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  • 1
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2015-11-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Tian -- New York, N.Y. -- Science. 2015 Nov 13;350(6262):738-9. doi: 10.1126/science.aad6452.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970 Horsholm, Denmark. zhang@biosustain.dtu.dk.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26564832" target="_blank"〉PubMed〈/a〉
    Keywords: Carbon Dioxide/chemistry ; *Chemistry Techniques, Synthetic ; Chemistry, Bioinorganic ; Escherichia coli ; Methanosarcina ; *Photosynthesis ; *Solar Energy
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2015-09-26
    Description: Assembly of protein complexes is considered a posttranslational process involving random collision of subunits. We show that within the Escherichia coli cytosol, bacterial luciferase subunits LuxA and LuxB assemble into complexes close to the site of subunit synthesis. Assembly efficiency decreases markedly if subunits are synthesized on separate messenger RNAs from genes integrated at distant chromosomal sites. Subunit assembly initiates cotranslationally on nascent LuxB in vivo. The ribosome-associated chaperone trigger factor delays the onset of cotranslational interactions until the LuxB dimer interface is fully exposed. Protein assembly is thus directly coupled to the translation process and involves spatially confined, actively chaperoned cotranslational subunit interactions. Bacterial gene organization into operons therefore reflects a fundamental cotranslational mechanism for spatial and temporal regulation that is vital to effective assembly of protein complexes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shieh, Yu-Wei -- Minguez, Pablo -- Bork, Peer -- Auburger, Josef J -- Guilbride, D Lys -- Kramer, Gunter -- Bukau, Bernd -- New York, N.Y. -- Science. 2015 Nov 6;350(6261):678-80. doi: 10.1126/science.aac8171. Epub 2015 Sep 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Molecular Biology of the University of Heidelberg (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany. ; European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany. ; European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany. Max-Delbruck-Centre for Molecular Medicine, Robert-Rossle-Strasse 10, 13125 Berlin, Germany. ; Center for Molecular Biology of the University of Heidelberg (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany. Malaria Research Foundation, Post Office Box 10420, Aspen, CO 81612, USA. ; Center for Molecular Biology of the University of Heidelberg (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany. bukau@zmbh.uni-heidelberg.de g.kramer@zmbh.uni-heidelberg.de.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26405228" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteria/*genetics/*metabolism ; Bacterial Proteins/chemistry/genetics/metabolism ; Escherichia coli ; *Gene Order ; Genes, Bacterial ; Green Fluorescent Proteins/chemistry/genetics/metabolism ; Luciferases, Bacterial/chemistry/*genetics/*metabolism ; Luminescent Proteins/chemistry/genetics/metabolism ; Molecular Chaperones/metabolism ; *Operon ; Protein Biosynthesis ; Protein Structure, Secondary ; Protein Subunits/chemistry/deficiency/genetics/metabolism ; RNA, Messenger/metabolism ; Recombinant Fusion Proteins/chemistry/genetics/metabolism ; Ribosomes/metabolism ; Vibrio/enzymology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2014-06-12
    Description: Spontaneous changes in the reading frame of translation are rare (frequency of 10(-3) to 10(-4) per codon), but can be induced by specific features in the messenger RNA (mRNA). In the presence of mRNA secondary structures, a heptanucleotide 'slippery sequence' usually defined by the motif X XXY YYZ, and (in some prokaryotic cases) mRNA sequences that base pair with the 3' end of the 16S ribosomal rRNA (internal Shine-Dalgarno sequences), there is an increased probability that a specific programmed change of frame occurs, wherein the ribosome shifts one nucleotide backwards into an overlapping reading frame (-1 frame) and continues by translating a new sequence of amino acids. Despite extensive biochemical and genetic studies, there is no clear mechanistic description for frameshifting. Here we apply single-molecule fluorescence to track the compositional and conformational dynamics of individual ribosomes at each codon during translation of a frameshift-inducing mRNA from the dnaX gene in Escherichia coli. Ribosomes that frameshift into the -1 frame are characterized by a tenfold longer pause in elongation compared to non-frameshifted ribosomes, which translate through unperturbed. During the pause, interactions of the ribosome with the mRNA stimulatory elements uncouple EF-G catalysed translocation from normal ribosomal subunit reverse-rotation, leaving the ribosome in a non-canonical intersubunit rotated state with an exposed codon in the aminoacyl-tRNA site (A site). tRNA(Lys) sampling and accommodation to the empty A site and EF-G action either leads to the slippage of the tRNAs into the -1 frame or maintains the ribosome into the 0 frame. Our results provide a general mechanistic and conformational framework for -1 frameshifting, highlighting multiple kinetic branchpoints during elongation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4472451/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4472451/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, Jin -- Petrov, Alexey -- Johansson, Magnus -- Tsai, Albert -- O'Leary, Sean E -- Puglisi, Joseph D -- GM099687/GM/NIGMS NIH HHS/ -- GM51266/GM/NIGMS NIH HHS/ -- R01 GM051266/GM/NIGMS NIH HHS/ -- R01 GM099687/GM/NIGMS NIH HHS/ -- England -- Nature. 2014 Aug 21;512(7514):328-32. doi: 10.1038/nature13428. Epub 2014 Jun 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Department of Applied Physics, Stanford University, Stanford, California 94305-4090, USA [2] Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA. ; Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24919156" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/genetics ; Codon/genetics ; DNA Polymerase III/genetics ; Escherichia coli ; *Frameshifting, Ribosomal ; Kinetics ; *Peptide Chain Elongation, Translational ; Peptide Elongation Factor G/metabolism ; RNA, Messenger/genetics ; RNA, Transfer, Amino Acyl/metabolism ; Reading Frames/genetics ; Ribosome Subunits/chemistry/metabolism ; Ribosomes/chemistry/*metabolism ; Rotation ; Time Factors
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2014-03-08
    Description: Little is known about how human genetic variation affects the responses to environmental stimuli in the context of complex diseases. Experimental and computational approaches were applied to determine the effects of genetic variation on the induction of pathogen-responsive genes in human dendritic cells. We identified 121 common genetic variants associated in cis with variation in expression responses to Escherichia coli lipopolysaccharide, influenza, or interferon-beta (IFN-beta). We localized and validated causal variants to binding sites of pathogen-activated STAT (signal transducer and activator of transcription) and IRF (IFN-regulatory factor) transcription factors. We also identified a common variant in IRF7 that is associated in trans with type I IFN induction in response to influenza infection. Our results reveal common alleles that explain interindividual variation in pathogen sensing and provide functional annotation for genetic variants that alter susceptibility to inflammatory diseases.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4124741/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4124741/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lee, Mark N -- Ye, Chun -- Villani, Alexandra-Chloe -- Raj, Towfique -- Li, Weibo -- Eisenhaure, Thomas M -- Imboywa, Selina H -- Chipendo, Portia I -- Ran, F Ann -- Slowikowski, Kamil -- Ward, Lucas D -- Raddassi, Khadir -- McCabe, Cristin -- Lee, Michelle H -- Frohlich, Irene Y -- Hafler, David A -- Kellis, Manolis -- Raychaudhuri, Soumya -- Zhang, Feng -- Stranger, Barbara E -- Benoist, Christophe O -- De Jager, Philip L -- Regev, Aviv -- Hacohen, Nir -- DP1 CA174427/CA/NCI NIH HHS/ -- DP1 MH100706/DP/NCCDPHP CDC HHS/ -- DP1 MH100706/MH/NIMH NIH HHS/ -- DP2 OD002230/OD/NIH HHS/ -- F32 AG043267/AG/NIA NIH HHS/ -- P30 DK043351/DK/NIDDK NIH HHS/ -- P50 HG006193/HG/NHGRI NIH HHS/ -- R01 AI091568/AI/NIAID NIH HHS/ -- R01 AR063759/AR/NIAMS NIH HHS/ -- R01 DK097768/DK/NIDDK NIH HHS/ -- R01 HG004037/HG/NHGRI NIH HHS/ -- RC2 GM093080/GM/NIGMS NIH HHS/ -- T32 GM007753/GM/NIGMS NIH HHS/ -- T32 HG002295/HG/NHGRI NIH HHS/ -- U19 AI082630/AI/NIAID NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2014 Mar 7;343(6175):1246980. doi: 10.1126/science.1246980.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24604203" target="_blank"〉PubMed〈/a〉
    Keywords: Adult ; Autoimmune Diseases/genetics ; Communicable Diseases/genetics ; Dendritic Cells/drug effects/*immunology ; Escherichia coli ; Female ; *Gene-Environment Interaction ; Genetic Loci ; Genome-Wide Association Study ; HEK293 Cells ; Host-Pathogen Interactions/*genetics ; Humans ; Influenza A virus ; Interferon Regulatory Factor-7/*genetics ; Interferon-beta/pharmacology ; Lipopolysaccharides/immunology ; Male ; Middle Aged ; Polymorphism, Single Nucleotide ; Quantitative Trait Loci ; STAT Transcription Factors/*genetics ; Transcriptome ; Young Adult
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
    Publication Date: 2014-08-12
    Description: An expanded GGGGCC repeat in C9orf72 is the most common genetic cause of frontotemporal dementia and amyotrophic lateral sclerosis. A fundamental question is whether toxicity is driven by the repeat RNA itself and/or by dipeptide repeat proteins generated by repeat-associated, non-ATG translation. To address this question, we developed in vitro and in vivo models to dissect repeat RNA and dipeptide repeat protein toxicity. Expression of pure repeats, but not stop codon-interrupted "RNA-only" repeats in Drosophila caused adult-onset neurodegeneration. Thus, expanded repeats promoted neurodegeneration through dipeptide repeat proteins. Expression of individual dipeptide repeat proteins with a non-GGGGCC RNA sequence revealed that both poly-(glycine-arginine) and poly-(proline-arginine) proteins caused neurodegeneration. These findings are consistent with a dual toxicity mechanism, whereby both arginine-rich proteins and repeat RNA contribute to C9orf72-mediated neurodegeneration.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mizielinska, Sarah -- Gronke, Sebastian -- Niccoli, Teresa -- Ridler, Charlotte E -- Clayton, Emma L -- Devoy, Anny -- Moens, Thomas -- Norona, Frances E -- Woollacott, Ione O C -- Pietrzyk, Julian -- Cleverley, Karen -- Nicoll, Andrew J -- Pickering-Brown, Stuart -- Dols, Jacqueline -- Cabecinha, Melissa -- Hendrich, Oliver -- Fratta, Pietro -- Fisher, Elizabeth M C -- Partridge, Linda -- Isaacs, Adrian M -- 089701/Wellcome Trust/United Kingdom -- 098565/Wellcome Trust/United Kingdom -- G0701441/Medical Research Council/United Kingdom -- G1000287/Medical Research Council/United Kingdom -- MR/J004022/1/Medical Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2014 Sep 5;345(6201):1192-4. doi: 10.1126/science.1256800. Epub 2014 Aug 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neurodegenerative Disease, UCL Institute of Neurology, London WC1N 3BG, UK. ; Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany. ; Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany. Department of Genetics, Evolution and Environment, Institute of Healthy Ageing, University College London, London WC1E 6BT, UK. ; Department of Neurodegenerative Disease, UCL Institute of Neurology, London WC1N 3BG, UK. Department of Genetics, Evolution and Environment, Institute of Healthy Ageing, University College London, London WC1E 6BT, UK. ; Department of Neurodegenerative Disease, UCL Institute of Neurology, London WC1N 3BG, UK. MRC Prion Unit, UCL Institute of Neurology, London WC1N 3BG, UK. ; Institute of Brain, Behaviour and Mental Health, Faculty of Human and Medical Sciences, University of Manchester, Manchester M13 9PT, UK. ; Department of Genetics, Evolution and Environment, Institute of Healthy Ageing, University College London, London WC1E 6BT, UK. ; Department of Neurodegenerative Disease, UCL Institute of Neurology, London WC1N 3BG, UK. MRC Centre for Neuromuscular Disease, UCL Institute of Neurology, London WC1N 3BG, UK. ; Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany. Department of Genetics, Evolution and Environment, Institute of Healthy Ageing, University College London, London WC1E 6BT, UK. a.isaacs@prion.ucl.ac.uk l.partridge@ucl.ac.uk. ; Department of Neurodegenerative Disease, UCL Institute of Neurology, London WC1N 3BG, UK. a.isaacs@prion.ucl.ac.uk l.partridge@ucl.ac.uk.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25103406" target="_blank"〉PubMed〈/a〉
    Keywords: Amyotrophic Lateral Sclerosis/*genetics/pathology ; Animals ; Cell Line, Tumor ; DNA Repeat Expansion/*genetics ; Dipeptides/metabolism ; Disease Models, Animal ; Drosophila melanogaster/*genetics ; Escherichia coli ; Frontotemporal Dementia/*genetics/pathology ; Humans ; Neurons/metabolism/pathology ; Proteins/*genetics
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  • 6
    Publication Date: 2014-03-08
    Description: The bicyclic beta-lactam/2-pyrrolidine precursor to all carbapenem antibiotics is biosynthesized by attachment of a carboxymethylene unit to C5 of L-proline followed by beta-lactam ring closure. Carbapenem synthase (CarC), an Fe(II) and 2-(oxo)glutarate (Fe/2OG)-dependent oxygenase, then inverts the C5 configuration. Here we report the structure of CarC in complex with its substrate and biophysical dissection of its reaction to reveal the stereoinversion mechanism. An Fe(IV)-oxo intermediate abstracts the hydrogen (H*) from C5, and tyrosine 165, a residue not visualized in the published structures of CarC lacking bound substrate, donates H* to the opposite face of the resultant radical. The reaction oxidizes the Fe(II) cofactor to Fe(III), limiting wild-type CarC to one turnover, but substitution of the H*-donating tyrosine disables stereoinversion and confers to CarC the capacity for catalytic substrate oxidation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4160820/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4160820/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chang, Wei-chen -- Guo, Yisong -- Wang, Chen -- Butch, Susan E -- Rosenzweig, Amy C -- Boal, Amie K -- Krebs, Carsten -- Bollinger, J Martin Jr -- GM 058518/GM/NIGMS NIH HHS/ -- GM 069657/GM/NIGMS NIH HHS/ -- GM 100011/GM/NIGMS NIH HHS/ -- R01 GM069657/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2014 Mar 7;343(6175):1140-4. doi: 10.1126/science.1248000.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24604200" target="_blank"〉PubMed〈/a〉
    Keywords: Carbapenems/*biosynthesis/*chemistry ; Catalysis ; Crystallography, X-Ray ; Enzymes/*chemistry/genetics ; Escherichia coli ; Hydrogen/chemistry ; Oxidation-Reduction ; Pectobacterium carotovorum/*enzymology ; Stereoisomerism ; Tyrosine/chemistry
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
    Publication Date: 2013-09-07
    Description: Organofluorines represent a rapidly expanding proportion of molecules that are used in pharmaceuticals, diagnostics, agrochemicals, and materials. Despite the prevalence of fluorine in synthetic compounds, the known biological scope is limited to a single pathway that produces fluoroacetate. Here, we demonstrate that this pathway can be exploited as a source of fluorinated building blocks for introduction of fluorine into natural-product scaffolds. Specifically, we have constructed pathways involving two polyketide synthase systems, and we show that fluoroacetate can be used to incorporate fluorine into the polyketide backbone in vitro. We further show that fluorine can be inserted site-selectively and introduced into polyketide products in vivo. These results highlight the prospects for the production of complex fluorinated natural products using synthetic biology.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4057101/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4057101/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Walker, Mark C -- Thuronyi, Benjamin W -- Charkoudian, Louise K -- Lowry, Brian -- Khosla, Chaitan -- Chang, Michelle C Y -- 1 DP2 OD008696/OD/NIH HHS/ -- 1 T32 GMO66698/PHS HHS/ -- 1S10RR023679-01/RR/NCRR NIH HHS/ -- F32 CA137994/CA/NCI NIH HHS/ -- R01 GM087934/GM/NIGMS NIH HHS/ -- S10 RR16634-01/RR/NCRR NIH HHS/ -- T32 GM066698/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Sep 6;341(6150):1089-94. doi: 10.1126/science.1242345.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-1460, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24009388" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/chemistry/genetics/metabolism ; Base Sequence ; Biological Products/chemistry/*metabolism ; Burkholderia/enzymology ; Coenzyme A Ligases/chemistry/genetics/metabolism ; Escherichia coli ; Fluoroacetates/chemistry/*metabolism ; Metabolic Networks and Pathways ; Molecular Sequence Data ; Polyketide Synthases/chemistry/genetics/*metabolism ; Polyketides/chemistry/*metabolism ; Protein Engineering ; Protein Structure, Tertiary ; Streptomyces coelicolor/enzymology
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  • 8
    Publication Date: 2012-01-24
    Description: Fic proteins that are defined by the ubiquitous FIC (filamentation induced by cyclic AMP) domain are known to catalyse adenylylation (also called AMPylation); that is, the transfer of AMP onto a target protein. In mammalian cells, adenylylation of small GTPases through Fic proteins injected by pathogenic bacteria can cause collapse of the actin cytoskeleton and cell death. It is unknown how this potentially deleterious adenylylation activity is regulated in the widespread Fic proteins that are found in all domains of life and that are thought to have critical roles in intrinsic signalling processes. Here we show that FIC-domain-mediated adenylylation is controlled by a conserved mechanism of ATP-binding-site obstruction that involves an inhibitory alpha-helix (alpha(inh)) with a conserved (S/T)XXXE(G/N) motif, and that in this mechanism the invariable glutamate competes with ATP gamma-phosphate binding. Consistent with this, FIC-domain-mediated growth arrest of bacteria by the VbhT toxin of Bartonella schoenbuchensis is intermolecularly repressed by the VbhA antitoxin through tight binding of its alpha(inh) to the FIC domain of VbhT, as shown by structure and function analysis. Furthermore, structural comparisons with other bacterial Fic proteins, such as Fic of Neisseria meningitidis and of Shewanella oneidensis, show that alpha(inh) frequently constitutes an amino-terminal or carboxy-terminal extension to the FIC domain, respectively, partially obstructing the ATP binding site in an intramolecular manner. After mutation of the inhibitory motif in various Fic proteins, including the human homologue FICD (also known as HYPE), adenylylation activity is considerably boosted, consistent with the anticipated relief of inhibition. Structural homology modelling of all annotated Fic proteins indicates that inhibition by alpha(inh) is universal and conserved through evolution, as the inhibitory motif is present in approximately 90% of all putatively adenylylation-active FIC domains, including examples from all domains of life and from viruses. Future studies should reveal how intrinsic or extrinsic factors modulate adenylylation activity by weakening the interaction of alpha(inh) with the FIC active site.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Engel, Philipp -- Goepfert, Arnaud -- Stanger, Frederic V -- Harms, Alexander -- Schmidt, Alexander -- Schirmer, Tilman -- Dehio, Christoph -- England -- Nature. 2012 Jan 22;482(7383):107-10. doi: 10.1038/nature10729.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Focal Area Infection Biology, Biozentrum, University of Basel, CH-4056 Basel, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22266942" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Bacterial Proteins/*chemistry/*metabolism ; Bartonella ; Carrier Proteins/chemistry/metabolism ; Catalysis ; Catalytic Domain ; Cyclic AMP/*metabolism ; Escherichia coli ; Escherichia coli Proteins/chemistry/metabolism ; Glutamic Acid/metabolism ; Humans ; Membrane Proteins/chemistry/metabolism ; Microbial Viability ; Models, Molecular ; Molecular Weight ; Neisseria meningitidis ; Protein Structure, Tertiary ; Shewanella
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 9
    Publication Date: 2011-05-21
    Description: During protein synthesis, the ribosome controls the movement of tRNA and mRNA by means of large-scale structural rearrangements. We describe structures of the intact bacterial ribosome from Escherichia coli that reveal how the ribosome binds tRNA in two functionally distinct states, determined to a resolution of ~3.2 angstroms by means of x-ray crystallography. One state positions tRNA in the peptidyl-tRNA binding site. The second, a fully rotated state, is stabilized by ribosome recycling factor and binds tRNA in a highly bent conformation in a hybrid peptidyl/exit site. The structures help to explain how the ratchet-like motion of the two ribosomal subunits contributes to the mechanisms of translocation, termination, and ribosome recycling.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3176341/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3176341/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dunkle, Jack A -- Wang, Leyi -- Feldman, Michael B -- Pulk, Arto -- Chen, Vincent B -- Kapral, Gary J -- Noeske, Jonas -- Richardson, Jane S -- Blanchard, Scott C -- Cate, Jamie H Doudna -- CA92584/CA/NCI NIH HHS/ -- GM074127-04S1/GM/NIGMS NIH HHS/ -- GM07739/GM/NIGMS NIH HHS/ -- GM079238/GM/NIGMS NIH HHS/ -- GM088674/GM/NIGMS NIH HHS/ -- GM65050/GM/NIGMS NIH HHS/ -- P01 CA092584/CA/NCI NIH HHS/ -- P01 GM063210/GM/NIGMS NIH HHS/ -- P01-GM63210/GM/NIGMS NIH HHS/ -- R01 GM065050/GM/NIGMS NIH HHS/ -- R01 GM065050-11/GM/NIGMS NIH HHS/ -- R01 GM074127/GM/NIGMS NIH HHS/ -- R01 GM079238/GM/NIGMS NIH HHS/ -- R01 GM088674/GM/NIGMS NIH HHS/ -- RR-15301/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2011 May 20;332(6032):981-4. doi: 10.1126/science.1202692.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21596992" target="_blank"〉PubMed〈/a〉
    Keywords: Anticodon/chemistry/metabolism ; Crystallography, X-Ray ; Escherichia coli ; Escherichia coli Proteins/metabolism ; Models, Molecular ; Nucleic Acid Conformation ; Protein Biosynthesis ; RNA, Bacterial/chemistry/*metabolism ; RNA, Messenger/chemistry/metabolism ; RNA, Ribosomal, 16S/chemistry/metabolism ; RNA, Ribosomal, 23S/chemistry/metabolism ; RNA, Transfer, Amino Acyl/chemistry/metabolism ; RNA, Transfer, Phe/chemistry/*metabolism ; Ribosomal Proteins/metabolism ; Ribosome Subunits, Large, Bacterial/*chemistry/*metabolism/ultrastructure ; Ribosome Subunits, Small, Bacterial/*chemistry/*metabolism/ultrastructure
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  • 10
    Publication Date: 2011-04-02
    Description: CRISPR/Cas systems constitute a widespread class of immunity systems that protect bacteria and archaea against phages and plasmids, and commonly use repeat/spacer-derived short crRNAs to silence foreign nucleic acids in a sequence-specific manner. Although the maturation of crRNAs represents a key event in CRISPR activation, the responsible endoribonucleases (CasE, Cas6, Csy4) are missing in many CRISPR/Cas subtypes. Here, differential RNA sequencing of the human pathogen Streptococcus pyogenes uncovered tracrRNA, a trans-encoded small RNA with 24-nucleotide complementarity to the repeat regions of crRNA precursor transcripts. We show that tracrRNA directs the maturation of crRNAs by the activities of the widely conserved endogenous RNase III and the CRISPR-associated Csn1 protein; all these components are essential to protect S. pyogenes against prophage-derived DNA. Our study reveals a novel pathway of small guide RNA maturation and the first example of a host factor (RNase III) required for bacterial RNA-mediated immunity against invaders.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070239/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070239/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Deltcheva, Elitza -- Chylinski, Krzysztof -- Sharma, Cynthia M -- Gonzales, Karine -- Chao, Yanjie -- Pirzada, Zaid A -- Eckert, Maria R -- Vogel, Jorg -- Charpentier, Emmanuelle -- P 17238/Austrian Science Fund FWF/Austria -- England -- Nature. 2011 Mar 31;471(7340):602-7. doi: 10.1038/nature09886.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Laboratory for Molecular Infection Medicine Sweden, Umea, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21455174" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/chemistry/genetics/immunology/metabolism ; Conserved Sequence ; DNA, Viral/genetics/metabolism ; Escherichia coli ; Models, Biological ; Prophages/genetics ; RNA Precursors/genetics/metabolism ; RNA Processing, Post-Transcriptional ; RNA, Bacterial/biosynthesis/*genetics/immunology/*metabolism ; RNA, Guide/*genetics ; Ribonuclease III/*metabolism ; Streptococcus pyogenes/*genetics/*immunology/metabolism/virology
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  • 11
    Publication Date: 2011-05-20
    Description: The boundaries between prokaryotes, unicellular eukaryotes and multicellular eukaryotes are accompanied by orders-of-magnitude reductions in effective population size, with concurrent amplifications of the effects of random genetic drift and mutation. The resultant decline in the efficiency of selection seems to be sufficient to influence a wide range of attributes at the genomic level in a non-adaptive manner. A key remaining question concerns the extent to which variation in the power of random genetic drift is capable of influencing phylogenetic diversity at the subcellular and cellular levels. Should this be the case, population size would have to be considered as a potential determinant of the mechanistic pathways underlying long-term phenotypic evolution. Here we demonstrate a phylogenetically broad inverse relation between the power of drift and the structural integrity of protein subunits. This leads to the hypothesis that the accumulation of mildly deleterious mutations in populations of small size induces secondary selection for protein-protein interactions that stabilize key gene functions. By this means, the complex protein architectures and interactions essential to the genesis of phenotypic diversity may initially emerge by non-adaptive mechanisms.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3121905/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3121905/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fernandez, Ariel -- Lynch, Michael -- R01 GM036827/GM/NIGMS NIH HHS/ -- R01 GM036827-17S1/GM/NIGMS NIH HHS/ -- R01GM036827/GM/NIGMS NIH HHS/ -- R01GM072614/GM/NIGMS NIH HHS/ -- England -- Nature. 2011 May 18;474(7352):502-5. doi: 10.1038/nature09992.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Computer Science, The University of Chicago, Chicago, Illinois 60637, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21593762" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Caenorhabditis elegans ; Computational Biology ; Escherichia coli ; *Evolution, Molecular ; *Genetic Drift ; Hemoglobins/chemistry/metabolism ; Humans ; Hydrogen Bonding ; Metabolic Networks and Pathways/genetics/*physiology ; Models, Genetic ; Models, Molecular ; Phenotype ; Phylogeny ; Population Density ; Protein Binding ; Protein Conformation ; Proteins/chemistry/genetics/*metabolism ; Selection, Genetic ; Solubility ; Species Specificity ; Superoxide Dismutase/chemistry/metabolism ; Water/chemistry
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  • 12
    Publication Date: 2011-05-21
    Description: The ordering of liquid crystals (LCs) is known to be influenced by surfaces and contaminants. Here, we report that picogram per milliliter concentrations of endotoxin in water trigger ordering transitions in micrometer-size LC droplets. The ordering transitions, which occur at surface concentrations of endotoxin that are less than 10(-5) Langmuir, are not due to adsorbate-induced changes in the interfacial energy of the LC. The sensitivity of the LC to endotoxin was measured to change by six orders of magnitude with the geometry of the LC (droplet versus slab), supporting the hypothesis that interactions of endotoxin with topological defects in the LC mediate the response of the droplets. The LC ordering transitions depend strongly on glycophospholipid structure and provide new designs for responsive soft matter.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3448959/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3448959/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lin, I-Hsin -- Miller, Daniel S -- Bertics, Paul J -- Murphy, Christopher J -- de Pablo, Juan J -- Abbott, Nicholas L -- CA105730/CA/NCI NIH HHS/ -- CA108467/CA/NCI NIH HHS/ -- R01 CA108467/CA/NCI NIH HHS/ -- R21 AI092004/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2011 Jun 10;332(6035):1297-300. doi: 10.1126/science.1195639. Epub 2011 May 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI 53706-1607, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21596951" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallization ; Endotoxins/*chemistry ; Escherichia coli ; Lipid A/chemistry ; Liquid Crystals/*chemistry ; Molecular Structure ; Surface Properties ; Water/*chemistry
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  • 13
    Publication Date: 2010-04-16
    Description: Translation by the ribosome occurs by a complex mechanism involving the coordinated interaction of multiple nucleic acid and protein ligands. Here we use zero-mode waveguides (ZMWs) and sophisticated detection instrumentation to allow real-time observation of translation at physiologically relevant micromolar ligand concentrations. Translation at each codon is monitored by stable binding of transfer RNAs (tRNAs)-labelled with distinct fluorophores-to translating ribosomes, which allows direct detection of the identity of tRNA molecules bound to the ribosome and therefore the underlying messenger RNA (mRNA) sequence. We observe the transit of tRNAs on single translating ribosomes and determine the number of tRNA molecules simultaneously bound to the ribosome, at each codon of an mRNA molecule. Our results show that ribosomes are only briefly occupied by two tRNA molecules and that release of deacylated tRNA from the exit (E) site is uncoupled from binding of aminoacyl-tRNA site (A-site) tRNA and occurs rapidly after translocation. The methods outlined here have broad application to the study of mRNA sequences, and the mechanism and regulation of translation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4466108/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4466108/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Uemura, Sotaro -- Aitken, Colin Echeverria -- Korlach, Jonas -- Flusberg, Benjamin A -- Turner, Stephen W -- Puglisi, Joseph D -- GM51266/GM/NIGMS NIH HHS/ -- R01 GM051266/GM/NIGMS NIH HHS/ -- England -- Nature. 2010 Apr 15;464(7291):1012-7. doi: 10.1038/nature08925.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20393556" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Codon/*genetics ; Escherichia coli ; Fluorescence ; Kinetics ; Ligands ; Luminescent Measurements ; Optical Tweezers ; Protein Biosynthesis/genetics/*physiology ; RNA, Transfer/genetics/*metabolism ; Ribosomes/chemistry/genetics/*metabolism ; Time Factors
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  • 14
    Publication Date: 2010-07-16
    Description: The translocation step of protein synthesis entails large-scale rearrangements of the ribosome-transfer RNA (tRNA) complex. Here we have followed tRNA movement through the ribosome during translocation by time-resolved single-particle electron cryomicroscopy (cryo-EM). Unbiased computational sorting of cryo-EM images yielded 50 distinct three-dimensional reconstructions, showing the tRNAs in classical, hybrid and various novel intermediate states that provide trajectories and kinetic information about tRNA movement through the ribosome. The structures indicate how tRNA movement is coupled with global and local conformational changes of the ribosome, in particular of the head and body of the small ribosomal subunit, and show that dynamic interactions between tRNAs and ribosomal residues confine the path of the tRNAs through the ribosome. The temperature dependence of ribosome dynamics reveals a surprisingly flat energy landscape of conformational variations at physiological temperature. The ribosome functions as a Brownian machine that couples spontaneous conformational changes driven by thermal energy to directed movement.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fischer, Niels -- Konevega, Andrey L -- Wintermeyer, Wolfgang -- Rodnina, Marina V -- Stark, Holger -- England -- Nature. 2010 Jul 15;466(7304):329-33. doi: 10.1038/nature09206.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉3D Electron Cryomicroscopy Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Gottingen, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20631791" target="_blank"〉PubMed〈/a〉
    Keywords: Cryoelectron Microscopy ; Escherichia coli ; Kinetics ; Models, Molecular ; Molecular Conformation ; *Movement ; *Protein Biosynthesis ; RNA, Transfer/genetics/*metabolism ; Ribosome Subunits, Large, Bacterial/chemistry/metabolism ; Ribosome Subunits, Small, Bacterial/chemistry/metabolism ; Ribosomes/chemistry/*metabolism ; Temperature ; Thermodynamics ; Time Factors
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  • 15
    Publication Date: 2010-07-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ehrenberg, Mans -- England -- Nature. 2010 Jul 15;466(7304):325-6. doi: 10.1038/466325a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20631789" target="_blank"〉PubMed〈/a〉
    Keywords: Cryoelectron Microscopy ; Escherichia coli ; Kinetics ; *Movement ; *Protein Biosynthesis ; RNA, Transfer/genetics/*metabolism ; Ribosomes/chemistry/*metabolism ; Temperature ; Thermodynamics
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  • 16
    Publication Date: 2010-05-14
    Description: Neurotransmitter:Na(+) symporters (NSS) remove neurotransmitters from the synapse in a reuptake process that is driven by the Na(+) gradient. Drugs that interfere with this reuptake mechanism, such as cocaine and antidepressants, profoundly influence behaviour and mood. To probe the nature of the conformational changes that are associated with substrate binding and transport, we have developed a single-molecule fluorescence imaging assay and combined it with functional and computational studies of the prokaryotic NSS homologue LeuT. Here we show molecular details of the modulation of intracellular gating of LeuT by substrates and inhibitors, as well as by mutations that alter binding, transport or both. Our direct observations of single-molecule transitions, reflecting structural dynamics of the intracellular region of the transporter that might be masked by ensemble averaging or suppressed under crystallographic conditions, are interpreted in the context of an allosteric mechanism that couples ion and substrate binding to transport.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2940119/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2940119/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhao, Yongfang -- Terry, Daniel -- Shi, Lei -- Weinstein, Harel -- Blanchard, Scott C -- Javitch, Jonathan A -- DA022413/DA/NIDA NIH HHS/ -- DA023694/DA/NIDA NIH HHS/ -- DA12408/DA/NIDA NIH HHS/ -- DA17293/DA/NIDA NIH HHS/ -- K05 DA022413/DA/NIDA NIH HHS/ -- K99 DA023694/DA/NIDA NIH HHS/ -- K99 DA023694-02/DA/NIDA NIH HHS/ -- R01 DA017293/DA/NIDA NIH HHS/ -- England -- Nature. 2010 May 13;465(7295):188-93. doi: 10.1038/nature09057.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Molecular Recognition, Columbia University College of Physicians and Surgeons, 630 W. 168th, New York, New York 10032, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20463731" target="_blank"〉PubMed〈/a〉
    Keywords: Alanine/metabolism ; Allosteric Regulation ; Aquifoliaceae/*chemistry ; Bacterial Proteins/*chemistry/genetics/*metabolism ; Crystallography, X-Ray ; Cysteine/chemistry/metabolism ; Escherichia coli ; Fluorescence Resonance Energy Transfer ; Leucine/metabolism ; Models, Molecular ; Molecular Dynamics Simulation ; Plasma Membrane Neurotransmitter Transport ; Proteins/*chemistry/genetics/*metabolism ; Protein Conformation ; Sodium/metabolism
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  • 17
    Publication Date: 2009-01-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gore, Jeff -- van Oudenaarden, Alexander -- K99 GM085279/GM/NIGMS NIH HHS/ -- R00 GM085279/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Jan 15;457(7227):271-2. doi: 10.1038/457271a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19148089" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biological Clocks/*physiology ; Circadian Rhythm/*physiology ; Escherichia coli ; *Feedback, Physiological ; Gene Expression Regulation/*genetics ; Genes, Synthetic/*genetics ; Genetic Engineering ; *Models, Biological
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  • 18
    Publication Date: 2009-10-13
    Description: Single-stranded DNA generated in the cell during DNA metabolism is stabilized and protected by binding of ssDNA-binding (SSB) proteins. Escherichia coli SSB, a representative homotetrameric SSB, binds to ssDNA by wrapping the DNA using its four subunits. However, such a tightly wrapped, high-affinity protein-DNA complex still needs to be removed or repositioned quickly for unhindered action of other proteins. Here we show, using single-molecule two- and three-colour fluorescence resonance energy transfer, that tetrameric SSB can spontaneously migrate along ssDNA. Diffusional migration of SSB helps in the local displacement of SSB by an elongating RecA filament. SSB diffusion also melts short DNA hairpins transiently and stimulates RecA filament elongation on DNA with secondary structure. This observation of diffusional movement of a protein on ssDNA introduces a new model for how an SSB protein can be redistributed, while remaining tightly bound to ssDNA during recombination and repair processes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2782680/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2782680/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Roy, Rahul -- Kozlov, Alexander G -- Lohman, Timothy M -- Ha, Taekjip -- R01 GM030498/GM/NIGMS NIH HHS/ -- R01 GM030498-28/GM/NIGMS NIH HHS/ -- R01 GM065367/GM/NIGMS NIH HHS/ -- R01 GM065367-08/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2009 Oct 22;461(7267):1092-7. doi: 10.1038/nature08442. Epub 2009 Oct 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Biophysics and Computational Biology, University of Illinois, Urbana-Champaign, Illinois 61801, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19820696" target="_blank"〉PubMed〈/a〉
    Keywords: DNA, Single-Stranded/chemistry/*metabolism ; DNA-Binding Proteins/*metabolism ; *Diffusion ; Escherichia coli ; Escherichia coli Proteins/*metabolism ; Fluorescence Resonance Energy Transfer ; *Movement ; Nucleic Acid Conformation ; Rec A Recombinases/*chemistry/*metabolism
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  • 19
    Publication Date: 2009-10-23
    Description: Maturation of precursor transfer RNA (pre-tRNA) includes excision of the 5' leader and 3' trailer sequences, removal of introns and addition of the CCA terminus. Nucleotide modifications are incorporated at different stages of tRNA processing, after the RNA molecule adopts the proper conformation. In bacteria, tRNA(Ile2) lysidine synthetase (TilS) modifies cytidine into lysidine (L; 2-lysyl-cytidine) at the first anticodon of tRNA(Ile2) (refs 4-9). This modification switches tRNA(Ile2) from a methionine-specific to an isoleucine-specific tRNA. However, the aminoacylation of tRNA(Ile2) by methionyl-tRNA synthetase (MetRS), before the modification by TilS, might lead to the misincorporation of methionine in response to isoleucine codons. The mechanism used by bacteria to avoid this pitfall is unknown. Here we show that the TilS enzyme specifically recognizes and modifies tRNA(Ile2) in its precursor form, thereby avoiding translation errors. We identified the lysidine modification in pre-tRNA(Ile2) isolated from RNase-E-deficient Escherichia coli and did not detect mature tRNA(Ile2) lacking this modification. Our kinetic analyses revealed that TilS can modify both types of RNA molecule with comparable efficiencies. X-ray crystallography and mutational analyses revealed that TilS specifically recognizes the entire L-shape structure in pre-tRNA(Ile2) through extensive interactions coupled with sequential domain movements. Our results demonstrate how TilS prevents the recognition of tRNA(Ile2) by MetRS and achieves high specificity for its substrate. These two key points form the basis for maintaining the fidelity of isoleucine codon translation in bacteria. Our findings also provide a rationale for the necessity of incorporating specific modifications at the precursor level during tRNA biogenesis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nakanishi, Kotaro -- Bonnefond, Luc -- Kimura, Satoshi -- Suzuki, Tsutomu -- Ishitani, Ryuichiro -- Nureki, Osamu -- England -- Nature. 2009 Oct 22;461(7267):1144-8. doi: 10.1038/nature08474.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Kanagawa 225-8501, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19847269" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acyl-tRNA Synthetases/*chemistry/genetics/*metabolism ; Apoproteins/genetics/metabolism ; Bacillus subtilis ; Bacterial Proteins/*chemistry/genetics/*metabolism ; Base Sequence ; Catalytic Domain ; Crystallography, X-Ray ; Escherichia coli ; Geobacillus ; Kinetics ; Lysine/analogs & derivatives/metabolism ; Mass Spectrometry ; Models, Molecular ; Molecular Sequence Data ; *Protein Biosynthesis ; Pyrimidine Nucleosides/metabolism ; RNA, Transfer, Ile/genetics/metabolism ; Substrate Specificity
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  • 20
    Publication Date: 2009-06-12
    Description: Natural products containing phosphorus-carbon bonds have found widespread use in medicine and agriculture. One such compound, phosphinothricin tripeptide, contains the unusual amino acid phosphinothricin attached to two alanine residues. Synthetic phosphinothricin (glufosinate) is a component of two top-selling herbicides (Basta and Liberty), and is widely used with resistant transgenic crops including corn, cotton and canola. Recent genetic and biochemical studies showed that during phosphinothricin tripeptide biosynthesis 2-hydroxyethylphosphonate (HEP) is converted to hydroxymethylphosphonate (HMP). Here we report the in vitro reconstitution of this unprecedented C(sp(3))-C(sp(3)) bond cleavage reaction and X-ray crystal structures of the enzyme. The protein is a mononuclear non-haem iron(ii)-dependent dioxygenase that converts HEP to HMP and formate. In contrast to most other members of this family, the oxidative consumption of HEP does not require additional cofactors or the input of exogenous electrons. The current study expands the scope of reactions catalysed by the 2-His-1-carboxylate mononuclear non-haem iron family of enzymes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2874955/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2874955/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cicchillo, Robert M -- Zhang, Houjin -- Blodgett, Joshua A V -- Whitteck, John T -- Li, Gongyong -- Nair, Satish K -- van der Donk, Wilfred A -- Metcalf, William W -- P01 GM077596/GM/NIGMS NIH HHS/ -- P01 GM077596-03/GM/NIGMS NIH HHS/ -- R01 GM059334/GM/NIGMS NIH HHS/ -- R01 GM059334-09/GM/NIGMS NIH HHS/ -- R01 GM59334/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Jun 11;459(7248):871-4. doi: 10.1038/nature07972.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19516340" target="_blank"〉PubMed〈/a〉
    Keywords: Aminobutyrates/*chemistry/*metabolism ; Biocatalysis ; Crystallography, X-Ray ; Dioxygenases/chemistry/genetics/*metabolism ; Escherichia coli ; Formates/metabolism ; Magnetic Resonance Spectroscopy ; Mass Spectrometry ; Models, Biological ; Models, Molecular ; Molecular Conformation ; Organophosphonates/metabolism
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  • 21
    Publication Date: 2009-10-23
    Description: 〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2819181/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2819181/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉George, Nicholas P -- Keck, James L -- R01 GM068061/GM/NIGMS NIH HHS/ -- R01 GM068061-07/GM/NIGMS NIH HHS/ -- R01 GM068061-07S1/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Oct 22;461(7267):1067-8. doi: 10.1038/4611067a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19847254" target="_blank"〉PubMed〈/a〉
    Keywords: DNA, Single-Stranded/chemistry/*metabolism ; DNA-Binding Proteins/*metabolism ; *Diffusion ; Escherichia coli ; Escherichia coli Proteins/*metabolism ; Fluorescence Resonance Energy Transfer ; *Movement ; Nucleic Acid Conformation ; Rec A Recombinases/*chemistry/*metabolism
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  • 22
    Publication Date: 2009-03-03
    Description: When Caenorhabditis elegans larvae hatch from the egg case in the absence of food, their development is arrested (L1 arrest), and they show increased stress resistance until food becomes available. To study nutritional control of larval development, we analyzed growth and gene expression profiles during L1 arrest and recovery. Larvae that were fed responded relatively slowly to starvation compared with the rapid response of arrested larvae to feeding. Chromatin immunoprecipitation of RNA polymerase II (Pol II) followed by deep sequencing showed that during L1 arrest, Pol II continued transcribing starvation-response genes, but the enzyme accumulated on the promoters of growth and development genes. In response to feeding, promoter accumulation decreased, and elongation and messenger RNA levels increased. Therefore, accumulation of Pol II at promoters anticipates nutritionally controlled gene expression during C. elegans development.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baugh, L Ryan -- Demodena, John -- Sternberg, Paul W -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2009 Apr 3;324(5923):92-4. doi: 10.1126/science.1169628. Epub 2009 Feb 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19251593" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Caenorhabditis elegans/*genetics/*growth & development/metabolism ; Chromatin Immunoprecipitation ; Cluster Analysis ; Escherichia coli ; Food ; Gene Expression Profiling ; *Gene Expression Regulation, Developmental ; Genes, Helminth ; Nutritional Physiological Phenomena ; Oligonucleotide Array Sequence Analysis ; Principal Component Analysis ; *Promoter Regions, Genetic ; RNA Polymerase II/*metabolism ; RNA, Helminth/genetics/metabolism ; RNA, Messenger/genetics/metabolism ; Signal Transduction ; Starvation ; Transcription, Genetic ; Up-Regulation
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  • 23
    Publication Date: 2008-10-14
    Description: The APOBEC family members are involved in diverse biological functions. APOBEC3G restricts the replication of human immunodeficiency virus (HIV), hepatitis B virus and retroelements by cytidine deamination on single-stranded DNA or by RNA binding. Here we report the high-resolution crystal structure of the carboxy-terminal deaminase domain of APOBEC3G (APOBEC3G-CD2) purified from Escherichia coli. The APOBEC3G-CD2 structure has a five-stranded beta-sheet core that is common to all known deaminase structures and closely resembles the structure of another APOBEC protein, APOBEC2 (ref. 5). A comparison of APOBEC3G-CD2 with other deaminase structures shows a structural conservation of the active-site loops that are directly involved in substrate binding. In the X-ray structure, these APOBEC3G active-site loops form a continuous 'substrate groove' around the active centre. The orientation of this putative substrate groove differs markedly (by 90 degrees) from the groove predicted by the NMR structure. We have introduced mutations around the groove, and have identified residues involved in substrate specificity, single-stranded DNA binding and deaminase activity. These results provide a basis for understanding the underlying mechanisms of substrate specificity for the APOBEC family.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2714533/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2714533/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Holden, Lauren G -- Prochnow, Courtney -- Chang, Y Paul -- Bransteitter, Ronda -- Chelico, Linda -- Sen, Udayaditya -- Stevens, Raymond C -- Goodman, Myron F -- Chen, Xiaojiang S -- R01 AI055926/AI/NIAID NIH HHS/ -- R01 AI055926-05/AI/NIAID NIH HHS/ -- England -- Nature. 2008 Nov 6;456(7218):121-4. doi: 10.1038/nature07357. Epub 2008 Oct 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18849968" target="_blank"〉PubMed〈/a〉
    Keywords: Antiviral Agents ; *Catalytic Domain ; Crystallography, X-Ray ; Cytidine Deaminase/*chemistry/genetics/isolation & purification/*metabolism ; DNA, Single-Stranded/metabolism ; Escherichia coli ; Humans ; Models, Molecular ; Muscle Proteins/chemistry ; Mutant Proteins/chemistry/genetics/metabolism ; Mutation ; Nuclear Magnetic Resonance, Biomolecular ; Protein Structure, Secondary ; Structural Homology, Protein ; Structure-Activity Relationship ; Substrate Specificity
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  • 24
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2008-05-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lutkenhaus, Joe -- R37GM09764/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 May 9;320(5877):755-6. doi: 10.1126/science.1158463.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS 66160, USA. jlutkenh@kumc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18467579" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/physiology ; Cell Cycle Proteins/physiology ; *Cell-Free System ; Cytokinesis/*physiology ; Cytoskeletal Proteins/physiology ; Escherichia coli ; Escherichia coli Proteins/physiology
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  • 25
    Publication Date: 2007-08-04
    Description: BtuCD is an adenosine triphosphate-binding cassette (ABC) transporter that translocates vitamin B12 from the periplasmic binding protein BtuF into the cytoplasm of Escherichia coli. The 2.6 angstrom crystal structure of a complex BtuCD-F reveals substantial conformational changes as compared with the previously reported structures of BtuCD and BtuF. The lobes of BtuF are spread apart, and B12 is displaced from the binding pocket. The transmembrane BtuC subunits reveal two distinct conformations, and the translocation pathway is closed to both sides of the membrane. Electron paramagnetic resonance spectra of spin-labeled cysteine mutants reconstituted in proteoliposomes are consistent with the conformation of BtuCD-F that was observed in the crystal structure. A comparison with BtuCD and the homologous HI1470/71 protein suggests that the structure of BtuCD-F may reflect a posttranslocation intermediate.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hvorup, Rikki N -- Goetz, Birke A -- Niederer, Martina -- Hollenstein, Kaspar -- Perozo, Eduardo -- Locher, Kaspar P -- New York, N.Y. -- Science. 2007 Sep 7;317(5843):1387-90. Epub 2007 Aug 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology and Biophysics, ETH Zurich, HPK D14.3, 8093 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17673622" target="_blank"〉PubMed〈/a〉
    Keywords: ATP-Binding Cassette Transporters/*chemistry ; Amino Acid Sequence ; Crystallography, X-Ray ; Electron Spin Resonance Spectroscopy ; Escherichia coli ; Escherichia coli Proteins/*chemistry ; Models, Molecular ; Molecular Sequence Data ; Periplasmic Binding Proteins/*chemistry ; Protein Binding ; Protein Conformation ; Recombinant Fusion Proteins/chemistry
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  • 26
    Publication Date: 2007-02-17
    Description: The type III ribulose-1,5-bisphosphate carboxylase-oxygenase (RuBisCO) present in the archaeon Thermococcus kodakaraensis was found to participate in adenosine 5'-monophosphate (AMP) metabolism, a role that is distinct from that of classical RuBisCOs of the Calvin-Benson-Bassham cycle. Genes annotated as thymidine phosphorylase (deoA) and eucaryal translation initiation factor 2B (e2b2) were found to encode AMP phosphorylase and ribose-1,5-bisphosphate isomerase, respectively. These enzymes supplied the RuBisCO substrate, ribulose-1,5-bisphosphate, from AMP and phosphate. Archaea with type III RuBisCOs all harbor both DeoA and the corresponding E2b2 homologs. In this pathway, adenine was released from AMP and the phosphoribose moiety entered central-carbon metabolism.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sato, Takaaki -- Atomi, Haruyuki -- Imanaka, Tadayuki -- New York, N.Y. -- Science. 2007 Feb 16;315(5814):1003-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17303759" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Monophosphate/*metabolism ; Archaea/enzymology/genetics/metabolism ; Archaeal Proteins/*metabolism ; Escherichia coli ; Metabolic Networks and Pathways ; Methionine/metabolism ; Pentosephosphates/metabolism ; Recombinant Proteins ; Ribulose-Bisphosphate Carboxylase/classification/*metabolism ; Thermococcus/*enzymology/genetics ; Thymidine Phosphorylase/genetics
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  • 27
    Publication Date: 2006-06-03
    Description: In Gram-negative bacteria, the import of essential micronutrients across the outer membrane requires a transporter, an electrochemical gradient of protons across the inner membrane, and an inner membrane protein complex (ExbB, ExbD, TonB) that couples the proton-motive force to the outer membrane transporter. The inner membrane protein TonB binds directly to a conserved region, called the Ton-box, of the transporter. We solved the structure of the cobalamin transporter BtuB in complex with the C-terminal domain of TonB. In contrast to its conformations in the absence of TonB, the Ton-box forms a beta strand that is recruited to the existing beta sheet of TonB, which is consistent with a mechanical pulling model of transport.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shultis, David D -- Purdy, Michael D -- Banchs, Christian N -- Wiener, Michael C -- DK59999/DK/NIDDK NIH HHS/ -- GM00Z055/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Jun 2;312(5778):1396-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16741124" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Outer Membrane Proteins/*chemistry/metabolism ; Biological Transport, Active ; Crystallography, X-Ray ; Escherichia coli ; Escherichia coli Proteins/*chemistry/metabolism ; Magnetic Resonance Spectroscopy ; Membrane Proteins/*chemistry/metabolism ; Membrane Transport Proteins/*chemistry/metabolism ; Models, Molecular ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary
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  • 28
    Publication Date: 2006-11-18
    Description: N-linked protein glycosylation is found in all domains of life. In eukaryotes, it is the most abundant protein modification of secretory and membrane proteins, and the process is coupled to protein translocation and folding. We found that in bacteria, N-glycosylation can occur independently of the protein translocation machinery. In an in vitro assay, bacterial oligosaccharyltransferase glycosylated a folded endogenous substrate protein with high efficiency and folded bovine ribonuclease A with low efficiency. Unfolding the eukaryotic substrate greatly increased glycosylation. We propose that in the bacterial system, glycosylation sites are located in flexible parts of folded proteins, whereas the eukaryotic cotranslational glycosylation evolved to a mechanism presenting the substrate in a flexible form before folding.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kowarik, Michael -- Numao, Shin -- Feldman, Mario F -- Schulz, Benjamin L -- Callewaert, Nico -- Kiermaier, Eva -- Catrein, Ina -- Aebi, Markus -- New York, N.Y. -- Science. 2006 Nov 17;314(5802):1148-50.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Microbiology, Department of Biology, Eidgenossische Technische Hochschule (ETH) Zurich, 8093 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17110579" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Bacterial Proteins/*metabolism ; Campylobacter jejuni ; Cattle ; Escherichia coli ; Glycoproteins/*metabolism ; Glycosylation ; Hexosyltransferases/metabolism ; Membrane Proteins/metabolism ; Molecular Sequence Data ; *Protein Folding ; Protein Transport ; Recombinant Proteins/metabolism
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  • 29
    Publication Date: 2005-03-05
    Description: Innate immunity in higher plants invokes a sophisticated surveillance system capable of recognizing bacterial effector proteins. In Arabidopsis, resistance to infection by strains of Pseudomonas syringae expressing the effector AvrRpt2 requires the plant resistance protein RPS2. AvrRpt2 was identified as a putative cysteine protease that results in the elimination of the Arabidopsis protein RIN4. RIN4 cleavage serves as a signal to activate RPS2-mediated resistance. AvrRpt2 is delivered into the plant cell, where it is activated by a eukaryotic factor that we identify as cyclophilin. This activation of AvrRpt2 is necessary for protease activity. Active AvrRpt2 can then directly cleave RIN4.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Coaker, Gitta -- Falick, Arnold -- Staskawicz, Brian -- R01-FM069680-01/PHS HHS/ -- New York, N.Y. -- Science. 2005 Apr 22;308(5721):548-50. Epub 2005 Mar 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15746386" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis/*immunology/*metabolism/microbiology ; Arabidopsis Proteins/genetics/*metabolism ; Bacterial Proteins/chemistry/*metabolism ; Carrier Proteins/genetics/*metabolism ; Cyclophilins/*metabolism ; Cyclosporine/pharmacology ; Cysteine Endopeptidases/metabolism ; Enzyme Activation ; Escherichia coli ; Mass Spectrometry ; Mutation ; Peptide Mapping ; Plant Diseases ; Pseudomonas syringae/*metabolism/pathogenicity ; Recombinant Fusion Proteins/metabolism ; Saccharomyces cerevisiae/genetics/metabolism ; Sirolimus/pharmacology
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  • 30
    Publication Date: 2005-02-26
    Description: Although structure determination of soluble proteins has become routine, our understanding of membrane proteins has been limited by experimental bottlenecks in obtaining both sufficient yields of protein and ordered crystals. Mistic is an unusual Bacillus subtilis integral membrane protein that folds autonomously into the membrane, bypassing the cellular translocon machinery. Using paramagnetic probes, we determined by nuclear magnetic resonance (NMR) spectroscopy that the protein forms a helical bundle with a surprisingly polar lipid-facing surface. Additional experiments suggest that Mistic can be used for high-level production of other membrane proteins in their native conformations, including many eukaryotic proteins that have previously been intractable to bacterial expression.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Roosild, Tarmo P -- Greenwald, Jason -- Vega, Mark -- Castronovo, Samantha -- Riek, Roland -- Choe, Senyon -- GM056653/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2005 Feb 25;307(5713):1317-21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Biology Laboratory, Salk Institute, San Diego, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15731457" target="_blank"〉PubMed〈/a〉
    Keywords: Bacillus subtilis/*chemistry ; Bacterial Proteins/*chemistry/*metabolism ; Cell Membrane/chemistry ; Crystallography, X-Ray ; Electron Spin Resonance Spectroscopy ; Escherichia coli ; Hydrogen Bonding ; Lipid Bilayers ; Membrane Proteins/*chemistry/*metabolism ; Micelles ; Models, Molecular ; Molecular Sequence Data ; Molecular Weight ; Mutation ; Nuclear Magnetic Resonance, Biomolecular ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Receptors, Transforming Growth Factor beta/chemistry/metabolism ; Recombinant Proteins/chemistry/metabolism
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  • 31
    Publication Date: 2005-04-12
    Description: Enzymes that produce retinal and related apocarotenoids constitute a sequence- and thus structure-related family, a member of which was analyzed by x-ray diffraction. This member is an oxygenase and contains an Fe2+-4-His arrangement at the axis of a seven-bladed beta-propeller chain fold covered by a dome formed by six large loops. The Fe2+ is accessible through a long nonpolar tunnel that holds a carotenoid derivative in one of the crystals. On binding, three consecutive double bonds of this carotenoid changed from a straight all-trans to a cranked cis-trans-cis conformation. The remaining trans bond is located at the dioxygen-ligated Fe2+ and cleaved by oxygen.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kloer, Daniel P -- Ruch, Sandra -- Al-Babili, Salim -- Beyer, Peter -- Schulz, Georg E -- R01 EY020551/EY/NEI NIH HHS/ -- New York, N.Y. -- Science. 2005 Apr 8;308(5719):267-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Organische Chemie und Biochemie, Albert-Ludwigs-Universitat, Albertstrasse 21, 79104 Freiburg im Breisgau, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15821095" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Cloning, Molecular ; Crystallography, X-Ray ; Escherichia coli ; Humans ; Molecular Sequence Data ; Oxygenases/*chemistry ; Protein Conformation ; Recombinant Proteins ; Retinaldehyde/*chemistry ; Synechocystis/*enzymology/genetics
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  • 32
    facet.materialart.
    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2003-05-17
    Description: During protein synthesis, transfer RNAs (tRNAs) are translocated from the aminoacyl to peptidyl to exit sites of the ribosome, coupled to the movement of messenger RNA (mRNA), in a reaction catalyzed by elongation factor G (EF-G) and guanosine triphosphate (GTP). Here, we show that the peptidyl transferase inhibitor sparsomycin triggers accurate translocation in vitro in the absence of EF-G and GTP. Our results provide evidence that translocation is a function inherent to the ribosome and that the energy to drive this process is stored in the tRNA-mRNA-ribosome complex after peptide-bond formation. These findings directly implicate the peptidyl transferase center of the 50S subunit in the mechanism of translocation, a process involving large-scale movement of tRNA and mRNA in the 30S subunit, some 70 angstroms away.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fredrick, Kurt -- Noller, Harry F -- GM17129/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2003 May 16;300(5622):1159-62.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California, Santa Cruz, CA 95064, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12750524" target="_blank"〉PubMed〈/a〉
    Keywords: Acylation ; Anti-Bacterial Agents/pharmacology ; Catalysis ; Codon ; Enzyme Inhibitors/pharmacology ; Escherichia coli ; Escherichia coli Proteins/drug effects/metabolism ; Peptide Elongation Factor G/metabolism ; Peptidyl Transferases/antagonists & inhibitors ; Protein Biosynthesis ; RNA, Bacterial/drug effects/metabolism ; RNA, Messenger/drug effects/*metabolism ; RNA, Transfer/drug effects/*metabolism ; Ribosomes/drug effects/*metabolism ; Sparsomycin/*pharmacology
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  • 33
    Publication Date: 2002-04-20
    Description: Aquaporins are transmembrane channels found in cell membranes of all life forms. We examine their apparently paradoxical property, facilitation of efficient permeation of water while excluding protons, which is of critical importance to preserving the electrochemical potential across the cell membrane. We have determined the structure of the Escherichia coli aquaglyceroporin GlpF with bound water, in native (2.7 angstroms) and in W48F/F200T mutant (2.1 angstroms) forms, and carried out 12-nanosecond molecular dynamics simulations that define the spatial and temporal probability distribution and orientation of a single file of seven to nine water molecules inside the channel. Two conserved asparagines force a central water molecule to serve strictly as a hydrogen bond donor to its neighboring water molecules. Assisted by the electrostatic potential generated by two half-membrane spanning loops, this dictates opposite orientations of water molecules in the two halves of the channel, and thus prevents the formation of a "proton wire," while permitting rapid water diffusion. Both simulations and observations revealed a more regular distribution of channel water and an increased water permeability for the W48F/F200T mutant.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tajkhorshid, Emad -- Nollert, Peter -- Jensen, Morten O -- Miercke, Larry J W -- O'Connell, Joseph -- Stroud, Robert M -- Schulten, Klaus -- New York, N.Y. -- Science. 2002 Apr 19;296(5567):525-30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Theoretical Biophysics Group, Beckman Institute, University of Illinois at Urbana-Champaign, 405 North Mathews, Urbana, IL 61801, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11964478" target="_blank"〉PubMed〈/a〉
    Keywords: Aquaporins/*chemistry/genetics/metabolism ; Asparagine/chemistry ; Chemistry, Physical ; Computer Simulation ; Crystallography, X-Ray ; Diffusion ; Electrochemistry ; Escherichia coli ; Escherichia coli Proteins/*chemistry/genetics/metabolism ; Glycerol/metabolism ; Hydrogen Bonding ; Models, Molecular ; Mutation ; Physicochemical Phenomena ; Protein Conformation ; Protein Structure, Secondary ; Protons ; Static Electricity ; Water/chemistry/*metabolism
    Print ISSN: 0036-8075
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  • 34
    Publication Date: 2002-09-21
    Description: The SecA adenosine triphosphatase (ATPase) mediates extrusion of the amino termini of secreted proteins from the eubacterial cytosol based on cycles of reversible binding to the SecYEG translocon. We have determined the crystal structure of SecA with and without magnesium-adenosine diphosphate bound to the high-affinity ATPase site at 3.0 and 2.7 angstrom resolution, respectively. Candidate sites for preprotein binding are located on a surface containing the SecA epitopes exposed to the periplasm upon binding to SecYEG and are thus positioned to deliver preprotein to SecYEG. Comparisons with structurally related ATPases, including superfamily I and II ATP-dependent helicases, suggest that the interaction geometry of the tandem motor domains in SecA is modulated by nucleotide binding, which is shown by fluorescence anisotropy experiments to reverse an endothermic domain-dissociation reaction hypothesized to gate binding to SecYEG.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hunt, John F -- Weinkauf, Sevil -- Henry, Lisa -- Fak, John J -- McNicholas, Paul -- Oliver, Donald B -- Deisenhofer, Johann -- New York, N.Y. -- Science. 2002 Sep 20;297(5589):2018-26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, 702A Fairchild Center, MC2434, Columbia University, New York, NY 10027, USA. hunt@sid.bio.columbia.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12242434" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Diphosphate/chemistry/*metabolism ; Adenosine Triphosphatases/*chemistry/*metabolism ; Adenosine Triphosphate/chemistry/*metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Bacillus subtilis/*enzymology ; Bacterial Proteins/*chemistry/metabolism ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; DNA Helicases/chemistry ; DNA, Bacterial/chemistry/metabolism ; DNA, Single-Stranded/chemistry/metabolism ; Dimerization ; Escherichia coli ; Escherichia coli Proteins/*chemistry/*metabolism ; Eukaryotic Initiation Factor-4A ; Fluorescence Polarization ; Fourier Analysis ; Hydrogen Bonding ; Ligands ; Membrane Transport Proteins/*chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Peptide Initiation Factors/chemistry ; Peptides/chemistry ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Precursors/metabolism ; Protein Structure, Secondary ; *Protein Structure, Tertiary ; Temperature
    Print ISSN: 0036-8075
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  • 35
    ISSN: 1572-8773
    Keywords: Escherichia coli ; heavy metals ; tellurite resistance ; ter genes ; transposon insertion mutagenesis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract The tellurite-resistant Escherichia coli strain KL53 was found during testing of the group of clinical isolates for antibiotics and heavy metal ion resistance (Burian et al. 1990). Determinant of the tellurite resistance of the strain was located on the large conjugative plasmid pTE53 and cloned into pACYC184. Three different Ter clones harboring pLK2, pLK18 and pLK20 were isolated (Burian et al. 1998). The smallest functional Ter clone harboring pLK18 was chosen for further analysis. Plasmid pLK18 have been subcloned to obtain convenient DNA fragments for sequencing of tellurite-resistance determinant. Sequencing of this DNA fragments provided complete DNA sequence of the determinant, 5250 bp in size. The sequence has been compared with nucleotide and protein databank (BLAST programs) and significant homology with the three known operons coding for tellurite resistance has been found (determinat on plasmid pR478 from Serratia marcescens, on plasmid pMER610 from Alcaligenes sp. and chromosomal tellurite resistance genes from Proteus mirabilis). We identified 5 ORFs coding for 5 genes named terB to terF. The clone harboring pLK18 was subjected to the transposition with Tn1737Km to disrupt determinant of the tellurite resistance. Plasmid DNA of several clones containing pLK18 with Tn1737Km was isolated to locate the target site of Tn1737Km. Analyses showed, the genes terB, terC, terD and terE are essential for conservation of the resistance whereas the gene terF is not important in this respect.
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  • 36
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    Bioscience reports 20 (2000), S. 277-288 
    ISSN: 1573-4935
    Keywords: potassium ion uptake ; proton-potassium exchange ; ATPase activity ; TrkA ; F0F1 ATP synthase ; fermentation ; growth at different pH ; Escherichia coli
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract Escherichia coli accumulates K+ by means of multiple transportsystems, of which TrkA is the most prominent at neutral and alkalinepH while Kup is major at acidic pH. In the present study, K+ uptakewas observed with cells grown under fermentative conditions at an initialpH of 9.0 and 7.3 (the medium pH decreased to 8.4 and 6.8, respectively,during the mid-logarithmic growth phase), washed with distilled water andresuspended in a K+ containing medium at pH 7.5 in the presence ofglucose. The kinetics for this K+ uptake and the amount of K+accumulated by the wild type and mutants having a functional TrkA orKup could confirm that K+ uptake by E. coli grown either at pH 9.0or pH 7.3 occurs mainly through TrkA. The following results distinguishpH dependent mode of TrkA operating: (1) K+ uptake was inhibited byDCCD in cells grown either at pH 9.0 or pH 7.3, although the stoichiometryof K+ influx to DCCD-inhibited H+ efflux for bacteria grownat pH 9.0 varied with external K+ concentration, but remained constantfor cells grown at pH 7.3; (2) K+ uptake was observed with an atpDmutant grown at pH 9.0 but not at pH 7.3; (3) The DCCD-inhibited H+efflux was increased 8-fold less by 5 mM K+ added into a K+ freemedium for bacteria grown at pH 9.0 than that for cells grown at pH 7.3;(4) the DCCD-inhibited ATPase activity of membrane vesicles from bacteriagrown at pH 9.0 was reduced a little in the presence of 100 mM K+,but stimulated more than 2.4-fold at pH 7.3.
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  • 37
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    Journal of bioenergetics and biomembranes 32 (2000), S. 341-346 
    ISSN: 1573-6881
    Keywords: F1-ATPase ; Escherichia coli ; small-angle X-ray scattering ; quaternary structure ; ab initio shape determination ; disulfide formation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology , Physics
    Notes: Abstract The structural organization and overall dimensions of the Escherichia coli F1-ATPase in solutionhas been analyzed by synchroton X-ray scattering. Using an independent ab initio approach,the low-resolution shape of the hydrated enzyme was determined at 3.2 nm resolution. Theshape permitted unequivocal identification of the volume occupied by the α3 β3 γ complex ofthe atomic model of the ECF1-ATPase. The position of the ^σ and ∈ subunits were found byinteractive fitting of the solution scattering data and by cross-linking studies. Laser-inducedcovalent incorporation of 2-azido-ATP established a direct relationship between nucleotidebinding affinity and the different interactions between the stalk subunits γ and ∈ with the threecatalytic subunits (β) of the F1-ATPase. Mutants of the ECF1-ATPase with the introductionof Trp-for-Tyr replacement in the catalytic site of the complex made it possible to monitorthe activated state for ATP synthesis (ATP conformation) in which the γ and ∈ subunits arein close proximity to the α subunits and the ADP conformation, with the stalk subunits arelinked to the β subunit.
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  • 38
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    Journal of bioenergetics and biomembranes 32 (2000), S. 357-364 
    ISSN: 1573-6881
    Keywords: ATP synthase ; F1F0 ; ab 2 subcomplex ; subunit a ; subunit b ; circular dichroism ; crosslinking ; Escherichia coli
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology , Physics
    Notes: Abstract Membrane-bound ATP synthases (F1F0) catalyze the synthesis of ATP via a rotary catalyticmechanism utilizing the energy of an electrochemical ion gradient. The transmembrane potentialis supposed to propel rotation of a subunit c ring of F0 together with subunits γ and ∈ of F1,hereby forming the rotor part of the enzyme, whereas the remainder of the F1F0 complexfunctions as a stator for compensation of the torque generated during rotation. This reviewfocuses on our recent work on the stator part of the F0 complex, e.g., subunits a and b. Usingepitope insertion and antibody binding, subunit a was shown to comprise six transmembranehelixes with both the N- and C-terminus oriented toward the cytoplasm. By use of circulardichroism (CD) spectroscopy, the secondary structure of subunit b incorporated intoproteoliposomes was determined to be 80% α-helical together with 14% β turn conformation, providingflexibility to the second stalk. Reconstituted subunit b together with isolated ac subcomplexwas shown to be active in proton translocation and functional F1 binding revealing the nativeconformation of the polypeptide chain. Chemical crosslinking in everted membrane vesiclesled to the formation of subunit b homodimers around residues bQ37 to bL65, whereas bA32Ccould be crosslinked to subunit a, indicating a close proximity of subunits a and b near themembrane. Further evidence for the proposed direct interaction between subunits a and b wasobtained by purification of a stable ab 2 subcomplex via affinity chromatography using Histags fused to subunit a or b. This ab 2 subcomplex was shown to be active in proton translocationand F1 binding, when coreconstituted with subunit c. Consequences of crosslink formationand subunit interaction within the F1F0 complex are discussed.
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  • 39
    ISSN: 1573-6881
    Keywords: Escherichia coli ; motor ; ATP synthase ; FoF1 ; catalytic residues ; ion pump ; ATPase ; mechanochemistry ; c-subunit ring ; energy conversion
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology , Physics
    Notes: Abstract Proton-translocating ATP synthase (FoF1) synthesizes ATP from ADP and phosphate, coupled with an electrochemical proton gradient across the biological membrane. It has been established that the rotation of a subunit assembly is an essential feature of the enzyme mechanism and that FoF1 can be regarded as a molecular motor. Thus, experimentally, in the reverse direction (ATP hydrolysis), the chemical reaction drives the rotation of a γεc 10-14 subunit assembly followed by proton translocation. We discuss our very recent results regarding subunit rotation in Escherichia coli FoF1 with a combined biophysical and mutational approach.
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  • 40
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    Journal of bioenergetics and biomembranes 32 (2000), S. 485-491 
    ISSN: 1573-6881
    Keywords: ATP synthase ; ATP hydrolsis ; ε subunit ; Escherichia coli ; F1-ATPase ; inhibition ; rotation ; ATP synthesis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology , Physics
    Notes: Abstract The ATP synthase from Escherichia coli is a prototype of the ATP synthases that are found in many bacteria, in the mitochondria of eukaryotes, and in the chloroplasts of plants. It contains eight different types of subunits that have traditionally been divided into F1, a water-soluble catalytic sector, and Fo, a membrane-bound ion transporting sector. In the current rotary model for ATP synthesis, the subunits can be divided into rotor and stator subunits. Several lines of evidence indicate that ε is one of the three rotor subunits, which rotate through 360 degrees. The three-dimensional structure of ε is known and its interactions with other subunits have been explored by several approaches. In light of recent work by our group and that of others, the role of ε in the ATP synthase from E. coli is discussed.
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  • 41
    ISSN: 1573-0972
    Keywords: Bacterial adherence ; bromodeoxyuridine (BrdU) ; Escherichia coli ; fimbria ; immunomax technique
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract Fimbriated and fimbria-less strains of Escherichia coli were isolated from urine of pyelonephritis patients, labelled with bromodeoxyuridine and their adhesion to human umbillical vein endothelial cells was studied employing ELISA and immunocytochemistry. No significant differences were noted in adhesion of the two types of strains.
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  • 42
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    World journal of microbiology and biotechnology 16 (2000), S. 719-724 
    ISSN: 1573-0972
    Keywords: Escherichia coli ; haemolytic uraemic syndrome ; haemorrhagic colitis ; pathogenicity ; Verocytotoxin ; VTEC
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract In 1977, Konowalchuk and colleagues (Konowalchuk, J., Speirs, J.I. & Stavric, S. 1977 Infection and Immunity 18, 775–779) were the first to describe Verocytotoxin-producing strains of Escherichia coli or VTEC. The surveillance of infection caused by VTEC demonstrated strains of E. coli belonging to serogroup O157 as the main cause of human infection capable of causing haemorrhagic colitis (HC) and haemolytic uraemic syndrome (HUS). Infection with O157 VTEC results in a range of disease manifestations including abdominal cramps, vomiting and fever. This frequently leads to cases with bloody diarrhoea and HC, and approximately 10% of patients develop HUS. The symptoms of disease caused by VTEC O157 have been well documented and the pathogenic mechanisms expressed by VTEC have been the focus of considerable attention. However, the role of putative pathogenic mechanisms in the pathogenesis of disease is not fully understood. The aim of this review is to consider the clinical aspects of infection with strains of VT-producing E. coli O157 in terms of the putative pathogenic mechanisms expressed by these bacteria.
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  • 43
    Publication Date: 2000-09-16
    Description: Extremely halophilic archaea contain retinal-binding integral membrane proteins called bacteriorhodopsins that function as light-driven proton pumps. So far, bacteriorhodopsins capable of generating a chemiosmotic membrane potential in response to light have been demonstrated only in halophilic archaea. We describe here a type of rhodopsin derived from bacteria that was discovered through genomic analyses of naturally occuring marine bacterioplankton. The bacterial rhodopsin was encoded in the genome of an uncultivated gamma-proteobacterium and shared highest amino acid sequence similarity with archaeal rhodopsins. The protein was functionally expressed in Escherichia coli and bound retinal to form an active, light-driven proton pump. The new rhodopsin exhibited a photochemical reaction cycle with intermediates and kinetics characteristic of archaeal proton-pumping rhodopsins. Our results demonstrate that archaeal-like rhodopsins are broadly distributed among different taxa, including members of the domain Bacteria. Our data also indicate that a previously unsuspected mode of bacterially mediated light-driven energy generation may commonly occur in oceanic surface waters worldwide.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Beja, O -- Aravind, L -- Koonin, E V -- Suzuki, M T -- Hadd, A -- Nguyen, L P -- Jovanovich, S B -- Gates, C M -- Feldman, R A -- Spudich, J L -- Spudich, E N -- DeLong, E F -- HG01775-02S1/HG/NHGRI NIH HHS/ -- R01GM27750/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Sep 15;289(5486):1902-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039-0628, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10988064" target="_blank"〉PubMed〈/a〉
    Keywords: Aerobiosis ; Amino Acid Sequence ; Archaea/classification/physiology ; Bacteria/genetics ; *Bacterial Physiological Phenomena ; Cloning, Molecular ; Escherichia coli ; Gammaproteobacteria/classification/genetics/*physiology ; Molecular Sequence Data ; Oceans and Seas ; Photochemistry ; Photosynthesis ; Phylogeny ; Phytoplankton/genetics/physiology ; Protein Binding ; Proton Pumps/physiology ; Retinaldehyde/metabolism ; Rhodopsin/*physiology ; Rhodopsins, Microbial ; *Water Microbiology
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  • 44
    Publication Date: 2000-07-15
    Description: p53 plays an essential pro-apoptotic role, a function thought to be shared with its family members p73 and p63. Here, we show that p73 is primarily present in developing neurons as a truncated isoform whose levels are dramatically decreased when sympathetic neurons apoptose after nerve growth factor (NGF) withdrawal. Increased expression of truncated p73 rescues these neurons from apoptosis induced by NGF withdrawal or p53 overexpression. In p73-/- mice, all isoforms of p73 are deleted and the apoptosis of developing sympathetic neurons is greatly enhanced. Thus, truncated p73 is an essential anti-apoptotic protein in neurons, serving to counteract the pro-apoptotic function of p53.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pozniak, C D -- Radinovic, S -- Yang, A -- McKeon, F -- Kaplan, D R -- Miller, F D -- New York, N.Y. -- Science. 2000 Jul 14;289(5477):304-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Neuronal Survival, Brain Tumor Research Center, Montreal Neurological Institute, McGill University, Montreal, Canada H3A 2B4.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10894779" target="_blank"〉PubMed〈/a〉
    Keywords: Adenoviridae/genetics ; Animals ; Apoptosis/*physiology ; Cells, Cultured ; DNA-Binding Proteins/biosynthesis/chemistry/*physiology ; Escherichia coli ; Genes, Tumor Suppressor ; Humans ; Mice ; Mice, Inbred BALB C ; Nerve Growth Factor/pharmacology ; Neurons/*physiology ; Nuclear Proteins/biosynthesis/chemistry/*physiology ; Protein Isoforms/biosynthesis/chemistry/physiology ; Recombinant Proteins ; Sympathetic Nervous System/cytology/*physiology ; Tumor Suppressor Protein p53/antagonists & inhibitors/*physiology ; Tumor Suppressor Proteins
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  • 45
    Publication Date: 2000-08-11
    Description: Biochemical and crystallographic evidence suggests that 23S ribosomal RNA (rRNA) is the catalyst of peptide bond formation. To explore the mechanism of this reaction, we screened for nucleotides in Escherichia coli 23S rRNA that may have a perturbed pKa (where Ka is the acid constant) based on the pH dependence of dimethylsulfate modification. A single universally conserved A (number 2451) within the central loop of domain V has a near neutral pKa of 7.6 +/- 0.2, which is about the same as that reported for the peptidyl transferase reaction. In vivo mutational analysis of this nucleotide indicates that it has an essential role in ribosomal function. These results are consistent with a mechanism wherein the nucleotide base of A2451 serves as a general acid base during peptide bond formation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Muth, G W -- Ortoleva-Donnelly, L -- Strobel, S A -- GM54839/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Aug 11;289(5481):947-50.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, CT 06520-8114, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10937997" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine/chemistry/*metabolism ; Binding Sites ; Catalysis ; Dimethyl Sulfoxide ; Escherichia coli ; Hydrogen Bonding ; Methylation ; Mutation ; *Peptide Biosynthesis ; Peptidyl Transferases/*chemistry/*metabolism ; Protons ; RNA, Bacterial/chemistry/genetics/metabolism ; RNA, Ribosomal, 23S/*chemistry/genetics/*metabolism ; Ribosomes/chemistry/*metabolism ; Tubercidin/metabolism
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  • 46
    ISSN: 1572-8773
    Keywords: photoaffinity labeling ; Escherichia coli ; FhuA ; siderophores ; ferrichrome ; azidobenzoyldesferriferricrocin
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract p-azidobenzoyloxy desferriferricrocin (AF) 2, a photoactivatable analog of ferrichrome, was prepared by selective acylation of the serine group of ferricrocin 1 in two steps: transesterification of ferricrocin followed by demetallation. A model compound, (L) 2-benzyloxycarbonylamino-3-p-azidobenzoyloxy N-isopropyl propionamide 8, was separately synthesized in order to set up optimal transesterification conditions to avoid α, β-elimination or epimerization of serine. Binding of iron-loaded AF (FeAF) to the FhuA outer membrane receptor protein of Escherichia coli AB2847 was demonstrated by inhibition of ferrichrome transport, interference with the infection by the bacteriophage φ80 and with killing of cells by albomycin and colicin M. FeAF transported iron only weakly which indicates that the photoaffinity moiety is incompatible with transport or intracellular iron release from the siderophore.
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  • 47
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    Journal of thermal analysis and calorimetry 58 (1999), S. 435-440 
    ISSN: 1572-8943
    Keywords: Escherichia coli ; microcalorimeter ; nutrient drug ; optimum concentration ; optimum promoter action
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The power vs. time curves of the promoter bacteria of a nutrient drug were determined by using a 2277 Thermal Activity Monitor (Sweden). A new experimental model of bacterial growth were established. The growth rate constant, heat output and optimum concentration of specific promoter bacterial of nutrient drug were calculated.
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  • 48
    ISSN: 1573-0972
    Keywords: Acetic acid production ; carbon metabolism ; continuous culture ; Escherichia coli ; metabolic engineering
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract The growth kinetics of an Escherichia coli wild type strain and two derivative mutants were examined in batch cultures and in glucose-limited chemostats. One mutant (PB12) had an inactive phosphotranferase transport system and the other (PB25) had interrupted pykA and pykF genes that code for the two pyruvate kinase isoenzymes. In both batch and continuous culture, important differences in acetic acid accumulation and other metabolic activities were found. Compared to the wild type strain, we observed a reduction in acetic acid accumulation of 25 and 80% in PB25 and PB12 strains respectively, in batch culture. Continuous culture experiments revealed that compared to the other two strains, PB25 accumulated less acetic acid as a function of dilution rate. In continuous cultures, oxidoreductase metabolic activities were substantially affected in the two mutant strains. These changes in turn were reflected in different levels of biomass and CO2 production, and in oxygen consumption.
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  • 49
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    World journal of microbiology and biotechnology 15 (1999), S. 65-71 
    ISSN: 1573-0972
    Keywords: Escherichia coli ; fedbatch cultivation ; growth rate ; high cell density ; plasmid stability
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract The effect of higher cell densities on the expression and segregational stability of a recombinant E. coli- B. subtilisshuttle plasmid coding for carboxymethylcellulase (CMCase) activity, was studied in E. coli DH5α. Of the various feeding policies adopted for maximal expression and stability, exponential feeding resulted in the highest biomass of 15g dry cell weight (DCW) l−1 and plasmid stability of 45%. A CMCase activity of 11400 Uml−1 was achieved as compared to 230 Uml−1 during batch cultivation. In the case of other feeding strategies viz., constant feeding, linear feeding or intermittent feeding, the plasmid stability varied between 20% to 60%. Biomass achieved ranged from 5.0 g DCW l−1 to 9.0 g DCW l−1 and enzyme activities were between 2550 Uml−1 and 6000 Uml−1.
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  • 50
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    World journal of microbiology and biotechnology 15 (1999), S. 475-480 
    ISSN: 1573-0972
    Keywords: α-Amylase ; Bacillus laterosporus ; cloning ; Escherichia coli ; secretion
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract α-Amylase gene from Bacillus laterosporus P3 was cloned and expressed in Escherichia coli HB101 and DH5α. Up to 92% of the cloned gene product was secreted into the medium by the recombinant E. coli. The recombinant crude enzyme showed improved functionality in terms of activity at a wider pH range and at higher temperature, as compared to the crude enzyme from the donor strain. The improved functionality of the cloned enzyme was due to the absence of a contaminating protease which was co-produced in the donor strain. Sub-cloning of the α-amylase gene using the promoter-probe vector, pKT240 in E. coli DH5α indicated the presence of a promoter of B. laterosporus P3 in the cloned fragment.
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  • 51
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    World journal of microbiology and biotechnology 15 (1999), S. 497-499 
    ISSN: 1573-0972
    Keywords: Amylose ; amylopectin ; Escherichia coli ; β-glucuronidase ; pullulan ; starch
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract Synthesis of β-glucuronidase in starch-degrading Escherichia coli (S1) was induced by amylose, amylopectin and pullulan supplied in mineral medium as the sole carbon source (1%, w/v). The maximum activity occurred after 4 days when cultures reached the stationary phase of growth, but induction was also evident during log-phase. The effects obtained with amylose, amylopectin and pullulan were higher than that obtained with maize starch.
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  • 52
    Publication Date: 1999-08-14
    Description: Many Gram-negative pathogens assemble architecturally and functionally diverse adhesive pili on their surfaces by the chaperone-usher pathway. Immunoglobulin-like periplasmic chaperones escort pilus subunits to the usher, a large protein complex that facilitates the translocation and assembly of subunits across the outer membrane. The crystal structure of the PapD-PapK chaperone-subunit complex, determined at 2.4 angstrom resolution, reveals that the chaperone functions by donating its G(1) beta strand to complete the immunoglobulin-like fold of the subunit via a mechanism termed donor strand complementation. The structure of the PapD-PapK complex also suggests that during pilus biogenesis, every subunit completes the immunoglobulin-like fold of its neighboring subunit via a mechanism termed donor strand exchange.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sauer, F G -- Futterer, K -- Pinkner, J S -- Dodson, K W -- Hultgren, S J -- Waksman, G -- R01AI29549/AI/NIAID NIH HHS/ -- R01DK51406/DK/NIDDK NIH HHS/ -- R01GM54033/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1999 Aug 13;285(5430):1058-61.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Microbiology, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10446050" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*chemistry/*metabolism ; Crystallography, X-Ray ; Escherichia coli ; *Escherichia coli Proteins ; Fimbriae Proteins ; Fimbriae, Bacterial/chemistry/*metabolism/ultrastructure ; Models, Molecular ; Molecular Chaperones/*chemistry/*metabolism ; Molecular Sequence Data ; *Periplasmic Proteins ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Sequence Alignment
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 53
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 1999-11-05
    Description: Phototropism of Arabidopsis thaliana seedlings in response to a blue light source is initiated by nonphototropic hypocotyl 1 (NPH1), a light-activated serine-threonine protein kinase. Mutations in three loci [NPH2, root phototropism 2 (RPT2), and NPH3] disrupt early signaling occurring downstream of the NPH1 photoreceptor. The NPH3 gene, now cloned, encodes a NPH1-interacting protein. NPH3 is a member of a large protein family, apparently specific to higher plants, and may function as an adapter or scaffold protein to bring together the enzymatic components of a NPH1-activated phosphorelay.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Motchoulski, A -- Liscum, E -- New York, N.Y. -- Science. 1999 Oct 29;286(5441):961-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10542152" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arabidopsis/genetics/*metabolism ; *Arabidopsis Proteins ; Cell Membrane/metabolism ; Cloning, Molecular ; Escherichia coli ; Molecular Sequence Data ; Phosphoproteins/genetics/*metabolism ; Photoreceptor Cells, Invertebrate/*metabolism ; Phototropism ; Plant Proteins/genetics/*metabolism ; Protein Binding ; Two-Hybrid System Techniques
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 54
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1999-09-11
    Description: Translational fidelity is established by ribosomal recognition of the codon-anticodon interaction within the aminoacyl-transfer RNA (tRNA) site (A site) of the ribosome. Experiments are presented that reveal possible contacts between 16S ribosomal RNA and the codon-anticodon complex. N1 methylation of adenine at position 1492 (A1492) and A1493 interfered with A-site tRNA binding. Mutation of A1492 and A1493 to guanine or cytosine also impaired A-site tRNA binding. The deleterious effects of A1492G or A1493G (or both) mutations were compensated by 2'fluorine substitutions in the mRNA codon. The results suggest that the ribosome recognizes the codon-anticodon complex by adenine contacts to the messenger RNA backbone and provide a mechanism for molecular discrimination of correct versus incorrect codon-anticodon pairs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yoshizawa, S -- Fourmy, D -- Puglisi, J D -- GM51266/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1999 Sep 10;285(5434):1722-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10481006" target="_blank"〉PubMed〈/a〉
    Keywords: Adenine/analogs & derivatives/metabolism ; Anticodon/chemistry/*metabolism ; Binding Sites ; Biotin ; Codon/chemistry/*metabolism ; Escherichia coli ; Hydrogen Bonding ; Methylation ; Mutagenesis, Site-Directed ; *Nucleic Acid Conformation ; Paromomycin/pharmacology ; Protein Biosynthesis ; RNA, Bacterial/chemistry/metabolism ; RNA, Ribosomal, 16S/chemistry/genetics/*metabolism ; RNA, Transfer, Met/metabolism ; RNA, Transfer, Phe/metabolism ; Ribosomes/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 55
    Electronic Resource
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    Springer
    BioMetals 11 (1998), S. 223-227 
    ISSN: 1572-8773
    Keywords: Escherichia coli ; metabolic rates of selenium ; selenium
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract Escherichia coli will reduce selenite (SeO 3 2- ) andselenate (SeO 4 2- ) to elemental selenium Se 0 . Seleniumwill also become incorporated intoproteins as part of the amino acids selenocysteine or selenomethionine.The reaction of selenitewith glutathione produces selenodiglutathione (GS-Se-GS). Selenodiglutathioneand itssubsequent reduction to glutathioselenol (GS-SeH) are likely the key intermediatesin the possiblemetabolic fates of selenium. This review presents the possible pathwaysinvolving selenium in E. coli. Identification of intermediates and potentialprocesses from uptake of the toxic oxyanions through to theirdetoxification will assist us inunderstanding the complexities of metalloid oxyanion metabolism in thesebacteria.
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  • 56
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    Springer
    Molecular and cellular biochemistry 183 (1998), S. 125-132 
    ISSN: 1573-4919
    Keywords: fission yeast ; Na+/H+ antiporter ; Escherichia coli ; expression ; lithium resistance
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology , Medicine
    Notes: Abstract Sod2 is the sodium-proton antiporter on the plasma membrane of the fission yeast Schizosaccharomyces pombe. It is vitally important for sodium export and pH homeostasis in this organism. Recently, the sod2 gene has been cloned and sequenced. However, initial attempts to express sod2 in Escherichia coli using the T7 promoter failed. In the present work we examined physiological consequences of expression of sod2 in E. coli. To alleviate problems caused by expression of sod2 we: (i) used sodium-free media at all steps; (ii) used the moderate tac promoter for expression and; (iii) used E. coli strain MH1 which has impaired sodium exchange. The effect of sod2 expression on E. coli varied depending on the E. coli genotype. When sod2 was expressed in BL21 cells which have normal N a+/H+ antiporters, the result was a Li+ sensitive phenotype. LiCl completely arrested or prevented growth of BL21 E. coli transformed with the sod2 gene. The effect on growth was pronounced in media of low external pH. Sod2 was then expressed in E. coli MH1 which is devoid of endogenous Na+/H+ antiporters. These cells became more resistant to external LiCl, but only in Na+ containing media. In the absence of external Na+, the presence of sod2 reduced growth. The results are explained in a model which demonstrates the physiological consequences of interference by expression of a foreign electroneutral Na+/H+ antiporter in conjunction with different housekeeping systems of E. coli host cells.
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  • 57
    ISSN: 1573-4943
    Keywords: Cyclic AMP receptor protein ; Escherichia coli ; protein stability ; denaturation kinetics ; fluorescence ; 8-anilino-1-naphthalenesulfonic acid
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract cAMP receptor protein (CRP) regulates expression of a number of genes in Escherichia coli. The protein is a homodimer and each monomer is folded into two structural domains. The biological activation of CRP upon cAMP binding may involve the subunit realignment as well as reorientation between the domains within each subunit. In order to study the interactions between the subunits or domains, we performed stopped-flow measurements of the guanidine hydrochloride (GuHCl)-induced denaturation of CRP. The changes in CRP structure induced by GuHCl were monitored using both intrinsic Trp fluorescence as well as the fluorescence of an extrinsic probe, 8-anilino-1-Naphthalenesulfonic acid (ANS). Results of CRP denaturation using Trp fluorescence detection are consistent with a two-step model [Malecki, and Wasylewski, (1997), Eur. J. Biochem. 243, 660], where the dissociation of dimer into subunits is followed by the monomer unfolding. The denaturation of CRP monitored by ANS fluorescence reveals the existence of two additional processes. One occurs before the dissociation of CRP into subunits, whereas the second takes place after the dissociation, but prior to proper subunit unfolding. These additional processes suggest that CRP denaturation is described by a more complicated mechanism than a simple three-state equilibrium and may involve additional changes in both inter- and intrasubunit interactions. We also report the effect of cAMP on the kinetics of CRP subunit unfolding and refolding.
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  • 58
    ISSN: 1573-4943
    Keywords: Cyclic AMP receptor protein ; Escherichia coli ; protein stability ; Trp fluorescence ; circular dichroism
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Kinetic measurements of denaturation and renaturation of two mutants of cAMP receptor protein (CRP) at position 128, namely Ser→Ala and Ser→Pro, were performed in order to assess changes introduced by the mutation in the quaternary structure and protein stability. No significant changes were found in the unfolding/refolding reactions. However, small perturbations in the dissociation of CRP dimer can be seen, which indicate that subunit interactions are influenced by the mutation. Studies of intrinsic fluorescence quenching of these two mutants are also reported, showing changes compared with wild-type protein. Near-UV circular dichroism measurements indicate, however, that Trp residues remain in the same environment as in the wild-type CRP. It is proposed that Ser at position 128 is involved in maintaining the proper domain alignment within CRP subunits.
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  • 59
    ISSN: 1573-4986
    Keywords: antiadhesives ; glycoclusters and glycodendrimers ; mannose sensitive adhesion ; type 1 fimbriae ; Escherichia coli
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
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  • 60
    ISSN: 1573-6881
    Keywords: Escherichia coli ; Quinol oxidase ; cytochrome bo3 ; cytochrome c oxidase ; nitric oxide reductase ; EPR spectroscopy ; MCD spectroscopy ; oxyferryl heme
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology , Physics
    Notes: Abstract For the study of the dinuclear center of heme-copper oxidases cytochrome bo 3 from Escherichia coli offers several advantages over the extensively charactererized bovine cytochrome c oxidase. The availability of strains with enhanced levels of expression allows purification of the significant amounts of enzyme required for detailed spectroscopic studies. Cytochrome bo 3 is readily prepared as the fast form, with a homogeneous dinuclear center which gives rise to characteristic broad EPR signals not seen in CcO. The absence of CuA and the incorporation of protohemes allows for a detailed interpretation of the MCD spectra arising from the dinuclear center heme o 3. Careful analysis allows us to distinguish between small molecules that bind to heme o 3, those which are ligands of CuB, and those which react to yield higher oxidation states of heme o 3. Here we review results from our studies of the reactions of fast cytochrome bo 3 with formate, fluoride, chloride, azide, cyanide, NO, and H2O2.
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  • 61
    ISSN: 0006-3592
    Keywords: Escherichia coli ; Chloramphenicol Acetyltransferase (CAT) ; Culture Redox Potential (CRP) ; Dithiothreitol (DTT) ; reducing agents ; molecular chaperones ; proteases ; heat shock ; stress response ; protein folding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The independent control of culture redox potential (CRP) by the regulated addition of a reducing agent, dithiothreitol (DTT) was demonstrated in aerated recombinant Escherichia coli fermentations. Moderate levels of DTT addition resulted in minimal changes to specific oxygen uptake, growth rate, and dissolved oxygen. Excessive levels of DTT addition were toxic to the cells resulting in cessation of growth. Chloramphenicol acetyltransferase (CAT) activity (nmoles/μg total protein min.) decreased in batch fermentation experiments with respect to increasing levels of DTT addition. To further investigate the mechanisms affecting CAT activity, experiments were performed to assay heat shock protein expression and specific CAT activity (nmoles/μg CAT min.). Expression of such molecular chaperones as GroEL and DnaK were found to increase after addition of DTT. Additionally, sigma factor 32 (σ32) and several proteases were seen to increase dramatically during addition of DTT. Specific CAT activity (nmoles/μg CAT min.) varied greatly as DTT was added, however, a minimum in activity was found at the highest level of DTT addition in E. coli strains RR1 [pBR329] and JM105 [pROEX-CAT]. In conjunction, cellular stress was found to reach a maximum at the same levels of DTT. Although DTT addition has the potential for directly affecting intracellular protein folding, the effects felt from the increased stress within the cell are likely the dominant effector. That the effects of DTT were measured within the cytoplasm of the cell suggests that the periplasmic redox potential was also altered. The changes in specific CAT activity, molecular chaperones, and other heat shock proteins, in the presence of minimal growth rate and oxygen uptake alterations, suggest that the ex vivo control of redox potential provides a new process for affecting the yield and conformation of heterologous proteins in aerated E. coli fermentations. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 59: 248-259, 1998.
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  • 62
    ISSN: 1573-0972
    Keywords: Escherichia coli ; diamines ; homospermidine synthase ; polyamines ; spermidine deficiency ; spermidine synthase
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract The Escherichia coli mutant speE deficient in the gene encoding for spermidine synthase has no absolute requirement for spermidine but shows a retarded growth rate. This growth retardation could be unspecifically restored to the respective wild type level by exogenously supplied polyamines such as spermidine, spermine and homospermidine as well as the diamines putrescine and cadaverine. In comparison to the respective wild type, the mutant shows a two-fold increased level of endogenous putrescine but displays a reduced ability to accumulate the diamines putrescine and cadaverine. The ability to accumulate polyamines is not affected. The deleted spermidine synthase gene of the mutant was substituted by heterologous expression of the hss gene from Rhodopseudomonas viridis encoding homospermidine synthase.
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  • 63
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    Biotechnology and Bioengineering 58 (1998), S. 325-328 
    ISSN: 0006-3592
    Keywords: poly(3-hydroxybutyrate) ; Escherichia coli ; filamentation suppression ; defined medium ; high cell density culture ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: A recombinant Escherichia coli strain XL1-Blue harboring a stable high-copy-number plasmid pSYL107 containing the Alcaligenes eutrophus polyhydroxyalkanoate biosynthesis genes and the Escherichia coli ftsZ gene was employed for the production of poly(3-hydroxybutyrate) (PHB) by fed-batch culture in a defined medium. Suppression of filamentation by overexpressing the cell division protein FtsZ allowed production of PHB to a high concentration (77 g/L) with high productivity (2 g/L/h) in a defined medium, which was not possible with the recombinant E. coli that underwent filamentation. Further optimization of fed-batch culture condition resulted in PHB concentration of 104 g/L in a defined medium, which was the highest value reported to date by employing recombinant E. coli. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 58:325-328, 1998.
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  • 64
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    Biotechnology and Bioengineering 60 (1998), S. 551-559 
    ISSN: 0006-3592
    Keywords: Escherichia coli ; SOS ; DNA repair ; recombinant proteins ; promoter ; proteolysis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The production of several non-related heterologous proteins in recombinant Escherichia coli cells promotes a significant transcription of recA and sfiA SOS DNA repair genes. The activation of the SOS system occurs when the expression of plasmid-encoded genes is directed by the strong lambda lytic promoters, but not by IPTG-controlled promoters either at 37 or at 42°C, and it is linked to an extensive degradation of the proteins after their synthesis. The triggering signal for the SOS response could be an important arrest of cell DNA replication observed within the first hour after the induction of recombinant gene expression. The stimulation of this DNA repair system can partially account for the toxicity exhibited by recombinant proteins on actively producing E. coli cells. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 60: 551-559, 1998.
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  • 65
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    Biotechnology and Bioengineering 57 (1998), S. 529-535 
    ISSN: 0006-3592
    Keywords: bacteriophage λ ; Q - mutant ; Escherichia coli ; recombinant protein ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: We previously demonstrated that the λ system integrated into the host chromosome can overcome the instability encountered in continuous operations of unstable plasmid-based expression vectors. High stability of a cloned gene in a lysogenic state and a high copy number in a lytic state provide cloned-gene stability and overexpression in a two-stage continuous operation. But the expression by the commonly used S- mutant λ was only twice as high as that of the single copy. To increase the expression in the λ system, we constructed a Q- mutant λ vector that can be used in long-term operations such as a two-stage continuous operation. The Q- mutant phage λ is deficient in the synthesis of proteins involved in cell lysis and λ DNA packaging, while the S- mutant is deficient in the synthesis of one of two phage proteins required for lysis of the host cell and liberation of the progeny phage. Therefore, it is expected that the replicated Q- λ DNA containing a cloned gene would not be coated by a phage head and would remain naked for ample expression of the cloned gene and host cells would not lyse easily and consequently would produce larger amounts of cloned-gene products. The β-galactosidase expression per unit cell by the Q- mutant in a lytic state was about 30 times higher than that in a lysogenic state, while the expression by the commonly used S- mutant in a lytic state was twice as high as that in a lysogenic state. The optimal switching time of the Q- mutant from the lysogenic state to the lytic state for the maximum production of β-galactosidase was 5.3 h, which corresponds to an early log phase in the batch operation. ©1998 John Wiley & Sons, Inc. Biotechnol Bioeng 57: 529-535, 1998.
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  • 66
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    Biotechnology and Bioengineering 60 (1998), S. 230-238 
    ISSN: 0006-3592
    Keywords: Escherichia coli ; metabolism ; flux ; linear optimization ; biomass composition ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The amino acid composition of proteins and the fatty acid composition of the cell membranes were measured in Escherichia coli growing exponentially in batch culture on glucose, succinate, glycerol, pyruvate, and acetate, and growing under continuous culture conditions on glucose at dilutions rates equivalent to the growth rates of the batch cultures. Although the fatty acid composition of the membranes did change significantly with carbon source and dilution rate, the amino acid content of proteins did not change significantly under either condition. A previously developed stoichiometric model of metabolism was used to calculate the fluxes through the metabolic reactions and to determine their sensitivity to changes in fatty acid and amino acid composition. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 60: 230-238, 1998.
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  • 67
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    Biotechnology and Bioengineering 57 (1998), S. 381-386 
    ISSN: 0006-3592
    Keywords: inclusion bodies ; recombinant protein ; IGF-I ; urea ; Escherichia coli ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: A method is presented for the direct extraction of the recombinant protein Long-R3-IGF-I from inclusion bodies located in the cytoplasm of intact Escherichia coli cells. Chemical treatment with 6M urea, 3 mM EDTA, and 20 mM dithiothreitol (DTT) at pH 9.0 proved an effective combination for extracting recombinant protein from intact cells. Comparable levels of Long-R3-IGF-I were recovered by direct extraction as achieved by in vitro dissolution following mechanical disruption. However, the purity of directly extracted recombinant protein was lower due to contamination by bacterial cell components. The kinetics of direct extraction are described using a first-order equation with the time constant of 3 min. Urea appears important for permeabilization of the cell and dissolution of the inclusion body. Conversely, EDTA is involved in permeabilization of the cell wall and DTT enhances protein release. pH proved to be important with lower levels of protein release achieved at low pH values (〈9). Cell concentration also had a minor effect on Long-R3-IGF-I release and caused an observable increase in viscosity. Advantages of the direct extraction method include its speed, simplicity, and efficiency at releasing product. ©1998 John Wiley & Sons, Inc. Biotechnol Bioeng 57:381-386, 1998.
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  • 68
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    Biotechnology and Bioengineering 58 (1998), S. 231-239 
    ISSN: 0006-3592
    Keywords: polyphosphate metabolism ; metabolic engineering ; Escherichia coli ; bioremediation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Polyphosphate metabolism plays an important role in the bioremediation of phosphate contamination in municiple wastewater, and may play a key role in heavy metal tolerance and bioremediation. However, little is known about the regulation of polyphosphate metabolism in microorganisms and its role in heavy metal toxicity. We have manipulated polyphosphate metabolism in Escherichia coli by overexpressing the genes for polyphosphate kinase (ppk) and for polyphosphatase (ppx) under control of their native promoters and inducible promoters. Overexpression of ppk results in high levels of intracellular polyphosphate, improved phosphate uptake, but no increase in tolerance to heavy metals. Overexpression of both ppk and ppx results in lower levels of intracellular polyphosphate, secretion of phosphate from the cell, and increased tolerance to heavy metals. Metabolic flux analysis indicates that the cell responds to increased flux through the PPK-PPX pathway by altering flux through the TCA cycle. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 58:231-239, 1998.
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  • 69
    ISSN: 0006-3592
    Keywords: Escherichia coli ; flow cytometry ; fluid mechanical stress ; membrane integrity ; membrane potential ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Continuous culture fermentations of Escherichia coli W3110 have been carried out at controlled dissolved oxygen levels of 40% and 10% of saturation. Satisfactory and reproducible results were obtained. Agitation speeds of 400 and 1200 rpm at an aeration rate of 1 vvm have been used as well as an aeration rate of 3 vvm at 400 rpm. The upper levels of these variables represent much higher agitation and aeration intensities than those normally used in practical fermentations. The fermentations were monitored by mass spectrometry and optical density, and cell samples were studied by flow cytometry, SEM, and TEM. Protocols were developed so the state of both cell membranes and cell size could be measured by flow cytometry. Under all the conditions of agitation and aeration, flow cytometric analysis indicated that both cell membranes were intact and that a cytoplasmic membrane potential existed; also the cell size did not change, results confirmed by SEM and TEM. There were no detectable changes in off-gas analysis or optical density during the continuous fermentation nor in the cell structure as revealed by SEM or TEM, except at the highest agitation intensity. Under the latter conditions, after 7 h, the outer polysaccharide layer on the cell was stripped away. It is concluded that any changes in biological performance of this E. coli cell line due to variations in agitation or aeration intensity or scale of operation cannot be attributed to fluid dynamic stresses associated with the turbulence generated by impellers or with bursting bubbles. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 59:612-620, 1998.
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  • 70
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    Biotechnology and Bioengineering 59 (1998), S. 754-761 
    ISSN: 0006-3592
    Keywords: polyphosphate ; Escherichia coli ; phosphate starvation ; phosphate secretion ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Polyphosphate degradation and phosphate secretion were optimized in Escherichia coli strains overexpressing the E. coli polyphosphate kinase gene (ppk) and either the E. coli polyphosphatase gene (ppx) or the Saccharomyces cerevisiae polyphosphatase gene (scPPX1) from different inducible promoters on medium- and high-copy plasmids. The use of a host strain without functional ppk or ppx genes on the chromosome yielded the highest levels of polyphosphate, as well as the fastest degradation of polyphosphate when the gene for polyphosphatase was induced. The introduction of a hybrid metabolic pathway consisting of the E. coli ppk gene and the S. cerevisiae polyphosphatase gene resulted in lower polyphosphate concentrations than when using both the ppk and ppx genes from E. coli, and did not significantly improve the degradation rate. It was also found that the rate of polyphosphate degradation was highest when ppx was induced late in growth, most likely due to the high intracellular polyphosphate concentration. The phosphate released from polyphosphate allowed the growth of phosphate-starved cells; excess phosphate was secreted into the medium, leading to a down-regulation of the phosphate-starvation (Pho) response. The production of alkaline phosphatase, an indicator of the Pho response, can be precisely controlled by manipulating the degree of ppx induction. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 59:754-761, 1998.
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  • 71
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    Biotechnology and Bioengineering 59 (1998), S. 386-391 
    ISSN: 0006-3592
    Keywords: Escherichia coli ; protein production ; secretion ; plasmid stability ; fed-batch ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Periplasmic secretion of overexpressed Bacillus stearothermophilus α-amylase was analyzed in batch and fed-batch cultivations of Escherichia coli MG1655:pCSS4-p and the mutant strain CWML2:pCSS4-p. Under all conditions investigated, growth and product formation of MG1655:pCSS4-p were severely impaired by heterologous protein expression and/or processing, while E. coli CWML2:pCSS4-p was found to be more robust and to accumulate 2- to 3-fold higher maximum α-amylase levels. While this strain is itself potentially interesting for applications, its properties also illustrate the potential of the selection procedure that was employed to obtain it from its progenitor MG1655 (Weikert, C., Sauer, U., Bailey, J. E., 1997. Microbiol. 143: 1567-1574. Application of this procedure to existing industrial strains may lead to significantly improved process organisms. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 59:386-391, 1998.
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  • 72
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    Biotechnology and Bioengineering 57 (1998), S. 228-237 
    ISSN: 0006-3592
    Keywords: AlkB ; Pseudomonas oleovorans ; alkane hydroxylase ; iron ; Escherichia coli ; alk + recombinants ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The alk genes enable Pseudomonas oleovorans to utilize alkanes as sole carbon and energy source. Expression of the alk genes in P. oleovorans and in two Escherichia coli recombinants induced iron limitation in minimal medium cultures. Further investigation showed that the expression of the alkB gene, encoding the integral cytoplasmic membrane protein AlkB, was responsible for the increase of the iron requirement of E. coli W3110 (pGEc47).AlkB is the non-heme iron monooxygenase component of the alkane hydroxylase system, and can be synthesized to levels up to 10% (w/w) of total cell protein in E. coli W3110 (pGEc47). Its synthesis is, however, strictly dependent on the presence of sufficient iron in the medium. Our results show that a glucose-grown E. coli alk+ strain can reach alkane hydroxylase activities of about 25 U/g cdw, and are consistent with the recent finding that catalytically active AlkB contains two, rather than one iron atom per polypeptide chain. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 57: 228-237, 1998.
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  • 73
    ISSN: 0173-0835
    Keywords: Membrane proteins ; Solubility ; Two-dimensional polyacrylamide gel electrophoresis ; Proteome ; Escherichia coli ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: We describe the extraction and enrichment of membrane proteins for separation by two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) after differential solubilization of an Escherichia coli cell lysate. In a simple three-step sequential solubilization protocol applicable for whole cell lysates, membrane proteins are partitioned from other cellular proteins by their insolubility in solutions conventionally used for isoelectric focusing (IEF). As the first step, Tris-base was used to solubilize many cytosolic proteins. The resultant pellet was then subjected to conventional solubilizing solutions (urea, 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate, dithiothreitol, Tris, carrier ampholytes). Following the completion of this step, 89% of the initial E. coli sample mass was solubilized. Finally, the membrane protein rich pellet was partially solubilized using a combination of urea, thiourea, tributyl phosphine and multiple zwitterionic surfactants. Using N-terminal sequence tagging and peptide mass fingerprinting we have identified 11 membrane proteins from this pellet. Two of these outer membrane proteins (Omp), OmpW and OmpX, have previously been known only as an open reading frame in E. coli, while OmpC, OmpT and OmpTOLC have not previously been identified on a 2-D gel. The prefractionation of an entire cell lysate into multiple fractions, based on solubility, results in simplified protein patterns following 2-D PAGE using broad-range pH 3.5-10 immobilized pH gradients (IPGs). Additional advantages of sample prefractionation are that protein identification and gel matching, for database construction, is a more manageable task, the procedure requires no specialized apparatus, and the sequential extraction is conducted in a single centrifuge tube, minimizing protein loss.
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  • 74
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    Electrophoresis 19 (1998), S. 536-544 
    ISSN: 0173-0835
    Keywords: Escherichia coli ; Bioinformatics ; Post-genome research ; Short open reading frames ; Small proteins ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: The EcoGene project involves the examination of Escherichia coli K-12 DNA sequences and accompanying annotation in the public databases in order to refine the representation and prediction of the entire set of E. coli K-12 chromosomally encoded protein sequences. The results of this ongoing effort have been deposited in the SWISSPROT protein sequence database as sequencing of the E. coli genome has progressed to completion in recent years. Through this continuing research, we have discovered that the prediction of low molecular weight (small) proteins, arbitrarily defined as protein sequences ≤ 150 amino acids (aa) in length, is problematic and requires special attention. We describe the small protein subset of EcoGene and the approach used to derive this subset from the complete E. coli genome sequence and database annotations. These E. coli proteins have helped to identify new small genes in other organisms and to identify conserved residues (motifs) using database searches and multiple alignments. Two thirds of the E. coli small proteins have not been characterized experimentally. The careful application of computer and laboratory methods to the analysis of small proteins is needed for accurate prediction, verification and characterization. The problem of accurate protein sequence identification is not limited to small proteins or to E. coli; these problems are encountered to varying degrees throughout all sequence databases.
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  • 75
    ISSN: 0173-0835
    Keywords: Two-dimensional polyacrylamide gel electrophoresis ; Escherichia coli ; SWISS-2DPAGE database ; Immobilized pH gradient ; Sequence tag ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: The combination of two-dimensional polyacrylamide gel electrophoresis (2-DPAGE), computer image analysis and several protein identification techniques allowed the Escherichia coli SWISS-2DPAGE database to be established. This is part of the ExPASy molecular biology server accessible through the WWW at the URL address http://www.expasy.ch/ch2d/ch2d-top.html. Here we report recent progress in the development of the E. coli SWISS-2DPAGE database. Proteins were separated with immobilized pH gradients in the first dimension and sodium dodecyl sulfate-polyacrylamide gel electrophoresis in the second dimension. To increase the resolution of the separation and thus the number of identified proteins, a variety of wide and narrow range immobilized pH gradients were used in the first dimension. Micropreparative gels were electroblotted onto polyvinylidene difluoride membranes and spots were visualized by amido black staining. Protein identification techniques such as amino acid composition analysis, gel comparison and microsequencing were used, as well as a recently described Edman “sequence tag” approach. Some of the above identification techniques were coupled with database searching tools. Currently 231 polypeptides are identified on the E. coli SWISS-2DPAGE map: 64 have been identified by N-terminal microsequencing, 39 by amino acid composition, and 82 by sequence tag. Of 153 proteins putatively identified by gel comparison, 65 have been confirmed. Many proteins have been identified using more than one technique. Faster progress in the E. coli proteome project will now be possible with advances in biochemical methodology and with the completion of the entire E. coli genome.
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  • 76
    Publication Date: 1998-05-02
    Description: In the ribosome, the aminoacyl-transfer RNA (tRNA) analog 4-thio-dT-p-C-p-puromycin crosslinks photochemically with G2553 of 23S ribosomal RNA (rRNA). This covalently linked substrate reacts with a peptidyl-tRNA analog to form a peptide bond in a peptidyl transferase-catalyzed reaction. This result places the conserved 2555 loop of 23S rRNA at the peptidyl transferase A site and suggests that peptide bond formation can occur uncoupled from movement of the A-site tRNA. Crosslink formation depends on occupancy of the P site by a tRNA carrying an intact CCA acceptor end, indicating that peptidyl-tRNA, directly or indirectly, helps to create the peptidyl transferase A site.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Green, R -- Switzer, C -- Noller, H F -- New York, N.Y. -- Science. 1998 Apr 10;280(5361):286-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California, Santa Cruz, CA 95064, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9535658" target="_blank"〉PubMed〈/a〉
    Keywords: Anti-Bacterial Agents/pharmacology ; Binding Sites ; Catalysis ; Enzyme Inhibitors/pharmacology ; Escherichia coli ; Nucleic Acid Conformation ; Peptidyl Transferases/antagonists & inhibitors/*metabolism ; Puromycin/analogs & derivatives/chemical synthesis/chemistry/*metabolism ; RNA, Bacterial/chemistry/metabolism ; RNA, Ribosomal, 23S/chemistry/*metabolism ; RNA, Transfer, Amino Acyl/chemistry/*metabolism ; RNA, Transfer, Phe/chemistry/genetics/*metabolism ; Ribosomes/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 77
    ISSN: 1432-1327
    Keywords: Key words Ribonucleotide reductase ; Iron metabolism ; Escherichia coli
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract  Protein R2, the small component of ribonucleotide reductase from Escherichia coli, contains a diferric center and a catalytically essential tyrosyl radical. In vitro, this radical can be produced in the protein from two inactive forms, metR2, containing an intact diiron center and lacking the tyrosyl radical, and apoR2, lacking both iron and the radical. While activation of apoR2 requires only a source of ferrous iron and exposure to O2, activation of metR2 was achieved using a multienzymatic system consisting of an NAD(P)H:flavin oxidoreductase, superoxide dismutase and a poorly defined protein fraction, named fraction b (Fontecave M, Eliasson R, Reichard P (1987) J Biol Chem 262 : 12325–12331). In both reactions, reduced R2, containing a diferrous center, is a key intermediate which is subsequently converted to active R2 during reaction with O2. By in vivo labeling of E. coli with radioactive 59Fe, we show that fraction b contains iron. Depletion of the iron in fraction b inactivates it, and fraction b can be substituted for by ferric citrate solutions. Furthermore, aqueous Fe2+ in the presence of dithiothreitol is able to convert metR2 into reduced R2. Therefore we propose that the function of fraction b is to provide, in association with the flavin reductase, ferrous iron for reduction of the endogenous diiron center. Since fraction b is not a single well-defined protein, it remains to be shown whether, in vivo, that function resides in a specific protein. Exogenous iron can thus participate in activation of both apoR2 and metR2, but it is incorporated into R2 only in the former case. A unifying mechanism is proposed.
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  • 78
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    World journal of microbiology and biotechnology 13 (1997), S. 159-161 
    ISSN: 1573-0972
    Keywords: Escherichia coli ; plasmid-containing bacteria ; pond water ; survival
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract The survival of Escherichia coli K-12 J62-1 containing the antibiotic-resistance plasmid R1 and an isogenic plasmid-free strain were studied in pond water microcosms. The number of plasmid-containing cells recovered from the microcosms remained constant over a sampling period of 31 days whereas plasmid-free cell numbers declined.
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  • 79
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    World journal of microbiology and biotechnology 14 (1997), S. 263-269 
    ISSN: 1573-0972
    Keywords: Escherichia coli ; fluorescence ; NAD(P)H ; nitrate reduction ; nitrite reduction
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract When nitrate was added to anaerobic resting cultures of Escherichia coli, two different profiles of NAD(P)H fluorescence were observed. E. coli is known to reduce nitrate to ammonia via nitrite as an anaerobic respiration mechanism. The profile showing single-stage response corresponded to situations where the nitrite formed from nitrate reduction was immediately converted to ammonia. The other profile showing two-stage response resulted from a much slower reduction of nitrite than nitrate. Nitrite thus accumulated during the first stage and was gradually reduced to ammonia when nitrate was depleted, i.e. in the second stage. An undamped oscillation of NAD(P)H fluorescence was also observed in the cultures showing the two-stage response. The oscillation was always detected during the second stage and seldom during either the first stage or the recovered anaerobic stage (after complete nitrite reduction). It never occurred in the cultures showing the single-stage response. The period of oscillation ranged from 1 to 5min. The possibility of the common glycolytic oscillation being responsible is low, as judged from the current knowledge of the nitrate/nitrite reductases of E. coli and the observations in this study. This is the first report on the occurrence of oscillatory NAD(P)H fluorescence in E. coli.
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  • 80
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    World journal of microbiology and biotechnology 13 (1997), S. 619-625 
    ISSN: 1573-0972
    Keywords: Alcohol ; biofuel ; corn fibre ; corn germ ; Escherichia coli ; fermentation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract Corn hulls and corn germ meal were both evaluated as feedstocks for production of ethanol for biofuel. Currently, these fibrous co-products are combined with corn steep liquor and the fermentation bottoms (if available) and marketed as cattle feed. Samples were obtained from wet and dry corn mills. The corn hulls and germ meal were evaluated for starch and hemicellulose compositions. Starch contents were 12 to 32% w/w and hemicellulose (arabinoxylans) contents were 23 to 64% w/w. Corn fibrous samples were hydrolysed, using dilute sulphuric acid, into mixed sugar streams containing arabinose, glucose and xylose. Total sugar concentrations in the hydrolysate varied from 8.4 to 10.8% w/v. The hydrolysates were fermented to ethanol using recombinant E. coli strains K011 and SL40. Ethanol yields were 0.38 to 0.41g ethanol produced/g total sugars consumed and fermentations were completed in 60h or less. However, residual xylose was detected for each hydrolysate fermentation and was especially significant for fermentations using strain SL40. Strain K011 was a superior ethanologenic strain compared with strain SL40 in terms of both ethanol yield and maximum productivity.
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  • 81
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    Journal of Bioluminescence and Chemiluminescence 12 (1997), S. 165-175 
    ISSN: 0884-3996
    Keywords: chemiluminescence ; β-galactosidase ; luminescent background ; quenching ; bacteriological growth media ; 1,2-dioxetanes ; coliforms ; Escherichia coli ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: The effects of the composition of bacteriological growth media on the light output in a chemiluminometric assay of β-galactosidase in Escherichia coli using 1,2-dioxetane substrates has been studied. In this assay a basic conflict exists between conditions that promote optimal bacterial growth and those conducive to maximal chemiluminescence. Common medium ingredients such as yeast or beef extract, protein hydrolysates and lactose suppress light emission and/or lead to high backgrounds. Quenching of light emission is probably partly due to light absorption by medium ingredients such as oxgall, and partly to interference with the reaction triggering the chemiluminescent process. Elevated backgrounds are caused by the presence of high concentrations of protein hydrolysates, which interact with the alkali in the accelerator solution. Only two purposely developed media, i.e. ILM and Colicult™ are shown to reconcile the requirements of growth support with that of optimal luminescent properties. © 1997 John Wiley & Sons, Ltd.
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  • 82
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    Biotechnology and Bioengineering 56 (1997), S. 583-590 
    ISSN: 0006-3592
    Keywords: 31P NMR ; PTS mutant ; Escherichia coli ; metabolism ; energetics ; glucose uptake system ; galactose symport system ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Modifying substrate uptake systems is a potentially powerful tool in metabolic engineering. This research investigates energetic and metabolic changes brought about by the genetic modification of the glucose uptake and phosphorylation system of Escherichia coli. The engineered strain PPA316, which lacks the E. coli phosphotransferase system (PTS) and uses instead the galactose-proton symport system for glucose uptake, exhibited significantly altered metabolic patterns relative to the parent strain PPA305 which retains PTS activity. Replacement of a PTS uptake system by the galactose-proton symport system is expected to lower the carbon flux to pyruvate in both aerobic and anaerobic cultivations. The extra energy cost in substrate uptake for the non-PTS strain PPA 316 had a greater effect on anaerobic specific growth rate, which was reduced by a factor of five relative to PPA 305, while PPA 316 reached a specific growth rate of 60% of that of the PTS strain under aerobic conditions. The maximal cell densities obtained with PPA 316 were approximately 8% higher than those of the PTS strain under aerobic conditions and 14% lower under anaerobic conditions. In vivo NMR results showed that the non-PTS strain possesses a dramatically different intracellular environment, as evidenced by lower levels of total sugar phosphate, NAD(H), nucleoside triphosphates and phosphoenolpyruvate, and higher levels of nucleoside diphosphates. The sugar phosphate compositions, as measured by extract NMR, were considerably different between these two strains. Data suggest that limitations in the rates of steps catalyzed by glucokinase, glyceraldehyde-3-phosphate dehydrogenase, phosphofructokinase, and pyruvate kinase may be responsible for the low overall rate of glucose metabolism in PPA316. © 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 56: 583-590, 1997.
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  • 83
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    Biotechnology and Bioengineering 53 (1997), S. 379-386 
    ISSN: 0006-3592
    Keywords: ppGpp ; recombinant protein synthesis ; translational machinery ; Escherichia coli ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Maintaining a metabolically productive state for recombinant Escherichia coli remains a central problem for a wide variety of growth-dependent biosynthesis. This problem becomes particularly acute under conditions of minimal cell growth such as fed-batch fermentations. In this, we investigated the possibility of manipulating the protein synthesis machinery of E. coli whereby synthesis of foreign proteins might be decoupled from cell growth. In particular, the effects of eliminating intracellular ppGpp on the synthesis of foreign proteins were studied in both batch and fed-batch operations. A significant increase in CAT production was observed from the ppGpp-deficient strain during both exponential and fed-batch phases. The increase in CAT production during exponential growth was accompanied by a simultaneous increase in CAT mRNA levels. Interestingly, CAT production was increased five-fold, while the level of CAT-specific mRNA increased only three-fold. Thus, eliminating intracellular ppGpp appears to have increase the production of recombinant protein by increasing not only the pool sizes of CAT mRNA but also possible alternations in the post-transcriptional processes. © 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 53: 379-386, 1997.
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  • 84
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    Biotechnology and Bioengineering 53 (1997), S. 453-458 
    ISSN: 0006-3592
    Keywords: chemical permeabilization ; cell disruption ; urea ; EDTA ; Escherichia coli ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Extraction of intracellular protein from Escherichia coli is traditionally achieved by mechanical disruption. A chemical treatment that destroys the integrity of the bacterial cell wall and could provide an alternative technique is examined in this study. Treatment with a combination of the chelating agent ethylenediaminetet-raacetate (EDTA) (greater than 0.3 mM) and the chaotropic agent urea (6 M) is highly effective at releasing protein from uninduced E. coli. The 6 M urea in the presence of 3 mM EDTA can release cytoplasmic protein from both logarithmic-phase and stationary-phase E. coli cells at levels equivalent to mechanical disruption. The concentrations of the two chemical agents were the major variables affecting the maximum levels of protein release. Several minor variables and interactions were also identified. The kinetics of protein release is first order. For 2, 4, and 6 M urea with 3 mM EDTA, the time constant is approximately 2.5 min independent of urea concentration. Kinetics for 3 mM EDTA without urea is considerably slower, with a time constant of 12.3 min. © 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 53: 453-458, 1997.
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  • 85
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    Biotechnology and Bioengineering 53 (1997), S. 487-496 
    ISSN: 0006-3592
    Keywords: bacterial chemotaxis ; Escherichia coli ; random motility ; mathematical model ; sand core ; porous media ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The migration of chemotactic bacteria in liquid media has previously been characterized in terms of two fundamental transport coefficients - the random motility coefficient and the chemotactic sensitivity coefficient. For modeling migration in porous media, we have shown that these coefficients which appear in macroscopic balance equations can be replaced by effective values that reflect the impact of the porous media on the swimming behavior of individual bacteria. Explicit relationships between values of the coefficients in porous and liquid media were derived. This type of quantitative analysis of bacterial migration is necessary for predicting bacterial population distributions in subsurface environments for applications such as in situ bioremediation in which bacteria respond chemotactically to the pollutants that they degrade.We analyzed bacterial penetration times through sand columns from two different experimental studies reported in the literature within the context of our mathematical model to evaluate the effective transport coefficients. Our results indicated that the presence of the porous medium reduced the random motility of the bacterial population by a factor comparable to the theoretical prediction. We were unable to determine the effect of the porous medium on the chemotactic sensitivity coefficient because no chemotactic response was observed in the experimental studies. However, the mathematical model was instrumental in developing a plausible explanation for why no chemotactic response was observed. The chemical gradients may have been too shallow over most of the sand core to elicit a measurable response. © 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 53: 487-496, 1997.
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  • 86
    ISSN: 0006-3592
    Keywords: recombinant protein production ; Escherichia coli ; heparinase ; bioprocess simulation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Heparinase I from flavobacterium heparinum has several potential clinical applications; the resulting high demands on protein purity and quantity can be met by recombinant expression in Escherichia coli. Based on laboratory scale experiments with insoluble heparinase I expression followed by renaturation, a process for production of 3 kg/year of heparinase I was designed. We present a comparative analysis of the production costs of soluble and insoluble heparinase I expression, as well as a generalized approach to sensitivity analysis, based on perturbation around a base case design scenario. This may assist focusing further development on process steps for which improvements both are feasible and result in significant cost saving. © 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 53: 575-582, 1997.
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  • 87
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    Biotechnology and Bioengineering 55 (1997), S. 556-564 
    ISSN: 0006-3592
    Keywords: cumulative sedimentation analysis ; cell debris size ; Escherichia coli ; homogenization ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: A new method to measure Escherichia coli cell debris size after homogenization is presented. It is based on cumulative sedimentation analysis under centrifugal force, coupled with Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis (SDS-PAGE) analysis of sedimented proteins. The effects that fermentation and homogenization conditions have on the resulting debris distributions were investigated using this method. Median debris size decreased significantly from approximately 0.5 μm to 0.3 μm as the number of homogenization passes increased from 2 to 10. Under identical homogenization conditions, uninduced host cells in stationary phase had a larger debris size than exponential cells after 5 homogenizer passes. This difference was not evident after 2 or 10 passes, possibly because of confounding intact cells and the existence of a minimum debris size for the conditions investigated. Recombinant cells containing protein inclusion bodies had the smallest debris size following homogenization. The method was also used to measure the size distribution of inclusion bodies. This result compared extremely well with an independent determination using centrifugal disc photosedimentation (CDS), thus validating the method. This is the first method that provides accurate size distributions of E. coli debris without the need for sample pretreatment, theoretical approximations (e.g. extinction coefficients), or the separation of debris and inclusion bodies prior to analysis. © 1997 John Wiley & Sons, Inc. Biotechnol Bioang 55: 556-564, 1997.
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  • 88
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    Biotechnology and Bioengineering 55 (1997), S. 747-757 
    ISSN: 0006-3592
    Keywords: microbial growth ; substrate mixtures ; multiple physiological quasi-steady states ; Escherichia coli ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Microbial growth on mixtures of substrates is of considerable engineering and biological interest. Most of the work until now has dealt with microbial growth on binary mixtures of sugars or polyols. In these cases, it is often found that no matter how the inoculum is precultured, only one of the two substrates is consumed in the first growth phase, leading to the diauxic growth pattern. The goal of the experiments reported here is to investigate growth on mixtures containing at least one organic acid. These experiments show that the substrate utilization patterns in such mixtures are qualitatively different from the diauxic growth pattern. For instance, during growth of Escherichia coli K12 on certain binary mixtures of organic acids, the two substrates are utilized simultaneously, and the mixed-substrate maximum specific growth rate exceeds the single-substrate maximum specific growth rate on either one of the two constituent substrates. Furthermore, the very same mixed-substrate maximum specific growth and substrate uptake rates are observed no matter how the inoculum is precultured. On the other hand, in a mixture of glucose and pyruvate, the maximum specific growth rate seems to depend on the preculturing conditions, thus suggesting the existence of multiple physiological quasi-steady states. © 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 55: 747-757, 1997.
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  • 89
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    Biotechnology and Bioengineering 56 (1997), S. 398-421 
    ISSN: 0006-3592
    Keywords: Escherichia coli ; metabolism ; flux ; linear optimization ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: A stoichiometric model of metabolism was developed to describe the balance of metabolic reactions during steady-state growth of Escherichia coli on glucose (or metabolic intermediates) and mineral salts. The model incorporates 153 reversible and 147 irreversible reactions and 289 metabolites from several metabolic data bases for the biosynthesis of the macromolecular precursors, coenzymes, and prosthetic groups necessary for synthesis of all cellular macromolecules. Correlations describing how the cellular composition changes with growth rate were developed from experimental data and were used to calculate the drain of precursors to macromolecules, coenzymes, and prosthetic groups from the metabolic network for the synthesis of those macromolecules at a specific growth rate. Energy requirements for macromolecular polymerization and proofreading, transport of metabolites, and maintenance of transmembrane gradients were included in the model rather than a lumped maintenance energy term. The underdetermined set of equations was solved using the Simplex algorithm, employing realistic objective functions and constraints; the drain of precursors, coenzymes, and prosthetic groups and the energy requirements for the synthesis of macromolecules served as the primary set of constraints. The model accurately predicted experimentally determined metabolic fluxes for aerobic growth on acetate or acetate plus glucose. In addition, the model predicted the genetic and metabolic regulation that must occur for growth under different conditions, such as the opening of the glyoxylate shunt during growth on acetate and the branching of the tricarboxylic acid cycle under anaerobic growth. Sensitivity analyses were performed to determine the flexibility of pathways and the effects of different rates and growth conditions on the distribution of fluxes. © 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 56: 398-421, 1997.
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  • 90
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    Biotechnology and Bioengineering 53 (1997), S. 238-241 
    ISSN: 0006-3592
    Keywords: Escherichia coli ; bacterial motility ; geometrical restriction ; capillary tube ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Motility of Escherichia coli K-12 cells was studied in a capillary tube with an inside diameter of 3 μm, which is comparable to the size of the cells' body. The extreme restriction, imposed by the capillary on the bacterial motility, caused a series of phenomena such as cell aggregation, swimming as a cluster, and break-up of aggregates, which were observable for the first time, and which are reported here. © 1997 John Wiley & Sons, Inc.
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  • 91
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    Biotechnology and Bioengineering 56 (1997), S. 304-310 
    ISSN: 0006-3592
    Keywords: crossflow membrane filtration ; Escherichia coli ; high pressure homogenization ; inclusion bodies ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Crossflow membrane filtration was used to process recombinant Escherichia coli cell lysates containing protein inclusion bodies after high pressure homogenization. The number of passes through the high pressure homogenizer changed the viscosities and average particle sizes of the cell lysates. The different cell lysates were processed with a hollow fiber unit containing microfiltration membranes and a plate and frame unit with either ultrafiltration or microfiltration membranes. There were differences in permeate flux and protein transmission for the various membranes with the best performing membranes giving permeate fluxes greater than 60 L m-2 h-1 and protein transmissions greater than 90%. For a given membrane, no differences were observed between the cell lysates following homogenization with one, two, and three passes at 83 MPa. The lack of a difference between the three lysates is due to their similarities with respect to the released macromolecules and the presence of small (〈0.1 μm) cell debris. © 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 56: 304-310, 1997.
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  • 92
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    Weinheim : Wiley-Blackwell
    Electroanalysis 9 (1997), S. 395-398 
    ISSN: 1040-0397
    Keywords: DNA biosensor ; Escherichia coli ; Bacteria ; Water quality ; Sequence-specific detection ; Hybridization ; Environmental monitoring ; Screen-printed electrode ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: An electrochemical biosensor for the specific detection of short DNA sequences from the E. coli pathogen is described. This hybridization device relies on the immobilization of a 25-mer oligonucleotide probe, from the E. coli lacZ gene, onto a screen-printed carbon electrode. Chronopotentiometric detection of the Co(bpy)3+3 indicator is used for monitoring the hybridization event. Numerous variables of the assay protocol, including those of the probe immobilization step, the hybridization event, and the indicator association/detection, are characterized and optimized. Hybridization times of 2- and 30-min are sufficient for detecting 300- and 50 ng/mL, respectively, of the E. coli DNA target. Applicability to analysis of untreated environmental water samples is illustrated. Such single-use electrochemical sensors hold great promise for decentralized environmental and food testing for the E. coli pathogen.
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  • 93
    Electronic Resource
    Electronic Resource
    Weinheim : Wiley-Blackwell
    Electrophoresis 18 (1997), S. 1243-1251 
    ISSN: 0173-0835
    Keywords: Escherichia coli ; Two-dimensional polyacrylamide gel electrophoresis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: The gene-protein database of Escherichia coli is a collection of data, largely generated from the separation of complex mixtures of cellular proteins on two-dimensional (2-D) polyacrylamide gel electrophoresis. The database currently contains about 1600 protein spots. The data are comprised of both identification information for many of these proteins and data on how the level or synthesis rates of proteins vary under different growth conditions. Three projects are underway to further elucidate the E. coli proteome including a project to localize on 2-D gels all of the open reading framed encoded by the E. coli chromosome, a project to determine the condition(s) under which each open reading frame is expressed and a project to determine the abundance and location of each protein in the cell. Applications for proteome databases for cell modeling are discussed and examples of applications in therapeutic drug discovery are given.
    Additional Material: 4 Ill.
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  • 94
    Electronic Resource
    Electronic Resource
    Weinheim : Wiley-Blackwell
    Electrophoresis 18 (1997), S. 1259-1313 
    ISSN: 0173-0835
    Keywords: Escherichia coli ; Functional genomics ; Proteome ; N-terminal sequencing ; Two-dimensional polyacrylamide gel electrophoresis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Mining the emerging abundance of microbial genome sequences for hypotheses is an exciting prospect of “functional genomics”. At the forefront of this effort, we compared the predictions of the complete Escherichia coli genomic sequence with the observed gene products by assessing 381 proteins for their mature N-termini, in vivo abundances, isoelectric points, molecular masses, and cellular locations. Two-dimensional gel electrophoresis (2-DE) and Edman sequencing were combined to sequence Coomassie-stained 2-DE spots representing the abundant proteins of wild-type E. coli K-12 strains. Greater than 90% of the abundant proteins in the E. coli proteome lie in a small isoelectric point and molecular mass window of 4-7 and 10-100 kDa, respectively. We identified several highly abundant proteins, YjbJ, YjbP, YggX, HdeA, and AhpC, which would not have been predicted from the genomic sequence alone. Of the 223 uniquely identified loci, 60% of the encoded proteins are proteolytically processed. As previously reported, the initiator methionine was efficiently cleaved when the penultimate amino acid was serine or alanine. In contrast, when the penultimate amino acid was threonine, glycine, or proline, cleavage was variable, and valine did not signal cleavage. Although signal peptide cleavage sites tended to follow predicted rules, the length of the putative signal sequence was occassionally greater than the consensus. For proteins predicted to be in the cytoplasm or inner membrane, the N-terminal amino acids were highly constrained compared to proteins localized to the periplasm or outer membrane. Although cytoplasmic proteins follow the N-end rule for protein stability, proteins in the periplasm or outer membrane do not follow this rule; several have N-terminal amino acids predicted to destabilize the proteins. Surprisingly, 18% of the identified 2-DE spots represent isoforms in which protein products of the same gene have different observed pI and Mr, suggesting they are post-translationally processed. Although most of the predicted and observed values for isoelectric point and molecular mass show reasonable concordance, for several proteins the observed values significantly deviate from the expected values. Such discrepancies may represent either highly processed proteins or misinterpretations of the genomic sequence. Our data suggest that AhpC, CspC, and HdeA exist as covalent homomultimers, and that IcdA exists as at least three isoforms even under conditions in which covalent modification is not predicted. We enriched for proteins based on subcellular location and found several proteins in unexpected subcellular locations.
    Additional Material: 15 Ill.
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  • 95
    ISSN: 0173-0835
    Keywords: Protein modelling ; Two-dimensional polyacrylamide gel electrophoresis ; Escherichia coli ; Database ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Knowledge-based molecular modelling of proteins has proven useful in many instances, including the rational design of mutagenesis experiments, but it has generally been limited by the availability of expensive computer hardware and software. To overcome these limitations, we developed the SWISS-MODEL sever for automated knowledge-based protein modelling. The SWISS-MODEL server uses the Brookhaven Protein Data Bank as a source of structural information and automatically generates protein models for sequences which share significant similarities with at least one protein of known three-dimensional structure. We have now used the software framework of the server to generate large collections of protein models, and established the SWISS-MODEL Repository, a new database for automatically generated and theoretical protein models. This repository is directly integrated with the SWISS-PROT and SWISS-2DPAGE databases through the ExPASy World Wide Web server (URL is http://expasy.hcuge.ch). Here we present an illustration of this process by an application to the Escherichia coli sequences.
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  • 96
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 1997-05-23
    Description: During translation errors of aminoacylation are corrected in editing reactions which ensure that an amino acid is stably attached to its corresponding transfer RNA (tRNA). Previous studies have not shown whether the tRNA nucleotides needed for effecting translational editing are the same as or distinct from those required for aminoacylation, but several considerations have suggested that they are the same. Here, designed tRNAs that are highly active for aminoacylation but are not active in translational editing are presented. The editing reaction can be controlled by manipulation of nucleotides at the corner of the L-shaped tRNA. In contrast, these manipulations do not affect aminoacylation. These results demonstrate the segregation of nucleotide determinants for the editing and aminoacylation functions of tRNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hale, S P -- Auld, D S -- Schmidt, E -- Schimmel, P -- GM15539/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1997 May 23;276(5316):1250-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9157882" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylation ; Base Sequence ; Binding Sites ; Cloning, Molecular ; Escherichia coli ; Molecular Sequence Data ; Nucleic Acid Conformation ; *RNA Editing ; RNA, Transfer/*metabolism ; RNA, Transfer, Ile/chemistry/metabolism ; RNA, Transfer, Val/chemistry/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 97
    Publication Date: 1997-11-05
    Description: Reactive and potentially toxic cofactors such as copper ions are imported into eukaryotic cells and incorporated into target proteins by unknown mechanisms. Atx1, a prototypical copper chaperone protein from yeast, has now been shown to act as a soluble cytoplasmic copper(I) receptor that can adopt either a two- or three-coordinate metal center in the active site. Atx1 also associated directly with the Atx1-like cytosolic domains of Ccc2, a vesicular protein defined in genetic studies as a member of the copper-trafficking pathway. The unusual structure and dynamics of Atx1 suggest a copper exchange function for this protein and related domains in the Menkes and Wilson disease proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pufahl, R A -- Singer, C P -- Peariso, K L -- Lin, S J -- Schmidt, P J -- Fahrni, C J -- Culotta, V C -- Penner-Hahn, J E -- O'Halloran, T V -- GM-38047/GM/NIGMS NIH HHS/ -- GM-50016/GM/NIGMS NIH HHS/ -- GM-54111/GM/NIGMS NIH HHS/ -- R01 GM054111/GM/NIGMS NIH HHS/ -- etc. -- New York, N.Y. -- Science. 1997 Oct 31;278(5339):853-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Northwestern University, Evanston, IL 60208, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9346482" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; *Carrier Proteins ; *Cation Transport Proteins ; Copper/*metabolism ; Escherichia coli ; Fungal Proteins/metabolism/*physiology ; Humans ; Molecular Chaperones/*physiology ; Molecular Sequence Data ; Recombinant Proteins ; Saccharomyces cerevisiae/metabolism/*physiology ; *Saccharomyces cerevisiae Proteins ; Sequence Homology, Amino Acid
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 98
    Electronic Resource
    Electronic Resource
    Springer
    Journal of polymers and the environment 4 (1996), S. 131-134 
    ISSN: 1572-8900
    Keywords: Escherichia coli ; poly(3-hydroxybutyrate) (PHB) ; filamentation ; fed-batch culture
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology , Energy, Environment Protection, Nuclear Power Engineering , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Abstract Fed-batch cultures of recombinantEscherichia coli strains were carried out for the production of poly(3-hydroxybutyric acid) (PHB) in a chemically defined medium. TheE. coli strains used were XL1-Blue, harboring pSYL105, a stable high-copy number plasmid containing theAlcaligenes eutrophus polyhydroxyalkanoate (PHA) genes, and XL1-Blue, harboring pSYL107, which is pSYL105 containing theE. coli ftsZ gene to suppress filamentation. With XL1-Blue(pSYL105) the final cell mass and PHB concentration obtained in 62 h were 102 and 22.5 g/L, respectively. Fed-batch culture of XL1-Blue(pSYL107) under identical conditions resulted in a final cell mass and PHB concentration of 127.5 and 48.2 g/L, respectively. The PHB contents obtained with XL1-Blue(pSYL105) and XL1-Blue(pSYL107) were 22.1 and 37.8%, respectively. Therefore, PHB was more efficiently produced in a defined medium by employing filamentation-suppressed recombinantE. coli.
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  • 99
    Electronic Resource
    Electronic Resource
    Springer
    Journal of industrial microbiology and biotechnology 16 (1996), S. 331-341 
    ISSN: 1476-5535
    Keywords: biofilms ; bacteriophages T4 and E79 ; Escherichia coli ; Pseudomonas aeruginosa ; SCLM ; fluorescence
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract Phages T4 and E79 were fluorescently-labeled with rhodamine isothiocyanate (RITC), fluoroscein isothiccyanate (FITC), and by the addition of 4′6-diamidino-2-phenylindole (DAPI) to phage-infected host cells ofEscherichia coli andPseudomonas aeruginosa. Comparisons of electron micrographs with scanning confocal laser microscope (SCLM) images indicated that single RITC-labeled phage particles could be visualized. Biofilms of each bacterium were infected by labeled phage. SCLM and epifluorescence microscopy were used to observe adsorption of phage to single-layer surface-attached bacteria and thicker biofilms. The spread of the recombinant T4 phage, YZA1 (containing an rll-LacZ fusion), within alac E. coli biofilm could be detected in the presence of chromogenic and fluorogenic homologs of galactose. Infected cells exhibited blue pigmentation and fluorescence from the cleavage products produced by the phage-encoded β-galactosidase activity. Fluorescent antibodies were used to detect nonlabeled progeny phage. Phage T4 infected both surface-attached and surface-associatedE. coli while phage E79 adsorbed toP. aeruginosa cells on the surface of the biofilm, but access to cells deep in biofilms was somewhat restricted. Temperature and nutrient concentration did not affect susceptibility to phage infection, but lower temperature and low nutrients extended the time-to-lysis and slowed the spread of infection within the biofilm.
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  • 100
    ISSN: 1476-5535
    Keywords: fermentation ; fermentation monitoring ; fermentation control ; fermentation software ; Escherichia coli
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract The advent of inexpensive computers and associated control and data acquisition software makes possible the development of sophisticated, configurable, integrated monitoring and control systems for small-scale laboratory and pilot-scale fermentors at low cost. We describe here the implementation of such a system, the interfacing of off-line instruments to enhance real time data analysis, low level process control and several substrate feeding protocols.
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