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  • 1
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    Structure of the integral membrane protein CAAX protease Ste24p (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-03-30
    Description: Posttranslational lipidation provides critical modulation of the functions of some proteins. Isoprenoids (i.e., farnesyl or geranylgeranyl groups) are attached to cysteine residues in proteins containing C-terminal CAAX sequence motifs (where A is an aliphatic residue and X is any residue). Isoprenylation is followed by cleavage of the AAX amino acid residues and, in some cases, by additional proteolytic cuts. We determined the crystal structure of the CAAX protease Ste24p, a zinc metalloprotease catalyzing two proteolytic steps in the maturation of yeast mating pheromone a-factor. The Ste24p core structure is a ring of seven transmembrane helices enclosing a voluminous cavity containing the active site and substrate-binding groove. The cavity is accessible to the external milieu by means of gaps between splayed transmembrane helices. We hypothesize that cleavage proceeds by means of a processive mechanism of substrate insertion, translocation, and ejection.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4136949/" 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/PMC4136949/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pryor, Edward E Jr -- Horanyi, Peter S -- Clark, Kathleen M -- Fedoriw, Nadia -- Connelly, Sara M -- Koszelak-Rosenblum, Mary -- Zhu, Guangyu -- Malkowski, Michael G -- Wiener, Michael C -- Dumont, Mark E -- P30 CA044579/CA/NCI NIH HHS/ -- U54 GM094611/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Mar 29;339(6127):1600-4. doi: 10.1126/science.1232048.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Membrane Protein Structural Biology Consortium, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23539602" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Catalytic Domain ; Cell Membrane/*enzymology ; Crystallography, X-Ray ; Membrane Proteins/*chemistry ; Metalloendopeptidases/*chemistry ; Molecular Sequence Data ; Protein Structure, Secondary ; Saccharomyces cerevisiae Proteins/*chemistry ; Substrate Specificity
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    The genome of Tetranychus urticae reveals herbivorous pest adaptations (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-11-25
    Description: The spider mite Tetranychus urticae is a cosmopolitan agricultural pest with an extensive host plant range and an extreme record of pesticide resistance. Here we present the completely sequenced and annotated spider mite genome, representing the first complete chelicerate genome. At 90 megabases T. urticae has the smallest sequenced arthropod genome. Compared with other arthropods, the spider mite genome shows unique changes in the hormonal environment and organization of the Hox complex, and also reveals evolutionary innovation of silk production. We find strong signatures of polyphagy and detoxification in gene families associated with feeding on different hosts and in new gene families acquired by lateral gene transfer. Deep transcriptome analysis of mites feeding on different plants shows how this pest responds to a changing host environment. The T. urticae genome thus offers new insights into arthropod evolution and plant-herbivore interactions, and provides unique opportunities for developing novel plant protection strategies.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Grbic, Miodrag -- Van Leeuwen, Thomas -- Clark, Richard M -- Rombauts, Stephane -- Rouze, Pierre -- Grbic, Vojislava -- Osborne, Edward J -- Dermauw, Wannes -- Ngoc, Phuong Cao Thi -- Ortego, Felix -- Hernandez-Crespo, Pedro -- Diaz, Isabel -- Martinez, Manuel -- Navajas, Maria -- Sucena, Elio -- Magalhaes, Sara -- Nagy, Lisa -- Pace, Ryan M -- Djuranovic, Sergej -- Smagghe, Guy -- Iga, Masatoshi -- Christiaens, Olivier -- Veenstra, Jan A -- Ewer, John -- Villalobos, Rodrigo Mancilla -- Hutter, Jeffrey L -- Hudson, Stephen D -- Velez, Marisela -- Yi, Soojin V -- Zeng, Jia -- Pires-daSilva, Andre -- Roch, Fernando -- Cazaux, Marc -- Navarro, Marie -- Zhurov, Vladimir -- Acevedo, Gustavo -- Bjelica, Anica -- Fawcett, Jeffrey A -- Bonnet, Eric -- Martens, Cindy -- Baele, Guy -- Wissler, Lothar -- Sanchez-Rodriguez, Aminael -- Tirry, Luc -- Blais, Catherine -- Demeestere, Kristof -- Henz, Stefan R -- Gregory, T Ryan -- Mathieu, Johannes -- Verdon, Lou -- Farinelli, Laurent -- Schmutz, Jeremy -- Lindquist, Erika -- Feyereisen, Rene -- Van de Peer, Yves -- England -- Nature. 2011 Nov 23;479(7374):487-92. doi: 10.1038/nature10640.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, The University of Western Ontario, London N6A 5B7, Canada. mgrbic@uwo.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22113690" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological/*genetics/physiology ; Animals ; Ecdysterone/analogs & derivatives/genetics ; Evolution, Molecular ; Fibroins/genetics ; Gene Expression Regulation ; Gene Transfer, Horizontal/genetics ; Genes, Homeobox/genetics ; Genome/*genetics ; Genomics ; Herbivory/*genetics/physiology ; Molecular Sequence Data ; Molting/genetics ; Multigene Family/genetics ; Nanostructures/chemistry ; Plants/parasitology ; Silk/biosynthesis/chemistry ; Tetranychidae/*genetics/*physiology ; Transcriptome/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 3
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    Ubiquitinated TDP-43 in frontotemporal lobar degeneration and amyotrophic lateral sclerosis (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-10-07
    Description: Ubiquitin-positive, tau- and alpha-synuclein-negative inclusions are hallmarks of frontotemporal lobar degeneration with ubiquitin-positive inclusions and amyotrophic lateral sclerosis. Although the identity of the ubiquitinated protein specific to either disorder was unknown, we showed that TDP-43 is the major disease protein in both disorders. Pathologic TDP-43 was hyper-phosphorylated, ubiquitinated, and cleaved to generate C-terminal fragments and was recovered only from affected central nervous system regions, including hippocampus, neocortex, and spinal cord. TDP-43 represents the common pathologic substrate linking these neurodegenerative disorders.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Neumann, Manuela -- Sampathu, Deepak M -- Kwong, Linda K -- Truax, Adam C -- Micsenyi, Matthew C -- Chou, Thomas T -- Bruce, Jennifer -- Schuck, Theresa -- Grossman, Murray -- Clark, Christopher M -- McCluskey, Leo F -- Miller, Bruce L -- Masliah, Eliezer -- Mackenzie, Ian R -- Feldman, Howard -- Feiden, Wolfgang -- Kretzschmar, Hans A -- Trojanowski, John Q -- Lee, Virginia M-Y -- AG10124/AG/NIA NIH HHS/ -- AG17586/AG/NIA NIH HHS/ -- T32 AG00255/AG/NIA NIH HHS/ -- New York, N.Y. -- Science. 2006 Oct 6;314(5796):130-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17023659" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amyotrophic Lateral Sclerosis/*metabolism/pathology ; Antibodies, Monoclonal ; *Brain Chemistry ; Cerebral Cortex/chemistry/pathology ; DNA-Binding Proteins/*analysis/chemistry/genetics/immunology ; Dementia/genetics/*metabolism/pathology ; Fluorescent Antibody Technique ; Hippocampus/chemistry/pathology ; Humans ; Immunoblotting ; Molecular Sequence Data ; Motor Neurons/chemistry/pathology ; Neurons/chemistry/pathology ; Peptide Fragments/chemistry ; Phosphorylation ; Spinal Cord/*chemistry/pathology ; Ubiquitin/*analysis
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 4
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    Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-07-21
    Description: The genomes of individuals from the same species vary in sequence as a result of different evolutionary processes. To examine the patterns of, and the forces shaping, sequence variation in Arabidopsis thaliana, we performed high-density array resequencing of 20 diverse strains (accessions). More than 1 million nonredundant single-nucleotide polymorphisms (SNPs) were identified at moderate false discovery rates (FDRs), and approximately 4% of the genome was identified as being highly dissimilar or deleted relative to the reference genome sequence. Patterns of polymorphism are highly nonrandom among gene families, with genes mediating interaction with the biotic environment having exceptional polymorphism levels. At the chromosomal scale, regional variation in polymorphism was readily apparent. A scan for recent selective sweeps revealed several candidate regions, including a notable example in which almost all variation was removed in a 500-kilobase window. Analyzing the polymorphisms we describe in larger sets of accessions will enable a detailed understanding of forces shaping population-wide sequence variation in A. thaliana.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Clark, Richard M -- Schweikert, Gabriele -- Toomajian, Christopher -- Ossowski, Stephan -- Zeller, Georg -- Shinn, Paul -- Warthmann, Norman -- Hu, Tina T -- Fu, Glenn -- Hinds, David A -- Chen, Huaming -- Frazer, Kelly A -- Huson, Daniel H -- Scholkopf, Bernhard -- Nordborg, Magnus -- Ratsch, Gunnar -- Ecker, Joseph R -- Weigel, Detlef -- New York, N.Y. -- Science. 2007 Jul 20;317(5836):338-42.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17641193" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Arabidopsis/*genetics ; Base Sequence ; Chromosomes, Plant/genetics ; Computational Biology ; Gene Frequency ; Genes, Plant ; *Genetic Variation ; *Genome, Plant ; Molecular Sequence Data ; *Polymorphism, Genetic ; *Polymorphism, Single Nucleotide ; Selection, Genetic ; Sequence Analysis, DNA
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 5
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    The evolution of selfing in Arabidopsis thaliana (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-07-28
    Description: Unlike most of its close relatives, Arabidopsis thaliana is capable of self-pollination. In other members of the mustard family, outcrossing is ensured by the complex self-incompatibility (S) locus,which harbors multiple diverged specificity haplotypes that effectively prevent selfing. We investigated the role of the S locus in the evolution of and transition to selfing in A. thaliana. We found that the S locus of A. thaliana harbored considerable diversity, which is an apparent remnant of polymorphism in the outcrossing ancestor. Thus, the fixation of a single inactivated S-locus allele cannot have been a key step in the transition to selfing. An analysis of the genome-wide pattern of linkage disequilibrium suggests that selfing most likely evolved roughly a million years ago or more.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tang, Chunlao -- Toomajian, Christopher -- Sherman-Broyles, Susan -- Plagnol, Vincent -- Guo, Ya-Long -- Hu, Tina T -- Clark, Richard M -- Nasrallah, June B -- Weigel, Detlef -- Nordborg, Magnus -- GM62932/GM/NIGMS NIH HHS/ -- P50 HG002790/HG/NHGRI NIH HHS/ -- R01 GM062932/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Aug 24;317(5841):1070-2. Epub 2007 Jul 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17656687" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Amino Acid Sequence ; Arabidopsis/*genetics/*physiology ; Arabidopsis Proteins/*genetics ; *Biological Evolution ; Chromosomes, Artificial, Bacterial ; *Genes, Plant ; Genetic Drift ; Haplotypes ; Linkage Disequilibrium ; Molecular Sequence Data ; Nuclear Proteins/*genetics ; Plant Proteins/*genetics ; Polymerase Chain Reaction ; Polymorphism, Genetic ; Protein Kinases/*genetics ; *Pseudogenes ; Reproduction/physiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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