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  • 1
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    Nitrite-driven anaerobic methane oxidation by oxygenic bacteria (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-03-26
    Description: Only three biological pathways are known to produce oxygen: photosynthesis, chlorate respiration and the detoxification of reactive oxygen species. Here we present evidence for a fourth pathway, possibly of considerable geochemical and evolutionary importance. The pathway was discovered after metagenomic sequencing of an enrichment culture that couples anaerobic oxidation of methane with the reduction of nitrite to dinitrogen. The complete genome of the dominant bacterium, named 'Candidatus Methylomirabilis oxyfera', was assembled. This apparently anaerobic, denitrifying bacterium encoded, transcribed and expressed the well-established aerobic pathway for methane oxidation, whereas it lacked known genes for dinitrogen production. Subsequent isotopic labelling indicated that 'M. oxyfera' bypassed the denitrification intermediate nitrous oxide by the conversion of two nitric oxide molecules to dinitrogen and oxygen, which was used to oxidize methane. These results extend our understanding of hydrocarbon degradation under anoxic conditions and explain the biochemical mechanism of a poorly understood freshwater methane sink. Because nitrogen oxides were already present on early Earth, our finding opens up the possibility that oxygen was available to microbial metabolism before the evolution of oxygenic photosynthesis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ettwig, Katharina F -- Butler, Margaret K -- Le Paslier, Denis -- Pelletier, Eric -- Mangenot, Sophie -- Kuypers, Marcel M M -- Schreiber, Frank -- Dutilh, Bas E -- Zedelius, Johannes -- de Beer, Dirk -- Gloerich, Jolein -- Wessels, Hans J C T -- van Alen, Theo -- Luesken, Francisca -- Wu, Ming L -- van de Pas-Schoonen, Katinka T -- Op den Camp, Huub J M -- Janssen-Megens, Eva M -- Francoijs, Kees-Jan -- Stunnenberg, Henk -- Weissenbach, Jean -- Jetten, Mike S M -- Strous, Marc -- England -- Nature. 2010 Mar 25;464(7288):543-8. doi: 10.1038/nature08883.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Radboud University Nijmegen, IWWR, Department of Microbiology, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands. k.ettwig@science.ru.nl〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20336137" target="_blank"〉PubMed〈/a〉
    Keywords: *Anaerobiosis ; Bacteria/classification/enzymology/genetics/*metabolism ; Genome, Bacterial/genetics ; Methane/*metabolism ; Molecular Sequence Data ; Nitrites/*metabolism ; Oxidation-Reduction ; Oxygen/metabolism ; Oxygenases/genetics ; Phylogeny ; Soil Microbiology
    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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  • 2
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    Complete nitrification by a single microorganism (2015)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2015-11-27
    Description: Nitrification is a two-step process where ammonia is first oxidized to nitrite by ammonia-oxidizing bacteria and/or archaea, and subsequently to nitrate by nitrite-oxidizing bacteria. Already described by Winogradsky in 1890, this division of labour between the two functional groups is a generally accepted characteristic of the biogeochemical nitrogen cycle. Complete oxidation of ammonia to nitrate in one organism (complete ammonia oxidation; comammox) is energetically feasible, and it was postulated that this process could occur under conditions selecting for species with lower growth rates but higher growth yields than canonical ammonia-oxidizing microorganisms. Still, organisms catalysing this process have not yet been discovered. Here we report the enrichment and initial characterization of two Nitrospira species that encode all the enzymes necessary for ammonia oxidation via nitrite to nitrate in their genomes, and indeed completely oxidize ammonium to nitrate to conserve energy. Their ammonia monooxygenase (AMO) enzymes are phylogenetically distinct from currently identified AMOs, rendering recent acquisition by horizontal gene transfer from known ammonia-oxidizing microorganisms unlikely. We also found highly similar amoA sequences (encoding the AMO subunit A) in public sequence databases, which were apparently misclassified as methane monooxygenases. This recognition of a novel amoA sequence group will lead to an improved understanding of the environmental abundance and distribution of ammonia-oxidizing microorganisms. Furthermore, the discovery of the long-sought-after comammox process will change our perception of the nitrogen cycle.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉van Kessel, Maartje A H J -- Speth, Daan R -- Albertsen, Mads -- Nielsen, Per H -- Op den Camp, Huub J M -- Kartal, Boran -- Jetten, Mike S M -- Lucker, Sebastian -- England -- Nature. 2015 Dec 24;528(7583):555-9. doi: 10.1038/nature16459. Epub 2015 Nov 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands. ; Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark. ; Laboratory for Microbiology, University of Gent, K. L. Ledeganckstraat 35, 9000 Gent, Belgium. ; Department of Biotechnology, TU Delft, Julianalaan 67, 2628 BC Delft, the Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26610025" target="_blank"〉PubMed〈/a〉
    Keywords: Ammonia/*metabolism ; Bacteria/enzymology/genetics/*metabolism ; Evolution, Molecular ; Genome, Bacterial/genetics ; Nitrates/*metabolism ; *Nitrification/genetics ; Nitrites/*metabolism ; Oxidation-Reduction ; Oxidoreductases/genetics/metabolism ; Phylogeny
    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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    Molecular mechanism of anaerobic ammonium oxidation (2011)
    Nature Publishing Group (NPG)
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    Publication Date: 2011-10-04
    Description: Two distinct microbial processes, denitrification and anaerobic ammonium oxidation (anammox), are responsible for the release of fixed nitrogen as dinitrogen gas (N(2)) to the atmosphere. Denitrification has been studied for over 100 years and its intermediates and enzymes are well known. Even though anammox is a key biogeochemical process of equal importance, its molecular mechanism is unknown, but it was proposed to proceed through hydrazine (N(2)H(4)). Here we show that N(2)H(4) is produced from the anammox substrates ammonium and nitrite and that nitric oxide (NO) is the direct precursor of N(2)H(4). We resolved the genes and proteins central to anammox metabolism and purified the key enzymes that catalyse N(2)H(4) synthesis and its oxidation to N(2). These results present a new biochemical reaction forging an N-N bond and fill a lacuna in our understanding of the biochemical synthesis of the N(2) in the atmosphere. Furthermore, they reinforce the role of nitric oxide in the evolution of the nitrogen cycle.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kartal, Boran -- Maalcke, Wouter J -- de Almeida, Naomi M -- Cirpus, Irina -- Gloerich, Jolein -- Geerts, Wim -- Op den Camp, Huub J M -- Harhangi, Harry R -- Janssen-Megens, Eva M -- Francoijs, Kees-Jan -- Stunnenberg, Hendrik G -- Keltjens, Jan T -- Jetten, Mike S M -- Strous, Marc -- England -- Nature. 2011 Oct 2;479(7371):127-30. doi: 10.1038/nature10453.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Water and Wetland Research, Department of Microbiology, Radboud University Nijmegen, Heyendaalseweg 135, 6525AJ Nijmegen, The Netherlands. kartal@science.ru.nl〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21964329" target="_blank"〉PubMed〈/a〉
    Keywords: Ammonia/metabolism ; *Anaerobiosis ; Atmosphere/chemistry ; Bacteria, Anaerobic/metabolism ; Biocatalysis ; Hydrazines/metabolism ; Nitrate Reductase/metabolism ; Nitric Oxide/biosynthesis/metabolism ; Nitrites/metabolism ; Nitrogen Cycle ; Nitrogen Fixation ; Oxidation-Reduction ; Quaternary Ammonium Compounds/chemistry/*metabolism
    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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  • 4
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    Evolution of a new enzyme for carbon disulphide conversion by an acidothermophilic archaeon (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-10-21
    Description: Extremophilic organisms require specialized enzymes for their exotic metabolisms. Acid-loving thermophilic Archaea that live in the mudpots of volcanic solfataras obtain their energy from reduced sulphur compounds such as hydrogen sulphide (H(2)S) and carbon disulphide (CS(2)). The oxidation of these compounds into sulphuric acid creates the extremely acidic environment that characterizes solfataras. The hyperthermophilic Acidianus strain A1-3, which was isolated from the fumarolic, ancient sauna building at the Solfatara volcano (Naples, Italy), was shown to rapidly convert CS(2) into H(2)S and carbon dioxide (CO(2)), but nothing has been known about the modes of action and the evolution of the enzyme(s) involved. Here we describe the structure, the proposed mechanism and evolution of a CS(2) hydrolase from Acidianus A1-3. The enzyme monomer displays a typical beta-carbonic anhydrase fold and active site, yet CO(2) is not one of its substrates. Owing to large carboxy- and amino-terminal arms, an unusual hexadecameric catenane oligomer has evolved. This structure results in the blocking of the entrance to the active site that is found in canonical beta-carbonic anhydrases and the formation of a single 15-A-long, highly hydrophobic tunnel that functions as a specificity filter. The tunnel determines the enzyme's substrate specificity for CS(2), which is hydrophobic. The transposon sequences that surround the gene encoding this CS(2) hydrolase point to horizontal gene transfer as a mechanism for its acquisition during evolution. Our results show how the ancient beta-carbonic anhydrase, which is central to global carbon metabolism, was transformed by divergent evolution into a crucial enzyme in CS(2) metabolism.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Smeulders, Marjan J -- Barends, Thomas R M -- Pol, Arjan -- Scherer, Anna -- Zandvoort, Marcel H -- Udvarhelyi, Aniko -- Khadem, Ahmad F -- Menzel, Andreas -- Hermans, John -- Shoeman, Robert L -- Wessels, Hans J C T -- van den Heuvel, Lambert P -- Russ, Lina -- Schlichting, Ilme -- Jetten, Mike S M -- Op den Camp, Huub J M -- England -- Nature. 2011 Oct 19;478(7369):412-6. doi: 10.1038/nature10464.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22012399" target="_blank"〉PubMed〈/a〉
    Keywords: Acidianus/classification/*enzymology/genetics ; Carbon Disulfide/*metabolism ; Catalytic Domain ; Crystallography, X-Ray ; *Evolution, Molecular ; Hydrolases/chemistry/*genetics ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Phylogeny ; Protein Structure, Tertiary
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 5
    Electronic Resource
    Electronic Resource
    A β-1,4-endoglucanase-encoding gene from Cellulomonas pachnodae (1999)
    Springer
    Applied microbiology and biotechnology 52 (1999), S. 232-239 
    Details
    ISSN: 1432-0614
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract  A gene library of Cellulomonas pachnodae was constructed in Escherichia coli and was screened for endoglucanase activity. Five endoglucanase-positive clones were isolated that carried identical DNA fragments. The gene, designated cel6A, encoding an endoglucanase enzyme, belongs to the glycosyl hydrolase family 6 (cellulase family B). The recombinant Cel6A had a molecular mass of 53 kDa, a pH optimum of 5.5, and a temperature optimum of 50–55 °C. The recombinant endoglucanase Cel6A bound to crystalline cellulose and beech litter. Based on amino acid sequence similarity, a clear cellulose-binding domain was not distinguished. However, the regions in the Cel6A amino acid sequence at the positions 262–319 and 448–473, which did not show similarity to any of the known family-6 glycosyl hydrolases, may be involved in substrate binding.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002530051514
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  • 6
    Electronic Resource
    Electronic Resource
    Growth of Bacillus fastidiosus on glycerol and the enzymes of ammonia assimilation (1986)
    Springer
    Archives of microbiology 146 (1986), S. 292-294 
    Details
    ISSN: 1432-072X
    Keywords: Bacillus fastidiosus ; Growth on glycerol ; Glycerol kinase ; Ammonia assimilation ; Glutamate dehydrogenase
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Bacillus fastidiosus was able to grow on glycerol as a carbon source when allantoin or urate was used as nitrogen source. The primary assimilatory enzyme for glycerol was glycerol kinase; glycerol dehydrogenase could not be detected. The glycerol kinase activity was increased 30-fold in allantoin/glycerol-grown cells as compared to alantoin-grown cells. Under both growth conditions high levels of glutamate dehydrogenase were found. Glutamine synthetase and glutamate synthase activities could not be demonstrated, while low levels of alanine dehydrogenase were present. It is concluded that B. fastidiosus assimilates ammonia by the NADP-dependent glutamate dehydrogenase.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00403232
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  • 7
    Electronic Resource
    Electronic Resource
    Effect of coculture of anaerobic fungi isolated from ruminants and non-ruminants with methanogenic bacteria on cellulolytic and xylanolytic enzyme activities (1992)
    Springer
    Archives of microbiology 157 (1992), S. 176-182 
    Details
    ISSN: 1432-072X
    Keywords: Anaerobic fungi ; Methanogenic bacteria ; Coculture Neocallimastix ; Cellulase secretion ; Enzyme location
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Neocallimastix strain N1, an isolate from a ruminant (sheep), was cocultured with three Methanobacterium formicicum strains, Methanosarcina barkeri, and Methanobrevibacter smithii. The coculture with Methanobacterium formicicum strains resulted in the highest production of cellulolytic and xylanolytic enzymes. Subsequently four anaerobic fungi, two Neocallimastix strains (N1 and N2) from a ruminant and two Piromyces species from non-ruminants (E2 and R1), were grown in coculture with Methanobacterium formicicum DSM 3637 on filter paper cellulose and monitored over a 7-day period for substrate utilisation, fermentation products, and secretion of cellulolytic and xylanolytic enzymes. Methanogens caused a shift in fermentation products to more acetate and less ethanol, lactate and succinate. Furthermore the cellulose digestion rate increased by coculture. For cocultures of Neoallimastix strains with Methanobacterium formicicum strains the cellulolytic and xylanolytic enzyme production increased. Avicelase, CMCase and xylanase were almost completely secreted into the medium, while 40–60% of the β-glucosidase was found to be cell bound. Coculture had no significant effect on the location of cellulolytic and xylanolytic enzymes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00245287
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  • 8
    Electronic Resource
    Electronic Resource
    Molecular characterization of the glnA gene encoding glutamine synthetase from the edible mushroom Agaricus bisporus (1997)
    Springer
    Molecular genetics and genomics 256 (1997), S. 179-186 
    Details
    ISSN: 1617-4623
    Keywords: Key wordsAgaricus bisporus ; Glutamine synthetase ; Molecular cloning ; Gene structure ; Mushroom
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The gene encoding glutamine synthetase (glnA) was isolated from an Agaricus bisporus H39 recombinant λ phage library. The deduced A. bisporus glutamine synthetase amino acid sequence contains 354 residues. The amino acid sequence is very similar to that derived from the gene coding for glutamine synthetase of the yeast Saccharomyces cerevisiae. The open reading frame is interrupted by four introns. Northern analysis revealed that transcription of the gene is repressed upon addition of ammonium to the culture but the repression was not as strong as that of the gene encoding NADP+-dependent glutamate dehydrogenase (gdhA). Enzyme activities are low in the presence of ammonium, glutamine and albumin and do not correlate with the mRNA levels revealed by Northern analysis. This suggests that glutamine synthetase expression in A. bisporus is also post-transcriptionally regulated by the nitrogen source.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00008612
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  • 9
    Electronic Resource
    Electronic Resource
    Conversion of cereal residues into biogas in a rumen-derived process (1992)
    Springer
    World journal of microbiology and biotechnology 8 (1992), S. 428-433 
    Details
    ISSN: 1573-0972
    Keywords: Anaerobic digestion ; biogas ; cereal residues ; rumen micro-organisms
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract A recently developed high-rate, two-phase process, which employs rumen microorganisms for efficient acidogenesis, was tested for anaerobic degradation of barley straw, rye straw, and maize stover. Under conditions similar to those of the rumen and loading rates varying between 9.8 and 26.0 g of organic matter/I/day in the first phase (acidogenic reactor), total fibre degradation efficiencies ranged between 42% and 57%, irrespective of the loading rate applied. Average specific production of volatile fatty acids and biogas/g volatile solid digested in the acidogenic reactor varied between 6.9 and 11.2 mmol and 0.10 and 0.25 l, respectively. The effect of varying solid retention times on the extent of degradation of barley straw was examined. Changing of retention times in the range of 60 to 156 h had no effect on degradation efficiency, but a decrease in efficiency was observed at retention times below 60 h. By connecting the acidogenic reactor in series to an Upflow Anaerobic Sludge Blanket (UASB) methanogenic reactor the volatile fatty acids were converted into biogas. Average methane contents of the gases produced in the acidogenic reactor and in the UASB reactor were 30±3% and 78±3%, respectively.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01198760
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  • 10
    Electronic Resource
    Electronic Resource
    Nucleotide sequence and expression of the gene encoding NADP+-dependent glutamate dehydrogenase (gdhA) fromAgaricus bisporus (1996)
    Springer
    Molecular genetics and genomics 250 (1996), S. 339-347 
    Details
    ISSN: 1617-4623
    Keywords: Agaricus bisporus ; NADP+-dependent glutamate dehydrogenase ; Molecular cloning ; Gene structure ; Mushroom
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The gene encoding NADP+-dependent glutamate dehydrogenase (gdhA) was isolated from anAgaricus bisporus recombinant phageλ library. The deduced amino acid sequence would specify a 457-amino acid protein that is highly homologous in sequence to those derived from previously isolated and characterized genes coding for microbial NADP+-GDH. The open reading frame is interrupted by six introns. None of the introns is located at either one of the positions of the two introns conserved in the corresponding open reading frames of the ascomycete fungiAspergillus nidulans andNeurospora crassa. Northern analysis suggests that theA. bisporus gdhA gene is transcriptionally regulated and that, unlike the case in ascomycetes, transcription of this gene is repressed upon the addition of ammonium to the culture.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02174392
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