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Distribution Of Nitrogen Fixation And Nitrogenase-like Sequences Amongst Microbial Genomes

P. D. Dos Santos, Z. Fang, Steven Mason, J. Setubal, R. Dixon
Published 2011 · Biology, Medicine

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BackgroundThe metabolic capacity for nitrogen fixation is known to be present in several prokaryotic species scattered across taxonomic groups. Experimental detection of nitrogen fixation in microbes requires species-specific conditions, making it difficult to obtain a comprehensive census of this trait. The recent and rapid increase in the availability of microbial genome sequences affords novel opportunities to re-examine the occurrence and distribution of nitrogen fixation genes. The current practice for computational prediction of nitrogen fixation is to use the presence of the nifH and/or nifD genes.ResultsBased on a careful comparison of the repertoire of nitrogen fixation genes in known diazotroph species we propose a new criterion for computational prediction of nitrogen fixation: the presence of a minimum set of six genes coding for structural and biosynthetic components, namely NifHDK and NifENB. Using this criterion, we conducted a comprehensive search in fully sequenced genomes and identified 149 diazotrophic species, including 82 known diazotrophs and 67 species not known to fix nitrogen. The taxonomic distribution of nitrogen fixation in Archaea was limited to the Euryarchaeota phylum; within the Bacteria domain we predict that nitrogen fixation occurs in 13 different phyla. Of these, seven phyla had not hitherto been known to contain species capable of nitrogen fixation. Our analyses also identified protein sequences that are similar to nitrogenase in organisms that do not meet the minimum-gene-set criteria. The existence of nitrogenase-like proteins lacking conserved co-factor ligands in both diazotrophs and non-diazotrophs suggests their potential for performing other, as yet unidentified, metabolic functions.ConclusionsOur predictions expand the known phylogenetic diversity of nitrogen fixation, and suggest that this trait may be much more common in nature than it is currently thought. The diverse phylogenetic distribution of nitrogenase-like proteins indicates potential new roles for anciently duplicated and divergent members of this group of enzymes.
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Biological dinitrogen (N2) fixation: introduction and nonsymbiotic
D. Zuberer (2021)
10.3390/life11040356
Natural Product Gene Clusters in the Filamentous Nostocales Cyanobacterium HT-58-2
Xiaohe Jin (2021)
10.1016/J.XCRP.2021.100444
An engineered, non-diazotrophic cyanobacterium and its application in bioelectrochemical nitrogen fixation
Fangyuan Dong (2021)
10.1111/gbi.12381
Reconstructing the evolutionary history of nitrogenases: Evidence for ancestral molybdenum‐cofactor utilization
Amanda K. Garcia (2020)
10.1128/mSystems.00291-20
GapMind: Automated Annotation of Amino Acid Biosynthesis
M. Price (2020)
10.1101/2020.05.01.064543
Radiation of nitrogen-metabolizing enzymes across the tree of life tracks environmental transitions in Earth history
C. Parsons (2020)
10.1007/s10533-020-00666-7
Biological nitrogen fixation by alternative nitrogenases in terrestrial ecosystems: a review
J. Bellenger (2020)
10.1101/2020.04.27.064337
Genomic characterization of a diazotrophic microbiota associated with maize aerial root mucilage
S. Higdon (2020)
10.1002/mbo3.1033
Rhodobacter capsulatus AnfA is essential for production of Fe‐nitrogenase proteins but dispensable for cofactor biosynthesis and electron supply
Lisa Demtröder (2020)
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