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Diversity and Activity of Alternative Nitrogenases in Sequenced Genomes and Coastal Environments

The nitrogenase enzyme, which catalyzes the reduction of N(2) gas to NH(4)(+), occurs as three separate isozyme that use Mo, Fe-only, or V. The majority of global nitrogen fixation is attributed to the more efficient ‘canonical’ Mo-nitrogenase, whereas Fe-only and V-(‘alternative’) nitrogenases are...

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Autores principales: McRose, Darcy L., Zhang, Xinning, Kraepiel, Anne M. L., Morel, François M. M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5328986/
https://www.ncbi.nlm.nih.gov/pubmed/28293220
http://dx.doi.org/10.3389/fmicb.2017.00267
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author McRose, Darcy L.
Zhang, Xinning
Kraepiel, Anne M. L.
Morel, François M. M.
author_facet McRose, Darcy L.
Zhang, Xinning
Kraepiel, Anne M. L.
Morel, François M. M.
author_sort McRose, Darcy L.
collection PubMed
description The nitrogenase enzyme, which catalyzes the reduction of N(2) gas to NH(4)(+), occurs as three separate isozyme that use Mo, Fe-only, or V. The majority of global nitrogen fixation is attributed to the more efficient ‘canonical’ Mo-nitrogenase, whereas Fe-only and V-(‘alternative’) nitrogenases are often considered ‘backup’ enzymes, used when Mo is limiting. Yet, the environmental distribution and diversity of alternative nitrogenases remains largely unknown. We searched for alternative nitrogenase genes in sequenced genomes and used PacBio sequencing to explore the diversity of canonical (nifD) and alternative (anfD and vnfD) nitrogenase amplicons in two coastal environments: the Florida Everglades and Sippewissett Marsh (MA). Genome-based searches identified an additional 25 species and 10 genera not previously known to encode alternative nitrogenases. Alternative nitrogenase amplicons were found in both Sippewissett Marsh and the Florida Everglades and their activity was further confirmed using newly developed isotopic techniques. Conserved amino acid sequences corresponding to cofactor ligands were also analyzed in anfD and vnfD amplicons, offering insight into environmental variants of these motifs. This study increases the number of available anfD and vnfD sequences ∼20-fold and allows for the first comparisons of environmental Mo-, Fe-only, and V-nitrogenase diversity. Our results suggest that alternative nitrogenases are maintained across a range of organisms and environments and that they can make important contributions to nitrogenase diversity and nitrogen fixation.
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spelling pubmed-53289862017-03-14 Diversity and Activity of Alternative Nitrogenases in Sequenced Genomes and Coastal Environments McRose, Darcy L. Zhang, Xinning Kraepiel, Anne M. L. Morel, François M. M. Front Microbiol Microbiology The nitrogenase enzyme, which catalyzes the reduction of N(2) gas to NH(4)(+), occurs as three separate isozyme that use Mo, Fe-only, or V. The majority of global nitrogen fixation is attributed to the more efficient ‘canonical’ Mo-nitrogenase, whereas Fe-only and V-(‘alternative’) nitrogenases are often considered ‘backup’ enzymes, used when Mo is limiting. Yet, the environmental distribution and diversity of alternative nitrogenases remains largely unknown. We searched for alternative nitrogenase genes in sequenced genomes and used PacBio sequencing to explore the diversity of canonical (nifD) and alternative (anfD and vnfD) nitrogenase amplicons in two coastal environments: the Florida Everglades and Sippewissett Marsh (MA). Genome-based searches identified an additional 25 species and 10 genera not previously known to encode alternative nitrogenases. Alternative nitrogenase amplicons were found in both Sippewissett Marsh and the Florida Everglades and their activity was further confirmed using newly developed isotopic techniques. Conserved amino acid sequences corresponding to cofactor ligands were also analyzed in anfD and vnfD amplicons, offering insight into environmental variants of these motifs. This study increases the number of available anfD and vnfD sequences ∼20-fold and allows for the first comparisons of environmental Mo-, Fe-only, and V-nitrogenase diversity. Our results suggest that alternative nitrogenases are maintained across a range of organisms and environments and that they can make important contributions to nitrogenase diversity and nitrogen fixation. Frontiers Media S.A. 2017-02-28 /pmc/articles/PMC5328986/ /pubmed/28293220 http://dx.doi.org/10.3389/fmicb.2017.00267 Text en Copyright © 2017 McRose, Zhang, Kraepiel and Morel. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
McRose, Darcy L.
Zhang, Xinning
Kraepiel, Anne M. L.
Morel, François M. M.
Diversity and Activity of Alternative Nitrogenases in Sequenced Genomes and Coastal Environments
title Diversity and Activity of Alternative Nitrogenases in Sequenced Genomes and Coastal Environments
title_full Diversity and Activity of Alternative Nitrogenases in Sequenced Genomes and Coastal Environments
title_fullStr Diversity and Activity of Alternative Nitrogenases in Sequenced Genomes and Coastal Environments
title_full_unstemmed Diversity and Activity of Alternative Nitrogenases in Sequenced Genomes and Coastal Environments
title_short Diversity and Activity of Alternative Nitrogenases in Sequenced Genomes and Coastal Environments
title_sort diversity and activity of alternative nitrogenases in sequenced genomes and coastal environments
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5328986/
https://www.ncbi.nlm.nih.gov/pubmed/28293220
http://dx.doi.org/10.3389/fmicb.2017.00267
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