pubmed.ncbi.nlm.nih.gov

Evolution of molybdenum nitrogenase during the transition from anaerobic to aerobic metabolism - PubMed

Evolution of molybdenum nitrogenase during the transition from anaerobic to aerobic metabolism

Eric S Boyd et al. J Bacteriol. 2015 May.

Abstract

Molybdenum nitrogenase (Nif), which catalyzes the reduction of dinitrogen to ammonium, has modulated the availability of fixed nitrogen in the biosphere since early in Earth's history. Phylogenetic evidence indicates that oxygen (O2)-sensitive Nif emerged in an anaerobic archaeon and later diversified into an aerobic bacterium. Aerobic bacteria that fix N2 have adapted a number of strategies to protect Nif from inactivation by O2, including spatial and temporal segregation of Nif from O2 and respiratory consumption of O2. Here we report the complement of Nif-encoding genes in 189 diazotrophic genomes. We show that the evolution of Nif during the transition from anaerobic to aerobic metabolism was accompanied by both gene recruitment and loss, resulting in a substantial increase in the number of nif genes. While the observed increase in the number of nif genes and their phylogenetic distribution are strongly correlated with adaptation to utilize O2 in metabolism, the increase is not correlated with any of the known O2 protection mechanisms. Rather, gene recruitment appears to have been in response to selective pressure to optimize Nif synthesis to meet fixed N demands associated with aerobic productivity and to more efficiently regulate Nif under oxic conditions that favor protein turnover. Consistent with this hypothesis, the transition of Nif from anoxic to oxic environments is associated with a shift from posttranslational regulation in anaerobes to transcriptional regulation in obligate aerobes and facultative anaerobes. Given that fixed nitrogen typically limits ecosystem productivity, our observations further underscore the dynamic interplay between the evolution of Earth's oxygen, nitrogen, and carbon biogeochemical cycles.

Importance: Molybdenum nitrogenase (Nif), which catalyzes the reduction of dinitrogen to ammonium, has modulated the availability of fixed nitrogen in the biosphere since early in Earth's history. Nif emerged in an anaerobe and later diversified into aerobes. Here we show that the transition of Nif from anaerobic to aerobic metabolism was accompanied by both gene recruitment and gene loss, resulting in a substantial increase in the number of nif genes. While the observed increase in the number of nif genes is strongly correlated with adaptation to utilize O2 in metabolism, the increase is not correlated with any of the known O2 protective mechanisms. Rather, gene recruitment was likely a response to more efficiently regulate Nif under oxic conditions that favor protein turnover.

Copyright © 2015, American Society for Microbiology. All Rights Reserved.

PubMed Disclaimer

Figures

FIG 1
FIG 1

(A) Schematic of the reduction of N2 to NH4+ by Nif, with the reaction stoichiometry indicated. Electrons carried by flavodoxin (yellow) are transferred to NifH (purple), which interacts with and transfers electrons to the P cluster, located between NifD (blue) and NifK (green), and ultimately to the FeMo-co cluster of NifD, where N2 reduction occurs. (B) Structure and composition of nif gene clusters in Azotobacter vinelandii AVoP (both major and minor nif clusters) and Methanocaldococcus sp. FS406-22. Asterisks and boldfaced letters delineate the minimal complement of genes required to form an active nitrogenase (nifHDKEB).

FIG 2
FIG 2

NifHDK chronogram from 189 taxa, with an overlay of aerobic/facultative anaerobic lineages in green. The outgroup lineage for the rooted tree is depicted by a dotted line. The terminals of lineages are depicted by a heat map indicating the complexity of the nif gene clusters. The presence (black boxes) or absence (white boxes) of individual nif gene cluster-associated loci as well as the phylum-level classification for each taxon are indicated. See Table S1 in the supplemental material for additional details of the nif gene contents and gene accession numbers for each taxon.

FIG 3
FIG 3

Principal coordinates analysis results for a matrix describing the Jaccard dissimilarity of 189 nif gene clusters. For simplicity, complements of nif genes that were identical in composition are depicted by a single dot. The calculated complexity of nif gene contents, as plotted on the surface of the PCO ordination, yielded a D2 of 0.95, indicating a near-perfect fit. nif gene complements from aerobic or facultative anaerobic taxa are indicated by green dots.

Similar articles

Cited by

References

    1. Falkowski PG. 1997. Evolution of the nitrogen cycle and its influence on the biological sequestration of CO2 in the ocean. Nature 387:272–275. doi:10.1038/387272a0. - DOI
    1. Falkowski PG, Fenchel T, Delong EF. 2008. The microbial engines that drive Earth's biogeochemical cycles. Science 320:1034–1039. doi:10.1126/science.1153213. - DOI - PubMed
    1. Boyd E, Peters JW. 2013. New insights into the evolutionary history of biological nitrogen fixation. Front Microbiol 4:201. doi:10.3389/fmicb.2013.00201. - DOI - PMC - PubMed
    1. Peters JW, Boyd ES, Hamilton TL, Rubio LM. 2011. Biochemistry of Mo-nitrogenase, p 59–99. In Moir JWB. (ed), Nitrogen cycling in bacteria: molecular analysis. Caister Academic Press, Norfolk, United Kingdom.
    1. Boyd ES, Anbar AD, Miller S, Hamilton TL, Lavin M, Peters JW. 2011. A late methanogen origin for molybdenum-dependent nitrogenase. Geobiology 9:221–232. doi:10.1111/j.1472-4669.2011.00278.x. - DOI - PubMed

Publication types

MeSH terms

Substances

LinkOut - more resources