Electron Transfer to Nitrogenase in Different Genomic and Metabolic Backgrounds

Abstract

Nitrogenase catalyzes the reduction of dinitrogen (N) using low potential electrons from ferredoxin (Fd) or flavodoxin (Fld) through an ATP dependent process. Since its emergence in an anaerobic chemoautotroph, this oxygen (O) sensitive enzyme complex has evolved to operate in a variety of genomic and metabolic backgrounds including those of aerobes, anaerobes, chemotrophs, and phototrophs. However, whether pathways of electron delivery to nitrogenase are influenced by these different metabolic backgrounds is not well understood. Here, we report the distribution of homologs of Fds, Flds, and Fd/Fld-reducing enzymes in 359 genomes of putative N fixers (diazotrophs). Six distinct lineages of nitrogenase were identified and their distributions largely corresponded to differences in the host cells' ability to integrate O or light into energy metabolism. Predicted pathways of electron transfer to nitrogenase in aerobes, facultative anaerobes, and phototrophs varied from those in anaerobes at the level of Fds/Flds used to reduce nitrogenase, the enzymes that generate reduced Fds/Flds, and the putative substrates of these enzymes. Proteins that putatively reduce Fd with hydrogen or pyruvate were enriched in anaerobes, while those that reduce Fd with NADH/NADPH were enriched in aerobes, facultative anaerobes, and anoxygenic phototrophs. The energy metabolism of aerobic, facultatively anaerobic, and anoxygenic phototrophic diazotrophs often yields reduced NADH/NADPH that is not sufficiently reduced to drive N reduction. At least two mechanisms have been acquired by these taxa to overcome this limitation and to generate electrons with potentials capable of reducing Fd. These include the bifurcation of electrons or the coupling of Fd reduction to reverse ion translocation. Nitrogen fixation supplies fixed nitrogen to cells from a variety of genomic and metabolic backgrounds including those of aerobes, facultative anaerobes, chemotrophs, and phototrophs. Here, using informatics approaches applied to genomic data, we show that pathways of electron transfer to nitrogenase in metabolically diverse diazotrophic taxa have diversified primarily in response to host cells' acquired ability to integrate O or light into their energy metabolism. Acquisition of two key enzyme complexes enabled aerobic and facultatively anaerobic phototrophic taxa to generate electrons of sufficiently low potential to reduce nitrogenase: the bifurcation of electrons via the Fix complex or the coupling of Fd reduction to reverse ion translocation via the nitrogen fixation (Rnf) complex.

Distinct trends in chemical composition of proteins from metagenomes in redox and salinity gradients

“…Cell membranes are permeable to uncharged species like hydrogen 19 , supporting the argument that oxidation-reduction conditions in the cytoplasm are affected by the external environment 20 . Oxygen diffuses rapidly through lipid membranes, depending on their composition and structure, and rates of diffusion increase with temperature 21 .…”

“…2A) is not unexpected. The findings of this study underscore an opportunity for integrating hydration state into evolutionary models that already consider changes in oxidation state or oxygen content of proteins 14,20 .…”

Carbon Oxidation State in Microbial Polar Lipids Suggests Adaptation to Hot Spring Temperature and Redox Gradients

“…Z C was chosen as a metric primarily because thermodynamic or kinetic relationships with redox potential have been implicated in a variety of natural processes. Examples include the predicted energetic favorability of amino acids biosynthesis in submarine hydrothermal vents (Amend and Shock, 1998), preservation and degradation of organic matter in sediments and soils (Likens, 2010;LaRowe and Van Cappellen, 2011;Boye et al, 2017), oxidation rates of atmospheric organic aerosols (Kroll et al, 2011(Kroll et al, , 2015, and evolutionary convergence on proteomes inferred from metagenomes of microbial communities in natural systems Shock, 2011, 2013;Dick, 2014;Dick et al, 2019;Fones et al, 2019), in aerobic and anaerobic nitrogen-fixing bacteria and archaea (Poudel et al, 2018), and in human cancer tissue (Dick, 2016(Dick, , 2017. Further, several of these studies have implicated Z C as a useful proxy for biosynthetic costs predicted from redox geochemistry (Amend and Shock, 1998;Dick and Shock, 2013;Dick et al, 2019).…”

The path of electron transfer to nitrogenase in a phototrophic alpha‐proteobacterium

“…The taxonomic distribution of Fer1, FerN and FldA in the 359 genomes was also determined. Additionally, homologs of the A. vinelandii Fld, NifF, were determined since NifF is not an ortholog of FldA and has been shown (Nieva‐Gómez et al ., ; Gennaro et al ., ) and hypothesized (Poudel et al ., ) to be involved in electron transport to nitrogenase in pathways that do not involve FixABCX. Fer1 and FerN were detected only in proteobacteria with the exception of one Verrucomicrobia genome that encoded FerN (Supporting Information Table S1).…”

“…Known electron transfer pathways to nitrogenase include pyruvate:ferredoxin/flavodoxin oxidoreductase (PFOR/ NifJ), the Rhodobacter nitrogen fixation (Rnf) complex, hydrogenases and FixABCX, and a number of nitrogenfixing organisms can utilize more than one pathway (Edgren and Nordlund, 2006;Herrmann et al, 2008;Khanna and Lindblad, 2015;Poudel et al, 2018;Ledbetter et al, 2017). R. palustris does not encode Rnf, but it encodes genes that are annotated as PFOR as well as FixABCX.…”