Exploring the alternatives of biological nitrogen fixation

Abstract

Most biological nitrogen fixation (BNF) results from the activity of the molybdenum nitrogenase (Mo-nitrogenase, Nif), an oxygen-sensitive metalloenzyme complex found in all known diazotrophs. Two alternative forms of nitrogenase, the vanadium nitrogenase (V-nitrogenase, Vnf) and the iron-only nitrogenase (Fe-only nitrogenase, Anf) have also been identified in the genome of some organisms that encode for Nif. It has been suggested that alternative nitrogenases were responsible for N2-fixation on early Earth because oceans were depleted of bioavailable Mo. Results of recent phylogenetic- and structure-based studies suggest, however, that such an evolutionary path is unlikely, and favor a new model for a stepwise evolution of nitrogenase where the V-nitrogenase and the Fe-only nitrogenase are not the ancestor of the Mo-nitrogenase. Rather, Mo-nitrogenase emerged within the methanogenic archaea and then gave rise to the alternative forms suggesting they arose later in response to the availability of fixed N2 and local environmental factors that influenced metal availability. This review summarizes the current state of knowledge on (1) the biochemistry of these complex systems highlighting the common and specific structural features and catalytic activities of the enzymes, (2) the recent progress in defining the discrete set of genes associated to N2-fixation and the regulatory features that coordinate the differential expression of genes in response to metal availability, and (3) the diverse taxonomic and phylogenic distribution of nitrogenase enzymes and the evolutionary history of BNF from the perspective of metal content and metal availability.

Carbon substrate re‐orders relative growth of a bacterium using Mo‐, V‐, or Fe‐nitrogenase for nitrogen fixation

“…There are three phylogenetically and structurally distinct isoforms of Nase: the molybdenum (Mo-) and 'alternative' vanadium (V-) and iron (Fe-) only Nases (Eady, 1996). These can be differentiated by a key active site metal atom (Mo, V, or Fe) in addition to their kinetics, stable isotope fractionation and reaction stoichiometry Robson et al, 1986;Eady, 1996;Gosse et al, 2010;McKinlay and Harwood, 2010b;Zhang et al, 2014;Mus et al, 2018). The metabolic costs of Mo-based diazotrophy are well characterized, including the direct energy and reducing power requirements of N 2 fixation and indirect costs related to oxygen protection (Andersen and Shanmugam, 1977;McKinlay and Harwood, 2010b;Großkopf and LaRoche, 2012;Inomura et al, 2016).…”

Genetic responses to carbon and nitrogen availability in Anabaena

“…In turn, electrons are received from an electron carrier such as ferredoxin or flavodoxin. Notably, alternative nitrogenases that use an Fe-V cofactor or an Fe-Fe cofactor are known (Mus et al, 2018). As in most N 2 -fixing bacteria, in Anabaena the nifHDK genes form an operon and are clustered with other genes encoding nitrogenase maturation proteins and electron donors including ferredoxins .…”

Coordinated regulation of nitrogen fixation and molybdate transport by molybdenum

“…Hence, both alternative nitrogenases are less efficient than Mo-nitrogenase in terms of ATP consumption per N 2 reduced. For details on nitrogenase structures and activities, see recent publications (Seefeldt et al, 2013;Hu and Ribbe, 2015;Sippel and Einsle, 2017;Mus et al, 2018). (Hoffmann et al, 2016), E. coli modA and moaA (Anderson et al, 1997;McNicholas et al, 1997), H. seropedicae modA2 (Souza et al, 2008), and R. capsulatus anfA, mopA, morA, and mop (Wiethaus et al, 2006) were verified by in vitro binding studies.…”

“…Hence, both alternative nitrogenases are less efficient than Mo‐nitrogenase in terms of ATP consumption per N 2 reduced. For details on nitrogenase structures and activities, see recent publications (Seefeldt et al , ; Hu and Ribbe, ; Sippel and Einsle, ; Mus et al , ).…”

“…In addition to Mo-nitrogenase, some diazotrophs synthesize one or two alternative Mo-free nitrogenases, a vanadium-dependent V-nitrogenase (vnf-encoded) carrying VFeco and/or an iron-only Fe-nitrogenase (anf-encoded) carrying FeFeco (Fig. 2, Table 1) (Loveless and Bishop, 1999;McGlynn et al, 2013;Thiel and Pratte, 2014;Hu and Ribbe, 2015;Mus et al, 2018). Like Mo-nitrogenase, the alternative nitrogenases consist of two components structurally and functionally similar to NifH (VnfH, AnfH) and NifDK (VnfDGK, AnfDGK).…”