Molecular Evolution of Nitrogen Fixation: The Evolutionary History of the nifD, nifK, nifE, and nifN Genes

Abstract

The pairs of nitrogen fixation genes nifDK and nifEN encode for the alpha and beta subunits of nitrogenase and for the two subunits of the NifNE protein complex, involved in the biosynthesis of the FeMo cofactor, respectively. Comparative analysis of the amino acid sequences of the four NifD, NifK, NifE, and NifN in several archaeal and bacterial diazotrophs showed extensive sequence similarity between them, suggesting that their encoding genes constitute a novel paralogous gene family. We propose a two-step model to reconstruct the possible evolutionary history of the four genes. Accordingly, an ancestor gene gave rise, by an in-tandem paralogous duplication event followed by divergence, to an ancestral bicistronic operon; the latter, in turn, underwent a paralogous operon duplication event followed by evolutionary divergence leading to the ancestors of the present-day nifDK and nifEN operons. Both these paralogous duplication events very likely predated the appearance of the last universal common ancestor. The possible role of the ancestral gene and operon in nitrogen fixation is also discussed.

Nitrogen fixation island and rhizosphere competence traits in the genome of root-associated Pseudomonas stutzeri A1501

“…The nitrogen fixation process is believed to have played a crucial role in early cellular evolution, in particular when the geochemical reserves of fixed nitrogen in the biosphere became depleted. Because nitrogen fixation is maintained in Bacteria and Archaea, it is often hypothesized that nif genes may originate from the last common ancestor, even though other scenarios are proposed (40,41). It can be presumed that nif genes were lost in most lineages of Bacteria and Archaea and that lateral gene transfer played a role in recent acquisition of nif genes in some lineages (16,42).…”

NifH and NifD phylogenies: an evolutionary basis for understanding nitrogen fixation capabilities of methanotrophic bacteria

“…The enzyme responsible for nitrogen fixation, nitrogenase, shows a high degree of conservation of structure and function across wide phylogenetic ranges (Dean & Jacobson, 1992). Nitrogenase is composed of two components, component I (dinitrogenase, or Fe-Mo protein), an a 2 b 2 tetramer encoded by the nifD and nifK genes, and component II (dinitrogenase reductase, or Fe protein), a homodimer encoded by the nifH gene (Fani et al, 2000;Zehr et al, 2003). The structural organization of the nif genes shows remarkable differences among nitrogen-fixing organisms (Zehr et al, 2003).…”

Role of Diazotrophic Bacteria in Biological Nitrogen Fixation and Plant Growth Improvement

“…The genes nifD and nifK are usually part of the same operon and appear in the same organization (as nifDK). Frequently, nifH is also included in the same operon (nifHDK) (Fani et al, 2000). The genes nifE and nifN, which play a role in the biosynthesis of the nitrogenase metal clusters (FeMo-co), usually appear together and may have arisen from paralogous ancestor of nifEN and nifDK operon (Fani et al, 2000).…”

“…Frequently, nifH is also included in the same operon (nifHDK) (Fani et al, 2000). The genes nifE and nifN, which play a role in the biosynthesis of the nitrogenase metal clusters (FeMo-co), usually appear together and may have arisen from paralogous ancestor of nifEN and nifDK operon (Fani et al, 2000). These core operons are supplemented by a number of other genes, which code for proteins involved in electron transport (e.g.…”