Distribution of nitrogen fixation and nitrogenase-like sequences amongst microbial genomes

Based on a careful comparison of the repertoire of nitrogen fixation genes in known diazotroph species we propose a new criterion for computational prediction of nitrogen fixation: the presence of a minimum set of six genes coding for structural and biosynthetic components, namely NifHDK and NifENB

Patricia C Dos Santos

2012

Scholarcy highlights

  • The metabolic capacity for nitrogen fixation is known to be present in several prokaryotic species scattered across taxonomic groups
  • Species containing NifD and NifH-like sequences The rapid expansion of microbial genome sequencing in the last few years affords novel opportunities to reexamine the distribution of nitrogen fixation genes
  • Based on the literature survey, we classified species with hits into two categories: known diazotrophs - with experimental demonstration, and potential diazotrophs - with no reports of experimental demonstration. During this literature search we found three recent reports providing experimental demonstration of diazotrophy motivated by an initial genomic identification of putative nitrogen fixation genes
  • The identification of a minimum gene set required for nitrogen fixation provides a more robust method for the in silico prediction of this biochemical pathway
  • The occurrence of nif-orphan sequences or incomplete gene sets in several species questions single-gene approaches used in phylogenetic studies of nitrogen fixation
  • The remaining 900 unique gene IDs were further filtered with a BLAST search against ChlB, BchB, ChlN and BchN to remove homologs of protochlorophylide reductase
  • BLAST searches used as queries the A. vinelandii nitrogen fixing protein sequences: NifH, NifD, NifK, NifE, NifN, NifU, NifS, NifV, NifB, NifQ, AnfG, and VnfG

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