Assessing horizontal transfer of nifHDK genes in eubacteria: nucleotide sequence of nifK from Frankia strain HFPCcI3

The structural genes for nitrogenase, nifK, nifD, and nifH, are crucial fornitrogen fixation. Previous phylogenetic analysis of the amino acidsequence of nifH suggested that this gene had been horizontally transferredfrom a proteobacterium to the gram-positive/cyanobacterial clade, althoughthe confounding effects of paralogous comparisons made interpretation ofthe data difficult. An additional test of nif gene horizontal transferusing nifD was made, but the NifD phylogeny lacked resolution. Here nifgene phylogeny is addressed with a phylogenetic analysis of a third andlonger nif gene, nifK. As part of the study, the nifK gene of the key taxonFrankia was sequenced. Parsimony and some distance analyses of the nifKamino acid sequences provide support for vertical descent of nifK, butother distance trees provide support for the lateral transfer of the gene.Bootstrap support was found for both hypotheses in all trees; the nifK datado not definitively favor one or the other hypothesis. A parsimony analysisof NifH provides support for horizontal transfer in accord with previousreports, although bootstrap analysis also shows some support for verticaldescent of the orthologous nifH genes. A wider sampling of taxa and moresophisticated methods of phylogenetic inference are needed to understandthe evolution of nif genes. The nif genes may also be powerful phylogenetictools. If nifK evolved by vertical descent, it provides strong evidencethat the cyanobacteria and proteobacteria are sister groups to theexclusion of the firmicutes, whereas 16S rRNA sequences are unable toresolve the relationships of these three major eubacterial lineages.