From β- to α-Proteobacteria: The Origin and Evolution of Rhizobial Nodulation Genes nodIJ

Abstract

Although many α- and some β-proteobacterial species are symbiotic with legumes, the evolutionary origin of nitrogen-fixing nodulation remains unclear. We examined α- and β-proteobacteria whose genomes were sequenced using large-scale phylogenetic profiling and revealed the evolutionary origin of two nodulation genes. These genes, nodI and nodJ (nodIJ), play key roles in the secretion of Nod factors, which are recognized by legumes during nodulation. We found that only the nodulating β-proteobacteria, including the novel strains isolated in this study, possess both nodIJ and their paralogous genes (DRA-ATPase/permease genes). Contrary to the widely accepted scenario of the α-proteobacterial origin of rhizobia, our exhaustive phylogenetic analysis showed that the entire nodIJ clade is included in the clade of Burkholderiaceae DRA-ATPase/permease genes, that is, the nodIJ genes originated from gene duplication in a lineage of the β-proteobacterial family. After duplication, the evolutionary rates of nodIJ were significantly accelerated relative to those of homologous genes, which is consistent with their novel function in nodulation. The likelihood analyses suggest that this accelerated evolution is not associated with changes in either nonsynonymous/synonymous substitution rates or transition/transversion rates, but rather, in the GC content. Although the low GC content of the nodulation genes has been assumed to reflect past horizontal transfer events from donor rhizobial genomes with low GC content, no rhizobial genome with such low GC content has yet been found. Our results encourage a reconsideration of the origin of nodulation and suggest new perspectives on the role of the GC content of bacterial genes in functional adaptation.

Origin and Evolution of Nitrogen Fixation Genes on Symbiosis Islands and Plasmid in <i>Bradyrhizobium</i>

“…In contrast, no apparent substitution bias was observed in the nif genes on symbiosis plasmids. Previous studies (2, 6, 8) analyzed nif genes across diverse taxonomic groups of α- and β-proteobacteria, and reported that rhizobial and non-rhizobial nitrogen-fixing strains were clustered in the same clade in phylogenetic trees. However, the nif genes of nodulation bacteria are closely related to those of non-rhizobial strains of the same or taxonomically-related groups.…”

Transient Hypermutagenesis Accelerates the Evolution of Legume Endosymbionts following Horizontal Gene Transfer

“…Horizontal transfer of essential symbiotic genes has been key in the conversion of soil bacteria into mutualistic symbionts of legumes [18]. Although compared phylogenies of rhizobia and nodulation genes predict that symbiotic genes have been transferred over large phylogenetic distances [19]–[21], transfer alone in lab conditions is usually unproductive between evolutionary distant taxa [22]–[24].…”

Evaluation of Ancestral Sequence Reconstruction Methods to Infer Nonstationary Patterns of Nucleotide Substitution

“…The same approach was used to construct the JTT matrix (Jones et al 1992) and to estimate relative rates of nucleotide substitution (Gojobori et al 1982). Other uses of the approach have included counting synonymous and nonsynonymous substitutions on the phylogeny to infer adaptive protein evolution affecting particular lineages (Messier and Stewart 1997;Zhang et al 1997) or sites (Fitch et al 1991;Suzuki and Gojobori 1999), inferring changes in nucleotide or amino acid compositions (Duret et al 2002;Gaucher et al 2003Gaucher et al , 2008Khelifi et al 2006;Groussin and Gouy 2011;Aoki et al 2013), and detecting coevolving nucleotides or amino acids (e.g., Shindyalov et al 1994;Tuffery and Darlu 2000;Osada and Akashi 2012;Liao et al 2014). In analysis of population data or data from closely related species, use of an outgroup species to "polarize" the changes to identify the ancestral and derived nucleotide states (e.g., Lohse and Barton 2011) is based on the same idea.…”