Evolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA gene

Abstract

Nodulation and nitrogen fixation genes of Mesorhizobium loti are encoded on the chromosome of the bacterium. Nevertheless, there is strong evidence that these genes can be transferred from an inoculant strain to nonsymbiotic mesorhizobia in the field environment. Here we report that the chromosomal symbiotic element of M. loti strain ICMP3153 is transmissible in laboratory matings to at least three genomic species of nonsymbiotic mesorhizobia. The element is 500 kb in size, integrates into a phe-tRNA gene, and encodes an integrase of the phage P4 family just within its left end. The entire phe-tRNA gene is reconstructed at the left end of the element upon integration, whereas the 3 17 nucleotides of the tRNA gene are present as a direct repeat at the right end. We termed the element a symbiosis island on the basis of its many similarities to pathogenicity islands. It may represent a class of genetic element that contributes to microbial evolution by acquisition.The considerable impact of horizontal gene transfer on microbial evolution has become apparent from recent molecular analyses (1-4). For example, many bacterial pathogens contain clusters of virulence genes not present in closely related nonpathogenic strains or species. These gene clusters may be located on transmissible phage or plasmids, but are often found as so-called pathogenicity islands on the chromosome (5-8). The acquisition of a pathogenicity island is likely to have been a key step in the evolution of the pathogen. For example, the SPI-1 pathogenicity island was probably acquired very early in the evolution of Salmonella and enabled that genus to invade epithelial cells (9, 10). Pathogenicity islands range up to 190 kb in size, and most are found adjacent to or integrated within tRNA genes or flanked by insertion sequences. tRNA genes are targets for integration of plasmids and phage in a wide variety of bacteria, and pathogenicity islands in Dichelobacter nodosus and Vibrio cholerae are linked to phagederived integrase genes, suggesting that pathogenicity islands may have been acquired by a phage-mediated process (11-13). However, transmissibility of pathogenicity islands has not been demonstrated and their evolutionary origin remains unknown.We are working with Mesorhizobium loti, a species previously named Rhizobium loti, that is able to form nodules on several Lotus species. Mesorhizobium was recently described as a new genus of root nodule bacteria phylogenetically distinct from other root nodule bacteria of the genera Rhizobium and Bradyrhizobium on the basis of 16S rRNA gene sequence and other properties (14). M. loti differs from Rhizobium species and some other Mesorhizobium species in that its symbiotic information is chromosome rather than plasmid encoded (15-17). Nevertheless, we observed that genetically diverse symbiotic mesorhizobia, isolated from nodules off a stand of Lotus corniculatus established with a single inoculant strain, M. loti strain ICMP3153, in an area devoid of naturalized rhizobia able to nodulate the pl...

Ribosomal protein biomarkers provide root nodule bacterial identification by MALDI-TOF MS

“…In contrast to legumes, which are monophyletic (Werner et al 2014), molecular techniques have demonstrated that rhizobia are polyphyletic, belonging to diverse bacterial genera of the Alphaproteobacteria and Betaproteobacteria (Masson-Boivin et al 2009). In RNB, symbiotic ability is conferred by genes for nodulation and nitrogen fixation that can be acquired via lateral transfer of plasmids or genomic islands (Broughton 2003;Freiberg et al 1997;Moulin et al 2004;Nandasena et al 2007;Sullivan and Ronson 1998). To date, 16 rhizobial genera and over 100 species have been validly described (ICSP Subcommittee on the taxonomy of Rhizobium and Agrobacterium-diversity, phylogeny, and systematics; http://edzna.ccg.unam.mx/rhizobial-taxonomy/node/4), and these numbers are expected to increase as more symbioses are studied.…”

The α-proteobacteria: the Darwin finches of the bacterial world

“…Such integration events serve to stabilize the auxiliary gene pool, thereby preventing its loss from the population. Most a-proteobacterial genomes also contain genomic islands that carry genes encoding important adaptive traits that can integrate, excise and be transferred across species (Sullivan & Ronson 1998).…”

Horizontal Transfer of Nodulation Genes in Soils and Microcosms from Bradyrhizobium japonicum to B. elkanii.

“…Recently, an alternative structure for horizontal gene transfer has been found for pathogenicity and symbiosis. These determinants were often detected as so-called pathogenicity and symbiosis islands on the chromosome 12,16,28) . These islands, ranging from 12 to 611 kb in size, are flanked by insertion elements and short direct repeats, and often lie within specific tRNA genes 12,16,28) .…”

“…These determinants were often detected as so-called pathogenicity and symbiosis islands on the chromosome 12,16,28) . These islands, ranging from 12 to 611 kb in size, are flanked by insertion elements and short direct repeats, and often lie within specific tRNA genes 12,16,28) . Gene transfer among bacteria has been studied for over half a century, but its importance and the mechanisms involved in natural environments still need further investigation, because most studies have been carried out under controlled conditions in microcosms containing specific donors 31) .…”

“…Horizontal gene transfer apparently plays an active role in many biological processes including the emergence and spread of virulence 7) , symbiosis 27,28) , the degradation of xenobiotic compounds 29) and resistance to antibiotics 6) . An overwhelming surge of bacterial genome information has provided evidence that horizontal gene transfer has frequently occurred in distinct evolutionary lineages 5,9,15) .…”