The conjugative plasmid of a bean-nodulating Sinorhizobium fredii strain is assembled from sequences of two Rhizobium plasmids and the chromosome of a Sinorhizobiumstrain

Abstract

BackgroundBean-nodulating Rhizobium etli originated in Mesoamerica, while soybean-nodulating Sinorhizobium fredii evolved in East Asia. S. fredii strains, such as GR64, have been isolated from bean nodules in Spain, suggesting the occurrence of conjugative transfer events between introduced and native strains. In R. etli CFN42, transfer of the symbiotic plasmid (pRet42d) requires cointegration with the endogenous self-transmissible plasmid pRet42a. Aiming at further understanding the generation of diversity among bean nodulating strains, we analyzed the plasmids of S. fredii GR64: pSfr64a and pSfr64b (symbiotic plasmid).ResultsThe conjugative transfer of the plasmids of strain GR64 was analyzed. Plasmid pSfr64a was self-transmissible, and required for transfer of the symbiotic plasmid. We sequenced pSfr64a, finding 166 ORFs. pSfr64a showed three large segments of different evolutionary origins; the first one presented 38 ORFs that were highly similar to genes located on the chromosome of Sinorhizobium strain NGR234; the second one harbored 51 ORFs with highest similarity to genes from pRet42d, including the replication, but not the symbiosis genes. Accordingly, pSfr64a was incompatible with the R. etli CFN42 symbiotic plasmid, but did not contribute to symbiosis. The third segment contained 36 ORFs with highest similarity to genes localized on pRet42a, 20 of them involved in conjugative transfer. Plasmid pRet42a was unable to substitute pSfr64a for induction of pSym transfer, and its own transfer was significantly diminished in GR64 background. The symbiotic plasmid pSfr64b was found to differ from typical R. etli symbiotic plasmids.ConclusionsS. fredii GR64 contains a chimeric transmissible plasmid, with segments from two R. etli plasmids and a S. fredii chromosome, and a symbiotic plasmid different from the one usually found in R. etli bv phaseoli. We infer that these plasmids originated through the transfer of a symbiotic-conjugative-plasmid cointegrate from R. etli to a S. fredii strain, and at least two recombination events among the R. etli plasmids and the S. fredii genome. As in R. etli CFN42, the S. fredii GR64 transmissible plasmid is required for the conjugative transfer of the symbiotic plasmid. In spite of the similarity in the conjugation related genes, the transfer process of these plasmids shows a host-specific behaviour.

Rhizobial communities in symbiosis with legumes: genetic diversity, competition and interactions with host plants

“…Some authors emphasize the role of lateral genetic transfer in rhizobial evolution [39,40,[100][101][102][103], whereas others suggest the lateral transfer of nodulation genes occurred in minority of cases [104,105]. Moreover, frequent genetic transfer and recombination events were evidenced within species (between sublineages) in different models [11,36,42,43,49,101]. There is an agreement, that (a) in numerous cases the world distribution of microsymbiont strains followed the distribution of their hosts, and the symbiosis-associated part of the genome (localized on symbiotic plasmid or symbiotic island) was subjected to the most intense evolution and fitting [103,104,106,107], and (b) other (non-symbiotic) parts of the rhizobial genome changed together with the symbiosis-related regions [105,108].…”

“…The frequency of plasmid transfer between rhizobial strains and the role of this genetic exchange in rhizobial evolution remains controversial [37][38][39][40]. However, the pool of plasmid replicons present in rhizobial cells is regarded as a (mostly) accessory genetic component which is evolving more rapidly than the chromosome [33], due to frequent changes (such as gene duplication, mutation or deletion) within particular replicons [41] or rearrangements between different replicons [42,43]. This distinction between the rhizobial chromosome and plasmids in the context of `evolutionary plasticity' and the role of these replicons in bacterial diversification resulted in the emergence of genomical concepts, which are similar to the pan-genome idea.…”

The tRNA arg Gene and engA Are Essential Genes on the 1.7-Mb pSymB Megaplasmid of Sinorhizobium meliloti and Were Translocated Together from the Chromosome in an Ancestral Strain

“…In many of these organisms, there is evidence that the chromosome and chromosome replicons coevolved with a shared evolutionary history and that the chromosome replicons were initially plasmids that did not carry any essential genes. The presence of multiple replicons in certain alphaproteobacteria is well known (11,12), and members of the Rhizobiaceae family contain a chromosome-like replicon of 3 to 4 Mb and multiple additional replicons (plasmids) that range in size from Ͻ100 kb to over 2 Mb (13)(14)(15)(16)(17)(18). In the root nodule bacteria, these plasmids were initially studied because they carried nodulation (nod) and nitrogen fixation (nif) genes.…”

Rhizobial plasmids — replication, structure and biological role

“…They are often maintained in the syntenic blocks and have a high level of nucleotide sequence identity among the homologous segments [55]. In Sfr GR64, a chimeric transmissible plasmid with segments from two Rhe plasmids and Sfr chromosome was detected [123]. The structural complexity and DNA sequence reiteration located in rhizobial extrachromosomal replicons could be one of the reasons of the tendency for genomic rearrangements.…”

“…In fact, some of these elements may be transferred to other bacterial cells by itself or in the presence of other mobilizing plasmids [73,92,110,111]. Cervantes et al [123] showed that Sfr plasmids might originate through the transfer of a symbiotic-conjugative-plasmid from the Rhe to a Sfr strain and at least two further recombination events among the Rhe plasmids and the Sfr genome. Recently, some (not only rhizobial) extrachromosomal replicons that have distinct properties from both chromosome and plasmids were reported and named "chromids" [128].…”