Genetic rearrangements of a Rhizobium phaseoli symbiotic plasmid

Abstract

Different structural changes of the Sym plasmid were found in a Rhizobium phaseoli strain that loses its symbiotic phenotype at a high frequency. These rearrangements affected both nif genes and TnS mob insertions in the plasmid, and in some cases they modified the expression of the bacterium's nodulation ability. One of the rearrangements was more frequent in heat-treated cells, but was also found under standard culture conditions; other structural changes appeared to be related to the conjugal transfer of the plasmid.The genus Rhizobium comprises the gram-negative bacteria that form nodules on legumes. In this association, the bacteria fix atmospheric nitrogen that is then assimilated by the plant.The genetic information controlling symbiotic activity in the fast-growing rhizobia is encoded in plasmids (10,11,13,19). A symbiotic (Sym) plasmid has been defined as one that determines the plant species specificity for nodulation and contains the nitrogenase enzyme structural genes (nifgenes) (12).Plasmids participate very frequently in recombination events (14,20). It has been proposed (27) that this plasticity enables the bacteria that harbor plasmids to adapt to different environmental changes and permits the rapid spread of newly created functions among very diverse bacteria. There is one report (24) of a change in the structure of a plasmid that resulted in modified metabolic activity in the recipient bacteria. This strongly suggests that plasmid plasticity is important in the generation of new functions in bacteria.In Rhizobium phaseoli, the nitrogen fixation gene sequences are reiterated (25). In strain CFN42, there are three regions of the Sym plasmid that contain nitrogenase structural genes (nifregions) (22). These three regions contain the nitrogenase reductase gene (nifH); the nucleotide sequence of the three copies is identical (26). In addition, two of the regions contain also nifD and nifK genes. The identity of the nifH genes suggests that a recombination event could be involved in the generation or maintenance of their reiteration. Reiterated sequences are not common in bacteria, but they have been found in some strains of R. phaseoli, Rhizobium trifolii, and Rhizobium japonicum (2) and also Streptomyces sp. (21), Halobacterium halobium (29), and Pseudomonas syringae p.v. "phaseolicola" (32). The presence of these reiterations may be related to the instability and genetic rearrangements of these organisms (1, 6, 23).We have found that symbiotically unstable isolates are very common among the R. phaseoli strains isolated in different regions of Mexico, and all have reiterated nifH genes (L. Castrejon and G. Soberon, manuscript in preparation). We suppose that the symbiotic instability of these R. phaseoli strains is due to genetic rearrangements caused by the presence of reiterated sequences. We report here that the loss of the symbiotic phenotype of an unstable R. phaseoli strain is due to changes in the structure of its Sym plasmid, * Corresponding author. and that this Sym plasmid can be involve...

Nitrogen-fixing nodules induced by Agrobacterium tumefaciens harboring Rhizobium phaseoli plasmids

“…We have found that pSym of CFN299 belongs to a different compatibility group than does pSym of CFN42 (the standard reference strain with nifH reiterations), since we have been able to maintain both symbiotic plasmids in GMI9023 (unpublished results). Other R. phaseoli plasmids show differences; pSym9 is a nonconjugative plasmid of 275 megadaltons (16), pRP2J1 is a conjugative plasmid of 190 megadaltons (20), and in pSym of CFN23 symbiotic instability is associated with genetic rearrangements (29). It would be interesting to see whether nodulation genes with P. vulgaris specificity are equivalent.…”

Genomic instability in Rhizobium phaseoli

“…These observations suggest that frequent genomic rearrangements are probably confined to certain regions of the genome. Soberon-Chavez et al (23) reported rearrangements that alter the symbiotic plasmid of another R. phaseoli strain with loss of nif genes as well as nodulation ability. In the case of some Archaebacteria, which have many repeated DNA sequences and present frequent genomic rearrangements (21), these appear to be circumscribed to only some zones of the genome, having a high A+T content (8,13).…”

The genomes of the family Rhizobiaceae: size, stability, and rarely cutting restriction endonucleases

“…Our present observations do rule out the occurrence of large-scale DNA rearrangements in mature bacteroids of B. japonicum. Genomic rearrangements are common in some Rhizobiaceae, notably in R. leguminosarum biovar phaseoli (13,39,40). Furthermore, repeated DNA sequences exist in B. japonicum (20), Sinorhizobium fredii (26,31), and other Rhizobiaceae (12 [7,15]), yet it still leaves questions unresolved.…”