An analysis of the conjugative transfer of pRetCFN42d, the symbiotic plasmid (pSym) of Rhizobium etli , has revealed a novel gene, rctA , as an essential element of a regulatory system for silencing the conjugative transfer of R. etli pSym by repressing the transcription of conjugal transfer genes in standard laboratory media. The rctA gene product lacks sequence conservation with other proteins of known function but may belong to the winged-helix DNA-binding subfamily of transcriptional regulators. Similar to that of many transcriptional repressors, rctA transcription seems to be positively autoregulated. rctA expression is greatly reduced upon overexpression of another gene, rctB , previously identified as a putative activator of R. etli pSym conjugal transfer. Thus, rctB seems to counteract the repressive action of rctA. rctA homologs are present in at least three other bacterial genomes within the order Rhizobiales , where they are invariably located adjacent to and divergently transcribed from putative virB -like operons. We show that similar to that of R. etli pSym, conjugative transfer of the 1.35-Mb symbiotic megaplasmid A of Sinorhizobium meliloti is also subjected to the inhibitory action of rctA . Our data provide strong evidence that the R. etli and S. meliloti pSym plasmids are indeed self-conjugative plasmids and that this property would only be expressed under optimal, as yet unknown conditions that entail inactivation of the rctA function. The rctA gene seems to represent novel but probably widespread regulatory systems controlling the transfer of conjugative elements within the order Rhizobiales .

Repetitive proteins are thought to have arisen through the amplification of subdomain-sized peptides. Many of these originated in a non-repetitive context as cofactors of RNA-based replication and catalysis, and required the RNA to assume their active conformation. In search of the origins of one of the most widespread repeat protein families, the tetratricopeptide repeat (TPR), we identified several potential homologs of its repeated helical hairpin in non-repetitive proteins, including the putatively ancient ribosomal protein S20 (RPS20), which only becomes structured in the context of the ribosome. We evaluated the ability of the RPS20 hairpin to form a TPR fold by amplification and obtained structures identical to natural TPRs for variants with 2–5 point mutations per repeat. The mutations were neutral in the parent organism, suggesting that they could have been sampled in the course of evolution. TPRs could thus have plausibly arisen by amplification from an ancestral helical hairpin.

The fungus Macrophomina phaseolina is the causal agent of charcoal rot in many crops, such as strawberries and beans. Symptoms include stem and root rot and chlorotic foliage. This disease’s management is complicated because the pathogen forms resistant microsclerotia. This work aimed to obtain bacterial isolates for the biocontrol of M. phaseolina in arid regions. Two strains that grew well under low pH and high salinity, named BsA3MX and BsC11MX, were isolated and identified as B. amyloliquefaciens, based on their morphology and analysis of the 16S ribosomal RNA. Both strains inhibited M. phaseolina up to 66.8% in vitro through the combined action of volatile and diffusible compounds. Furthermore, they produce siderophores and indole-3-acetic acid (IAA), have ACC-deaminase activity, solubilize phosphate and zinc, and decrease microsclerotia germination. Moreover, in greenhouse assays using cowpea plants (Vigna unguiculata L.), strain BsA3MX reduced lesions caused by M. phaseolina and induced a significant increase in foliage and root biomass. Overall, these results suggest B. amyloliquefaciens BsA3MX and BsC11MX can be used as biological control agents against M. phaseolina in arid zones.

Bacteria of the order Rhizobiales are able to establish nitrogen-fixing symbioses with legumes. Commonly, genes for symbiosis are harbored on large symbiotic plasmids. Although the transfer of symbiotic plasmids is commonly detected in nature, there are few experimentally characterized examples. In Rhizobium etli , the product of rctA inhibits the conjugation of the symbiotic plasmid by reducing the transcription of the virB operon. rctA is transcribed divergently from this operon, and its product is predicted to have a DNA binding domain. In the present study, using DNase I footprinting and binding assays, we demonstrated the specific binding of RctA to the virB operon promoter. A 9-bp motif in the spacer region of this promoter (the rctA binding motif box) and the presence of a functional −10 region were critical elements for RctA binding. Transcriptional fusion analyses revealed that the elimination of either element provoked a relief of RctA-mediated repression. These data support a model in which RctA inhibits the access of the RNA polymerase to the virB promoter. Interestingly, rctA expression levels were modulated by transcriptional interference from transcripts emanating from the virB promoter. This phenomenon adds another level of regulation for this system, thus revealing a novel mechanism of plasmid transfer regulation in the Rhizobiales .

Plant growth-promoting rhizobacteria are often utilized to improve crop health and productivity. Nevertheless, their positive effects can be hindered if they fail to withstand the environmental and ecological conditions of the regions where they are applied. An alternative approach to circumvent this problem is a tailored selection of bacteria for specific agricultural systems. In this work, we evaluated the plant growth promoting and pathogen inhibition activity of rhizobacteria obtained from the rhizosphere of Mariola (Solanum hindsianum), an endemic shrub from Baja California. Eight strains were capable of inhibiting Fusarium oxysporum in vitro, and thirteen strains were found to possess three or more plant-growth-promotion traits. Molecular identification of these strains, using 16 s rRNA partial sequences, identified them as belonging to the genera Arthrobacter, Bacillus, Paenibacillus, Pseudomonas, and Streptomyces. Finally, the effect of selected plant growth-promoting rhizobacteria (PGPR) strains on the growth and suppression of Fusarium wilt in tomato was evaluated. Results showed that these strains improved tomato plants growth under greenhouse conditions and reduced Fusarium wilt effects, as reflected in several variables such as length and weight of roots and stem. This work highlights the potential of native plants related to regionally important crops as a valuable source of beneficial bacteria.

The CrbS/R system is a two-component signal transduction system that regulates acetate utilization in Vibrio cholerae, P. aeruginosa, and P. entomophila. CrbS is a hybrid histidine kinase that belongs to a recently identified family, in which the signaling domain is fused to an SLC5 solute symporter domain through aSTAC domain. Upon activation by CrbS, CrbR activates transcription of the acs gene, which encodes an acetyl-CoA synthase (ACS), and the actP gene, which encodes an acetate/solute symporter. In this work, we characterized the CrbS/R system in Pseudomonas fluorescens SBW25. Through the quantitative proteome analysis of different mutants, we were able to identify a new set of genes under its control, which play an important role during growth on acetate. These results led us to the identification of a conserved DNA motif in the putative promoter region of acetate-utilization genes in the Gammaproteobacteria that is essential for the CrbR-mediated transcriptional activation of genes under acetate-utilizing conditions. Finally, we took advantage of the existence of a second SLC5-containing two-component signal transduction system in P. fluorescens, CbrA/B, to demonstrate that the activation of the response regulator by the histidine kinase is not dependent on substrate transport through the SLC5 domain.