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SRNAs in Rhizobium etli differentially expressed during free-living and host-associated growth

ABSTRACT: 89 small non-coding RNAs (ncRNAs) were identified in the soil-dwelling alpha-proteobacterium Rhizobium etli by comparing an extensive compilation of ncRNA predictions to intergenic expression data of a whole-genome tiling array. The differential expression levels of some of these ncRNAs during free-living growth and during interaction with the eukaryotic host plant may indicate a role in adaptation to changing environmental conditions.

ORGANISM(S): Rhizobium etli CFN 42

PROVIDER: GSE18580 | GEO | 2009/11/17

SECONDARY ACCESSION(S): PRJNA120289

REPOSITORIES: GEO

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Project description:Background Regulation of transcription is essential for any organism and Rhizobium etli (a multi-replicon, nitrogen-fixing symbiotic bacterium) is no exception. This bacterium is commonly found in the rhizosphere (free-living) or inside of root-nodules of the common bean (Phaseolus vulgaris) in a symbiotic relationship. Abiotic stresses, such as high soil temperatures and salinity, compromise the genetic stability of R. etli and therefore its symbiotic interaction with P. vulgaris. However, it is still unclear which genes are up- or down-regulated to cope with these stress conditions. The aim of this study was to identify the genes and non-coding RNAs (ncRNAs) that are differentially expressed under heat and saline shock, as well as the promoter regions of the up-regulated loci. Results Analysing the heat and saline shock responses of R. etli CE3 through RNA-Seq, we identified 756 and 392 differentially expressed genes, respectively, and 106 were up-regulated under both conditions. Notably, the set of genes over-expressed under either condition was preferentially encoded on plasmids, although this observation was more significant for the heat shock response. In contrast, during either saline shock or heat shock, the down-regulated genes were principally chromosomally encoded. Our functional analysis shows that genes encoding chaperone proteins were up-regulated during the heat shock response, whereas genes involved in the metabolism of compatible solutes were up-regulated following saline shock. Furthermore, we identified thirteen and nine ncRNAs that were differentially expressed under heat and saline shock, respectively, as well as eleven ncRNAs that had not been previously identified. Finally, using an in silico analysis, we studied the promoter motifs in all of the non-coding regions associated with the genes and ncRNAs up-regulated under both conditions. Conclusions Our data suggest that the replicon contribution is different for different stress responses and that the heat shock response is more complex than the saline shock response. In general, this work exemplifies how strategies that not only consider differentially regulated genes but also regulatory elements of the stress response provide a more comprehensive view of bacterial gene regulation. mRNA of nine independent cultures of wild type strain Rhizobium etli CE3 were sequenced using Illumina GAIIx. Our parameters were: all cultures were taken from exponential phase, at 30M-BM-0C for 30min in control condition; 42M-BM-0C for 30min for the culture subject to heat -shock, and 30min at 30M-BM-0C in supplementary PY medium with 80mM NaCl for the saline shock condition.

Project description:A core component of the α-proteobacterial general stress response is the extracytoplasmic function (ECF) sigma factor EcfG, exclusively present in this taxonomic class. Half of the completed α-proteobacterial genome sequences contain two or more copies of genes encoding σEcfG-like sigma factors, with the primary copy typically located adjacent to genes coding for a cognate anti-sigma factor (NepR) and two-component response regulator (PhyR). So far, the widespread occurrence of additional, non-canonical σEcfG copies has not satisfactorily been explained. This work explores the hierarchical relation between Rhizobium etli σEcfG1 and σEcfG2, canonical and non-canonical σEcfG proteins, respectively. Contrary to reports in other species, we find that σEcfG1 and σEcfG2 act in parallel, as nodes of a complex regulatory network, rather than in series, as elements of a linear regulatory cascade. We demonstrate that both sigma factors control unique yet also shared target genes, corroborating phenotypic evidence. σEcfG1 drives expression of rpoH2, explaining the increased heat sensitivity of an ecfG1 mutant, while katG is under control of σEcfG2, accounting for reduced oxidative stress resistance of an ecfG2 mutant. We also identify non-coding RNA genes as novel σEcfG targets. We propose a modified model for general stress response regulation in R. etli, in which σEcfG1 and σEcfG2 function largely independently. Based on a phylogenetic analysis and considering the prevalence of α-proteobacterial genomes with multiple σEcfG copies, this model may also be applicable to numerous other species. In this study, we investigate to which degree R. etli EcfG1 and EcfG2 regulation is interdependent. Furthermore, we demonstrate that both sigma factors control distinct regulons and pinpoint unique EcfG2 target genes. We also identify non-coding RNAs (ncRNAs) as novel targets of EcfG1 and EcfG2 and show that expression of at least one of these ncRNAs is under direct EcfG control. The presence of ncRNAs in the regulon of an EcfG type sigma factor has not been described previously and adds an extra level of complexity to the regulation of the general stress response in Alpha-proteobacteria. Moreover, considering the widespread existence of Alpha-proteobacterial genomes with multiple EcfG copies, the here presented results not only lead to a better understanding of the general stress response in R. etli, but also contribute to a conceptual paradigm for general stress response regulation by multiple EcfG proteins in Alpha-proteobacteria.

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SRNAs in Rhizobium etli differentially expressed during free-living and host-associated growth

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