Genome-wide detection of predicted non-coding RNAs in Rhizobium etli expressed during free-living and host-associated growth using a high-resolution tiling array

Abstract

BackgroundNon-coding RNAs (ncRNAs) play a crucial role in the intricate regulation of bacterial gene expression, allowing bacteria to quickly adapt to changing environments. In the past few years, a growing number of regulatory RNA elements have been predicted by computational methods, mostly in well-studied γ-proteobacteria but lately in several α-proteobacteria as well. Here, we have compared an extensive compilation of these non-coding RNA predictions to intergenic expression data of a whole-genome high-resolution tiling array in the soil-dwelling α-proteobacterium Rhizobium etli.ResultsExpression of 89 candidate ncRNAs was detected, both on the chromosome and on the six megaplasmids encompassing the R. etli genome. Of these, 11 correspond to functionally well characterized ncRNAs, 12 were previously identified in other α-proteobacteria but are as yet uncharacterized and 66 were computationally predicted earlier but had not been experimentally identified and were therefore classified as novel ncRNAs. The latter comprise 17 putative sRNAs and 49 putative cis-regulatory ncRNAs. A selection of these candidate ncRNAs was validated by RT-qPCR, Northern blotting and 5' RACE, confirming the existence of 4 ncRNAs. Interestingly, individual transcript levels of numerous ncRNAs varied during free-living growth and during interaction with the eukaryotic host plant, pointing to possible ncRNA-dependent regulation of these specialized processes.ConclusionsOur data support the practical value of previous ncRNA prediction algorithms and significantly expand the list of candidate ncRNAs encoded in the intergenic regions of R. etli and, by extension, of α-proteobacteria. Moreover, we show high-resolution tiling arrays to be suitable tools for studying intergenic ncRNA transcription profiles across the genome. The differential expression levels of some of these ncRNAs may indicate a role in adaptation to changing environmental conditions.

Riboregulation in plant-associated α-proteobacteria

“…Recent high-throughput analyses revealed that these α-proteobacterial species harbor hundreds of RNAs with regulatory potential. [5][6][7][8][9][10][11][12] It is the challenge now to understand their physiological roles and the underlying molecular mechanisms. A systematic comparison of the sRNA repertoires of selected model organisms may help to understand the commonalities and differences between these phylogenetically and ecologically related bacteria.…”

“…This view is supported by the large amount of cis-and trans-encoded sRNAs detected by genome-wide analyses in these plant-associated bacteria. [5][6][7][8][9][10][11][12] Since conservation of sRNAs is mostly limited to closely related bacteria, the phylogenetic relationships between α-rhizobia and Agrobacterium species allow the functional comparison of sRNAs with different degrees of conservation in function and regulation. Here, we summarize the current knowledge on the non-coding RNome as inferred from genome-wide surveys and discuss the incipient insights into biological functions and mechanisms of riboregulation in these organisms.…”

The novel regulatory ncRNA, NfiS, optimizes nitrogen fixation via base pairing with the nitrogenase gene nifK mRNA in Pseudomonas stutzeri A1501

“…Despite the identification of a number of genes potentially involved in rhizosphere competence in the A1501 genome, little is known about the mechanisms of adaptation and survival in the rhizosphere (17). A search for ncRNAs in other nitrogen-fixing organisms was reported (5,6,14,(27)(28)(29), but none have been described so far as being involved in the regulation of nif gene expression.…”

Small RNAs of theBradyrhizobium/Rhodopseudomonaslineage and their analysis

“…[23][24][25][26][27][28] Changes in the amount of some of the sRNAs under different stresses, in different media, and at different growth stages suggest that they are involved in adaptation to stress, changing environmental conditions and in symbiosis. [23][24][25][26][27][28] In the a-proteobacterium Agrobacterium tumefaciens the sRNA AbcR1, which is homologous to the Hfq-dependent sRNA SmrC16 of S. meliloti, controls the expression of a periplasmic substrate binding protein required for uptake of the plant-derived defense signal GABA. 22,23,29 Here we describe the prediction, verification and analysis of seven novel sRNAs in the Bradyrhizobium/Rhodopseudomonas lineage.…”