Small RNAs of theBradyrhizobium/Rhodopseudomonaslineage and their analysis

Abstract

Evguenieva-Hackenberg (2012) Small RNAs (sRNAs) play a pivotal role in bacterial gene regulation. However, the sRNAs of the vast majority of bacteria with sequenced genomes still remain unknown since sRNA genes are usually difficult to recognize and thus not annotated. Here, expression of seven sRNAs (BjrC2a, BjrC2b, BjrC2c, BjrC68, BjrC80, BjrC174 and BjrC1505) predicted by genome comparison of Bradyrhizobium and Rhodopseudomonas members, was verified by RNA gel blot hybridization, microarray and deep sequencing analyses of RNA from the soybean symbiont Bradyrhizobium japonicum USDA 110. BjrC2a, BjrC2b and BjrC2c belong to the RNA family RF00519, while the other sRNAs are novel. For some of the sRNAs we observed expression differences between free-living bacteria and bacteroids in root nodules. The amount of BjrC1505 was decreased in nodules. By contrast, the amount of BjrC2a, BjrC68, BjrC80, BjrC174 and the previously described 6S RNA was increased in nodules, and accumulation of truncated forms of these sRNAs was observed. Comparative genomics and deep sequencing suggest that BjrC2a is an antisense RNA regulating the expression of inositol-monophosphatase. The analyzed sRNAs show a different degree of conservation in Rhizobiales, and expression of homologs of BjrC2, BjrC68, BjrC1505, and 6S RNA was confirmed in the free-living purple bacterium Rhodopseudomonas palustris 5D.

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.…”

“…10 Approximately 100 so-called "clusters" representing potential trans-sRNAs were predicted, and seven candidate sRNAs (BjrC2a, BjrC2b, BjrC2c, BjrC68, BjrC80, BjrC174 and BjrC1505) were verified by northern blot hybridization in addition to conserved sRNAs with housekeeping function like SRP RNA, RNase P RNA, tmRNA and 6S rRNA. The detected sRNA candidates have a different degree of conservation.…”

“…The least conserved BjrC68 corresponds to the 3′-UTR of blr0613 and its homologs are found only in the closely related genera Bradyrhizobium and Rhodopseudomonas. 10 As in most similar studies, the expression of the verified sRNAs was monitored by northern blot hybridization under diverse stresses and at different growth phases. The results were directly compared with data from microarray and dRNA-seq analyses and displayed similar tendencies -increases or decreases in the amounts of the particular sRNA in bacteroids were supported by at least two of the methods.…”

Daily Expression Pattern of Protein-Encoding Genes and Small Noncoding RNAs in Synechocystis sp. Strain PCC 6803

“…In many bacteria, including cyanobacteria, small regulatory RNAs (sRNAs) have been reported as important regulators of gene expression (25)(26)(27)(28)(29). By base pairing with their target mRNA(s), small RNAs can interfere with the ribosome binding site or other sequence stretches and, consequently, alter mRNA translation and stability.…”