Role of an sRNA repeat in general stress response of alpha-proteobacteria and mechanisms of regulation

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The identification of small non-coding RNAs in alpha-proteobacteria is still at an early stage and little is known in regard to biological functions or mechanisms of action. We have identified 17 sRNAs, which are abundant under high oxygen tension in the facultatively photosynthetic bacterium Rhodobacter sphaeroides. The sRNA RSs0680 was found in four consecutive copies (a-d) on the chromosome and is co-transcribed together with an upstream gene of unknown function. Its abundance is increased under various stress conditions, i.e. by peroxide, singlet oxygen, superoxide, and heat stress. Sequences with strong similarity to RSs0680 are found in other alpha-proteobacteria, in all cases in repeats of more than one copy. To learn more about the function of this sRNA repeat we will delete or over-express some or all of the copies in R. sphaeroides and/or the upstream ORF and analyze how important the presence of several copies is for function. The transcriptome and proteome of the resulting mutants will be investigated. We will identify the target mRNAs and elucidate their interaction to RSs0680 and the consequences for regulation. The processing events leading to the generation of the individual sRNAs will be analyzed. We will also test the response of the homologs identified in Paracoccus denitrificans and Sinorhizobium meliloti to different stresses and investigate whether RSs0680 has a similar role in other alpha-proteobacteria.