Involvement of the small RNA suhb on carbon catbolite repression of tetralin degradation genes in Sphingopyxis granuli strain TFA

Abstract

[Backgrounds]: Sphingopyxis granuli strain TFA is able to use the organic solvent tetralin as the sole carbon and energy source. Structural thn genes are induced in the presence of tetralin by ThnR, a LysR-like transcriptional regulator, and ThnY, a ThnR co-activator. Besides, the expression of thn genes is under carbon catabolite repression (CCR) by a preferential carbon source, such as β-hydroxybutyrate (β-HB). [Objectives]: The main objective is to stablish the role of a small RNA (sRNA) in thn genes expression control under CCR conditions. [Methods]: Comparison of the global gene expression in tetralin- and β-HB-grown cells revealed the presence of a sRNA expressed preferentially in β-HB, which was annotated by Infernal software 1.1. Northern Blot and β-galactosidase assays confirmed the differential expression of this sRNA. The effect on CCR over thn genes of mutant lacking the sRNA was evaluated. Furthermore, its putative targets were detected by IntaRNA software and the interaction validated by RNA-RNA EMSA. [Conclusions]: The sRNA is predicted as belonging to the family RF00519 (SuhB), which is highly conserved in α-proteobacteria. The thn genes are partially de-repressed in a mutant lacking SuhB under CCR conditions. Furthermore, the 5' UTR of thnR mRNA is identified as a target of SuhB in which would block the ribosomal binding site. Accordingly, ThnR levels are higher in the mutant strain. The available data so far indicate that SuhB is involved in CCR of thn genes.