SuhB, a small non‐coding RNA involved in catabolite repression of tetralin degradation genes in Sphingopyxis granuli strain TFA

Abstract

Global dRNA-seq analysis of transcription start sites combined with in silico annotation using Infernal software revealed the expression of 91 putative non-coding sRNA in Sphingopyxis granuli TFA cells grown on different carbon sources. Excluding housekeeping sRNAs, only one additional sRNA, which belongs to the Rfam SuhB family (RF00519), was detected by Infernal but with an incorrect size according to the experimental results. SuhB is highly conserved across the Sphingopyxis genus. Expression data revealed that SuhB is present in rapidly growing TFA cells. A suhB deletion mutant exhibited de-repression of tetralin degradation (thn) gene expression and higher amounts of their LysR-type activator, ThnR, under conditions of carbon catabolite repression (CCR). Interaction between SuhB and the 5'UTR of thnR mRNA was demonstrated in vitro. Moreover, co-immunoprecipitation experiments, combined with fluorescence measurements of gfp fusions to the 5'UTR of thnR mRNA and the phenotype of an hfq deletion mutant, suggest the involvement of Hfq in this interaction. Taken together, these data support an Hfq-mediated repressive role for SuhB, on ThnR mRNA translation that prevents thn gene induction. SuhB, which is a highly conserved sRNA in the Sphingopyxis genus, is the first identified element directly involved in CCR of thn gene expression in S. granuli strain TFA.

Two paralogous EcfG σ factors hierarchically orchestrate the activation of the General Stress Response in Sphingopyxis granuli TFA

“…Although nepR genes are not usually automatically annotated due to their small size, the TFA genome revealed that it contains two short orfs that could actually code for NepR-like proteins and were therefore designated as nepR1 (SGRAN_0992) and nepR2 (SGRAN_1162). The one designated nepR2 is located upstream ecfG1, shares the same transcription start site (TSS) 21 and actually overlaps with ecfG1 by 4 bp (Fig. 1).…”

“…In order to know the specific contribution of EcfG1 and EcfG2 to the transcription of different GSR promoters, in vitro transcription assays were performed with either EcfG1 or EcfG2 forms of the RNAP using five putative promoter regions, representatives of the most frequent -10 boxes, as templates. In order to restrict the regulatory inputs to the effect of the σ factor alone, the DNA regions used as templates would only extend from the putative TSS 21 to the -35 sequence. Among the chosen templates, nepR2 and gsp (general stress protein, SGRAN_0888) were selected for having a consensus CGTT -10 box, but also for differing in the -35 element (they present a GGAAC and a GCAAC -35 box, respectively, the two most frequent in the GSR-dependent promoters, see Supp.…”

Understanding the metabolism of the tetralin degrader Sphingopyxis granuli strain TFA through genome-scale metabolic modelling

“…In addition, beyond providing more accurate predictions, GEMs provide useful computational workflows for the incorporation of -omics data within biological networks 31 . We thus included available transcriptomic data for strain TFA grown aerobically with tetralin and 3-HB 32 in an attempt to optimize iIG743 predictions for the strain grown on each of the two carbon sources. To do this, we reduced the solution space of iIG743 by using the GIMME method 33 .…”

Genome-Wide Analysis Reveals Genetic Potential for Aromatic Compounds Biodegradation of Sphingopyxis

“…C-1 isolated from an eutrophic lake in China has been shown to harbor the ability of MCs degradation [9]. Sphingopyxis fribergensis Kp5.2, originally isolated from soils, was reported to degrade styrene [14]. In addition, Sphingopyxis granuli TFA isolated from the Rhine river was able to grow in organic solvent tetralin [15].…”