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

Immaculada García-Romero, Konrad U. Förstner, Eduardo Santero, Belen Floriano

Research output: Contribution to journalArticle

4 Citations (Scopus)

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.
Original languageEnglish
Pages (from-to)3671-3683
Number of pages13
JournalEnvironmental Microbiology
Volume20
Issue number10
Early online date22 Jul 2018
DOIs
Publication statusPublished - Oct 2018

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Catabolite Repression
Sphingomonas
Small Untranslated RNA
RNA
metabolites
Gene Expression
Housekeeping
Messenger RNA
degradation
gene expression
gene
carbon
Transcription Initiation Site
Protein Biosynthesis
Computer Simulation
Genes
mutants
Carbon
Software
genes

Cite this

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title = "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.",
author = "Immaculada Garc{\'i}a-Romero and F{\"o}rstner, {Konrad U.} and Eduardo Santero and Belen Floriano",
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SuhB, a small non-coding RNA involved in catabolite repression of tetralin degradation genes in Sphingopyxis granuli strain TFA. / García-Romero, Immaculada; Förstner, Konrad U.; Santero, Eduardo; Floriano, Belen.

In: Environmental Microbiology, Vol. 20, No. 10, 10.2018, p. 3671-3683.

Research output: Contribution to journalArticle

TY - JOUR

T1 - SuhB, a small non-coding RNA involved in catabolite repression of tetralin degradation genes in Sphingopyxis granuli strain TFA

AU - García-Romero, Immaculada

AU - Förstner, Konrad U.

AU - Santero, Eduardo

AU - Floriano, Belen

PY - 2018/10

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AB - 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.

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