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GcvB small RNA uses two distinct seed regions to regulate an extensive targetome
Author(s) -
Lalaouna David,
Eyraud Alex,
Devinck Aurélie,
Prévost Karine,
Massé Eric
Publication year - 2019
Publication title -
molecular microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.857
H-Index - 247
eISSN - 1365-2958
pISSN - 0950-382X
DOI - 10.1111/mmi.14168
Subject(s) - biology , rnase p , rna , transfer rna , messenger rna , small rna , base pair , genetics , microbiology and biotechnology , gene
Summary GcvB small RNA is described as post‐transcriptional regulator of 1–2% of all mRNAs in Escherichia coli and Salmonella Typhimurium. At least 24 GcvB:mRNA interactions have been validated in vivo , establishing the largest characterized sRNA targetome. By performing MS2‐affinity purification coupled with RNA sequencing (MAPS) technology, we identified seven additional mRNAs negatively regulated by GcvB in E. coli . Contrary to the vast majority of previously known targets, which pair to the well‐conserved GcvB R1 region, we validated four mRNAs targeted by GcvB R3 region. This indicates that base‐pairing through R3 seed sequence seems relatively common. We also noticed unusual GcvB pairing sites in the coding sequence of two target mRNAs. One of these target mRNAs has a pairing site displaying a unique ACA motif, suggesting that GcvB could hijack a translational enhancer element. The second target mRNA is likely regulated via an active RNase E‐mediated mRNA degradation mechanism. Remarkably, we confirmed the importance of the sRNA sponge SroC in the fine‐tuning control of GcvB activity in function of growth conditions such as growth phase and nutrient availability.