Post-transcriptional gene regulation by an Hfq-independent small RNA in Caulobacter crescentus.

TitlePost-transcriptional gene regulation by an Hfq-independent small RNA in Caulobacter crescentus.
Publication TypeJournal Article
Year of Publication2018
AuthorsFröhlich, KS, Förstner, KU, Gitai, Z
JournalNucleic Acids Res
Volume46
Issue20
Pagination10969-10982
Date Published2018 11 16
ISSN1362-4962
KeywordsBacterial Proteins, Base Pairing, Base Sequence, Caulobacter crescentus, DNA Damage, Gene Expression Profiling, Gene Expression Regulation, Bacterial, Host Factor 1 Protein, Models, Molecular, Nucleic Acid Conformation, Protein Binding, RNA, Bacterial, RNA, Messenger, RNA, Small Untranslated
Abstract

<p>Bacterial small RNAs (sRNAs) are a heterogeneous group of post-transcriptional regulators that often act at the heart of large networks. Hundreds of sRNAs have been discovered by genome-wide screens and most of these sRNAs exert their functions by base-pairing with target mRNAs. However, studies addressing the molecular roles of sRNAs have been largely confined to gamma-proteobacteria, such as Escherichia coli. Here we identify and characterize a novel sRNA, ChvR, from the alpha-proteobacterium Caulobacter crescentus. Transcription of chvR is controlled by the conserved two-component system ChvI-ChvG and it is expressed in response to DNA damage, low pH, and growth in minimal medium. Transient over-expression of ChvR in combination with genome-wide transcriptome profiling identified the mRNA of the TonB-dependent receptor ChvT as the sole target of ChvR. Genetic and biochemical analyses showed that ChvR represses ChvT at the post-transcriptional level through direct base-pairing. Fine-mapping of the ChvR-chvT interaction revealed the requirement of two distinct base-pairing sites for full target regulation. Finally, we show that ChvR-controlled repression of chvT is independent of the ubiquitous RNA-chaperone Hfq, and therefore distinct from previously reported mechanisms employed by prototypical bacterial sRNAs. These findings have implications for the mechanism and evolution of sRNA function across bacterial species.</p>

DOI10.1093/nar/gky765
Alternate JournalNucleic Acids Res.
PubMed ID30165530
PubMed Central IDPMC6237742
Grant ListDP1 AI124669 / AI / NIAID NIH HHS / United States
R01 GM107384 / GM / NIGMS NIH HHS / United States