Premium
Specific and pleiotropic patterns of mRNA regulation by ArcZ, a conserved, Hfq‐dependent small RNA
Author(s) -
Papenfort Kai,
Said Nelly,
Welsink Tim,
Lucchini Sacha,
Hinton Jay C. D.,
Vogel Jörg
Publication year - 2009
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/j.1365-2958.2009.06857.x
Subject(s) - biology , messenger rna , rna , genetics , small rna , computational biology , microbiology and biotechnology , evolutionary biology , gene
Summary The small RNA, ArcZ (previously RyhA/SraH), was discovered in several genome‐wide screens in Escherichia coli and Salmonella . Its high degree of genomic conservation, its frequent recovery by shotgun sequencing, and its association with the RNA chaperone, Hfq, identified ArcZ as an abundant enterobacterial ‘core’ small RNA, yet its function remained unknown. Here, we report that ArcZ acts as a post‐transcriptional regulator in Salmonella , repressing the mRNAs of the widely distributed sdaCB (serine uptake) and tpx (oxidative stress) genes, and of STM3216, a horizontally acquired methyl‐accepting chemotaxis protein (MCP). Both sdaCB and STM3216 are regulated by sequestration of the ribosome binding site. In contrast, the tpx mRNA is targeted in the coding sequence (CDS), arguing that CDS targeting is more common than appreciated. Transcriptomic analysis of an arcZ deletion strain further argued for the existence of a distinct set of Salmonella loci specifically regulated by ArcZ. In contrast, increased expression of the sRNA altered the steady‐state levels of > 16% (> 750) of all Salmonella mRNAs, and rendered the bacteria non‐motile. Deep sequencing detected a dramatically changed profile of Hfq‐bound sRNAs and mRNAs, suggesting that the unprecedented pleiotropic effects by a single sRNA might in part be caused by altered post‐transcriptional regulation.