RRC ID 66221
Author Miyakoshi M, Matera G, Maki K, Sone Y, Vogel J.
Title Functional expansion of a TCA cycle operon mRNA by a 3' end-derived small RNA.
Journal Nucleic Acids Res
Abstract Global RNA profiling studies in bacteria have predicted the existence of many of small noncoding RNAs (sRNAs) that are processed off mRNA 3' ends to regulate other mRNAs via the RNA chaperones Hfq and ProQ. Here, we present targets of SdhX (RybD), an Hfq-dependent sRNA that is generated by RNase E mediated 3' processing of the ∼10 000-nt mRNA of the TCA cycle operon sdhCDAB-sucABCD in enteric bacteria. An in silico search predicted ackA mRNA, which encodes acetate kinase, as a conserved primary target of SdhX. Through base pairing, SdhX represses AckA synthesis during growth of Salmonella on acetate. Repression can be achieved by a naturally occurring 38-nucleotide SdhX variant, revealing the shortest functional Hfq-associated sRNA yet. Salmonella SdhX also targets the mRNAs of fumB (anaerobic fumarase) and yfbV, a gene of unknown function adjacent to ackA. Instead, through a slightly different seed sequence, SdhX can repress other targets in Escherichia coli, namely katG (catalase) and fdoG (aerobic formate dehydrogenase). This study illustrates how a key operon from central metabolism is functionally connected to other metabolic pathways through a 3' appended sRNA, and supports the notion that mRNA 3'UTRs are a playground for the evolution of regulatory RNA networks in bacteria.
Volume 47(4)
Pages 2075-2088
Published 2019-2-28
DOI 10.1093/nar/gky1243
PII 5239034
PMID 30541135
PMC PMC6393394
MeSH Endoribonucleases / genetics Escherichia coli / genetics* Escherichia coli / metabolism Escherichia coli Proteins / genetics* Gene Expression Regulation, Bacterial Host Factor 1 Protein / genetics Operon RNA, Messenger / genetics RNA, Small Untranslated / genetics* RNA-Binding Proteins / genetics*
IF 11.502
Prokaryotes E. coli