Journal
NUCLEIC ACIDS RESEARCH
Volume 47, Issue 4, Pages 2075-2088Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gky1243
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Funding
- Japan Society for the Promotion of Science [JSPS KAKENHI] [JP15H06528, JP16H06190]
- Bavarian BioSysNet program
- German Research Foundation [DFG Vo875-14/1]
- MEXT LEADER program
- Tomizawa Jun-ichi & Keiko Fund of Molecular Biology Society of Japan for Young Scientist
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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 approximate to 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 3UTRs are a playground for the evolution of regulatory RNA networks in bacteria.
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