Regulation of acetate metabolism and coordination with the TCA cycle via a processed small RNA.

Abstract

Bacterial regulatory small RNAs act as crucial regulators in central carbon metabolism by modulating translation initiation and degradation of target mRNAs in metabolic pathways. Here, we demonstrate that a noncoding small RNA, SdhX, is produced by RNase E-dependent processing from the 3'UTR of the <i>sdhCDAB-sucABCD</i> operon, encoding enzymes of the tricarboxylic acid (TCA) cycle. In <i>Escherichia coli</i>, SdhX negatively regulates <i>ackA</i>, which encodes an enzyme critical for degradation of the signaling molecule acetyl phosphate, while the downstream <i>pta</i> gene, encoding the enzyme critical for acetyl phosphate synthesis, is not significantly affected. This discoordinate regulation of <i>pta</i> and <i>ackA</i> increases the accumulation of acetyl phosphate when SdhX is expressed. Mutations in <i>sdhX</i> that abolish regulation of <i>ackA</i> lead to more acetate in the medium (more overflow metabolism), as well as a strong growth defect in the presence of acetate as sole carbon source, when the AckA-Pta pathway runs in reverse. SdhX overproduction confers resistance to hydroxyurea, via regulation of <i>ackA</i> SdhX abundance is tightly coupled to the transcription signals of TCA cycle genes but escapes all known posttranscriptional regulation. Therefore, SdhX expression directly correlates with transcriptional input to the TCA cycle, providing an effective mechanism for the cell to link the TCA cycle with acetate metabolism pathways.