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 thesdhCDAB-sucABCDoperon, encoding enzymes of the tricarboxylic acid (TCA) cycle. InEscherichia coli, SdhX negatively regulatesackA, which encodes an enzyme critical for degradation of the signaling molecule acetyl phosphate, while the downstreamptagene, encoding the enzyme critical for acetyl phosphate synthesis, is not significantly affected. This discoordinate regulation ofptaandackAincreases the accumulation of acetyl phosphate when SdhX is expressed. Mutations insdhXthat abolish regulation ofackAlead 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 ofackA. 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.