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Abstract Bacteria use a multi-layered regulatory strategy to precisely and rapidly tune gene expression in response to environmental cues. Small RNAs (sRNAs) form an important layer of gene expression control and most act post-transcriptionally to control translation and stability of mRNAs. We have shown that at least five different sRNAs inEscherichia coliregulate the cyclopropane fatty acid synthase (cfa) mRNA. These sRNAs bind at different sites in the long 5’ untranslated region (UTR) ofcfamRNA and previous work suggested that they modulate RNase E-dependent mRNA turnover. Recently, thecfa5’ UTR was identified as a site of Rho-dependent transcription termination, leading us to hypothesize that the sRNAs might also regulatecfatranscription elongation. In this study we find that a pyrimidine-rich region flanked by sRNA binding sites in thecfa5’ UTR is required for premature Rho-dependent termination. We discovered that both the activating sRNA RydC and repressing sRNA CpxQ regulatecfaprimarily by modulating Rho-dependent termination ofcfatranscription, with only a minor effect on RNase E-mediated turnover ofcfamRNA. A stem-loop structure in thecfa5’ UTR sequesters the pyrimidine-rich region required for Rho-dependent termination. CpxQ binding to the 5’ portion of the stem increases Rho-dependent termination whereas RydC binding downstream of the stem decreases termination. These results reveal the versatile mechanisms sRNAs use to regulate target gene expression at transcriptional and post-transcriptional levels and demonstrate that regulation by sRNAs in long UTRs can involve modulation of transcription elongation. ImportanceBacteria respond to stress by rapidly regulating gene expression. Regulation can occur through control of messenger RNA (mRNA) production (transcription elongation), stability of mRNAs, or translation of mRNAs. Bacteria can use small RNAs (sRNAs) to regulate gene expression at each of these steps, but we often do not understand how this works at a molecular level. In this study, we find that sRNAs inEscherichia coliregulate gene expression at the level of transcription elongation by promoting or inhibiting transcription termination by a protein called Rho. These results help us understand new molecular mechanisms of gene expression regulation in bacteria.
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Re-defining how mRNA degradation is coordinated with transcription and translation in bacteria
Abstract In eukaryotic cells, transcription, translation, and mRNA degradation occur in distinct subcellular regions. How these mRNA processes are organized in bacteria, without employing membrane-bound compartments, remains unclear. Here, we present generalizable principles underlying coordination between these processes in bacteria. InEscherichia coli, we found that co-transcriptional degradation is rare for mRNAs except for those encoding inner membrane proteins, due to membrane localization of the main ribonuclease, RNase E. We further found, by varying ribosome binding sequences, that translation affects mRNA stability not because ribosomes protect mRNA from degradation, but because low translation leads to premature transcription termination in the absence of transcription-translation coupling. Extending our analyses toBacillus subtilisandCaulobacter crescentus, we established subcellular localization of RNase E (or its homolog) and premature transcription termination in the absence of transcription-translation coupling as key determinants that explain differences in transcriptional and translational coupling to mRNA degradation across genes and species.
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- Award ID(s):
- 2243257
- PAR ID:
- 10595292
- Publisher / Repository:
- bioRxiv
- Date Published:
- Format(s):
- Medium: X
- Institution:
- bioRxiv
- Sponsoring Org:
- National Science Foundation
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Accepted Manuscript1.0
- Posted Content:
- https://doi.org/10.1101/2024.04.18.588412
