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Transcriptomic Profiling of Escherichia coli Reveals Regulatory Roles of the 3′ UTR-Derived sRNA UhpU Under Various Growth Conditions

ABSTRACT: 1.To investigate the biological function and regulatory impact of the 3′ UTR-derived small RNA (sRNA) UhpU, we performed comparative transcriptomic analysis of wild-type and ΔuhpTU deletion strains during growth in M9CA medium supplemented with Glucose-6-phosphate as the sole carbon source. 2:To investigate the biological function and regulatory impact of the transcriptional repressor MprA, we performed transcriptomic analyses in Escherichia coli with short-term pulse expression of MprA during LB growth.

ORGANISM(S): Escherichia coli

PROVIDER: GSE310329 | GEO | 2025/11/30

REPOSITORIES: GEO

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Project description:N-Acyl homoserine lactone (AHL) quorum sensing (QS) controls expression of over 200 genes in Pseudomonas aeruginosa. There are two AHL regulatory systems: the LasR-LasI circuit and the RhlR-RhlI system. We mapped transcription termination sites affected by AHL QS in P. aeruginosa, and in doing so we identified AHL-regulated small RNAs (sRNAs). Of interest, we noted that one particular sRNA was located within the rhlI locus. We found that rhlI, which encodes the enzyme that produces the AHL N-butanoyl-homoserine lactone (C4-HSL), is controlled by a 5' untranslated region (UTR)-derived sRNA we name RhlS. We also identified an antisense RNA encoded opposite the beginning of the rhlI open reading frame, which we name asRhlS. RhlS accumulates as wild-type cells enter stationary phase and is required for the production of normal levels of C4-HSL through activation of rhlI translation. RhlS also directly posttranscriptionally regulates at least one other unlinked gene, fpvA. The asRhlS appears to be expressed at maximal levels during logarithmic growth, and we suggest RhlS may act antagonistically to the asRhlS to regulate rhlI translation. The rhlI-encoded sRNAs represent a novel aspect of RNA-mediated tuning of P. aeruginosa QS.IMPORTANCE The opportunistic human pathogen Pseudomonas aeruginosa possesses multiple quorum sensing systems that regulate and coordinate production of virulence factors and adaptation to different environments. Despite extensive research, the regulatory elements that play a role in this complex network are still not fully understood. By using several RNA sequencing techniques, we were able to identify a small regulatory RNA we named RhlS. RhlS increases translation of RhlI, a key enzyme in the quorum sensing pathway, and represses the fpvA mRNA encoding one of the siderophore pyoverdine receptors. Our results highlight a new regulatory layer of P. aeruginosa quorum sensing and contribute to the growing understanding of the role regulatory RNAs play in bacterial physiology.

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Transcriptomic Profiling of Escherichia coli Reveals Regulatory Roles of the 3′ UTR-Derived sRNA UhpU Under Various Growth Conditions

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