{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T14:26:54Z","timestamp":1768487214879,"version":"3.49.0"},"posted":{"date-parts":[[2024,11,19]]},"group-title":"Microbiology","reference-count":74,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2024,11,19]],"date-time":"2024-11-19T00:00:00Z","timestamp":1731974400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/publicdomain\/zero\/1.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2024,11,19]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                <jats:p>\n                  Bacterial sRNAs together with the RNA chaperone Hfq post-transcriptionally regulate gene expression by affecting ribosome binding or mRNA stability. In the human pathogen\n                  <jats:italic>Bordetella pertussis<\/jats:italic>\n                  , the causative agent of whooping cough, hundreds of sRNAs have been identified, but their roles in\n                  <jats:italic>B. pertussis<\/jats:italic>\n                  biology are mostly unknown. Here we characterize a Hfq-dependent sRNA (S17), whose level is dramatically higher in the virulence (Bvg\n                  <jats:sup>+<\/jats:sup>\n                  ) mode. We show that transcription from a \u03c3\n                  <jats:sup>A<\/jats:sup>\n                  -dependent promoter yields a long form of 190 nucleotides (nts) that is processed by RNase E to generate a shorter, more stable form (S17S) of 67 nts. Using RNA-seq and RT-qPCR, we identify 92 genes whose expression significantly increases in the absence of S17. Of these genes, 70 contain sequences at\/near their ribosome binding sites (RBSs) that are complementary to single-stranded (ss) regions (Sites 1 or 2) of S17S. The identified genes include those encoding multiple transporters and 3 transcriptional regulators. Using a\n                  <jats:italic>lacZ<\/jats:italic>\n                  translational reporter system, we demonstrate that S17S directly represses one of these genes,\n                  <jats:italic>BP2158<\/jats:italic>\n                  , a \u03c3\n                  <jats:sup>54<\/jats:sup>\n                  - dependent transcriptional regulator, suggesting the repression of a \u03c3\n                  <jats:sup>54<\/jats:sup>\n                  regulon in the Bvg\n                  <jats:sup>+<\/jats:sup>\n                  mode. We find that the S17S region containing Sites 1 and 2 is 100% conserved throughout various Betaproteobacteria species, and the S17S target sites are often conserved in the homologs of the\n                  <jats:italic>B. pertussis<\/jats:italic>\n                  target genes. We speculate that S17S regulation represents a highly conserved process that fine-tunes gene expression in the Bvg\n                  <jats:sup>+<\/jats:sup>\n                  mode of\n                  <jats:italic>B. pertussis<\/jats:italic>\n                  and perhaps under other conditions in related bacteria.\n                <\/jats:p>\n                <jats:sec>\n                  <jats:title>IMPORTANCE<\/jats:title>\n                  <jats:p>\n                    Regulation of gene expression involves controlling transcription, translation, and transcript degradation. sRNAs with short sequences complementary to an mRNA sequence are involved in post-transcriptional regulation by aiding or interfering with either ribosome binding or nuclease attack. In the human pathogen\n                    <jats:italic>Bordetella pertussis<\/jats:italic>\n                    , the causative agent of whooping cough, hundreds of sRNA have been identified, but their functions remain largely unknown. We have characterized a sRNA that is abundant in the virulence mode of\n                    <jats:italic>B. pertussis<\/jats:italic>\n                    and serves to down-regulate multiple genes including transcriptional regulators and various transporters. We demonstrate that this sRNA directly represses a transcriptional factor, suggesting that it influences the regulation of specific\n                    <jats:italic>B. pertussis<\/jats:italic>\n                    regulons. The high conservation of this sRNA and its targets within Betaproteobacteria suggests a conserved pathway for gene regulation.\n                  <\/jats:p>\n                <\/jats:sec>","DOI":"10.1101\/2024.11.19.624354","type":"posted-content","created":{"date-parts":[[2024,11,19]],"date-time":"2024-11-19T22:45:13Z","timestamp":1732056313000},"source":"Crossref","is-referenced-by-count":2,"title":["A highly conserved sRNA downregulates multiple genes, including a \u03c3\n                  <sup>54<\/sup>\n                  transcriptional activator, in the virulence mode of\n                  <i>Bordetella pertussis<\/i>"],"prefix":"10.64898","author":[{"given":"Minji","family":"Sim","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jeffers","family":"Nguyen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Karol\u00edna","family":"\u0160kopov\u00e1","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kyungyoon","family":"Yoo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chin-Hsien","family":"Tai","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Leslie","family":"Knipling","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qing","family":"Chen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David","family":"Kim","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Summer","family":"Nolan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rawan","family":"Elaksher","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5223-0882","authenticated-orcid":false,"given":"Nadim","family":"Majdalani","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hernan","family":"Lorenzi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Scott","family":"Stibitz","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kyung","family":"Moon","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7254-9495","authenticated-orcid":false,"given":"Deborah M.","family":"Hinton","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"54368","reference":[{"key":"2024112219503014000_2024.11.19.624354v1.1","doi-asserted-by":"crossref","unstructured":"Gottesman S , Storz G . 2011. 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