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We have determined the transcriptional landscape of <jats:italic>R. conorii<\/jats:italic> during infection of <jats:underline>H<\/jats:underline>uman <jats:underline>M<\/jats:underline>icrovascular <jats:underline>E<\/jats:underline>ndothelial <jats:underline>C<\/jats:underline>ells (HMECs) by strand-specific RNA sequencing to identify 4 riboswitches, 13 trans-acting (intergenic), and 22 cis-acting (antisense) small RNAs (termed \u2018<jats:italic>Rc<\/jats:italic>_sR\u2019s). Independent expression of four novel trans-acting sRNAs (<jats:italic>Rc<\/jats:italic>_sR31, <jats:italic>Rc<\/jats:italic>_sR33, <jats:italic>Rc<\/jats:italic>_sR35, and <jats:italic>Rc<\/jats:italic>_sR42) and known bacterial sRNAs (6S, RNaseP_bact_a, ffs, and \u03b1-tmRNA) was next confirmed by Northern hybridization. Comparative analysis during infection of HMECs vis-\u00e0-vis tick AAE2 cells revealed significantly higher expression of <jats:italic>Rc<\/jats:italic>_sR35 and <jats:italic>Rc<\/jats:italic>_sR42 in HMECs, whereas <jats:italic>Rc<\/jats:italic>_sR31 and <jats:italic>Rc<\/jats:italic>_sR33 were expressed at similar levels in both cell types. We further predicted a total of 502 genes involved in all important biological processes as potential targets of <jats:italic>Rc<\/jats:italic>_sRs and validated the interaction of <jats:italic>Rc<\/jats:italic>_sR42 with <jats:italic>cydA<\/jats:italic> (cytochrome d ubiquinol oxidase subunit I). Our findings constitute the first evidence of the existence of post-transcriptional riboregulatory mechanisms in <jats:italic>R. conorii<\/jats:italic> and interactions between a novel <jats:italic>Rc<\/jats:italic>_sR and its target mRNA.<\/jats:p>","DOI":"10.1038\/srep36728","type":"journal-article","created":{"date-parts":[[2016,11,11]],"date-time":"2016-11-11T10:30:32Z","timestamp":1478860232000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":25,"title":["Small Regulatory RNAs of Rickettsia conorii"],"prefix":"10.1038","volume":"6","author":[{"given":"Hema P.","family":"Narra","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Casey L. 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