{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T07:59:37Z","timestamp":1772179177964,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pntd.0008671","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2020,12,4]],"date-time":"2020-12-04T00:00:00Z","timestamp":1607040000000}}],"reference-count":74,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2020,11,20]],"date-time":"2020-11-20T00:00:00Z","timestamp":1605830400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["R21AI128575"],"award-info":[{"award-number":["R21AI128575"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["AI133023, DE028409"],"award-info":[{"award-number":["AI133023, DE028409"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosntds.org"],"crossmark-restriction":false},"short-container-title":["PLoS Negl Trop Dis"],"abstract":"<jats:p>\n                    <jats:italic>Bartonella bacilliformis<\/jats:italic>\n                    , the etiological agent of Carri\u00f3n\u2019s disease, is a Gram-negative, facultative intracellular alphaproteobacterium. Carri\u00f3n\u2019s disease is an emerging but neglected tropical illness endemic to Peru, Colombia, and Ecuador.\n                    <jats:italic>B<\/jats:italic>\n                    .\n                    <jats:italic>bacilliformis<\/jats:italic>\n                    is spread between humans through the bite of female phlebotomine sand flies. As a result, the pathogen encounters significant and repeated environmental shifts during its life cycle, including changes in pH and temperature. In most bacteria, small non-coding RNAs (sRNAs) serve as effectors that may post-transcriptionally regulate the stress response to such changes. However, sRNAs have not been characterized in\n                    <jats:italic>B<\/jats:italic>\n                    .\n                    <jats:italic>bacilliformis<\/jats:italic>\n                    , to date. We therefore performed total RNA-sequencing analyses on\n                    <jats:italic>B<\/jats:italic>\n                    .\n                    <jats:italic>bacilliformis<\/jats:italic>\n                    grown\n                    <jats:italic>in vitro<\/jats:italic>\n                    then shifted to one of ten distinct conditions that simulate various environments encountered by the pathogen during its life cycle. From this, we identified 160 sRNAs significantly expressed under at least one of the conditions tested. sRNAs included the highly-conserved tmRNA, 6S RNA, RNase P RNA component, SRP RNA component,\n                    <jats:italic>ffH<\/jats:italic>\n                    leader RNA, and the alphaproteobacterial sRNAs \u03b1r45 and\n                    <jats:italic>speF<\/jats:italic>\n                    leader RNA. In addition, 153 other potential sRNAs of unknown function were discovered. Northern blot analysis was used to confirm the expression of eight novel sRNAs. We also characterized a\n                    <jats:underline>\n                      <jats:bold>\n                        <jats:italic>B<\/jats:italic>\n                      <\/jats:bold>\n                    <\/jats:underline>\n                    <jats:italic>artonella<\/jats:italic>\n                    <jats:underline>\n                      <jats:bold>\n                        <jats:italic>b<\/jats:italic>\n                      <\/jats:bold>\n                    <\/jats:underline>\n                    <jats:italic>acilliformis<\/jats:italic>\n                    <jats:underline>\n                      <jats:bold>g<\/jats:bold>\n                    <\/jats:underline>\n                    rou\n                    <jats:underline>\n                      <jats:bold>p I<\/jats:bold>\n                    <\/jats:underline>\n                    intron (BbgpI) that disrupts an un-annotated tRNA\n                    <jats:sub>CCU<\/jats:sub>\n                    <jats:sup>Arg<\/jats:sup>\n                    gene and determined that the intron splices\n                    <jats:italic>in vivo<\/jats:italic>\n                    and self-splices\n                    <jats:italic>in vitro<\/jats:italic>\n                    . Furthermore, we demonstrated the molecular targeting of\n                    <jats:underline>\n                      <jats:bold>\n                        <jats:italic>B<\/jats:italic>\n                      <\/jats:bold>\n                    <\/jats:underline>\n                    <jats:italic>artonella<\/jats:italic>\n                    <jats:underline>\n                      <jats:bold>\n                        <jats:italic>b<\/jats:italic>\n                      <\/jats:bold>\n                    <\/jats:underline>\n                    <jats:italic>acilliformis<\/jats:italic>\n                    <jats:underline>\n                      <jats:bold>s<\/jats:bold>\n                    <\/jats:underline>\n                    mall\n                    <jats:underline>\n                      <jats:bold>R<\/jats:bold>\n                    <\/jats:underline>\n                    NA\n                    <jats:underline>\n                      <jats:bold>9<\/jats:bold>\n                    <\/jats:underline>\n                    (BbsR9) to transcripts of the\n                    <jats:italic>ftsH<\/jats:italic>\n                    ,\n                    <jats:italic>nuoF<\/jats:italic>\n                    , and\n                    <jats:italic>gcvT<\/jats:italic>\n                    genes,\n                    <jats:italic>in vitro<\/jats:italic>\n                    .\n                  <\/jats:p>","DOI":"10.1371\/journal.pntd.0008671","type":"journal-article","created":{"date-parts":[[2020,11,20]],"date-time":"2020-11-20T14:26:53Z","timestamp":1605882413000},"page":"e0008671","update-policy":"https:\/\/doi.org\/10.1371\/journal.pntd.corrections_policy","source":"Crossref","is-referenced-by-count":6,"title":["Novel small RNAs expressed by Bartonella bacilliformis under multiple conditions reveal potential mechanisms for persistence in the sand fly vector and human host"],"prefix":"10.1371","volume":"14","author":[{"given":"Shaun","family":"Wachter","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Linda D.","family":"Hicks","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rahul","family":"Raghavan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1131-7930","authenticated-orcid":true,"given":"Michael F.","family":"Minnick","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2020,11,20]]},"reference":[{"issue":"4","key":"pntd.0008671.ref001","doi-asserted-by":"crossref","first-page":"503","DOI":"10.4269\/ajtmh.1968.17.503","article-title":"A history of bartonellosis (Carri\u00f3n\u2019s disease).","volume":"17","author":"MG Schultz","year":"1968","journal-title":"Am J Trop Med Hyg"},{"issue":"1","key":"pntd.0008671.ref002","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1186\/s40249-016-0197-7","article-title":"Carrion\u2019s disease: an eradicable illness?","volume":"5","author":"C Gomes","year":"2016","journal-title":"Infect Dis Poverty"},{"issue":"3","key":"pntd.0008671.ref003","doi-asserted-by":"crossref","first-page":"215","DOI":"10.4269\/ajtmh.1990.42.215","article-title":"An epidemic of Oroya fever in the Peruvian Andes","volume":"42","author":"GC Gray","year":"1990","journal-title":"Am J Trop Med Hyg"},{"issue":"3","key":"pntd.0008671.ref004","doi-asserted-by":"crossref","first-page":"598","DOI":"10.3181\/00379727-37-9655P","article-title":"Carri\u00f3n\u2019s disease. V. Studies on Phlebotomus as the possible vector","volume":"37","author":"M Hertig","year":"1937","journal-title":"Proc Soc Exp Biol Med"},{"issue":"10","key":"pntd.0008671.ref005","doi-asserted-by":"crossref","first-page":"e0004128","DOI":"10.1371\/journal.pntd.0004128","article-title":"Colonization of Lutzomyia verrucarum and Lutzomyia longipalpis sand flies (Diptera: Psychodidae) by Bartonella bacilliformis, the etiologic agent of Carri\u00f3n\u2019s disease","volume":"9","author":"JM Battisti","year":"2015","journal-title":"PLoS Negl Trop Dis"},{"issue":"1","key":"pntd.0008671.ref006","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/S0891-5520(05)70215-4","article-title":"Bartonellosis.","volume":"14","author":"C Magui\u00f1a","year":"2000","journal-title":"New and old. Infect Dis Clin North Am"},{"issue":"7","key":"pntd.0008671.ref007","doi-asserted-by":"crossref","first-page":"e2919","DOI":"10.1371\/journal.pntd.0002919","article-title":"Oroya fever and verruga peruana: bartonelloses unique to South America","volume":"8","author":"MF Minnick","year":"2014","journal-title":"PLoS Negl Trop Dis"},{"issue":"6","key":"pntd.0008671.ref008","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1086\/322614","article-title":"Bartonellosis (Carri\u00f3n\u2019s disease) in the modern era","volume":"33","author":"C Magui\u00f1a","year":"2001","journal-title":"Clin Infect Dis"},{"key":"pntd.0008671.ref009","doi-asserted-by":"crossref","first-page":"562","DOI":"10.1182\/blood.V17.5.562.562","article-title":"The hemolytic anemia of human bartonellosis","volume":"17","author":"C Reynafarje","year":"1961","journal-title":"Blood"},{"issue":"3","key":"pntd.0008671.ref010","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1016\/j.clindermatol.2008.10.006","volume":"27","author":"C Magui\u00f1a","year":"2009","journal-title":"Bartonellosis. Clin Dermatol"},{"issue":"2","key":"pntd.0008671.ref011","doi-asserted-by":"crossref","first-page":"174","DOI":"10.4269\/ajtmh.1997.57.174","article-title":"Bartonellosis in Ecuador: serosurvey and current status of cutaneous verrucous disease","volume":"57","author":"Y Amano","year":"1997","journal-title":"Am J Trop Med Hyg"},{"issue":"7","key":"pntd.0008671.ref012","doi-asserted-by":"crossref","first-page":"1111","DOI":"10.3201\/eid1907.121718","article-title":"Novel Bartonella agent as cause of verruga peruana","volume":"19","author":"DL Blazes","year":"2013","journal-title":"Emerg Infect Dis"},{"issue":"23","key":"pntd.0008671.ref013","doi-asserted-by":"crossref","first-page":"2381","DOI":"10.1056\/NEJMoa065987","article-title":"Bacteremia, fever, and splenomegaly caused by a newly recognized Bartonella species","volume":"356","author":"ME Eremeeva","year":"2007","journal-title":"N Engl J Med"},{"issue":"5","key":"pntd.0008671.ref014","doi-asserted-by":"crossref","first-page":"1229","DOI":"10.4269\/ajtmh.18-0520","article-title":"Molecular detection of Bartonella bacilliformis in Lutzomyia maranonensis in Cajamarca, Peru: a new potential vector of Carrion\u2019s disease in Peru","volume":"99","author":"GM Ulloa","year":"2018","journal-title":"Am J Trop Med Hyg"},{"issue":"5","key":"pntd.0008671.ref015","doi-asserted-by":"crossref","first-page":"799","DOI":"10.4269\/ajtmh.1999.60.799","article-title":"Survey of Bartonella species infecting intradomicillary animals in the Huayllacall\u00e0n Valley, Ancash, Peru, a region endemic for human bartonellosis","volume":"60","author":"RJ Birtles","year":"1999","journal-title":"Am J Trop Med Hyg"},{"key":"pntd.0008671.ref016","first-page":"S1","article-title":"Phlebotomus and Carri\u00f3n\u2019s disease III. Field studies on Phlebotomus","author":"M Hertig","year":"1942","journal-title":"Am J Trop Med Hyg"},{"issue":"1","key":"pntd.0008671.ref017","first-page":"76","article-title":"Susceptibility of owl monkeys (Aotus nancymaae) to experimental infection with Bartonella bacilliformis","volume":"58","author":"DE Bentzel","year":"2008","journal-title":"Comp Med."},{"issue":"2","key":"pntd.0008671.ref018","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1128\/IAI.54.2.347-353.1986","article-title":"Entry of Bartonella bacilliformis into erythrocytes","volume":"54","author":"LA Benson","year":"1986","journal-title":"Infect Immun"},{"issue":"12","key":"pntd.0008671.ref019","doi-asserted-by":"crossref","first-page":"4962","DOI":"10.1128\/IAI.61.12.4962-4971.1993","article-title":"Characterization of Bartonella bacilliformis flagella and effect of antiflagellin antibodies on invasion of human erythrocytes","volume":"61","author":"DC Scherer","year":"1993","journal-title":"Infect Immun"},{"issue":"4","key":"pntd.0008671.ref020","doi-asserted-by":"crossref","first-page":"1552","DOI":"10.1128\/IAI.63.4.1552-1562.1995","article-title":"Characterization of a two-gene locus from Bartonella bacilliformis associated with the ability to invade human erythrocytes","volume":"63","author":"SJ Mitchell","year":"1995","journal-title":"Infect Immun"},{"issue":"7","key":"pntd.0008671.ref021","doi-asserted-by":"crossref","first-page":"4373","DOI":"10.1128\/IAI.69.7.4373-4381.2001","article-title":"Establishing a direct role for the Bartonella bacilliformis invasion-associated locus B (IalB) protein in human erythrocyte parasitism","volume":"69","author":"SA Coleman","year":"2001","journal-title":"Infect Immun"},{"issue":"1","key":"pntd.0008671.ref022","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1111\/j.1574-6968.2000.tb08884.x","article-title":"Contact-dependent hemolytic activity distinct from deforming activity of Bartonella bacilliformis","volume":"182","author":"LR Hendrix","year":"2000","journal-title":"FEMS Microbiol Lett"},{"issue":"9","key":"pntd.0008671.ref023","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1046\/j.1462-5822.2002.00217.x","article-title":"Activation of Rac, Cdc42 and other downstream signaling molecules by Bartonella bacilliformis during entry into human endothelial cells","volume":"4","author":"A Verma","year":"2002","journal-title":"Cell Microbiol"},{"issue":"5","key":"pntd.0008671.ref024","first-page":"1125","article-title":"Bartonella bacilliformis stimulates endothelial cells in vitro and is angiogenic in vivo","volume":"136","author":"FU Garcia","year":"1990","journal-title":"Am J Pathol"},{"issue":"12","key":"pntd.0008671.ref025","doi-asserted-by":"crossref","first-page":"6933","DOI":"10.1128\/IAI.71.12.6933-6942.2003","article-title":"Mitogenic effect of Bartonella bacilliformis on human vascular endothelial cells and involvement of GroEL","volume":"71","author":"MF Minnick","year":"2003","journal-title":"Infect Immun"},{"issue":"4","key":"pntd.0008671.ref026","doi-asserted-by":"crossref","first-page":"e0008236","DOI":"10.1371\/journal.pntd.0008236","article-title":"Human vascular endothelial cells express epithelial growth factor in response to infection by Bartonella bacilliformis","volume":"14","author":"LD Hicks","year":"2020","journal-title":"PLoS Negl Trop Dis"},{"issue":"6","key":"pntd.0008671.ref027","doi-asserted-by":"crossref","first-page":"485","DOI":"10.1590\/S0036-46651993000600002","article-title":"Geographic distribution of Lutzomyia verrucarum (Townsend, 1913) (Diptera, Psychodidae, Phlebotominae), vector of human bartonellosis in Peru.","volume":"35","author":"AG Caceres","year":"1993","journal-title":"Rev Inst Med Trop Sao Paulo"},{"key":"pntd.0008671.ref028","doi-asserted-by":"crossref","first-page":"3","DOI":"10.5194\/adgeo-22-3-2009","article-title":"The Andes climate and weather","volume":"22","author":"RD Garreaud","year":"2009","journal-title":"Adv. Geosci."},{"issue":"Pt 17","key":"pntd.0008671.ref029","first-page":"2792","article-title":"The physiology of the midgut of Lutzomyia longipalpis (Lutz and Neiva 1912): pH in different physiological conditions and mechanisms involved in its control","volume":"211","author":"VC Santos","year":"2008"},{"issue":"3","key":"pntd.0008671.ref030","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1006\/expr.1998.4336","article-title":"Lutzomyia longipalpis: pH in the gut, digestive glycosidases, and some speculations upon Leishmania development","volume":"90","author":"NF Gontijo","year":"1998","journal-title":"Exp Parasitol"},{"issue":"1","key":"pntd.0008671.ref031","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1146\/annurev-micro-090817-062607","article-title":"Broadening the definition of bacterial small RNAs: characteristics and mechanisms of action","volume":"72","author":"MC Carrier","year":"2018","journal-title":"Annu Rev Microbiol"},{"issue":"15","key":"pntd.0008671.ref032","doi-asserted-by":"crossref","first-page":"3993","DOI":"10.1002\/j.1460-2075.1996.tb00773.x","article-title":"The small RNA, DsrA, is essential for the low temperature expression of RpoS during exponential growth in Escherichia coli","volume":"15","author":"DD Sledjeski","year":"1996","journal-title":"EMBO J"},{"key":"pntd.0008671.ref033","doi-asserted-by":"crossref","first-page":"24","DOI":"10.3389\/fcimb.2016.00024","article-title":"A novel small RNA regulates tolerance and virulence in Shigella flexneri by responding to acidic environmental changes","volume":"6","author":"L Wang","year":"2016","journal-title":"Front Cell Infect Microbiol"},{"issue":"2","key":"pntd.0008671.ref034","doi-asserted-by":"crossref","first-page":"e00420","DOI":"10.1002\/mbo3.420","article-title":"A family of genus-specific RNAs in tandem with DNA-binding proteins control expression of the badA major virulence factor gene in Bartonella henselae","volume":"6","author":"N Tu","year":"2017","journal-title":"Microbiologyopen"},{"key":"pntd.0008671.ref035","doi-asserted-by":"crossref","first-page":"104272","DOI":"10.1016\/j.micpath.2020.104272","article-title":"A non-coding RNA controls transcription of a gene encoding a DNA binding protein that modulates biofilm development in Bartonella henselae","volume":"147","author":"U Okaro","year":"2020","journal-title":"Microb Pathog"},{"issue":"22","key":"pntd.0008671.ref036","doi-asserted-by":"crossref","first-page":"e00524","DOI":"10.1128\/JB.00524-19","article-title":"A CsrA-binding, trans-acting sRNA of Coxiella burnetii is necessary for optimal intracellular growth and vacuole formation during early infection of host cells","volume":"201","author":"S Wachter","year":"2019","journal-title":"J Bacteriol"},{"issue":"16","key":"pntd.0008671.ref037","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map (SAM) format and SAMtools","volume":"25","author":"H Li","year":"2009","journal-title":"Bioinformatics"},{"issue":"4","key":"pntd.0008671.ref038","doi-asserted-by":"crossref","first-page":"464","DOI":"10.1093\/bioinformatics\/btr703","article-title":"Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data","volume":"28","author":"T Carver","year":"2012","journal-title":"Bioinformatics"},{"issue":"Pt 6","key":"pntd.0008671.ref039","doi-asserted-by":"crossref","first-page":"1751","DOI":"10.1099\/mic.0.28743-0","article-title":"Promoter prediction in the rhizobia","volume":"152","author":"SR MacLellan","year":"2006","journal-title":"Microbiology"},{"issue":"7","key":"pntd.0008671.ref040","doi-asserted-by":"crossref","first-page":"923","DOI":"10.1093\/bioinformatics\/btt656","article-title":"featureCounts: an efficient general purpose program for assigning sequence reads to genomic features","volume":"30","author":"Y Liao","year":"2014","journal-title":"Bioinformatics"},{"issue":"12","key":"pntd.0008671.ref041","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"MI Love","year":"2014","journal-title":"Genome Biol"},{"issue":"12","key":"pntd.0008671.ref042","doi-asserted-by":"crossref","first-page":"1461","DOI":"10.1093\/bioinformatics\/btn209","article-title":"fdrtool: a versatile R package for estimating local and tail area-based false discovery rates","volume":"24","author":"K Strimmer","year":"2008","journal-title":"Bioinformatics"},{"issue":"W1","key":"pntd.0008671.ref043","doi-asserted-by":"crossref","first-page":"W435","DOI":"10.1093\/nar\/gkx279","article-title":"IntaRNA 2.0: enhanced and customizable prediction of RNA-RNA interactions","volume":"45","author":"M Mann","year":"2017","journal-title":"Nucleic Acids Res"},{"issue":"10","key":"pntd.0008671.ref044","doi-asserted-by":"crossref","first-page":"3420","DOI":"10.1093\/nar\/gkn176","article-title":"High-throughput functional annotation and data mining with the Blast2GO suite","volume":"36","author":"S G\u00f6tz","year":"2008","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"pntd.0008671.ref045","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1038\/nprot.2008.211","article-title":"Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources","volume":"4","author":"DW Huang","year":"2009","journal-title":"Nat Protoc"},{"issue":"18","key":"pntd.0008671.ref046","doi-asserted-by":"crossref","first-page":"2938","DOI":"10.1093\/bioinformatics\/btx364","article-title":"UpSetR: an R package for the visualization of intersecting sets and their properties","volume":"33","author":"JR Conway","year":"2017","journal-title":"Bioinformatics"},{"key":"pntd.0008671.ref047","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-319-24277-4","volume-title":"ggplot2: Elegant Graphics for Data Analysis","author":"H Wickham","year":"2016","edition":"1"},{"issue":"7","key":"pntd.0008671.ref048","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1038\/nmeth.2019","article-title":"Fiji: an open-source platform for biological-image analysis.","volume":"9","author":"J Schindelin","year":"2012","journal-title":"Nat Methods"},{"issue":"12","key":"pntd.0008671.ref049","doi-asserted-by":"crossref","first-page":"1983","DOI":"10.1109\/TVCG.2014.2346248","article-title":"UpSet: Visualization of intersecting sets","volume":"20","author":"A Lex","year":"2014","journal-title":"IEEE Trans Vis Comput Graph"},{"issue":"4","key":"pntd.0008671.ref050","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1093\/bioinformatics\/btp692","article-title":"RNA-Seq gene expression estimation with read mapping uncertainty","volume":"26","author":"B Li","year":"2010","journal-title":"Bioinformatics"},{"issue":"3","key":"pntd.0008671.ref051","doi-asserted-by":"crossref","first-page":"1049","DOI":"10.1128\/JB.181.3.1049-1053.1999","article-title":"Sporadic distribution of tRNA(Arg)CCU introns among alpha-purple bacteria: evidence for horizontal transmission and transposition of a group I intron","volume":"181","author":"B Paquin","year":"1999","journal-title":"J Bacteriol"},{"issue":"1","key":"pntd.0008671.ref052","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1186\/1759-8753-5-8","article-title":"Bacterial group I introns: mobile RNA catalysts","volume":"5","author":"G Hausner","year":"2014","journal-title":"Mob DNA"},{"key":"pntd.0008671.ref053","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/978-1-4939-9173-0_1","article-title":"tRNAscan-SE: searching for tRNA genes in genomic sequences","volume":"1962","author":"PP Chan","year":"2019","journal-title":"Methods Mol Biol"},{"issue":"W1","key":"pntd.0008671.ref054","doi-asserted-by":"crossref","first-page":"W124","DOI":"10.1093\/nar\/gku317","article-title":"TargetRNA2: identifying targets of small regulatory RNAs in bacteria","volume":"42","author":"MB Kery","year":"2014","journal-title":"Nucleic Acids Res"},{"issue":"W1","key":"pntd.0008671.ref055","doi-asserted-by":"crossref","first-page":"W119","DOI":"10.1093\/nar\/gku359","article-title":"CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains","volume":"42","author":"PR Wright","year":"2014","journal-title":"Nucleic Acids Res"},{"issue":"13","key":"pntd.0008671.ref056","doi-asserted-by":"crossref","first-page":"3406","DOI":"10.1093\/nar\/gkg595","article-title":"Mfold web server for nucleic acid folding and hybridization prediction","volume":"31","author":"M Zuker","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"pntd.0008671.ref057","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1016\/j.gene.2019.05.036","article-title":"Riboswitch distribution, structure, and function in bacteria","volume":"708","author":"N Pavlova","year":"2019","journal-title":"Gene"},{"issue":"2","key":"pntd.0008671.ref058","doi-asserted-by":"crossref","first-page":"119","DOI":"10.4161\/rna.18643","article-title":"A survey of sRNA families in \u03b1-proteobacteria","volume":"9","author":"C del Val","year":"2012","journal-title":"RNA Biol"},{"key":"pntd.0008671.ref059","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1186\/1471-2180-10-71","article-title":"The Sinorhizobium meliloti RNA chaperone Hfq influences central carbon metabolism and the symbiotic interaction with alfalfa","volume":"10","author":"O Torres-Quesada","year":"2010","journal-title":"BMC Microbiol"},{"key":"pntd.0008671.ref060","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1016\/j.mib.2016.02.003","article-title":"Hfq: The flexible RNA matchmaker","volume":"30","author":"TB Updergrove","year":"2016","journal-title":"Curr Opin Microbiol"},{"issue":"8","key":"pntd.0008671.ref061","doi-asserted-by":"crossref","first-page":"R70","DOI":"10.1186\/gb-2005-6-8-r70","article-title":"Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria","volume":"6","author":"KA Corbino","year":"2005","journal-title":"Genome Biol"},{"issue":"7395","key":"pntd.0008671.ref062","doi-asserted-by":"crossref","first-page":"538","DOI":"10.1038\/nature10965","article-title":"The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria","volume":"484","author":"G-W Li","year":"2012","journal-title":"Nature"},{"issue":"6","key":"pntd.0008671.ref063","doi-asserted-by":"crossref","first-page":"1722","DOI":"10.1093\/gbe\/evw107","article-title":"The frequency of internal Shine-Dalgarno-like motifs in prokaryotes","volume":"8","author":"GD Diwan","year":"2016","journal-title":"Genome Biol Evol"},{"issue":"7","key":"pntd.0008671.ref064","doi-asserted-by":"crossref","first-page":"4620","DOI":"10.1073\/pnas.032066599","article-title":"A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli","volume":"99","author":"E Mass\u00e9","year":"2002","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"3","key":"pntd.0008671.ref065","doi-asserted-by":"crossref","DOI":"10.1128\/microbiolspec.RWR-0019-2018","article-title":"6S RNA, a global regulator of transcription","volume":"6","author":"KM Wassarman","year":"2018","journal-title":"Microbiol Spectr"},{"issue":"11","key":"pntd.0008671.ref066","doi-asserted-by":"crossref","first-page":"e1000660","DOI":"10.1371\/journal.ppat.1000660","article-title":"The bacterial defensing resistance protein MprF consists of separable domains for lipid lysinylation and antimicrobial peptide repulsion","volume":"5","author":"CM Ernst","year":"2009","journal-title":"PLoS Pathog"},{"key":"pntd.0008671.ref067","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1146\/annurev.biochem.72.121801.161828","article-title":"The many faces of vitamin B12: catalysis by cobalamin-dependent enzymes","volume":"72","author":"R Banerjee","year":"2003","journal-title":"Annu Rev Biochem"},{"key":"pntd.0008671.ref068","doi-asserted-by":"crossref","first-page":"151","DOI":"10.3389\/fcimb.2014.00151","article-title":"Sibling rivalry: related bacterial small RNAs and their redundant and non-redundant roles","volume":"4","author":"CC Caswell","year":"2014","journal-title":"Front Cell Infect Microbiol"},{"issue":"6374","key":"pntd.0008671.ref069","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1038\/357173a0","article-title":"Self-splicing introns in tRNA genes of widely divergent bacteria","volume":"357","author":"B Reinhold-Hurek","year":"1992","journal-title":"Nature"},{"issue":"5\u20136","key":"pntd.0008671.ref070","doi-asserted-by":"crossref","first-page":"625","DOI":"10.1515\/hsz-2016-0302","article-title":"When, how, and why? Regulated proteolysis by the essential FtsH protease in Escherichia coli","volume":"398","author":"LM Bittner","year":"2017","journal-title":"Biol Chem"},{"issue":"5","key":"pntd.0008671.ref071","doi-asserted-by":"crossref","first-page":"1174","DOI":"10.1128\/JB.180.5.1174-1184.1998","article-title":"Genetic analysis of the nuo locus, which encodes the proton-translocating NADH dehydrogenase in Escherichia coli","volume":"180","author":"HJ Falk-Krzesinski","year":"1998","journal-title":"J Bacteriol"},{"issue":"7","key":"pntd.0008671.ref072","doi-asserted-by":"crossref","first-page":"246","DOI":"10.2183\/pjab.84.246","article-title":"Glycine cleavage system: reaction mechanism, physiological significance, and hyperglycinemia","volume":"84","author":"G Kikuchi","year":"2008","journal-title":"Proc Jpn Acad Ser B Phys Biol Sci"},{"issue":"11","key":"pntd.0008671.ref073","doi-asserted-by":"crossref","first-page":"485","DOI":"10.1016\/S0966-842X(02)02457-5","article-title":"Versatile persistence pathways for pathogens of animals and plants","volume":"10","author":"D Vereecke","year":"2002","journal-title":"Trends Microbiol"},{"issue":"7","key":"pntd.0008671.ref074","doi-asserted-by":"crossref","first-page":"4102","DOI":"10.1128\/IAI.68.7.4102-4107.2000","article-title":"Identification of genes required for chronic persistence of Brucella abortus in mice","volume":"68","author":"PC Hong","year":"2000","journal-title":"Infect Immun"}],"updated-by":[{"DOI":"10.1371\/journal.pntd.0008671","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2020,12,4]],"date-time":"2020-12-04T00:00:00Z","timestamp":1607040000000}}],"container-title":["PLOS Neglected Tropical Diseases"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pntd.0008671","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,11,28]],"date-time":"2022-11-28T22:44:28Z","timestamp":1669675468000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pntd.0008671"}},"subtitle":[],"editor":[{"given":"Joseph M.","family":"Vinetz","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2020,11,20]]},"references-count":74,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2020,11,20]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pntd.0008671","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2020.08.04.235903","asserted-by":"object"}]},"ISSN":["1935-2735"],"issn-type":[{"value":"1935-2735","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,11,20]]}}}