{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,26]],"date-time":"2026-09-26T10:29:35Z","timestamp":1790418575915,"version":"4.1.0"},"reference-count":89,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2016,10,5]],"date-time":"2016-10-05T00:00:00Z","timestamp":1475625600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R03-AI113648"],"award-info":[{"award-number":["R03-AI113648"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R21-AI120602"],"award-info":[{"award-number":["R21-AI120602"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0164165","type":"journal-article","created":{"date-parts":[[2016,10,5]],"date-time":"2016-10-05T18:41:40Z","timestamp":1475692900000},"page":"e0164165","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":63,"title":["RNA-Seq of Borrelia burgdorferi in Multiple Phases of Growth Reveals Insights into the Dynamics of Gene Expression, Transcriptome Architecture, and Noncoding RNAs"],"prefix":"10.1371","volume":"11","author":[{"given":"William K.","family":"Arnold","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christina R.","family":"Savage","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Catherine A.","family":"Brissette","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Janakiram","family":"Seshu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonathan","family":"Livny","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brian","family":"Stevenson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2016,10,5]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1038\/nrmicro2714","article-title":"Of ticks, mice, and men: understanding the dual-host lifestyle of Lyme disease spirochaetes","volume":"10","author":"JD Radolf","year":"2012","journal-title":"Nature Rev Microbiol"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"2909","DOI":"10.1073\/pnas.92.7.2909","article-title":"Induction of an outer surface protein on <italic>Borrelia burgdorferi<\/italic> during tick feeding","volume":"92","author":"TG Schwan","year":"1995","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"382","DOI":"10.1128\/JCM.38.1.382-388.2000","article-title":"Temporal changes in outer surface proteins A and C of the Lyme disease-associated spirochete, <italic>Borrelia burgdorferi<\/italic>, during the chain of infection in ticks and mice","volume":"38","author":"TG Schwan","year":"2000","journal-title":"J Clin Microbiol"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"799","DOI":"10.1016\/S1286-4579(01)01435-6","article-title":"Analysis of <italic>Borrelia burgdorferi<\/italic> gene expression during life cycle phases of the tick vector <italic>Ixodes scapularis<\/italic>","volume":"3","author":"RD Gilmore","year":"2001","journal-title":"Microbes Infect"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"3122","DOI":"10.1128\/JB.184.11.3122-3125.2002","article-title":"Examination of the <italic>Borrelia burgdorferi<\/italic> transcriptome in <italic>Ixodes scapularis<\/italic> during feeding","volume":"184","author":"S Narasimhan","year":"2002","journal-title":"J Bacteriol"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"6943","DOI":"10.1128\/IAI.71.12.6943-6952.2003","article-title":"Temporal analysis of <italic>Borrelia burgdorferi<\/italic> Erp protein expression throughout the mammal-tick infectious cycle","volume":"71","author":"JC Miller","year":"2003","journal-title":"Infect Immun"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"4879","DOI":"10.1128\/JB.00229-06","article-title":"Transcriptional regulation of the <italic>Borrelia burgdorferi<\/italic> antigenically variable VlsE surface protein","volume":"188","author":"T Bykowski","year":"2006","journal-title":"J Bacteriol"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"4227","DOI":"10.1128\/IAI.00604-07","article-title":"Coordinated expression of <italic>Borrelia burgdorferi<\/italic> complement regulator-acquiring surface proteins during the Lyme disease spirochete\u2019s mammal-tick infection cycle","volume":"75","author":"T Bykowski","year":"2007","journal-title":"Infect Immun"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"e0118063","DOI":"10.1371\/journal.pone.0118063","article-title":"Characterization of the RelBbu regulon in <italic>Borrelia burgdorferi<\/italic> reveals modulation of glycerol metabolism by (p)ppGpp","volume":"10","author":"JV Bugrysheva","year":"2015","journal-title":"PLoS ONE"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1111\/mmi.12882","article-title":"Stage-specific global alterations in the transcriptomes of Lyme disease spirochetes during tick feeding and following mammalian host-adaptation","volume":"95","author":"R Iyer","year":"2015","journal-title":"Mol Microbiol"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"11001","DOI":"10.1073\/pnas.1834315100","article-title":"The response regulator Rrp2 is essential for the expression of major membrane lipoproteins in <italic>Borrelia burgdorferi<\/italic>","volume":"100","author":"XF Yang","year":"2003","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"4972","DOI":"10.1128\/IAI.73.8.4972-4981.2005","article-title":"<italic>Borrelia burgdorferi rel<\/italic> is responsible for generation of guanosine-3&apos;-diphosphate-5&apos;-triphosphate and growth control","volume":"73","author":"JV Bugrysheva","year":"2005","journal-title":"Infect Immun"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"1551","DOI":"10.1111\/j.1365-2958.2009.06621.x","article-title":"Rrp1, a cyclic-di-GMP-producing response regulator, is an important regulator of <italic>Borrelia burgdorferi<\/italic> core cellular functions","volume":"71","author":"EA Rogers","year":"2009","journal-title":"Mol Microbiol"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1146\/annurev.micro.112408.134040","article-title":"Gene regulation in <italic>Borrelia burgdorferi<\/italic>","volume":"65","author":"DS Samuels","year":"2011","journal-title":"Annu Rev Microbiol"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"26220","DOI":"10.1074\/jbc.M113.491357","article-title":"Bpur, the Lyme disease spirochete&apos;s PUR-domain protein: identification as a transcriptional modulator and characterization of nucleic acid interactions","volume":"288","author":"BL Jutras","year":"2013","journal-title":"J Biol Chem"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"1840","DOI":"10.1128\/IAI.00030-14","article-title":"DhhP, a cyclic di-AMP phosphodiesterase of <italic>Borrelia burgdorferi<\/italic>, is essential for cell growth and virulence","volume":"82","author":"M Ye","year":"2014","journal-title":"Infect Immun"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"3043","DOI":"10.1128\/IAI.00315-15","article-title":"Cyclic di-GMP modulates gene expression in Lyme disease spirochetes at the tick-mammal interface to promote spirochete survival during the blood meal and tick-to-mammal transmission","volume":"83","author":"MJ Caimano","year":"2015","journal-title":"Infect Immun"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"e0125440","DOI":"10.1371\/journal.pone.0125440","article-title":"Intracellular concentrations of <italic>Borrelia burgdorferi<\/italic> cyclic di-AMP are not changed by altered expression of the CdaA synthase","volume":"10","author":"CR Savage","year":"2015","journal-title":"PLoS One"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"4535","DOI":"10.1128\/IAI.63.11.4535-4539.1995","article-title":"Temperature-related differential expression of antigens in the Lyme disease spirochete, <italic>Borrelia burgdorferi<\/italic>","volume":"63","author":"B Stevenson","year":"1995","journal-title":"Infect Immun"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"3181","DOI":"10.1128\/IAI.67.7.3181-3187.1999","article-title":"Effects of environmental pH on membrane proteins in <italic>Borrelia burgdorferi<\/italic>","volume":"67","author":"JA Carroll","year":"1999","journal-title":"Infect Immun"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"1562","DOI":"10.1073\/pnas.032667699","article-title":"DNA microarray analysis of differential gene expression in <italic>Borrelia burgdorferi<\/italic>, the Lyme disease spirochete","volume":"99","author":"AT Revel","year":"2002","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"1689","DOI":"10.1128\/IAI.71.4.1689-1705.2003","article-title":"Profiling of temperature-induced changes in <italic>Borrelia burgdorferi<\/italic> gene expression by using whole genome arrays","volume":"71","author":"C Ojaimi","year":"2003","journal-title":"Infect Immun"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"5162","DOI":"10.1073\/pnas.0408536102","article-title":"<italic>Borrelia burgdorferi<\/italic> \u03c3<sup>54<\/sup> is required for mammalian infection and vector transmission but not for tick colonization","volume":"102","author":"MA Fisher","year":"2005","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"6791","DOI":"10.1128\/IAI.73.10.6791-6802.2005","article-title":"Comparative transcriptional profiling of <italic>Borrelia burgdorferi<\/italic> clinical isolates differing in capacities for hematogenous dissemination","volume":"73","author":"C Ojaimi","year":"2005","journal-title":"Infect Immun"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"2599","DOI":"10.1099\/mic.0.28996-0","article-title":"Transcriptional profiling of <italic>Borrelia burgdorferi<\/italic> containing a unique <italic>bosR<\/italic> allele identifies a putative stress regulon","volume":"152","author":"JA Hyde","year":"2006","journal-title":"Microbiology"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"1193","DOI":"10.1111\/j.1365-2958.2007.05860.x","article-title":"Analysis of the RpoS regulon in <italic>Borrelia burgdorferi<\/italic> in response to mammalian host signals provides insight into RpoS function during the enzootic cycle","volume":"65","author":"MJ Caimano","year":"2007","journal-title":"Mol Microbiol"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"2139","DOI":"10.1128\/JB.01653-06","article-title":"Evidence that RpoS (\u03c3<sup>S<\/sup>) in <italic>Borrelia burgdorferi<\/italic> is controlled directly by RpoN (\u03c3<sup>54<\/sup>\/\u03c3<sup>N<\/sup>)","volume":"189","author":"AH Smith","year":"2007","journal-title":"J Bacteriol"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"2641","DOI":"10.1099\/mic.0.2008\/019992-0","article-title":"Transcriptional interplay among the regulators Rrp2, RpoN and RpoS in <italic>Borrelia burgdorferi<\/italic>","volume":"154","author":"Z Ouyang","year":"2008","journal-title":"Microbiology"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"e1002133","DOI":"10.1371\/journal.ppat.1002133","article-title":"Cyclic di-GMP is essential for the survival of the Lyme disease spirochete in ticks","volume":"7","author":"M He","year":"2011","journal-title":"PLoS Pathog"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"e22168","DOI":"10.1371\/journal.pone.0022168","article-title":"HrpA, a DEAH-box RNA helicase, is involved in global gene regulation in the Lyme disease spirochete","volume":"6","author":"A Salman-Dilgimen","year":"2011","journal-title":"PLoS One"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"3395","DOI":"10.1128\/JB.00252-12","article-title":"EbfC (YbaB) is a new type of bacterial nucleoid-associated protein, and a global regulator of gene expression in the Lyme disease spirochete","volume":"194","author":"BL Jutras","year":"2012","journal-title":"J Bacteriol"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1111\/mmi.12171","article-title":"Borrelia host adaptation regulator (BadR) regulates <italic>rpoS<\/italic> to modulate host adaptation and virulence factors in <italic>Borrelia burgdorferi<\/italic>","volume":"88","author":"CL Miller","year":"2013","journal-title":"Mol Microbiol"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"e1005160","DOI":"10.1371\/journal.ppat.1005160","article-title":"The <italic>Borrelia burgdorferi<\/italic> RelA\/SpoT homolog and stringent response regulate survival in the tick vector and global gene expression during starvation","volume":"11","author":"D Drecktrah","year":"2015","journal-title":"PLoS Pathog"},{"key":"ref34","doi-asserted-by":"crossref","DOI":"10.3390\/microarrays5020009","article-title":"Microarray-based comparative genomic and transcriptome analysis of <italic>Borrelia burgdorferi<\/italic>","volume":"5","author":"R Iyer","year":"2016","journal-title":"Microarrays"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"615","DOI":"10.1016\/j.cell.2009.01.043","article-title":"Regulatory RNAs in bacteria","volume":"136","author":"LS Waters","year":"2009","journal-title":"Cell"},{"key":"ref36","doi-asserted-by":"crossref","DOI":"10.1016\/j.molcel.2011.08.022","article-title":"Regulation by small RNAs in bacteria: expanding frontiers","volume":"43","author":"G Storz","year":"2011","journal-title":"Mol Cell"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"774","DOI":"10.1261\/rna.7286705","article-title":"6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter","volume":"11","author":"JE Barrick","year":"2005","journal-title":"RNA"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1016\/j.cbpa.2015.09.016","article-title":"Dynamics of co-translational protein targeting","volume":"29","author":"MM Elvekrog","year":"2015","journal-title":"Curr Opin Chem Biol"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1093\/femsre\/fuv022","article-title":"Small RNAs, 5&apos; UTR elements and RNA-binding proteins in intracellular bacteria: impact on metabolism and virulence","volume":"39","author":"G Oliva","year":"2015","journal-title":"FEMS Microbiol Rev"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"362","DOI":"10.1093\/femsre\/fuv016","article-title":"Target activation by regulatory RNAs in bacteria","volume":"39","author":"K Papenfort","year":"2015","journal-title":"FEMS Microbiol Rev"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"8472","DOI":"10.1128\/JB.186.24.8472-8477.2004","article-title":"The etiological agent of Lyme disease, <italic>Borrelia burgdorferi<\/italic>, appears to contain only a few small RNA molecules","volume":"186","author":"Y \u00d6stberg","year":"2004","journal-title":"J Bacteriol"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"1075","DOI":"10.1111\/j.1365-2958.2007.05716.x","article-title":"Temperature-induced regulation of RpoS by a small RNA in <italic>Borrelia burgdorferi<\/italic>","volume":"64","author":"MC Lybecker","year":"2007","journal-title":"Mol Microbiol"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"622","DOI":"10.1111\/j.1365-2958.2010.07374.x","article-title":"Identification and function of the RNA chaperone Hfq in the Lyme disease spirochete <italic>Borrelia burgdorferi<\/italic>","volume":"78","author":"MC Lybecker","year":"2010","journal-title":"Mol Microbiol"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"5119","DOI":"10.1128\/IAI.66.11.5119-5124.1998","article-title":"Differential expression of <italic>Borrelia burgdorferi<\/italic> proteins during growth in vitro","volume":"66","author":"R Ramamoorthy","year":"1998","journal-title":"Infect Immun"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"2909","DOI":"10.1128\/JB.182.10.2909-2918.2000","article-title":"Altered stationary-phase response in a <italic>Borrelia burgdorferi rpoS<\/italic> mutant","volume":"182","author":"AF Elias","year":"2000","journal-title":"J Bacteriol"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1038\/nmeth.3313","article-title":"Simultaneous generation of many RNA-seq libraries in a single reaction","volume":"12","author":"AA Shishkin","year":"2015","journal-title":"Nat Methods"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"580","DOI":"10.1038\/37551","article-title":"Genomic sequence of a Lyme disease spirochaete, <italic>Borrelia burgdorferi<\/italic>","volume":"390","author":"CM Fraser","year":"1997","journal-title":"Nature"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"490","DOI":"10.1046\/j.1365-2958.2000.01698.x","article-title":"A bacterial genome in flux: the twelve linear and nine circular extrachromosomal DNAs of an infectious isolate of the Lyme disease spirochete <italic>Borrelia burgdorferi<\/italic>","volume":"35","author":"S Casjens","year":"2000","journal-title":"Mol Microbiol"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"2139","DOI":"10.1128\/IAI.70.4.2139-2150.2002","article-title":"Clonal polymorphism of <italic>Borrelia burgdorferi<\/italic> strain B31 MI: implications for mutagenesis in an infectious strain background","volume":"70","author":"AF Elias","year":"2002","journal-title":"Infect Immun"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"13865","DOI":"10.1073\/pnas.97.25.13865","article-title":"Correlation between plasmid content and infectivity in <italic>Borrelia burgdorferi<\/italic>","volume":"97","author":"JE Purser","year":"2000","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"446","DOI":"10.1128\/IAI.69.1.446-455.2001","article-title":"Decreased infectivity in <italic>Borrelia burgdorferi<\/italic> strain B31 is associated with loss of linear plasmid 25 or 28\u20131","volume":"69","author":"M Labandeira-Rey","year":"2001","journal-title":"Infect Immun"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1016\/j.mimet.2011.05.004","article-title":"Multiplex PCR as a tool for validating plasmid content of <italic>Borrelia burgdorferi<\/italic>","volume":"86","author":"I Bunikis","year":"2011","journal-title":"J Microbiol Methods"},{"key":"ref53","first-page":"1","article-title":"Laboratory maintenance of <italic>Borrelia burgdorferi<\/italic>","volume":"12C","author":"WR Z\u00fcckert","year":"2007","journal-title":"Curr Protocols Microbiol"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"757","DOI":"10.1128\/JB.01956-12","article-title":"Changes in bacterial growth rate govern expression of the <italic>Borrelia burgdorferi<\/italic> OspC and Erp infection-associated surface proteins","volume":"195","author":"BL Jutras","year":"2013","journal-title":"J Bacteriol"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"12212","DOI":"10.1093\/nar\/gku891","article-title":"Comparative RNA-Seq based dissection of the regulatory networks and environmental stimuli underlying <italic>Vibrio parahaemolyticus<\/italic> gene expression during infection","volume":"42","author":"J Livny","year":"2014","journal-title":"Nucl Acids Res"},{"key":"ref56","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"H Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/gb-2010-11-10-r106","article-title":"Differential expression analysis for sequence count data","volume":"11","author":"S Anders","year":"2010","journal-title":"Genome Biology"},{"key":"ref58","article-title":"Example of real-time quantitative reverse transcription-PCR (Q-RT-PCR) analysis of bacterial gene expression during mammalian infection: <italic>Borrelia burgdorferi<\/italic> in mouse tissues","volume":"1D","author":"JC Miller","year":"2005","journal-title":"Current Protocols In Microbiology"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"4724","DOI":"10.1093\/nar\/29.22.4724","article-title":"RNAMotif, an RNA secondary structure definition and search algorithm","volume":"29","author":"TJ Macke","year":"2001","journal-title":"Nucleic Acids Research"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"D72","DOI":"10.1093\/nar\/gkn763","article-title":"Transterm: a database to aid the analysis of regulatory sequences in mRNAs","volume":"37","author":"GH Jacobs","year":"2009","journal-title":"Nucleic Acids Research"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"941","DOI":"10.1016\/S0960-9822(01)00270-6","article-title":"Novel small RNA-encoding genes in the intergenic regions of <italic>Escherichia coli<\/italic>","volume":"11","author":"L Argaman","year":"2001","journal-title":"Curr Biol"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1007\/978-1-61779-949-5_1","article-title":"Bioinformatic discovery of bacterial regulatory RNAs using SIPHT","volume":"905","author":"J Livny","year":"2012","journal-title":"Methods Mol Biol"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"835","DOI":"10.1038\/nmeth.3478","article-title":"Efficient and quantitative high-throughput tRNA sequencing","volume":"12","author":"G Zheng","year":"2015","journal-title":"Nat Methods"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"e170","DOI":"10.1093\/nar\/gku945","article-title":"Diverse cell stresses induce unique patterns of tRNA up- and down-regulation: tRNA-seq for quantifying changes in tRNA copy number","volume":"42","author":"YL Pang","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"ref65","first-page":"87","article-title":"The Spirochetes: Molecular and Cellular Biology","author":"B Stevenson","year":"2001"},{"key":"ref66","first-page":"35","article-title":"The Spirochetes: Molecular and Cellular Biology","author":"CH Eggers","year":"2001"},{"key":"ref67","doi-asserted-by":"crossref","first-page":"7985","DOI":"10.1128\/JB.187.23.7985-7995.2005","article-title":"Demonstration of cotranscription and 1-methyl-3-nitroso-nitroguanidine induction of a 30-gene operon of <italic>Borrelia burgdorferi<\/italic>: evidence that the 32-kilobase circular plasmids are prophages","volume":"187","author":"H Zhang","year":"2005","journal-title":"J Bacteriol"},{"key":"ref68","doi-asserted-by":"crossref","first-page":"1165","DOI":"10.1128\/IAI.65.4.1165-1171.1997","article-title":"Cell-density-dependent expression of <italic>Borrelia burgdorferi<\/italic> lipoproteins in vitro","volume":"65","author":"KJ Indest","year":"1997","journal-title":"Infect Immun"},{"key":"ref69","doi-asserted-by":"crossref","first-page":"1033","DOI":"10.1099\/00221287-144-4-1033","article-title":"Oligopeptide permease in <italic>Borrelia burgdorferi<\/italic>: putative peptide-binding components encoded by both chromosomal and plasmid loci","volume":"144","author":"JL Bono","year":"1998","journal-title":"Microbiology"},{"key":"ref70","doi-asserted-by":"crossref","first-page":"987","DOI":"10.1128\/JCM.37.4.987-992.1999","article-title":"Rapid and sensitive quantification of <italic>Borrelia burgdorferi<\/italic>-infected mouse tissues by continuous fluorescent monitoring of PCR","volume":"37","author":"TB Morrison","year":"1999","journal-title":"J Clin Microbiol"},{"key":"ref71","doi-asserted-by":"crossref","first-page":"4134","DOI":"10.1128\/JB.186.13.4134-4141.2004","article-title":"Telomere exchange between linear replicons of <italic>Borrelia burgdorferi<\/italic>","volume":"186","author":"WM Huang","year":"2004","journal-title":"J Bacteriol"},{"key":"ref72","doi-asserted-by":"crossref","DOI":"10.1038\/nature08756","article-title":"The primary transcriptome of the major human pathogen Helicobacter pylori","volume":"464","author":"CM Sharma","year":"2010","journal-title":"Nature"},{"key":"ref73","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12864-015-1555-8","article-title":"An empirical strategy to detect bacterial transcript structure from directional RNA-seq transcriptome data","volume":"16","author":"Y Wang","year":"2015","journal-title":"BMC Genomics"},{"key":"ref74","article-title":"The TamB ortholog of <italic>Borrelia burgdorferi<\/italic> interacts with the \u03b2-barrel assembly machine (BAM) complex protein BamA","author":"H Iqbal","year":"2016","journal-title":"Mol Microbiol"},{"key":"ref75","doi-asserted-by":"crossref","first-page":"926","DOI":"10.1128\/jb.175.4.926-932.1993","article-title":"Transcriptional analyses and mapping of the <italic>ospC<\/italic> gene in Lyme disease spirochetes","volume":"175","author":"RT Marconi","year":"1993","journal-title":"J Bacteriol"},{"key":"ref76","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1016\/S0378-1119(97)00196-0","article-title":"Cloning and expression of the <italic>Borrelia burgdorferi lon<\/italic> gene","volume":"194","author":"JL Cloud","year":"1997","journal-title":"Gene"},{"key":"ref77","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1111\/j.1574-6968.2000.tb08930.x","article-title":"Transcriptional analysis of a superoxide dismutase gene of <italic>Borrelia burgdorferi<\/italic>","volume":"183","author":"TL Nichols","year":"2000","journal-title":"FEMS Microbiol Lett"},{"key":"ref78","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1186\/1471-2180-9-108","article-title":"Chitobiose utilization in <italic>Borrelia burgdorferi<\/italic> is dually regulated by RpoD and RpoS","volume":"9","author":"RG Rhodes","year":"2009","journal-title":"BMC Microbiol"},{"key":"ref79","doi-asserted-by":"crossref","first-page":"4915","DOI":"10.1128\/JB.00819-13","article-title":"Post-transcriptional autoregulation of the Lyme disease bacterium&apos;s BpuR DNA\/RNA-binding protein","volume":"195","author":"BL Jutras","year":"2013","journal-title":"J Bacteriol"},{"key":"ref80","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1126\/science.284.5414.611","article-title":"Mechanism of intrinsic transcription termination and antitermination","volume":"284","author":"WS Yarnell","year":"1999","journal-title":"Science"},{"key":"ref81","doi-asserted-by":"crossref","first-page":"1453","DOI":"10.1126\/science.277.5331.1453","article-title":"The complete genome sequence of <italic>Escherichia coli<\/italic> K-12","volume":"277","author":"FR Blattner","year":"1997","journal-title":"Science"},{"key":"ref82","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1111\/j.1574-6968.2009.01542.x","article-title":"The <italic>Borrelia burgdorferi flaB<\/italic> promoter has an extended -10 element and includes a T-rich -35\/-10 spacer sequence that is essential for optimal activity","volume":"293","author":"A Gautam","year":"2009","journal-title":"FEMS Microbiol Lett"},{"key":"ref83","doi-asserted-by":"crossref","first-page":"370","DOI":"10.1046\/j.1365-2958.2001.02220.x","article-title":"Two independent transcriptional units control the complex and simultaneous expression of the <italic>bmp<\/italic> paralogous chromosomal gene family in <italic>Borrelia burgdorferi<\/italic>","volume":"39","author":"EY Dobrikova","year":"2001","journal-title":"Mol Microbiol"},{"key":"ref84","doi-asserted-by":"crossref","first-page":"2592","DOI":"10.1128\/JB.187.8.2592-2600.2005","article-title":"Expression of the <italic>bmpB<\/italic> gene of <italic>Borrelia burgdorferi<\/italic> is modulated by two distinct transcription termination events","volume":"187","author":"R Ramamoorthy","year":"2005","journal-title":"J Bacteriol"},{"key":"ref85","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1126\/science.284.5414.611","article-title":"Mechanism of Intrinsic Transcription Termination and Antitermination","volume":"284","author":"WS Yarnell","year":"1999","journal-title":"Science"},{"key":"ref86","doi-asserted-by":"crossref","first-page":"12724","DOI":"10.1073\/pnas.231442498","article-title":"Expression of <italic>Borrelia burgdorferi<\/italic> OspC and DbpA is controlled by a RpoN-RpoS regulatory pathway","volume":"98","author":"A H\u00fcbner","year":"2001","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref87","doi-asserted-by":"crossref","first-page":"e1002102","DOI":"10.1371\/journal.ppat.1002102","article-title":"<italic>Borrelia burgdorferi<\/italic> requires glycerol for maximum fitness during the tick phase of the enzootic cycle","volume":"7","author":"CJ Pappas","year":"2011","journal-title":"PLoS Pathog"},{"key":"ref88","doi-asserted-by":"crossref","first-page":"e75643","DOI":"10.1371\/journal.pone.0075643","article-title":"BB0347, from the Lyme disease spirochete <italic>Borrelia burgdorferi<\/italic>, is surface exposed and interacts with the CS1 heparin-binding domain of human fibronectin","volume":"8","author":"RA Gaultney","year":"2013","journal-title":"PLoS ONE"},{"key":"ref89","doi-asserted-by":"crossref","first-page":"e1004004","DOI":"10.1371\/journal.ppat.1004004","article-title":"A model system for studying the transcriptomic and physiological changes associated with mammalian host-adaptation by <italic>Leptospira interrogans<\/italic> serovar Copenhageni","volume":"10","author":"MJ Caimano","year":"2014","journal-title":"PLoS Pathog"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0164165","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,19]],"date-time":"2024-06-19T19:46:34Z","timestamp":1718826394000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0164165"}},"subtitle":[],"editor":[{"given":"Utpal","family":"Pal","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2016,10,5]]},"references-count":89,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2016,10,5]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0164165","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,10,5]]}}}