{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T02:32:09Z","timestamp":1791340329706,"version":"4.3.1"},"reference-count":59,"publisher":"Public Library of Science (PLoS)","issue":"12","content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0015321","type":"journal-article","created":{"date-parts":[[2010,12,21]],"date-time":"2010-12-21T19:27:26Z","timestamp":1292959646000},"page":"e15321","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":9,"title":["Coxiella burnetii Transcriptional Analysis Reveals Serendipity Clusters of Regulation in Intracellular Bacteria"],"prefix":"10.1371","volume":"5","author":[{"given":"Quentin","family":"Leroy","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kevin","family":"Lebrigand","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fabrice","family":"Armougom","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pascal","family":"Barbry","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard","family":"Thi\u00e9ry","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Didier","family":"Raoult","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2010,12,21]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"518","DOI":"10.1128\/CMR.12.4.518","article-title":"Q fever.","volume":"12","author":"M Maurin","year":"1999","journal-title":"Clin Microbiol Rev"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1128\/IAI.48.2.359-365.1985","article-title":"Lipopolysaccharide variation in Coxiella burnetti: intrastrain heterogeneity in structure and antigenicity.","volume":"48","author":"T Hackstadt","year":"1985","journal-title":"Infect Immun"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"5455","DOI":"10.1073\/pnas.0931379100","article-title":"Complete genome sequence of the Q-fever pathogen <italic>Coxiella burnetii<\/italic>.","volume":"100","author":"R Seshadri","year":"2003","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"642","DOI":"10.1128\/IAI.01141-08","article-title":"Comparative genomics reveal extensive transposon-mediated genomic plasticity and diversity among potential effector proteins within the genus Coxiella.","volume":"77","author":"PA Beare","year":"2009","journal-title":"Infect Immun"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"1063","DOI":"10.1128\/JB.147.3.1063-1076.1981","article-title":"Developmental cycle of Coxiella burnetii: structure and morphogenesis of vegetative and sporogenic differentiations.","volume":"147","author":"TF McCaul","year":"1981","journal-title":"J Bacteriol"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1128\/JB.110.1.368-377.1972","article-title":"Isolation and characterization of two cell types of Coxiella burneti phase I.","volume":"110","author":"ME Wiebe","year":"1972","journal-title":"J Bacteriol"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"982","DOI":"10.1128\/JB.160.3.982-988.1984","article-title":"Biochemical and immunological properties of Coxiella burnetii cell wall and peptidoglycan-protein complex fractions.","volume":"160","author":"K Amano","year":"1984","journal-title":"J Bacteriol"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1016\/S0966-842X(99)01475-4","article-title":"Developmental biology of Coxiella burnettii.","volume":"7","author":"RA Heinzen","year":"1999","journal-title":"Trends Microbiol"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"2661","DOI":"10.1007\/s00018-009-0041-3","article-title":"Microbial thermosensors.","volume":"66","author":"B Klinkert","year":"2009","journal-title":"Cell Mol Life Sci"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1038\/24094","article-title":"The genome sequence of <italic>Rickettsia prowazekii<\/italic> and the origin of mitochondria.","volume":"396","author":"SG Andersson","year":"1998","journal-title":"Nature"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"1800","DOI":"10.1101\/gr.1474603","article-title":"<italic>Tropheryma whipplei<\/italic> Twist: a human pathogenic Actinobacteria with a reduced genome.","volume":"13","author":"D Raoult","year":"2003","journal-title":"Genome Res"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"2093","DOI":"10.1126\/science.1061471","article-title":"Mechanisms of evolution in <italic>Rickettsia conorii<\/italic> and <italic>R. prowazekii<\/italic>.","volume":"293","author":"H Ogata","year":"2001","journal-title":"Science"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"5228","DOI":"10.1128\/JB.00507-06","article-title":"Global transcriptome analysis of Tropheryma whipplei in response to temperature stresses.","volume":"188","author":"N Crapoulet","year":"2006","journal-title":"J Bacteriol"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"7809","DOI":"10.1128\/AEM.00896-08","article-title":"DNA microarray analysis of the heat shock transcriptome of the obligate intracytoplasmic pathogen <italic>Rickettsia prowazekii<\/italic>.","volume":"74","author":"JP Audia","year":"2008","journal-title":"Appl Environ Microbiol"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1186\/1471-2180-8-61","article-title":"Genome-wide screen for temperature-regulated genes of the obligate intracellular bacterium, <italic>Rickettsia typhi<\/italic>.","volume":"8","author":"SM Dreher-Lesnick","year":"2008","journal-title":"BMC Microbiol"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"e5612","DOI":"10.1371\/journal.pone.0005612","article-title":"Limited transcriptional responses of <italic>Rickettsia rickettsii<\/italic> exposed to environmental stimuli.","volume":"4","author":"DW Ellison","year":"2009","journal-title":"PLoS One"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"4430","DOI":"10.1073\/pnas.0812074106","article-title":"Host cell-free growth of the Q fever bacterium <italic>Coxiella burnetii<\/italic>.","volume":"106","author":"A Omsland","year":"2009","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"950","DOI":"10.1038\/nature08080","article-title":"The Listeria transcriptional landscape from saprophytism to virulence.","volume":"459","author":"A Toledo-Arana","year":"2009","journal-title":"Nature"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"7533","DOI":"10.1073\/pnas.0911764107","article-title":"Legionella pneumophila 6S RNA optimizes intracellular multiplication.","volume":"107","author":"SP Faucher","year":"2010","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"868","DOI":"10.1093\/nar\/gkp1032","article-title":"Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome.","volume":"38","author":"M Albrecht","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"ref21","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 Escherichia coli.","volume":"11","author":"L Argaman","year":"2001","journal-title":"Curr Biol"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"827","DOI":"10.1016\/j.molcel.2008.10.027","article-title":"Small RNA binding to 5\u2032 mRNA coding region inhibits translational initiation.","volume":"32","author":"M Bouvier","year":"2008","journal-title":"Mol Cell"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"674","DOI":"10.1016\/j.mib.2009.09.009","article-title":"Activation of gene expression by small RNA.","volume":"12","author":"KS Frohlich","year":"2009","journal-title":"Curr Opin Microbiol"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1016\/j.mib.2009.01.012","article-title":"Expanding roles for metabolite-sensing regulatory RNAs.","volume":"12","author":"MD Dambach","year":"2009","journal-title":"Curr Opin Microbiol"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1093\/nar\/28.1.33","article-title":"The COG database: a tool for genome-scale analysis of protein functions and evolution.","volume":"28","author":"RL Tatusov","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"D412","DOI":"10.1093\/nar\/gkn760","article-title":"STRING 8\u2013a global view on proteins and their functional interactions in 630 organisms.","volume":"37","author":"LJ Jensen","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1016\/S0097-8485(01)00099-7","article-title":"Application of a time-delay neural network to promoter annotation in the Drosophila melanogaster genome.","volume":"26","author":"MG Reese","year":"2001","journal-title":"Comput Chem"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"e3681","DOI":"10.1371\/journal.pone.0003681","article-title":"<italic>Rickettsia conorii<\/italic> transcriptional response within inoculation eschar.","volume":"3","author":"P Renesto","year":"2008","journal-title":"PLoS One"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1016\/j.mimet.2007.09.017","article-title":"Development of a method for recovering rickettsial RNA from infected cells to analyze gene expression profiling of obligate intracellular bacteria.","volume":"71","author":"MV La","year":"2007","journal-title":"J Microbiol Methods"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1016\/j.mimet.2010.02.008","article-title":"Review of microarray studies for host-intracellular pathogen interactions.","volume":"81","author":"Q Leroy","year":"2010","journal-title":"J Microbiol Methods"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"9","DOI":"10.3184\/003685003783238707","article-title":"Bacterial cold shock responses.","volume":"86","author":"MH Weber","year":"2003","journal-title":"Sci Prog"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"2946","DOI":"10.1128\/jb.177.10.2946-2949.1995","article-title":"Characterization of the 23S and 5S rRNA genes of Coxiella burnetii and identification of an intervening sequence within the 23S rRNA gene.","volume":"177","author":"G Afseth","year":"1995","journal-title":"J Bacteriol"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"6572","DOI":"10.1128\/JB.00812-07","article-title":"The unusual 23S rRNA gene of Coxiella burnetii: two self-splicing group I introns flank a 34-base-pair exon, and one element lacks the canonical omegaG.","volume":"189","author":"R Raghavan","year":"2007","journal-title":"J Bacteriol"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1186\/1471-2164-8-349","article-title":"Comparative genomic analysis of <italic>Tropheryma whipplei<\/italic> strains reveals that diversity among clinical isolates is mainly related to the WiSP proteins.","volume":"8","author":"MV La","year":"2007","journal-title":"BMC Genomics"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"588","DOI":"10.1111\/j.1365-2958.2004.04283.x","article-title":"Bacterial cell division and the septal ring.","volume":"54","author":"DS Weiss","year":"2004","journal-title":"Mol Microbiol"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"2053","DOI":"10.1099\/mic.0.27899-0","article-title":"ftsZ mutations affecting cell division frequency, placement and morphology in Bacillus subtilis.","volume":"151","author":"A Feucht","year":"2005","journal-title":"Microbiology"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"1369","DOI":"10.1128\/JB.01580-08","article-title":"Characterization of a Coxiella burnetii ftsZ mutant generated by Himar1 transposon mutagenesis.","volume":"191","author":"PA Beare","year":"2009","journal-title":"J Bacteriol"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1111\/j.1365-2958.2005.04933.x","article-title":"P1 plasmid partition: in vivo evidence for the ParA- and ParB-mediated formation of an anchored parS complex in the absence of a partner parS.","volume":"59","author":"R Edgar","year":"2006","journal-title":"Mol Microbiol"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1111\/j.1365-2958.1992.tb01510.x","article-title":"Genes and their organization in the replication origin region of the bacterial chromosome.","volume":"6","author":"N Ogasawara","year":"1992","journal-title":"Mol Microbiol"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"5892","DOI":"10.1093\/nar\/gkl752","article-title":"Further insights into the tRNA modification process controlled by proteins MnmE and GidA of Escherichia coli.","volume":"34","author":"L Yim","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1111\/j.1574-6968.2006.00532.x","article-title":"The role of the omega subunit of RNA polymerase in expression of the relA gene in Escherichia coli.","volume":"267","author":"D Chatterji","year":"2007","journal-title":"FEMS Microbiol Lett"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1016\/S1369-5274(00)00182-X","article-title":"Revisiting the stringent response, ppGpp and starvation signaling.","volume":"4","author":"D Chatterji","year":"2001","journal-title":"Curr Opin Microbiol"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1128\/JB.01322-07","article-title":"Conditional lethality, division defects, membrane involution, and endocytosis in mre and mrd shape mutants of Escherichia coli.","volume":"190","author":"FO Bendezu","year":"2008","journal-title":"J Bacteriol"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"1128","DOI":"10.1111\/j.1365-2958.2008.06229.x","article-title":"The global, ppGpp-mediated stringent response to amino acid starvation in Escherichia coli.","volume":"68","author":"MF Traxler","year":"2008","journal-title":"Mol Microbiol"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"1394","DOI":"10.1271\/bbb.80093","article-title":"Interaction of the molecular chaperone HtpG with uroporphyrinogen decarboxylase in the cyanobacterium Synechococcus elongatus PCC 7942.","volume":"72","author":"M Saito","year":"2008","journal-title":"Biosci Biotechnol Biochem"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"3526","DOI":"10.1128\/JB.01812-08","article-title":"In Escherichia coli, MreB and FtsZ direct the synthesis of lateral cell wall via independent pathways that require PBP 2.","volume":"191","author":"A Varma","year":"2009","journal-title":"J Bacteriol"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1099\/mic.0.033266-0","article-title":"New insights into the regulatory networks of paralogous genes in bacteria.","volume":"156","author":"MA Martinez-Nunez","year":"2010","journal-title":"Microbiology"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1146\/annurev.micro.62.081307.162903","article-title":"(p)ppGpp: still magical?","volume":"62","author":"K Potrykus","year":"2008","journal-title":"Annu Rev Microbiol"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1128\/MMBR.00046-09","article-title":"ppGpp conjures bacterial virulence.","volume":"74","author":"ZD Dalebroux","year":"2010","journal-title":"Microbiol Mol Biol Rev"},{"key":"ref50","article-title":"Genomic, proteomic, and transcriptomic analysis of virulent and avirulent Rickettsia prowazekii reveals its adaptive mutation capabilities.","author":"Y Bechah","year":"2010","journal-title":"Genome Res"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"250","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":"ref52","doi-asserted-by":"crossref","first-page":"3383","DOI":"10.1101\/gad.1747308","article-title":"Riboswitch RNAs: using RNA to sense cellular metabolism.","volume":"22","author":"TM Henkin","year":"2008","journal-title":"Genes Dev"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"440","DOI":"10.1111\/j.1574-6976.2008.00103.x","article-title":"Regulation of whole bacterial pathogen transcription within infected hosts.","volume":"32","author":"MV La","year":"2008","journal-title":"FEMS Microbiol Rev"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1093\/bioinformatics\/18.3.486","article-title":"OligoArray: genome-scale oligonucleotide design for microarrays.","volume":"18","author":"JM Rouillard","year":"2002","journal-title":"Bioinformatics"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"3057","DOI":"10.1093\/nar\/gkg426","article-title":"OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach.","volume":"31","author":"JM Rouillard","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"ref56","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":"ref57","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkp919","article-title":"MicrobesOnline: an integrated portal for comparative and functional genomics.","volume":"38","author":"PS Dehal","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: multiple sequence alignment with high accuracy and high throughput.","volume":"32","author":"RC Edgar","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"1596","DOI":"10.1093\/molbev\/msm092","article-title":"MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0.","volume":"24","author":"K Tamura","year":"2007","journal-title":"Mol Biol Evol"}],"container-title":["PLoS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0015321","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,4]],"date-time":"2023-06-04T15:36:02Z","timestamp":1685892962000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0015321"}},"subtitle":[],"editor":[{"given":"Stefan","family":"Bereswill","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2010,12,21]]},"references-count":59,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2010,12,21]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0015321","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2010,12,21]]}}}