{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:27:26Z","timestamp":1790814446945,"version":"4.1.0"},"update-to":[{"DOI":"10.1371\/journal.pgen.1010857","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2023,8,7]],"date-time":"2023-08-07T00:00:00Z","timestamp":1691366400000}}],"reference-count":84,"publisher":"Public Library of Science (PLoS)","issue":"7","license":[{"start":{"date-parts":[[2023,7,26]],"date-time":"2023-07-26T00:00:00Z","timestamp":1690329600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"NIH NIGMS","award":["R01GM141242 and R01GM143182"],"award-info":[{"award-number":["R01GM141242 and R01GM143182"]}]},{"DOI":"10.13039\/100000875","name":"Pew Charitable Trusts","doi-asserted-by":"publisher","award":["Innovation Fund"],"award-info":[{"award-number":["Innovation Fund"]}],"id":[{"id":"10.13039\/100000875","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000076","name":"Directorate for Biological Sciences","doi-asserted-by":"publisher","award":["2022049"],"award-info":[{"award-number":["2022049"]}],"id":[{"id":"10.13039\/100000076","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosgenetics.org"],"crossmark-restriction":false},"short-container-title":["PLoS Genet"],"abstract":"<jats:p><jats:italic>Borrelia burgdorferi<\/jats:italic>, a causative agent of Lyme disease, contains the most segmented bacterial genome known to date, with one linear chromosome and over twenty plasmids. How this unusually complex genome is organized, and whether and how the different replicons interact are unclear. We recently demonstrated that<jats:italic>B<\/jats:italic>.<jats:italic>burgdorferi<\/jats:italic>is polyploid and that the copies of the chromosome and plasmids are regularly spaced in each cell, which is critical for faithful segregation of the genome to daughter cells. Regular spacing of the chromosome is controlled by two separate partitioning systems that involve the protein pairs ParA\/ParZ and ParB\/Smc. Here, using chromosome conformation capture (Hi-C), we characterized the organization of the<jats:italic>B<\/jats:italic>.<jats:italic>burgdorferi<\/jats:italic>genome and the interactions between the replicons. We uncovered that although the linear chromosome lacks contacts between the two replication arms, the two telomeres are in frequent contact. Moreover, several plasmids specifically interact with the chromosome<jats:italic>oriC<\/jats:italic>region, and a subset of plasmids interact with each other more than with others. We found that Smc and the Smc-like MksB protein mediate long-range interactions on the chromosome, but they minimally affect plasmid-chromosome or plasmid-plasmid interactions. Finally, we found that disruption of the two partition systems leads to chromosome restructuring, correlating with the mis-positioning of chromosome<jats:italic>oriC<\/jats:italic>. Altogether, this study revealed the conformation of a complex genome and analyzed the contribution of the partition systems and SMC family proteins to this organization. This work expands the understanding of the organization and maintenance of multipartite bacterial genomes.<\/jats:p>","DOI":"10.1371\/journal.pgen.1010857","type":"journal-article","created":{"date-parts":[[2023,7,26]],"date-time":"2023-07-26T18:46:40Z","timestamp":1690397200000},"page":"e1010857","update-policy":"https:\/\/doi.org\/10.1371\/journal.pgen.corrections_policy","source":"Crossref","is-referenced-by-count":10,"title":["Organization and replicon interactions within the highly segmented genome of Borrelia burgdorferi"],"prefix":"10.1371","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1788-5362","authenticated-orcid":true,"given":"Zhongqing","family":"Ren","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4553-0668","authenticated-orcid":true,"given":"Constantin N.","family":"Takacs","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5496-0638","authenticated-orcid":true,"given":"Hugo B.","family":"Brand\u00e3o","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0980-5334","authenticated-orcid":true,"given":"Christine","family":"Jacobs-Wagner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6458-180X","authenticated-orcid":true,"given":"Xindan","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2023,7,26]]},"reference":[{"issue":"3","key":"pgen.1010857.ref001","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1016\/j.idc.2022.03.004","article-title":"Epidemiology of Lyme Disease","volume":"36","author":"P. Mead","year":"2022","journal-title":"Infect Dis Clin North Am"},{"issue":"2","key":"pgen.1010857.ref002","doi-asserted-by":"crossref","first-page":"616","DOI":"10.3201\/eid2702.202731","article-title":"Estimating the Frequency of Lyme Disease Diagnoses, United States, 2010\u20132018","volume":"27","author":"KJ Kugeler","year":"2021","journal-title":"Emerg Infect Dis"},{"issue":"6660","key":"pgen.1010857.ref003","doi-asserted-by":"crossref","first-page":"580","DOI":"10.1038\/37551","article-title":"Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi","volume":"390","author":"CM Fraser","year":"1997","journal-title":"Nature"},{"issue":"3","key":"pgen.1010857.ref004","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 in an infectious isolate of the Lyme disease spirochete Borrelia burgdorferi","volume":"35","author":"S Casjens","year":"2000","journal-title":"Mol Microbiol"},{"key":"pgen.1010857.ref005","first-page":"409","article-title":"Multipartite Genome of Lyme Disease Borrelia: Structure, Variation and Prophages","volume":"42","author":"I Schwartz","year":"2021","journal-title":"Curr Issues Mol Biol"},{"issue":"3","key":"pgen.1010857.ref006","doi-asserted-by":"crossref","DOI":"10.1128\/MMBR.00019-17","article-title":"The Divided Bacterial Genome: Structure, Function, and Evolution","volume":"81","author":"GC diCenzo","year":"2017","journal-title":"Microbiol Mol Biol Rev"},{"issue":"1","key":"pgen.1010857.ref007","doi-asserted-by":"crossref","first-page":"7173","DOI":"10.1038\/s41467-022-34876-4","article-title":"Polyploidy, regular patterning of genome copies, and unusual control of DNA partitioning in the Lyme disease spirochete","volume":"13","author":"CN Takacs","year":"2022","journal-title":"Nat Commun"},{"issue":"6","key":"pgen.1010857.ref008","doi-asserted-by":"crossref","DOI":"10.1128\/microbiolspec.PLAS-0023-2014","article-title":"Plasmid Partition Mechanisms","volume":"2","author":"JC Baxter","year":"2014","journal-title":"Microbiol Spectr"},{"key":"pgen.1010857.ref009","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1007\/978-3-030-46886-6_3","article-title":"Physical Views on ParABS-Mediated DNA Segregation","volume":"1267","author":"B Guilhas","year":"2020","journal-title":"Adv Exp Med Biol"},{"issue":"6","key":"pgen.1010857.ref010","doi-asserted-by":"crossref","first-page":"200097","DOI":"10.1098\/rsob.200097","article-title":"Bacterial chromosome segregation by the ParABS system","volume":"10","author":"ASB Jalal","year":"2020","journal-title":"Open Biol"},{"issue":"6","key":"pgen.1010857.ref011","doi-asserted-by":"crossref","first-page":"1271","DOI":"10.1016\/j.cell.2018.01.014","article-title":"Subcellular Organization: A Critical Feature of Bacterial Cell Replication","volume":"172","author":"IV Surovtsev","year":"2018","journal-title":"Cell"},{"issue":"8","key":"pgen.1010857.ref012","doi-asserted-by":"crossref","first-page":"791","DOI":"10.1038\/ncb2083","article-title":"A spindle-like apparatus guides bacterial chromosome segregation","volume":"12","author":"JL Ptacin","year":"2010","journal-title":"Nat Cell Biol"},{"issue":"4","key":"pgen.1010857.ref013","doi-asserted-by":"crossref","first-page":"697","DOI":"10.1016\/j.cell.2009.04.044","article-title":"Recruitment of SMC by ParB-parS organizes the origin region and promotes efficient chromosome segregation","volume":"137","author":"NL Sullivan","year":"2009","journal-title":"Cell"},{"issue":"4","key":"pgen.1010857.ref014","doi-asserted-by":"crossref","first-page":"685","DOI":"10.1016\/j.cell.2009.02.035","article-title":"Recruitment of condensin to replication origin regions by ParB\/SpoOJ promotes chromosome segregation in B. subtilis","volume":"137","author":"S Gruber","year":"2009","journal-title":"Cell"},{"issue":"23","key":"pgen.1010857.ref015","doi-asserted-by":"crossref","first-page":"3269","DOI":"10.1101\/gad.1496506","article-title":"A dynamic, mitotic-like mechanism for bacterial chromosome segregation","volume":"20","author":"MA Fogel","year":"2006","journal-title":"Genes Dev"},{"issue":"6","key":"pgen.1010857.ref016","doi-asserted-by":"crossref","first-page":"927","DOI":"10.1016\/j.cell.2010.05.033","article-title":"Pushing and pulling in prokaryotic DNA segregation","volume":"141","author":"K Gerdes","year":"2010","journal-title":"Cell"},{"issue":"2","key":"pgen.1010857.ref017","doi-asserted-by":"crossref","first-page":"270","DOI":"10.1038\/sj.emboj.7600530","article-title":"Bacterial chromosome segregation: structure and DNA binding of the Soj dimer\u2014a conserved biological switch","volume":"24","author":"TA Leonard","year":"2005","journal-title":"EMBO J"},{"issue":"9","key":"pgen.1010857.ref018","doi-asserted-by":"crossref","first-page":"1455","DOI":"10.1111\/j.1365-2958.1990.tb02056.x","article-title":"A family of ATPases involved in active partitioning of diverse bacterial plasmids","volume":"4","author":"M Motallebi-Veshareh","year":"1990","journal-title":"Mol Microbiol"},{"issue":"1","key":"pgen.1010857.ref019","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1111\/j.1365-2958.2010.07314.x","article-title":"ATP control of dynamic P1 ParA-DNA interactions: a key role for the nucleoid in plasmid partition","volume":"78","author":"AG Vecchiarelli","year":"2010","journal-title":"Mol Microbiol"},{"issue":"5401","key":"pgen.1010857.ref020","doi-asserted-by":"crossref","first-page":"546","DOI":"10.1126\/science.283.5401.546","article-title":"Silencing of genes flanking the P1 plasmid centromere","volume":"283","author":"O Rodionov","year":"1999","journal-title":"Science"},{"issue":"7","key":"pgen.1010857.ref021","doi-asserted-by":"crossref","first-page":"1512","DOI":"10.1016\/j.cell.2019.11.015","article-title":"ParB-type DNA Segregation Proteins Are CTP-Dependent Molecular Switches","volume":"179","author":"M Osorio-Valeriano","year":"2019","journal-title":"Cell"},{"issue":"5","key":"pgen.1010857.ref022","doi-asserted-by":"crossref","first-page":"1352","DOI":"10.1111\/j.1365-2958.2006.05316.x","article-title":"The bacterial chromosome segregation protein Spo0J spreads along DNA from parS nucleation sites","volume":"61","author":"H Murray","year":"2006","journal-title":"Mol Microbiol"},{"issue":"3","key":"pgen.1010857.ref023","doi-asserted-by":"crossref","first-page":"744","DOI":"10.1016\/j.bbrc.2006.01.173","article-title":"Characterization of the Soj\/Spo0J chromosome segregation proteins and identification of putative parS sequences in Helicobacter pylori","volume":"342","author":"MJ Lee","year":"2006","journal-title":"Biochem Biophys Res Commun"},{"issue":"5","key":"pgen.1010857.ref024","doi-asserted-by":"crossref","first-page":"1365","DOI":"10.1046\/j.1365-2958.2002.03102.x","article-title":"The ParB protein of Streptomyces coelicolor A3(2) recognizes a cluster of parS sequences within the origin-proximal region of the linear chromosome","volume":"45","author":"D Jakimowicz","year":"2002","journal-title":"Mol Microbiol"},{"issue":"6469","key":"pgen.1010857.ref025","doi-asserted-by":"crossref","first-page":"1129","DOI":"10.1126\/science.aay3965","article-title":"Self-organization of parS centromeres by the ParB CTP hydrolase","volume":"366","author":"YM Soh","year":"2019","journal-title":"Science"},{"issue":"20","key":"pgen.1010857.ref026","doi-asserted-by":"crossref","first-page":"6076","DOI":"10.1093\/emboj\/17.20.6076","article-title":"Probing the structure of complex macromolecular interactions by homolog specificity scanning: the P1 and P7 plasmid partition systems","volume":"17","author":"L Radnedge","year":"1998","journal-title":"EMBO J"},{"issue":"46","key":"pgen.1010857.ref027","doi-asserted-by":"crossref","first-page":"E7268","DOI":"10.1073\/pnas.1616118113","article-title":"DNA-relay mechanism is sufficient to explain ParA-dependent intracellular transport and patterning of single and multiple cargos","volume":"113","author":"IV Surovtsev","year":"2016","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"12","key":"pgen.1010857.ref028","doi-asserted-by":"crossref","first-page":"2790","DOI":"10.1016\/j.bpj.2016.05.014","article-title":"The Slow Mobility of the ParA Partitioning Protein Underlies Its Steady-State Patterning in Caulobacter","volume":"110","author":"IV Surovtsev","year":"2016","journal-title":"Biophys J"},{"issue":"7","key":"pgen.1010857.ref029","doi-asserted-by":"crossref","first-page":"1489","DOI":"10.1016\/j.bpj.2017.02.039","article-title":"Brownian Ratchet Mechanism for Faithful Segregation of Low-Copy-Number Plasmids","volume":"112","author":"L Hu","year":"2017","journal-title":"Biophys J"},{"key":"pgen.1010857.ref030","doi-asserted-by":"crossref","first-page":"e02758","DOI":"10.7554\/eLife.02758","article-title":"Evidence for a DNA-relay mechanism in ParABS-mediated chromosome segregation","volume":"3","author":"HC Lim","year":"2014","journal-title":"Elife"},{"issue":"2","key":"pgen.1010857.ref031","doi-asserted-by":"crossref","first-page":"028101","DOI":"10.1103\/PhysRevLett.119.028101","article-title":"Surfing on Protein Waves: Proteophoresis as a Mechanism for Bacterial Genome Partitioning","volume":"119","author":"JC Walter","year":"2017","journal-title":"Phys Rev Lett"},{"key":"pgen.1010857.ref032","doi-asserted-by":"crossref","first-page":"77","DOI":"10.2142\/biophysics.7.77","article-title":"Chemophoresis as a driving force for intracellular organization: Theory and application to plasmid partitioning","volume":"7","author":"T Sugawara","year":"2011","journal-title":"Biophysics"},{"issue":"6324","key":"pgen.1010857.ref033","doi-asserted-by":"crossref","first-page":"524","DOI":"10.1126\/science.aai8982","article-title":"Bacillus subtilis SMC complexes juxtapose chromosome arms as they travel from origin to terminus","volume":"355","author":"X Wang","year":"2017","journal-title":"Science"},{"issue":"15","key":"pgen.1010857.ref034","doi-asserted-by":"crossref","first-page":"1661","DOI":"10.1101\/gad.265876.115","article-title":"Condensin promotes the juxtaposition of DNA flanking its loading site in Bacillus subtilis","volume":"29","author":"X Wang","year":"2015","journal-title":"Genes Dev"},{"issue":"9","key":"pgen.1010857.ref035","doi-asserted-by":"crossref","first-page":"2057","DOI":"10.1016\/j.celrep.2017.08.026","article-title":"SMC Progressively Aligns Chromosomal Arms in Caulobacter crescentus but Is Antagonized by Convergent Transcription","volume":"20","author":"NT Tran","year":"2017","journal-title":"Cell Rep"},{"issue":"6159","key":"pgen.1010857.ref036","doi-asserted-by":"crossref","first-page":"731","DOI":"10.1126\/science.1242059","article-title":"High-resolution mapping of the spatial organization of a bacterial chromosome","volume":"342","author":"TB Le","year":"2013","journal-title":"Science"},{"issue":"4","key":"pgen.1010857.ref037","doi-asserted-by":"crossref","first-page":"771","DOI":"10.1016\/j.cell.2017.12.027","article-title":"Multiscale Structuring of the E. coli Chromosome by Nucleoid-Associated and Condensin Proteins","volume":"172","author":"VS Lioy","year":"2018","journal-title":"Cell"},{"issue":"1","key":"pgen.1010857.ref038","doi-asserted-by":"crossref","first-page":"1485","DOI":"10.1038\/s41467-020-15238-4","article-title":"Chromosome organization by a conserved condensin-ParB system in the actinobacterium Corynebacterium glutamicum","volume":"11","author":"K Bohm","year":"2020","journal-title":"Nat Commun"},{"issue":"5","key":"pgen.1010857.ref039","doi-asserted-by":"crossref","first-page":"108344","DOI":"10.1016\/j.celrep.2020.108344","article-title":"Distinct Activities of Bacterial Condensins for Chromosome Management in Pseudomonas aeruginosa","volume":"33","author":"VS Lioy","year":"2020","journal-title":"Cell Rep"},{"issue":"3","key":"pgen.1010857.ref040","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1016\/j.molcel.2020.12.013","article-title":"Euryarchaeal genomes are folded into SMC-dependent loops and domains, but lack transcription-mediated compartmentalization","volume":"81","author":"C Cockram","year":"2021","journal-title":"Mol Cell"},{"issue":"6","key":"pgen.1010857.ref041","article-title":"Conformation and dynamic interactions of the multipartite genome in Agrobacterium tumefaciens","volume":"119","author":"Z Ren","year":"2022","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"3","key":"pgen.1010857.ref042","doi-asserted-by":"crossref","first-page":"e0050822","DOI":"10.1128\/mbio.00508-22","article-title":"Centromere Interactions Promote the Maintenance of the Multipartite Genome in Agrobacterium tumefaciens","volume":"13","author":"Z Ren","year":"2022","journal-title":"mBio"},{"key":"pgen.1010857.ref043","doi-asserted-by":"crossref","first-page":"e0429022","DOI":"10.1128\/spectrum.04290-22","article-title":"High-Resolution 3D Genome Map of Brucella Chromosomes in Exponential and Stationary Phases","author":"YF Huang","year":"2023","journal-title":"Microbiol Spectr"},{"issue":"4","key":"pgen.1010857.ref044","doi-asserted-by":"crossref","first-page":"e1501914","DOI":"10.1126\/sciadv.1501914","article-title":"A checkpoint control orchestrates the replication of the two chromosomes of Vibrio cholerae","volume":"2","author":"ME Val","year":"2016","journal-title":"Sci Adv"},{"issue":"44","key":"pgen.1010857.ref045","doi-asserted-by":"crossref","first-page":"26404","DOI":"10.1074\/jbc.R115.651679","article-title":"Formaldehyde crosslinking: a tool for the study of chromatin complexes","volume":"290","author":"EA Hoffman","year":"2015","journal-title":"J Biol Chem"},{"key":"pgen.1010857.ref046","article-title":"Longitudinal map of transcriptome changes in the Lyme pathogen Borrelia burgdorferi during tick-borne transmission","author":"AL Sapiro","year":"2023","journal-title":"Elife"},{"issue":"1","key":"pgen.1010857.ref047","doi-asserted-by":"crossref","first-page":"5221","DOI":"10.1038\/s41467-021-25462-1","article-title":"Dynamics of the compartmentalized Streptomyces chromosome during metabolic differentiation","volume":"12","author":"VS Lioy","year":"2021","journal-title":"Nat Commun"},{"issue":"1","key":"pgen.1010857.ref048","doi-asserted-by":"crossref","first-page":"5222","DOI":"10.1038\/s41467-021-25461-2","article-title":"Spatial rearrangement of the Streptomyces venezuelae linear chromosome during sporogenic development","volume":"12","author":"MJ Szafran","year":"2021","journal-title":"Nat Commun"},{"issue":"10","key":"pgen.1010857.ref049","doi-asserted-by":"crossref","first-page":"999","DOI":"10.1038\/nmeth.2148","article-title":"Iterative correction of Hi-C data reveals hallmarks of chromosome organization","volume":"9","author":"M Imakaev","year":"2012","journal-title":"Nature methods"},{"issue":"7","key":"pgen.1010857.ref050","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1038\/nrm.2016.30","article-title":"SMC complexes: from DNA to chromosomes","volume":"17","author":"F. Uhlmann","year":"2016","journal-title":"Nat Rev Mol Cell Biol"},{"key":"pgen.1010857.ref051","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1146\/annurev-genet-112618-043633","article-title":"Organization of Chromosomal DNA by SMC Complexes","volume":"53","author":"S Yatskevich","year":"2019","journal-title":"Annu Rev Genet"},{"issue":"3","key":"pgen.1010857.ref052","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1038\/nrg3375","article-title":"Organization and segregation of bacterial chromosomes","volume":"14","author":"X Wang","year":"2013","journal-title":"Nat Rev Genet"},{"key":"pgen.1010857.ref053","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1146\/annurev-cellbio-100814-125211","article-title":"Bacterial chromosome organization and segregation","volume":"31","author":"A Badrinarayanan","year":"2015","journal-title":"Annu Rev Cell Dev Biol"},{"key":"pgen.1010857.ref054","first-page":"2825","article-title":"Scikit-learn: Machine learning in Python","volume":"12","author":"F Pedregosa","year":"2011","journal-title":"the Journal of machine Learning research"},{"key":"pgen.1010857.ref055","doi-asserted-by":"crossref","first-page":"10200","DOI":"10.1038\/ncomms10200","article-title":"Multistep assembly of DNA condensation clusters by SMC","volume":"7","author":"H Kim","year":"2016","journal-title":"Nat Commun"},{"issue":"6471","key":"pgen.1010857.ref056","doi-asserted-by":"crossref","first-page":"1338","DOI":"10.1126\/science.aaz3418","article-title":"DNA loop extrusion by human cohesin","volume":"366","author":"IF Davidson","year":"2019","journal-title":"Science"},{"issue":"6384","key":"pgen.1010857.ref057","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1126\/science.aar7831","article-title":"Real-time imaging of DNA loop extrusion by condensin","volume":"360","author":"M Ganji","year":"2018","journal-title":"Science"},{"issue":"6471","key":"pgen.1010857.ref058","doi-asserted-by":"crossref","first-page":"1345","DOI":"10.1126\/science.aaz4475","article-title":"Human cohesin compacts DNA by loop extrusion","volume":"366","author":"Y Kim","year":"2019","journal-title":"Science"},{"issue":"6363","key":"pgen.1010857.ref059","doi-asserted-by":"crossref","first-page":"672","DOI":"10.1126\/science.aan6516","article-title":"The condensin complex is a mechanochemical motor that translocates along DNA","volume":"358","author":"T Terakawa","year":"2017","journal-title":"Science"},{"issue":"2","key":"pgen.1010857.ref060","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1016\/j.plasmid.2013.05.002","article-title":"Peaceful coexistence amongst Borrelia plasmids: getting by with a little help from their friends","volume":"70","author":"G Chaconas","year":"2013","journal-title":"Plasmid"},{"issue":"10","key":"pgen.1010857.ref061","doi-asserted-by":"crossref","first-page":"e47532","DOI":"10.1371\/journal.pone.0047532","article-title":"Analysis of an ordered, comprehensive STM mutant library in infectious Borrelia burgdorferi: insights into the genes required for mouse infectivity","volume":"7","author":"T Lin","year":"2012","journal-title":"PLoS One"},{"issue":"1","key":"pgen.1010857.ref062","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.plasmid.2012.01.009","article-title":"Requirements for Borrelia burgdorferi plasmid maintenance","volume":"68","author":"K Tilly","year":"2012","journal-title":"Plasmid"},{"issue":"16","key":"pgen.1010857.ref063","doi-asserted-by":"crossref","first-page":"5443","DOI":"10.1093\/nar\/gkq284","article-title":"BpaB, a novel protein encoded by the Lyme disease spirochete\u2019s cp32 prophages, binds to erp Operator 2 DNA","volume":"38","author":"LH Burns","year":"2010","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"pgen.1010857.ref064","doi-asserted-by":"crossref","first-page":"1436","DOI":"10.1128\/jb.154.3.1436-1439.1983","article-title":"Bacteriophage in the Ixodes dammini spirochete, etiological agent of Lyme disease","volume":"154","author":"SF Hayes","year":"1983","journal-title":"J Bacteriol"},{"issue":"3","key":"pgen.1010857.ref065","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1016\/S0934-8840(11)80363-4","article-title":"Bacteriophages induced by ciprofloxacin in a Borrelia burgdorferi skin isolate","volume":"279","author":"U Neubert","year":"1993","journal-title":"Zentralbl Bakteriol"},{"issue":"1","key":"pgen.1010857.ref066","doi-asserted-by":"crossref","first-page":"198","DOI":"10.1038\/s41467-023-35897-3","article-title":"Coupled induction of prophage and virulence factors during tick transmission of the Lyme disease spirochete","volume":"14","author":"J Wachter","year":"2023","journal-title":"Nat Commun"},{"issue":"23","key":"pgen.1010857.ref067","doi-asserted-by":"crossref","first-page":"7308","DOI":"10.1128\/JB.181.23.7308-7313.1999","article-title":"Molecular evidence for a new bacteriophage of Borrelia burgdorferi","volume":"181","author":"CH Eggers","year":"1999","journal-title":"J Bacteriol"},{"issue":"23","key":"pgen.1010857.ref068","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 Borrelia burgdorferi: evidence that the 32-kilobase circular plasmids are prophages","volume":"187","author":"H Zhang","year":"2005","journal-title":"J Bacteriol"},{"issue":"4","key":"pgen.1010857.ref069","first-page":"521","article-title":"Isolation and cultivation of Lyme disease spirochetes","volume":"57","author":"AG Barbour","year":"1984","journal-title":"Yale J Biol Med"},{"key":"pgen.1010857.ref070","article-title":"Laboratory maintenance of Borrelia burgdorferi","author":"WR Zuckert","year":"2007","journal-title":"Curr Protoc Microbiol"},{"issue":"9","key":"pgen.1010857.ref071","doi-asserted-by":"crossref","first-page":"2445","DOI":"10.1128\/JB.182.9.2445-2452.2000","article-title":"Efficient targeted mutagenesis in Borrelia burgdorferi","volume":"182","author":"JL Bono","year":"2000","journal-title":"J Bacteriol"},{"issue":"22","key":"pgen.1010857.ref072","doi-asserted-by":"crossref","first-page":"6723","DOI":"10.1128\/JB.185.22.6723-6727.2003","article-title":"aadA confers streptomycin resistance in Borrelia burgdorferi","volume":"185","author":"KL Frank","year":"2003","journal-title":"J Bacteriol"},{"issue":"1","key":"pgen.1010857.ref073","first-page":"29","article-title":"New antibiotic resistance cassettes suitable for genetic studies in Borrelia burgdorferi","volume":"6","author":"AF Elias","year":"2003","journal-title":"J Mol Microbiol Biotechnol"},{"issue":"7","key":"pgen.1010857.ref074","doi-asserted-by":"crossref","first-page":"3864","DOI":"10.1128\/IAI.00189-06","article-title":"Serologic proteome analysis of Borrelia burgdorferi membrane-associated proteins","volume":"74","author":"AJ Nowalk","year":"2006","journal-title":"Infect Immun"},{"issue":"1","key":"pgen.1010857.ref075","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1093\/bioinformatics\/btz540","article-title":"Cooler: scalable storage for Hi-C data and other genomically labeled arrays","volume":"36","author":"N Abdennur","year":"2020","journal-title":"Bioinformatics"},{"issue":"3","key":"pgen.1010857.ref076","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1109\/MCSE.2007.55","article-title":"Matplotlib: A 2D graphics environment","volume":"9","author":"JD Hunter","year":"2007","journal-title":"Comput Sci Eng"},{"key":"pgen.1010857.ref077","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/0377-0427(87)90125-7","article-title":"Silhouettes\u2014a Graphical Aid to the Interpretation and Validation of Cluster-Analysis","volume":"20","author":"PJ Rousseeuw","year":"1987","journal-title":"J Comput Appl Math"},{"issue":"5","key":"pgen.1010857.ref078","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1038\/nmeth.1318","article-title":"Enzymatic assembly of DNA molecules up to several hundred kilobases","volume":"6","author":"DG Gibson","year":"2009","journal-title":"Nature methods"},{"issue":"12","key":"pgen.1010857.ref079","first-page":"2016","article-title":"Precipitation of DNA with Ethanol","author":"MR Green","year":"2016","journal-title":"Cold Spring Harb Protoc"},{"key":"pgen.1010857.ref080","first-page":"253","article-title":"Electrotransformation of the spirochete Borrelia burgdorferi","volume":"47","author":"DS Samuels","year":"1995","journal-title":"Methods Mol Biol"},{"key":"pgen.1010857.ref081","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1007\/978-1-4939-7383-5_15","article-title":"Genetic Transformation and Complementation","volume":"1690","author":"DS Samuels","year":"2018","journal-title":"Methods Mol Biol"},{"issue":"4","key":"pgen.1010857.ref082","first-page":"433","article-title":"DNA exchange and insertional inactivation in spirochetes","volume":"2","author":"K Tilly","year":"2000","journal-title":"J Mol Microbiol Biotechnol"},{"issue":"4","key":"pgen.1010857.ref083","doi-asserted-by":"crossref","DOI":"10.1128\/AEM.02519-20","article-title":"A CRISPR interference platform for selective downregulation of gene expression in Borrelia burgdorferi","volume":"87","author":"CN Takacs","year":"2020","journal-title":"Appl Environ Microbiol"},{"issue":"2","key":"pgen.1010857.ref084","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 Borrelia burgdorferi","volume":"86","author":"I Bunikis","year":"2011","journal-title":"J Microbiol Methods"}],"updated-by":[{"DOI":"10.1371\/journal.pgen.1010857","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2023,8,7]],"date-time":"2023-08-07T00:00:00Z","timestamp":1691366400000}}],"container-title":["PLOS Genetics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pgen.1010857","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,12,17]],"date-time":"2023-12-17T21:56:34Z","timestamp":1702850194000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pgen.1010857"}},"subtitle":[],"editor":[{"given":"Frederic","family":"Boccard","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2023,7,26]]},"references-count":84,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2023,7,26]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pgen.1010857","relation":{"new_version":[{"id-type":"doi","id":"10.1371\/journal.pgen.1010857","asserted-by":"object"}]},"ISSN":["1553-7404"],"issn-type":[{"value":"1553-7404","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,7,26]]}}}