{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T12:46:57Z","timestamp":1790858817412,"version":"4.1.0"},"reference-count":54,"publisher":"Oxford University Press (OUP)","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,3]]},"DOI":"10.1093\/gbe\/evx042","type":"journal-article","created":{"date-parts":[[2017,3,3]],"date-time":"2017-03-03T07:13:12Z","timestamp":1488525192000},"page":"761-776","source":"Crossref","is-referenced-by-count":43,"title":["Evolutionary Dynamics of Pathoadaptation Revealed by Three Independent Acquisitions of the VirB\/D4 Type IV Secretion System in Bartonella"],"prefix":"10.1093","volume":"9","author":[{"given":"Alexander","family":"Harms","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francisca H.I.D.","family":"Segers","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maxime","family":"Quebatte","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claudia","family":"Mistl","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pablo","family":"Manfredi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonas","family":"K\u00f6rner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bruno B.","family":"Chomel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Kosoy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Soichi","family":"Maruyama","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philipp","family":"Engel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christoph","family":"Dehio","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2017,3,1]]},"reference":[{"key":"key\n\t\t\t\t20170725021508_evx042-B1","doi-asserted-by":"crossref","first-page":"e1002983","DOI":"10.1371\/journal.pgen.1002983","article-title":"The non-flagellar type III secretion system evolved from the bacterial flagellum and diversified into host-cell adapted systems","volume":"8","year":"2012","journal-title":"PLoS Genet."},{"key":"key\n\t\t\t\t20170725021508_evx042-B2","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1016\/j.ijantimicag.2014.04.006","article-title":"Pathogenicity and treatment of Bartonella infections","volume":"44","year":"2014","journal-title":"Int J Antimicrob Agents"},{"key":"key\n\t\t\t\t20170725021508_evx042-B3","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1016\/j.tig.2015.07.002","article-title":"The genomics of organismal diversification illuminated by adaptive radiations","volume":"31","year":"2015","journal-title":"Trends Genet."},{"key":"key\n\t\t\t\t20170725021508_evx042-B4","doi-asserted-by":"crossref","first-page":"1111","DOI":"10.3201\/eid1907.121718","article-title":"Novel Bartonella agent as cause of verruga peruana","volume":"19","year":"2013","journal-title":"Emerg Infect Dis"},{"key":"key\n\t\t\t\t20170725021508_evx042-B5","doi-asserted-by":"crossref","first-page":"118","DOI":"10.4161\/mge.1.2.16733","article-title":"Potential origins and horizontal transfer of type III secretion systems and effectors","volume":"1","year":"2011","journal-title":"Mob Genet Elements"},{"key":"key\n\t\t\t\t20170725021508_evx042-B6","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1038\/ng.3481","article-title":"Genomic analysis of 38 Legionella species identifies large and diverse effector repertoires","volume":"48","year":"2016","journal-title":"Nat Genet."},{"key":"key\n\t\t\t\t20170725021508_evx042-B7","first-page":"81","article-title":"Towards an integrated model of bacterial conjugation","volume":"39","year":"2015","journal-title":"FEMS Microbiol Rev"},{"key":"key\n\t\t\t\t20170725021508_evx042-B8","doi-asserted-by":"crossref","first-page":"1972","DOI":"10.1093\/bioinformatics\/btp348","article-title":"trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses","volume":"25","year":"2009","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170725021508_evx042-B9","doi-asserted-by":"crossref","first-page":"811","DOI":"10.1038\/nchembio.1364","article-title":"The Fic protein Doc uses an inverted substrate to phosphorylate and inactivate EF-Tu","volume":"9","year":"2013","journal-title":"Nat Chem Biol."},{"key":"key\n\t\t\t\t20170725021508_evx042-B10","doi-asserted-by":"crossref","first-page":"563","DOI":"10.1038\/nmeth.2474","article-title":"Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data","volume":"10","year":"2013","journal-title":"Nat Methods"},{"key":"key\n\t\t\t\t20170725021508_evx042-B11","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1038\/nrmicro3456","article-title":"Secretion systems in Gram-negative bacteria: structural and mechanistic insights","volume":"13","year":"2015","journal-title":"Nat Rev Microbiol."},{"key":"key\n\t\t\t\t20170725021508_evx042-B12","doi-asserted-by":"crossref","first-page":"1164","DOI":"10.1093\/bioinformatics\/btr088","article-title":"ProtTest 3: fast selection of best-fit models of protein evolution","volume":"27","year":"2011","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170725021508_evx042-B13","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1186\/s13059-015-0721-2","article-title":"OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy","volume":"16","year":"2015","journal-title":"Genome Biol."},{"key":"key\n\t\t\t\t20170725021508_evx042-B14","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1038\/nature10729","article-title":"Adenylylation control by intra- or intermolecular active-site obstruction in Fic proteins","volume":"482","year":"2012","journal-title":"Nature"},{"key":"key\n\t\t\t\t20170725021508_evx042-B15","doi-asserted-by":"crossref","first-page":"e1001296","DOI":"10.1371\/journal.pgen.1001296","article-title":"Parallel evolution of a type IV secretion system in radiating lineages of the host-restricted bacterial pathogen Bartonella","volume":"7","year":"2011","journal-title":"PLoS Genet."},{"key":"key\n\t\t\t\t20170725021508_evx042-B16","doi-asserted-by":"crossref","first-page":"1325","DOI":"10.1093\/molbev\/msi124","article-title":"Functional divergence and horizontal transfer of type IV secretion systems","volume":"22","year":"2005","journal-title":"Mol Biol Evol."},{"issue":"3","key":"key\n\t\t\t\t20170725021508_evx042-B17","article-title":"Mechanism and function of type IV secretion during infection of the human host","volume":"4","year":"2016","journal-title":"Microbiol Spectr"},{"key":"key\n\t\t\t\t20170725021508_evx042-B18","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1093\/molbev\/mss221","article-title":"Evolution of conjugation and type IV secretion systems","volume":"30","year":"2013","journal-title":"Mol Biol Evol."},{"key":"key\n\t\t\t\t20170725021508_evx042-B19","doi-asserted-by":"crossref","first-page":"2334","DOI":"10.1093\/bioinformatics\/btq413","article-title":"genoPlotR: comparative gene and genome visualization in R","volume":"26","year":"2010","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170725021508_evx042-B20","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1186\/1471-2148-12-65","article-title":"A genome-wide study of recombination rate variation in Bartonella henselae","volume":"12","year":"2012","journal-title":"BMC Evol Biol."},{"key":"key\n\t\t\t\t20170725021508_evx042-B21","doi-asserted-by":"crossref","first-page":"e1003393","DOI":"10.1371\/journal.pgen.1003393","article-title":"A gene transfer agent and a dynamic repertoire of secretion systems hold the keys to the explosive radiation of the emerging pathogen Bartonella","volume":"9","year":"2013","journal-title":"PLoS Genet."},{"key":"key\n\t\t\t\t20170725021508_evx042-B22","article-title":"Complete genome sequence of Bartonella ancashensis strain 20.00, isolated from the blood of a patient with verruga peruana","volume":"3(6):pii: e01217-15","year":"2015","journal-title":"Genome Announc"},{"key":"key\n\t\t\t\t20170725021508_evx042-B23","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1128\/CMR.05009-11","article-title":"Intruders below the radar: molecular pathogenesis of Bartonella spp","volume":"25","year":"2012","journal-title":"Clin Microbiol Rev"},{"key":"key\n\t\t\t\t20170725021508_evx042-B24","article-title":"Biological diversity and molecular plasticity of FIC domain proteins","year":"2016","journal-title":"Annu Rev Microbiol. 70:341\u2013360"},{"key":"key\n\t\t\t\t20170725021508_evx042-B25","doi-asserted-by":"crossref","first-page":"1497","DOI":"10.1016\/j.celrep.2015.07.056","article-title":"Adenylylation of gyrase and topo IV by FicT toxins disrupts bacterial DNA topology","volume":"12","year":"2015","journal-title":"Cell Rep"},{"key":"key\n\t\t\t\t20170725021508_evx042-B26","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1111\/cmi.12040","article-title":"Bacterial EPIYA effectors: where do they come from? What are they? Where are they going?","volume":"15","year":"2013","journal-title":"Cell Microbiol."},{"key":"key\n\t\t\t\t20170725021508_evx042-B27","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","year":"2012","journal-title":"Nat Methods"},{"key":"key\n\t\t\t\t20170725021508_evx042-B28","doi-asserted-by":"crossref","first-page":"1984","DOI":"10.3201\/eid1512.081692","article-title":"Bartonella rochalimae in raccoons, coyotes, and red foxes","volume":"15","year":"2009","journal-title":"Emerg Infect Dis"},{"key":"key\n\t\t\t\t20170725021508_evx042-B29","doi-asserted-by":"crossref","first-page":"2411","DOI":"10.1128\/JCM.02539-06","article-title":"Gray foxes (Urocyon cinereoargenteus) as a potential reservoir of a Bartonella clarridgeiae-like bacterium and domestic dogs as part of a sentinel system for surveillance of zoonotic arthropod-borne pathogens in northern California","volume":"45","year":"2007","journal-title":"J Clin Microbiol."},{"key":"key\n\t\t\t\t20170725021508_evx042-B30","doi-asserted-by":"crossref","first-page":"2947","DOI":"10.1093\/bioinformatics\/btm404","article-title":"Clustal W and clustal X version 2.0","volume":"23","year":"2007","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170725021508_evx042-B31","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1186\/2047-217X-1-18","article-title":"SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler","volume":"1","year":"2012","journal-title":"Gigascience"},{"key":"key\n\t\t\t\t20170725021508_evx042-B32","doi-asserted-by":"crossref","first-page":"D560","DOI":"10.1093\/nar\/gkt963","article-title":"IMG 4 version of the integrated microbial genomes comparative analysis system","volume":"42","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170725021508_evx042-B33","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","year":"2014","journal-title":"PLoS Negl Trop Dis"},{"key":"key\n\t\t\t\t20170725021508_evx042-B34","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1038\/nature10335","article-title":"Modulation of Rab GTPase function by a protein phosphocholine transferase","volume":"477","year":"2011","journal-title":"Nature"},{"key":"key\n\t\t\t\t20170725021508_evx042-B35","doi-asserted-by":"crossref","first-page":"3865","DOI":"10.1128\/JCM.01226-13","article-title":"Molecular typing of \u201cCandidatus Bartonella ancashi,\u201d a new human pathogen causing verruga peruana","volume":"51","year":"2013","journal-title":"J Clin Microbiol."},{"key":"key\n\t\t\t\t20170725021508_evx042-B36","doi-asserted-by":"crossref","first-page":"3635","DOI":"10.1093\/nar\/gkg584","article-title":"Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs","volume":"31","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170725021508_evx042-B37","doi-asserted-by":"crossref","first-page":"e1004187","DOI":"10.1371\/journal.ppat.1004187","article-title":"A translocated effector required for Bartonella dissemination from derma to blood safeguards migratory host cells from damage by co-translocated effectors","volume":"10","year":"2014","journal-title":"PLoS Pathog"},{"issue":"3","key":"key\n\t\t\t\t20170725021508_evx042-B38","first-page":"492","article-title":"Fic domain catalyzed adenylylation: insight provided by the structural analysis of the type IV secretion system effector BepA","volume":"20","year":"2010","journal-title":"Protein Sci."},{"key":"key\n\t\t\t\t20170725021508_evx042-B39","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1093\/bioinformatics\/btg412","article-title":"APE: analyses of phylogenetics and evolution in R language","volume":"20","year":"2004","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170725021508_evx042-B40","doi-asserted-by":"crossref","first-page":"1048","DOI":"10.1002\/pmic.201300470","article-title":"An experimental strategy for the identification of AMPylation targets from complex protein samples","volume":"14","year":"2014","journal-title":"Proteomics"},{"key":"key\n\t\t\t\t20170725021508_evx042-B41","doi-asserted-by":"crossref","first-page":"9581","DOI":"10.1073\/pnas.1117651109","article-title":"Bacterial effector binds host cell adenylyl cyclase to potentiate Galphas-dependent cAMP production","volume":"109","year":"2012","journal-title":"Proc Natl Acad Sci U S A."},{"key":"key\n\t\t\t\t20170725021508_evx042-B42","doi-asserted-by":"crossref","first-page":"3352","DOI":"10.1128\/JB.01676-09","article-title":"The BatR\/BatS two-component regulatory system controls the adaptive response of Bartonella henselae during human endothelial cell infection","volume":"192","year":"2010","journal-title":"J Bacteriol"},{"key":"key\n\t\t\t\t20170725021508_evx042-B43","doi-asserted-by":"crossref","first-page":"756","DOI":"10.1111\/mmi.12396","article-title":"Dual input control: activation of the Bartonella henselae VirB\/D4 type IV secretion system by the stringent sigma factor RpoH1 and the BatR\/BatS two-component system","volume":"90","year":"2013","journal-title":"Mol Microbiol."},{"key":"key\n\t\t\t\t20170725021508_evx042-B44","doi-asserted-by":"crossref","first-page":"1469","DOI":"10.1038\/ng.2007.38","article-title":"Genomic analysis of Bartonella identifies type IV secretion systems as host adaptability factors","volume":"39","year":"2007","journal-title":"Nat Genet."},{"key":"key\n\t\t\t\t20170725021508_evx042-B45","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1016\/j.vetmic.2012.07.012","article-title":"Isolation and phylogenetic analysis of Bartonella species from wild carnivores of the suborder Caniformia in Japan","volume":"161","year":"2012","journal-title":"Vet Microbiol."},{"key":"key\n\t\t\t\t20170725021508_evx042-B46","doi-asserted-by":"crossref","first-page":"575","DOI":"10.1016\/j.cimid.2012.07.001","article-title":"Prevalence and genetic diversity of Bartonella species in sika deer (Cervus nippon) in Japan","volume":"35","year":"2012","journal-title":"Comp Immunol Microbiol Infect Dis"},{"key":"key\n\t\t\t\t20170725021508_evx042-B47","article-title":"Genomic changes associated with the evolutionary transition of an insect gut commensal into a blood-borne pathogen","year":"2017","journal-title":"ISME J."},{"key":"key\n\t\t\t\t20170725021508_evx042-B48","doi-asserted-by":"crossref","first-page":"856","DOI":"10.1073\/pnas.0406796102","article-title":"A bipartite signal mediates the transfer of type IV secretion substrates of Bartonella henselae into human cells","volume":"102","year":"2005","journal-title":"Proc Natl Acad Sci U S A."},{"key":"key\n\t\t\t\t20170725021508_evx042-B49","doi-asserted-by":"crossref","first-page":"397","DOI":"10.1016\/j.chom.2009.03.004","article-title":"Host cell interactome of tyrosine-phosphorylated bacterial proteins","volume":"5","year":"2009","journal-title":"Cell Host Microbe"},{"key":"key\n\t\t\t\t20170725021508_evx042-B50","doi-asserted-by":"crossref","first-page":"1253","DOI":"10.1046\/j.1365-2958.2003.03650.x","article-title":"A bacterial conjugation machinery recruited for pathogenesis","volume":"49","year":"2003","journal-title":"Mol Microbiol."},{"key":"key\n\t\t\t\t20170725021508_evx042-B51","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1016\/j.mib.2014.11.007","article-title":"New insights into the role of Bartonella effector proteins in pathogenesis","volume":"23","year":"2015","journal-title":"Curr Opin Microbiol."},{"key":"key\n\t\t\t\t20170725021508_evx042-B52","doi-asserted-by":"crossref","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","article-title":"RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies","volume":"30","year":"2014","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170725021508_evx042-B53","doi-asserted-by":"crossref","first-page":"2725","DOI":"10.1093\/molbev\/mst197","article-title":"MEGA6: Molecular Evolutionary Genetics Analysis version 6.0","volume":"30","year":"2013","journal-title":"Mol Biol Evol."},{"key":"key\n\t\t\t\t20170725021508_evx042-B54","doi-asserted-by":"crossref","first-page":"2156","DOI":"10.1093\/gbe\/evu169","article-title":"Horizontal transfers and gene losses in the phospholipid pathway of Bartonella reveal clues about early ecological niches","volume":"6","year":"2014","journal-title":"Genome Biol Evol."}],"container-title":["Genome Biology and Evolution"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/gbe\/article-pdf\/9\/3\/761\/19270681\/evx042.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2017,8,24]],"date-time":"2017-08-24T15:40:37Z","timestamp":1503589237000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/gbe\/article-lookup\/doi\/10.1093\/gbe\/evx042"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,3]]},"references-count":54,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2017,3,1]]},"published-print":{"date-parts":[[2017,3]]}},"URL":"https:\/\/doi.org\/10.1093\/gbe\/evx042","relation":{},"ISSN":["1759-6653"],"issn-type":[{"value":"1759-6653","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,3]]}}}