{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,10]],"date-time":"2026-07-10T20:28:42Z","timestamp":1783715322596,"version":"3.55.0"},"reference-count":148,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2019,9,24]],"date-time":"2019-09-24T00:00:00Z","timestamp":1569283200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Genet."],"DOI":"10.3389\/fgene.2019.00797","type":"journal-article","created":{"date-parts":[[2019,9,24]],"date-time":"2019-09-24T04:48:01Z","timestamp":1569300481000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":24,"title":["Bioinformatic Exploration of Metal-Binding Proteome of Zoonotic Pathogen Orientia tsutsugamushi"],"prefix":"10.3389","volume":"10","author":[{"given":"Dixit","family":"Sharma","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ankita","family":"Sharma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Birbal","family":"Singh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shailender Kumar","family":"Verma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2019,9,24]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.1042\/BSR20160179","article-title":"Computational approaches for de novo design and redesign of metal-binding sites on proteins","volume":"37","author":"Akcapinar","year":"2017","journal-title":"Biosci. Rep."},{"key":"B2","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"B3","doi-asserted-by":"publisher","first-page":"1427","DOI":"10.1093\/nar\/30.7.1427","article-title":"Comparative genomics and evolution of proteins involved in RNA metabolism","volume":"30","author":"Anantharaman","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"B4","doi-asserted-by":"publisher","first-page":"317","DOI":"10.1002\/prot.21324","article-title":"Non-heme iron through the three domains of life","volume":"67","author":"Andreini","year":"2007","journal-title":"Proteins"},{"key":"B5","doi-asserted-by":"publisher","first-page":"209","DOI":"10.1021\/pr070480u","article-title":"Occurrence of copper proteins through the three domains of life: a bioinformatic approach","volume":"7","author":"Andreini","year":"2007","journal-title":"J. Proteome Res."},{"key":"B6","doi-asserted-by":"publisher","first-page":"4582","DOI":"10.1128\/AAC.00511-10","article-title":"Efficacy of calcium-EDTA as an inhibitor for metallo-\u03b2-lactamase in a mouse model of Pseudomonas aeruginosa pneumonia","volume":"54","author":"Aoki","year":"2010","journal-title":"Antimicrob. Agents Chemother."},{"key":"B7","doi-asserted-by":"publisher","first-page":"469","DOI":"10.1016\/S0968-0004(98)01293-6","article-title":"The HD domain defines a new superfamily of metal-dependent phosphohydrolases","volume":"23","author":"Aravind","year":"1998","journal-title":"Trends Biochem. Sci."},{"key":"B8","doi-asserted-by":"publisher","first-page":"7528","DOI":"10.1021\/jacs.5b01156","article-title":"Reaction mechanisms in carbohydrate-active enzymes: glycoside hydrolases and glycosyltransferases. Insights from ab initio quantum mechanics\/molecular mechanics dynamic simulations","volume":"137","author":"Ard\u00e8vol","year":"2015","journal-title":"J. Am. Chem. Soc."},{"key":"B9","doi-asserted-by":"publisher","first-page":"136","DOI":"10.1007\/s12275-016-5599-5","article-title":"Inhibition of eukaryotic translation by tetratricopeptide-repeat proteins of Orientia tsutsugamushi","volume":"54","author":"Bang","year":"2016","journal-title":"J. Microbiol."},{"key":"B10","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0006566","article-title":"Long-read whole genome sequencing and comparative analysis of six strains of the human pathogen Orientia tsutsugamushi","volume":"12","author":"Batty","year":"2018","journal-title":"PLoS Negl. Trop. Dis."},{"key":"B11","doi-asserted-by":"publisher","first-page":"580","DOI":"10.1128\/IAI.00858-12","article-title":"Helicobacter pylori stores nickel to aid its host colonization","volume":"81","author":"Benoit","year":"2013","journal-title":"Infect. Immun."},{"key":"B12","doi-asserted-by":"publisher","first-page":"1071","DOI":"10.1007\/s00775-010-0666-6","article-title":"The annotation of full zinc proteomes","volume":"15","author":"Bertini","year":"2010","journal-title":"J. Biol. Inorg. Chem."},{"key":"B13","doi-asserted-by":"publisher","first-page":"3097","DOI":"10.1128\/JB.00276-15","article-title":"Orientia tsutsugamushi strain Ikeda ankyrin repeat-containing proteins recruit SCF1 ubiquitin ligase machinery via poxvirus-like F-box motifs","volume":"197","author":"Beyer","year":"2015","journal-title":"J. Bacteriol."},{"key":"B14","doi-asserted-by":"publisher","first-page":"1091","DOI":"10.1093\/bioinformatics\/btp101","article-title":"ClueGO: A Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks","volume":"25","author":"Bindea","year":"2009","journal-title":"Bioinformatics"},{"key":"B15","doi-asserted-by":"publisher","first-page":"713","DOI":"10.1016\/S0969-2126(02)00761-X","article-title":"Tandem DNA recognition by PhoB, a two-component signal transduction transcriptional activator","volume":"10","author":"Blanco","year":"2002","journal-title":"Structure"},{"key":"B16","doi-asserted-by":"publisher","first-page":"13750","DOI":"10.1073\/pnas.1613610113","article-title":"An HD domain phosphohydrolase active site tailored for oxetanocin-A biosynthesis","volume":"113","author":"Bridwell-Rabb","year":"2016","journal-title":"Proc. Natl. Acad. Sci."},{"key":"B17","doi-asserted-by":"publisher","first-page":"1469","DOI":"10.1038\/emboj.2013.82","article-title":"Structure of the Legionella effector AnkX reveals the mechanism of phosphocholine transfer by the FIC domain","volume":"32","author":"Campanacci","year":"2013","journal-title":"EMBO J."},{"key":"B18","doi-asserted-by":"publisher","first-page":"795","DOI":"10.1046\/j.1365-2958.2001.02673.x","article-title":"The TolQ\u2013TolR proteins energize TolA and share homologies with the flagellar motor proteins MotA\u2013MotB","volume":"42","author":"Cascales","year":"2001","journal-title":"Mol. Microbiol."},{"key":"B19","doi-asserted-by":"publisher","first-page":"1357","DOI":"10.1007\/s00894-010-0653-4","article-title":"Exploring the molecular basis for selective binding of Mycobacterium tuberculosis Asp kinase toward its natural substrates and feedback inhibitors: a docking and molecular dynamics study","volume":"16","author":"Chaitanya","year":"2010","journal-title":"J. Mol. Model."},{"key":"B20","doi-asserted-by":"publisher","first-page":"D615","DOI":"10.1093\/nar\/gkr942","article-title":"DBETH: a database of bacterial exotoxins for human","volume":"40","author":"Chakraborty","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"B21","doi-asserted-by":"publisher","DOI":"10.1128\/JB.00268-17","article-title":"Pseudomonas aeruginosa magnesium transporter MgtE inhibits type III secretion system gene expression by stimulating rsmYZ transcription","volume":"199","author":"Chakravarty","year":"2017","journal-title":"J. Bacteriol."},{"key":"B22","doi-asserted-by":"publisher","first-page":"561","DOI":"10.1046\/j.1365-2958.2002.02917.x","article-title":"Mg2+ homeostasis and avoidance of metal toxicity","volume":"44","author":"Chamnongpol","year":"2002","journal-title":"Mol. Microbiol."},{"key":"B23","doi-asserted-by":"publisher","first-page":"369","DOI":"10.18388\/abp.2013_1994","article-title":"The toxic Doppelganger: on the ionic and molecular mimicry of cadmium","volume":"60","author":"Chmielowska-B\u0105k","year":"2013","journal-title":"Acta Biochim. Pol."},{"key":"B24","doi-asserted-by":"publisher","first-page":"1699","DOI":"10.1002\/pmic.200900633","article-title":"Global gene expression profile of Orientia tsutsugamushi","volume":"10","author":"Cho","year":"2010","journal-title":"Proteomics"},{"key":"B25","doi-asserted-by":"publisher","first-page":"7981","DOI":"10.1073\/pnas.0611553104","article-title":"The Orientia tsutsugamushi genome reveals massive proliferation of conjugative type IV secretion system and host\u2013cell interaction genes","volume":"104","author":"Cho","year":"2007","journal-title":"Proc. Natl. Acad. Sci."},{"key":"B26","doi-asserted-by":"publisher","first-page":"2671","DOI":"10.1002\/pro.5560061225","article-title":"Crystal structures of the cadmium-and mercury-substituted metallo-\u03b2-lactamase from Bacteroides fragilis","volume":"6","author":"Concha","year":"1997","journal-title":"Protein Sci."},{"key":"B27","doi-asserted-by":"publisher","first-page":"291","DOI":"10.1111\/j.1365-2958.2004.04276.x","article-title":"Calcium signalling in bacteria","volume":"54","author":"Dominguez","year":"2004","journal-title":"Mol. Microbiol."},{"key":"B28","doi-asserted-by":"publisher","first-page":"1093","DOI":"10.1002\/jccs.200300155","article-title":"Metal binding and selectivity in zinc proteins","volume":"50","author":"Dudev","year":"2003","journal-title":"J. Chin. Chem. Soc."},{"key":"B29","doi-asserted-by":"publisher","first-page":"269","DOI":"10.7537\/marsjas061010.31","article-title":"Cytotoxic activities of some Escherichia coli isolates: possible mechanisms and approaches for inhibition","volume":"6","author":"El-Housseiny","year":"2010","journal-title":"J. Am. Sci."},{"key":"B30","doi-asserted-by":"publisher","first-page":"504","DOI":"10.1128\/MMBR.00021-10","article-title":"FtsZ in bacterial cytokinesis: cytoskeleton and force generator all in one","volume":"74","author":"Erickson","year":"2010","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"B31","doi-asserted-by":"publisher","first-page":"R877","DOI":"10.1016\/j.cub.2011.09.040","article-title":"Copper: an essential metal in biology","volume":"21","author":"Festa","year":"2011","journal-title":"Curr. Biol."},{"key":"B32","doi-asserted-by":"publisher","first-page":"50293","DOI":"10.1074\/jbc.M205042200","article-title":"Characterization of a new type of phosphopantetheinyl transferase for fatty acid and siderophore synthesis in Pseudomonas aeruginosa","volume":"277","author":"Finking","year":"2002","journal-title":"J. Biol. Chem."},{"key":"B33","doi-asserted-by":"publisher","first-page":"D279","DOI":"10.1093\/nar\/gkv1344","article-title":"The Pfam protein families database: towards a more sustainable future","volume":"44","author":"Finn","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"B34","doi-asserted-by":"publisher","first-page":"597","DOI":"10.1128\/MMBR.00082-15","article-title":"Bacterial sphingomyelinases and phospholipases as virulence factors","volume":"80","author":"Flores-D\u00edaz","year":"2016","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"B35","doi-asserted-by":"publisher","first-page":"225","DOI":"10.1093\/bib\/bbl004","article-title":"Automated protein function prediction\u2014the genomic challenge","volume":"7","author":"Friedberg","year":"2006","journal-title":"Brief. Bioinformatics"},{"key":"B36","doi-asserted-by":"publisher","first-page":"2878","DOI":"10.1039\/C3DT52810C","article-title":"Structural and computational insights into the versatility of cadmium binding to proteins","volume":"43","author":"Friedman","year":"2014","journal-title":"Dalton Trans."},{"key":"B37","doi-asserted-by":"publisher","first-page":"6757","DOI":"10.1128\/IAI.72.12.6757-6763.2004","article-title":"ATP-binding cassette transporters are targets for the development of antibacterial vaccines and therapies","volume":"72","author":"Garmory","year":"2004","journal-title":"Infect. Immun."},{"key":"B38","first-page":"1910","article-title":"Isolation and some properties of phospholipase D from Bacillus subtilis G-22","volume":"42","author":"Garutskas","year":"1977","journal-title":"Biokhimiia"},{"key":"B39","doi-asserted-by":"publisher","first-page":"3784","DOI":"10.1093\/nar\/gkg563","article-title":"ExPASy: The proteomics server for in-depth protein knowledge and analysis","volume":"31","author":"Gasteiger","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"B40","doi-asserted-by":"publisher","first-page":"625","DOI":"10.1146\/annurev-genet-051313-051025","article-title":"Bacterial Mg2+ homeostasis, transport, and virulence","volume":"47","author":"Groisman","year":"2013","journal-title":"Annu. Rev. Genet."},{"key":"B41","doi-asserted-by":"publisher","first-page":"91","DOI":"10.2174\/1874285801509010091","article-title":"Iron acquisition mechanisms: promising target against Mycobacterium tuberculosis","volume":"9","author":"Hameed","year":"2015","journal-title":"Open Microbiol. J."},{"key":"B42","doi-asserted-by":"publisher","first-page":"W236","DOI":"10.1093\/nar\/gkw370","article-title":"Evolview v2: an online visualization and management tool for customized and annotated phylogenetic trees","volume":"44","author":"He","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"B43","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1146\/annurev.cb.08.110192.000435","article-title":"ABC transporters: from microorganisms to man","volume":"8","author":"Higgins","year":"1992","journal-title":"Annu. Rev. Cell Biol."},{"key":"B44","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1186\/s12977-015-0198-9","article-title":"dUTPase: the frequently overlooked enzyme encoded by many retroviruses","volume":"12","author":"Hizi","year":"2015","journal-title":"Retrovirology"},{"key":"B45","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2007-8-9-r183","article-title":"The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists","volume":"8","author":"Huang","year":"2007","journal-title":"Genome Biol."},{"key":"B46","doi-asserted-by":"publisher","first-page":"E747","DOI":"10.1073\/pnas.1416485112","article-title":"An HD-domain phosphodiesterase mediates cooperative hydrolysis of c-di-AMP to affect bacterial growth and virulence","volume":"112","author":"Huynh","year":"2015","journal-title":"Proc. Natl. Acad. Sci."},{"key":"B47","doi-asserted-by":"publisher","first-page":"1895","DOI":"10.1093\/oxfordjournals.jbchem.a133168","article-title":"Thermostability and aliphatic index of globular proteins","volume":"88","author":"Ikai","year":"1980","journal-title":"J. Biochem."},{"key":"B48","doi-asserted-by":"publisher","first-page":"10358","DOI":"10.1073\/pnas.1605442113","article-title":"Insights into the molecular basis for substrate binding and specificity of the wild-type L-arginine\/agmatine antiporter AdiC","volume":"113","author":"Ilg\u00fc","year":"2016","journal-title":"Proc. Natl. Acad. Sci."},{"key":"B49","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0006346","article-title":"Emergence of Orientia tsutsugamushi as an important cause of acute encephalitis syndrome in India","volume":"121","author":"Jain","year":"2018","journal-title":"PLoS Negl. Trop. Dis."},{"key":"B50","doi-asserted-by":"publisher","first-page":"361","DOI":"10.1038\/nrd1087","article-title":"Drug discovery with engineered zinc-finger proteins","volume":"2","author":"Jamieson","year":"2003","journal-title":"Nat. Rev. Drug Discov."},{"key":"B51","doi-asserted-by":"publisher","first-page":"816","DOI":"10.3389\/fimmu.2018.00816","article-title":"Dissemination of Orientia tsutsugamushi, a causative agent of scrub typhus, and immunological responses in the humanized DRAGA mouse","volume":"9","author":"Jiang","year":"2018","journal-title":"Front. Immunol."},{"key":"B52","doi-asserted-by":"publisher","first-page":"1236","DOI":"10.1093\/bioinformatics\/btu031","article-title":"InterProScan 5: genome-scale protein function classification","volume":"30","author":"Jones","year":"2014","journal-title":"Bioinformatics"},{"key":"B53","doi-asserted-by":"publisher","first-page":"3558","DOI":"10.1128\/JB.185.12.3558-3566.2003","article-title":"Posttranscriptional control of quorum-sensing-dependent virulence genes by DksA in Pseudomonas aeruginosa","volume":"185","author":"Jude","year":"2003","journal-title":"J. Bacteriol."},{"key":"B54","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1002\/ddr.21465","article-title":"Reaching toward underexplored targets in antibacterial drug design","volume":"80","author":"Juki\u010d","year":"2019","journal-title":"Drug Dev. Res."},{"key":"B55","doi-asserted-by":"publisher","first-page":"800","DOI":"10.1107\/S0907444907024353","article-title":"Structure and stability of designed TPR protein superhelices: unusual crystal packing and implications for natural TPR proteins","volume":"63","author":"Kajander","year":"2007","journal-title":"Acta Crystallogr. D. Biol. Crystallogr."},{"key":"B56","doi-asserted-by":"publisher","first-page":"9774","DOI":"10.1093\/nar\/gks704","article-title":"The role of Ca 2+ in the activity of Mycobacterium tuberculosis DNA gyrase","volume":"40","author":"Karkare","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"B57","doi-asserted-by":"publisher","first-page":"845","DOI":"10.1038\/nprot.2015.053","article-title":"The Phyre2 web portal for protein modeling, prediction and analysis","volume":"10","author":"Kelley","year":"2015","journal-title":"Nat. Protoc."},{"key":"B58","doi-asserted-by":"publisher","first-page":"63","DOI":"10.3390\/tropicalmed2040063","article-title":"The historical case for and the future study of antibiotic-resistant scrub typhus","volume":"2","author":"Kelly","year":"2017","journal-title":"Trop. Med. Infect. Dis."},{"key":"B59","doi-asserted-by":"publisher","first-page":"148","DOI":"10.3201\/eid2301.161038","article-title":"Scrub typhus leading to acute encephalitis syndrome, Assam, India","volume":"23","author":"Khan","year":"2017","journal-title":"Emerging Infect. Dis."},{"key":"B60","doi-asserted-by":"publisher","first-page":"176","DOI":"10.1038\/nchembio.72","article-title":"Mechanisms for copper acquisition, distribution and regulation","volume":"4","author":"Kim","year":"2008","journal-title":"Nat. Chem. Biol."},{"key":"B61","doi-asserted-by":"publisher","first-page":"2720","DOI":"10.1128\/AEM.02738-08","article-title":"Effect of iron concentration on the growth rate of Pseudomonas syringae and the expression of virulence factors in hrp-inducing minimal medium","volume":"75","author":"Kim","year":"2009","journal-title":"Appl. Environ. Microbiol."},{"key":"B62","doi-asserted-by":"publisher","first-page":"1098","DOI":"10.1039\/c1mt00073j","article-title":"Bacterial ATP-driven transporters of transition metals: physiological roles, mechanisms of action, and roles in bacterial virulence","volume":"3","author":"Klein","year":"2011","journal-title":"Metallomics"},{"key":"B63","doi-asserted-by":"publisher","first-page":"326","DOI":"10.1016\/j.micpath.2011.02.007","article-title":"Involvement of Ca2+ signaling in intracellular invasion of non-phagocytic host cells by Orientia tsutsugamushi","volume":"50","author":"Ko","year":"2011","journal-title":"Microb. Pathog."},{"key":"B64","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01732-17","article-title":"Orientia tsutsugamushi is highly susceptible to the RNA polymerase switch region inhibitor corallopyronin A in vitro and in vivo","volume":"62","author":"Kock","year":"2018","journal-title":"Antimicrob. Agents Chemother."},{"key":"B65","doi-asserted-by":"publisher","first-page":"8894","DOI":"10.1021\/bi049083c","article-title":"Structural characterization of the stringent response related exopolyphosphatase\/guanosine pentaphosphate phosphohydrolase protein family","volume":"43","author":"Kristensen","year":"2004","journal-title":"Biochemistry"},{"key":"B66","doi-asserted-by":"publisher","first-page":"2287","DOI":"10.1021\/acs.jcim.6b00407","article-title":"MIB: metal ion-binding site prediction and docking server","volume":"56","author":"Lin","year":"2016","journal-title":"J. Chem. Inf. Model."},{"key":"B67","doi-asserted-by":"publisher","first-page":"4366","DOI":"10.1021\/cr400479b","article-title":"Metalloproteins containing cytochrome, iron\u2013sulfur, or copper redox centers","volume":"114","author":"Liu","year":"2014","journal-title":"Chem. Rev."},{"key":"B68","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0039252","article-title":"Prediction of metal ion-binding sites in proteins using the fragment transformation method","volume":"7","author":"Lu","year":"2012","journal-title":"PLoS One"},{"key":"B69","doi-asserted-by":"publisher","first-page":"1394","DOI":"10.1096\/fj.12-223305","article-title":"Inhibition of bacterial thioredoxin reductase: an antibiotic mechanism targeting bacteria lacking glutathione","volume":"27","author":"Lu","year":"2013","journal-title":"FASEB J."},{"key":"B70","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1128\/MMBR.00055-15","article-title":"Bacterial transcription as a target for antibacterial drug development","volume":"80","author":"Ma","year":"2016","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"B71","doi-asserted-by":"publisher","first-page":"1541","DOI":"10.1039\/C5MT00170F","article-title":"Iron and zinc exploitation during bacterial pathogenesis","volume":"7","author":"Ma","year":"2015","journal-title":"Metallomics"},{"key":"B72","doi-asserted-by":"publisher","first-page":"4644","DOI":"10.1021\/cr900077w","article-title":"Coordination chemistry of bacterial metal transport and sensing","volume":"109","author":"Ma","year":"2009","journal-title":"Chem. Rev."},{"key":"B73","doi-asserted-by":"publisher","first-page":"1641","DOI":"10.3201\/eid1610.100456","article-title":"Scrub typhus involving central nervous system, India, 2004\u20132006","volume":"16","author":"Mahajan","year":"2010","journal-title":"Emerging Infect. Dis."},{"key":"B74","doi-asserted-by":"publisher","first-page":"66","DOI":"10.3390\/ijms17010066","article-title":"The metals in the biological periodic system of the elements: concepts and conjectures","volume":"17","author":"Maret","year":"2016","journal-title":"Int. J. Mol. Sci."},{"key":"B75","doi-asserted-by":"publisher","first-page":"359","DOI":"10.1111\/j.1749-6632.2003.tb07391.x","article-title":"Outbreak of scrub typhus in Southern India during the cooler months","volume":"990","author":"Mathai","year":"2003","journal-title":"Ann. N. Y. Acad. Sci."},{"key":"B76","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1016\/S0966-842X(01)02284-3","article-title":"The functions of Ca2+ in bacteria: a role for EF-hand proteins","volume":"10","author":"Michiels","year":"2002","journal-title":"Trends Microbiol."},{"key":"B77","doi-asserted-by":"publisher","first-page":"5850","DOI":"10.1093\/nar\/gky323","article-title":"The structure of the TsaB\/TsaD\/TsaE complex reveals an unexpected mechanism for the bacterial t6A tRNA-modification","volume":"46","author":"Missoury","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"B78","doi-asserted-by":"publisher","first-page":"1029","DOI":"10.2174\/1389450116666151001105622","article-title":"B1-Metallo-\u03b2-lactamases: where do we stand","volume":"17","author":"Mojica","year":"2016","journal-title":"Curr. Drug Targets"},{"key":"B79","doi-asserted-by":"publisher","first-page":"459","DOI":"10.1016\/S1359-6446(03)02689-8","article-title":"Reverse vaccinology","volume":"8","author":"Mora","year":"2003","journal-title":"Drug Discov. Today"},{"key":"B80","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1016\/j.tube.2015.01.006","article-title":"Structural and functional features of enzymes of Mycobacterium tuberculosis peptidoglycan biosynthesis as targets for drug development","volume":"95","author":"Moraes","year":"2015","journal-title":"Tuberculosis"},{"key":"B81","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0060143","article-title":"Characterisation of ATP-dependent Mur ligases involved in the biogenesis of cell wall peptidoglycan in Mycobacterium tuberculosis","volume":"8","author":"Munshi","year":"2013","journal-title":"PloS one"},{"key":"B82","doi-asserted-by":"publisher","first-page":"35801","DOI":"10.1074\/jbc.M113.519496","article-title":"Structures of the Bacillus subtilis glutamine synthetase dodecamer reveal large intersubunit catalytic conformational changes linked to a unique feedback inhibition mechanism","volume":"288","author":"Murray","year":"2013","journal-title":"J. Biol. Chem."},{"key":"B83","doi-asserted-by":"publisher","first-page":"ec269","DOI":"10.1126\/scisignal.aal3828","article-title":"A ribosomal strategy for magnesium deficiency","volume":"9","author":"Mushegian","year":"2016","journal-title":"Sci. Signal."},{"key":"B84","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1093\/dnares\/dsn011","article-title":"The whole-genome sequencing of the obligate intracellular bacterium orientia tsutsugamushi revealed massive gene amplification during reductive genome evolution","volume":"15","author":"Nakayama","year":"2008","journal-title":"DNA Res."},{"key":"B85","doi-asserted-by":"publisher","first-page":"17496","DOI":"10.1074\/jbc.M117.804799","article-title":"Mechanisms of zinc binding to the solute-binding protein AztC and transfer from the metallochaperone AztD","volume":"292","author":"Neupane","year":"2017","journal-title":"J. Biol. Chem."},{"key":"B86","doi-asserted-by":"publisher","first-page":"2347","DOI":"10.1093\/jac\/dkq311","article-title":"Targeting the chromosome partitioning protein ParA in tuberculosis drug discovery","volume":"65","author":"Nisa","year":"2010","journal-title":"J. Antimicrob. Chemother."},{"key":"B87","first-page":"357","article-title":"Bacterial bioinformatics: pathogenesis and the genome","volume":"4","author":"Paine","year":"2002","journal-title":"J. Mol. Microbiol. Biotechnol."},{"key":"B88","doi-asserted-by":"publisher","first-page":"1594","DOI":"10.1016\/j.bbamcr.2012.01.013","article-title":"Role of metal in folding and stability of copper proteins in vitro","volume":"1823","author":"Palm-Espling","year":"2012","journal-title":"BBA-Mol. Cell Res."},{"key":"B89","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1146\/annurev-genet-120215-035146","article-title":"Transition metals and virulence in bacteria","volume":"50","author":"Palmer","year":"2016","journal-title":"Annu. Rev. Genet."},{"key":"B90","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1111\/j.1749-6632.2012.06796.x","article-title":"Metallo-\u03b2-lactamase structure and function","volume":"1277","author":"Palzkill","year":"2013","journal-title":"Ann. N. Y. Acad. Sci."},{"key":"B91","doi-asserted-by":"publisher","DOI":"10.4137\/DTI.S19728","article-title":"Genome-wide analysis of Mycoplasma hominis for the identification of putative therapeutic targets","volume":"8","author":"Parvege","year":"2014","journal-title":"Drug Target Insights"},{"key":"B92","doi-asserted-by":"publisher","first-page":"36322","DOI":"10.1074\/jbc.M112.402149","article-title":"Hallmarks of processivity in glycoside hydrolases from crystallographic and computational studies of the Serratia marcescens chitinases","volume":"287","author":"Payne","year":"2012","journal-title":"J. Biol. Chem."},{"key":"B93","doi-asserted-by":"publisher","first-page":"90","DOI":"10.3389\/fcimb.2013.00090","article-title":"Iron, copper, zinc, and manganese transport and regulation in pathogenic Enterobacteria: correlations between strains, site of infection and the relative importance of the different metal transport systems for virulence","volume":"3","author":"Porcheron","year":"2013","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"B94","doi-asserted-by":"publisher","first-page":"D61","DOI":"10.1093\/nar\/gkl842","article-title":"NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins","volume":"35","author":"Pruitt","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"B95","doi-asserted-by":"publisher","first-page":"D459","DOI":"10.1093\/nar\/gkx989","article-title":"MetalPDB in 2018: a database of metal sites in biological macromolecular structures","volume":"46","author":"Putignano","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"B96","doi-asserted-by":"publisher","first-page":"329","DOI":"10.1016\/S0969-2126(02)00721-9","article-title":"Structure of acetylglutamate kinase, a key enzyme for arginine biosynthesis and a prototype for the amino acid kinase enzyme family, during catalysis","volume":"10","author":"Ram\u00f3n-Maiques","year":"2002","journal-title":"Structure"},{"key":"B97","doi-asserted-by":"publisher","first-page":"183","DOI":"10.1016\/0076-6879(95)48015-3","article-title":"[13] Evolutionary families of metallopeptidases","volume":"248","author":"Rawlings","year":"1995","journal-title":"Methods Enzymol."},{"key":"B98","doi-asserted-by":"publisher","first-page":"730","DOI":"10.1111\/mmi.12126","article-title":"The Staphylococcus aureus Opp1 ABC transporter imports nickel and cobalt in zinc-depleted conditions and contributes to virulence","volume":"87","author":"Remy","year":"2013","journal-title":"Mol. Microbiol."},{"key":"B99","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1016\/j.femsre.2004.09.002","article-title":"Some lessons from Rickettsia genomics","volume":"29","author":"Renesto","year":"2005","journal-title":"FEMS Microbiol. Rev."},{"key":"B100","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1016\/S0168-6445(03)00049-4","article-title":"Escherichia coli mechanisms of copper homeostasis in a changing environment","volume":"27","author":"Rensing","year":"2003","journal-title":"FEMS Microbiol. Rev."},{"key":"B101","doi-asserted-by":"publisher","first-page":"162","DOI":"10.1186\/1471-2164-6-162","article-title":"Assessing the precision of high-throughput computational and laboratory approaches for the genome-wide identification of protein subcellular localization in bacteria","volume":"6","author":"Rey","year":"2005","journal-title":"BMC Genomics"},{"key":"B102","doi-asserted-by":"publisher","first-page":"4172","DOI":"10.1128\/JB.185.14.4172-4185.2003","article-title":"Mycobacterium tuberculosis chaperonin 10 heptamers self-associate through their biologically active loops","volume":"185","author":"Roberts","year":"2003","journal-title":"J. Bacteriol."},{"key":"B103","doi-asserted-by":"publisher","first-page":"352","DOI":"10.2174\/138945012799424598","article-title":"Architecture and conservation of the bacterial DNA replication machinery, an underexploited drug target","volume":"13","author":"Robinson","year":"2012","journal-title":"Curr. Drug Targets"},{"key":"B104","doi-asserted-by":"publisher","first-page":"20150023","DOI":"10.1098\/rstb.2015.0023","article-title":"Outer membrane protein biogenesis in Gram-negative bacteria","volume":"370","author":"Rollauer","year":"2015","journal-title":"Philos. Trans. R. Soc. Lond., B, Biol. Sci."},{"key":"B105","doi-asserted-by":"publisher","first-page":"1299","DOI":"10.1111\/j.1432-1033.2004.04037.x","article-title":"Escherichia coli thioredoxin inhibition by cadmium: two mutually exclusive binding sites involving Cys32 and Asp26","volume":"271","author":"Rollin-Genetet","year":"2004","journal-title":"Eur. J. Biochem."},{"key":"B106","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1093\/protein\/12.2.85","article-title":"Twilight zone of protein sequence alignments","volume":"12","author":"Rost","year":"1999","journal-title":"Protein Eng."},{"key":"B107","doi-asserted-by":"publisher","first-page":"8327","DOI":"10.1128\/JB.01079-06","article-title":"Cyclic di-GMP signaling in bacteria: recent advances and new puzzles","volume":"188","author":"Ryan","year":"2006","journal-title":"J. Bacteriol."},{"key":"B108","doi-asserted-by":"publisher","first-page":"106","DOI":"10.1016\/j.chom.2012.01.009","article-title":"Copper in microbial pathogenesis: meddling with the metal","volume":"11","author":"Samanovic","year":"2012","journal-title":"Cell Host Microbe"},{"key":"B109","doi-asserted-by":"publisher","first-page":"3800","DOI":"10.1128\/jb.174.11.3800-3806.1992","article-title":"Localization of TraC, a protein involved in assembly of the F conjugative pilus","volume":"174","author":"Schandel","year":"1992","journal-title":"J. Bacteriol."},{"key":"B110","doi-asserted-by":"publisher","first-page":"182","DOI":"10.3389\/fmicb.2016.00182","article-title":"Bacterial glycosyltransferases: challenges and opportunities of a highly diverse enzyme class toward tailoring natural products","volume":"7","author":"Schmid","year":"2016","journal-title":"Front. Microbiol."},{"key":"B111","doi-asserted-by":"publisher","first-page":"863","DOI":"10.1016\/j.jmb.2009.04.046","article-title":"The three-dimensional structure of a mycobacterial DapD provides insights into DapD diversity and reveals unexpected particulars about the enzymatic mechanism","volume":"389","author":"Schuldt","year":"2009","journal-title":"J. Mol. Biol."},{"key":"B112","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1002856","article-title":"Surface proteome analysis and characterization of surface cell antigen (Sca) or autotransporter family of Rickettsia typhi","volume":"8","author":"Sears","year":"2012","journal-title":"PLoS Pathog."},{"key":"B113","doi-asserted-by":"publisher","first-page":"1047","DOI":"10.1111\/mmi.12256","article-title":"The role of zinc in the interplay between pathogenic streptococci and their hosts","volume":"88","author":"Shafeeq","year":"2013","journal-title":"Mol. Microbiol."},{"key":"B114","doi-asserted-by":"publisher","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"cytoscape: a software environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res."},{"key":"B115","doi-asserted-by":"publisher","first-page":"127","DOI":"10.1007\/s10534-017-9991-3","article-title":"Proteome wide identification of iron binding proteins of Xanthomonas translucens pv. undulosa: focus on secretory virulent proteins","volume":"30","author":"Sharma","year":"2017","journal-title":"Biometals"},{"key":"B116","doi-asserted-by":"publisher","first-page":"1838","DOI":"10.3389\/fmicb.2018.01838","article-title":"In silico study of Iron, zinc and copper binding proteins of Pseudomonas syringae pv. lapsa: emphasis on secreted metalloproteins","volume":"9","author":"Sharma","year":"2018","journal-title":"Front. Microbiol."},{"key":"B117","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1016\/j.pmpp.2019.02.005","article-title":"In silico identification of copper-binding proteins of Xanthomonas translucens pv. undulosa for their probable role in plant\u2013pathogen interactions","volume":"106","author":"Sharma","year":"2019","journal-title":"Physiol. Mol. Plant Pathol."},{"key":"B118","doi-asserted-by":"publisher","DOI":"10.1002\/jmr.2766","article-title":"Targeting metabolic pathways proteins of Orientia tsutsugamushi using combined hierarchical approach to combat scrub typhus","volume":"32","author":"Sharma","year":"2018","journal-title":"J. Mol. Recognit."},{"key":"B119","doi-asserted-by":"publisher","first-page":"19842","DOI":"10.1038\/srep19842","article-title":"Essential proteins and possible therapeutic targets of Wolbachia endosymbiont and development of FiloBase-a comprehensive drug target database for lymphatic filariasis","volume":"6","author":"Sharma","year":"2016","journal-title":"Sci. Rep."},{"key":"B120","doi-asserted-by":"publisher","first-page":"326","DOI":"10.1016\/j.jtbi.2010.01.018","article-title":"Gneg-mPLoc: a top\u2013down strategy to enhance the quality of predicting subcellular localization of Gram-negative bacterial proteins","volume":"264","author":"Shen","year":"2010","journal-title":"J. Theor. Biol."},{"key":"B121","doi-asserted-by":"publisher","DOI":"10.4155\/fsoa-2016-0066","article-title":"In silico functional elucidation of uncharacterized proteins of Chlamydia abortus strain LLG","volume":"3","author":"Singh","year":"2017","journal-title":"Future Sci. OA"},{"key":"B122","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1000949","article-title":"The battle for iron between bacterial pathogens and their vertebrate hosts","volume":"6","author":"Skaar","year":"2010","journal-title":"PLoS Pathog."},{"key":"B123","doi-asserted-by":"publisher","first-page":"1046","DOI":"10.1107\/S0907444906024541","article-title":"The cofactor-induced pre-active conformation in PhoB","volume":"62","author":"Sola","year":"2006","journal-title":"Acta Crystallogr. D. Biol. Crystallogr."},{"key":"B124","doi-asserted-by":"publisher","first-page":"6828","DOI":"10.1093\/nar\/gkg895","article-title":"Functional characterization of Helicobacter pylori DnaB helicase","volume":"31","author":"Soni","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"B125","doi-asserted-by":"publisher","first-page":"3845","DOI":"10.1128\/IAI.02025-05","article-title":"The novel Helicobacter pylori CznABC metal efflux pump is required for cadmium, zinc, and nickel resistance, urease modulation, and gastric colonization","volume":"74","author":"St\u00e4hler","year":"2006","journal-title":"Infect. Immun."},{"key":"B126","doi-asserted-by":"publisher","first-page":"8772","DOI":"10.1128\/JB.00911-07","article-title":"Analysis of promoter targets for Escherichia coli transcription elongation factor GreA in vivo and in vitro","volume":"189","author":"Stepanova","year":"2007","journal-title":"J. Bacteriol."},{"key":"B127","doi-asserted-by":"publisher","first-page":"928","DOI":"10.1039\/c3mt00126a","article-title":"Putative cobalt-and nickel-binding proteins and motifs in Streptococcus pneumoniae","volume":"5","author":"Sun","year":"2013","journal-title":"Metallomics"},{"key":"B128","doi-asserted-by":"publisher","first-page":"272","DOI":"10.1016\/j.febslet.2009.11.085","article-title":"Discovery and characterization of tRNAIle lysidine synthetase (TilS)","volume":"584","author":"Suzuki","year":"2010","journal-title":"FEBS Lett."},{"key":"B129","doi-asserted-by":"publisher","first-page":"2725","DOI":"10.1093\/molbev\/mst197","article-title":"MEGA6: molecular evolutionary genetics analysis version 6.0","volume":"30","author":"Tamura","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"B130","doi-asserted-by":"publisher","first-page":"964","DOI":"10.1016\/j.bbabio.2012.01.003","article-title":"The roles of Rhodobacter sphaeroides copper chaperones PCuAC and Sco (PrrC) in the assembly of the copper centers of the aa3-type and the cbb3-type cytochrome c oxidases","volume":"1817","author":"Thompson","year":"2012","journal-title":"Biochim. Biophys. Acta."},{"key":"B131","doi-asserted-by":"publisher","first-page":"52","DOI":"10.3389\/fcimb.2014.00052","article-title":"Ribonucleotide reductases: essential enzymes for bacterial life","volume":"4","author":"Torrents","year":"2014","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"B132","doi-asserted-by":"publisher","first-page":"2566","DOI":"10.2174\/092986709788682029","article-title":"DD-ligases as a potential target for antibiotics: past, present and future","volume":"16","author":"Tytgat","year":"2009","journal-title":"Curr. Med. Chem."},{"key":"B133","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/s00253-019-09697-z","article-title":"Function, essentiality, and expression of cytochrome P450 enzymes and their cognate redox partners in Mycobacterium tuberculosis: are they drug targets","volume":"103","author":"Ugalde","year":"2019","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"B134","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1004175","article-title":"The highly conserved bacterial RNase YbeY is essential in Vibrio cholerae, playing a critical role in virulence, stress regulation, and RNA processing","volume":"10","author":"Vercruysse","year":"2014","journal-title":"PLoS Pathog."},{"key":"B135","doi-asserted-by":"publisher","first-page":"331","DOI":"10.3389\/fmicb.2019.00331","article-title":"Cell wall hydrolases in bacteria: insight on the diversity of cell wall amidases, glycosidases and peptidases towards peptidoglycan","volume":"10","author":"Vermassen","year":"2019","journal-title":"Front. Microbiol."},{"key":"B136","doi-asserted-by":"publisher","first-page":"186","DOI":"10.3389\/fcimb.2014.00186","article-title":"Orientia tsutsugamushi ankyrin repeat-containing protein family members are type 1 secretion system substrates that traffic to the host cell endoplasmic reticulum","volume":"4","author":"VieBrock","year":"2015","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"B137","doi-asserted-by":"publisher","first-page":"181","DOI":"10.1186\/1471-2164-9-181","article-title":"Genome-wide subcellular localization of putative outer membrane and extracellular proteins in Leptospira interrogans serovar Lai genome using bioinformatics approaches","volume":"9","author":"Viratyosin","year":"2008","journal-title":"BMC Genomics"},{"key":"B138","doi-asserted-by":"publisher","first-page":"4232","DOI":"10.1128\/JB.01656-08","article-title":"The Coxiella burnetii ankyrin repeat domain-containing protein family is heterogeneous, with C-terminal truncations that influence Dot\/Icm-mediated secretion","volume":"191","author":"Voth","year":"2009","journal-title":"J. Bacteriol."},{"key":"B139","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1038\/nrmicro2057","article-title":"How do bacterial cells ensure that metalloproteins get the correct metal","volume":"7","author":"Waldron","year":"2009","journal-title":"Nat. Rev. Microbiol."},{"key":"B140","doi-asserted-by":"publisher","first-page":"913","DOI":"10.1056\/NEJMp1608499","article-title":"Scrub typhus\u2014 scientific neglect, ever-widening impact","volume":"375","author":"Walker","year":"2016","journal-title":"N. Engl. J. Med."},{"key":"B141","doi-asserted-by":"publisher","first-page":"86","DOI":"10.1016\/S0140-6736(96)02501-9","article-title":"Scrub typhus infections poorly responsive to antibiotics in northern Thailand","volume":"348","author":"Watt","year":"1996","journal-title":"Lancet"},{"key":"B142","doi-asserted-by":"publisher","first-page":"D1074","DOI":"10.1093\/nar\/gkx1037","article-title":"DrugBank 5.0: a major update to the DrugBank database for 2018","volume":"46","author":"Wishart","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"B143","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1107\/S139900471303366X","article-title":"Structures of SAICAR synthetase (PurC) from Streptococcus pneumoniae with ADP, Mg2+, AIR and Asp","volume":"70","author":"Wolf","year":"2014","journal-title":"Acta Crystallogr. D Biol. Crystallogr."},{"key":"B144","doi-asserted-by":"publisher","first-page":"24142","DOI":"10.1074\/jbc.M202467200","article-title":"Substrate-activated zinc binding of metallo-\u03b2-lactamases physiological importance of the mononuclear enzymes","volume":"277","author":"Wommer","year":"2002","journal-title":"J. Biol. Chem."},{"key":"B145","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0006062","article-title":"A review of the global epidemiology of scrub typhus","volume":"11","author":"Xu","year":"2017","journal-title":"PLoS Negl. Trop. Dis."},{"key":"B146","doi-asserted-by":"publisher","first-page":"1402","DOI":"10.1110\/ps.03479604","article-title":"Predicting subcellular localization of proteins for Gram-negative bacteria by support vector machines based on n-peptide compositions","volume":"13","author":"Yu","year":"2004","journal-title":"Protein Sci."},{"key":"B147","doi-asserted-by":"publisher","first-page":"1608","DOI":"10.1093\/bioinformatics\/btq249","article-title":"PSORTb 3.0: Improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes","volume":"26","author":"Yu","year":"2010","journal-title":"Bioinformatics"},{"key":"B148","doi-asserted-by":"publisher","first-page":"558","DOI":"10.1039\/C4MB00645C","article-title":"Predicting the subcellular localization of mycobacterial proteins by incorporating the optimal tripeptides into the general form of pseudo amino acid composition","volume":"11","author":"Zhu","year":"2015","journal-title":"Mol. Biosyst."}],"container-title":["Frontiers in Genetics"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/article\/10.3389\/fgene.2019.00797\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,9,24]],"date-time":"2019-09-24T04:48:05Z","timestamp":1569300485000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/article\/10.3389\/fgene.2019.00797\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,9,24]]},"references-count":148,"alternative-id":["10.3389\/fgene.2019.00797"],"URL":"https:\/\/doi.org\/10.3389\/fgene.2019.00797","relation":{},"ISSN":["1664-8021"],"issn-type":[{"value":"1664-8021","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,9,24]]},"article-number":"797"}}