{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,27]],"date-time":"2025-10-27T00:48:24Z","timestamp":1761526104849,"version":"build-2065373602"},"reference-count":51,"publisher":"Elsevier BV","issue":"10","license":[{"start":{"date-parts":[[2016,10,1]],"date-time":"2016-10-01T00:00:00Z","timestamp":1475280000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2016,10,1]],"date-time":"2016-10-01T00:00:00Z","timestamp":1475280000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2020,9,11]],"date-time":"2020-09-11T00:00:00Z","timestamp":1599782400000},"content-version":"vor","delay-in-days":1441,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["mcponline.org","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Molecular & Cellular Proteomics"],"published-print":{"date-parts":[[2016,10]]},"DOI":"10.1074\/mcp.m116.059337","type":"journal-article","created":{"date-parts":[[2016,8,3]],"date-time":"2016-08-03T22:49:11Z","timestamp":1470264551000},"page":"3220-3232","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":0,"title":["Cell-free Determination of Binary Complexes That Comprise Extended Protein-Protein Interaction Networks of Yersinia pestis"],"prefix":"10.1016","volume":"15","author":[{"given":"Sarah L.","family":"Keasey","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mohan","family":"Natesan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christine","family":"Pugh","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Teddy","family":"Kamata","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stefan","family":"Wuchty","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Robert G.","family":"Ulrich","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"78","reference":[{"key":"10.1074\/mcp.M116.059337_bib1","unstructured":".World Health Organization.(2014) Plague-Madagascar. (WHO Global Alert and Response, Disease Outbreak News). Geneva, Switzerland. Retrieved from http:\/\/www.who.int\/csr\/don\/21-november-2014-plague\/en\/,"},{"key":"10.1074\/mcp.M116.059337_bib2","first-page":"918","article-title":"Human plague \u2013 United States, 2015","volume":"64","author":"Kwit","year":"2015","journal-title":"M. M. W. R"},{"key":"10.1074\/mcp.M116.059337_bib3","doi-asserted-by":"crossref","first-page":"677","DOI":"10.1056\/NEJM199709043371004","article-title":"Multidrug resistance in Yersinia pestis mediated by a transferable plasmid","volume":"337","author":"Galimand","year":"1997","journal-title":"N. Engl. J. Med"},{"key":"10.1074\/mcp.M116.059337_bib4","doi-asserted-by":"crossref","first-page":"13826","DOI":"10.1073\/pnas.0404012101","article-title":"Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis","volume":"101","author":"Chain","year":"2004","journal-title":"Proc. Natl. Acad. Sci. U.S.A"},{"year":"2012","series-title":"Yersinia: Systems Biology and Control","author":"Carniel","key":"10.1074\/mcp.M116.059337_bib5"},{"key":"10.1074\/mcp.M116.059337_bib6","doi-asserted-by":"crossref","first-page":"686","DOI":"10.1101\/gr.4527806","article-title":"Large-scale identification of protein-protein interaction of Escherichia coli K-12","volume":"16","author":"Arifuzzaman","year":"2006","journal-title":"Genome Res"},{"key":"10.1074\/mcp.M116.059337_bib7","doi-asserted-by":"crossref","first-page":"531","DOI":"10.1038\/nature03239","article-title":"Interaction network containing conserved and essential protein complexes in Escherichia coli","volume":"433","author":"Butland","year":"2005","journal-title":"Nature"},{"key":"10.1074\/mcp.M116.059337_bib8","doi-asserted-by":"crossref","first-page":"e96","DOI":"10.1371\/journal.pbio.1000096","article-title":"Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins","volume":"7","author":"Hu","year":"2009","journal-title":"PLos Biol"},{"key":"10.1074\/mcp.M116.059337_bib9","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1038\/nbt.2831","article-title":"The binary protein-protein interaction landscape of Escherichia coli","volume":"32","author":"Rajagopala","year":"2014","journal-title":"Nat. Biotech"},{"key":"10.1074\/mcp.M116.059337_bib10","doi-asserted-by":"crossref","first-page":"e1000523","DOI":"10.1371\/journal.pcbi.1000523","article-title":"The modular organization of protein interactions in Escherichia coli","volume":"5","author":"Peregrin-Alvarez","year":"2009","journal-title":"PLoS Comp. Biol"},{"key":"10.1074\/mcp.M116.059337_bib11","doi-asserted-by":"crossref","first-page":"282","DOI":"10.1002\/pmic.200500115","article-title":"A protein network for phospholipid synthesis uncovered by a variant of the tandem affinity purification method in Escherichia coli","volume":"6","author":"Gully","year":"2006","journal-title":"Proteomics"},{"key":"10.1074\/mcp.M116.059337_bib12","doi-asserted-by":"crossref","first-page":"R130","DOI":"10.1186\/gb-2007-8-7-r130","article-title":"A proteome-wide protein interaction map for Campylobacter jejuni","volume":"8","author":"Parrish","year":"2007","journal-title":"Genome Biol"},{"key":"10.1074\/mcp.M116.059337_bib13","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1038\/35051615","article-title":"The protein-protein interaction map of Helicobacter pylori","volume":"409","author":"Rain","year":"2001","journal-title":"Nature"},{"key":"10.1074\/mcp.M116.059337_bib14","doi-asserted-by":"crossref","first-page":"2429","DOI":"10.1074\/mcp.M800160-MCP200","article-title":"In vivo interactome of Helicobacter pylori urease revealed by tandem affinity purification","volume":"7","author":"Stingl","year":"2008","journal-title":"Mol. Cell. Proteomics"},{"key":"10.1074\/mcp.M116.059337_bib15","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1093\/dnares\/dsm028","article-title":"A large scale analysis of protein-protein interactions in the nitrogen-fixing bacterium Mesorhizobium loti","volume":"15","author":"Shimoda","year":"2008","journal-title":"D. N. A. Res"},{"key":"10.1074\/mcp.M116.059337_bib16","doi-asserted-by":"crossref","first-page":"1418","DOI":"10.1021\/jm301499r","article-title":"Novel HldE-K inhibitors leading to attenuated Gram negative bacterial virulence","volume":"56","author":"Desroy","year":"2013","journal-title":"J. Med. Chem"},{"key":"10.1074\/mcp.M116.059337_bib17","doi-asserted-by":"crossref","first-page":"4569","DOI":"10.1073\/pnas.061034498","article-title":"A comprehensive two-hybrid analysis to explore the yeast protein interactome","volume":"98","author":"Ito","year":"2001","journal-title":"Proc. Natl. Acad. Sci. U.S.A"},{"key":"10.1074\/mcp.M116.059337_bib18","doi-asserted-by":"crossref","first-page":"924","DOI":"10.1074\/mcp.M800213-MCP200","article-title":"Extensive antibody cross-reactivity among infectious gram-negative bacteria revealed by proteome microarray analysis","volume":"8","author":"Keasey","year":"2009","journal-title":"Mol. Cell. Proteomics"},{"key":"10.1074\/mcp.M116.059337_bib19","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene Ontology: tool for the unification of biology. The Gene Ontology Consortium","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat. Genet"},{"key":"10.1074\/mcp.M116.059337_bib20","doi-asserted-by":"crossref","first-page":"4337","DOI":"10.1073\/pnas.0607879104","article-title":"Predicting protein-protein interactions based only on sequences information","volume":"104","author":"Shen","year":"2007","journal-title":"Proc. Natl. Acad. Sci. U.S.A"},{"key":"10.1074\/mcp.M116.059337_bib21","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1023\/A:1010933404324","article-title":"Random forests","volume":"45","author":"Breiman","year":"2001","journal-title":"Mach. Learn"},{"key":"10.1074\/mcp.M116.059337_bib22","doi-asserted-by":"crossref","first-page":"1069","DOI":"10.1038\/nmeth.2212","article-title":"A travel guide to Cytoscape plugins","volume":"9","author":"Saito","year":"2012","journal-title":"Nat. Methods"},{"key":"10.1074\/mcp.M116.059337_bib23","doi-asserted-by":"crossref","first-page":"W444","DOI":"10.1093\/nar\/gkn336","article-title":"NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways","volume":"36","author":"Brohee","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"10.1074\/mcp.M116.059337_bib24","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1186\/1471-2105-4-2","article-title":"An automated method for finding molecular complexes in large protein interaction networks","volume":"4","author":"Bader","year":"2003","journal-title":"BMC Bioinform"},{"key":"10.1074\/mcp.M116.059337_bib25","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1038\/nprot.2008.211","article-title":"Systematic and integrative analysis of large gene lists using DAVID Bioinformatics Resources","volume":"4","author":"Huang","year":"2009","journal-title":"Nat. Protoc"},{"key":"10.1074\/mcp.M116.059337_bib26","doi-asserted-by":"crossref","first-page":"D336","DOI":"10.1093\/nar\/gkv1194","article-title":"PANTHER version 10: expanded protein families and functions, and analysis tools","volume":"44","author":"Mi","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"10.1074\/mcp.M116.059337_bib27","doi-asserted-by":"crossref","first-page":"D459","DOI":"10.1093\/nar\/gkt1103","article-title":"The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway\/Genome Databases","volume":"42","author":"Caspi","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"10.1074\/mcp.M116.059337_bib28","doi-asserted-by":"crossref","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":"10.1074\/mcp.M116.059337_bib29","doi-asserted-by":"crossref","first-page":"4601","DOI":"10.1128\/JB.184.16.4601-4611.2002","article-title":"Genome sequence of Yersinia pestis KIM","volume":"184","author":"Deng","year":"2002","journal-title":"J. Bacteriol"},{"key":"10.1074\/mcp.M116.059337_bib30","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1093\/bib\/bbn019","article-title":"The relative value of operon predictions","volume":"9","author":"Brouwer","year":"2008","journal-title":"Brief. Bioinform"},{"key":"10.1074\/mcp.M116.059337_bib31","doi-asserted-by":"crossref","first-page":"e26960","DOI":"10.1371\/journal.pone.0026960","article-title":"Computational prediction of host-parasite protein interactions between Plasmodium falciparum and Homo sapiens","volume":"6","author":"Wuchty","year":"2011","journal-title":"PloS One"},{"key":"10.1074\/mcp.M116.059337_bib32","doi-asserted-by":"crossref","first-page":"412","DOI":"10.1126\/science.1173299","article-title":"Scale-free networks: a decade and beyond","volume":"325","author":"Barabasi","year":"2009","journal-title":"Science"},{"key":"10.1074\/mcp.M116.059337_bib33","doi-asserted-by":"crossref","first-page":"440","DOI":"10.1038\/30918","article-title":"Collective dynamics of \u2018small-world\u2019 networks","volume":"393","author":"Watts","year":"1998","journal-title":"Nature"},{"key":"10.1074\/mcp.M116.059337_bib34","doi-asserted-by":"crossref","first-page":"789","DOI":"10.1016\/S0092-8674(03)00427-6","article-title":"Study of the structural dynamics of the E. coli 70S ribosome using real-space refinement","volume":"113","author":"Gao","year":"2003","journal-title":"Cell"},{"key":"10.1074\/mcp.M116.059337_bib35","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1128\/AAC.48.2.525-532.2004","article-title":"New class of bacterial phenylalanyl-tRNA synthetase inhibitors with high potency and broad-spectrum activity","volume":"48","author":"Beyer","year":"2004","journal-title":"Antimicrob. Agents Chemother"},{"key":"10.1074\/mcp.M116.059337_bib36","doi-asserted-by":"crossref","first-page":"725","DOI":"10.1016\/S0960-9822(98)70282-9","article-title":"Formation of RuvABC Holliday junction complexes in vitro","volume":"8","author":"Davies","year":"1998","journal-title":"Curr. Biol"},{"key":"10.1074\/mcp.M116.059337_bib37","doi-asserted-by":"crossref","first-page":"2707","DOI":"10.1128\/AAC.00012-06","article-title":"Novel bacterial acetyl coenzyme A carboxylase inhibitors with antibiotic efficacy in vivo","volume":"50","author":"Freiberg","year":"2006","journal-title":"Antimicrob. Agents Chemother"},{"key":"10.1074\/mcp.M116.059337_bib38","doi-asserted-by":"crossref","first-page":"432","DOI":"10.1016\/j.sbi.2011.03.011","article-title":"Intrinsically disordered proteins: regulation and disease","volume":"21","author":"Babu","year":"2011","journal-title":"Curr. Opin. Struct. Biol"},{"key":"10.1074\/mcp.M116.059337_bib39","doi-asserted-by":"crossref","first-page":"W340","DOI":"10.1093\/nar\/gkt381","article-title":"Scalable web services for the PSIPRED Protein Analysis Workbench","volume":"41","author":"Buchan","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"10.1074\/mcp.M116.059337_bib40","doi-asserted-by":"crossref","first-page":"635","DOI":"10.1093\/protein\/gzr025","article-title":"Transient protein-protein interactions","volume":"24","author":"Ozbabacan","year":"2011","journal-title":"Protein Eng. Des. Sel"},{"key":"10.1074\/mcp.M116.059337_bib41","doi-asserted-by":"crossref","first-page":"3700","DOI":"10.1128\/IAI.00062-10","article-title":"Global gene expression profiling of Yersinia pestis replicating inside macrophages reveals the roles of a putative stress-induced operon in regulating type III secretion and intracellular cell division","volume":"78","author":"Fukuto","year":"2010","journal-title":"Infect. Immun"},{"key":"10.1074\/mcp.M116.059337_bib42","doi-asserted-by":"crossref","first-page":"38693","DOI":"10.1074\/jbc.M405217200","article-title":"Novel protein-protein interactions of the Yersinia pestis type III secretion system elucidated with a matrix analysis by surface plasmon resonance and mass spectrometry","volume":"279","author":"Swietnicki","year":"2004","journal-title":"J. Biol. Chem"},{"key":"10.1074\/mcp.M116.059337_bib43","doi-asserted-by":"crossref","first-page":"2763","DOI":"10.3390\/ijms10062763","article-title":"Yeast Two-Hybrid, a Powerful Tool for Systems Biology","volume":"10","author":"Bruckner","year":"2009","journal-title":"Int. J. Mol. Sci"},{"key":"10.1074\/mcp.M116.059337_bib44","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1126\/science.1188308","article-title":"Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells","volume":"329","author":"Taniguchi","year":"2010","journal-title":"Science"},{"key":"10.1074\/mcp.M116.059337_bib45","doi-asserted-by":"crossref","first-page":"678","DOI":"10.1126\/science.aac8171","article-title":"Operon structure and cotranslational subunit association direct protein assembly in bacteria","volume":"350","author":"Shieh","year":"2015","journal-title":"Science"},{"key":"10.1074\/mcp.M116.059337_bib46","doi-asserted-by":"crossref","first-page":"S388","DOI":"10.1097\/CCM.0b013e31817e3236","article-title":"Critical care medicine at Walter Reed Army Medical Center in support of the global war on terrorism","volume":"36","author":"Colombo","year":"2008","journal-title":"Crit. Care Med"},{"key":"10.1074\/mcp.M116.059337_bib47","doi-asserted-by":"crossref","first-page":"2623","DOI":"10.1128\/AAC.01374-10","article-title":"Comparative efficacies of candidate antibiotics against Yersinia pestis in an in vitro pharmacodynamic model","volume":"55","author":"Louie","year":"2011","journal-title":"Antimicrob. Agents Chemother"},{"key":"10.1074\/mcp.M116.059337_bib48","doi-asserted-by":"crossref","first-page":"57","DOI":"10.20506\/rst.31.1.2095","article-title":"Antibiotics that affect the ribosome","volume":"31","author":"Lambert","year":"2012","journal-title":"Rev. Sci. Tech"},{"key":"10.1074\/mcp.M116.059337_bib49","doi-asserted-by":"crossref","first-page":"e78216","DOI":"10.1371\/journal.pone.0078216","article-title":"Post-transcriptional regulator Hfq binds catalase HPII: Crystal structure of the complex","volume":"8","author":"Yonekura","year":"2013","journal-title":"PLoS ONE"},{"key":"10.1074\/mcp.M116.059337_bib50","doi-asserted-by":"crossref","first-page":"2034","DOI":"10.1128\/IAI.01046-09","article-title":"The small RNA chaperone Hfq is required for the virulence of Yersinia pseudotuberculosis","volume":"78","author":"Schiano","year":"2010","journal-title":"Infect. Immun"},{"key":"10.1074\/mcp.M116.059337_bib51","doi-asserted-by":"crossref","first-page":"4239","DOI":"10.1128\/JB.00504-10","article-title":"The importance of the small RNA chaperone Hfq for growth of epidemic Yersinia pestis, but not Yersinia pseudotuberculosis, with implications for plague biology","volume":"192","author":"Bai","year":"2010","journal-title":"J. Bacteriol"}],"container-title":["Molecular & Cellular Proteomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1535947620333545?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1535947620333545?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1074\/mcp.M116.059337","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,27]],"date-time":"2025-10-27T00:46:41Z","timestamp":1761526001000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1535947620333545"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,10]]},"references-count":51,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2016,10]]}},"alternative-id":["S1535947620333545"],"URL":"https:\/\/doi.org\/10.1074\/mcp.m116.059337","relation":{},"ISSN":["1535-9476"],"issn-type":[{"type":"print","value":"1535-9476"}],"subject":[],"published":{"date-parts":[[2016,10]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Cell-free Determination of Binary Complexes That Comprise Extended Protein-Protein Interaction Networks of Yersinia pestis","name":"articletitle","label":"Article Title"},{"value":"Molecular & Cellular Proteomics","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1074\/mcp.M116.059337","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2016 ASBMB. Currently published by Elsevier Inc; originally published by American Society for Biochemistry and Molecular Biology.","name":"copyright","label":"Copyright"}]}}