{"id":"https://openalex.org/W4377053501","doi":"https://doi.org/10.1101/2022.12.16.520825","title":"A computational model of Pseudomonas syringae metabolism unveils the role of branched-chain amino acids in virulence expression at the early stages of Arabidopsis colonization","display_name":"A computational model of Pseudomonas syringae metabolism unveils the role of branched-chain amino acids in virulence expression at the early stages of Arabidopsis colonization","publication_year":2022,"publication_date":"2022-12-17","ids":{"openalex":"https://openalex.org/W4377053501","doi":"https://doi.org/10.1101/2022.12.16.520825"},"language":"en","primary_location":{"id":"doi:10.1101/2022.12.16.520825","doi":"https://doi.org/10.1101/2022.12.16.520825","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2022.12.16.520825","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2022/12/17/2022.12.16.520825.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","indexed_in":["crossref","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2022/12/17/2022.12.16.520825.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5014234555","display_name":"Philip J. Tubergen","orcid":"https://orcid.org/0000-0002-5077-7024","observed_orcids":["https://orcid.org/0000-0002-5077-7024"]},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Philip J. Tubergen","raw_affiliation_strings":["Department of Biology, University of Virginia, Charlottesville, VA, USA"],"raw_orcid":"https://orcid.org/0000-0002-5077-7024","affiliations":[{"raw_affiliation_string":"Department of Biology, University of Virginia, Charlottesville, VA, USA","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069219439","display_name":"Gregory L. Medlock","orcid":"https://orcid.org/0000-0002-1571-0801","observed_orcids":["https://orcid.org/0000-0002-1571-0801"]},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Greg Medlock","raw_affiliation_strings":["Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Anni Moore","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anni Moore","raw_affiliation_strings":["Department of Biology, University of Virginia, Charlottesville, VA, USA","Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA","Department of Biology and Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, University of Virginia, Charlottesville, VA, USA","institution_ids":["https://openalex.org/I51556381"]},{"raw_affiliation_string":"Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA","institution_ids":["https://openalex.org/I51556381"]},{"raw_affiliation_string":"Department of Biology and Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Xiaomu Zhang","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiaomu Zhang","raw_affiliation_strings":["Department of Biology, University of Virginia, Charlottesville, VA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, University of Virginia, Charlottesville, VA, USA","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000119406","display_name":"Jason A. Papin","orcid":"https://orcid.org/0000-0002-2769-5805","observed_orcids":["https://orcid.org/0000-0002-2769-5805"]},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jason A. Papin","raw_affiliation_strings":["Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5051994970","display_name":"Cristian H. Danna","orcid":"https://orcid.org/0000-0001-5517-9739","observed_orcids":["https://orcid.org/0000-0001-5517-9739"]},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Cristian H. Danna","raw_affiliation_strings":["Department of Biology, University of Virginia, Charlottesville, VA, USA"],"raw_orcid":"https://orcid.org/0000-0001-5517-9739","affiliations":[{"raw_affiliation_string":"Department of Biology, University of Virginia, Charlottesville, VA, USA","institution_ids":["https://openalex.org/I51556381"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5051994970"],"corresponding_institution_ids":["https://openalex.org/I51556381"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.5967000126838684,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.5967000126838684,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11578","display_name":"Plant Pathogenic Bacteria Studies","score":0.3285999894142151,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10076","display_name":"Plant-Microbe Interactions and Immunity","score":0.023900000378489494,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/pseudomonas-syringae-pv-tomato-dc3000","display_name":"Pseudomonas syringae pv. tomato DC3000","score":0.9599999785423279},{"id":"https://openalex.org/keywords/bacterial-metabolism","display_name":"bacterial metabolism","score":0.8199999928474426},{"id":"https://openalex.org/keywords/genome-scale-metabolic-reconstruction","display_name":"genome-scale metabolic reconstruction","score":0.7319999933242798},{"id":"https://openalex.org/keywords/branched-chain-amino-acids","display_name":"branched-chain amino acids","score":0.8709999918937683},{"id":"https://openalex.org/keywords/arabidopsis-thaliana","display_name":"Arabidopsis thaliana","score":0.8999999761581421},{"id":"https://openalex.org/keywords/plant-pathogen-interaction","display_name":"plant-pathogen interaction","score":0.7450000047683716},{"id":"https://openalex.org/keywords/plant-immunity","display_name":"plant immunity","score":0.6990000009536743},{"id":"https://openalex.org/keywords/gene-essentiality","display_name":"gene essentiality","score":0.7149999737739563},{"id":"https://openalex.org/keywords/metabolic-flux-analysis","display_name":"metabolic flux analysis","score":0.8019999861717224},{"id":"https://openalex.org/keywords/bacterial-colonization","display_name":"bacterial colonization","score":0.39899998903274536}],"concepts":[{"id":"https://openalex.org/C2780381237","wikidata":"https://www.wikidata.org/wiki/Q311202","display_name":"Pseudomonas syringae","level":3,"score":0.9574395418167114},{"id":"https://openalex.org/C2776927270","wikidata":"https://www.wikidata.org/wiki/Q815962","display_name":"Colonization","level":2,"score":0.8130910396575928},{"id":"https://openalex.org/C2779491563","wikidata":"https://www.wikidata.org/wiki/Q157892","display_name":"Arabidopsis","level":4,"score":0.7788373231887817},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5310673713684082},{"id":"https://openalex.org/C2775988993","wikidata":"https://www.wikidata.org/wiki/Q158695","display_name":"Arabidopsis thaliana","level":4,"score":0.4900780916213989},{"id":"https://openalex.org/C62231903","wikidata":"https://www.wikidata.org/wiki/Q1057","display_name":"Metabolism","level":2,"score":0.44841188192367554},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4069678485393524},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.30086636543273926},{"id":"https://openalex.org/C89423630","wikidata":"https://www.wikidata.org/wiki/Q7193","display_name":"Microbiology","level":1,"score":0.26647281646728516},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.21391886472702026},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","level":2,"score":0.17069044709205627},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.16903945803642273},{"id":"https://openalex.org/C143065580","wikidata":"https://www.wikidata.org/wiki/Q3285695","display_name":"Mutant","level":3,"score":0.15887528657913208}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1101/2022.12.16.520825","doi":"https://doi.org/10.1101/2022.12.16.520825","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2022.12.16.520825","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2022/12/17/2022.12.16.520825.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmh:oai:zenodo.org:7942779","doi":null,"is_oa":true,"landing_page_url":"https://zenodo.org/record/7942779","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"},{"id":"doi:10.5281/zenodo.7942778","doi":"https://doi.org/10.5281/zenodo.7942778","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.7942778","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"JournalArticle"},{"id":"doi:10.5281/zenodo.7942779","doi":"https://doi.org/10.5281/zenodo.7942779","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.7942779","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"JournalArticle"}],"best_oa_location":{"id":"doi:10.1101/2022.12.16.520825","doi":"https://doi.org/10.1101/2022.12.16.520825","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2022.12.16.520825","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2022/12/17/2022.12.16.520825.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[{"score":0.5666999816894531,"id":"https://metadata.un.org/sdg/2","display_name":"Zero hunger"}],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4377053501.pdf","grobid_xml":"https://content.openalex.org/works/W4377053501.grobid-xml"},"referenced_works_count":61,"referenced_works":["https://openalex.org/W193034086","https://openalex.org/W1581918372","https://openalex.org/W1614221105","https://openalex.org/W1924867606","https://openalex.org/W1930484445","https://openalex.org/W1975806134","https://openalex.org/W1982658095","https://openalex.org/W1987148148","https://openalex.org/W1987545960","https://openalex.org/W1996939399","https://openalex.org/W2004548026","https://openalex.org/W2011586678","https://openalex.org/W2014851585","https://openalex.org/W2019854769","https://openalex.org/W2033160598","https://openalex.org/W2041211295","https://openalex.org/W2045204781","https://openalex.org/W2051056433","https://openalex.org/W2057994970","https://openalex.org/W2085993965","https://openalex.org/W2091319608","https://openalex.org/W2095838576","https://openalex.org/W2100084634","https://openalex.org/W2103971647","https://openalex.org/W2107007801","https://openalex.org/W2115059363","https://openalex.org/W2115404289","https://openalex.org/W2116308838","https://openalex.org/W2117807796","https://openalex.org/W2131033489","https://openalex.org/W2135235433","https://openalex.org/W2138542468","https://openalex.org/W2142597537","https://openalex.org/W2146391755","https://openalex.org/W2147674484","https://openalex.org/W2149840315","https://openalex.org/W2150050125","https://openalex.org/W2151313241","https://openalex.org/W2153544866","https://openalex.org/W2160128694","https://openalex.org/W2161343058","https://openalex.org/W2161827792","https://openalex.org/W2162237022","https://openalex.org/W2162666840","https://openalex.org/W2168733762","https://openalex.org/W2202347610","https://openalex.org/W2470340022","https://openalex.org/W2553505543","https://openalex.org/W2605875623","https://openalex.org/W2773560904","https://openalex.org/W2791004613","https://openalex.org/W2791224469","https://openalex.org/W2792666293","https://openalex.org/W2890797363","https://openalex.org/W2922405027","https://openalex.org/W2931056090","https://openalex.org/W2945438038","https://openalex.org/W2950018499","https://openalex.org/W2999288267","https://openalex.org/W4280531250","https://openalex.org/W4318543008"],"related_works":["https://openalex.org/W4390264123","https://openalex.org/W4311833230","https://openalex.org/W6925257125","https://openalex.org/W2274129615","https://openalex.org/W4414382730","https://openalex.org/W1930484445","https://openalex.org/W2070807697","https://openalex.org/W2790296650","https://openalex.org/W2011586678","https://openalex.org/W2057994970"],"abstract_inverted_index":{"ABSTRACT":[0],"Leaf":[1],"mesophyll-colonizing":[2],"bacterial":[3,28,63,80,164,204,253],"pathogens":[4],"infect":[5],"their":[6,11],"plant":[7,43,53,194,241,256],"hosts":[8],"by":[9],"adjusting":[10],"metabolism":[12,81,246],"to":[13,47,62,83,238],"the":[14,20,26,100,174,180,184,192,199,202,210,218],"leaf":[15,189],"mesophyll":[16],"environment.":[17],"Soon":[18],"after":[19],"inoculation":[21],"of":[22,95,104,176,183,191,201,212,252],"na\u00efve,":[23],"susceptible":[24],"plants,":[25],"model":[27],"pathogen":[29],"Pseudomonas":[30],"syringae":[31],"pv.":[32],"tomato":[33],"DC3000":[34,66,110,245],"(":[35],"Pst":[36,65,109,244],"DC3000)":[37],"expresses":[38],"virulence":[39,69,159,177,213,226],"factors":[40],"that":[41,115,123,142,156,222],"suppress":[42,158,173],"immunity,":[44],"a":[45],"requirement":[46],"produce":[48],"robust":[49],"infections.":[50,76],"However,":[51],"if":[52],"immunity":[54,242],"was":[55],"elicited":[56],"with":[57,106],"Microbe-Associated":[58],"Molecular-Patterns":[59],"(MAMPs)":[60],"prior":[61],"inoculation,":[64],"slows":[67],"down":[68],"expression":[70,112,153,161,175,211],"and":[71,151,186,247,255],"only":[72],"produces":[73],"symptomless":[74],"mild":[75],"To":[77],"understand":[78,239],"how":[79,240],"adapts":[82],"these":[84],"two":[85],"contrasting":[86],"conditions,":[87],"we":[88],"created":[89],"iPst19,":[90],"an":[91],"in":[92,101,107,121,127,140,146,166],"silico":[93,102],"ensemble":[94],"genome-scale":[96],"metabolic":[97],"reconstructions.":[98],"Constraining":[99],"growth":[103,150,165],"iPst19":[105],"planta":[108,169],"gene":[111,152,160],"data":[113,234],"revealed":[114],"sugar":[116],"catabolism":[117,136],"is":[118,137],"highly":[119,138],"active":[120,139],"bacteria":[122,141],"have":[124,143],"been":[125,144],"inoculated":[126,145],"mock-treated":[128],"plants.":[129,148],"In":[130,168],"contrast,":[131],"branched-chain":[132],"amino":[133],"acids":[134],"(BCAAs)":[135],"MAMP-pretreated":[147],"Bacterial":[149],"analysis":[154],"showed":[155],"BCAAs":[157,172],"without":[162],"affecting":[163],"vitro.":[167],",":[170],"however,":[171],"genes":[178],"at":[179],"early":[181],"stages":[182],"infection":[185],"significantly":[187],"impair":[188],"colonization":[190],"host":[193],"Arabidopsis":[195],"thaliana":[196],".":[197],"While":[198],"overexpression":[200],"conserved":[203],"leucine-responsive":[205],"transcriptional":[206],"regulator":[207],"Lrp":[208,224,229],"induced":[209],"genes,":[214],"its":[215],"downregulation":[216],"had":[217],"opposite":[219],"effect,":[220],"suggesting":[221],"BCAA-free":[223],"induces":[225],"while":[227],"BCAA-":[228],"does":[230],"not.":[231],"Overall,":[232],"our":[233,250],"provide":[235],"mechanistic":[236],"connections":[237],"impacts":[243],"virulence,":[248],"furthering":[249],"understanding":[251],"pathogenesis":[254],"disease.":[257]},"counts_by_year":[{"year":2024,"cited_by_count":1}],"updated_date":"2026-11-05T12:25:35.769452","created_date":"2023-05-19T00:00:00"}
