{"id":"https://openalex.org/W1998296691","doi":"https://doi.org/10.1128/jb.186.23.7988-7999.2004","title":"Sequence Tolerance of the Phage \u03bb P RM Promoter: Implications for Evolution of Gene Regulatory Circuitry","display_name":"Sequence Tolerance of the Phage \u03bb P RM Promoter: Implications for Evolution of Gene Regulatory Circuitry","publication_year":2004,"publication_date":"2004-11-16","ids":{"openalex":"https://openalex.org/W1998296691","doi":"https://doi.org/10.1128/jb.186.23.7988-7999.2004","mag":"1998296691","pmid":"https://pubmed.ncbi.nlm.nih.gov/15547271","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/529058"},"language":"en","primary_location":{"id":"doi:10.1128/jb.186.23.7988-7999.2004","doi":"https://doi.org/10.1128/jb.186.23.7988-7999.2004","is_oa":false,"landing_page_url":"https://doi.org/10.1128/jb.186.23.7988-7999.2004","pdf_url":null,"source":{"id":"https://openalex.org/S133274750","display_name":"Journal of Bacteriology","issn_l":"0021-9193","issn":["0021-9193","1067-8832","1098-5530"],"is_oa":false,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-b","doyens","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2"],"host_organization":"https://openalex.org/P4310320263","host_organization_name":"American Society for Microbiology","host_organization_lineage":["https://openalex.org/P4310320263"],"host_organization_lineage_names":["American Society for Microbiology"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bacteriology","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/529058","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5113635583","display_name":"Christine B. Michalowski","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Christine B. Michalowski","raw_affiliation_strings":["Department of Biochemistry and Molecular Biophysics"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biophysics","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054661306","display_name":"Megan D. Short","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Megan D. Short","raw_affiliation_strings":["Department of Biochemistry and Molecular Biophysics"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biophysics","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5103404455","display_name":"John William Little","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I138006243","display_name":"University of Arizona","ror":"https://ror.org/03m2x1q45","country_code":"US","type":"education","lineage":["https://openalex.org/I138006243"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"John W. Little","raw_affiliation_strings":["Department of Biochemistry and Molecular Biophysics","Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biophysics","institution_ids":[]},{"raw_affiliation_string":"Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona","institution_ids":["https://openalex.org/I138006243"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5103404455"],"corresponding_institution_ids":["https://openalex.org/I138006243"],"apc_list":null,"apc_paid":null,"fwci":1.7489,"has_fulltext":false,"cited_by_count":34,"citation_normalized_percentile":{"value":0.83187653,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":87,"max":97},"biblio":{"volume":"186","issue":"23","first_page":"7988","last_page":"7999"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.8413000106811523,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.8413000106811523,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11764","display_name":"Evolution and Genetic Dynamics","score":0.09430000185966492,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.025499999523162842,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/bacteriophage-lambda","display_name":"bacteriophage lambda","score":0.8709999918937683},{"id":"https://openalex.org/keywords/ci-repressor","display_name":"cI repressor","score":0.7509999871253967},{"id":"https://openalex.org/keywords/promoter-mutagenesis","display_name":"promoter mutagenesis","score":0.671999990940094},{"id":"https://openalex.org/keywords/lysogeny","display_name":"lysogeny","score":0.7509999871253967},{"id":"https://openalex.org/keywords/prophage-induction","display_name":"prophage induction","score":0.9980000257492065}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8027138710021973},{"id":"https://openalex.org/C158448853","wikidata":"https://www.wikidata.org/wiki/Q425218","display_name":"Repressor","level":4,"score":0.7866898775100708},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.7440921068191528},{"id":"https://openalex.org/C73445445","wikidata":"https://www.wikidata.org/wiki/Q1712327","display_name":"Prophage","level":5,"score":0.6380929946899414},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.6025670766830444},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5936311483383179},{"id":"https://openalex.org/C21592294","wikidata":"https://www.wikidata.org/wiki/Q3238407","display_name":"Regulatory sequence","level":4,"score":0.5068019032478333},{"id":"https://openalex.org/C121050878","wikidata":"https://www.wikidata.org/wiki/Q5135020","display_name":"Cloning (programming)","level":2,"score":0.48808586597442627},{"id":"https://openalex.org/C136199206","wikidata":"https://www.wikidata.org/wiki/Q1148110","display_name":"Lysogenic cycle","level":5,"score":0.4569372236728668},{"id":"https://openalex.org/C16318435","wikidata":"https://www.wikidata.org/wiki/Q149299","display_name":"Mutagenesis","level":4,"score":0.44538843631744385},{"id":"https://openalex.org/C81089528","wikidata":"https://www.wikidata.org/wiki/Q5134986","display_name":"clone (Java method)","level":3,"score":0.4388159513473511},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.41104230284690857},{"id":"https://openalex.org/C2776441376","wikidata":"https://www.wikidata.org/wiki/Q165028","display_name":"Bacteriophage","level":4,"score":0.4078165292739868},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.3183773159980774},{"id":"https://openalex.org/C143065580","wikidata":"https://www.wikidata.org/wiki/Q3285695","display_name":"Mutant","level":3,"score":0.31813836097717285},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2792670726776123},{"id":"https://openalex.org/C547475151","wikidata":"https://www.wikidata.org/wiki/Q25419","display_name":"Escherichia coli","level":3,"score":0.17924049496650696},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003001","descriptor_name":"Cloning, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005809","descriptor_name":"Genes, Regulator","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010582","descriptor_name":"Bacteriophage lambda","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D039002","descriptor_name":"Prophages","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1128/jb.186.23.7988-7999.2004","doi":"https://doi.org/10.1128/jb.186.23.7988-7999.2004","is_oa":false,"landing_page_url":"https://doi.org/10.1128/jb.186.23.7988-7999.2004","pdf_url":null,"source":{"id":"https://openalex.org/S133274750","display_name":"Journal of Bacteriology","issn_l":"0021-9193","issn":["0021-9193","1067-8832","1098-5530"],"is_oa":false,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-b","doyens","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2"],"host_organization":"https://openalex.org/P4310320263","host_organization_name":"American Society for Microbiology","host_organization_lineage":["https://openalex.org/P4310320263"],"host_organization_lineage_names":["American Society for Microbiology"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bacteriology","raw_type":"journal-article"},{"id":"pmh:oai:europepmc.org:1999827","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/529058","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"Text"},{"id":"pmid:15547271","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15547271","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of bacteriology","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:529058","doi":null,"is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC529058/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"J Bacteriol","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:europepmc.org:1999827","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/529058","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"Text"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G5988882226","display_name":"Behavior of the Phage Lambda Gene regulatory Circuitry","funder_award_id":"R01GM024178","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":56,"referenced_works":["https://openalex.org/W643035040","https://openalex.org/W758067990","https://openalex.org/W1483197227","https://openalex.org/W1495116103","https://openalex.org/W1535401479","https://openalex.org/W1546783991","https://openalex.org/W1561222718","https://openalex.org/W1576795553","https://openalex.org/W1585692887","https://openalex.org/W1606928272","https://openalex.org/W1684234548","https://openalex.org/W1855493718","https://openalex.org/W1947813675","https://openalex.org/W1966192701","https://openalex.org/W1967829049","https://openalex.org/W1979159575","https://openalex.org/W1983793826","https://openalex.org/W1984657015","https://openalex.org/W1991998153","https://openalex.org/W1994926732","https://openalex.org/W1998492964","https://openalex.org/W2001715343","https://openalex.org/W2008405377","https://openalex.org/W2009875303","https://openalex.org/W2012748022","https://openalex.org/W2012847227","https://openalex.org/W2018011810","https://openalex.org/W2019460535","https://openalex.org/W2024809219","https://openalex.org/W2028544954","https://openalex.org/W2045765967","https://openalex.org/W2051449352","https://openalex.org/W2055208835","https://openalex.org/W2056484551","https://openalex.org/W2062997771","https://openalex.org/W2069982266","https://openalex.org/W2070538799","https://openalex.org/W2075375092","https://openalex.org/W2080076677","https://openalex.org/W2080973820","https://openalex.org/W2081070106","https://openalex.org/W2082148398","https://openalex.org/W2085973760","https://openalex.org/W2086976399","https://openalex.org/W2100762397","https://openalex.org/W2102334149","https://openalex.org/W2104341696","https://openalex.org/W2108210068","https://openalex.org/W2111478804","https://openalex.org/W2113495126","https://openalex.org/W2117086910","https://openalex.org/W2123992498","https://openalex.org/W2134759932","https://openalex.org/W2164927343","https://openalex.org/W2174616248","https://openalex.org/W2465977606"],"related_works":["https://openalex.org/W2108210068","https://openalex.org/W1869889887","https://openalex.org/W1998492964","https://openalex.org/W2077827578","https://openalex.org/W2088894479","https://openalex.org/W4388245502","https://openalex.org/W2108316907","https://openalex.org/W2521863855","https://openalex.org/W7073750756","https://openalex.org/W2092699911"],"abstract_inverted_index":{"Much":[0],"of":[1,6,38,57,62,80,102,134,141,154,159,181,187,207,211,213,219,232,252,269],"the":[2,15,55,59,78,122,135,160,164,176,188,197,233,240,267],"gene":[3,270],"regulatory":[4,26,199,271],"circuitry":[5,200],"phage":[7],"lambda":[8,112,198],"centers":[9],"on":[10,47],"a":[11,81,99,111,152,179,204,217],"complex":[12],"region":[13,21,40],"called":[14],"O(R)":[16,123],"region.":[17,124],"This":[18],"approximately":[19],"100-bp":[20],"is":[22,41,145,201],"densely":[23],"packed":[24],"with":[25,203],"sites,":[27],"including":[28],"two":[29],"promoters":[30,238],"and":[31,64,144,166,171,236,262],"three":[32],"repressor-binding":[33],"sites.":[34],"The":[35],"dense":[36],"packing":[37],"this":[39,107,127,173,250],"likely":[42],"to":[43,50,70,118,193,230,246],"impose":[44],"severe":[45],"constraints":[46],"its":[48,90,264],"ability":[49],"change":[51],"during":[52],"evolution,":[53],"raising":[54],"question":[56],"how":[58],"specific":[60],"arrangement":[61],"sites":[63],"their":[65,71,237,244],"exact":[66],"sequences":[67,254],"could":[68,96],"evolve":[69],"present":[72],"form.":[73],"Here":[74],"we":[75,109,129],"ask":[76],"whether":[77],"sequence":[79],"cis-acting":[82],"site":[83],"can":[84],"be":[85],"widely":[86],"varied":[87],"while":[88],"retaining":[89],"function;":[91],"if":[92],"it":[93],"can,":[94],"evolution":[95,268],"proceed":[97],"by":[98,147],"larger":[100],"number":[101],"paths.":[103],"To":[104],"help":[105],"address":[106],"question,":[108],"developed":[110],"cloning":[113],"vector":[114],"that":[115,196],"allowed":[116],"us":[117],"clone":[119],"fragments":[120,155],"spanning":[121],"By":[125],"using":[126],"vector,":[128,177],"carried":[130],"out":[131],"intensive":[132],"mutagenesis":[133],"P(RM)":[136,182,189,208],"promoter,":[137],"which":[138,157],"drives":[139],"expression":[140],"CI":[142,148],"repressor":[143],"activated":[146],"itself.":[149],"We":[150,248],"made":[151],"pool":[153,174,180],"in":[156,163,221,243,266],"8":[158],"12":[161],"positions":[162],"-35":[165],"-10":[167],"regions":[168],"were":[169,191],"randomized":[170],"cloned":[172],"into":[175],"making":[178],"variant":[183],"phage.":[184],"About":[185],"10%":[186],"variants":[190],"able":[192],"lysogenize,":[194],"suggesting":[195],"compatible":[202],"wide":[205],"range":[206,218],"sequences.":[209],"Analysis":[210],"several":[212],"these":[214],"phages":[215],"indicated":[216],"behaviors":[220],"prophage":[222],"induction.":[223],"Several":[224],"isolates":[225],"had":[226],"induction":[227],"properties":[228],"similar":[229],"those":[231],"wild":[234,241],"type,":[235],"resembled":[239],"type":[242],"responses":[245],"CI.":[247],"term":[249],"property":[251],"different":[253],"allowing":[255],"roughly":[256],"equivalent":[257],"function":[258],"\"sequence":[259],"tolerance":[260],"\"":[261],"discuss":[263],"role":[265],"circuitry.":[272]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":1}],"updated_date":"2026-11-10T11:39:43.021295","created_date":"2016-06-24T00:00:00"}
