{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,19]],"date-time":"2026-03-19T11:44:32Z","timestamp":1773920672552,"version":"3.50.1"},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2024,5,10]],"date-time":"2024-05-10T00:00:00Z","timestamp":1715299200000},"content-version":"vor","delay-in-days":6188,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-sa\/3.0\/"}],"funder":[{"DOI":"10.13039\/501100002360","name":"Beijing Institute of Genomics, Chinese Academy of Sciences","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002360","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["30571009"],"award-info":[{"award-number":["30571009"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The cry gene family, produced during the late exponential phase of growth in Bacillus thuringiensis, is a large, still-growing family of homologous genes, in which each gene encodes a protein with strong specific activity against only one or a few insect species. Extensive studies are mostly focusing on the structural and functional relationships of Cry proteins, and have revealed several residues or domains that are important for the target recognition and receptor attachment. In this study, we have employed a maximum likelihood method to detect evidence of adaptive evolution in Cry proteins, and have identified 24 positively selected residues, which are all located in Domain II or III. Combined with known data from mutagenesis studies, the majority of these residues, at the molecular level, contribute much to the insect specificity determination. We postulate that the potential pressures driving the diversification of Cry proteins may be in an attempt to adapt for the \u201carm race\u201d between \u03b4-endotoxins and the targeted insects, or to enlarge their target spectra, hence result in the functional divergence. The sites identified to be under positive selection would provide targets for further structural and functional analyses on Cry proteins.<\/jats:p>","DOI":"10.1016\/s1672-0229(07)60020-5","type":"journal-article","created":{"date-parts":[[2007,9,23]],"date-time":"2007-09-23T11:12:24Z","timestamp":1190545944000},"page":"102-110","source":"Crossref","is-referenced-by-count":14,"title":["Adaptive Evolution of <i>Cry<\/i> Genes in <i>Bacillus Thuringiensis<\/i>: Implications for Their Specificity Determination"],"prefix":"10.1093","volume":"5","author":[{"given":"Jin-Yu","family":"Wu","sequence":"first","affiliation":[{"name":"Institute of Biomedical Informatics, Wenzhou Medical College , Wenzhou, 325000 , China"}]},{"given":"Fang-Qing","family":"Zhao","sequence":"additional","affiliation":[{"name":"Insititute of Oceanology, Chinese Academy of Sciences , Qingdao, 266071 , China"}]},{"given":"Jie","family":"Bai","sequence":"additional","affiliation":[{"name":"Institute of Biomedical Informatics, Wenzhou Medical College , Wenzhou, 325000 , China"}]},{"given":"Gang","family":"Deng","sequence":"additional","affiliation":[{"name":"Institute of Biomedical Informatics, Wenzhou Medical College , Wenzhou, 325000 , China"}]},{"given":"Song","family":"Qin","sequence":"additional","affiliation":[{"name":"Insititute of Oceanology, Chinese Academy of Sciences , Qingdao, 266071 , China"}]},{"given":"Qi-Yu","family":"Bao","sequence":"additional","affiliation":[{"name":"Institute of Biomedical Informatics, Wenzhou Medical College , Wenzhou, 325000 , China"}]}],"member":"286","published-online":{"date-parts":[[2007,9,22]]},"reference":[{"key":"2024051008232383400_bib1","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1128\/mr.53.2.242-255.1989","article-title":"Insecticidal crystal proteins of Bacillus thuringiensis","volume":"53","author":"H\u04e7fte","year":"1989","journal-title":"Microbiol. Rev."},{"key":"2024051008232383400_bib2","doi-asserted-by":"crossref","first-page":"2793","DOI":"10.1128\/jb.179.9.2793-2801.1997","article-title":"Phylogenetic relationships of Bacillus thuringiensis delta-endotoxin family proteins and their functional domains","volume":"179","author":"Bravo","year":"1997","journal-title":"J. Bacteriol."},{"key":"2024051008232383400_bib3","doi-asserted-by":"crossref","first-page":"775","DOI":"10.1128\/MMBR.62.3.775-806.1998","article-title":"Bacillus thuringiensis and its pesticidal crystal proteins","volume":"62","author":"Schnepf","year":"1998","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"2024051008232383400_bib4","doi-asserted-by":"crossref","first-page":"807","DOI":"10.1128\/MMBR.62.3.807-813.1998","article-title":"Revision of the nomenclature for the Bacillus thuringiensis pesticidal crystal proteins","volume":"62","author":"Crickmore","year":"1998","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"2024051008232383400_bib5","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1016\/j.jmb.2005.02.013","article-title":"Crystal structure of the mosquito-larvicidal toxin Cry4Ba and its biological implications","volume":"348","author":"Boonserm","year":"2005","journal-title":"J. Mol. Biol."},{"key":"2024051008232383400_bib6","doi-asserted-by":"crossref","first-page":"1617","DOI":"10.1099\/13500872-142-7-1617","article-title":"Mutagenesis of three surface-exposed loops of a Bacillus thuringiensis insecticidal toxin reveals residues important for toxicity, receptor recognition and possibly membrane insertion","volume":"142","author":"Smedley","year":"1996","journal-title":"Microbiology"},{"key":"2024051008232383400_bib7","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1016\/j.femsle.2004.11.026","article-title":"Targeted mutagenesis of loop residues in the receptor-binding domain of the Bacillus thuringiensis Cry4Ba toxin affects larvicidal activity","volume":"242","author":"Tuntitippawan","year":"2005","journal-title":"FEMS Microbiol. Lett."},{"key":"2024051008232383400_bib8","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1046\/j.1365-2958.1999.01188.x","article-title":"Domain III of the Bacillus thuringiensis delta-endotoxin Cry1Ac is involved in binding to Manduca sexta brush border membranes and to its purified aminopeptidase N","volume":"31","author":"de Maagd","year":"1999","journal-title":"Mol. Microbiol."},{"key":"2024051008232383400_bib9","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1042\/BJ20041094","article-title":"Mutations in the Bacillus thuringiensis Cry1Ca toxin demonstrate the role of domains II and III in specificity towards Spodoptera exigua larvae","volume":"384","author":"Herrero","year":"2004","journal-title":"J. Biochem."},{"key":"2024051008232383400_bib10","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1016\/S0378-1119(02)01039-9","article-title":"An algorithm for detecting directional and non-directional positive selection, neutrality and negative selection in protein coding DNA sequences","volume":"300","author":"Creevey","year":"2002","journal-title":"Gene"},{"key":"2024051008232383400_bib11","first-page":"555","article-title":"PAML: a program for package for phylogenetic analysis by maximum likelihood","volume":"13","author":"Yang","year":"1997","journal-title":"Comput. Appl. Biosci."},{"key":"2024051008232383400_bib12","doi-asserted-by":"crossref","first-page":"1041","DOI":"10.1534\/genetics.104.031153","article-title":"Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites","volume":"168","author":"Wong","year":"2004","journal-title":"Genetics"},{"key":"2024051008232383400_bib13","doi-asserted-by":"crossref","first-page":"716","DOI":"10.1109\/TAC.1974.1100705","article-title":"A new look at the statistical model identification","volume":"19","author":"Akaike","year":"1974","journal-title":"IEEE Trans. Autom. Control"},{"key":"2024051008232383400_bib14","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1016\/S1672-0229(07)60007-2","article-title":"KaKs_Calculator: calculating Ka and Ks through model selection and model averaging","volume":"4","author":"Zhang","year":"2006","journal-title":"Genomics Proteomics Bioinformatics"},{"key":"2024051008232383400_bib15","doi-asserted-by":"crossref","first-page":"496","DOI":"10.1016\/S0169-5347(00)01994-7","article-title":"Statistical methods for detecting molecular adaptation","volume":"15","author":"Yang","year":"2000","journal-title":"Trends Ecol. Evol."},{"key":"2024051008232383400_bib16","doi-asserted-by":"crossref","first-page":"426","DOI":"10.1007\/s00239-004-0137-1","article-title":"Accuracy and power of the likelihood ratio test for comparing evolutionary rates among genes","volume":"60","author":"Aagaard","year":"2005","journal-title":"J. Mol. Evol."},{"key":"2024051008232383400_bib17","doi-asserted-by":"crossref","first-page":"3179","DOI":"10.1073\/pnas.0500371102","article-title":"The power of phylogenetic comparison in revealing protein function","volume":"102","author":"Yang","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2024051008232383400_bib18","doi-asserted-by":"crossref","first-page":"1107","DOI":"10.1093\/molbev\/msi097","article-title":"Bayes empirical Bayes inference of amino acid sites under positive selection","volume":"22","author":"Yang","year":"2005","journal-title":"Mol. Biol. Evol."},{"key":"2024051008232383400_bib19","doi-asserted-by":"crossref","first-page":"1341","DOI":"10.1093\/oxfordjournals.molbev.a004195","article-title":"Host-symbiont conflicts: positive selection on an outer membrane protein of parasitic but not mutualistic Rickettsiaceae","volume":"19","author":"Jiggins","year":"2002","journal-title":"Mol. Biol. Evol."},{"key":"2024051008232383400_bib20","first-page":"178","article-title":"Protein engineering of \u03b4-endotoxins of Bacillus thuringiensis","volume":"7","author":"Saraswathy","year":"2004","journal-title":"Electron. J. Biotechnol."},{"key":"2024051008232383400_bib21","doi-asserted-by":"crossref","first-page":"4059","DOI":"10.1128\/jb.177.14.4059-4065.1995","article-title":"Mutagenesis of specificity and toxicity regions of a Bacillus thuringiensis protoxin gene","volume":"177","author":"Aronson","year":"1995","journal-title":"J. Bacteriol."},{"key":"2024051008232383400_bib22","doi-asserted-by":"crossref","first-page":"4369","DOI":"10.1128\/AEM.65.10.4369-4374.1999","article-title":"Identification of Bacillus thuringiensis delta-endotoxin Cry1C domain III amino acid residues involved in insect specificity","volume":"65","author":"de Maagd","year":"1999","journal-title":"Appl. Environ. Microbiol."},{"key":"2024051008232383400_bib23","doi-asserted-by":"crossref","first-page":"4513","DOI":"10.1128\/AEM.65.10.4513-4520.1999","article-title":"Identification of residues in domain III of Bacillus thuringiensis Cry1Ac toxin that affect binding and toxicity","volume":"65","author":"Lee","year":"1999","journal-title":"Appl. Environ. Microbiol."},{"key":"2024051008232383400_bib24","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1146\/annurev.genet.37.110801.143042","article-title":"Structure, diversity, and evolution of protein toxins from spore-forming entomopathogenic bacteria","volume":"37","author":"de Maagd","year":"2003","journal-title":"Annu. Rev. Genet."},{"key":"2024051008232383400_bib25","doi-asserted-by":"crossref","first-page":"4876","DOI":"10.1093\/nar\/25.24.4876","article-title":"The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools","volume":"25","author":"Thompson","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"2024051008232383400_bib26","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1093\/bib\/5.2.150","article-title":"MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment","volume":"5","author":"Kumar","year":"2004","journal-title":"Brief. Bioinform."},{"key":"2024051008232383400_bib27","first-page":"164","article-title":"PHYLIP\u2014phylogeny inference package (version 3.2)","volume":"5","author":"Felsenstein","year":"1989","journal-title":"Cladistics"},{"key":"2024051008232383400_bib28","doi-asserted-by":"crossref","first-page":"929","DOI":"10.1093\/genetics\/148.3.929","article-title":"Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene","volume":"148","author":"Nielsen","year":"1998","journal-title":"Genetics"},{"key":"2024051008232383400_bib29","doi-asserted-by":"crossref","first-page":"908","DOI":"10.1093\/oxfordjournals.molbev.a004148","article-title":"Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages","volume":"19","author":"Yang","year":"2002","journal-title":"Mol. Biol. Evol."},{"key":"2024051008232383400_bib30","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1186\/1471-2148-6-44","article-title":"Computing Ka and Ks with a consideration of unequal transitional substitutions","volume":"6","author":"Zhang","year":"2006","journal-title":"BMC Evol. Biol."},{"key":"2024051008232383400_bib31","doi-asserted-by":"crossref","first-page":"2714","DOI":"10.1002\/elps.1150181505","article-title":"SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling","volume":"18","author":"Guex","year":"1997","journal-title":"Electrophoresis"}],"container-title":["Genomics, Proteomics &amp; Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1672022907600205?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1672022907600205?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/academic.oup.com\/gpb\/article-pdf\/5\/2\/102\/57482831\/gpb_5_2_102.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/gpb\/article-pdf\/5\/2\/102\/57482831\/gpb_5_2_102.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,5,10]],"date-time":"2024-05-10T08:23:57Z","timestamp":1715329437000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/gpb\/article\/5\/2\/102\/7210682"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,6,1]]},"references-count":31,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2007,6,1]]}},"URL":"https:\/\/doi.org\/10.1016\/s1672-0229(07)60020-5","relation":{},"ISSN":["1672-0229","2210-3244"],"issn-type":[{"value":"1672-0229","type":"print"},{"value":"2210-3244","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2007,6]]},"published":{"date-parts":[[2007,6,1]]}}}