{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T05:29:15Z","timestamp":1772083755767,"version":"3.50.1"},"reference-count":51,"publisher":"Springer Science and Business Media LLC","issue":"6","license":[{"start":{"date-parts":[[2023,11,26]],"date-time":"2023-11-26T00:00:00Z","timestamp":1700956800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2023,11,26]],"date-time":"2023-11-26T00:00:00Z","timestamp":1700956800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Mol Evol"],"published-print":{"date-parts":[[2023,12]]},"DOI":"10.1007\/s00239-023-10144-x","type":"journal-article","created":{"date-parts":[[2023,11,26]],"date-time":"2023-11-26T10:01:16Z","timestamp":1700992876000},"page":"912-921","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Unusual Evolution of Cephalopod Tryptophan Indole-Lyases"],"prefix":"10.1007","volume":"91","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1581-4552","authenticated-orcid":false,"given":"Hajime Julie","family":"Yuasa","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2023,11,26]]},"reference":[{"key":"10144_CR1","doi-asserted-by":"publisher","first-page":"1711","DOI":"10.1093\/molbev\/msz093","volume":"36","author":"G Abrus\u00e1n","year":"2019","unstructured":"Abrus\u00e1n G, Marsh JA (2019) Ligand-binding-site structure shapes allosteric signal transduction and the evolution of allostery in protein complexes. Mol Biol Evol 36:1711\u20131727. https:\/\/doi.org\/10.1093\/molbev\/msz093","journal-title":"Mol Biol Evol"},{"key":"10144_CR2","doi-asserted-by":"publisher","first-page":"2427","DOI":"10.1038\/s41467-022-29748-w","volume":"13","author":"CB Albertin","year":"2022","unstructured":"Albertin CB, Medina-Ruiz S, Mitros T, Schmidbaur H, Sanchez G, Wang ZY, Grimwood J, Rosenthal JJC, Ragsdale CW, Simakov O, Rokhsar DS (2022) Genome and transcriptome mechanisms driving cephalopod evolution. Nat Commun 13:2427. https:\/\/doi.org\/10.1038\/s41467-022-29748-w","journal-title":"Nat Commun"},{"key":"10144_CR3","doi-asserted-by":"publisher","first-page":"a017996","DOI":"10.1101\/cshperspect.a017996","volume":"7","author":"DI Andersson","year":"2015","unstructured":"Andersson DI, Jerlstr\u00f6m-Hultqvist J, N\u00e4svall J (2015) Evolution of new functions de novo and from preexisting genes. Cold Spring Harb Perspect Biol 7:a017996. https:\/\/doi.org\/10.1101\/cshperspect.a017996","journal-title":"Cold Spring Harb Perspect Biol"},{"key":"10144_CR4","doi-asserted-by":"publisher","first-page":"104","DOI":"10.1126\/science.1240810","volume":"342","author":"CR Baker","year":"2013","unstructured":"Baker CR, Hanson-Smith V, Johnson AD (2013) Following gene duplication, paralog interference constrains transcriptional circuit evolution. Science 342:104\u2013108. https:\/\/doi.org\/10.1126\/science.1240810","journal-title":"Science"},{"key":"10144_CR5","doi-asserted-by":"publisher","first-page":"203","DOI":"10.1016\/j.gene.2007.04.010","volume":"396","author":"HJ Ball","year":"2007","unstructured":"Ball HJ, Sanchez-Perez A, Weiser S, Austin CJ, Astelbauer F, Miu J, McQuillan JA, Stocker R, Jermiin LS, Hunt NH (2007) Characterization of an indoleamine 2,3-dioxygenase-like protein found in humans and mice. Gene 396:203\u2013213. https:\/\/doi.org\/10.1016\/j.gene.2007.04.010","journal-title":"Gene"},{"key":"10144_CR6","doi-asserted-by":"publisher","first-page":"2156","DOI":"10.3390\/microorganisms9102156","volume":"9","author":"BR Boya","year":"2021","unstructured":"Boya BR, Kumar P, Lee JH, Lee J (2021) Diversity of the tryptophanase gene and its evolutionary implications in living organisms. Microorganisms 9:2156. https:\/\/doi.org\/10.3390\/microorganisms9102156","journal-title":"Microorganisms"},{"key":"10144_CR7","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1111\/j.1365-2958.2006.05481.x","volume":"63","author":"EL Chant","year":"2007","unstructured":"Chant EL, Summers DK (2007) Indole signalling contributes to the stable maintenance of Escherichia coli multicopy plasmids. Mol Microbiol 63:35\u201343. https:\/\/doi.org\/10.1111\/j.1365-2958.2006.05481.x","journal-title":"Mol Microbiol"},{"key":"10144_CR8","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1007\/s10482-006-9097-3","volume":"91","author":"A Collet","year":"2007","unstructured":"Collet A, Vilain S, Cosette P, Junter GA, Jouenne T, Phillips RS, Di Martino P (2007) Protein expression in Escherichia coli S17\u20131 biofilms: impact of indole. Antonie Van Leeuwenhoek 91:71\u201385. https:\/\/doi.org\/10.1007\/s10482-006-9097-3","journal-title":"Antonie Van Leeuwenhoek"},{"key":"10144_CR9","doi-asserted-by":"publisher","first-page":"938","DOI":"10.1038\/nrg2482","volume":"9","author":"GC Conant","year":"2008","unstructured":"Conant GC, Wolfe KH (2008) Turning a hobby into a job: how duplicated genes find new functions. Nat Rev Genet 9:938\u2013950. https:\/\/doi.org\/10.1038\/nrg2482","journal-title":"Nat Rev Genet"},{"key":"10144_CR10","doi-asserted-by":"publisher","first-page":"1792","DOI":"10.1093\/nar\/gkh340","volume":"32","author":"RC Edgar","year":"2004","unstructured":"Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792\u20131797. https:\/\/doi.org\/10.1093\/nar\/gkh340","journal-title":"Nucleic Acids Res"},{"key":"10144_CR11","doi-asserted-by":"publisher","first-page":"e2018731118","DOI":"10.1073\/pnas.2018731118","volume":"118","author":"JR Emlaw","year":"2021","unstructured":"Emlaw JR, Tessier CJG, McCluskey GD, McNulty MS, Sheikh Y, Burkett KM, Musgaard M, daCosta CJB (2021) A single historical substitution drives an increase in acetylcholine receptor complexity. Proc Natl Acad Sci USA 118:e2018731118. https:\/\/doi.org\/10.1073\/pnas.2018731118","journal-title":"Proc Natl Acad Sci USA"},{"key":"10144_CR12","doi-asserted-by":"publisher","first-page":"360","DOI":"10.1038\/nature10724","volume":"481","author":"GC Finnigan","year":"2012","unstructured":"Finnigan GC, Hanson-Smith V, Stevens TH, Thornton JW (2012) Evolution of increased complexity in a molecular machine. Nature 481:360\u2013364. https:\/\/doi.org\/10.1038\/nature10724","journal-title":"Nature"},{"key":"10144_CR13","doi-asserted-by":"publisher","first-page":"603","DOI":"10.1006\/jmbi.1997.1561","volume":"276","author":"MN Isupov","year":"1988","unstructured":"Isupov MN, Antson AA, Dodson EJ, Dodson GG, Dementieva IS, Zakomirdina LN, Wilson KS, Dauter Z, Lebedev AA, Harutyunyan EH (1988) Crystal structure of tryptophanase. J Mol Biol 276:603\u2013623. https:\/\/doi.org\/10.1006\/jmbi.1997.1561","journal-title":"J Mol Biol"},{"key":"10144_CR14","doi-asserted-by":"publisher","first-page":"814","DOI":"10.1016\/j.tplants.2015.10.003","volume":"20","author":"E Kaltenegger","year":"2015","unstructured":"Kaltenegger E, Ober D (2015) Paralogue interference affects the dynamics after gene duplication. Trends Plant Sci 20:814\u2013821. https:\/\/doi.org\/10.1016\/j.tplants.2015.10.003","journal-title":"Trends Plant Sci"},{"key":"10144_CR15","doi-asserted-by":"publisher","first-page":"D563","DOI":"10.1093\/nar\/gkp871","volume":"38","author":"PJ Kersey","year":"2010","unstructured":"Kersey PJ, Lawson D, Birney E, Derwent PS, Haimel M, Herrero J, Keenan S, Kerhornou A, Koscielny G, K\u00e4h\u00e4ri A, Kinsella RJ, Kulesha E, Maheswari U, Megy K, Nuhn M, Proctor G, Staines D, Valentin F, Vilella AJ, Yates A (2010) Ensembl Genomes: extending Ensembl across the taxonomic space. Nucleic Acids Res 38:D563-569. https:\/\/doi.org\/10.1093\/nar\/gkp871","journal-title":"Nucleic Acids Res"},{"key":"10144_CR16","doi-asserted-by":"publisher","first-page":"286","DOI":"10.1107\/S2053230X15000850","volume":"71","author":"A Kogan","year":"2015","unstructured":"Kogan A, Raznov L, Gdalevsky GY, Cohen-Luria R, Almog O, Parola AH, Goldgur Y (2015) Structures of Escherichia coli tryptophanase in holo and \u201csemi-holo\u201d forms. Acta Crystallogr F Struct Biol Commun 71:286\u2013290. https:\/\/doi.org\/10.1107\/S2053230X15000850","journal-title":"Acta Crystallogr F Struct Biol Commun"},{"key":"10144_CR17","doi-asserted-by":"publisher","first-page":"814","DOI":"10.1107\/S0907444906019895","volume":"62","author":"SY Ku","year":"2006","unstructured":"Ku SY, Yip P, Howell PL (2006) Structure of Escherichia coli tryptophanase. Acta Crystallogr D Biol Crystallogr 62:814\u2013823. https:\/\/doi.org\/10.1107\/S0907444906019895","journal-title":"Acta Crystallogr D Biol Crystallogr"},{"key":"10144_CR18","doi-asserted-by":"publisher","first-page":"1307","DOI":"10.1093\/molbev\/msn067","volume":"25","author":"SQ Le","year":"2008","unstructured":"Le SQ, Gascuel O (2008) An improved general amino acid replacement matrix. Mol Biol Evol 25:1307\u20131320. https:\/\/doi.org\/10.1093\/molbev\/msn067","journal-title":"Mol Biol Evol"},{"key":"10144_CR19","doi-asserted-by":"publisher","first-page":"1703","DOI":"10.1128\/AEM.02081-08","volume":"75","author":"J Lee","year":"2009","unstructured":"Lee J, Maeda T, Hong SH, Wood TK (2009) Reconfiguring the quorum-sensing regulator SdiA of Escherichia coli to control biofilm formation via indole and N-acylhomoserine lactones. Appl Environ Microbiol 75:1703\u20131716. https:\/\/doi.org\/10.1128\/AEM.02081-08","journal-title":"Appl Environ Microbiol"},{"key":"10144_CR20","doi-asserted-by":"publisher","first-page":"82","DOI":"10.1038\/nature09354","volume":"467","author":"HH Lee","year":"2010","unstructured":"Lee HH, Molla MN, Cantor CR, Collins JJ (2010) Bacterial charity work leads to population-wide resistance. Nature 467:82\u201385. https:\/\/doi.org\/10.1038\/nature09354","journal-title":"Nature"},{"key":"10144_CR21","doi-asserted-by":"publisher","first-page":"e1008145","DOI":"10.1371\/journal.pcbi.1008145","volume":"16","author":"S Mallik","year":"2020","unstructured":"Mallik S, Tawfik DS (2020) Determining the interaction status and evolutionary fate of duplicated homomeric proteins. PLoS Comput Biol 16:e1008145. https:\/\/doi.org\/10.1371\/journal.pcbi.1008145","journal-title":"PLoS Comput Biol"},{"key":"10144_CR22","doi-asserted-by":"publisher","DOI":"10.1016\/j.gde.2022.101966","volume":"76","author":"S Mallik","year":"2022","unstructured":"Mallik S, Tawfik DS, Levy ED (2022) How gene duplication diversifies the landscape of protein oligomeric state and function. Curr Opin Genet Dev 76:101966. https:\/\/doi.org\/10.1016\/j.gde.2022.101966","journal-title":"Curr Opin Genet Dev"},{"key":"10144_CR23","doi-asserted-by":"publisher","first-page":"443","DOI":"10.1139\/w03-056","volume":"49","author":"PD Martino","year":"2003","unstructured":"Martino PD, Fursy R, Bret L, Sundararaju B, Phillips RS (2003) Indole can act as an extracellular signal to regulate biofilm formation of Escherichia coli and other indole-producing bacteria. Can J Microbiol 49:443\u2013449. https:\/\/doi.org\/10.1139\/w03-056","journal-title":"Can J Microbiol"},{"key":"10144_CR24","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1186\/1757-4749-4-5","volume":"4","author":"E Nikaido","year":"2012","unstructured":"Nikaido E, Giraud E, Baucheron S, Yamasaki S, Wiedemann A, Okamoto K, Takagi T, Yamaguchi A, Cloeckaert A, Nishino K (2012) Effects of indole on drug resistance and virulence of Salmonella enterica serovar Typhimurium revealed by genome-wide analyses. Gut Pathog 4:5. https:\/\/doi.org\/10.1186\/1757-4749-4-5","journal-title":"Gut Pathog"},{"key":"10144_CR25","doi-asserted-by":"publisher","first-page":"243","DOI":"10.1007\/s12010-014-1263-x","volume":"175","author":"T Nuidate","year":"2015","unstructured":"Nuidate T, Tansila N, Chomchuen P, Phattaranit P, Eangchuan S, Vuddhakul V (2015) Characterization of tryptophanase from Vibrio cholerae. Appl Biochem Biotechnol 175:243\u2013252. https:\/\/doi.org\/10.1007\/s12010-014-1263-x","journal-title":"Appl Biochem Biotechnol"},{"key":"10144_CR26","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-642-86659-3","volume-title":"Evolution by gene duplication","author":"S Ohno","year":"1970","unstructured":"Ohno S (1970) Evolution by gene duplication. Springer, Berlin"},{"key":"10144_CR27","doi-asserted-by":"publisher","first-page":"1605","DOI":"10.1002\/jcc.20084","volume":"25","author":"EF Pettersen","year":"2004","unstructured":"Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) UCSF Chimera\u2013 a visualization system for exploratory research and analysis. J Comput Chem 25:1605\u20131612. https:\/\/doi.org\/10.1002\/jcc.20084","journal-title":"J Comput Chem"},{"key":"10144_CR28","doi-asserted-by":"publisher","first-page":"4012","DOI":"10.1021\/bi015838t","volume":"41","author":"RS Phillips","year":"2002","unstructured":"Phillips RS, Johnson N, Kamath AV (2002) Formation in vitro of hybrid dimers of H463F and Y74F mutant Escherichia coli tryptophan indole-lyase rescues activity with L-tryptophan. Biochemistry 41:4012\u20134019. https:\/\/doi.org\/10.1021\/bi015838t","journal-title":"Biochemistry"},{"key":"10144_CR29","doi-asserted-by":"publisher","first-page":"198","DOI":"10.1016\/j.bioorg.2014.06.002","volume":"57","author":"RS Phillips","year":"2014","unstructured":"Phillips RS, Demidkina TV, Faleev NG (2014) The role of substrate strain in the mechanism of the carbon-carbon lyases. Bioorg Chem 57:198\u2013205. https:\/\/doi.org\/10.1016\/j.bioorg.2014.06.002","journal-title":"Bioorg Chem"},{"key":"10144_CR30","doi-asserted-by":"publisher","first-page":"503","DOI":"10.1016\/s1046-5928(02)00024-4","volume":"25","author":"DV Rial","year":"2002","unstructured":"Rial DV, Ceccarelli EA (2002) Removal of DnaK contamination during fusion protein purifications. Protein Expr Purif 25:503\u2013507. https:\/\/doi.org\/10.1016\/s1046-5928(02)00024-4","journal-title":"Protein Expr Purif"},{"key":"10144_CR31","doi-asserted-by":"publisher","first-page":"4260","DOI":"10.1128\/AEM.00166-10","volume":"76","author":"T Sasaki-Imamura","year":"2010","unstructured":"Sasaki-Imamura T, Yano A, Yoshida Y (2010) Production of indole from L-tryptophan and effects of these compounds on biofilm formation by Fusobacterium nucleatum ATCC 25586. Appl Environ Microbiol 76:4260\u20134268. https:\/\/doi.org\/10.1128\/AEM.00166-10","journal-title":"Appl Environ Microbiol"},{"key":"10144_CR32","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1111\/j.1574-6968.2011.02329.x","volume":"322","author":"T Sasaki-Imamura","year":"2011","unstructured":"Sasaki-Imamura T, Yoshida Y, Suwabe K, Yoshimura F, Kato H (2011) Molecular basis of indole production catalyzed by tryptophanase in the genus Prevotella. FEMS Microbiol Lett 322:51\u201359. https:\/\/doi.org\/10.1111\/j.1574-6968.2011.02329.x","journal-title":"FEMS Microbiol Lett"},{"key":"10144_CR33","doi-asserted-by":"publisher","first-page":"102339","DOI":"10.1016\/j.sbi.2022.102339","volume":"73","author":"L Schulz","year":"2022","unstructured":"Schulz L, Sendker FL, Hochberg GKA (2022) Non-adaptive complexity and biochemical function. Curr Opin Struct Biol 73:102339. https:\/\/doi.org\/10.1016\/j.sbi.2022.102339","journal-title":"Curr Opin Struct Biol"},{"key":"10144_CR34","doi-asserted-by":"publisher","first-page":"686","DOI":"10.1016\/j.protis.2017.09.003","volume":"168","author":"M Sugiura","year":"2017","unstructured":"Sugiura M, Yuasa HJ, Harumoto T (2017) Novel specificity of IDO enzyme involved in the biosynthesis of mating pheromone in the ciliate Blepharisma stoltei. Protist 168:686\u2013696. https:\/\/doi.org\/10.1016\/j.protis.2017.09.003","journal-title":"Protist"},{"key":"10144_CR35","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1080\/1120009X.2019.1678913","volume":"32","author":"F Sun","year":"2020","unstructured":"Sun F, Yuan Q, Wang Y, Cheng L, Li X, Feng W, Xia P (2020) Sub-minimum inhibitory concentration ceftazidime inhibits Escherichia coli biofilm formation by influencing the levels of the ibpA gene and extracellular indole. J Chemother 32:7\u201314. https:\/\/doi.org\/10.1080\/1120009X.2019.1678913","journal-title":"J Chemother"},{"key":"10144_CR36","doi-asserted-by":"publisher","first-page":"3022","DOI":"10.1093\/molbev\/msab120","volume":"38","author":"K Tamura","year":"2021","unstructured":"Tamura K, Stecher G, Kumar S (2021) MEGA11: molecular evolutionary genetics analysis version 11. Mol Biol Evol 38:3022\u20133027. https:\/\/doi.org\/10.1093\/molbev\/msab120","journal-title":"Mol Biol Evol"},{"key":"10144_CR37","doi-asserted-by":"publisher","first-page":"20162818","DOI":"10.1098\/rspb.2016.2818","volume":"284","author":"AR Tanner","year":"2017","unstructured":"Tanner AR, Fuchs D, Winkelmann IE, Gilbert MT, Pankey MS, Ribeiro \u00c2M, Kocot KM, Halanych KM, Oakley TH, da Fonseca RR, Pisani D, Vinther J (2017) Molecular clocks indicate turnover and diversification of modern coleoid cephalopods during the mesozoic marine revolution. Proc Biol Sci 284:20162818. https:\/\/doi.org\/10.1098\/rspb.2016.2818","journal-title":"Proc Biol Sci"},{"key":"10144_CR38","doi-asserted-by":"publisher","first-page":"1589","DOI":"10.1007\/pl00012485","volume":"59","author":"S Walter","year":"2002","unstructured":"Walter S (2002) Structure and function of the GroE chaperone. Cell Mol Life Sci 59:1589\u20131597. https:\/\/doi.org\/10.1007\/pl00012485","journal-title":"Cell Mol Life Sci"},{"key":"10144_CR39","doi-asserted-by":"publisher","first-page":"968","DOI":"10.1099\/mic.0.024174-0","volume":"155","author":"Y Yoshida","year":"2009","unstructured":"Yoshida Y, Sasaki T, Ito S, Tamura H, Kunimatsu K, Kato H (2009) Identification and molecular characterization of tryptophanase encoded by tnaA in Porphyromonas gingivalis. Microbiology 155:968\u2013978. https:\/\/doi.org\/10.1099\/mic.0.024174-0","journal-title":"Microbiology"},{"key":"10144_CR40","doi-asserted-by":"publisher","first-page":"3651","DOI":"10.1111\/febs.13834","volume":"283","author":"HJ Yuasa","year":"2016","unstructured":"Yuasa HJ (2016) High l-Trp affinity of indoleamine 2,3-dioxygenase 1 is attributed to two residues located in the distal heme pocket. FEBS J 283:3651\u20133661. https:\/\/doi.org\/10.1111\/febs.13834","journal-title":"FEBS J"},{"key":"10144_CR41","doi-asserted-by":"publisher","first-page":"140247","DOI":"10.1016\/j.bbapap.2019.06.014","volume":"1868","author":"HJ Yuasa","year":"2020","unstructured":"Yuasa HJ (2020) A comprehensive comparison of the metazoan tryptophan degrading enzymes. Biochim Biophys Acta Proteins Proteom 1868:140247. https:\/\/doi.org\/10.1016\/j.bbapap.2019.06.014","journal-title":"Biochim Biophys Acta Proteins Proteom"},{"key":"10144_CR42","doi-asserted-by":"publisher","first-page":"110801","DOI":"10.1016\/j.cbpb.2022.110801","volume":"263","author":"HJ Yuasa","year":"2023","unstructured":"Yuasa HJ (2023) Metazoan tryptophan indole-lyase: are they still active? Comp Biochem Physiol B Biochem Mol Biol 263:110801. https:\/\/doi.org\/10.1016\/j.cbpb.2022.110801","journal-title":"Comp Biochem Physiol B Biochem Mol Biol"},{"key":"10144_CR43","doi-asserted-by":"publisher","first-page":"64","DOI":"10.1016\/j.gene.2012.04.082","volume":"501","author":"HJ Yuasa","year":"2012","unstructured":"Yuasa HJ, Ball HJ (2012) The evolution of three types of indoleamine 2,3 dioxygenases in fungi with distinct molecular and biochemical characteristics. Gene 501:64\u201374. https:\/\/doi.org\/10.1016\/j.gene.2012.04.082","journal-title":"Gene"},{"key":"10144_CR44","doi-asserted-by":"publisher","first-page":"98","DOI":"10.1016\/j.fgb.2013.03.003","volume":"56","author":"HJ Yuasa","year":"2013","unstructured":"Yuasa HJ, Ball HJ (2013) Indoleamine 2,3-dioxygenases with very low catalytic activity are well conserved across kingdoms: IDOs of Basidiomycota. Fungal Genet Biol 56:98\u2013106. https:\/\/doi.org\/10.1016\/j.fgb.2013.03.003","journal-title":"Fungal Genet Biol"},{"key":"10144_CR45","doi-asserted-by":"publisher","first-page":"128","DOI":"10.1002\/jez.b.22608","volume":"324","author":"HJ Yuasa","year":"2015","unstructured":"Yuasa HJ, Ball HJ (2015) Efficient tryptophan-catabolizing activity is consistently conserved through evolution of TDO enzymes, but not IDO enzymes. J Exp Zool B Mol Dev Evol 324:128\u2013140. https:\/\/doi.org\/10.1002\/jez.b.22608","journal-title":"J Exp Zool B Mol Dev Evol"},{"key":"10144_CR46","doi-asserted-by":"publisher","first-page":"705","DOI":"10.1007\/s00239-007-9049-1","volume":"65","author":"HJ Yuasa","year":"2007","unstructured":"Yuasa HJ, Takubo M, Takahashi A, Hasegawa T, Noma H, Suzuki T (2007) Evolution of vertebrate indoleamine 2,3-dioxygenases. J Mol Evol 65:705\u2013714. https:\/\/doi.org\/10.1007\/s00239-007-9049-1","journal-title":"J Mol Evol"},{"key":"10144_CR47","doi-asserted-by":"publisher","first-page":"2735","DOI":"10.1111\/febs.13316","volume":"282","author":"HJ Yuasa","year":"2015","unstructured":"Yuasa HJ, Mizuno K, Ball HJ (2015) Low efficiency IDO2 enzymes are conserved in lower vertebrates, whereas higher efficiency IDO1 enzymes are dispensable. FEBS J 282:2735\u20132745. https:\/\/doi.org\/10.1111\/febs.13316","journal-title":"FEBS J"},{"key":"10144_CR48","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.abb.2017.12.019","volume":"640","author":"HJ Yuasa","year":"2018","unstructured":"Yuasa HJ, Sugiura M, Harumoto T (2018) A single amino acid residue regulates the substrate affinity and specificity of indoleamine 2,3-dioxygenase. Arch Biochem Biophys 640:1\u20139. https:\/\/doi.org\/10.1016\/j.abb.2017.12.019","journal-title":"Arch Biochem Biophys"},{"key":"10144_CR49","doi-asserted-by":"publisher","first-page":"1189","DOI":"10.1023\/a:1020975610046","volume":"67","author":"LN Zakomirdina","year":"2002","unstructured":"Zakomirdina LN, Kulikova VV, Gogoleva OI, Dementieva IS, Faleev NG, Demidkina TV (2002) Tryptophan indole-lyase from Proteus vulgaris: kinetic and spectral spectral properties. Biochemistry (mosc) 67:1189\u20131196. https:\/\/doi.org\/10.1023\/a:1020975610046","journal-title":"Biochemistry (mosc)"},{"key":"10144_CR50","doi-asserted-by":"publisher","first-page":"108673","DOI":"10.1016\/j.celrep.2020.108673","volume":"34","author":"T Zelante","year":"2021","unstructured":"Zelante T, Choera T, Beauvais A, Fallarino F, Paolicelli G, Pieraccini G, Pieroni M, Galosi C, Beato C, De Luca A, Boscaro F, Romoli R, Liu X, Warris A, Verweij PE, Ballard E, Borghi M, Pariano M, Costantino G, Calvitti M, Vacca C, Oikonomou V, Gargaro M, Wong AYW, Boon L, den Hartog M, Sp\u00e1\u010dil Z, Puccetti P, Latg\u00e8 JP, Keller NP, Romani L (2021) Aspergillus fumigatus tryptophan metabolic route differently affects host immunity. Cell Rep 34:108673. https:\/\/doi.org\/10.1016\/j.celrep.2020.108673","journal-title":"Cell Rep"},{"key":"10144_CR51","doi-asserted-by":"publisher","first-page":"292","DOI":"10.1016\/S0169-5347(03)00033-8","volume":"18","author":"J Zhang","year":"2003","unstructured":"Zhang J (2003) Evolution by gene duplication: an update. Trends Ecol Evol 18:292\u2013298. https:\/\/doi.org\/10.1016\/S0169-5347(03)00033-8","journal-title":"Trends Ecol Evol"}],"container-title":["Journal of Molecular Evolution"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00239-023-10144-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s00239-023-10144-x\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00239-023-10144-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,12,20]],"date-time":"2023-12-20T02:05:12Z","timestamp":1703037912000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s00239-023-10144-x"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,11,26]]},"references-count":51,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2023,12]]}},"alternative-id":["10144"],"URL":"https:\/\/doi.org\/10.1007\/s00239-023-10144-x","relation":{},"ISSN":["0022-2844","1432-1432"],"issn-type":[{"value":"0022-2844","type":"print"},{"value":"1432-1432","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,11,26]]},"assertion":[{"value":"17 July 2023","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"7 November 2023","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"26 November 2023","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The author declares no conflict of interest.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of interest"}}]}}