{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,19]],"date-time":"2026-01-19T14:35:30Z","timestamp":1768833330561,"version":"3.49.0"},"reference-count":72,"publisher":"American Society for Microbiology","issue":"4","license":[{"start":{"date-parts":[[2019,7,23]],"date-time":"2019-07-23T00:00:00Z","timestamp":1563840000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2019,8,27]],"date-time":"2019-08-27T00:00:00Z","timestamp":1566864000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/501100002920","name":"Research Grants Council, University Grants Committee","doi-asserted-by":"publisher","award":["11206514"],"award-info":[{"award-number":["11206514"]}],"id":[{"id":"10.13039\/501100002920","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007567","name":"City University of Hong Kong","doi-asserted-by":"publisher","award":["9678175"],"award-info":[{"award-number":["9678175"]}],"id":[{"id":"10.13039\/100007567","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["mSystems"],"published-print":{"date-parts":[[2019,8,27]]},"abstract":"<jats:p>\n            Microbial methane oxidation plays a fundamental role in the biogeochemical cycle of Earth\u2019s system. Recent reports have provided evidence for the acquisition of methane monooxygenases by horizontal gene transfer in methane-oxidizing bacteria from different environments, but how evolution has shaped the coding sequences to execute methanotrophy efficiently remains unexplored. In this work, we provide genomic evidence that among the different types of methanotrophs, type Ia methanotrophs possess a unique coding sequence of the\n            <jats:italic>pmoCAB<\/jats:italic>\n            operon that is under positive selection for optimal resource allocation and efficient synthesis of transcripts and proteins. This adaptive trait possibly enables type Ia methanotrophs to respond robustly to fluctuating methane availability and explains their global prevalence.\n          <\/jats:p>","DOI":"10.1128\/msystems.00342-19","type":"journal-article","created":{"date-parts":[[2019,7,22]],"date-time":"2019-07-22T13:09:12Z","timestamp":1563800952000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":11,"title":["Genomic Evidence for Simultaneous Optimization of Transcription and Translation through Codon Variants in the\n            <i>pmoCAB<\/i>\n            Operon of Type Ia Methanotrophs"],"prefix":"10.1128","volume":"4","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2216-4279","authenticated-orcid":false,"given":"Juan C.","family":"Villada","sequence":"first","affiliation":[{"name":"School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong SAR, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8598-0172","authenticated-orcid":false,"given":"Maria F.","family":"Duran","sequence":"additional","affiliation":[{"name":"School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong SAR, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0911-5317","authenticated-orcid":false,"given":"Patrick K. H.","family":"Lee","sequence":"additional","affiliation":[{"name":"School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong SAR, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"235","reference":[{"key":"e_1_3_2_2_2","doi-asserted-by":"publisher","DOI":"10.1002\/2017RG000559"},{"key":"e_1_3_2_3_2","doi-asserted-by":"publisher","DOI":"10.1002\/lno.10312"},{"key":"e_1_3_2_4_2","doi-asserted-by":"publisher","DOI":"10.1038\/ngeo2992"},{"key":"e_1_3_2_5_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41558-018-0095-z"},{"key":"e_1_3_2_6_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-017-01776-x"},{"key":"e_1_3_2_7_2","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2017.146"},{"key":"e_1_3_2_8_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2015.01346"},{"key":"e_1_3_2_9_2","doi-asserted-by":"publisher","DOI":"10.1128\/MMBR.00058-15"},{"key":"e_1_3_2_10_2","doi-asserted-by":"publisher","DOI":"10.1038\/ngeo3006"},{"key":"e_1_3_2_11_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.tim.2018.01.011"},{"key":"e_1_3_2_12_2","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2013.145"},{"key":"e_1_3_2_13_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ympev.2018.08.010"},{"key":"e_1_3_2_14_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2018.02493"},{"key":"e_1_3_2_15_2","doi-asserted-by":"publisher","DOI":"10.1093\/femsle\/fnz096"},{"key":"e_1_3_2_16_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.1257503"},{"key":"e_1_3_2_17_2","doi-asserted-by":"publisher","DOI":"10.1038\/msb.2013.32"},{"key":"e_1_3_2_18_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1518976113"},{"key":"e_1_3_2_19_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrm.2017.91"},{"key":"e_1_3_2_20_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1810022115"},{"key":"e_1_3_2_21_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature16509"},{"key":"e_1_3_2_22_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2015.07.018"},{"key":"e_1_3_2_23_2","doi-asserted-by":"publisher","DOI":"10.1038\/nsmb.2919"},{"key":"e_1_3_2_24_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2016.11.007"},{"key":"e_1_3_2_25_2","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms11334"},{"key":"e_1_3_2_26_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1606724113"},{"key":"e_1_3_2_27_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1719375115"},{"key":"e_1_3_2_28_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-6968.2011.02340.x"},{"key":"e_1_3_2_29_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.2896904"},{"key":"e_1_3_2_30_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0912989107"},{"key":"e_1_3_2_31_2","doi-asserted-by":"publisher","DOI":"10.1038\/msb.2011.14"},{"key":"e_1_3_2_32_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2015.05.035"},{"key":"e_1_3_2_33_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00239-009-9199-4"},{"key":"e_1_3_2_34_2","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.00131-10"},{"key":"e_1_3_2_35_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1219530110"},{"key":"e_1_3_2_36_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12934-015-0377-3"},{"key":"e_1_3_2_37_2","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms3785"},{"key":"e_1_3_2_38_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1619871114"},{"key":"e_1_3_2_39_2","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2012.63"},{"key":"e_1_3_2_40_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0102561"},{"key":"e_1_3_2_41_2","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms11728"},{"key":"e_1_3_2_42_2","doi-asserted-by":"publisher","DOI":"10.1128\/MMBR.63.2.479-506.1999"},{"key":"e_1_3_2_43_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1462-2920.2011.02464.x"},{"key":"e_1_3_2_44_2","doi-asserted-by":"publisher","DOI":"10.1038\/nchembio.1509"},{"key":"e_1_3_2_45_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-016-1087-9"},{"key":"e_1_3_2_46_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-018-1480-7"},{"key":"e_1_3_2_47_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.00959-15"},{"key":"e_1_3_2_48_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2017.02392"},{"key":"e_1_3_2_49_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-6968.1995.tb07834.x"},{"key":"e_1_3_2_50_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-6968.1998.tb13288.x"},{"key":"e_1_3_2_51_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1758-2229.2010.00192.x"},{"key":"e_1_3_2_52_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0959-437X(00)00143-X"},{"key":"e_1_3_2_53_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkr054"},{"key":"e_1_3_2_54_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.64.3.1091-1098.1998"},{"key":"e_1_3_2_55_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.coisb.2018.01.004"},{"key":"e_1_3_2_56_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkt919"},{"key":"e_1_3_2_57_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv1189"},{"key":"e_1_3_2_58_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2015.11.006"},{"key":"e_1_3_2_59_2","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms3304"},{"key":"e_1_3_2_60_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0066643"},{"key":"e_1_3_2_61_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv033"},{"key":"e_1_3_2_62_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv638"},{"key":"e_1_3_2_63_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.186072.114"},{"key":"e_1_3_2_64_2","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.3893"},{"key":"e_1_3_2_65_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu153"},{"key":"e_1_3_2_66_2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msx148"},{"key":"e_1_3_2_67_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-540-35306-5_10"},{"key":"e_1_3_2_68_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/15.3.1281"},{"key":"e_1_3_2_69_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkh834"},{"key":"e_1_3_2_70_2","doi-asserted-by":"publisher","DOI":"10.1016\/0378-1119(90)90491-9"},{"key":"e_1_3_2_71_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0168-9525(00)02024-2"},{"key":"e_1_3_2_72_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.1239303"},{"key":"e_1_3_2_73_2","doi-asserted-by":"publisher","DOI":"10.1093\/dnares\/dsx014"}],"container-title":["mSystems"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/mSystems.00342-19","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/mSystems.00342-19","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,3,8]],"date-time":"2022-03-08T05:51:19Z","timestamp":1646718679000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/mSystems.00342-19"}},"subtitle":[],"editor":[{"given":"Karen G.","family":"Lloyd","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2019,8,27]]},"references-count":72,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2019,8,27]]}},"alternative-id":["10.1128\/mSystems.00342-19"],"URL":"https:\/\/doi.org\/10.1128\/msystems.00342-19","relation":{},"ISSN":["2379-5077"],"issn-type":[{"value":"2379-5077","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,8,27]]},"assertion":[{"value":"2019-05-30","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2019-07-08","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2019-07-23","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e00342-19"}}