{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,5,20]],"date-time":"2025-05-20T04:02:28Z","timestamp":1747713748477,"version":"3.40.5"},"reference-count":25,"publisher":"Springer Science and Business Media LLC","issue":"6","license":[{"start":{"date-parts":[[2025,5,9]],"date-time":"2025-05-09T00:00:00Z","timestamp":1746748800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2025,5,9]],"date-time":"2025-05-09T00:00:00Z","timestamp":1746748800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"funder":[{"DOI":"10.13039\/501100003819","name":"Natural Science Foundation of Hubei Province","doi-asserted-by":"crossref","award":["2024AFD151","2024AFD151"],"award-info":[{"award-number":["2024AFD151","2024AFD151"]}],"id":[{"id":"10.13039\/501100003819","id-type":"DOI","asserted-by":"crossref"}]},{"name":"the National Key Research and Development Program","award":["2021YFC2100400","2021YFC2100400"],"award-info":[{"award-number":["2021YFC2100400","2021YFC2100400"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"crossref","award":["32272276"],"award-info":[{"award-number":["32272276"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Arch Microbiol"],"published-print":{"date-parts":[[2025,6]]},"DOI":"10.1007\/s00203-025-04339-7","type":"journal-article","created":{"date-parts":[[2025,5,9]],"date-time":"2025-05-09T05:33:01Z","timestamp":1746768781000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Transcriptomic insights into methanol utilization in Pichia pastoris lacking AOX genes under co-feeding conditions"],"prefix":"10.1007","volume":"207","author":[{"given":"Xueyun","family":"Zheng","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhifang","family":"Ye","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiao","family":"Gao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuechuo","family":"Hao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cheng","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hongsen","family":"Xie","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ying","family":"Lin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shuli","family":"Liang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2025,5,9]]},"reference":[{"key":"4339_CR8","doi-asserted-by":"crossref","unstructured":"Bertau M, Offermanns H, Plass L, Schmidt F, Wernicke H-J (2014) Methanol: the basic chemical and energy feedstock of the future. Springer:; Vol. 1","DOI":"10.1007\/978-3-642-39709-7"},{"key":"4339_CR24","doi-asserted-by":"crossref","unstructured":"Boojari MA, Rajabi Ghaledari F, Motamedian E, Soleimani M, Shojaosadati SA (2023) Developing a metabolic model-based fed\u2010batch feeding strategy for Pichia pastoris fermentation through fine\u2010tuning of the methanol utilization pathway. Microb Biotechnol","DOI":"10.22541\/au.165397868.89805525\/v1"},{"key":"4339_CR4","doi-asserted-by":"publisher","first-page":"1781","DOI":"10.1021\/jacsau.2c00344","volume":"2","author":"JS Cho","year":"2022","unstructured":"Cho JS, Kim GB, Eun H, Moon CW, Lee SY (2022) Designing microbial cell factories for the production of chemicals. JACS Au 2:1781\u20131799","journal-title":"JACS Au"},{"key":"4339_CR20","doi-asserted-by":"publisher","first-page":"321","DOI":"10.1016\/j.jbiotec.2004.12.010","volume":"116","author":"O Cos","year":"2005","unstructured":"Cos O, Serrano A, Montesinos JL, Ferrer P, Cregg JM, Valero F (2005) Combined effect of the methanol utilization (Mut) phenotype and gene dosage on Recombinant protein production in Pichia pastoris fed-batch cultures. J Biotechnol 116:321\u2013335","journal-title":"J Biotechnol"},{"key":"4339_CR9","doi-asserted-by":"publisher","first-page":"293","DOI":"10.1042\/EBC20200138","volume":"65","author":"S De","year":"2021","unstructured":"De S, Mattanovich D, Ferrer P, Gasser B (2021) Established tools and emerging trends for the production of Recombinant proteins and metabolites in Pichia pastoris. Essays Biochem 65:293\u2013307","journal-title":"Essays Biochem"},{"key":"4339_CR7","doi-asserted-by":"publisher","first-page":"322","DOI":"10.1002\/cssc.201501013","volume":"9","author":"X-L Du","year":"2016","unstructured":"Du X-L, Jiang Z, Su DS, Wang J-Q (2016) Research progress on the indirect hydrogenation of carbon dioxide to methanol. Chemsuschem 9:322\u2013332","journal-title":"Chemsuschem"},{"key":"4339_CR11","doi-asserted-by":"publisher","first-page":"100081","DOI":"10.1016\/j.engmic.2023.100081","volume":"3","author":"Y Gan","year":"2023","unstructured":"Gan Y, Meng X, Gao C, Song W, Liu L, Chen X (2023) Metabolic engineering strategies for microbial utilization of methanol. Eng Microbiol 3:100081","journal-title":"Eng Microbiol"},{"key":"4339_CR6","doi-asserted-by":"publisher","first-page":"1066","DOI":"10.1016\/j.tibtech.2023.03.006","volume":"41","author":"F Guo","year":"2023","unstructured":"Guo F, Qiao Y, Xin F, Zhang W, Jiang M (2023) Bioconversion of C1 feedstocks for chemical production using Pichia pastoris. Trends Biotechnol 41:1066\u20131079","journal-title":"Trends Biotechnol"},{"key":"4339_CR3","doi-asserted-by":"publisher","first-page":"845","DOI":"10.1038\/s41589-021-00836-0","volume":"17","author":"W Jiang","year":"2021","unstructured":"Jiang W, Hern\u00e1ndez Villamor D, Peng H, Chen J, Liu L, Haritos V, Ledesma-Amaro R (2021) Metabolic engineering strategies to enable microbial utilization of C1 feedstocks. Nat Chem Biol 17:845\u2013855","journal-title":"Nat Chem Biol"},{"key":"4339_CR1","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1186\/s13068-023-02342-y","volume":"16","author":"Y Jin","year":"2023","unstructured":"Jin Y, Hu J, Su J, Aslan S, Lin Y, Jin L, Isaksson S, Liu C, Wang F, Schn\u00fcrer A, Sitbon F, Hofvander P, Sun C (2023) Improved bioenergy value of residual rice straw by increased lipid levels from upregulation of fatty acid biosynthesis. Biotechnol Biofuels Bioprod 16:90","journal-title":"Biotechnol Biofuels Bioprod"},{"key":"4339_CR21","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1016\/S1389-1723(00)88050-0","volume":"89","author":"K Kobayashi","year":"2000","unstructured":"Kobayashi K, Kuwae S, Ohya T, Ohda T, Ohyama M, Ohi H, Tomomitsu K, Ohmura T (2000) High-level expression of Recombinant human serum albumin from the Methylotrophic yeast Pichia pastoris with minimal protease production and activation. J Biosci Bioeng 89:55\u201361","journal-title":"J Biosci Bioeng"},{"key":"4339_CR14","doi-asserted-by":"publisher","first-page":"422","DOI":"10.3390\/jof9040422","volume":"9","author":"S Liu","year":"2023","unstructured":"Liu S, Dong H, Hong K, Meng J, Lin L, Wu X (2023) Improving methanol utilization by reducing alcohol oxidase activity and adding Co-Substrate of sodium citrate in Pichia pastoris. J Fungi 9:422","journal-title":"J Fungi"},{"key":"4339_CR10","doi-asserted-by":"publisher","first-page":"249","DOI":"10.1002\/yea.1208","volume":"22","author":"S Macauley-Patrick","year":"2005","unstructured":"Macauley-Patrick S, Fazenda ML, McNeil B, Harvey LM (2005) Heterologous protein production using the Pichia pastoris expression system. Yeast 22:249\u2013270","journal-title":"Yeast"},{"key":"4339_CR22","doi-asserted-by":"crossref","unstructured":"Mu H, Chen J, Huang W, Huang G, Deng M, Hong S, Ai P, Gao C, Zhou H (2024) OmicShare tools: A zero-code interactive online platform for biological data analysis and visualization. iMeta 3, e228","DOI":"10.1002\/imt2.228"},{"key":"4339_CR19","doi-asserted-by":"publisher","first-page":"292","DOI":"10.1111\/j.1567-1364.2011.00716.x","volume":"11","author":"R Pan","year":"2011","unstructured":"Pan R, Zhang J, Shen W-L, Tao Z-Q, Li S-P, Yan X (2011) Sequential deletion of Pichia pastoris genes by a self-excisable cassette. FEMS Yeast Res 11:292\u2013298","journal-title":"FEMS Yeast Res"},{"key":"4339_CR23","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12915-015-0186-5","volume":"13","author":"H Ru\u00dfmayer","year":"2015","unstructured":"Ru\u00dfmayer H, Buchetics M, Gruber C, Valli M, Grillitsch K, Modarres G, Guerrasio R, Klavins K, Neubauer S, Drexler H (2015) Systems-level organization of yeast Methylotrophic lifestyle. BMC Biol 13:1\u201325","journal-title":"BMC Biol"},{"key":"4339_CR17","unstructured":"Sambrook J, Fritsch EF, Maniatis T (1982) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory:; p 895\u2013909"},{"key":"4339_CR25","doi-asserted-by":"publisher","first-page":"134","DOI":"10.1016\/j.ymben.2017.06.008","volume":"42","author":"M Su\u00e1stegui","year":"2017","unstructured":"Su\u00e1stegui M, Ng CY, Chowdhury A, Sun W, Cao M, House E, Maranas CD, Shao Z (2017) Multilevel engineering of the upstream module of aromatic amino acid biosynthesis in Saccharomyces cerevisiae for high production of polymer and drug precursors. Metab Eng 42:134\u2013144","journal-title":"Metab Eng"},{"key":"4339_CR2","doi-asserted-by":"publisher","first-page":"167548","DOI":"10.1016\/j.scitotenv.2023.167548","volume":"906","author":"R Wang","year":"2024","unstructured":"Wang R, Li D, Deng F, Cao Z, Zheng G (2024) Production of artificial humic acid from rice straw for fertilizer production and soil improvement. Sci Total Environ 906:167548","journal-title":"Sci Total Environ"},{"key":"4339_CR5","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1186\/s13068-022-02210-1","volume":"15","author":"V Wegat","year":"2022","unstructured":"Wegat V, Fabarius JT, Sieber V (2022) Synthetic Methylotrophic yeasts for the sustainable fuel and chemical production. Biotechnol Biofuels Bioprod 15:113","journal-title":"Biotechnol Biofuels Bioprod"},{"key":"4339_CR18","doi-asserted-by":"publisher","first-page":"152","DOI":"10.2144\/04361DD02","volume":"36","author":"S Wu","year":"2004","unstructured":"Wu S, Letchworth GJ (2004) High efficiency transformation by electroporation of Pichia pastoris pretreated with lithium acetate and dithiothreitol. Biotechniques 36:152\u2013154","journal-title":"Biotechniques"},{"key":"4339_CR16","doi-asserted-by":"crossref","unstructured":"Wurm DJ, Spadiut O (2019) Efficient Development of a Mixed Feed Process for Pichia pastoris. In Recombinant Protein Production in Yeast, Gasser, B.; Mattanovich, D., Eds. Springer New York: New York, NY,; pp 323-333","DOI":"10.1007\/978-1-4939-9024-5_15"},{"key":"4339_CR12","doi-asserted-by":"publisher","first-page":"366","DOI":"10.1186\/s12864-022-08592-8","volume":"23","author":"Y-f Yu","year":"2022","unstructured":"Yu Y-f, Yang J, Zhao F, Lin Y, Han S (2022) Comparative transcriptome and metabolome analyses reveal the methanol dissimilation pathway of Pichia pastoris. BMC Genomics 23:366","journal-title":"BMC Genomics"},{"key":"4339_CR13","doi-asserted-by":"publisher","first-page":"foab009","DOI":"10.1093\/femsyr\/foab009","volume":"21","author":"D Zavec","year":"2021","unstructured":"Zavec D, Troyer C, Maresch D, Altmann F, Hann S, Gasser B, Mattanovich D (2021) Beyond alcohol oxidase: the Methylotrophic yeast Komagataella phaffii utilizes methanol also with its native alcohol dehydrogenase Adh2. FEMS Yeast Res 21:foab009","journal-title":"FEMS Yeast Res"},{"key":"4339_CR15","doi-asserted-by":"publisher","first-page":"210","DOI":"10.1007\/s10295-003-0035-3","volume":"30","author":"W Zhang","year":"2003","unstructured":"Zhang W, Hywood Potter KJ, Plantz BA, Schlegel VL, Smith LA, Meagher MM (2003) Pichia pastoris fermentation with mixed-feeds of glycerol and methanol: growth kinetics and production improvement. J Ind Microbiol Biotechnol 30:210\u2013215","journal-title":"J Ind Microbiol Biotechnol"}],"container-title":["Archives of Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00203-025-04339-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s00203-025-04339-7\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00203-025-04339-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,5,19]],"date-time":"2025-05-19T09:21:06Z","timestamp":1747646466000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s00203-025-04339-7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,5,9]]},"references-count":25,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2025,6]]}},"alternative-id":["4339"],"URL":"https:\/\/doi.org\/10.1007\/s00203-025-04339-7","relation":{},"ISSN":["0302-8933","1432-072X"],"issn-type":[{"type":"print","value":"0302-8933"},{"type":"electronic","value":"1432-072X"}],"subject":[],"published":{"date-parts":[[2025,5,9]]},"assertion":[{"value":"5 January 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"10 April 2025","order":2,"name":"revised","label":"Revised","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"21 April 2025","order":3,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"9 May 2025","order":4,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"This article does not contain any studies with human participants or animals performed by any of the authors.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethical approval"}},{"value":"The authors declare no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"140"}}