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dc.contributor.authorPriest, Margaret
dc.contributor.authorBorowsky, Jonathan
dc.contributor.authorYoung, Sarah K.
dc.contributor.authorLove, Kerry R.
dc.contributor.authorWhittaker, Charles A
dc.contributor.authorLove, John C
dc.contributor.authorWu, Jie
dc.contributor.authorMa, Duanduan
dc.contributor.authorShah, Kartik A
dc.contributor.authorBartlett, Mary Catherine
dc.contributor.authorLeeson, Rachel
dc.date.accessioned2017-04-07T21:05:43Z
dc.date.available2017-04-07T21:05:43Z
dc.date.issued2016-08
dc.date.submitted2016-03
dc.identifier.issn1471-2164
dc.identifier.urihttp://hdl.handle.net/1721.1/107984
dc.description.abstractBackground Pichia pastoris has emerged as an important alternative host for producing recombinant biopharmaceuticals, owing to its high cultivation density, low host cell protein burden, and the development of strains with humanized glycosylation. Despite its demonstrated utility, relatively little strain engineering has been performed to improve Pichia, due in part to the limited number and inconsistent frameworks of reported genomes and transcriptomes. Furthermore, the co-mingling of genomic, transcriptomic and fermentation data collected about Komagataella pastoris and Komagataella phaffii, the two strains co-branded as Pichia, has generated confusion about host performance for these genetically distinct species. Generation of comparative high-quality genomes and transcriptomes will enable meaningful comparisons between the organisms, and potentially inform distinct biotechnological utilies for each species. Results Here, we present a comprehensive and standardized comparative analysis of the genomic features of the three most commonly used strains comprising the tradename Pichia: K. pastoris wild-type, K. phaffii wild-type, and K. phaffii GS115. We used a combination of long-read (PacBio) and short-read (Illumina) sequencing technologies to achieve over 1000X coverage of each genome. Construction of individual genomes was then performed using as few as seven individual contigs to create gap-free assemblies. We found substantial syntenic rearrangements between the species and characterized a linear plasmid present in K. phaffii. Comparative analyses between K. phaffii genomes enabled the characterization of the mutational landscape of the GS115 strain. We identified and examined 35 non-synonomous coding mutations present in GS115, many of which are likely to impact strain performance. Additionally, we investigated transcriptomic profiles of gene expression for both species during cultivation on various carbon sources. We observed that the most highly transcribed genes in both organisms were consistently highly expressed in all three carbon sources examined. We also observed selective expression of certain genes in each carbon source, including many sequences not previously reported as promoters for expression of heterologous proteins in yeasts. Conclusions Our studies establish a foundation for understanding critical relationships between genome structure, cultivation conditions and gene expression. The resources we report here will inform and facilitate rational, organism-wide strain engineering for improved utility as a host for protein production.en_US
dc.description.sponsorshipSpace and Naval Warfare Systems Center San Diego (U.S.)en_US
dc.description.sponsorshipUnited States. Defense Advanced Research Projects Agency (Contract No. N66001-13-C-4025)en_US
dc.description.sponsorshipW. M. Keck Foundationen_US
dc.description.sponsorshipNational Cancer Institute (U.S.) (Koch Institute Support (core) Grant P30-CA14051)en_US
dc.description.sponsorshipMazumdar-Shaw International Fellowshipen_US
dc.publisherBiomed Central Ltd.en_US
dc.relation.isversionofhttp://dx.doi.org/10.1186/s12864-016-2876-yen_US
dc.rightsCreative Commons Attributionen_US
dc.sourceBioMed Centralen_US
dc.titleComparative genomics and transcriptomics of Pichia pastorisen_US
dc.typeArticleen_US
dc.identifier.citationLove, Kerry R. et al. “Comparative Genomics and Transcriptomics of Pichia Pastoris.” BMC Genomics 17.1 (2016): n. pag.en_US
dc.contributor.departmentDavid H. Koch Institute for Integrative Cancer Research at MITen_US
dc.contributor.departmentMassachusetts Institute of Technology. Department of Chemical Engineeringen_US
dc.contributor.departmentMassachusetts Institute of Technology. Department of Chemistryen_US
dc.contributor.mitauthorLove, Kerry R.
dc.contributor.mitauthorWhittaker, Charles A
dc.contributor.mitauthorLove, John C
dc.contributor.mitauthorWu, Jie
dc.contributor.mitauthorMa, Duanduan
dc.contributor.mitauthorShah, Kartik A
dc.contributor.mitauthorBartlett, Mary Catherine
dc.contributor.mitauthorLeeson, Rachel
dc.relation.journalBMC Genomicsen_US
dc.eprint.versionFinal published versionen_US
dc.type.urihttp://purl.org/eprint/type/JournalArticleen_US
eprint.statushttp://purl.org/eprint/status/PeerRevieweden_US
dc.date.updated2016-08-06T04:01:58Z
dc.language.rfc3066en
dc.rights.holderThe Author(s).
dspace.orderedauthorsLove, Kerry R.; Shah, Kartik A.; Whittaker, Charles A.; Wu, Jie; Bartlett, M. Catherine; Ma, Duanduan; Leeson, Rachel L.; Priest, Margaret; Borowsky, Jonathan; Young, Sarah K.; Love, J. Christopheren_US
dspace.embargo.termsNen_US
dc.identifier.orcidhttps://orcid.org/0000-0003-0921-3144
dc.identifier.orcidhttps://orcid.org/0000-0003-0495-4795
dc.identifier.orcidhttps://orcid.org/0000-0002-7504-2948
mit.licensePUBLISHER_CCen_US


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