OPENPichia: licence-free Komagataella phaffii chassis strains and toolkit for protein expression.
Journal
Nature microbiology
ISSN: 2058-5276
Titre abrégé: Nat Microbiol
Pays: England
ID NLM: 101674869
Informations de publication
Date de publication:
Mar 2024
Mar 2024
Historique:
received:
23
03
2023
accepted:
01
12
2023
medline:
6
3
2024
pubmed:
6
3
2024
entrez:
5
3
2024
Statut:
ppublish
Résumé
The industrial yeast Komagataella phaffii (formerly named Pichia pastoris) is commonly used to synthesize recombinant proteins, many of which are used as human therapeutics or in food. However, the basic strain, named NRRL Y-11430, from which all commercial hosts are derived, is not available without restrictions on its use. Comparative genome sequencing leaves little doubt that NRRL Y-11430 is derived from a K. phaffii type strain deposited in the UC Davis Phaff Yeast Strain Collection in 1954. We analysed four equivalent type strains in several culture collections and identified the NCYC 2543 strain, from which we started to develop an open-access Pichia chassis strain that anyone can use to produce recombinant proteins to industry standards. NRRL Y-11430 is readily transformable, which we found to be due to a HOC1 open-reading-frame truncation that alters cell-wall mannan. We introduced the HOC1 open-reading-frame truncation into NCYC 2543, which increased the transformability and improved secretion of some but not all of our tested proteins. We provide our genome-sequenced type strain, the hoc1
Identifiants
pubmed: 38443579
doi: 10.1038/s41564-023-01574-w
pii: 10.1038/s41564-023-01574-w
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
864-876Informations de copyright
© 2024. The Author(s).
Références
Karbalaei, M., Rezaee, S. A. & Farsiani, H. Pichia pastoris: a highly successful expression system for optimal synthesis of heterologous proteins. J. Cell. Physiol. https://doi.org/10.1002/jcp.29583 (2020).
Adivitiya, Dagar, V. K. & Khasa, Y. P. in Yeast Diversity in Human Welfare (eds Satyanarayana, T. & Kunze, G.) 215–250 (Springer, 2017).
Yang, Z. & Zhang, Z. Engineering strategies for enhanced production of protein and bio-products in Pichia pastoris: a review. Biotechnol. Adv. 36, 182–195 (2018).
pubmed: 29129652
doi: 10.1016/j.biotechadv.2017.11.002
Phaff, H. J., Miller, M. W. & Shifrine, M. The taxonomy of yeasts isolated from Drosophila in the Yosemite region of California. Antonie van Leeuwenhoek 22, 145–161 (1956).
pubmed: 13340701
doi: 10.1007/BF02538322
Phaff, H. J. A proposal for amendment of the diagnosis of the genus Pichia hansen. Antonie van Leeuwenhoek 22, 113–116 (1956).
pubmed: 13340697
doi: 10.1007/BF02538318
Kurtzman, C. P. Description of Komagataella phaffii sp. nov. and the transfer of Pichia pseudopastoris to the methylotrophic yeast genus Komagataella. Int. J. Syst. Evol. 55, 973–976 (2005).
doi: 10.1099/ijs.0.63491-0
Ogata, K., Nishikawa, H. & Ohsugi, M. A yeast capable of utilizing methanol. Agric. Biol. Chem. 33, 1519–1520 (1969).
doi: 10.1080/00021369.1969.10859497
Tani, Y., Miya, T., Nishikawa, H. & Ogata, K. The microbial metabolism of methanol. Part I. Formation and crystallization of methanol-oxidizing enzyme in a methanol-utilizing yeast, Kloeckera sp. no. 2201. Agric. Biol. Chem. 36, 68–83 (1972).
Tani, Y., Miya, T. & Ogata, K. The microbial metabolism of methanol part II. Properties of crystalline alcohol oxidase from Kloeckera sp. no. 2201. Agric. Biol. Chem. 36, 76–83 (1972).
doi: 10.1271/bbb1961.36.76
Wegner, E. H. A process for producing single cell protein material and culture. European patent EP0017853B2 (1980).
De Schutter, K. et al. Genome sequence of the recombinant protein production host Pichia pastoris. Nat. Biotechnol. 27, 561–566 (2009).
pubmed: 19465926
doi: 10.1038/nbt.1544
Sturmberger, L. et al. Refined Pichia pastoris reference genome sequence. J. Biotechnol. 235, 121–131 (2016).
pmcid: 5089815
doi: 10.1016/j.jbiotec.2016.04.023
Mattanovich, D. et al. Open access to sequence: browsing the Pichia pastoris genome. Microb. Cell Fact. 8, 53 (2009).
pubmed: 19835590
pmcid: 2768684
doi: 10.1186/1475-2859-8-53
Brady, J. R. et al. Comparative genome‐scale analysis of Pichia pastoris variants informs selection of an optimal base strain. Biotechnol. Bioeng. 117, 543–555 (2020).
pubmed: 31654411
doi: 10.1002/bit.27209
Prielhofer, R. et al. GoldenPiCS: a Golden Gate-derived modular cloning system for applied synthetic biology in the yeast Pichia pastoris. BMC Syst. Biol. 11, 123 (2017).
pubmed: 29221460
pmcid: 5723102
doi: 10.1186/s12918-017-0492-3
Love, K. R. et al. Comparative genomics and transcriptomics of Pichia pastoris. BMC Genomics 17, 550 (2016).
pubmed: 27495311
pmcid: 4974788
doi: 10.1186/s12864-016-2876-y
Braun-Galleani, S. et al. Genomic diversity and meiotic recombination among isolates of the biotech yeast Komagataella phaffii (Pichia pastoris). Microb. Cell Fact. 18, 211 (2019).
pubmed: 31801527
pmcid: 6894112
doi: 10.1186/s12934-019-1260-4
Offei, B. et al. Identification of genetic variants of the industrial yeast Komagataella phaffii (Pichia pastoris) that contribute to increased yields of secreted heterologous proteins. PLoS Biol. 20, e3001877 (2022).
pubmed: 36520709
pmcid: 9754263
doi: 10.1371/journal.pbio.3001877
Lu, L., Roberts, G. G., Oszust, C. & Hudson, A. P. The YJR127C/ZMS1 gene product is involved in glycerol-based respiratory growth of the yeast Saccharomyces cerevisiae. Curr. Genet. 48, 235–246 (2005).
pubmed: 16208474
doi: 10.1007/s00294-005-0023-4
Jungmann, J. & Munro, S. Multi-protein complexes in the cis Golgi of Saccharomyces cerevisiae with α-1,6-mannosyltransferase activity. EMBO J. 17, 423–434 (1998).
pubmed: 9430634
pmcid: 1170393
doi: 10.1093/emboj/17.2.423
Vogl, T., Gebbie, L., Palfreyman, R. W. & Speight, R. Effect of plasmid design and type of integration event on recombinant protein expression in Pichia pastoris. Appl. Environ. Microbiol. 84, e02712-17 (2018).
pubmed: 29330186
pmcid: 5835746
doi: 10.1128/AEM.02712-17
Laroy, W., Contreras, R. & Callewaert, N. Glycome mapping on DNA sequencing equipment. Nat. Protoc. 1, 397–405 (2006).
pubmed: 17406262
doi: 10.1038/nprot.2006.60
Conde, R., Pablo, G., Cueva, R. & Larriba, G. Screening for new yeast mutants affected in mannosylphosphorylation of cell wall mannoproteins. Yeast 20, 1189–1211 (2003).
pubmed: 14587103
doi: 10.1002/yea.1032
Friis, J. & Ottolenghi, P. The genetically determined binding of alcian blue by a minor fraction of yeast cell walls. C. R. Trav. Lab. Carlsberg 37, 327–341 (1970).
pubmed: 4194860
Casini, A., Storch, M., Baldwin, G. S. & Ellis, T. Bricks and blueprints: methods and standards for DNA assembly. Nat. Rev. Mol. Cell Biol. 16, 568–576 (2015).
pubmed: 26081612
doi: 10.1038/nrm4014
OPENPichia Plasmid Set. Belgian Coordinated Collections of Microorganisms https://bccm.belspo.be/catalogues/plasmid-sets/openpichia (2022).
Moore, S. J. et al. EcoFlex: a multifunctional MoClo kit for E. coli synthetic biology. ACS Synth. Biol. 5, 1059–1069 (2016).
pubmed: 27096716
doi: 10.1021/acssynbio.6b00031
Lee, M. E., DeLoache, W. C., Cervantes, B. & Dueber, J. E. A highly characterized yeast toolkit for modular, multipart assembly. ACS Synth. Biol. 4, 975–986 (2015).
pubmed: 25871405
doi: 10.1021/sb500366v
van Dolleweerd, C. J. et al. MIDAS: a modular DNA assembly system for synthetic biology. ACS Synth. Biol. 7, 1018–1029 (2018).
pubmed: 29620866
doi: 10.1021/acssynbio.7b00363
Hernanz-Koers, M. et al. FungalBraid: a GoldenBraid-based modular cloning platform for the assembly and exchange of DNA elements tailored to fungal synthetic biology. Fungal Genet. Biol. 116, 51–61 (2018).
pubmed: 29680684
doi: 10.1016/j.fgb.2018.04.010
Sarrion-Perdigones, A. et al. GoldenBraid: an iterative cloning system for standardized assembly of reusable genetic modules. PLoS ONE 6, e21622 (2011).
pubmed: 21750718
pmcid: 3131274
doi: 10.1371/journal.pone.0021622
Obst, U., Lu, T. K. & Sieber, V. A modular toolkit for generating Pichia pastoris secretion libraries. ACS Synth. Biol. 6, 1016–1025 (2017).
pubmed: 28252957
doi: 10.1021/acssynbio.6b00337
Andreou, A. I. & Nakayama, N. Mobius assembly: a versatile Golden-Gate framework towards universal DNA assembly. PLoS ONE 13, e0189892 (2018).
pubmed: 29293531
pmcid: 5749717
doi: 10.1371/journal.pone.0189892
Engler, C. et al. A Golden Gate modular cloning toolbox for plants. ACS Synth. Biol. 3, 839–843 (2014).
pubmed: 24933124
doi: 10.1021/sb4001504
Weber, E., Engler, C., Gruetzner, R., Werner, S. & Marillonnet, S. A modular cloning system for standardized assembly of multigene constructs. PLoS ONE 6, e16765 (2011).
pubmed: 21364738
pmcid: 3041749
doi: 10.1371/journal.pone.0016765
Potapov, V. et al. Comprehensive profiling of four base overhang ligation fidelity by T4 DNA ligase and application to DNA assembly. ACS Synth. Biol. 7, 2665–2674 (2018).
pubmed: 30335370
doi: 10.1021/acssynbio.8b00333
Lin, Y.-C. et al. Genome dynamics of the human embryonic kidney 293 lineage in response to cell biology manipulations. Nat. Commun. 5, 4767 (2014).
pubmed: 25182477
doi: 10.1038/ncomms5767
Andrews, S. FastQCc: a quality control tool for high throughput sequence data v.0.11.9 (Babraham Bioinformatics, 2019); http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).
pubmed: 24695404
pmcid: 4103590
doi: 10.1093/bioinformatics/btu170
Deatherage, D. E. & Barrick, J. E. in Engineering and Analyzing Multicellular Systems, Vol. 1151 (eds Sun, L. & Shou, W.) 165–188 (Springer, 2014).
Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35, 1547–1549 (2018).
pubmed: 29722887
pmcid: 5967553
doi: 10.1093/molbev/msy096
Heiss, S., Maurer, M., Hahn, R., Mattanovich, D. & Gasser, B. Identification and deletion of the major secreted protein of Pichia pastoris. Appl. Microbiol. Biotechnol. 97, 1241–1249 (2013).
pubmed: 22801711
doi: 10.1007/s00253-012-4260-4
Näätsaari, L. et al. Deletion of the Pichia pastoris KU70 homologue facilitates platform strain generation for gene expression and synthetic biology. PLoS ONE 7, e39720 (2012).
pubmed: 22768112
pmcid: 3387205
doi: 10.1371/journal.pone.0039720
Weninger, A., Hatzl, A.-M., Schmid, C., Vogl, T. & Glieder, A. Combinatorial optimization of CRISPR/Cas9 expression enables precision genome engineering in the methylotrophic yeast Pichia pastoris. J. Biotechnol. 235, 139–149 (2016).
pubmed: 27015975
doi: 10.1016/j.jbiotec.2016.03.027
Wu, S. & Letchworth, G. J. High efficiency transformation by electroporation of Pichia pastoris pretreated with lithium acetate and dithiothreitol. BioTechniques 36, 152–154 (2004).
pubmed: 14740498
doi: 10.2144/04361DD02
Livak, K. J. & Schmittgen, T. D. Analysis of relative gene expression data using real-time quantitative PCR and the [Formula: see text] method. Methods 25, 402–408 (2001).
pubmed: 11846609
doi: 10.1006/meth.2001.1262
Boone, M. et al. Massively parallel interrogation of protein fragment secretability using SECRiFY reveals features influencing secretory system transit. Nat. Commun. 12, 6414 (2021).
pubmed: 34741024
pmcid: 8571348
doi: 10.1038/s41467-021-26720-y
Vandesompele, J. et al. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol. 3, research0034.1 (2002).
doi: 10.1186/gb-2002-3-7-research0034
R Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2009).
Lüdecke, D. ggeffects: Tidy data frames of marginal effects from regression models. J. Open Source Softw. 3, 772 (2018).
Zeileis, A., Köll, S. & Graham, N. Various versatile variances: an object-oriented implementation of clustered covariances in R. J. Stat. Softw. 95, 1–36 (2020).
doi: 10.18637/jss.v095.i01
Ram, A. F. J. & Klis, F. M. Identification of fungal cell wall mutants using susceptibility assays based on Calcofluor white and Congo red. Nat. Protoc. 1, 2253–2256 (2006).
pubmed: 17406464
doi: 10.1038/nprot.2006.397
Arendt, P. et al. An endoplasmic reticulum-engineered yeast platform for overproduction of triterpenoids. Metab. Eng. 40, 165–175 (2017).
pubmed: 28216107
doi: 10.1016/j.ymben.2017.02.007
McDonald, K. L. & Webb, R. I. Freeze substitution in 3 hours or less. J. Microsc. 243, 227–233 (2011).
pubmed: 21827481
doi: 10.1111/j.1365-2818.2011.03526.x