{{Short description|Genus of fungus used industrially and as model organism}} {{Automatic taxobox | image = Pichia pastoris GS115 (Yang 2017).jpg | image_caption = ''Komagataella phaffii''<ref name="De Schutter, K., Lin, Y., Tiels, P. (2009)"/> GS115 | taxon = Komagataella | authority = Y. Yamada, M. Matsuda, K. Maeda & Mikata, 1995 | subdivision_ranks = Species | subdivision = See text | synonyms_ref = | synonyms = }}
'''''Komagataella''''' is a methylotrophic yeast within the order Pichiales. It was found in the 1960s as ''Pichia pastoris'', with its feature of using methanol as a source of carbon and energy.<ref name="Koichi Ogata, Hideo Nishikawa & Masahiro Ohsugi (1969)">{{Cite journal | author=Koichi Ogata, Hideo Nishikawa & Masahiro Ohsugi | title=A Yeast Capable of Utilizing Methanol | journal=Agricultural and Biological Chemistry | year=1969 | volume=33 | issue=10 | pages=1519–1520 | doi=10.1080/00021369.1969.10859497 | doi-access=free }}</ref> In 1995, ''P. pastoris'' was reassigned into the sole representative of genus ''Komagataella'', becoming ''Komagataella pastoris''.<ref>{{cite journal |last1=Yamada |first1=Yuzo |last2=Matsuda |first2=Minako |last3=Maeda |first3=Kojiro |last4=Mikata |first4=Kozaburo |title=The Phylogenetic Relationships of Methanol-assimilating Yeasts Based on the Partial Sequences of 18S and 26S Ribosomal RNAs: The Proposal of Komagataella Gen. Nov. (Saccharomycetaceae) |journal=Bioscience, Biotechnology, and Biochemistry |date=January 1995 |volume=59 |issue=3 |pages=439–444 |doi=10.1271/bbb.59.439|pmid=7766181 |doi-access=free }}</ref> In 2005, it was found that almost all strains used industrially and in labs are a separate species, ''K. phaffii''. Later studies have further distinguished new species in this genus, resulting in a total of 7 recognized species.<ref name="gbif"/> It is not uncommon to see the old name still in use in the context of protein production, as of 2023;<ref name=Heistinger2020/> in less formal use, the yeast may confusingly be referred to as ''pichia''.
After years of study, ''Komagataella'' is widely used in biochemical research and biotech industries. With strong potential for being an expression system for protein production, as well as being a model organism for genetic study, ''Komagataella phaffii'' has become important for biological research and biotech applications.<ref name="De Schutter, K., Lin, Y., Tiels, P. (2009)">{{Cite journal | author=De Schutter, K., Lin, Y., Tiels, P. | title=Genome sequence of the recombinant protein production host Pichia pastoris. | journal=Nature Biotechnology | year=2009 | volume=27 | issue=6 | pages=561–566 | doi=10.1038/nbt.1544 | pmid=19465926 | doi-access=free }}</ref><ref name=Heistinger2020>{{Cite journal|last1=Heistinger|first1=Lina|last2=Gasser|first2=Brigitte|last3=Mattanovich|first3=Diethard|date=2020-07-01|title=Microbe Profile: Komagataella phaffii: a methanol devouring biotech yeast formerly known as Pichia pastoris|journal=Microbiology|language=en|volume=166|issue=7|pages=614–616|doi=10.1099/mic.0.000958|pmid=32720891|issn=1350-0872|doi-access=free}}</ref>
== Taxonomy == <!-- years are actually from NCBI. They are useful here: you get a rough idea of whether studies know about the various splits from pastoris. --> <!-- oh and the links are pointless for now. not enough literature knows exactly which they are using, so unless you search up the strains one by one, you really can't make these smaller articles. --> According to GBIF:<ref name="gbif">{{cite web |title=Komagataella Y.Yamada, M.Matsuda, K.Maeda & Mikata, 1995 |url=https://www.gbif.org/species/7934007 |website=www.gbif.org |language=en}}</ref> * ''Komagataella kurtzmanii'' {{Au|1=G.I.Naumov, E.S.Naumova, Tyurin & Kozlov, 2013}} * ''Komagataella mondaviorum'' {{Au|1=G.I.Naumov, E.S.Naumova & K.L.Boundy-Mills, 2018}} * ''Komagataella pastoris'' {{Au|1=(Guillierm., 1919) Y.Yamada, M.Matsuda, K.Maeda & Mikata, 1995}} * ''Komagataella phaffii'' {{Au|1=Kurtzman, 2005}} – responsible for most, if not all, industrial & research use<ref>{{cite journal |last1=Kurtzman |first1=Cletus Paul |title=Biotechnological strains of Komagataella (Pichia) pastoris are Komagataella phaffii as determined from multigene sequence analysis |journal=Journal of Industrial Microbiology & Biotechnology |date=November 2009 |volume=36 |issue=11 |pages=1435–1438 |doi=10.1007/s10295-009-0638-4|doi-access=free|pmid=19760441 }}</ref> * ''Komagataella populi'' {{Au|1=Kurtzman, 2012}} * ''Komagataella pseudopastoris'' {{Au|1=(Dlauchy, Tornai-Leh., Fülöp & G.Péter, 2003) Kurtzman, 2005}} * ''Komagataella ulmi'' {{Au|1=Kurtzman, 2012}}
==''Komagataella'' in nature==
===Natural habitat=== In nature, ''Komagataella'' is found on trees, such as chestnut trees.<ref name="pmid35468837">{{cite journal |last1=Heistinger |first1=L |last2=Dohm |first2=JC |last3=Paes |first3=BG |last4=Koizar |first4=D |last5=Troyer |first5=C |last6=Ata |first6=Ö |last7=Steininger-Mairinger |first7=T |last8=Mattanovich |first8=D |title=Genotypic and phenotypic diversity among Komagataella species reveals a hidden pathway for xylose utilization. |journal=Microbial Cell Factories |date=25 April 2022 |volume=21 |issue=1 |page=70 |doi=10.1186/s12934-022-01796-3 |pmid=35468837|pmc=9036795 |doi-access=free }}</ref> They are heterotrophs and they can use several carbon sources for living, like glucose, glycerol and methanol.<ref name="Rebnegger, C., Vos, T., Graf, A. B., Valli, M., Pronk, J. T., Daran-Lapujade, P., & Mattanovich, D. (2016)">{{Cite journal | author=Rebnegger, C., Vos, T., Graf, A. B., Valli, M., Pronk, J. T., Daran-Lapujade, P., & Mattanovich, D. | title=Pichia pastoris exhibits high viability and a low maintenance energy requirement at near-zero specific growth rates | journal=Applied and Environmental Microbiology | year=2016 | volume=82 | issue=15 | pages=4570–4583 | doi=10.1128/AEM.00638-16 | pmid=27208115 | pmc=4984280 | bibcode=2016ApEnM..82.4570R | doi-access=free }}</ref> However, they cannot use lactose.
===Reproduction=== ''Komagataella'' can undergo both asexual reproduction and sexual reproduction, by budding and ascospore.<ref name="Kurtzman. (1998)">{{Cite journal | author=Kurtzman | title=42 - Pichia E.C. Hansen emend. Kurtzman | journal=The Yeasts: A Taxonomic Study | volume=1 | year=1998 | pages=273–352 | doi=10.1016/B978-044481312-1/50046-0 | isbn=978-0-444-81312-1 }}</ref> In this case, two types of cells of ''Komagataella'' exist: haploid and diploid cells. In the asexual life cycle, haploid cells undergo mitosis for reproduction. In the sexual life cycle, diploid cells undergo sporulation and meiosis.<ref name="Zörgö E, Chwialkowska K, Gjuvsland AB, Garré E, Sunnerhagen P, Liti G, Blomberg A, Omholt SW, Warringer J (2013)">{{Cite journal | author=Zörgö E, Chwialkowska K, Gjuvsland AB, Garré E, Sunnerhagen P, Liti G, Blomberg A, Omholt SW, Warringer J | title=Ancient Evolutionary Trade-Offs between Yeast Ploidy States | journal=PLOS Genetics | year=2013 | volume=9 | issue=3 | article-number=e1003388 | doi=10.1371/journal.pgen.1003388 | pmid=23555297 | pmc=3605057 | doi-access=free }}</ref> The growth rate of its colonies can vary by a large range, from near to 0 to a doubling time of one hour, which is suitable for industrial processes.<ref name="Kastilan, R., Boes, A., Spiegel, H.(2017)">{{Cite journal | author=Kastilan, R., Boes, A., Spiegel, H. | title=Improvement of a fermentation process for the production of two PfAMA1-DiCo-based malaria vaccine candidates in Pichia pastoris | journal=Nature | volume=1 | year=2017 | issue=1 | page=7 | doi=10.1038/s41598-017-11819-4 | pmid=28931852 | pmc=5607246 | bibcode=2017NatSR...711991K | doi-access=free }}</ref>
==''Komagataella'' as a model organism== In the last few years, ''Komagataella'' was investigated and identified as a good model organism with several advantages. First of all, ''Komagataella'' can be grown and used easily in lab. Like other widely used yeast models, it has relatively short life span and fast regeneration time. Moreover, some inexpensive culture media have been designed, so that ''Komagataella'' can grow quickly on them, with high cell density.<ref name="M. M. Guarna G. J. Lesnicki B. M. Tam J. Robinson C. Z. Radziminski D. Hasenwinkle A. Boraston E. Jervis R. T. A. MacGillivray R. F. B. Turner D. G. Kilburn(1997)">{{Cite journal | author=M. M. Guarna G. J. Lesnicki B. M. Tam J. Robinson C. Z. Radziminski D. Hasenwinkle A. Boraston E. Jervis R. T. A. MacGillivray R. F. B. Turner D. G. Kilburn | title=On-line monitoring and control of methanol concentration in shake-flask cultures of Pichia pastoris | journal=Biotechnology and Bioengineering | volume=56 | year=1997 | issue=3 | pages=279–286 |doi=10.1002/(SICI)1097-0290(19971105)56:3<279::AID-BIT5>3.0.CO;2-G| pmid=18636643 }}</ref> Whole genome sequencing for ''Komagataella'' has been performed. The ''K. phaffii'' GS115 genome has been sequenced by the Flanders Institute for Biotechnology and Ghent University, and published in ''Nature Biotechnology''.<ref name = "De Schutter">{{cite journal | vauthors = De Schutter K, Lin YC, Tiels P, Van Hecke A, Glinka S, Weber-Lehmann J, Rouzé P, Van de Peer Y, Callewaert N | title = Genome sequence of the recombinant protein production host Pichia pastoris | journal = Nature Biotechnology | volume = 27 | issue = 6 | pages = 561–6 | date = June 2009 | pmid = 19465926 | doi = 10.1038/nbt.1544 | doi-access = free }}</ref> The genome sequence and gene annotation can be browsed through the [http://bioinformatics.psb.ugent.be/orcae/overview/Picpa ORCAE] system. The complete genomic data allows scientists to identify homologous proteins and evolutionary relationships between other yeast species and ''Komagataella''. In addition, all seven species were sequenced by 2022.<ref name="pmid35468837"/> Furthermore, ''Komagataella'' are single eukaryotic cells, which means researchers could investigate the proteins inside ''Komagataella''. Then the homologous comparison to other more complicated eukaryotic species can be processed, to obtain their functions and origins.<ref name="Brigitte Gasser, Roland Prielhofer, Hans Marx, Michael Maurer, Justyna Nocon, Matthias Steiger, Verena Puxbaum, Michael Sauer & Diethard Mattanovich(2013)">{{Cite journal | author=Brigitte Gasser, Roland Prielhofer, Hans Marx, Michael Maurer, Justyna Nocon, Matthias Steiger, Verena Puxbaum, Michael Sauer & Diethard Mattanovich | title=Pichia pastoris: protein production host and model organism for biomedical research | journal=Future Microbiology | volume=8 | year=2013 | issue=2 | pages=191–208 | doi=10.2217/fmb.12.133 | pmid=23374125 }}</ref>
Another advantage of ''Komagataella'' is its similarity to the well-studied yeast model — ''Saccharomyces cerevisiae''. As a model organism for biology, ''S. cerevisiae'' have been well studied for decades and used by researchers for various purposes throughout history. The two yeast genera; ''Pichia'' (sensu lato) and ''Saccharomyces'', have similar growth conditions and tolerances; thus, the culture of ''Komagataella'' can be adopted by labs without many modifications.<ref name="Tran, A., Nguyen, T., Nguyen, C.(2017)">{{Cite journal | author=Tran, A., Nguyen, T., Nguyen, C. | title=Pichia pastoris versus Saccharomyces cerevisiae: a case study on the recombinant production of human granulocyte-macrophage colony-stimulating factor | journal=BMC Res Notes | volume=10 | year=2017 | issue=1 | page=148 |doi=10.1186/s13104-017-2471-6| pmid=28376863 | pmc=5379694 | doi-access=free }}</ref> Moreover, unlike ''S. cerevisiae'', ''Komagataella'' has the ability to functionally process proteins with large molecular weight, which is useful in a translational host.<ref name="Heidebrecht, Aniela, and Thomas Scheibel(2013)">{{Cite journal | author=Heidebrecht, Aniela, and Thomas Scheibel | title=Recombinant production of spider silk proteins | journal=Advances in Applied Microbiology | volume=82 | year=2013 |pages=115–153 |doi=10.1016/B978-0-12-407679-2.00004-1| pmid=23415154 | isbn=978-0-12-407679-2 }}</ref> Considering all the advantages, ''Komagataella'' can be usefully employed as both a genetic and experimental model organism.
===''Komagataella'' as a genetic model organism=== As a genetic model organism, ''Komagataella'' can be used for genetic analysis and large-scale genetic crossing, with complete genome data and its ability to carry out complex eukaryotic genetic processing in a relatively small genome. The functional genes for peroxisome assembly were investigated by comparing wild-type and mutant strains of ''Komagataella''.<ref name="Gould, S. J., McCollum, D., Spong, A. P., Heyman, J. A., & Subramani, S. (1992).">{{Cite journal | author=Gould, S. J., McCollum, D., Spong, A. P., Heyman, J. A., & Subramani, S. | title=Development of the yeast Pichia pastoris as a model organism for a genetic and molecular analysis of peroxisome assembly. | journal=The Yeasts: A Taxonomic Study | volume=8 | year=1992 | issue=8 |pages=613–628 |doi=10.1002/yea.320080805| pmid=1441741 | s2cid=8840145 }}</ref>
===''Komagataella'' as an experimental model organism=== As an experimental model organism, ''Komagataella'' was mainly used as the host system for transformation. Due to its abilities of recombination with foreign DNA and processing large proteins, much research has been carried out to investigate the possibility of producing new proteins and the function of artificially designed proteins, using ''Komagataella'' as a transformation host.<ref name="Cregg, J. M., Barringer, K. J., Hessler, A. Y., & Madden, K. R. (1985).">{{Cite journal | author=Cregg, J. M., Barringer, K. J., Hessler, A. Y., & Madden, K. R. | title=Pichia pastoris as a host system for transformations | journal=Molecular and Cellular Biology | volume=5 | year=1985 | issue=12 |pages=3376–3385 |doi=10.1128/MCB.5.12.3376| pmid=3915774 | pmc=369166 }}</ref> In the last decade, ''Komagataella'' was engineered to build expression system platforms, which is a typical application for a standard experimental model organism, as described below.
==''Komagataella'' as expression system platform== ''Komagataella'' is frequently used as an expression system for the production of heterologous proteins. Several properties make ''Komagataella'' suited for this task. Currently, several strains of ''Komagataella'' are used for biotechnical purposes, with significant differences among them in growth and protein production.<ref name="Brady, J. R. (2020). ">{{Cite journal | author=Brady, J.R. | title=Comparative genome-scale analysis of Pichia pastoris variants informs selection of an optimal base strain | journal=Biotechnology and Bioengineering | year=2020 | volume=117 | issue=2 | pages=543–555 | doi=10.1002/bit.27209 | pmid=31654411 | pmc=7003935 }}</ref> Some common variants possess a mutation in the HIS4 gene, leading to the selection of cells which are transformed successfully with expression vectors. The technology for vector integration into ''Komagataella'' genome is similar to that in ''Saccharomyces cerevisiae''.<ref name="Higgins, D. R., & Cregg, J. M. (1998). ">{{Cite book | author=Higgins, D. R., & Cregg, J. M. | title=Pichia Protocols | chapter=Introduction to Pichia pastoris | series=Methods in Molecular Biology | year=1998 | volume=103 |pages=1–15|doi=10.1385/0-89603-421-6:1| pmid=9680629 | isbn=0-89603-421-6 }}</ref>
===Advantage=== #''Komagataella'' is able to grow on simple, inexpensive medium, with high growth rate. ''Komagataella'' can grow in either shake flasks or a fermenter, which makes it suitable for both small- and large-scale production.<ref name="Wenhui Zhang Mark A. Bevins Bradley A. Plantz Leonard A. Smith Michael M. Meagher(2000)">{{Cite journal | author=Wenhui Zhang Mark A. Bevins Bradley A. Plantz Leonard A. Smith Michael M. Meagher. | title=Modeling Pichia pastoris growth on methanol and optimizing the production of a recombinant protein, the heavy-chain fragment C of botulinum neurotoxin, serotype A | journal=Biotechnology and Bioengineering | volume=70 | year=2000 | issue=1 |pages=1–8|doi=10.1002/1097-0290(20001005)70:1<1::AID-BIT1>3.0.CO;2-Y| pmid=10940857 | url=http://digitalcommons.unl.edu/cgi/viewcontent.cgi?article=1017&context=chemeng_biotechnology | url-access=subscription }}</ref> #''Komagataella'' has two alcohol oxidase genes, ''Aox1'' and ''Aox2'', which include strongly inducible promoters.<ref name="pmid15565717">{{cite journal | vauthors = Daly R, Hearn MT | title = Expression of heterologous proteins in Pichia pastoris: a useful experimental tool in protein engineering and production | journal = Journal of Molecular Recognition | volume = 18 | issue = 2 | pages = 119–38 | year = 2005 | pmid = 15565717 | doi = 10.1002/jmr.687 | s2cid = 7476149 }}</ref> These two genes allow ''Komagataella'' to use methanol as a carbon and energy source. The AOX promoters are induced by methanol, and repressed by glucose. Usually, the gene for the desired protein is introduced under the control of the ''Aox1'' promoter, which means that protein production can be induced by the addition of methanol on medium. After several researches, scientists found that the promoter derived from ''AOX1'' gene in ''Komagataella'' is extremely suitable to control the expression of foreign genes, which had been transformed into the ''Komagataella'' genome, producing heterologous proteins.<ref name="Romanos, Mike.(1995)">{{Cite journal | author=Romanos, Mike. | title=Advances in the use of Pichia pastoris for high-level gene expression | journal=Current Opinion in Biotechnology | volume=6 | year=1995 | issue=5 |pages=527–533|doi=10.1016/0958-1669(95)80087-5}}</ref> # With a key trait, ''Komagataella'' can grow with extremely high cell density on the culture. This feature is compatible with heterologous protein expression, giving higher yields of production.<ref name="Zhou, X., Yu, Y., Tao, J., & Yu, L. (2014). ">{{Cite journal | author=Zhou, X., Yu, Y., Tao, J., & Yu, L. | title=Production of LYZL6, a novel human c-type lysozyme, in recombinant Pichia pastoris employing high cell density fed-batch fermentation | journal=Journal of Bioscience and Bioengineering | volume=118 | year=2014 | issue=4 |pages=420–425|doi=10.1016/j.jbiosc.2014.03.009| pmid=24745549 }}</ref> # ''Komagataella'' has a well-developed secretory pathway involving the Endoplasmic reticulum and a stacked Golgi apparatus, which is more similar to those of higher eukaryotes to that of ''Saccharomyces cerevisiae''. This enables the efficient folding and post-translational modification of heterologous proteins, including the formation of disulfide bonds and glycosylation. This process allows many recombinant proteins to be secreted as soluble, physiologically active forms into the culture medium.<ref>{{Cite journal |last=Zou |first=Chenwei |last2=Lu |first2=Lingfang |last3=Wang |first3=Shengyan |last4=Zhang |first4=Chenshan |last5=Chen |first5=Xuequn |last6=Lin |first6=Yao |last7=Huang |first7=Yide |date=2022-12-16 |title=The α-mating factor secretion signals and endogenous signal peptides for recombinant protein secretion in Komagataella phaffii |journal=Biotechnology for Biofuels and Bioproducts |language=en |volume=15 |issue=1 |page=140 |doi=10.1186/s13068-022-02243-6 |doi-access=free|issn=2731-3654 |pmc=9756452 |pmid=36527112}}</ref><ref name=":0">{{Cite journal |last=Chen |first=Hongtao |last2=Niu |first2=Yueheng |last3=Zhang |first3=Liuxia |last4=Wang |first4=Yunpeng |last5=Luo |first5=Ao |last6=Dai |first6=Zhihui |last7=Du |first7=Guocheng |last8=Zhao |first8=Xinrui |date=2025-09-01 |title=The optimized signal peptide and feeding strategy to enhance secretory expression of LegH in Komagataella phaffii |url=https://www.sciencedirect.com/science/article/pii/S1359511325001813 |journal=Process Biochemistry |volume=156 |pages=255–262 |doi=10.1016/j.procbio.2025.06.005 |issn=1359-5113|url-access=subscription }}</ref> # The technology required for genetic manipulation of ''Komagataella'' is similar to that of ''Saccharomyces cerevisiae'', which is one of the most well-studied yeast model organisms. As a result, the experiment protocol and materials are easy to build for ''Komagataella''.<ref name="Morton, C. L., & Potter, P. M. (2000). ">{{Cite journal | author=Morton, C. L., & Potter, P. M. | s2cid=22792748 | title=Comparison of Escherichia coli, Saccharomyces cerevisiae, Pichia pastoris, Spodoptera frugiperda, and COS7 cells for recombinant gene expression. | journal=Molecular Biotechnology | volume=16 | year=2000 | issue=3 |pages=193–202|doi=10.1385/MB:16:3:193| pmid=11252804 }}</ref>
===Disadvantage=== As some proteins require chaperonin for proper folding, ''Komagataella'' is unable to produce a number of proteins, since it does not contain the appropriate chaperones. The technologies of introducing genes of mammalian chaperonins into the yeast genome and overexpressing existing chaperonins still require improvement.<ref>{{cite journal |last1=Bankefa |first1=OE |last2=Wang |first2=M |last3=Zhu |first3=T |last4=Li |first4=Y |s2cid=29155989 |title=Hac1p homologues from higher eukaryotes can improve the secretion of heterologous proteins in the yeast Pichia pastoris. |journal=Biotechnology Letters |date=July 2018 |volume=40 |issue=7 |pages=1149–1156 |doi=10.1007/s10529-018-2571-y |pmid=29785668|doi-access=free }}</ref><ref>{{cite journal |last1=Yu |first1=Xiao-Wei |last2=Sun |first2=Wei-Hong |last3=Wang |first3=Ying-Zheng |last4=Xu |first4=Yan |title=Identification of novel factors enhancing recombinant protein production in multi-copy Komagataella phaffii based on transcriptomic analysis of overexpression effects |journal=Scientific Reports |date=24 November 2017 |volume=7 |issue=1 |page=16249 |doi=10.1038/s41598-017-16577-x |pmid=29176680 |pmc=5701153 |doi-access=free|bibcode=2017NatSR...716249Y }}</ref>
===Comparison with other expression systems=== In standard molecular biology research, the bacterium ''Escherichia coli'' is the most frequently used organism for expression system, to produce heterologous proteins, due to its features of fast growth rate, high protein production rate, as well as undemanding growth conditions. Protein production in ''E. coli'' is usually faster than that in ''Komagataella'', with reasons: Competent ''E. coli'' cells can be stored frozen, and thawed before use, whereas ''Komagataella'' cells have to be produced immediately before use. Expression yields in ''Komagataella'' vary between different clones, so that a large number of clones has to be screened for protein production, to find the best producer. The biggest advantage of ''Komagataella'' over ''E. coli'' is that ''Komagataella'' is capable of forming disulfide bonds and glycosylations in proteins, but ''E. coli'' cannot.<ref name="pmid19892173">{{Cite book |vauthors=Cregg JM, Tolstorukov I, Kusari A, Sunga J, Madden K, Chappell T |title=Guide to Protein Purification, 2nd Edition |chapter=Chapter 13 Expression in the Yeast Pichia pastoris |volume=463 |pages=169–89 |year=2009 |pmid=19892173 |doi=10.1016/S0076-6879(09)63013-5 |series=Methods in Enzymology |isbn=978-0-12-374536-1}}</ref> ''E. coli'' might produce a misfolded protein when disulfides are included in final product, leading to inactive or insoluble forms of proteins.<ref name="pmid19892171">{{Cite book |author=Brondyk WH |title=Guide to Protein Purification, 2nd Edition |chapter=Chapter 11 Selecting an Appropriate Method for Expressing a Recombinant Protein |volume=463 |pages=131–47 |year=2009 |pmid=19892171 |doi=10.1016/S0076-6879(09)63011-1 |series=Methods in Enzymology |isbn=978-0-12-374536-1}}</ref>
The well-studied ''Saccharomyces cerevisiae'' is also used as an expression system with similar advantages over ''E. coli'' as ''Komagataella''. However ''Komagataella'' has two main advantages over ''S. cerevisiae'' in laboratory and industrial settings: #''Komagataella'', as mentioned above, is a methylotroph, meaning that it can grow with the simple methanol, as the only source of energy — ''Komagataella'' can grow fast in cell suspension with reasonably strong methanol solution, which would kill most other micro-organisms. In this case, the expression system is cheap to set up and maintain. #''Komagataella'' can grow up to a very high cell density. Under ideal conditions, it can multiply to the point where the cell suspension is practically a paste. As the protein yield from expression system in a microbe is roughly equal to the product of the proteins produced per cell, which makes ''Komagataella'' of great use when trying to produce large quantities of protein without expensive equipment.<ref name="pmid19892173"/>
Comparing to other expression systems, such as S2-cells from ''Drosophila melanogaster'' and Chinese hamster ovary cells, ''Komagataella'' usually gives much better yields. Generally, cell lines from multicellular organisms require complex and expensive types of media, including amino acids, vitamins, as well as other growth factors. These types of media significantly increase the cost of producing heterologous proteins. Additionally, ''Komagataella'' can grow in media containing only one carbon source and one nitrogen source, which is suitable for isotopic labelling applications, like protein NMR.<ref name="pmid19892173"/>
==Industrial applications== ''Komagataella'' have been used in several kinds of biotech industries, such as pharmaceutical industry. All the applications are based on its feature of expressing proteins.
===Biotherapeutic production=== In the last few years, ''Komagataella'' had been used for the production of over 500 types of biotherapeutics, such as IFNγ. At the beginning, one drawback of this protein expression system is the over-glycosylation with high density of mannose structure, which is a potential cause of immunogenicity.<ref>{{cite journal | vauthors = Razaghi A, Tan E, Lua LH, Owens L, Karthikeyan OP, Heimann K | title = Is Pichia pastoris a realistic platform for industrial production of recombinant human interferon gamma? | journal = Biologicals | volume = 45 | pages = 52–60 | date = January 2017 | pmid = 27810255 | doi = 10.1016/j.biologicals.2016.09.015 | s2cid = 28204059 | url = https://zenodo.org/record/1312349 }}</ref><ref>{{cite journal | title=Increased expression and secretion of recombinant hIFNγ through amino acid starvation-induced selective pressure on the adjacent HIS4 gene in Pichia pastoris | author=Ali Razaghi|author2=Roger Huerlimann|author3=Leigh Owens|author4=Kirsten Heimann | journal=European Pharmaceutical Journal | year=2015 | volume=62 | issue=2 | pages=43–50 | doi=10.1515/afpuc-2015-0031| doi-access=free | url=https://researchonline.jcu.edu.au/42240/1/Razaghi%20et%20al_AFPUC_2015_LXII%282%29_1-8.pdf }}</ref> In 2006, a research group managed to create a new strain called YSH597.{{efn|YSH597 is based on strain NRRL-Y11430, now considered part of ''K. phaffi''.}} This strain can express erythropoietin in its normal glycosylation form, by exchanging the enzymes responsible for the fungal type glycosylation, with the mammalian homologs. Thus, the altered glycosylation pattern allowed the protein to be fully functional.<ref name="pmid16960007">{{cite journal | vauthors = Hamilton SR, Davidson RC, Sethuraman N, Nett JH, Jiang Y, Rios S, Bobrowicz P, Stadheim TA, Li H, Choi BK, Hopkins D, Wischnewski H, Roser J, Mitchell T, Strawbridge RR, Hoopes J, Wildt S, Gerngross TU | s2cid = 43334198 | title = Humanization of yeast to produce complex terminally sialylated glycoproteins | journal = Science | volume = 313 | issue = 5792 | pages = 1441–3 | date = September 2006 | pmid = 16960007 | doi = 10.1126/science.1130256 | bibcode = 2006Sci...313.1441H }}</ref>
===Enzyme production=== A significant milestone in the use of ''K. phaffii'' in food technology was its GRAS classification by the US Food and Drug Administration, alongside their approval of recombinant proteins.<ref>{{Cite web |title=GRAS Notices |url=https://hfpappexternal.fda.gov/scripts/fdcc/index.cfm?set=grasnotices&id=1202 |access-date=2026-02-23 |website=hfpappexternal.fda.gov |language=en-US}}</ref> It is now used to produce various enzymes that serve as processing aids and food additives. In bakery production, enzymes produced by genetically modified ''Komagataella'' can maintain bread freshness and compensate for variations in flour and malt quality. In brewing, they can reduce beer's alcohol content or modify the flavour and filtration properties of wine.<ref name="Spohner, S. C., Müller, H., Quitmann, H., & Czermak, P. (2015)).">{{Cite journal | author=Spohner, S. C., Müller, H., Quitmann, H., & Czermak, P. | title= Expression of enzymes for the usage in food and feed industry with Pichia pastoris | journal=Journal of Biotechnology | volume=202 | year=2015 |pages=420–425|doi=10.1016/j.jbiotec.2015.01.027| pmid= 25687104 }}</ref> Recombinant expressed phospholipase C is used to degum high-phosphorus vegetable oils by hydrolysing phospholipids. In animal feed, phytase produced by ''K. phaffii'' breaks down phytic acid, an antinutrient.<ref name="pmid36979376">{{cite journal |last1=Barone |first1=GD |last2=Emmerstorfer-Augustin |first2=A |last3=Biundo |first3=A |last4=Pisano |first4=I |last5=Coccetti |first5=P |last6=Mapelli |first6=V |last7=Camattari |first7=A |title=Industrial Production of Proteins with Pichia pastoris-Komagataella phaffii. |journal=Biomolecules |date=26 February 2023 |volume=13 |issue=3 |page=441 |doi=10.3390/biom13030441 |pmid=36979376 |pmc=10046876 |doi-access=free }}</ref>
Recently, ''K. phaffii'' has been used increasingly to produce soy leghemoglobin, a plant heme protein that gives plant-based meat analogues their colour and flavour.<ref>{{Cite web |title=Sage Journals: Discover world-class research |url=https://journals.sagepub.com/action/cookieAbsent |access-date=2026-02-23 |website=Sage Journals |language=en |doi=10.1177/1091581818766318 |pmc=5956568 |pmid=29642729}}</ref> This expands the industrial application of ''K. phaffii'' from technical enzymes towards functional food ingredients. For this purpose, the yeast utilises its strong methanol-inducible promoters and efficient secretion to produce functional leghemoglobin for use as a food ingredient. Through strain engineering, including optimisation of heme biosynthesis and signal peptides, and controlled fed-batch fermentation, gram-per-litre titres of secreted leghemoglobin have been achieved. This makes large-scale production for meat analogues economically viable.<ref>{{Cite journal |last=Shao |first=Youran |last2=Xue |first2=Changlu |last3=Liu |first3=Wenqian |last4=Zuo |first4=Siqi |last5=Wei |first5=Peilian |last6=Huang |first6=Lei |last7=Lian |first7=Jiazhang |last8=Xu |first8=Zhinan |date=2022-11-01 |title=High-level secretory production of leghemoglobin in Pichia pastoris through enhanced globin expression and heme biosynthesis |url=https://www.sciencedirect.com/science/article/pii/S0960852422012147 |journal=Bioresource Technology |volume=363 |article-number=127884 |doi=10.1016/j.biortech.2022.127884 |issn=0960-8524|url-access=subscription }}</ref><ref name=":0" />
== References == {{Notelist}} {{Reflist}}
{{Taxonbar|from1=Q148697|from2=Q10547278}} {{Authority control}}
Category:Pichiomycetes Category:Fungal models Category:Yeasts Category:Taxa described in 1995 Category:Ascomycota genera