Journal of Guangxi Normal University(Natural Science Edition) ›› 2024, Vol. 42 ›› Issue (3): 17-26.doi: 10.16088/j.issn.1001-6600.2023081702

Previous Articles     Next Articles

Komagataella phaffii Serves as a Model Organism for Emerging Basic Research

AI Congcong1,2, GONG Guoli1,2*, JIAO Xiaoyu1,2, TIAN Lu1,2, GAI Zhongchao1,2, GOU Jingxuan1,2, LI Hui1,2   

  1. 1. School of Biological and Pharmaceutical Sciences, Shaanxi University of Science and Technology, Xi'an Shaanxi 710021, China;
    2. School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an Shaanxi 710021, China
  • Received:2023-08-17 Revised:2023-09-17 Published:2024-05-31

Abstract: Komagataella phaffii has been widely used in the pharmaceutical and biotechnology industries. In recent years, its potential as a research model organism has gained attention. Although baker's yeast is the most commonly used yeast model in research, it limits our understanding of the same organism. K. phaffii, which diverged from baker's yeast 250 million years ago, evolves at a slower rate and retains characteristics of ancient yeast ancestors, making it more similar to higher eukaryotic cells. K. phaffii can efficiently assimilate methanol as the sole carbon source, making it a valuable model organism for studying molecular cell biology of eukaryotes. This article reviews the research progress of using K. phaffii as a model organism, including methanol assimilation, peroxisome formation, mating and sporulation behavior, as well as protein secretion, lipid synthesis, and cell wall formation processes. By comparing the data of K. phaffii with other yeast species such as baker's yeast, this article highlights the great potential of K. phaffii in basic research, aiming to present a comprehensive and systematic review of the research progress on K. phaffii as a model organism.

Key words: Komagataella phaffii, methyltrophic yeast, eukaryote, recombinat expression, model organism

CLC Number:  Q78
[1] GOFFEAU B A, BARRELL B G, BUSSEY H, et al. Life with 6000 genes[J]. Science, 1996, 274(5287): 546-567. DOI: 10.1126/science.274.5287.546.
[2] KARBALAEI M, REZAEE S A, FARSIANI H. Pichia pastoris: a highly successful expression system for optimal synthesis of heterologous proteins[J]. Journal of Cellular Physiology, 2020, 235(9): 5867-5881. DOI: 10.1002/jcp.29583.
[3] 谷洋, 连佳长, 黄磊, 等. 毕赤酵母基因编辑技术研究进展[J]. 微生物学通报, 2020, 47(2): 602-614. DOI: 10.13344/j.microbiol.china.190257.
[4] RILEY R, HARIDAS S, WOLFE K H, et al. Comparative genomics of biotechnologically important yeasts[J]. Proceedings of the National Academy Sciences of the United States of America, 2016, 113(35): 9882-9887. DOI: 10.1073/pnas.1603941113.
[5] SHEN X X, OPULENTE D A, KOMINEK J, et al. Tempo and mode of genome evolution in the budding yeast subphylum[J]. Cell, 2018, 175(6): 1533-1545. DOI: 10.1016/j.cell.2018.10.023.
[6] YAMADA Y, MATSUDA M, MAEDA K, et al. 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)[J]. Bioscience, Biotechnology, and Biochemistry, 1995, 59(3): 439-444. DOI: 10.1271/bbb.59.439.
[7] KURTZMAN C P. Description of Komagataella phaffii sp. nov. and the transfer of Pichia pseudopastoris to the methylotrophic yeast genus Komagataella[J]. International Journal of Systematic and Evolutionary Microbiology, 2005, 55(Pt2): 973-976. DOI: 10.1099/ijs.0.63491-0.
[8] CEREGHINO J L, CREGG J M. Heterologous protein expression in the methylotrophic yeast Pichia pastoris[J]. FEMS Microbiology Reviews, 2000, 24(1): 45-66. DOI: 10.1111/j.1574-6976.2000.tb00532.x.
[9] AHMAD M, HIRZ M, PICHLER H, et al. Protein expression in Pichia pastoris: recent achievements and perspectives for heterologous protein production[J]. Applied Microbiology and Biotechnology, 2014, 98(12): 5301-5317. DOI: 10.1007/s00253-014-5732-5.
[10] 吴瑕, 刘志军, 查健, 等. 蛋清溶菌酶的重组合成及粗酶生化特性研究[J]. 食品与发酵工业, 2023, 49(4): 209-215. DOI: 10.13995/j.cnki.11-1802/ts.033346.
[11] AHMAD M, WINKLER C M, KOLMBAUER M, et al. Pichia pastoris protease-deficient and auxotrophic strains generated by a novel, user-friendly vector toolbox for genedeletion[J]. Yeast, 2019, 36(9): 557-570. DOI: 10.1002/yea.3426.
[12] BERNAUER L, RADKOHL A, LEHMAYER L G K, et al. Komagataella phaffii as emerging model organism in fundamental research[J]. Frontiers Microbiology, 2020, 11:607028. DOI: 10.3389/fmicb.2020.607028.
[13] BRAUN-GALLEANI S, DIAS J A, COUGHLAN A Y, et al. Genomic diversity and meiotic recombination among isolates of the biotech yeast Komagataella phaffii (Pichia pastoris)[J]. Microbial Cell Factories, 2019, 18(1): 211. DOI: 10.1186/s12934-019-1260-4.
[14] NAZARKO T Y, POLUPANOV A S, MANJITHAYA R R, et al. The requirement of sterol glucoside for pexophagy in yeast is dependent on the species and nature of peroxisome inducers[J]. Molecular Biology of the Cell, 2007, 18(1): 106-118. DOI: 10.1091/mbc.e06-06-0554.
[15] STURMBERGER L, CHAPPELL T, GEIER M, et al. Refined Pichia pastoris reference genome sequence[J]. Journal of Biotechnology, 2016, 235: 121-131. DOI: 10.1016/j.jbiotec.2016.04.023.
[16] KÜBERL A, SCHNEIDER J, THALLINGER G G, et al. High-quality genome sequence of Pichia pastoris CBS7435[J]. Journal of Biotechnology, 2011, 154(4): 312-320. DOI: 10.1016/j.jbiotec.2011.04.014.
[17] MATTANOVICH D, CALLEWAERT N, ROUZÉ P, et al. Open access to sequence: browsing the Pichia pastoris genome[J]. Microbial Cell Factories, 2009, 8: 53. DOI: 10.1186/1475-2859-8-53.
[18] VALLI M, TATTO N E, PEYMANN A, et al. Curation of the genome annotation of Pichia pastoris (Komagataella phaffii) CBS7435 from gene level to protein function[J]. FEMS Yeast Research, 2016, 16(6): fow051. DOI: 10.1093/femsyr/fow051.
[19] COSANO I, ALVAREZ P, MOLINA M, et al. Cloning and sequence analysis of the Pichia pastoris TRP1, IPP1 and HIS3 genes[J]. Yeast, 1998, 14(9): 861-867. DOI: 10.1002/(SICI)1097-0061(19980630)14:9<861::AID-YEA276>3.0.CO;2-N.
[20] LIN CEREGHINO G P, LIN CEREGHINO J, SUNGA A J, et al. New selectable marker/auxotrophic host strain combinations for molecular genetic manipulation of Pichia pastoris[J]. Gene, 2001, 263(1/2): 159-169. DOI: 10.1016/S0378-1119(00)00576-x.
[21] ZHU J X, GONG R Q, ZHU Q Y, et al. Genome-wide determination of gene essentiality by transposon insertion sequencing in yeast Pichia pastoris[J]. Scientific Reports, 2018, 8(1): 10223. DOI: 10.1038/s41598-018-28217-z.
[22] CHUNG B K S, LAKSHMANAN M, KLEMENT M, et al. Metabolic reconstruction and flux analysis of industrial Pichia yeasts[J]. Applied Microbiology and Biotechnology, 2013, 97(5): 1865-1873. DOI: 10.1007/s00253-013-4702-7.
[23] COUGHLAN A Y, HANSON S J, BYNE K P, et al. Centromeres of the yeast Komagataella phaffii (Pichia pastoris) have a simple inverted-repeat structure[J]. Genome Biology and Evolution, 2016, 8(8): 2482-2492. DOI: 10.1093/gbe/evw178.
[24] FITZGERALD-HAYES M, CLARKE L, CARBON J. Nucleotide sequence comparisons and functional analysis of yeast centromere DNAs[J]. Cell, 1982, 29(1): 235-244. DOI: 10.1016/0092-8674(82)90108-8.
[25] WOOD V, GWILLIAM R, RAJANDREAM M A, et al. The genome sequence of Schizosaccharomyces pombe[J]. Nature, 2002, 415(6874): 871-880. DOI: 10.1038/nature724.
[26] HANSON S J, WOLFE K H. An evolutionary perspective on yeast mating-type switching[J]. Genetics, 2017, 206(1): 9-32. DOI: 10.1534/genetics.117.202036.
[27] HABER J E. Mating-type genes and MAT switching in Saccharomyces cerevisiae[J]. Genetics, 2012, 191(1): 33-64. DOI: 10.1534/genetics.111.134577.
[28] MAEKAWA H, KANEKO Y. Inversion of the chromosomal region between two mating type loci switches the mating type in Hansenula polymorpha[J]. PLoS Genetics, 2014, 10(11): e1004796. DOI: 10.1371/journal.pgen.1004796.
[29] HANSON S J, BYRNE K P, WOLFE K H. Mating-type switching by chromosomal inversion in methylotrophic yeasts suggests an origin for the three-locus Saccharomyces cerevisiae system[J]. Proceedings of the National Academy of Sciences of the United States of America, 2014, 111(45): E4851-E4858. DOI: 10.1073/pnas.1416014111.
[30] 赵禹, 赵雅坤, 刘士琦, 等. 非常规酵母的分子遗传学及合成生物学研究进展[J]. 微生物学报, 2020, 60(8): 1574-1591. DOI: 10.13343/j.cnki.wsxb.20190512.
[31] SCHRICK K, GARVIK B, HARTWELL L H, et al. Mating in Saccharomyces cerevisiae: the role of the pheromone signal transduction pathway in the chemotropic response to pheromone[J]. Genetics ,1997, 147(1): 19-32. DOI: 10.1093/genetics/147.1.19.
[32] HEISTINGER L, GASSER B, MATTANOVICH D. Creation of stable heterothallic strains of Komagataella phaffii enables dissection of mating gene regulation[J]. Molecuar and Cellular Biology, 2017, 38(2): e00398-17. DOI: 10.1128/MCB.00398-17.
[33] HEISTINGER L, MOSER J, TATTO N E, et al. Identification and characterization of the Komagataella phaffii mating pheromone genes[J]. FEMS Yeast Research, 2018, 18(5): foy051. DOI: 10.1093/femsyr/foy051.
[34] GOLEMIS EA, KHAZAK V. Alternative yeast two-hybrid systems. The interaction trap and interaction mating[J]. Methods in Molecular Biology, 1997, 63: 197-218. DOI: 10.1385/0-89603-481-X:197.
[35] 欧阳立明, 张惠展, 张嗣同,等. 巴斯德毕赤酵母的基因表达系统研究进展[J]. 生物化学与生物物理进展, 2000, 27(2): 151-154. DOI: 10.3321/j.issn:1000-3282.2000.02.001.
[36] VAN DER KLEI I J, YURIMOTO H, SAKAI Y, et al. The significance of peroxisomes in methanol metabolism in methylotrophic yeast[J]. Biochimica et Biophysica Acta-Molecular Cell Research, 2006, 1763(12): 1453-1462. DOI: 10.1016/j.bbamcr.2006.07.016.
[37] YURIMOTO H, OKU M, SAKAI Y. Yeast methylotrophy: metabolism,gene regulation and peroxisome homeostasis[J]. International Journal of Microbiology, 2011, 2011: 101298. DOI: 10.1155/2011/101298.
[38] AGRAWAL G, SUBRAMANI S. De novo peroxisome biogenesis: evolving concepts and conundrums[J]. Biochimica et Biophysica Acta-Molecular Cell Research, 2016, 1863(5):892-901. DOI: 10.1016/j.bbamcr.2015.09.014.
[39] YUAN W, VEENHUIS M, VAN DER KLEI I J. The birth of yeast peroxisomes[J]. Biochimica et Biophysica Acta-Molecular Cell Research, 2016, 1863(5): 902-910. DOI: 10.1016/j.bbamcr.2015.09.008.
[40] DUNN W A, Jr, CREGG J M, KIEL J A K W, et al. Pexophagy: the selective autophagy of peroxisomes[J]. Autophagy, 2005, 1(2): 75-83. DOI: 10.4161/auto.1.2.1737.
[41] OKU M, SAKAI Y. Pexophagy in yeasts[J]. Biochimica et Biophysica Acta-Molecular Cell Research, 2016, 1863(5): 992-998. DOI: 10.1016/j.bbamcr.2015.09.023.
[42] MUKAIYAMA H, BABA M, OSUMI M, et al. Modification of a ubiquitin-like protein Paz2 conducted macropexophagy through formation of a novel membrane structure[J]. Molecular Biology of the Cell, 2004, 15(1): 58-70. DOI: 10.1091/mbc.e03-05-0340.
[43] CHIANG H L, SCHEKMAN R, HAMAMOTO S. Selective uptake of cytosolic, peroxisomal, and plasma membrane proteins into the yeast lysosome for degradation[J]. Journal of Biological Chemistry, 1996, 271(17): 9934-9941. DOI: 10.1074/jbc.271.17.9934.
[44] TIAN L, FU J P, WU M, et al. Evaluation of gallic acid on membrane damage of Yersinia enterocolitica and its application as a food preservative in pork[J]. International Journal of Food Microbiology, 2022, 374: 109720. DOI: 10.1016/j.ijfoodmicro.2022.109720.
[45] TIAN L, WANG X Y, ZHANG D, et al. Evaluation of the membrane damage mechanism of protocatechualdehyde against Yersinia enterocolitica and simulation of growth inhibition in pork[J]. Food Chemistry, 2021, 363: 130340. DOI: 10.1016/j.foodchem.2021.130340.
[46] YANG S Q, TIAN L, WANG X Y, et al. Metabolomics analysis and membrane damage measurement reveal the antibacterial mechanism of lipoic acid against Yersinia enterocolitica[J]. Food & Function, 2022, 13(22): 11476-11488. DOI: 10.1039/D2FO01306A.
[47] PICHLER H, EMMERSTORFER-AUGUSTIN A. Modification of membrane lipid compositions in single-celled organisms-from basics to applications[J]. Methods, 2018, 147: 50-65. DOI: 10.1016/j.ymeth.2018.06.009.
[48] WRIESSNEGGER T, LEITNER E, BELEGRATIS M R, et al. Lipid analysis of mitochondrial membranes from the yeast Pichia pastoris[J]. Biochimica et Biophysica Acta-Molecular and Cell Biology of Lipids, 2009,1791(3): 166-172. DOI: 10.1016/j.bbalip.2008.12.017.
[49] WRIESSNEGGER T, GÜBITZ G, LEITNER E, et al. Lipid composition of peroxisomes from the yeast Pichia pastoris grown on different carbon sources[J]. Biochimica et Biophysica Acta-Molecular and Cell Biology of Lipids, 2007, 1771(4): 455-461. DOI: 10.1016/j.bbalip.2007.01.004.
[50] KLUG L, TARAZONA P, GRUBER C, et al. The lipidome and proteome of microsomes from the methylotrophic yeast Pichia pastoris[J]. Biochimica et Biophysica Acta-Molecular and Cell Biology of Lipids, 2014, 1841(2): 215-226. DOI: 10.1016/j.bbalip.2013.11.005.
[51] WEI D, LI J, SHEN M D, et al. Cellular production of n-3 PUFAs and reduction of n-6-to-n-3 ratios in the pancreatic beta-cells and islets enhance insulin secretion and confer protection against cytokine-induced cell death[J]. Diabetes, 2010, 59(2): 471-478. DOI: 10.2337/db09-0284.
[52] ZINSER E, PALTAU F, DAUM G. Sterol composition of yeast organelle membranes and subcellular distribution of enzymes involved in sterol metabolism[J]. Journal of Bacteriology, 1993, 175(10): 2853-2858. DOI: 10.1128/jb.175.10.2853-2858.1993.
[53] MICHAELSON L V, ZÄUNER S, MARKHAM J E, et al. Functional characterization of a higher plant sphingolipid Delta4-desaturase: defining the role of sphingosine and sphingosine-1-phosphate in Arabidopsis[J]. Plant Physiology, 2009, 149(1): 487-498. DOI: 10.1104/pp.108.129411.
[54] KOCH B, SCHMIDT C, DAUM G. Storage lipids of yeasts: a survey of nonpolar lipid metabolism in Saccharomyces cerevisiae, Pichia pastoris, and Yarrowia lipolytica[J]. FEMS Microbiology Reviews, 2014, 38(5): 892-915. DOI: 10.1111/1574-6976.12069.
[55] TIAN L, WU M, LI H, et al. Transcriptome analysis of Micrococcus luteus in response to treatment with protocatechuic acid[J]. Journal of Applied Microbiology, 2022, 133(5): 3139-3149. DOI: 10.1111/jam.15743.
[56] WU M, TIAN L, FU J P, et al. Antibacterial mechanism of Protocatechuic acid against Yersinia enterocolitica and its application in pork[J]. Food Control, 2022, 133(Part A): 108573. DOI: 10.1016/j.foodcont.2021.108573.
[57] KOCK C, DUFRÊNE Y F, HEINISCH J J. Up against the wall: is yeast cell wall integrity ensured by mechanosensing in plasma membrane microdomains?[J]. Applied and Environmental Microbiology, 2015, 81(3): 806-811. DOI: 10.1128/AEM.03273-14.
[58] OHSAWA S, YURIMOTO H, SAKAI Y. Novel function of Wsc proteins as a methanol-sensing machinery in the yeast Pichia pastoris[J]. Molecular Microbiology, 2017, 104(2): 349-363. DOI: 10.1111/mmi.13631.
[59] COSANO I C, MARTÍN H, FLÁNDEZ M, et al. Pim1, a MAP kinase involved in cell wall integrity in Pichia pastoris[J]. Molecular Genetics and Genomics, 2001, 265(4): 604-614. DOI: 10.1007/s004380100452.
[60] ZHANG C B, MA Y, MIAO H B, et al. Transcriptomic analysis of Pichia pastoris (Komagataella phaffii) GS115 during heterologous protein production using a high-cell-density fed-batch cultivation strategy[J]. Frontiers in Microbiology, 2020, 11: 463. DOI: 10.3389/fmicb.2020.00463.
[61] BRADY J R, WHITTAKER C A, TAN M C, et al. Comparative genome-scale analysis of Pichia pastoris variants informs selection of an optimal base strain[J]. Biotechnology and Bioengineering, 2020, 117(2): 543-555. DOI: 10.1002/bit.27209.
[62] LARSEN S, WEAVER J, DE SA CAMPOS K, et al. Mutant strains of Pichia pastoris with enhanced secretion of recombinant proteins[J]. Biotechnology Letters, 2013, 35(11): 1925-1935. DOI: 10.1007/s10529-013-1290-7.
[63] 彭毅, 杨希才, 康良仪. 影响甲醇酵母外源蛋白表达的因素[J]. 生物技术通报, 2000, 16(4): 33-36. DOI: 10.3969/j.issn.1002-5464.2000.04.0D7.
[64] Invitrogen. Pichia Expression Kit[Z]. Carlsbad, CA: Invitrogen Corporation, 2014.
[65] CREGG J M, TSCHOPP J F, STILLMAN C, et al. High-level expression and efficient assembly of hepatitis B surface antigen in the methylotrophic yeast Pichia pastoris[J]. Bio/Technology, 1987, 5(5): 479-485. DOI: 10.1038/nbt0587-479.
[66] SREEKRISHNA K, NELLES L, POTENZ R, et al. High-level expression, purification, and characterization of recombinant human tumor necrosis factor synthesized in the methylotrophic yeast Pichia pastoris[J]. Biochemistry, 1989, 28(9): 4117-4125. DOI: 10.1021/bi00435a074.
[67] SIEGEL R S, BUCKHOLZ R G, THILL G P, et al. Production of epider growth factor in methylotrophic yeast cells:WO9010697[P]. 1990-03-15.
[68] MATTEWS B J, VOSSHALL L B. How to turn an organism into a model organism in 10 ‘easy’ steps[J]. The Journal of Experimental Biology, 2020, 223(Pt Suppl 1): jeb218198. DOI: 10.1242/jeb.218198.
[69] DICARLO J E, CONLEY A J, PENTTILÄ M, et al. Yeast oligo-mediated genome engineering (YOGE)[J]. ACS Synthetic Biology, 2013, 2(12): 741-749. DOI: 10.1021/sb400117c.
[70] GIAEVER G, NISLOW C. The yeast deletion collection: a decade of functional genomics[J]. Genetics, 2014, 197(2): 451-465. DOI: 10.1534/genetics.114.161620.
[71] BERNAUER L, RADKOHL A, GABRIELA L, et al. Komagataella phaffii as emerging model organism in fundamental research[J]. Frontiers in Microbiology, 2021, 11: 607028. DOI: 10.3389/fmicb.2020.607028.
[1] LI Yayuan, WANG Guangxing, LI Xinwen, GUO Zhenhua, GUAN Guijun. Expression of nup58 in Medaka and Its Potential Role in Sex Differentiation [J]. Journal of Guangxi Normal University(Natural Science Edition), 2024, 42(1): 168-179.
[2] ZOU Lei, XING Bing, YANG Liu. Construction of AC16 Human Cardiomyocyte Cell Line with Mutant LMNA Gene by CRISPR/Cas9 [J]. Journal of Guangxi Normal University(Natural Science Edition), 2023, 41(3): 163-170.
[3] ZHOU Jing, LI Yinling, CHEN Qiaoyuan, LIN Wanhua. Construction of Sdr9c7 Gene Conditional Knockout Mice and Phenotypic Analysis [J]. Journal of Guangxi Normal University(Natural Science Edition), 2023, 41(2): 147-153.
[4] JIANG Jiao-yun, FENG Long, QU Xian-cheng, TIAN Wen-fei. Clone and Expression of a Novel Sex-related Gene (F4) in Gonads During Sex Reversal in the Rice Field Eel (Monopterus albus) [J]. Journal of Guangxi Normal University(Natural Science Edition), 2013, 31(4): 121-127.
[5] ZHAO Zhi-chang, ZHANG Jian-jun, ZHANG Wan-rong, LIU Zhen, LI Xu-feng, YANG Yi. Over-expression of Arabidopsis DnaJ (Hsp40) Contributes to NaCl-stress Tolerance of Escherichia coli [J]. Journal of Guangxi Normal University(Natural Science Edition), 2010, 28(1): 54-57.
[6] CHEN Dun-xue, SHI Chang-you, BIN Shi-yu, CHU Wu-ying, TANG Wang-lin, LIN Qian. CAT1,EAAC1 and Pept1 mRNA in Intestinal for Detection Developmental Expression in Tibetan [J]. Journal of Guangxi Normal University(Natural Science Edition), 2010, 28(1): 63-67.
[7] ZHAO Fa-lan, BING Shi-yu, CHEN Dun-xue, NONG Xiao-xian, LIU Xi-liang. cDNA Cloning and Sequence Analysis of the Myosin Light Chain 1 Gene in Siniperca scherzeri [J]. Journal of Guangxi Normal University(Natural Science Edition), 2011, 29(2): 99-103.
[8] WU Yajie, YANG Yuefei, FAN Bojun, XU Lei, JU Huiming. Construction and Efficiency Detection of a Porcine PPARD Vector Using Improved CRISPR/Cas9 System [J]. Journal of Guangxi Normal University(Natural Science Edition), 2023, 41(6): 132-138.
Viewed
Full text


Abstract

Cited

  Shared   
  Discussed   
No Suggested Reading articles found!