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Tsuda M, Nonaka K. Recent progress on heterologous protein production in methylotrophic yeast systems. World J Microbiol Biotechnol 2024; 40:200. [PMID: 38730212 PMCID: PMC11087369 DOI: 10.1007/s11274-024-04008-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 04/27/2024] [Indexed: 05/12/2024]
Abstract
Recombinant protein production technology is widely applied to the manufacture of biologics used as drug substances and industrial proteins such as recombinant enzymes and bioactive proteins. Various heterologous protein production systems have been developed using prokaryotic and eukaryotic hosts. Especially methylotrophic yeast in eukaryotic hosts is suggested to be particularly valuable because such systems have the following advantages: protein secretion into culture broth, eukaryotic quality control systems, a post-translational modification system, rapid growth, and established recombinant DNA tools and technologies such as strong promoters, effective selection markers, and gene knock-in and -out systems. Many methylotrophic yeasts such as the genera Candida, Ogataea, and Komagataella have been studied since methylotrophic yeast was first isolated in 1969. The methanol-consumption-related genes in methylotrophic yeast are strongly and strictly regulated under methanol-containing conditions. The well-regulated gene expression systems under the methanol-inducible gene promoter lead to the potential application of heterologous protein production in methylotrophic yeast. In this review, we describe the recent progress of heterologous protein production technology in methylotrophic yeast and introduce Ogataea minuta as an alternative production host as a substitute for K. phaffii and O. polymorpha.
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Affiliation(s)
- Masashi Tsuda
- Biologics Technology Research Laboratories I, Daiichi Sankyo Co., Ltd., 2716-1 Kurakake, Akaiwa, Chiyoda, Gunma, 370-0503, Japan.
| | - Koichi Nonaka
- Biologics Technology Research Laboratories I, Daiichi Sankyo Co., Ltd., 2716-1 Kurakake, Akaiwa, Chiyoda, Gunma, 370-0503, Japan
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Selection of the methylotrophic yeast Ogataea minuta as a high-producing host for heterologous protein expression. J Biosci Bioeng 2023; 135:196-202. [PMID: 36702678 DOI: 10.1016/j.jbiosc.2022.12.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/28/2022] [Accepted: 12/11/2022] [Indexed: 01/26/2023]
Abstract
Three Ogataea minuta var. minuta strains have been deposited as NBRC 0975, NBRC 10402, and NBRC 10746 in the National Institute of Technology and Evaluation (NITE) Biological Resource Center (NBRC) collection. We investigated the ability to produce secretory proteins and several genotypic and phenotypic characteristics in order to select the best strain for heterologous protein expression. NBRC 10746 showed the best performance as evaluated by Cypridina noctiluca luciferase expression. Subsequently, clone #5-30 named tat06213, which was obtained by single-colony isolation from NBRC 10746, was established as a promising host for heterologous protein expression. To deepen our understanding of the characteristics of O.minuta var. minuta strains, sequence analysis of the D1/D2 domain of large subunit rRNA was conducted and the resulting phylogenetic tree derived from the D1/D2 domain showed that NBRC 10402 and NBRC 10746 were grouped into a different cluster far from NBRC 0975. Furthermore, a chromosome structure topology with electrophoretic karyotype and AOX1 loci analyzed by pulsed-field gel electrophoresis with Southern blotting showed different chromosome patterns and AOX1-hybridization loci among the strains. Additionally, the sequences of the promoter regions of the cloned AOX1 genes were not identical among the three strains. These findings might explain the differences in heterologous protein expression among the tested O. minuta var. minuta strains.
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Calderón CE, Rotem N, Harris R, Vela‐Corcía D, Levy M. Pseudozyma aphidis activates reactive oxygen species production, programmed cell death and morphological alterations in the necrotrophic fungus Botrytis cinerea. MOLECULAR PLANT PATHOLOGY 2019; 20:562-574. [PMID: 30537338 PMCID: PMC6637909 DOI: 10.1111/mpp.12775] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Many types of yeast have been studied in the last few years as potential biocontrol agents against different phytopathogenic fungi. Their ability to control plant diseases is mainly through combined modes of action. Among them, antibiosis, competition for nutrients and niches, induction of systemic resistance in plants and mycoparasitism have been the most studied. In previous work, we have established that the epiphytic yeast Pseudozyma aphidis inhibits Botrytis cinerea through induced resistance and antibiosis. Here, we demonstrate that P. aphidis adheres to B. cinerea hyphae and competes with them for nutrients. We further show that the secreted antifungal compounds activate the production of reactive oxygen species and programmed cell death in B. cinerea mycelium. Finally, P. aphidis and its secreted compounds negatively affect B. cinerea hyphae, leading to morphological alterations, including hyphal curliness, vacuolization and branching, which presumably affects the colonization ability and infectivity of B. cinerea. This study demonstrates additional modes of action for P. aphidis and its antifungal compounds against the plant pathogen B. cinerea.
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Affiliation(s)
- Claudia E. Calderón
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and EnvironmentThe Hebrew University of JerusalemRehovot76100Israel
| | - Neta Rotem
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and EnvironmentThe Hebrew University of JerusalemRehovot76100Israel
| | - Raviv Harris
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and EnvironmentThe Hebrew University of JerusalemRehovot76100Israel
| | - David Vela‐Corcía
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and EnvironmentThe Hebrew University of JerusalemRehovot76100Israel
| | - Maggie Levy
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and EnvironmentThe Hebrew University of JerusalemRehovot76100Israel
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Yoko-O T, Komatsuzaki A, Yoshihara E, Umemura M, Chiba Y. Mating type switching, formation of diploids, and sporulation in the methylotrophic yeast Ogataea minuta. J Biosci Bioeng 2018; 127:1-7. [PMID: 30064813 DOI: 10.1016/j.jbiosc.2018.07.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 06/08/2018] [Accepted: 07/09/2018] [Indexed: 10/28/2022]
Abstract
Ogataea minuta is a methylotrophic yeast that is closely related to Ogataea (Hansenula) polymorpha. Like other methylotrophic yeasts, O. minuta also possesses strongly methanol-inducible genes, such as AOX1. We have focused on O. minuta as a host for the production of therapeutic glycoproteins. However, genetic methods, which are required for the construction of strains by breeding, have not yet been established in this organism. In this study, we investigated the O. minuta mechanisms of mating and sporulation, which would facilitate genetic analysis in this species. Specifically, we determined DNA sequences around the MAT locus in O. minuta strain NBRC 10746, and found that two MAT loci were flanked by a pair of inverted repeat sequences, as reported in O.polymorpha (Maekawa and Kaneko, PLOS Genet., 10, e1004796, 2014). As in O. polymorpha, mating type in O. minuta appears to be switched by inversion of the chromosomal region between the two MAT loci. We successfully obtained O. minuta diploid cells, which showed vegetative growth on rich medium. The size of the diploid cells was 1.3-fold larger than haploid cells of this species. Diploid cells formed ascospores, which contained 2-4 spores, under nutrient starvation conditions. Phenotypes of the resultant haploid cells exhibited Mendelian segregation, indicating that genetic approaches are applicable to O. minuta.
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Affiliation(s)
- Takehiko Yoko-O
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Umezono, Tsukuba 305-8568, Japan.
| | - Akiko Komatsuzaki
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Umezono, Tsukuba 305-8568, Japan
| | - Erina Yoshihara
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Umezono, Tsukuba 305-8568, Japan; The School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Mariko Umemura
- The School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Yasunori Chiba
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Umezono, Tsukuba 305-8568, Japan
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Starmer WT, Ganter PF, Phaff HJ. QUANTUM AND CONTINUOUS EVOLUTION OF DNA BASE COMPOSITION IN THE YEAST GENUS PICHIA. Evolution 2017; 40:1263-1274. [PMID: 28563510 DOI: 10.1111/j.1558-5646.1986.tb05750.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/1985] [Accepted: 07/07/1986] [Indexed: 11/29/2022]
Abstract
This paper investigates the noncontinuous nature and evolution of the base composition of nuclear DNA (expressed as mol% guanine + cytosine) in species of the yeast genus Pichia (sensu Kurtzman, 1984b). The pattern of change in the G + C contents in species of this genus, which range from about 27 to 52 mol%, was evaluated. When specifically those species of Pichia were analyzed that have evolved in necroses of cactus species and associated Drosophila, a periodic change in the G + C contents of approximately 3.0-3.2 mol% was detected by a "bootstrapping" method, Fourier analysis, and a nonlinear trigonometric model. Pichia species occurring in exudates of broad-leaved deciduous trees or associated Drosophila and substrates such as soil and water ("other") showed a periodicity of 2.5-2.6 mol%, whereas species associated with conifers and associated bark beetles showed no significant periodicity. Periodicity in the most recent association (cactus and resident Drosophila) as compared to the lack of periodicity in the oldest association (conifer-beetle) may indicate mixed evolutionary processes. Low mol% G + C values appear more frequently in the relatively recent cactus and Drosophila-associated yeast species. In addition, low mol% G + C species do not display the ancestral bud-meiosis mode of sexual reproduction which occurs frequently in medium to high mol% G + C yeasts. It was found that the mol% G + C content of the Drosophila- and cactus-associated Pichia species is positively correlated with the number of compounds fermented or respired by these yeast species. Possible reasons for the periodic changes in mol% G + C content accompanying speciation include aneuploidy, allopolyploidy, the presence of nuclear plasmids, and regular differences in moderately repetitive portions of DNA. Since significant DNA complementarity is virtually limited to species within a relatively narrow G + C group, this suggests that there are at least two processes which alter the G + C content between species, one saltational and one continuous.
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Affiliation(s)
| | - Philip F Ganter
- Biology Department, Syracuse University, Syracuse, NY, 13210
| | - Herman J Phaff
- Department of Food Science and Technology, University of California, Davis, Davis, CA, 95616
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Gafni A, Calderon CE, Harris R, Buxdorf K, Dafa-Berger A, Zeilinger-Reichert E, Levy M. Biological control of the cucurbit powdery mildew pathogen Podosphaera xanthii by means of the epiphytic fungus Pseudozyma aphidis and parasitism as a mode of action. FRONTIERS IN PLANT SCIENCE 2015; 6:132. [PMID: 25814995 PMCID: PMC4356082 DOI: 10.3389/fpls.2015.00132] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 02/18/2015] [Indexed: 05/13/2023]
Abstract
Epiphytic yeasts, which colonize plant surfaces, may possess activity that can be harnessed to help plants defend themselves against various pathogens. Due to their unique characteristics, epiphytic yeasts belonging to the genus Pseudozyma hold great potential for use as biocontrol agents. We identified a unique, biologically active isolate of the epiphytic yeast Pseudozyma aphidis that is capable of inhibiting Botrytis cinerea via a dual mode of action, namely induced resistance and antibiosis. Here, we show that strain L12 of P. aphidis can reduce the severity of powdery mildew caused by Podosphaera xanthii on cucumber plants with an efficacy of 75%. Confocal and scanning electron microscopy analyses demonstrated P. aphidis proliferation on infected tissue and its production of long hyphae that parasitize the powdery mildew hyphae and spores as an ectoparasite. We also show that crude extract of P. aphidis metabolites can inhibit P. xanthii spore germination in planta. Our results suggest that in addition to its antibiosis as mode of action, P. aphidis may also act as an ectoparasite on P. xanthii. These results indicate that P. aphidis strain L12 has the potential to control powdery mildew.
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Affiliation(s)
- Aviva Gafni
- Plant Pathology and Microbiology, Hebrew University of JerusalemJerusalem, Israel
| | - Claudia E. Calderon
- Plant Pathology and Microbiology, Hebrew University of JerusalemJerusalem, Israel
| | - Raviv Harris
- Plant Pathology and Microbiology, Hebrew University of JerusalemJerusalem, Israel
| | - Kobi Buxdorf
- Plant Pathology and Microbiology, Hebrew University of JerusalemJerusalem, Israel
| | - Avis Dafa-Berger
- Plant Pathology and Microbiology, Hebrew University of JerusalemJerusalem, Israel
| | - Einat Zeilinger-Reichert
- The Interdepartmental Equipment Facility, The Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of JerusalemJerusalem, Israel
| | - Maggie Levy
- Plant Pathology and Microbiology, Hebrew University of JerusalemJerusalem, Israel
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Buxdorf K, Rahat I, Gafni A, Levy M. The epiphytic fungus Pseudozyma aphidis induces jasmonic acid- and salicylic acid/nonexpressor of PR1-independent local and systemic resistance. PLANT PHYSIOLOGY 2013; 161:2014-22. [PMID: 23388119 PMCID: PMC3613472 DOI: 10.1104/pp.112.212969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2012] [Accepted: 02/02/2013] [Indexed: 05/07/2023]
Abstract
Pseudozyma spp. are yeast-like fungi, classified in the Ustilaginales, which are mostly epiphytic or saprophytic and are not pathogenic to plants. Several Pseudozyma species have been reported to exhibit biological activity against powdery mildews. However, previous studies have reported that Pseudozyma aphidis, which can colonize plant surfaces, is not associated with the collapse of powdery mildew colonies. In this report, we describe a novel P. aphidis strain and study its interactions with its plant host and the plant pathogen Botrytis cinerea. This isolate was found to secrete extracellular metabolites that inhibit various fungal pathogens in vitro and significantly reduce B. cinerea infection in vivo. Moreover, P. aphidis sensitized Arabidopsis (Arabidopsis thaliana) plants' defense machinery via local and systemic induction of pathogenesis-related1 (PR1) and plant defensin1.2 (PDF1.2) expression. P. aphidis also reduced B. cinerea infection, locally and systemically, in Arabidopsis mutants impaired in jasmonic acid (JA) or salicylic acid (SA) signaling. Thus, in addition to direct inhibition, P. aphidis may inhibit B. cinerea infection via induced resistance in a manner independent of SA, JA, and Nonexpressor of PR1 (NPR1). P. aphidis primed the plant defense machinery and induced stronger activation of PDF1.2 after B. cinerea infection. Finally, P. aphidis fully or partially reconstituted PR1 and PDF1.2 expression in npr1-1 mutant and in plants with the SA hydroxylase NahG transgene, but not in a jasmonate resistant1-1 mutant, after B. cinerea infection, suggesting that P. aphidis can bypass the SA/NPR1, but not JA, pathway to activate PR genes. Thus, either partial gene activation is sufficient to induce resistance, or the resistance is not directed solely through PR1 and PDF1.2 but probably through other pathogen-resistance genes or pathways as well.
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Affiliation(s)
| | | | | | - Maggie Levy
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
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Tani Y, Kato N, Yamada H. Utilization of methanol by yeasts. ADVANCES IN APPLIED MICROBIOLOGY 1978; 24:165-86. [PMID: 367098 DOI: 10.1016/s0065-2164(08)70639-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Craveri R, Cavazzoni V, Sarra PG, Succi G, Molteni L, Cardini G, Di Fiore L. Taxonomical examination and characterization of a methanol-utilizing yeast. Antonie Van Leeuwenhoek 1976; 42:533-40. [PMID: 1087866 DOI: 10.1007/bf00410184] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The morphological, cultural, and physiological characteristics are described of a yeast, LI70, which uses methanol as its source of energy and carbon; these characteristics have made it possible to identify the strain as Candida boidinii Ramirez. The identification was confirmed by a DNA-DNA genetic homology of 99.43% with the type strain of C. boidinii. Strain LI70 is not pathogenic.
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