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Claes K, Van Herpe D, Vanluchene R, Roels C, Van Moer B, Wyseure E, Vandewalle K, Eeckhaut H, Yilmaz S, Vanmarcke S, Çıtak E, Fijalkowska D, Grootaert H, Lonigro C, Meuris L, Michielsen G, Naessens J, van Schie L, De Rycke R, De Bruyne M, Borghgraef P, Callewaert N. OPENPichia: licence-free Komagataella phaffii chassis strains and toolkit for protein expression. Nat Microbiol 2024; 9:864-876. [PMID: 38443579 PMCID: PMC10914597 DOI: 10.1038/s41564-023-01574-w] [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: 03/23/2023] [Accepted: 12/01/2023] [Indexed: 03/07/2024]
Abstract
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 hoc1tr derivative that we named OPENPichia as well as a synthetic, modular expression vector toolkit under liberal end-user distribution licences as an unencumbered OPENPichia resource for the microbial biotechnology community.
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Affiliation(s)
- Katrien Claes
- Center for Medical Biotechnology, VIB, Ghent, Belgium.
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.
| | - Dries Van Herpe
- Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Inbiose NV, Ghent, Belgium
| | - Robin Vanluchene
- Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Charlotte Roels
- Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Berre Van Moer
- Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Elise Wyseure
- Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Kristof Vandewalle
- Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Hannah Eeckhaut
- Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Semiramis Yilmaz
- Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Sandrine Vanmarcke
- Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Erhan Çıtak
- Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Daria Fijalkowska
- Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Hendrik Grootaert
- Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Chiara Lonigro
- Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Leander Meuris
- Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Gitte Michielsen
- Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Justine Naessens
- Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Loes van Schie
- Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Riet De Rycke
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- BioImaging Core, VIB, Ghent, Belgium
| | - Michiel De Bruyne
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- BioImaging Core, VIB, Ghent, Belgium
| | | | - Nico Callewaert
- Center for Medical Biotechnology, VIB, Ghent, Belgium.
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.
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Dutreux F, Dutta A, Peltier E, Bibi-Triki S, Friedrich A, Llorente B, Schacherer J. Lessons from the meiotic recombination landscape of the ZMM deficient budding yeast Lachancea waltii. PLoS Genet 2023; 19:e1010592. [PMID: 36608114 PMCID: PMC9851511 DOI: 10.1371/journal.pgen.1010592] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 01/19/2023] [Accepted: 12/22/2022] [Indexed: 01/09/2023] Open
Abstract
Meiotic recombination is a driving force for genome evolution, deeply characterized in a few model species, notably in the budding yeast Saccharomyces cerevisiae. Interestingly, Zip2, Zip3, Zip4, Spo16, Msh4, and Msh5, members of the so-called ZMM pathway that implements the interfering meiotic crossover pathway in S. cerevisiae, have been lost in Lachancea yeast species after the divergence of Lachancea kluyveri from the rest of the clade. In this context, after investigating meiosis in L. kluyveri, we determined the meiotic recombination landscape of Lachancea waltii. Attempts to generate diploid strains with fully hybrid genomes invariably resulted in strains with frequent whole-chromosome aneuploidy and multiple extended regions of loss of heterozygosity (LOH), which mechanistic origin is so far unclear. Despite the lack of multiple ZMM pro-crossover factors in L. waltii, numbers of crossovers and noncrossovers per meiosis were higher than in L. kluyveri but lower than in S. cerevisiae, for comparable genome sizes. Similar to L. kluyveri but opposite to S. cerevisiae, L. waltii exhibits an elevated frequency of zero-crossover bivalents. Lengths of gene conversion tracts for both crossovers and non-crossovers in L. waltii were comparable to those observed in S. cerevisiae and shorter than in L. kluyveri despite the lack of Mlh2, a factor limiting conversion tract size in S. cerevisiae. L. waltii recombination hotspots were not shared with either S. cerevisiae or L. kluyveri, showing that meiotic recombination hotspots can evolve at a rather limited evolutionary scale within budding yeasts. Finally, L. waltii crossover interference was reduced relative to S. cerevisiae, with interference being detected only in the 25 kb distance range. Detection of positive inference only at short distance scales in the absence of multiple ZMM factors required for interference-sensitive crossovers in other systems likely reflects interference between early recombination precursors such as DSBs.
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Affiliation(s)
- Fabien Dutreux
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Abhishek Dutta
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Emilien Peltier
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | | | - Anne Friedrich
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Bertrand Llorente
- CNRS UMR7258, INSERM U1068, Aix Marseille Université UM105, Institut Paoli-Calmettes, CRCM, Marseille, France,* E-mail: (BL); (JS)
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France,Institut Universitaire de France (IUF), Paris, France,* E-mail: (BL); (JS)
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Offei B, Braun-Galleani S, Venkatesh A, Casey WT, O’Connor KE, Byrne KP, Wolfe KH. Identification of genetic variants of the industrial yeast Komagataella phaffii (Pichia pastoris) that contribute to increased yields of secreted heterologous proteins. PLoS Biol 2022; 20:e3001877. [PMID: 36520709 PMCID: PMC9754263 DOI: 10.1371/journal.pbio.3001877] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 10/13/2022] [Indexed: 12/23/2022] Open
Abstract
The yeast Komagataella phaffii (formerly called Pichia pastoris) is used widely as a host for secretion of heterologous proteins, but only a few isolates of this species exist and all the commonly used expression systems are derived from a single genetic background, CBS7435 (NRRL Y-11430). We hypothesized that other genetic backgrounds could harbor variants that affect yields of secreted proteins. We crossed CBS7435 with 2 other K. phaffii isolates and mapped quantitative trait loci (QTLs) for secretion of a heterologous protein, β-glucosidase, by sequencing individual segregant genomes. A major QTL mapped to a frameshift mutation in the mannosyltransferase gene HOC1, which gives CBS7435 a weaker cell wall and higher protein secretion than the other isolates. Inactivation of HOC1 in the other isolates doubled β-glucosidase secretion. A second QTL mapped to an amino acid substitution in IRA1 that tripled β-glucosidase secretion in 1-week batch cultures but reduced cell viability, and its effects are specific to this heterologous protein. Our results demonstrate that QTL analysis is a powerful method for dissecting the basis of biotechnological traits in nonconventional yeasts, and a route to improving their industrial performance.
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Affiliation(s)
- Benjamin Offei
- UCD Conway Institute and School of Medicine, University College Dublin, Dublin, Ireland
| | - Stephanie Braun-Galleani
- UCD Conway Institute and School of Medicine, University College Dublin, Dublin, Ireland
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Anjan Venkatesh
- UCD Conway Institute and School of Medicine, University College Dublin, Dublin, Ireland
| | - William T. Casey
- Bioplastech Ltd., NovaUCD, Belfield Innovation Park, University College Dublin, Dublin, Ireland
| | - Kevin E. O’Connor
- UCD Earth Institute and School of Biomolecular & Biomedical Science, University College Dublin, Dublin, Ireland
- BiOrbic Bioeconomy SFI Research Centre, University College Dublin, Dublin, Ireland
| | - Kevin P. Byrne
- UCD Conway Institute and School of Medicine, University College Dublin, Dublin, Ireland
| | - Kenneth H. Wolfe
- UCD Conway Institute and School of Medicine, University College Dublin, Dublin, Ireland
- * E-mail:
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Heterologous Expression of Extracellular Proteinase pAsPs of Aspergillus pseudotamarii in Komagataella phaffii. Int J Mol Sci 2022; 23:ijms232315035. [PMID: 36499360 PMCID: PMC9739362 DOI: 10.3390/ijms232315035] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/25/2022] [Accepted: 11/26/2022] [Indexed: 12/02/2022] Open
Abstract
Neutral protease pAsPs gene was obtained by sequence optimization of NpI protease from Aspergillus pseudotamarii. pAsPs was for the first time integrated in the genome of yeast strain Komagataella phaffii T07, and then produced in a 5 L bioreactor with an enzyme yield of 150,800 U/mL of culture liquid towards casein. The specific activity of the pAsPs was 7,657,000 U/mg toward casein, 2320 U/mg toward hemoglobin, and 25,344 U/mg toward azocasein per 1 mg of the protein. The enzyme was found to be inhibited by Cu2+. Optimal activity pH was shown in the range of pH 6.5-8.0, and optimal temperature-50-60 °C. The molecular mass of the recombinant protease pAsPs was shown to be 67.5 kDa. Mass-spectrometric analysis confirmed the identity of the amino acid sequence of the obtained pAsPs preparation with the predicted sequence, with 17% coverage and protein score 288. Thus, the novel neutral protease pAsPs is a promising candidate for large-scale use in manufacturing, including the food industry.
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The teenage years of yeast population genomics trace history, admixing and getting wilder. Curr Opin Genet Dev 2022; 75:101942. [PMID: 35753210 DOI: 10.1016/j.gde.2022.101942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 11/22/2022]
Abstract
Population genomics studies the evolutionary processes that shape intraspecies genetic variations. In this review, I explore the insights into yeast-population genomics that have emerged from recent advances in sequencing. Genomes of the model Saccharomyces cerevisiae and many new yeast species from around the world are being used to address various aspects of population biology, including geographical origin, the level of introgression, domestication signatures, and outcrossing frequency. New long-read sequencing has enabled a greater capacity to quantify these variations at a finer resolution from complete de novo genomes at the population scale to phasing subgenomes of different origins. These resources provide a platform to dissect the relationship between phenotypes across environmental niches.
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Heistinger L, Dohm JC, Paes BG, Koizar D, Troyer C, Ata Ö, Steininger-Mairinger T, Mattanovich D. Genotypic and phenotypic diversity among Komagataella species reveals a hidden pathway for xylose utilization. Microb Cell Fact 2022; 21:70. [PMID: 35468837 PMCID: PMC9036795 DOI: 10.1186/s12934-022-01796-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 03/06/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The yeast genus Komagataella currently consists of seven methylotrophic species isolated from tree environments. Well-characterized strains of K. phaffii and K. pastoris are important hosts for biotechnological applications, but the potential of other species from the genus remains largely unexplored. In this study, we characterized 25 natural isolates from all seven described Komagataella species to identify interesting traits and provide a comprehensive overview of the genotypic and phenotypic diversity available within this genus. RESULTS Growth tests on different carbon sources and in the presence of stressors at two different temperatures allowed us to identify strains with differences in tolerance to high pH, high temperature, and growth on xylose. As Komagataella species are generally not considered xylose-utilizing yeasts, xylose assimilation was characterized in detail. Growth assays, enzyme activity measurements and 13C labeling confirmed the ability of K. phaffii to utilize D-xylose via the oxidoreductase pathway. In addition, we performed long-read whole-genome sequencing to generate genome assemblies of all Komagataella species type strains and additional K. phaffii and K. pastoris isolates for comparative analysis. All sequenced genomes have a similar size and share 83-99% average sequence identity. Genome structure analysis showed that K. pastoris and K. ulmi share the same rearrangements in difference to K. phaffii, while the genome structure of K. kurtzmanii is similar to K. phaffii. The genomes of the other, more distant species showed a larger number of structural differences. Moreover, we used the newly assembled genomes to identify putative orthologs of important xylose-related genes in the different Komagataella species. CONCLUSIONS By characterizing the phenotypes of 25 natural Komagataella isolates, we could identify strains with improved growth on different relevant carbon sources and stress conditions. Our data on the phenotypic and genotypic diversity will provide the basis for the use of so-far neglected Komagataella strains with interesting characteristics and the elucidation of the genetic determinants of improved growth and stress tolerance for targeted strain improvement.
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Affiliation(s)
- Lina Heistinger
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), 1190, Vienna, Austria.
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093, Zürich, Switzerland.
| | - Juliane C Dohm
- Department of Biotechnology, Institute of Computational Biology, University of Natural Resources and Life Sciences Vienna (BOKU), 1190, Vienna, Austria
| | - Barbara G Paes
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), 1190, Vienna, Austria
- Department of Cell Biology, Institute of Biological Sciences, University of Brasilia (UnB), Brasilia, Brazil
| | - Daniel Koizar
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), 1190, Vienna, Austria
| | - Christina Troyer
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences Vienna (BOKU), 1190, Vienna, Austria
| | - Özge Ata
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), 1190, Vienna, Austria
- Austrian Centre of Industrial Biotechnology (Acib GmbH), 1190, Vienna, Austria
| | - Teresa Steininger-Mairinger
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences Vienna (BOKU), 1190, Vienna, Austria
| | - Diethard Mattanovich
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), 1190, Vienna, Austria
- Austrian Centre of Industrial Biotechnology (Acib GmbH), 1190, Vienna, Austria
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Bustos C, Quezada J, Veas R, Altamirano C, Braun-Galleani S, Fickers P, Berrios J. Advances in Cell Engineering of the Komagataella phaffii Platform for Recombinant Protein Production. Metabolites 2022; 12:346. [PMID: 35448535 PMCID: PMC9027633 DOI: 10.3390/metabo12040346] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/01/2022] [Accepted: 04/06/2022] [Indexed: 12/11/2022] Open
Abstract
Komagataella phaffii (formerly known as Pichia pastoris) has become an increasingly important microorganism for recombinant protein production. This yeast species has gained high interest in an industrial setting for the production of a wide range of proteins, including enzymes and biopharmaceuticals. During the last decades, relevant bioprocess progress has been achieved in order to increase recombinant protein productivity and to reduce production costs. More recently, the improvement of cell features and performance has also been considered for this aim, and promising strategies with a direct and substantial impact on protein productivity have been reported. In this review, cell engineering approaches including metabolic engineering and energy supply, transcription factor modulation, and manipulation of routes involved in folding and secretion of recombinant protein are discussed. A lack of studies performed at the higher-scale bioreactor involving optimisation of cultivation parameters is also evidenced, which highlights new research aims to be considered.
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Affiliation(s)
- Cristina Bustos
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaíso 2362803, Chile; (C.B.); (J.Q.); (R.V.); (C.A.); (S.B.-G.)
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, Av. de la Faculté 2B, 5030 Gembloux, Belgium;
| | - Johan Quezada
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaíso 2362803, Chile; (C.B.); (J.Q.); (R.V.); (C.A.); (S.B.-G.)
| | - Rhonda Veas
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaíso 2362803, Chile; (C.B.); (J.Q.); (R.V.); (C.A.); (S.B.-G.)
| | - Claudia Altamirano
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaíso 2362803, Chile; (C.B.); (J.Q.); (R.V.); (C.A.); (S.B.-G.)
| | - Stephanie Braun-Galleani
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaíso 2362803, Chile; (C.B.); (J.Q.); (R.V.); (C.A.); (S.B.-G.)
| | - Patrick Fickers
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, Av. de la Faculté 2B, 5030 Gembloux, Belgium;
| | - Julio Berrios
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaíso 2362803, Chile; (C.B.); (J.Q.); (R.V.); (C.A.); (S.B.-G.)
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Jennifer S, Corinna R, Thomas D, Nils L, Diethard M, Brigitte G. Going beyond the limit: Increasing global translation activity leads to increased productivity of recombinant secreted proteins in Pichia pastoris. Metab Eng 2022; 70:181-195. [DOI: 10.1016/j.ymben.2022.01.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/12/2022] [Accepted: 01/20/2022] [Indexed: 01/06/2023]
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Papaioannou IA, Dutreux F, Peltier FA, Maekawa H, Delhomme N, Bardhan A, Friedrich A, Schacherer J, Knop M. Sex without crossing over in the yeast Saccharomycodes ludwigii. Genome Biol 2021; 22:303. [PMID: 34732243 PMCID: PMC8567612 DOI: 10.1186/s13059-021-02521-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 10/20/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Intermixing of genomes through meiotic reassortment and recombination of homologous chromosomes is a unifying theme of sexual reproduction in eukaryotic organisms and is considered crucial for their adaptive evolution. Previous studies of the budding yeast species Saccharomycodes ludwigii suggested that meiotic crossing over might be absent from its sexual life cycle, which is predominated by fertilization within the meiotic tetrad. RESULTS We demonstrate that recombination is extremely suppressed during meiosis in Sd. ludwigii. DNA double-strand break formation by the conserved transesterase Spo11, processing and repair involving interhomolog interactions are required for normal meiosis but do not lead to crossing over. Although the species has retained an intact meiotic gene repertoire, genetic and population analyses suggest the exceptionally rare occurrence of meiotic crossovers in its genome. A strong AT bias of spontaneous mutations and the absence of recombination are likely responsible for its unusually low genomic GC level. CONCLUSIONS Sd. ludwigii has followed a unique evolutionary trajectory that possibly derives fitness benefits from the combination of frequent mating between products of the same meiotic event with the extreme suppression of meiotic recombination. This life style ensures preservation of heterozygosity throughout its genome and may enable the species to adapt to its environment and survive with only minimal levels of rare meiotic recombination. We propose Sd. ludwigii as an excellent natural forum for the study of genome evolution and recombination rates.
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Affiliation(s)
| | - Fabien Dutreux
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - France A. Peltier
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Hiromi Maekawa
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
- Current affiliation: Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Nicolas Delhomme
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Amit Bardhan
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Anne Friedrich
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
- Institut Universitaire de France (IUF), Paris, France
| | - Michael Knop
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
- German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
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Hanson SJ, Cinnéide EÓ, Salzberg LI, Wolfe KH, McGowan J, Fitzpatrick DA, Matlin K. Genomic diversity, chromosomal rearrangements, and interspecies hybridization in the Ogataea polymorpha species complex. G3 (BETHESDA, MD.) 2021; 11:jkab211. [PMID: 34849824 PMCID: PMC8496258 DOI: 10.1093/g3journal/jkab211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/11/2021] [Indexed: 11/13/2022]
Abstract
The methylotrophic yeast Ogataea polymorpha has long been a useful system for recombinant protein production, as well as a model system for methanol metabolism, peroxisome biogenesis, thermotolerance, and nitrate assimilation. It has more recently become an important model for the evolution of mating-type switching. Here, we present a population genomics analysis of 47 isolates within the O. polymorpha species complex, including representatives of the species O. polymorpha, Ogataea parapolymorpha, Ogataea haglerorum, and Ogataea angusta. We found low levels of nucleotide sequence diversity within the O. polymorpha species complex and identified chromosomal rearrangements both within and between species. In addition, we found that one isolate is an interspecies hybrid between O. polymorpha and O. parapolymorpha and present evidence for loss of heterozygosity following hybridization.
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Affiliation(s)
- Sara J Hanson
- Department of Molecular Biology, Colorado College, Colorado Springs, CO 80903, USA
| | - Eoin Ó Cinnéide
- School of Medicine, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Letal I Salzberg
- School of Medicine, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Kenneth H Wolfe
- School of Medicine, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Jamie McGowan
- Genome Evolution Laboratory, Department of Biology, Maynooth University, Maynooth, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Ireland
| | - David A Fitzpatrick
- Genome Evolution Laboratory, Department of Biology, Maynooth University, Maynooth, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Ireland
| | - Kate Matlin
- Department of Molecular Biology, Colorado College, Colorado Springs, CO 80903, USA
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11
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Bernauer L, Radkohl A, Lehmayer LGK, Emmerstorfer-Augustin A. Komagataella phaffii as Emerging Model Organism in Fundamental Research. Front Microbiol 2021; 11:607028. [PMID: 33505376 PMCID: PMC7829337 DOI: 10.3389/fmicb.2020.607028] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 12/14/2020] [Indexed: 01/11/2023] Open
Abstract
Komagataella phaffii (Pichia pastoris) is one of the most extensively applied yeast species in pharmaceutical and biotechnological industries, and, therefore, also called the biotech yeast. However, thanks to more advanced strain engineering techniques, it recently started to gain attention as model organism in fundamental research. So far, the most studied model yeast is its distant cousin, Saccharomyces cerevisiae. While these data are of great importance, they limit our knowledge to one organism only. Since the divergence of the two species 250 million years ago, K. phaffii appears to have evolved less rapidly than S. cerevisiae, which is why it remains more characteristic of the common ancient yeast ancestors and shares more features with metazoan cells. This makes K. phaffii a valuable model organism for research on eukaryotic molecular cell biology, a potential we are only beginning to fully exploit. As methylotrophic yeast, K. phaffii has the intriguing property of being able to efficiently assimilate methanol as a sole source of carbon and energy. Therefore, major efforts have been made using K. phaffii as model organism to study methanol assimilation, peroxisome biogenesis and pexophagy. Other research topics covered in this review range from yeast genetics including mating and sporulation behavior to other cellular processes such as protein secretion, lipid biosynthesis and cell wall biogenesis. In this review article, we compare data obtained from K. phaffii with S. cerevisiae and other yeasts whenever relevant, elucidate major differences, and, most importantly, highlight the big potential of using K. phaffii in fundamental research.
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Affiliation(s)
- Lukas Bernauer
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, BioTechMed-Graz, Graz, Austria
| | - Astrid Radkohl
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, BioTechMed-Graz, Graz, Austria
| | | | - Anita Emmerstorfer-Augustin
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, BioTechMed-Graz, Graz, Austria
- acib—Austrian Centre of Industrial Biotechnology, Graz, Austria
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12
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Radoman B, Grünwald-Gruber C, Schmelzer B, Zavec D, Gasser B, Altmann F, Mattanovich D. The Degree and Length of O-Glycosylation of Recombinant Proteins Produced in Pichia pastoris Depends on the Nature of the Protein and the Process Type. Biotechnol J 2020; 16:e2000266. [PMID: 32975831 DOI: 10.1002/biot.202000266] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 09/09/2020] [Indexed: 12/16/2022]
Abstract
The methylotrophic yeast Pichia pastoris is known as an efficient host for the production of heterologous proteins. While N-linked protein glycosylation is well characterized in P. pastoris there is less knowledge of the patterns of O-glycosylation. O-glycans produced by P. pastoris consist of short linear mannose chains, which in the case of recombinant biopharmaceuticals can trigger an immune response in humans. This study aims to reveal the influence of different cultivation strategies on O-mannosylation profiles in P. pastoris. Sixteen different model proteins, produced by different P. pastoris strains, are analyzed for their O-glycosylation profile. Based on the obtained data, human serum albumin (HSA) is chosen to be produced in fast and slow growth fed batch fermentations by using common promoters, PGAP and PAOX1 . After purification and protein digestion, glycopeptides are analyzed by LC/ESI-MS. In the samples expressed with PGAP it is found that the degree of glycosylation is slightly higher when a slow growth rate is used, regardless of the efficiency of the producing strain. The highest glycosylation intensity is observed in HSA produced with PAOX1 . The results indicate that the O-glycosylation level is markedly higher when the protein is produced in a methanol-based expression system.
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Affiliation(s)
- Bojana Radoman
- Austrian Centre of Industrial Biotechnology (ACIB), Vienna, 1190, Austria.,Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Vienna, 1190, Austria
| | - Clemens Grünwald-Gruber
- Department of Chemistry, BOKU-University of Natural Resources and Life Sciences, Vienna, 1190, Austria
| | - Bernhard Schmelzer
- Austrian Centre of Industrial Biotechnology (ACIB), Vienna, 1190, Austria.,Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Vienna, 1190, Austria
| | - Domen Zavec
- Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Vienna, 1190, Austria
| | - Brigitte Gasser
- Austrian Centre of Industrial Biotechnology (ACIB), Vienna, 1190, Austria.,Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Vienna, 1190, Austria
| | - Friedrich Altmann
- Austrian Centre of Industrial Biotechnology (ACIB), Vienna, 1190, Austria.,Department of Chemistry, BOKU-University of Natural Resources and Life Sciences, Vienna, 1190, Austria
| | - Diethard Mattanovich
- Austrian Centre of Industrial Biotechnology (ACIB), Vienna, 1190, Austria.,Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Vienna, 1190, Austria
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13
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Rodríguez Mallón A, Javier González L, Encinosa Guzmán PE, Bechara GH, Sanches GS, Pousa S, Cabrera G, Cabrales A, Garay H, Mejías R, López Álvarez JR, Bello Soto Y, Almeida F, Guirola O, Rodríguez Fernández R, Fuentes Castillo A, Méndez L, Jiménez S, Licea-Navarro A, Portela M, Durán R, Estrada MP. Functional and Mass Spectrometric Evaluation of an Anti-Tick Antigen Based on the P0 Peptide Conjugated to Bm86 Protein. Pathogens 2020; 9:pathogens9060513. [PMID: 32630414 PMCID: PMC7350365 DOI: 10.3390/pathogens9060513] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/20/2020] [Accepted: 06/21/2020] [Indexed: 11/16/2022] Open
Abstract
A synthetic 20 amino acid peptide of the ribosomal protein P0 from ticks, when conjugated to keyhole limpet hemocyanin from Megathura crenulata and used as an immunogen against Rhipicephalus microplus and Rhipicephalus sanguineus s.l. species, has shown efficacies of around 90%. There is also experimental evidence of a high efficacy of this conjugate against Amblyomma mixtum and Ixodes ricinus species, which suggest that this antigen could be a good broad-spectrum anti-tick vaccine candidate. In this study, the P0 peptide (pP0) was chemically conjugated to Bm86 as a carrier protein. SDS-PAGE analysis of this conjugate demonstrated that it is highly heterogeneous in size, carrying from 1 to 18 molecules of pP0 per molecule of Bm86. Forty-nine out of the 54 lysine residues and the N-terminal end of Bm86 were found partially linked to pP0 by using LC-MS/MS analysis and the combination of four different softwares. Several post-translational modifications of Bm86 protein were also identified by mass spectrometry. High immunogenicity and efficacy were achieved when dogs and cattle were vaccinated with the pP0-Bm86 conjugate and challenged with R. sanguineus s.l. and R. microplus, respectively. These results encourage the development of this antigen with promising possibilities as an anti-tick vaccine.
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Affiliation(s)
- Alina Rodríguez Mallón
- Animal Biotechnology Department, Center for Genetic Engineering and Biotechnology (CIGB), Havana 10600, Cuba; (P.E.E.G.); (Y.B.S.); (M.P.E.)
- Correspondence: ; Tel.: +53-72504407
| | - Luis Javier González
- Mass Spectrometry Laboratory and GlycoLab, Department of Proteomics, CIGB, Havana 10600, Cuba; (L.J.G.); (S.P.); (G.C.); (F.A.)
| | - Pedro Enrique Encinosa Guzmán
- Animal Biotechnology Department, Center for Genetic Engineering and Biotechnology (CIGB), Havana 10600, Cuba; (P.E.E.G.); (Y.B.S.); (M.P.E.)
| | - Gervasio Henrique Bechara
- Programa de Pós-graduação em Ciência Animal, Pontifícia Universidade Católica do Paraná (PUCPR), Paraná 80215-901, Brazil; (G.H.B.); (G.S.S.)
- Departamento de Patologia Veterinária, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (FCAV-UNESP), São Paulo 14884-900, Brazil
| | - Gustavo Seron Sanches
- Programa de Pós-graduação em Ciência Animal, Pontifícia Universidade Católica do Paraná (PUCPR), Paraná 80215-901, Brazil; (G.H.B.); (G.S.S.)
- Departamento de Patologia Veterinária, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (FCAV-UNESP), São Paulo 14884-900, Brazil
| | - Satomy Pousa
- Mass Spectrometry Laboratory and GlycoLab, Department of Proteomics, CIGB, Havana 10600, Cuba; (L.J.G.); (S.P.); (G.C.); (F.A.)
| | - Gleysin Cabrera
- Mass Spectrometry Laboratory and GlycoLab, Department of Proteomics, CIGB, Havana 10600, Cuba; (L.J.G.); (S.P.); (G.C.); (F.A.)
| | - Ania Cabrales
- Synthetic Peptides Group, CIGB, Havana 10600, Cuba; (A.C.); (H.G.)
| | - Hilda Garay
- Synthetic Peptides Group, CIGB, Havana 10600, Cuba; (A.C.); (H.G.)
| | - Raúl Mejías
- Instituto de Ciencia Animal (ICA), San José de las Lajas 32700, Cuba; (R.M.); (J.R.L.Á.)
| | | | - Yamil Bello Soto
- Animal Biotechnology Department, Center for Genetic Engineering and Biotechnology (CIGB), Havana 10600, Cuba; (P.E.E.G.); (Y.B.S.); (M.P.E.)
| | - Fabiola Almeida
- Mass Spectrometry Laboratory and GlycoLab, Department of Proteomics, CIGB, Havana 10600, Cuba; (L.J.G.); (S.P.); (G.C.); (F.A.)
| | | | | | - Alier Fuentes Castillo
- National Laboratory for Parasitology, San Antonio de los Banos 32500, Cuba; (R.R.F.); (A.F.C.); (L.M.)
| | - Luis Méndez
- National Laboratory for Parasitology, San Antonio de los Banos 32500, Cuba; (R.R.F.); (A.F.C.); (L.M.)
| | - Samanta Jiménez
- Departamento de Innovación Biomédica, CICESE, Ensenada 22860, Mexico; (S.J.); (A.L.-N.)
| | - Alexei Licea-Navarro
- Departamento de Innovación Biomédica, CICESE, Ensenada 22860, Mexico; (S.J.); (A.L.-N.)
| | - Madelón Portela
- Unidad de Bioquímica y Proteómica Analítica, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay; (M.P.); (R.D.)
- Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo 11600, Uruguay
| | - Rosario Durán
- Unidad de Bioquímica y Proteómica Analítica, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay; (M.P.); (R.D.)
- Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo 11600, Uruguay
| | - Mario Pablo Estrada
- Animal Biotechnology Department, Center for Genetic Engineering and Biotechnology (CIGB), Havana 10600, Cuba; (P.E.E.G.); (Y.B.S.); (M.P.E.)
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