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Kruasuwan W, Puseenam A, Tanapongpipat S, Roongsawang N. Multiplexed CRISPR-mediated engineering of protein secretory pathway genes in the thermotolerant methylotrophic yeast Ogataea thermomethanolica. PLoS One 2021; 16:e0261754. [PMID: 34941944 PMCID: PMC8699913 DOI: 10.1371/journal.pone.0261754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 12/07/2021] [Indexed: 11/19/2022] Open
Abstract
CRISPR multiplex gRNA systems have been employed in genome engineering in various industrially relevant yeast species. The thermotolerant methylotrophic yeast Ogataea thermomethanolica TBRC 656 is an alternative host for heterologous protein production. However, the limited secretory capability of this yeast is a bottleneck for protein production. Here, we refined CRISPR-based genome engineering tools for simultaneous mutagenesis and activation of multiple protein secretory pathway genes to improve heterologous protein secretion. We demonstrated that multiplexed CRISPR-Cas9 mutation of up to four genes (SOD1, VPS1, YPT7 and YPT35) in one single cell is practicable. We also developed a multiplexed CRISPR-dCas9 system which allows simultaneous activation of multiple genes in this yeast. 27 multiplexed gRNA combinations were tested for activation of three genes (SOD1, VPS1 and YPT7), three of which were demonstrated to increase the secretion of fungal xylanase and phytase up to 29% and 41%, respectively. Altogether, our study provided a toolkit for mutagenesis and activation of multiple genes in O. thermomethanolica, which could be useful for future strain engineering to improve heterologous protein production in this yeast.
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Affiliation(s)
- Worarat Kruasuwan
- Microbial Cell Factory Research Team, Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Nueng, Khlong Luang, Pathum Thani, Thailand
| | - Aekkachai Puseenam
- Microbial Cell Factory Research Team, Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Nueng, Khlong Luang, Pathum Thani, Thailand
| | - Sutipa Tanapongpipat
- Microbial Cell Factory Research Team, Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Nueng, Khlong Luang, Pathum Thani, Thailand
| | - Niran Roongsawang
- Microbial Cell Factory Research Team, Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Nueng, Khlong Luang, Pathum Thani, Thailand
- * E-mail:
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Kruasuwan W, Puseenam A, Phithakrotchanakoon C, Tanapongpipat S, Roongsawang N. Modulation of heterologous protein secretion in the thermotolerant methylotrophic yeast Ogataea thermomethanolica TBRC 656 by CRISPR-Cas9 system. PLoS One 2021; 16:e0258005. [PMID: 34582499 PMCID: PMC8478189 DOI: 10.1371/journal.pone.0258005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 09/16/2021] [Indexed: 11/18/2022] Open
Abstract
The thermotolerant methylotrophic yeast Ogataea thermomethanolica TBRC 656 is a potential host strain for industrial protein production. Heterologous proteins are often retained intracellularly in yeast resulting in endoplasmic reticulum (ER) stress and poor secretion, and despite efforts to engineer protein secretory pathways, heterologous protein production is often lower than expected. We hypothesized that activation of genes involved in the secretory pathway could mitigate ER stress. In this study, we created mutants defective in protein secretory-related functions using clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) tools. Secretion of the model protein xylanase was significantly decreased in loss of function mutants for oxidative stress (sod1Δ) and vacuolar and protein sorting (vps1Δ and ypt7Δ) genes. However, xylanase secretion was unaffected in an autophagy related atg12Δ mutant. Then, we developed a system for sequence-specific activation of target gene expression (CRISPRa) in O. thermomethanolica and used it to activate SOD1, VPS1 and YPT7 genes. Production of both non-glycosylated xylanase and glycosylated phytase was enhanced in the gene activated mutants, demonstrating that CRISPR-Cas9 systems can be used as tools for understanding O. thermomethanolica genes involved in protein secretion, which could be applied for increasing heterologous protein secretion in this yeast.
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Affiliation(s)
- Worarat Kruasuwan
- Microbial Cell Factory Research Team, Microbial Biotechnology and Biochemicals Research Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Nueng, Khlong Luang, Pathum Thani, Thailand
| | - Aekkachai Puseenam
- Microbial Cell Factory Research Team, Microbial Biotechnology and Biochemicals Research Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Nueng, Khlong Luang, Pathum Thani, Thailand
| | - Chitwadee Phithakrotchanakoon
- Microbial Systems and Computational Biology Research Team, Thailand Bioresource Research Center, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Nueng, Khlong Luang, Pathum Thani, Thailand
| | - Sutipa Tanapongpipat
- Microbial Cell Factory Research Team, Microbial Biotechnology and Biochemicals Research Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Nueng, Khlong Luang, Pathum Thani, Thailand
| | - Niran Roongsawang
- Microbial Cell Factory Research Team, Microbial Biotechnology and Biochemicals Research Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Nueng, Khlong Luang, Pathum Thani, Thailand
- * E-mail:
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Phithakrotchanakoon C, Puseenam A, Kruasuwan W, Likhitrattanapisal S, Phaonakrop N, Roytrakul S, Ingsriswang S, Tanapongpipat S, Roongsawang N. Identification of proteins responsive to heterologous protein production in thermotolerant methylotrophic yeast Ogataea thermomethanolica TBRC656. Yeast 2021; 38:316-325. [PMID: 33445217 DOI: 10.1002/yea.3548] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 11/09/2022] Open
Abstract
The thermotolerant methylotrophic yeast Ogataea thermomethanolica TBRC656 is a potential host for heterologous protein production. However, overproduction of heterologous protein can induce cellular stress and limit the level of its secretion. To improve the secretion of heterologous protein, we identified the candidate proteins with altered production during production of heterologous protein in O. thermomethanolica by using a label-free comparative proteomic approach. Four hundred sixty-four proteins with various biological functions showed differential abundance between O. thermomethanolica expressing fungal xylanase (OT + Xyl) and a control strain. The induction of proteins in transport and proteasomal proteolysis was prominently observed. Eight candidate proteins involved in cell wall biosynthesis (Chs3, Gas4), chaperone (Sgt2, Pex19), glycan metabolism (Csf1), protein transport (Ypt35), and vacuole and protein sorting (Cof1, Npr2) were mutated by a CRISPR/Cas9 approach. An Sgt2 mutant showed higher phytase and xylanase activity compared with the control strain (13%-20%), whereas mutants of other genes including Cof1, Pex19, Gas4, and Ypt35 showed lower xylanase activity compared with the control strain (15%-25%). In addition, an Npr2 mutant showed defective growth, while overproduction of Npr2 enhanced xylanase activity. These results reveal genes that can be mutated to modulate heterologous protein production and growth of O. thermomethanolica TBRC656.
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Affiliation(s)
- Chitwadee Phithakrotchanakoon
- Microbial Systems and Computational Biology Research Team, Thailand Bioresource Research Center, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Aekkachai Puseenam
- Microbial Cell Factory Research Team, Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Worarat Kruasuwan
- Microbial Cell Factory Research Team, Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Somsak Likhitrattanapisal
- Microbial Systems and Computational Biology Research Team, Thailand Bioresource Research Center, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Narumon Phaonakrop
- Functional Proteomics Technology, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Sittiruk Roytrakul
- Functional Proteomics Technology, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Supawadee Ingsriswang
- Microbial Systems and Computational Biology Research Team, Thailand Bioresource Research Center, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Sutipa Tanapongpipat
- Microbial Cell Factory Research Team, Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Niran Roongsawang
- Microbial Cell Factory Research Team, Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
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Rozanov AS, Pershina EG, Bogacheva NV, Shlyakhtun V, Sychev AA, Peltek SE. Diversity and occurrence of methylotrophic yeasts used in genetic engineering. Vavilovskii Zhurnal Genet Selektsii 2020; 24:149-157. [PMID: 33659794 PMCID: PMC7716571 DOI: 10.18699/vj20.602] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Methylotrophic yeasts have been used as the platform for expression of heterologous proteins since the
1980’s. They are highly productive and allow producing eukaryotic proteins with an acceptable glycosylation level.
The first Pichia pastoris-based system for expression of recombinant protein was developed on the basis of the treeexudate-
derived strain obtained in the US southwest. Being distributed free of charge for scientific purposes, this system
has become popular around the world. As methylotrophic yeasts were classified in accordance with biomolecular
markers, strains used for production of recombinant protein were reclassified as Komagataella phaffii. Although patent
legislation suggests free access to these yeasts, they have been distributed on a contract basis. Whereas their status
for commercial use is undetermined, the search for alternative stains for expression of recombinant protein continues.
Strains of other species of methylotrophic yeasts have been adapted, among which the genus Ogataea representatives
prevail. Despite the phylogenetic gap between the genus Ogataea and the genus Komagataella representatives,
it turned out possible to use classic vectors and promoters for expression of recombinant protein in all cases. There
exist expression systems based on other strains of the genus Komagataella as well as the genus Candida. The potential
of these microorganisms for genetic engineering is far from exhausted. Both improvement of existing expression systems
and development of new ones on the basis of strains obtained from nature are advantageous. Historically, strains
obtained on the southwest of the USA were used as expression systems up to 2009. Currently, expression systems
based on strains obtained in Thailand are gaining popularity. Since this group of microorganisms is widely represented
around the world both in nature and in urban environments, it may reasonably be expected that new expression systems
for recombinant proteins based on strains obtained in other regions of the globe will appear.
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Affiliation(s)
- A S Rozanov
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - E G Pershina
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - N V Bogacheva
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - V Shlyakhtun
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A A Sychev
- Innovation Centre Biruch-NT, Belgorod region, Russia
| | - S E Peltek
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Phithakrotchanakoon C, Phaonakrop N, Roytrakul S, Tanapongpipat S, Roongsawang N. Protein secretion in wild-type and Othac1 mutant strains of thermotolerant methylotrophic yeast Ogataea thermomethanolica TBRC656. Mol Biol Rep 2019; 47:461-468. [DOI: 10.1007/s11033-019-05149-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 10/18/2019] [Indexed: 12/12/2022]
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Yebra-Pimentel ES, Gebert M, Jansen HJ, Jong-Raadsen SA, Dirks RPH. Deep transcriptome analysis of the heat shock response in an Atlantic sturgeon (Acipenser oxyrinchus) cell line. FISH & SHELLFISH IMMUNOLOGY 2019; 88:508-517. [PMID: 30862517 DOI: 10.1016/j.fsi.2019.03.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 01/28/2019] [Accepted: 03/08/2019] [Indexed: 06/09/2023]
Abstract
Despite efforts to restore Atlantic sturgeon in European rivers, aquaculture techniques result in animals with high post-release mortality due to, among other reasons, their low tolerance to increasing water temperature. Marker genes to monitor heat stress are needed in order to identify heat-resistant fish. Therefore, an Atlantic sturgeon cell line was exposed to different heat shock protocols (30 °C and 35 °C) and differences in gene expression were investigated. In total 3020 contigs (∼1.5%) were differentially expressed. As the core of the upregulated contigs corresponded to heat shock proteins (HSP), the heat shock factor (HSF) and the HSP gene families were annotated in Atlantic sturgeon and mapped via Illumina RNA sequencing to identify heat-inducible family members. Up to 6 hsf and 76 hsp genes were identified in the Atlantic sturgeon transcriptome resources, 16 of which were significantly responsive to the applied heat shock. The previously studied hspa1 (hsp70) gene was only significantly upregulated at the highest heat shock (35 °C), while a set of 5 genes (hspc1, hsph3a, hspb1b, hspb11a, and hspb11b) was upregulated at all conditions. Although the hspc1 (hsp90a) gene was previously used as heat shock-marker in sturgeons, we found that hspb11a is the most heat-inducible gene, with up to 3296-fold higher expression in the treated cells, constituting the candidate gene markers for in vivo trials.
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Affiliation(s)
- Elena Santidrián Yebra-Pimentel
- ZF-screens B.V., 2333CH, Leiden, the Netherlands; Department of Basic Sciences and Aquatic Medicine, Norwegian University of Life Sciences, 0454, Oslo, Norway.
| | - Marina Gebert
- Working Group Aquatic Cell Technology and Aquaculture, Fraunhofer Research Institution for Marine Biotechnology and Cell Technology, 23562, Lübeck, Germany
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