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Krappinger JC, Aguilar Gomez CM, Hoenikl A, Schusterbauer V, Hatzl AM, Feichtinger J, Glieder A. dMAD7 is a promising tool for targeted gene regulation in the methylotrophic yeast Komagataella phaffii. N Biotechnol 2024; 83:110-120. [PMID: 38960022 DOI: 10.1016/j.nbt.2024.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 06/07/2024] [Accepted: 06/30/2024] [Indexed: 07/05/2024]
Abstract
The methylotrophic yeast Komagataella phaffii is a popular host system for the pharmaceutical and biotechnological production of recombinant proteins. CRISPR-Cas9 and its derivative CRISPR interference (CRISPRi) offer a promising avenue to further enhance and exploit the full capabilities of this host. MAD7 and its catalytically inactive variant "dead" MAD7 (dMAD7) represent an interesting alternative to established CRISPR-Cas9 systems and are free to use for industrial and academic research. CRISPRi utilizing dMAD7 does not introduce double-strand breaks but only binds to the DNA to regulate gene expression. Here, we report the first use of dMAD7 in K. phaffii to regulate the expression of the enhanced green fluorescent protein (eGFP). A reduction of eGFP fluorescence level (up to 88 %) was achieved in random integration experiments using dMAD7 plasmids. Integration loci/events of investigated strains were assessed through whole genome sequencing. Additionally, RNA-sequencing experiments corroborated the whole genome sequencing results and showed a significantly reduced expression of eGFP in strains containing a dMAD7 plasmid, among others. Our findings conclusively demonstrate the utility of dMAD7 in K. phaffii through successfully regulating eGFP expression.
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Affiliation(s)
- Julian C Krappinger
- Christian Doppler Laboratory for Innovative Pichia pastoris Host and Vector Systems, Graz, Austria; Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria
| | - Carla M Aguilar Gomez
- Christian Doppler Laboratory for Innovative Pichia pastoris Host and Vector Systems, Graz, Austria; Institute of Molecular Biotechnology, Graz University of Technology, Graz, Austria
| | - Andrea Hoenikl
- Institute of Molecular Biotechnology, Graz University of Technology, Graz, Austria
| | | | - Anna-Maria Hatzl
- Christian Doppler Laboratory for Innovative Pichia pastoris Host and Vector Systems, Graz, Austria; Institute of Molecular Biotechnology, Graz University of Technology, Graz, Austria
| | - Julia Feichtinger
- Christian Doppler Laboratory for Innovative Pichia pastoris Host and Vector Systems, Graz, Austria; Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria.
| | - Anton Glieder
- Christian Doppler Laboratory for Innovative Pichia pastoris Host and Vector Systems, Graz, Austria; Institute of Molecular Biotechnology, Graz University of Technology, Graz, Austria
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2
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Yang J, Yang L, Zhao F, Ye C, Han S. De novo biosynthesis of β-Arbutin in Komagataella phaffii based on metabolic engineering strategies. Microb Cell Fact 2024; 23:261. [PMID: 39350198 PMCID: PMC11440761 DOI: 10.1186/s12934-024-02525-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Accepted: 09/09/2024] [Indexed: 10/04/2024] Open
Abstract
BACKGROUND β-Arbutin, found in the leaves of bearberry, stands out as one of the globally acknowledged eco-friendly whitening additives in recent years. However, the natural abundance of β-Arbutin is low, and the cost-effectiveness of using chemical synthesis or plant extraction methods is low, which cannot meet the requirements. While modifying the β-Arbutin synthesis pathway of existing strains is a viable option, it is hindered by the limited synthesis capacity of these strains, which hinders further development and application. RESULTS In this study, we established a biosynthetic pathway in Komagataella phaffii for β-Arbutin production with a titer of 1.58 g/L. Through diverse metabolic strategies, including fusion protein construction, enhancing shikimate pathway flux, and augmenting precursor supplies (PEP, E4P, and UDPG), we significantly increased β-Arbutin titer to 4.32 g/L. Further optimization of methanol concentration in shake flasks led to a titer of 6.32 g/L titer after 120 h of fermentation, representing a fourfold increase over the initial titer. In fed-batch fermentation, strain UA3-10 set a record with the highest production to date, reaching 128.6 g/L in a 5 L fermenter. CONCLUSIONS This is the highest yield in the fermentation tank level of using microbial cell factories for de novo synthesis of β-Arbutin. Applying combinatorial engineering strategies has significantly improved the β-Arbutin yield in K. phaffii and is a promising approach for synthesizing functional products using a microbial cell factory. This study not only advances low-cost fermentation-based production of β-Arbutin but also establishes K. phaffii as a promising chassis cell for synthesizing other aromatic amino acid metabolites.
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Affiliation(s)
- Jiashuo Yang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China
| | - Liu Yang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China
| | - Fengguang Zhao
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China
| | - Chunting Ye
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China
| | - Shuangyan Han
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China.
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3
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Vijayakumar VE, Venkataraman K. A Systematic Review of the Potential of Pichia pastoris (Komagataella phaffii) as an Alternative Host for Biologics Production. Mol Biotechnol 2024; 66:1621-1639. [PMID: 37400712 DOI: 10.1007/s12033-023-00803-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/20/2023] [Indexed: 07/05/2023]
Abstract
The methylotrophic yeast Pichia pastoris is garnering interest as a chassis cell factory for the manufacture of recombinant proteins because it effectively satisfies the requirements of both laboratory and industrial set up. The optimisation of P. pastoris cultivation is still necessary due to strain- and product-specific problems such as promoter strength, methanol utilisation type, and culturing conditions to realize the high yields of heterologous protein(s) of interest. Techniques integrating genetic and process engineering have been used to overcome these problems. Insight into the Pichia as an expression system utilizing MUT pathway and the development of methanol free systems are highlighted in this systematic review. Recent developments in the improved production of proteins in P. pastoris by (i) diverse genetic engineering such as codon optimization and gene dosage; (ii) cultivating tactics including co-expression of chaperones; (iii) advances in the use of the 2A peptide system, and (iv) CRISPR/Cas technologies are widely discussed. We believe that by combining these strategies, P. pastoris will become a formidable platform for the production of high value therapeutic proteins.
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Affiliation(s)
- Vijay Elakkya Vijayakumar
- Centre for Bio-Separation Technology (CBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India
| | - Krishnan Venkataraman
- Centre for Bio-Separation Technology (CBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India.
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4
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Albacar M, Casamayor A, Ariño J. Harnessing alkaline-pH regulatable promoters for efficient methanol-free expression of enzymes of industrial interest in Komagataella Phaffii. Microb Cell Fact 2024; 23:99. [PMID: 38566096 PMCID: PMC10985989 DOI: 10.1186/s12934-024-02362-9] [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: 11/04/2023] [Accepted: 03/11/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND The yeast Komagataella phaffii has become a very popular host for heterologous protein expression, very often based on the use of the AOX1 promoter, which becomes activated when cells are grown with methanol as a carbon source. However, the use of methanol in industrial settings is not devoid of problems, and therefore, the search for alternative expression methods has become a priority in the last few years. RESULTS We recently reported that moderate alkalinization of the medium triggers a fast and wide transcriptional response in K. phaffii. Here, we present the utilization of three alkaline pH-responsive promoters (pTSA1, pHSP12 and pPHO89) to drive the expression of a secreted phytase enzyme by simply shifting the pH of the medium to 8.0. These promoters offer a wide range of strengths, and the production of phytase could be modulated by adjusting the pH to specific values. The TSA1 and PHO89 promoters offered exquisite regulation, with virtually no enzyme production at acidic pH, while limitation of Pi in the medium further potentiated alkaline pH-driven phytase expression from the PHO89 promoter. An evolved strain based on this promoter was able to produce twice as much phytase as the reference pAOX1-based strain. Functional mapping of the TSA1 and HSP12 promoters suggests that both contain at least two alkaline pH-sensitive regulatory regions. CONCLUSIONS Our work shows that the use of alkaline pH-regulatable promoters could be a useful alternative to methanol-based expression systems, offering advantages in terms of simplicity, safety and economy.
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Affiliation(s)
- Marcel Albacar
- Institut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193, Spain
| | - Antonio Casamayor
- Institut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193, Spain
| | - Joaquín Ariño
- Institut de Biotecnologia i Biomedicina & Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193, Spain.
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5
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Bampidis V, Azimonti G, Bastos MDL, Christensen H, Dusemund B, Durjava M, Kouba M, López‐Alonso M, López Puente S, Marcon F, Mayo B, Pechová A, Petkova M, Ramos F, Villa RE, Woutersen R, Martelli G, Brozzi R, Galobart J, Innocenti ML, Ortuño J, Pettenati E, Pizzo F, Tarrés‐Call J, Vettori MV, Radovnikovic A. Safety and efficacy of a feed additive consisting of fumonisin esterase produced with Komagataella phaffii NCAIM (P) Y001485 for all pigs (piglets, pigs for fattening, sows and minor growing and reproductive porcine species) (Dr. Bata Ltd.). EFSA J 2024; 22:e8614. [PMID: 38464413 PMCID: PMC10921364 DOI: 10.2903/j.efsa.2024.8614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024] Open
Abstract
Following a request from the European Commission, EFSA was asked to deliver a scientific opinion on the safety and efficacy of the additive based on fumonisin esterase (Free Yeast® F), produced with a genetically modified strain of Komagataella phaffii. The additive is categorised as a technological feed additive, for the reduction of the contamination of feed by mycotoxins and intended for use in all pigs species (piglets, pigs for fattening, sows and minor growing and reproductive porcine species). It was shown that the production strain and its recombinant genes are not present in the additive. The FEEDAP Panel concluded that the additive is safe for weaned and suckling piglets and pigs for fattening, and all minor growing porcine species up to 60 U/kg complete feed. No conclusions can be drawn on the safety of the additive in sows. The use of the additive in animal nutrition is of no concern for consumer safety. The additive is dust-free, and therefore, respiratory sensitisation/irritation is unlikely. The additive is non-irritant to the eyes and the skin. No conclusion could be made on skin sensitisation. The use of the additive as a feed additive is considered safe for the environment. The Panel concluded that the additive is efficacious as technological feed additive for the reduction of feed contamination by fumonisins, when used at the minimum recommended concentration of 60 U/kg. This conclusion can be extrapolated to all growing and reproductive pigs and other minor porcine species.
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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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7
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Abramczyk D, Del Carmen Sanchez Olmos M, Rojas AAR, Schindler D, Robertson D, McColm S, Marston AL, Barlow PN. A supernumerary synthetic chromosome in Komagataella phaffii as a repository for extraneous genetic material. Microb Cell Fact 2023; 22:259. [PMID: 38104077 PMCID: PMC10724962 DOI: 10.1186/s12934-023-02262-4] [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: 08/17/2023] [Accepted: 11/29/2023] [Indexed: 12/19/2023] Open
Abstract
BACKGROUND Komagataella phaffii (Pichia pastoris) is a methylotrophic commercially important non-conventional species of yeast that grows in a fermentor to exceptionally high densities on simple media and secretes recombinant proteins efficiently. Genetic engineering strategies are being explored in this organism to facilitate cost-effective biomanufacturing. Small, stable artificial chromosomes in K. phaffii could offer unique advantages by accommodating multiple integrations of extraneous genes and their promoters without accumulating perturbations of native chromosomes or exhausting the availability of selection markers. RESULTS Here, we describe a linear "nano"chromosome (of 15-25 kb) that, according to whole-genome sequencing, persists in K. phaffii over many generations with a copy number per cell of one, provided non-homologous end joining is compromised (by KU70-knockout). The nanochromosome includes a copy of the centromere from K. phaffii chromosome 3, a K. phaffii-derived autonomously replicating sequence on either side of the centromere, and a pair of K. phaffii-like telomeres. It contains, within its q arm, a landing zone in which genes of interest alternate with long (approx. 1-kb) non-coding DNA chosen to facilitate homologous recombination and serve as spacers. The landing zone can be extended along the nanochromosome, in an inch-worming mode of sequential gene integrations, accompanied by recycling of just two antibiotic-resistance markers. The nanochromosome was used to express PDI, a gene encoding protein disulfide isomerase. Co-expression with PDI allowed the production, from a genomically integrated gene, of secreted murine complement factor H, a plasma protein containing 40 disulfide bonds. As further proof-of-principle, we co-expressed, from a nanochromosome, both PDI and a gene for GFP-tagged human complement factor H under the control of PAOX1 and demonstrated that the secreted protein was active as a regulator of the complement system. CONCLUSIONS We have added K. phaffii to the list of organisms that can produce human proteins from genes carried on a stable, linear, artificial chromosome. We envisage using nanochromosomes as repositories for numerous extraneous genes, allowing intensive engineering of K. phaffii without compromising its genome or weakening the resulting strain.
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Affiliation(s)
| | | | | | - Daniel Schindler
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
| | - Daniel Robertson
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Adele L Marston
- The Wellcome Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Paul N Barlow
- School of Chemistry, University of Edinburgh, Edinburgh, UK.
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
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8
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Kobalter S, Voit A, Bekerle-Bogner M, Rudalija H, Haas A, Wriessnegger T, Pichler H. Tuning Fatty Acid Profile and Yield in Pichia pastoris. Bioengineering (Basel) 2023; 10:1412. [PMID: 38136003 PMCID: PMC10741089 DOI: 10.3390/bioengineering10121412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 11/29/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
Fatty acids have been supplied for diverse non-food, industrial applications from plant oils and animal fats for many decades. Due to the massively increasing world population demanding a nutritious diet and the thrive to provide feedstocks for industrial production lines in a sustainable way, i.e., independent from food supply chains, alternative fatty acid sources have massively gained in importance. Carbohydrate-rich side-streams of agricultural production, e.g., molasses, lignocellulosic waste, glycerol from biodiesel production, and even CO2, are considered and employed as carbon sources for the fermentative accumulation of fatty acids in selected microbial hosts. While certain fatty acid species are readily accumulated in native microbial metabolic routes, other fatty acid species are scarce, and host strains need to be metabolically engineered for their high-level production. We report the metabolic engineering of Pichia pastoris to produce palmitoleic acid from glucose and discuss the beneficial and detrimental engineering steps in detail. Fatty acid secretion was achieved through the deletion of fatty acyl-CoA synthetases and overexpression of the truncated E. coli thioesterase 'TesA. The best strains secreted >1 g/L free fatty acids into the culture medium. Additionally, the introduction of C16-specific ∆9-desaturases and fatty acid synthases, coupled with improved cultivation conditions, increased the palmitoleic acid content from 5.5% to 22%.
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Affiliation(s)
- Simon Kobalter
- Austrian Centre of Industrial Biotechnology (acib GmbH), Petersgasse 14, 8010 Graz, Austria; (S.K.)
| | - Alena Voit
- Austrian Centre of Industrial Biotechnology (acib GmbH), Petersgasse 14, 8010 Graz, Austria; (S.K.)
| | - Myria Bekerle-Bogner
- Austrian Centre of Industrial Biotechnology (acib GmbH), Petersgasse 14, 8010 Graz, Austria; (S.K.)
| | - Haris Rudalija
- Austrian Centre of Industrial Biotechnology (acib GmbH), Petersgasse 14, 8010 Graz, Austria; (S.K.)
| | - Anne Haas
- Austrian Centre of Industrial Biotechnology (acib GmbH), Petersgasse 14, 8010 Graz, Austria; (S.K.)
| | - Tamara Wriessnegger
- Austrian Centre of Industrial Biotechnology (acib GmbH), Petersgasse 14, 8010 Graz, Austria; (S.K.)
| | - Harald Pichler
- Austrian Centre of Industrial Biotechnology (acib GmbH), Petersgasse 14, 8010 Graz, Austria; (S.K.)
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, BioTechMed Graz, Petersgasse 14, 8010 Graz, Austria
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9
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Tan H, Wang L, Wang H, Cheng Y, Li X, Wan H, Liu C, Liu T, Li Q. Engineering Komagataella phaffii to biosynthesize cordycepin from methanol which drives global metabolic alterations at the transcription level. Synth Syst Biotechnol 2023; 8:242-252. [PMID: 37007278 PMCID: PMC10060148 DOI: 10.1016/j.synbio.2023.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 02/22/2023] [Accepted: 03/02/2023] [Indexed: 03/18/2023] Open
Abstract
Cordycepin has the potential to be an alternative to the disputed herbicide glyphosate. However, current laborious and time-consuming production strategies at low yields based on Cordyceps militaris lead to extremely high cost and restrict its application in the field of agriculture. In this study, Komagataella phaffii (syn. Pichia pastoris) was engineered to biosynthesize cordycepin from methanol, which could be converted from CO2. Combined with fermentation optimization, cordycepin content in broth reached as high as 2.68 ± 0.04 g/L within 168 h, around 15.95 mg/(L·h) in productivity. Additionally, a deaminated product of cordycepin was identified at neutral or weakly alkaline starting pH during fermentation. Transcriptome analysis found the yeast producing cordycepin was experiencing severe inhibition in methanol assimilation and peroxisome biogenesis, responsible for delayed growth and decreased carbon flux to pentose phosphate pathway (PPP) which led to lack of precursor supply. Amino acid interconversion and disruption in RNA metabolism were also due to accumulation of cordycepin. The study provided a unique platform for the manufacture of cordycepin based on the emerging non-conventional yeast and gave practical strategies for further optimization of the microbial cell factory.
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Affiliation(s)
- Huiping Tan
- Department of Life and Health, Dalian University, No. 10 Xuefu Street, Dalian Economic and Technological Development Zone, Dalian, 116622, China
| | - Liang Wang
- School of Biological Engineering, Dalian Polytechnic University, No. 1 Qinggongyuan Road, Ganjingzi District, Dalian, 116034, China
| | - Huiguo Wang
- Department of Life and Health, Dalian University, No. 10 Xuefu Street, Dalian Economic and Technological Development Zone, Dalian, 116622, China
| | - Yanghao Cheng
- Department of Life and Health, Dalian University, No. 10 Xuefu Street, Dalian Economic and Technological Development Zone, Dalian, 116622, China
| | - Xiang Li
- Department of Life and Health, Dalian University, No. 10 Xuefu Street, Dalian Economic and Technological Development Zone, Dalian, 116622, China
| | - Huihui Wan
- Analytical Instrumentation Centre, Dalian University of Technology, No.2 Linggong Road, Dalian, 116024, China
| | - Chenguang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Science, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Tian Liu
- School of Bioengineering, Dalian University of Technology, No.2 Linggong Road, Dalian, 116024, China
| | - Qian Li
- Department of Life and Health, Dalian University, No. 10 Xuefu Street, Dalian Economic and Technological Development Zone, Dalian, 116622, China
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10
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Besleaga M, Vignolle GA, Kopp J, Spadiut O, Mach RL, Mach-Aigner AR, Zimmermann C. Evaluation of reference genes for transcript analyses in Komagataella phaffii (Pichia pastoris). Fungal Biol Biotechnol 2023; 10:7. [PMID: 36991508 DOI: 10.1186/s40694-023-00154-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 03/10/2023] [Indexed: 03/30/2023] Open
Abstract
Abstract
Background
The yeast Komagataella phaffii (Pichia pastoris) is routinely used for heterologous protein expression and is suggested as a model organism for yeast. Despite its importance and application potential, no reference gene for transcript analysis via RT-qPCR assays has been evaluated to date. In this study, we searched publicly available RNASeq data for stably expressed genes to find potential reference genes for relative transcript analysis by RT-qPCR in K. phaffii. To evaluate the applicability of these genes, we used a diverse set of samples from three different strains and a broad range of cultivation conditions. The transcript levels of 9 genes were measured and compared using commonly applied bioinformatic tools.
Results
We could demonstrate that the often-used reference gene ACT1 is not very stably expressed and could identify two genes with outstandingly low transcript level fluctuations. Consequently, we suggest the two genes, RSC1, and TAF10 to be simultaneously used as reference genes in transcript analyses by RT-qPCR in K. phaffii in future RT-qPCR assays.
Conclusion
The usage of ACT1 as a reference gene in RT-qPCR analysis might lead to distorted results due to the instability of its transcript levels. In this study, we evaluated the transcript levels of several genes and found RSC1 and TAF10 to be extremely stable. Using these genes holds the promise for reliable RT-qPCR results.
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11
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Bernat-Camps N, Ebner K, Schusterbauer V, Fischer JE, Nieto-Taype MA, Valero F, Glieder A, Garcia-Ortega X. Enabling growth-decoupled Komagataella phaffii recombinant protein production based on the methanol-free P DH promoter. Front Bioeng Biotechnol 2023; 11:1130583. [PMID: 37034257 PMCID: PMC10076887 DOI: 10.3389/fbioe.2023.1130583] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 03/01/2023] [Indexed: 04/07/2023] Open
Abstract
The current transition towards the circular bioeconomy requires a rational development of biorefineries to sustainably fulfill the present demands. The use of Komagataella phaffii (Pichia pastoris) can meet this challenge, since it has the capability to use crude glycerol as a carbon-source, a by-product from the biodiesel industry, while producing high- and low-added value products. Recombinant protein production (RPP) using K. phaffii has often been driven either by the methanol induced AOX1 promoter (PAOX1) and/or the constitutive GAP promoter (PGAP). In the last years, strong efforts have been focused on developing novel expression systems that expand the toolbox variety of K. phaffii to efficiently produce diverse proteins that requires different strategies. In this work, a study was conducted towards the development of methanol-free expression system based on a heat-shock gene promoter (PDH) using glycerol as sole carbon source. Using this promoter, the recombinant expression is strongly induced in carbon-starving conditions. The classical PGAP was used as a benchmark, taking for both strains the lipase B from Candida antarctica (CalB) as model protein. Titer of CalB expressed under PDH outperformed PGAP controlled expression in shake-flask cultivations when using a slow-release continuous feeding technology, confirming that PDH is induced under pseudo-starving conditions. This increase was also confirmed in fed-batch cultivations. Several optimization rounds were carried out for PDH under different feeding and osmolarity conditions. In all of them the PDH controlled process outperformed the PGAP one in regard to CalB titer. The best PDH approach reached 3.6-fold more specific productivity than PGAP fed-batch at low μ. Compared to the optimum approach for PGAP-based process, the best PDH fed-batch strategy resulted in 2.3-fold higher titer, while the specific productivity was very similar. To summarize, PDH is an inducible promoter that exhibited a non-coupled growth regulation showing high performance, which provides a methanol-free additional solution to the usual growth-coupled systems for RPP. Thus, this novel system emerges as a potential alternative for K. phaffii RPP bioprocess and for revaluing crude glycerol, promoting the transition towards a circular economy.
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Affiliation(s)
- Núria Bernat-Camps
- Department of Chemical, Biological, and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, Bellaterra, Spain
- Austrian Centre of Industrial Biotechnology (ACIB), Graz, Austria
| | | | | | | | - Miguel Angel Nieto-Taype
- Department of Chemical, Biological, and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Francisco Valero
- Department of Chemical, Biological, and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, Bellaterra, Spain
- Austrian Centre of Industrial Biotechnology (ACIB), Graz, Austria
| | | | - Xavier Garcia-Ortega
- Department of Chemical, Biological, and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, Bellaterra, Spain
- Austrian Centre of Industrial Biotechnology (ACIB), Graz, Austria
- *Correspondence: Xavier Garcia-Ortega,
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12
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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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13
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Schusterbauer V, Fischer JE, Gangl S, Schenzle L, Rinnofner C, Geier M, Sailer C, Glieder A, Thallinger GG. Whole Genome Sequencing Analysis of Effects of CRISPR/Cas9 in Komagataella phaffii: A Budding Yeast in Distress. J Fungi (Basel) 2022; 8:jof8100992. [PMID: 36294556 PMCID: PMC9605565 DOI: 10.3390/jof8100992] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/12/2022] [Accepted: 09/15/2022] [Indexed: 11/16/2022] Open
Abstract
The industrially important non-conventional yeast Komagataella phaffii suffers from low rates of homologous recombination, making site specific genetic engineering tedious. Therefore, genome editing using CRISPR/Cas represents a simple and efficient alternative. To characterize on- and off-target mutations caused by CRISPR/Cas9 followed by non-homologous end joining repair, we chose a diverse set of CRISPR/Cas targets and conducted whole genome sequencing on 146 CRISPR/Cas9 engineered single colonies. We compared the outcomes of single target CRISPR transformations to double target experiments. Furthermore, we examined the extent of possible large deletions by targeting a large genomic region, which is likely to be non-essential. The analysis of on-target mutations showed an unexpectedly high number of large deletions and chromosomal rearrangements at the CRISPR target loci. We also observed an increase of on-target structural variants in double target experiments as compared to single target experiments. Targeting of two loci within a putatively non-essential region led to a truncation of chromosome 3 at the target locus in multiple cases, causing the deletion of 20 genes and several ribosomal DNA repeats. The identified de novo off-target mutations were rare and randomly distributed, with no apparent connection to unspecific CRISPR/Cas9 off-target binding sites.
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Affiliation(s)
- Veronika Schusterbauer
- bisy GmbH, Wuenschendorf 292, 8200 Hofstaetten, Austria
- Institute of Biomedical Imaging, Graz University of Technology, Stremayrgasse 16, 8010 Graz, Austria
| | | | - Sarah Gangl
- bisy GmbH, Wuenschendorf 292, 8200 Hofstaetten, Austria
| | - Lisa Schenzle
- bisy GmbH, Wuenschendorf 292, 8200 Hofstaetten, Austria
| | | | - Martina Geier
- bisy GmbH, Wuenschendorf 292, 8200 Hofstaetten, Austria
| | - Christian Sailer
- Institute of Biomedical Informatics, Graz University of Technology, Stremayrgasse 16, 8010 Graz, Austria
| | - Anton Glieder
- bisy GmbH, Wuenschendorf 292, 8200 Hofstaetten, Austria
| | - Gerhard G. Thallinger
- Institute of Biomedical Informatics, Graz University of Technology, Stremayrgasse 16, 8010 Graz, Austria
- OMICS Center Graz, BioTechMed Graz, Stiftingtalstraße 24, 8010 Graz, Austria
- Correspondence: ; Tel.: +43-316-873-5343
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14
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Bampidis V, Azimonti G, Bastos MDL, Christensen H, Dusemund B, Fašmon Durjava M, Kouba M, López‐Alonso M, López Puente S, Marcon F, Mayo B, Pechová A, Petkova M, Ramos F, Sanz Y, Villa RE, Woutersen R, Glandorf B, Svensson K, Zeljezic D, Anguita M, Brozzi R, Galobart J, Ortuño J, Revez J, Tarrés‐Call J, Pettenati E. Safety and efficacy of a feed additive consisting of endo-1,4-β-xylanase produced by Komagataella phaffii DSM 33574 (Xylamax) for chickens and turkeys for fattening, chickens reared for laying/breeding, turkeys reared for breeding and minor poultry species for fattening or raised to the point of lay (BioResource international, Inc.). EFSA J 2022; 20:e07428. [PMID: 35898296 PMCID: PMC9310697 DOI: 10.2903/j.efsa.2022.7428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Following a request from the European Commission, the EFSA Panel on Additives and Products of Substances used in Animal Feed (FEEDAP) was asked to deliver a scientific opinion on the safety and efficacy of the product containing endo-1,4-β-xylanase produced by Komagataella phaffii DSM 33574 (Xylamax) as a zootechnical additive in chickens for fattening, chickens reared for laying/breeding, turkeys for fattening, turkeys reared for breeding and minor poultry species for fattening or raised to the point of lay. The production strain is genetically modified. No viable cells nor recombinant DNA of the production strain were detected in the final product. Therefore, the Panel concluded that the additive does not pose any safety concern regarding the production strain. Based on the no observed adverse effect level identified in a subchronic oral toxicity study in rats, the Panel concluded that Xylamax is safe for all poultry species for fattening or reared to the point of lay. Considering the production strain and the results obtained in the genotoxicity studies, the Panel concluded that the additive is safe for the consumers. The Panel also concluded that Xylamax is not irritant to the skin but should be considered a potential eye irritant and a respiratory sensitiser. No conclusions could be drawn on the potential of the additive to cause skin sensitisation. The use of the product as a feed additive is of no concern for the environment. The FEEDAP Panel concluded that the additive has the potential to be efficacious at 10,000 XU/kg feed in chickens for fattening. This conclusion was extended/extrapolated to chickens reared for laying/breeding, turkeys for fattening, turkeys reared for breeding and minor poultry species for fattening or raised to the point of lay.
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15
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Freitas M, Souza P, Homem-de-Mello M, Fonseca-Bazzo YM, Silveira D, Ferreira Filho EX, Pessoa Junior A, Sarker D, Timson D, Inácio J, Magalhães PO. L-Asparaginase from Penicillium sizovae Produced by a Recombinant Komagataella phaffii Strain. Pharmaceuticals (Basel) 2022; 15:ph15060746. [PMID: 35745665 PMCID: PMC9227789 DOI: 10.3390/ph15060746] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 12/10/2022] Open
Abstract
L-asparaginase is an important enzyme in the pharmaceutical field used as treatment for acute lymphoblastic leukemia due to its ability to hydrolyze L-asparagine, an essential amino acid synthesized by normal cells, but not by neoplastic cells. Adverse effects of L-asparaginase formulations are associated with its glutaminase activity and bacterial origin; therefore, it is important to find new sources of L-asparaginase produced by eukaryotic microorganisms with low glutaminase activity. This work aimed to identify the L-asparaginase gene sequence from Penicillium sizovae, a filamentous fungus isolated from the Brazilian Savanna (Cerrado) soil with low glutaminase activity, and to biosynthesize higher yields of this enzyme in the yeast Komagataella phaffii. The L-asparaginase gene sequence of P. sizovae was identified by homology to L-asparaginases from species of Penicillium of the section Citrina: P. citrinum and P. steckii. Partial L-asparaginase from P. sizovae, lacking the periplasmic signaling sequence, was cloned, and expressed intracellularly with highest enzymatic activity achieved by a MUT+ clone cultured in BMM expression medium; a value 5-fold greater than that obtained by native L-asparaginase in P. sizovae cells. To the best of our knowledge, this is the first literature report of the heterologous production of an L-asparaginase from a filamentous fungus by a yeast.
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Affiliation(s)
- Marcela Freitas
- Health Sciences School, University of Brasilia, Brasilia 70910-900, Brazil; (M.F.); (P.S.); (M.H.-d.-M.); (Y.M.F.-B.); (D.S.)
| | - Paula Souza
- Health Sciences School, University of Brasilia, Brasilia 70910-900, Brazil; (M.F.); (P.S.); (M.H.-d.-M.); (Y.M.F.-B.); (D.S.)
| | - Mauricio Homem-de-Mello
- Health Sciences School, University of Brasilia, Brasilia 70910-900, Brazil; (M.F.); (P.S.); (M.H.-d.-M.); (Y.M.F.-B.); (D.S.)
| | - Yris M. Fonseca-Bazzo
- Health Sciences School, University of Brasilia, Brasilia 70910-900, Brazil; (M.F.); (P.S.); (M.H.-d.-M.); (Y.M.F.-B.); (D.S.)
| | - Damaris Silveira
- Health Sciences School, University of Brasilia, Brasilia 70910-900, Brazil; (M.F.); (P.S.); (M.H.-d.-M.); (Y.M.F.-B.); (D.S.)
| | | | - Adalberto Pessoa Junior
- Department of Biochemical and Pharmaceutical Technology, University of Sao Paulo, Sao Paulo 05508-000, Brazil;
| | - Dipak Sarker
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton BN2 4GJ, UK; (D.S.); (D.T.); (J.I.)
| | - David Timson
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton BN2 4GJ, UK; (D.S.); (D.T.); (J.I.)
| | - João Inácio
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton BN2 4GJ, UK; (D.S.); (D.T.); (J.I.)
| | - Pérola O. Magalhães
- Health Sciences School, University of Brasilia, Brasilia 70910-900, Brazil; (M.F.); (P.S.); (M.H.-d.-M.); (Y.M.F.-B.); (D.S.)
- Correspondence:
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16
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Producing Natural Flavours from Isoamyl Alcohol and Fusel Oil by Using Immobilised Rhizopus oryzae Lipase. Catalysts 2022. [DOI: 10.3390/catal12060639] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Enzymatic synthesis of short-chain esters (flavours) might enable their labelling as natural, increasing their value. Covalently immobilised Rhizopus oryzae lipase (EO-proROL) was used to synthesise isoamyl butyrate and acetate. In cyclohexane, the best performer reaction solvent, 1.8 times higher yield of isoamyl butyrate (ca. 100%) than isoamyl acetate (ca. 55%) was obtained. Optimum initial acid concentration (410 mM) and acid:alcohol mole ratio (0.5) were established by a central composite rotatable design to maximise isoamyl butyrate single-batch and cumulative production with reused enzyme. These conditions were used to scale up the esterification (150 mL) and to assess yield, initial esterification rate, productivity and enzyme operational stability. Commercial isoamyl alcohol and fusel oil results were found to be similar as regards yield (91% vs. 84%), initial reaction rate (5.4 µM min−1 with both substrates), operational stability (40% activity loss after five runs with both) and productivity (31.09 vs. 28.7 mM h−1). EO-proROL specificity for the structural isomers of isoamyl alcohol was also evaluated. Thus, a successful biocatalyst and product conditions ready to be used for isoamyl ester industrial production are here proposed.
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17
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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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18
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Kjeldsen A, Kay JE, Baxter S, McColm S, Serrano‐Amatriain C, Parker S, Robb E, Arnold SA, Gilmour C, Raper A, Robertson G, Fleming R, Smith BO, Fotheringham IG, Christie JM, Magneschi L. The fluorescent protein iLOV as a reporter for screening of high‐yield production of antimicrobial peptides in
Pichia pastoris. Microb Biotechnol 2022; 15:2126-2139. [PMID: 35312165 PMCID: PMC9249318 DOI: 10.1111/1751-7915.14034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 03/03/2022] [Accepted: 03/05/2022] [Indexed: 11/28/2022] Open
Abstract
The methylotrophic yeast Pichia pastoris is commonly used for the production of recombinant proteins at scale. The identification of an optimally overexpressing strain following transformation can be time and reagent consuming. Fluorescent reporters like GFP have been used to assist identification of superior producers, but their relatively big size, maturation requirements and narrow temperature range restrict their applications. Here, we introduce the use of iLOV, a flavin‐based fluorescent protein, as a fluorescent marker to identify P. pastoris high‐yielding strains easily and rapidly. The use of this fluorescent protein as a fusion partner is exemplified by the production of the antimicrobial peptide NI01, a difficult target to overexpress in its native form. iLOV fluorescence correlated well with protein expression level and copy number of the chromosomally integrated gene. An easy and simple medium‐throughput plate‐based screen directly following transformation is demonstrated for low complexity screening, while a high‐throughput method using fluorescence‐activated cell sorting (FACS) allowed for comprehensive library screening. Both codon optimization of the iLOV_NI01 fusion cassettes and different integration strategies into the P. pastoris genome were tested to produce and isolate a high‐yielding strain. Checking the genetic stability, process reproducibility and following the purification of the active native peptide are eased by visualization of and efficient cleavage from the iLOV reporter. We show that this system can be used for expression and screening of several different antimicrobial peptides recombinantly produced in P. pastoris.
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Affiliation(s)
- Annemette Kjeldsen
- Ingenza Ltd Roslin Innovation Centre Charnock Bradley Building Roslin EH25 9RG UK
- Institute of Molecular, Cell and Systems Biology College of Medical, Veterinary and Life Sciences University of Glasgow Bower Building Glasgow G12 8QQ UK
| | - Jack E. Kay
- Ingenza Ltd Roslin Innovation Centre Charnock Bradley Building Roslin EH25 9RG UK
| | - Scott Baxter
- Ingenza Ltd Roslin Innovation Centre Charnock Bradley Building Roslin EH25 9RG UK
| | - Stephen McColm
- Ingenza Ltd Roslin Innovation Centre Charnock Bradley Building Roslin EH25 9RG UK
| | | | - Scott Parker
- Ingenza Ltd Roslin Innovation Centre Charnock Bradley Building Roslin EH25 9RG UK
| | - Ellis Robb
- Ingenza Ltd Roslin Innovation Centre Charnock Bradley Building Roslin EH25 9RG UK
| | - S. Alison Arnold
- Ingenza Ltd Roslin Innovation Centre Charnock Bradley Building Roslin EH25 9RG UK
| | - Craig Gilmour
- Ingenza Ltd Roslin Innovation Centre Charnock Bradley Building Roslin EH25 9RG UK
| | - Anna Raper
- The Roslin Institute & Royal (Dick) School of Veterinary Studies University of Edinburgh Easter Bush Midlothian EH25 9RG UK
| | - Graeme Robertson
- The Roslin Institute & Royal (Dick) School of Veterinary Studies University of Edinburgh Easter Bush Midlothian EH25 9RG UK
| | - Robert Fleming
- The Roslin Institute & Royal (Dick) School of Veterinary Studies University of Edinburgh Easter Bush Midlothian EH25 9RG UK
| | - Brian O. Smith
- Institute of Molecular, Cell and Systems Biology College of Medical, Veterinary and Life Sciences University of Glasgow Bower Building Glasgow G12 8QQ UK
| | - Ian G. Fotheringham
- Ingenza Ltd Roslin Innovation Centre Charnock Bradley Building Roslin EH25 9RG UK
| | - John M. Christie
- Institute of Molecular, Cell and Systems Biology College of Medical, Veterinary and Life Sciences University of Glasgow Bower Building Glasgow G12 8QQ UK
| | - Leonardo Magneschi
- Ingenza Ltd Roslin Innovation Centre Charnock Bradley Building Roslin EH25 9RG UK
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19
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Nishi T, Ito Y, Nakamura Y, Yamaji T, Hashiba N, Tamai M, Yasohara Y, Ishii J, Kondo A. One-Step In Vivo Assembly of Multiple DNA Fragments and Genomic Integration in Komagataella phaffii. ACS Synth Biol 2022; 11:644-654. [PMID: 35094517 DOI: 10.1021/acssynbio.1c00302] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The methylotrophic yeast species Komagataella phaffii (synonym: Pichia pastoris) is widely used as a host for recombinant protein production. Although several genetic engineering techniques are being employed on K. phaffii, advanced methods such as in vivo DNA assembly in this yeast species are required for synthetic biology applications. In this study, we established a technique for accomplishing one-step in vivo assembly of multiple DNA fragments and genomic integration in K. phaffii. To concurrently achieve an accurate multiple DNA assembly and a high-efficient integration into the target genomic locus in vivo, a K. phaffii strain, lacking a non-homologous end joining-related protein, DNA ligase IV (Dnl4p), that has been reported to improve gene targeting efficiency by homologous recombination, was used. Using green fluorescent protein along with the lycopene biosynthesis, we showed that our method that included a Dnl4p-defective strain permits direct and easy engineering of K. phaffii strains.
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Affiliation(s)
- Teruyuki Nishi
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe 657-8501, Japan
- Biotechnology Research Laboratories, Pharma & Supplemental Nutrition Solutions Vehicle, Kaneka Corporation, Takasago 676-8688, Japan
| | - Yoichiro Ito
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe 657-8501, Japan
- Engineering Biology Research Center, Kobe University, Kobe 657-8501, Japan
| | - Yasuyuki Nakamura
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe 657-8501, Japan
- Engineering Biology Research Center, Kobe University, Kobe 657-8501, Japan
| | - Taiki Yamaji
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe 657-8501, Japan
- Technology Research Association of Highly Efficient Gene Design (TRAHED), Kobe 650-0047, Japan
| | - Noriko Hashiba
- Technology Research Association of Highly Efficient Gene Design (TRAHED), Kobe 650-0047, Japan
| | - Masaya Tamai
- Technology Research Association of Highly Efficient Gene Design (TRAHED), Kobe 650-0047, Japan
| | - Yoshihiko Yasohara
- Biotechnology Research Laboratories, Pharma & Supplemental Nutrition Solutions Vehicle, Kaneka Corporation, Takasago 676-8688, Japan
| | - Jun Ishii
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe 657-8501, Japan
- Engineering Biology Research Center, Kobe University, Kobe 657-8501, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe 657-8501, Japan
- Engineering Biology Research Center, Kobe University, Kobe 657-8501, Japan
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe 657-8501, Japan
- Center for Sustainable Resource Science, RIKEN, Yokohama 230-0045, Japan
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20
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Liu Q, Song L, Peng Q, Zhu Q, Shi X, Xu M, Wang Q, Zhang Y, Cai M. A programmable high-expression yeast platform responsive to user-defined signals. SCIENCE ADVANCES 2022; 8:eabl5166. [PMID: 35148182 PMCID: PMC8836803 DOI: 10.1126/sciadv.abl5166] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Rapidly growing yeasts with appropriate posttranslational modifications are favored hosts for protein production in the biopharmaceutical industry. However, limited production capacity and intricate transcription regulation restrict their application and adaptability. Here, we describe a programmable high-expression yeast platform, SynPic-X, which responds to defined signals and is broadly applicable. We demonstrated that a synthetic improved transcriptional signal amplification device (iTSAD) with a bacterial-yeast transactivator and bacterial-yeast promoter markedly increased expression capacity in Pichia pastoris. CRISPR activation and interference devices were designed to strictly regulate iTSAD in response to defined signals. Engineered switches were then constructed to exemplify the response of SynPic-X to exogenous signals. Expression of α-amylase by SynPic-R, a specific SynPic-X, in a bioreactor proved a methanol-free high-production process of recombinant protein. Our SynPic-X platform provides opportunities for protein production in customizable yeast hosts with high expression and regulatory flexibility.
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Affiliation(s)
- Qi Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Lili Song
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Qiangqiang Peng
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Qiaoyun Zhu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Xiaona Shi
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Mingqiang Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Qiyao Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Yuanxing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
- Shanghai Collaborative Innovation Center for Biomanufacturing, 130 Meilong Road, Shanghai 200237, China
| | - Menghao Cai
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
- Corresponding author.
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21
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Rinnofner C, Felber M, Pichler H. Strains and Molecular Tools for Recombinant Protein Production in Pichia pastoris. Methods Mol Biol 2022; 2513:79-112. [PMID: 35781201 DOI: 10.1007/978-1-0716-2399-2_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Within the last two decades, the methylotrophic yeast Pichia pastoris (Komagataella phaffii) has become an important alternative to E. coli or mammalian cell lines for the production of recombinant proteins. Easy handling, strong promoters, and high cell density cultivations as well as the capability of posttranslational modifications are some of the major benefits of this yeast. The high secretion capacity and low level of endogenously secreted proteins further promoted the rapid development of a versatile Pichia pastoris toolbox. This chapter reviews common and new "Pichia tools" and their specific features. Special focus is given to expression strains, such as different methanol utilization, protease-deficient or glycoengineered strains, combined with application highlights. Different promoters and signal sequences are also discussed.
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Affiliation(s)
- Claudia Rinnofner
- Austrian Centre of Industrial Biotechnology (ACIB), Graz, Austria.
- Bisy GmbH, Hofstaetten/Raab, Austria.
| | - Michael Felber
- Austrian Centre of Industrial Biotechnology (ACIB), Graz, Austria
| | - Harald Pichler
- Austrian Centre of Industrial Biotechnology (ACIB), Graz, Austria
- Institute of Molecular Biotechnology, Graz University of Technology, Graz, Austria
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22
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Ata Ö, Ergün BG, Fickers P, Heistinger L, Mattanovich D, Rebnegger C, Gasser B. What makes Komagataella phaffii non-conventional? FEMS Yeast Res 2021; 21:6440159. [PMID: 34849756 PMCID: PMC8709784 DOI: 10.1093/femsyr/foab059] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/23/2021] [Indexed: 12/30/2022] Open
Abstract
The important industrial protein production host Komagataella phaffii (syn Pichia pastoris) is classified as a non-conventional yeast. But what exactly makes K. phaffii non-conventional? In this review, we set out to address the main differences to the 'conventional' yeast Saccharomyces cerevisiae, but also pinpoint differences to other non-conventional yeasts used in biotechnology. Apart from its methylotrophic lifestyle, K. phaffii is a Crabtree-negative yeast species. But even within the methylotrophs, K. phaffii possesses distinct regulatory features such as glycerol-repression of the methanol-utilization pathway or the lack of nitrate assimilation. Rewiring of the transcriptional networks regulating carbon (and nitrogen) source utilization clearly contributes to our understanding of genetic events occurring during evolution of yeast species. The mechanisms of mating-type switching and the triggers of morphogenic phenotypes represent further examples for how K. phaffii is distinguished from the model yeast S. cerevisiae. With respect to heterologous protein production, K. phaffii features high secretory capacity but secretes only low amounts of endogenous proteins. Different to S. cerevisiae, the Golgi apparatus of K. phaffii is stacked like in mammals. While it is tempting to speculate that Golgi architecture is correlated to the high secretion levels or the different N-glycan structures observed in K. phaffii, there is recent evidence against this. We conclude that K. phaffii is a yeast with unique features that has a lot of potential to explore both fundamental research questions and industrial applications.
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Affiliation(s)
- Özge Ata
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria.,Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria
| | - Burcu Gündüz Ergün
- UNAM-National Nanotechnology Research Center, Bilkent University, Ankara, Turkey.,Biotechnology Research Center, Ministry of Agriculture and Forestry, Ankara, Turkey
| | - 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
| | - Lina Heistinger
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria.,Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Christian Doppler Laboratory for Innovative Immunotherapeutics, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Diethard Mattanovich
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria.,Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria
| | - Corinna Rebnegger
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria.,Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Christian Doppler Laboratory for Growth-Decoupled Protein Production in Yeast, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Brigitte Gasser
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria.,Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Biotechnology Research Center, Ministry of Agriculture and Forestry, Ankara, Turkey
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23
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Schultz JC, Cao M, Mejia A, Zhao H. CUT&RUN Identifies Centromeric DNA Regions of Rhodotorula toruloides IFO0880. FEMS Yeast Res 2021; 21:6460484. [PMID: 34902017 DOI: 10.1093/femsyr/foab066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 12/10/2021] [Indexed: 11/14/2022] Open
Abstract
Rhodotorula toruloides has been increasingly explored as a host for bioproduction of lipids, fatty acid derivatives, and terpenoids. Various genetic tools have been developed, but neither a centromere nor an autonomously replicating sequence (ARS), both necessary elements for stable episomal plasmid maintenance, have yet been reported. In this study, Cleavage Under Targets and Release Using Nuclease (CUT&RUN), a method used for genome-wide mapping DNA-protein interactions, was used to identify R. toruloides IFO0880 genomic regions associated with the centromeric histone H3 protein Cse4, a marker of centromeric DNA. Fifteen putative centromeres ranging from 8 to 19 kb in length were identified and analyzed, and four were tested for, but did not show, ARS activity. These centromeric sequences contained below average GC content, corresponded to transcriptional cold-spots, were primarily nonrepetitive, and shared some vestigial transposon-related sequences but otherwise did not show significant sequence conservation. Future efforts to identify an ARS in this yeast can utilize these centromeric DNA sequences to improve the stability of episomal plasmids derived from putative ARS elements.
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Affiliation(s)
- J Carl Schultz
- Department of Chemical and Biomolecular Engineering, U.S. Department of Energy Center for Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Mingfeng Cao
- Department of Chemical and Biomolecular Engineering, U.S. Department of Energy Center for Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Andrea Mejia
- Department of Chemical and Biomolecular Engineering, U.S. Department of Energy Center for Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, U.S. Department of Energy Center for Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.,Departments of Chemistry, Biochemistry, and Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
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24
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Constitutive Expression in Komagataella phaffii of Mature Rhizopus oryzae Lipase Jointly with Its Truncated Prosequence Improves Production and the Biocatalyst Operational Stability. Catalysts 2021. [DOI: 10.3390/catal11101192] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Rhizopus oryzae lipase (ROL) containing 28 C-terminal amino acids of the prosequence fused to the N-terminal mature sequence in ROL (proROL) was successfully expressed in the methylotrophic yeast Komagataella phaffii (Pichia pastoris) under the constitutive glyceraldehyde-3-phosphate dehydrogenase promoter (PGAP). Although the sequence encoding the mature lipase (rROL) was also transformed, no clones were obtained after three transformation cycles, which highlights the importance of the truncated prosequence to obtain viable transformed clones. Batch cultures of the K. phaffii strain constitutively expressing proROL scarcely influenced growth rate and exhibited a final activity and volumetric productivity more than six times higher than those obtained with proROL from K. phaffii under the methanol-inducible alcohol oxidase 1 promoter (PAOX1). The previous differences were less marked in fed-batch cultures. N-terminal analysis confirmed the presence of the 28 amino acids in proROL. In addition, immobilized proROL exhibited increased tolerance of organic solvents and an operational stability 0.25 and 3 times higher than that of immobilized rROL in biodiesel and ethyl butyrate production, respectively. Therefore, the truncated prosequence enables constitutive proROL production, boosts bioprocess performance and provides a more stable biocatalyst in two reactions in which lipases are mostly used at industrial level, esterification (ethyl butyrate) and transesterification (biodiesel).
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25
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Fessner ND, Nelson DR, Glieder A. Evolution and enrichment of CYP5035 in Polyporales: functionality of an understudied P450 family. Appl Microbiol Biotechnol 2021; 105:6779-6792. [PMID: 34459954 PMCID: PMC8426240 DOI: 10.1007/s00253-021-11444-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 05/29/2021] [Accepted: 07/03/2021] [Indexed: 11/29/2022]
Abstract
Abstract Bioprospecting for innovative basidiomycete cytochrome P450 enzymes (P450s) is highly desirable due to the fungi’s enormous enzymatic repertoire and outstanding ability to degrade lignin and detoxify various xenobiotics. While fungal metagenomics is progressing rapidly, the biocatalytic potential of the majority of these annotated P450 sequences usually remains concealed, although functional profiling identified several P450 families with versatile substrate scopes towards various natural products. Functional knowledge about the CYP5035 family, for example, is largely insufficient. In this study, the families of the putative P450 sequences of the four white-rot fungi Polyporus arcularius, Polyporus brumalis, Polyporus squamosus and Lentinus tigrinus were assigned, and the CYPomes revealed an unusual enrichment of CYP5035, CYP5136 and CYP5150. By computational analysis of the phylogeny of the former two P450 families, the evolution of their enrichment could be traced back to the Ganoderma macrofungus, indicating their evolutionary benefit. In order to address the knowledge gap on CYP5035 functionality, a representative subgroup of this P450 family of P. arcularius was expressed and screened against a test set of substrates. Thereby, the multifunctional enzyme CYP5035S7 converting several plant natural product classes was discovered. Aligning CYP5035S7 to 102,000 putative P450 sequences of 36 fungal species from Joint Genome Institute-provided genomes located hundreds of further CYP5035 family members, which subfamilies were classified if possible. Exemplified by these specific enzyme analyses, this study gives valuable hints for future bioprospecting of such xenobiotic-detoxifying P450s and for the identification of their biocatalytic potential. Graphical abstract ![]()
Key points • The P450 families CYP5035 and CYP5136 are unusually enriched in P. arcularius. • Functional screening shows CYP5035 assisting in the fungal detoxification mechanism. • Some Polyporales encompass an unusually large repertoire of detoxification P450s. Supplementary Information The online version contains supplementary material available at 10.1007/s00253-021-11444-2.
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Affiliation(s)
- Nico D Fessner
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, Petersgasse 14, 8010, Graz, Austria
| | - David R Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
| | - Anton Glieder
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, Petersgasse 14, 8010, Graz, Austria.
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26
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Rieder L, Ebner K, Glieder A, Sørlie M. Novel molecular biological tools for the efficient expression of fungal lytic polysaccharide monooxygenases in Pichia pastoris. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:122. [PMID: 34044872 PMCID: PMC8161572 DOI: 10.1186/s13068-021-01971-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 05/13/2021] [Indexed: 05/13/2023]
Abstract
BACKGROUND Lytic polysaccharide monooxygenases (LPMOs) are attracting large attention due their ability to degrade recalcitrant polysaccharides in biomass conversion and to perform powerful redox chemistry. RESULTS We have established a universal Pichia pastoris platform for the expression of fungal LPMOs using state-of-the-art recombination cloning and modern molecular biological tools to achieve high yields from shake-flask cultivation and simple tag-less single-step purification. Yields are very favorable with up to 42 mg per liter medium for four different LPMOs spanning three different families. Moreover, we report for the first time of a yeast-originating signal peptide from the dolichyl-diphosphooligosaccharide-protein glycosyltransferase subunit 1 (OST1) form S. cerevisiae efficiently secreting and successfully processes the N-terminus of LPMOs yielding in fully functional enzymes. CONCLUSION The work demonstrates that the industrially most relevant expression host P. pastoris can be used to express fungal LPMOs from different families in high yields and inherent purity. The presented protocols are standardized and require little equipment with an additional advantage with short cultivation periods.
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Affiliation(s)
- Lukas Rieder
- Faculty of Chemistry, Biotechnology, and Food Sciences, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | | | - Anton Glieder
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, Graz, Austria
| | - Morten Sørlie
- Faculty of Chemistry, Biotechnology, and Food Sciences, Norwegian University of Life Sciences (NMBU), Ås, Norway.
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27
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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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28
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Ruchala J, Sibirny AA. Pentose metabolism and conversion to biofuels and high-value chemicals in yeasts. FEMS Microbiol Rev 2020; 45:6034013. [PMID: 33316044 DOI: 10.1093/femsre/fuaa069] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 12/09/2020] [Indexed: 12/15/2022] Open
Abstract
Pentose sugars are widespread in nature and two of them, D-xylose and L-arabinose belong to the most abundant sugars being the second and third by abundance sugars in dry plant biomass (lignocellulose) and in general on planet. Therefore, it is not surprising that metabolism and bioconversion of these pentoses attract much attention. Several different pathways of D-xylose and L-arabinose catabolism in bacteria and yeasts are known. There are even more common and really ubiquitous though not so abundant pentoses, D-ribose and 2-deoxy-D-ribose, the constituents of all living cells. Thus, ribose metabolism is example of endogenous metabolism whereas metabolism of other pentoses, including xylose and L-arabinose, represents examples of the metabolism of foreign exogenous compounds which normally are not constituents of yeast cells. As a rule, pentose degradation by the wild-type strains of microorganisms does not lead to accumulation of high amounts of valuable substances; however, productive strains have been obtained by random selection and metabolic engineering. There are numerous reviews on xylose and (less) L-arabinose metabolism and conversion to high value substances; however, they mostly are devoted to bacteria or the yeast Saccharomyces cerevisiae. This review is devoted to reviewing pentose metabolism and bioconversion mostly in non-conventional yeasts, which naturally metabolize xylose. Pentose metabolism in the recombinant strains of S. cerevisiae is also considered for comparison. The available data on ribose, xylose, L-arabinose transport, metabolism, regulation of these processes, interaction with glucose catabolism and construction of the productive strains of high-value chemicals or pentose (ribose) itself are described. In addition, genome studies of the natural xylose metabolizing yeasts and available tools for their molecular research are reviewed. Metabolism of other pentoses (2-deoxyribose, D-arabinose, lyxose) is briefly reviewed.
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Affiliation(s)
- Justyna Ruchala
- Department of Microbiology and Molecular Genetics, University of Rzeszow, Zelwerowicza 4, Rzeszow 35-601, Poland.,Department of Molecular Genetics and Biotechnology, Institute of Cell Biology NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
| | - Andriy A Sibirny
- Department of Microbiology and Molecular Genetics, University of Rzeszow, Zelwerowicza 4, Rzeszow 35-601, Poland.,Department of Molecular Genetics and Biotechnology, Institute of Cell Biology NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
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29
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Brady JR, Tan MC, Whittaker CA, Colant NA, Dalvie NC, Love KR, Love JC. Identifying Improved Sites for Heterologous Gene Integration Using ATAC-seq. ACS Synth Biol 2020; 9:2515-2524. [PMID: 32786350 PMCID: PMC7506950 DOI: 10.1021/acssynbio.0c00299] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
![]()
Constructing efficient cellular factories
often requires integration
of heterologous pathways for synthesis of novel compounds and improved
cellular productivity. Few genomic sites are routinely used, however,
for efficient integration and expression of heterologous genes, especially
in nonmodel hosts. Here, a data-guided framework for informing suitable
integration sites for heterologous genes based on ATAC-seq was developed
in the nonmodel yeast Komagataella phaffii. Single-copy
GFP constructs were integrated using CRISPR/Cas9 into 38 intergenic
regions (IGRs) to evaluate the effects of IGR size, intensity of ATAC-seq
peaks, and orientation and expression of adjacent genes. Only the
intensity of accessibility peaks was observed to have a significant
effect, with higher expression observed from IGRs with low- to moderate-intensity
peaks than from high-intensity peaks. This effect diminished for tandem,
multicopy integrations, suggesting that the additional copies of exogenous
sequence buffered the transcriptional unit of the transgene against
effects from endogenous sequence context. The approach developed from
these results should provide a basis for nominating suitable IGRs
in other eukaryotic hosts from an annotated genome and ATAC-seq data.
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Affiliation(s)
- Joseph R. Brady
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Melody C. Tan
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Charles A. Whittaker
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Noelle A. Colant
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Neil C. Dalvie
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Kerry Routenberg Love
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - J. Christopher Love
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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30
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Hashem C, Stolterfoht H, Rinnofner C, Steinberger S, Winkler M, Pichler H. Secretion of Pseudomonas aeruginosa Lipoxygenase by Pichia pastoris upon Glycerol Feed. Biotechnol J 2020; 15:e2000089. [PMID: 32749051 DOI: 10.1002/biot.202000089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/07/2020] [Indexed: 01/17/2023]
Abstract
Pseudomonas aeruginosa lipoxygenase (PaLOX) catalyzes the peroxidation of unsaturated fatty acids. Not only linoleic acid, but also linolenic acid and oleic acid are oxidized. The natural host secretes PaLOX into the periplasmic space. Herein, the aim is to secrete PaLOX to the culture supernatant of Pichia pastoris. Since protein background in the culture supernatant is typically rather low, this strategy allows for almost pure production of PaLOX applicable for the valorization of renewable fatty acids, for example for the production of green leaf volatiles. Using the CAT1 promoter system and the well-established α-factor signal sequence for secretion, methanol- and glycerol-induced secretion are compared and the latter shows four times more LOX activity in the culture supernatant under methanol-free conditions. In addition, secreted PaLOX is purified and the specific activity with enzyme in culture supernatant is compared. Notably, the predominant specific activity is achieved for enzyme in culture supernatant - 11.6 U mg-1 - reaching five times higher specific activity than purified PaLOX.
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Affiliation(s)
- Chiam Hashem
- Austrian Centre of Industrial Biotechnology, Krenngasse 37, Graz, 8010, Austria
- TU Graz, NAWI Graz, BioTechMed Graz, Institute of Molecular Biotechnology, Petersgasse 14, Graz, 8010, Austria
| | - Holly Stolterfoht
- Austrian Centre of Industrial Biotechnology, Krenngasse 37, Graz, 8010, Austria
| | - Claudia Rinnofner
- Austrian Centre of Industrial Biotechnology, Krenngasse 37, Graz, 8010, Austria
- bisy GmbH, Wuenschendorf 292, Hofstaetten, 8200, Austria
| | - Stefan Steinberger
- Austrian Centre of Industrial Biotechnology, Krenngasse 37, Graz, 8010, Austria
| | - Margit Winkler
- Austrian Centre of Industrial Biotechnology, Krenngasse 37, Graz, 8010, Austria
- TU Graz, NAWI Graz, BioTechMed Graz, Institute of Molecular Biotechnology, Petersgasse 14, Graz, 8010, Austria
| | - Harald Pichler
- Austrian Centre of Industrial Biotechnology, Krenngasse 37, Graz, 8010, Austria
- TU Graz, NAWI Graz, BioTechMed Graz, Institute of Molecular Biotechnology, Petersgasse 14, Graz, 8010, Austria
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31
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De S, Rebnegger C, Moser J, Tatto N, Graf AB, Mattanovich D, Gasser B. Pseudohyphal differentiation in Komagataella phaffii: investigating the FLO gene family. FEMS Yeast Res 2020; 20:5884885. [PMID: 32766781 PMCID: PMC7419694 DOI: 10.1093/femsyr/foaa044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 08/05/2020] [Indexed: 12/12/2022] Open
Abstract
Many yeasts differentiate into multicellular phenotypes in adverse environmental conditions. Here, we investigate pseudohyphal growth in Komagataella phaffii and the involvement of the flocculin (FLO) gene family in its regulation. The K. phaffii FLO family consists of 13 members, and the conditions inducing pseudohyphal growth are different from Saccharomyces cerevisiae. So far, this phenotype was only observed when K. phaffii was cultivated at slow growth rates in glucose-limited chemostats, but not upon nitrogen starvation or the presence of fusel alcohols. Transcriptional analysis identified that FLO11, FLO400 and FLO5-1 are involved in the phenotype, all being controlled by the transcriptional regulator Flo8. The three genes exhibit a complex mechanism of expression and repression during transition from yeast to pseudohyphal form. Unlike in S. cerevisiae, deletion of FLO11 does not completely prevent the phenotype. In contrast, deletion of FLO400 or FLO5-1 prevents pseudohyphae formation, and hampers FLO11 expression. FAIRE-Seq data shows that the expression and repression of FLO400 and FLO5-1 are correlated to open or closed chromatin regions upstream of these genes, respectively. Our findings indicate that K. phaffii Flo400 and/or Flo5-1 act as upstream signals that lead to the induction of FLO11 upon glucose limitation in chemostats at slow growth and chromatin modulation is involved in the regulation of their expression.
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Affiliation(s)
- Sonakshi De
- Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria.,Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Corinna Rebnegger
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria.,CD-Laboratory for Growth-decoupled Protein Production in Yeast, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Josef Moser
- Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria.,School of Bioengineering, University of Applied Sciences-FH Campus Wien, Muthgasse 11, 1190 Vienna, Austria
| | - Nadine Tatto
- Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria.,Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Alexandra B Graf
- Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria.,School of Bioengineering, University of Applied Sciences-FH Campus Wien, Muthgasse 11, 1190 Vienna, Austria
| | - Diethard Mattanovich
- Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria.,Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Brigitte Gasser
- Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria.,Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria.,CD-Laboratory for Growth-decoupled Protein Production in Yeast, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
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32
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Piva LC, De Marco JL, de Moraes LMP, Reis VCB, Torres FAG. Construction and characterization of centromeric plasmids for Komagataella phaffii using a color-based plasmid stability assay. PLoS One 2020; 15:e0235532. [PMID: 32614905 PMCID: PMC7332064 DOI: 10.1371/journal.pone.0235532] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 06/16/2020] [Indexed: 02/06/2023] Open
Abstract
The yeast Komagataella phaffii is widely used as a microbial host for heterologous protein production. However, molecular tools for this yeast are basically restricted to a few integrative and replicative plasmids. Four sequences that have recently been proposed as the K. phaffii centromeres could be used to develop a new class of mitotically stable vectors. In this work, we designed a color-based genetic assay to investigate plasmid stability in K. phaffii and constructed vectors bearing K. phaffii centromeres and the ADE3 marker. These genetic tools were evaluated in terms of mitotic stability by transforming an ade2/ade3 auxotrophic strain and regarding plasmid copy number by quantitative PCR (qPCR). Our results confirmed that the centromeric plasmids were maintained at low copy numbers as a result of typical chromosome-like segregation during cell division. These features, combined with in vivo assembly possibilities, prompt these plasmids as a new addition to the K. phaffii genetic toolbox.
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Affiliation(s)
- Luiza Cesca Piva
- Departamento de Biologia Celular, Bloco K, primeiro andar, Universidade de Brasília, Brasília, Brazil
| | - Janice Lisboa De Marco
- Departamento de Biologia Celular, Bloco K, primeiro andar, Universidade de Brasília, Brasília, Brazil
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33
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Douglass AP, Byrne KP, Wolfe KH. The Methylotroph Gene Order Browser (MGOB) reveals conserved synteny and ancestral centromere locations in the yeast family Pichiaceae. FEMS Yeast Res 2020; 19:5545594. [PMID: 31397853 DOI: 10.1093/femsyr/foz058] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 08/08/2019] [Indexed: 12/15/2022] Open
Abstract
The yeast family Pichiaceae, also known as the 'methylotrophs clade', is a relatively little studied group of yeasts despite its economic and clinical relevance. To explore the genome evolution and synteny relationships within this family, we developed the Methylotroph Gene Order Browser (MGOB, http://mgob.ucd.ie) similar to our previous gene order browsers for other yeast families. The dataset contains genome sequences from nine Pichiaceae species, including our recent reference sequence of Pichia kudriavzevii. As an example, we demonstrate the conservation of synteny around the MOX1 locus among species both containing and lacking the MOX1 gene for methanol assimilation. We found ancient clusters of genes that are conserved as adjacent between Pichiaceae and Saccharomycetaceae. Surprisingly, we found evidence that the locations of some centromeres have been conserved among Pichiaceae species, and between Pichiaceae and Saccharomycetaceae, even though the centromeres fall into different structural categories-point centromeres, inverted repeats and retrotransposon cluster centromeres.
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Affiliation(s)
- Alexander P Douglass
- UCD Conway Institute, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Kevin P Byrne
- UCD Conway Institute, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Kenneth H Wolfe
- UCD Conway Institute, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
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34
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Brady JR, Whittaker CA, Tan MC, Kristensen DL, Ma D, Dalvie NC, Love KR, Love JC. Comparative genome-scale analysis of Pichia pastoris variants informs selection of an optimal base strain. Biotechnol Bioeng 2020; 117:543-555. [PMID: 31654411 PMCID: PMC7003935 DOI: 10.1002/bit.27209] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/04/2019] [Accepted: 10/22/2019] [Indexed: 01/08/2023]
Abstract
Komagataella phaffii, also known as Pichia pastoris, is a common host for the production of biologics and enzymes, due to fast growth, high productivity, and advancements in host engineering. Several K. phaffii variants are commonly used as interchangeable base strains, which confounds efforts to improve this host. In this study, genomic and transcriptomic analyses of Y-11430 (CBS7435), GS115, X-33, and eight other variants enabled a comparative assessment of the relative fitness of these hosts for recombinant protein expression. Cell wall integrity explained the majority of the variation among strains, impacting transformation efficiency, growth, methanol metabolism, and secretion of heterologous proteins. Y-11430 exhibited the highest activity of genes involved in methanol utilization, up to two-fold higher transcription of heterologous genes, and robust growth. With a more permeable cell wall, X-33 displayed a six-fold higher transformation efficiency and up to 1.2-fold higher titers than Y-11430. X-33 also shared nearly all mutations, and a defective variant of HIS4, with GS115, precluding robust growth. Transferring two beneficial mutations identified in X-33 into Y-11430 resulted in an optimized base strain that provided up to four-fold higher transformation efficiency and three-fold higher protein titers, while retaining robust growth. The approach employed here to assess unique banked variants in a species and then transfer key beneficial variants into a base strain should also facilitate rational assessment of a broad set of other recombinant hosts.
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Affiliation(s)
- Joseph R. Brady
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMassachusetts
- Department of Chemical EngineeringMassachusetts Institute of TechnologyCambridgeMassachusetts
| | - Charles A. Whittaker
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMassachusetts
| | - Melody C. Tan
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMassachusetts
| | - D. Lee Kristensen
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMassachusetts
| | - Duanduan Ma
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMassachusetts
| | - Neil C. Dalvie
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMassachusetts
- Department of Chemical EngineeringMassachusetts Institute of TechnologyCambridgeMassachusetts
| | - Kerry Routenberg Love
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMassachusetts
| | - J. Christopher Love
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMassachusetts
- Department of Chemical EngineeringMassachusetts Institute of TechnologyCambridgeMassachusetts
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35
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Braun-Galleani S, Dias JA, Coughlan AY, Ryan AP, Byrne KP, Wolfe KH. Genomic diversity and meiotic recombination among isolates of the biotech yeast Komagataella phaffii (Pichia pastoris). Microb Cell Fact 2019; 18:211. [PMID: 31801527 PMCID: PMC6894112 DOI: 10.1186/s12934-019-1260-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 11/25/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Komagataella phaffii is a yeast widely used in the pharmaceutical and biotechnology industries, and is one of the two species that were previously called Pichia pastoris. However, almost all laboratory work on K. phaffii has utilized strains derived from a single natural isolate, CBS7435. There is little information about the sequence diversity of K. phaffii or the genetic properties of this species. RESULTS We sequenced the genomes of all the known isolates of K. phaffii. We made a genetic cross between derivatives of two isolates that differ at 44,000 single nucleotide polymorphism sites, and used this cross to analyze the rate and landscape of meiotic recombination. We conducted tetrad analysis by making use of the property that K. phaffii haploids do not mate in rich media, which enabled us to isolate and sequence the four types of haploid cell that are present in the colony that forms when a tetra-type ascus germinates. CONCLUSIONS We found that only four distinct natural isolates of K. phaffii exist in public yeast culture collections. The meiotic recombination rate in K. phaffii is approximately 3.5 times lower than in Saccharomyces cerevisiae, with an average of 25 crossovers per meiosis. Recombination is suppressed, and genetic diversity among natural isolates is low, in a region around centromeres that is much larger than the centromeres themselves. Our work lays a foundation for future quantitative trait locus analysis in K. phaffii.
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Affiliation(s)
| | - Julie A Dias
- UCD Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland
- Department of Mathematics and Statistics, McGill University, Montreal, QC, Canada
| | - Aisling Y Coughlan
- UCD Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland
| | - Adam P Ryan
- UCD Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland
| | - Kevin P Byrne
- UCD Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland
| | - Kenneth H Wolfe
- UCD Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland.
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36
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Specific growth rate governs AOX1 gene expression, affecting the production kinetics of Pichia pastoris (Komagataella phaffii) P AOX1-driven recombinant producer strains with different target gene dosage. Microb Cell Fact 2019; 18:187. [PMID: 31675969 PMCID: PMC6824138 DOI: 10.1186/s12934-019-1240-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 10/23/2019] [Indexed: 12/02/2022] Open
Abstract
Background The PAOX1-based expression system is the most widely used for producing recombinant proteins in the methylotrophic yeast Pichia pastoris (Komagataella phaffii). Despite relevant recent advances in regulation of the methanol utilization (MUT) pathway have been made, the role of specific growth rate (µ) in AOX1 regulation remains unknown, and therefore, its impact on protein production kinetics is still unclear. Results The influence of heterologous gene dosage, and both, operational mode and strategy, on culture physiological state was studied by cultivating the two PAOX1-driven Candida rugosa lipase 1 (Crl1) producer clones. Specifically, a clone integrating a single expression cassette of CRL1 was compared with one containing three cassettes over broad dilution rate and µ ranges in both chemostat and fed-batch cultivations. Chemostat cultivations allowed to establish the impact of µ on the MUT-related MIT1 pool which leads to a bell-shaped relationship between µ and PAOX1-driven gene expression, influencing directly Crl1 production kinetics. Also, chemostat and fed-batch cultivations exposed the favorable effects of increasing the CRL1 gene dosage (up to 2.4 fold in qp) on Crl1 production with no significant detrimental effects on physiological capabilities. Conclusions PAOX1-driven gene expression and Crl1 production kinetics in P. pastoris were successfully correlated with µ. In fact, µ governs MUT-related MIT1 amount that triggers PAOX1-driven gene expression—heterologous genes included—, thus directly influencing the production kinetics of recombinant protein.
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37
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Fischer JE, Glieder A. Current advances in engineering tools for Pichia pastoris. Curr Opin Biotechnol 2019; 59:175-181. [DOI: 10.1016/j.copbio.2019.06.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 06/02/2019] [Accepted: 06/18/2019] [Indexed: 12/13/2022]
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38
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Ahmad M, Winkler CM, Kolmbauer M, Pichler H, Schwab H, Emmerstorfer‐Augustin A. Pichia pastoris protease-deficient and auxotrophic strains generated by a novel, user-friendly vector toolbox for gene deletion. Yeast 2019; 36:557-570. [PMID: 31148217 PMCID: PMC6771850 DOI: 10.1002/yea.3426] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/28/2019] [Accepted: 05/26/2019] [Indexed: 01/24/2023] Open
Abstract
Targeted gene knockouts play an important role in the study of gene function. For the generation of knockouts in the industrially important yeast Pichia pastoris, several protocols have been published to date. Nevertheless, creating a targeted knockout in P. pastoris still is a time-consuming process, as the existing protocols are labour intensive and/or prone to accumulate nucleotide mutations. In this study, we introduce a novel, user-friendly vector-based system for the generation of targeted knockouts in P. pastoris. Upon confirming the successful knockout, respective selection markers can easily be recycled. Excision of the marker is mediated by Flippase (Flp) recombinase and occurs at high frequency (≥95%). We validated our knockout system by deleting 20 (confirmed and putative) protease genes and five genes involved in biosynthetic pathways. For the first time, we describe gene deletions of PRO3 and PHA2 in P. pastoris, genes involved in proline, and phenylalanine biosynthesis, respectively. Unexpectedly, knockout strains of PHA2 did not display the anticipated auxotrophy for phenylalanine but rather showed a bradytroph phenotype on minimal medium hinting at an alternative but less efficient pathway for production of phenylalanine exists in P. pastoris. Overall, all knockout vectors can easily be adapted to the gene of interest and strain background by efficient exchange of target homology regions and selection markers in single cloning steps. Average knockout efficiencies for all 25 genes were shown to be 40%, which is comparably high.
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Affiliation(s)
- Mudassar Ahmad
- Institute of Molecular BiotechnologyGraz University of TechnologyGrazAustria
| | | | - Markus Kolmbauer
- Institute of Molecular BiotechnologyGraz University of TechnologyGrazAustria
| | - Harald Pichler
- Institute of Molecular BiotechnologyGraz University of TechnologyGrazAustria,Austrian Centre of Industrial Biotechnology (ACIB)GrazAustria
| | - Helmut Schwab
- Institute of Molecular BiotechnologyGraz University of TechnologyGrazAustria,Austrian Centre of Industrial Biotechnology (ACIB)GrazAustria
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39
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Braun-Galleani S, Henríquez MJ, Nesbeth DN. Whole cell biosynthesis of 1-methyl-3-phenylpropylamine and 2-amino-1,3,4-butanetriol using Komagataella phaffii ( Pichia pastoris) strain BG-10 engineered with a transgene encoding Chromobacterium violaceum ω-transaminase. Heliyon 2019; 5:e02338. [PMID: 31467995 PMCID: PMC6710532 DOI: 10.1016/j.heliyon.2019.e02338] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 04/04/2019] [Accepted: 08/14/2019] [Indexed: 12/13/2022] Open
Abstract
We have engineered strain BG-10 of the methylotrophic yeast Komagataella phaffii for use as an effective whole cell biocatalyst. We introduced into the yeast a transgene encoding a Chromobacterium violaceum ω-transaminase for transcription in response to methanol induction. The strain was then assessed with respect to its growth performance and biotransformation of a fed ketoalcohol substrate to an amino-alcohol. In the resultant strain, BG-TAM, methanol induction did not compromise cell growth. Successful bioconversion of fed substrates to the by-product, acetophenone, indicated transaminase activity in shake flask-cultivated BG-TAM cells. We then used bioreactor cultivation to exploit the high levels of biomass achievable by Komagataella phaffii. In a 900 μL reaction the BG-TAM strain at OD600 = 1024 achieved up to 0.41 mol mol−1 (molproduct molsubstrate−1) yield on substrate (Yp/s) for production of 1-methyl-3-phenylpropylamine and a space time yield (STY) of 0.29 g L−1 h−1 for production of 2-amino-1,3,4-butanetriol. We have shown that transamination, an important step for bespoke synthesis of small molecule medicines, is biologically realisable using enzymes with a broad substrate range, such as ω-transaminases, within living yeast cells that are fed low-cost substrates for bioconversion.
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Affiliation(s)
- Stephanie Braun-Galleani
- Department of Biochemical Engineering, University College London, Bernard Katz Building, London, WC1E 6BT, United Kingdom
| | - Maria-José Henríquez
- Department of Biochemical Engineering, University College London, Bernard Katz Building, London, WC1E 6BT, United Kingdom
| | - Darren N Nesbeth
- Department of Biochemical Engineering, University College London, Bernard Katz Building, London, WC1E 6BT, United Kingdom
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40
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Amann T, Schmieder V, Faustrup Kildegaard H, Borth N, Andersen MR. Genetic engineering approaches to improve posttranslational modification of biopharmaceuticals in different production platforms. Biotechnol Bioeng 2019; 116:2778-2796. [PMID: 31237682 DOI: 10.1002/bit.27101] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 03/27/2019] [Accepted: 06/18/2019] [Indexed: 12/18/2022]
Abstract
The number of approved biopharmaceuticals, where product quality attributes remain of major importance, is increasing steadily. Within the available variety of expression hosts, the production of biopharmaceuticals faces diverse limitations with respect to posttranslational modifications (PTM), while different biopharmaceuticals demand different forms and specifications of PTMs for proper functionality. With the growing toolbox of genetic engineering technologies, it is now possible to address general as well as host- or biopharmaceutical-specific product quality obstacles. In this review, we present diverse expression systems derived from mammalians, bacteria, yeast, plants, and insects as well as available genetic engineering tools. We focus on genes for knockout/knockdown and overexpression for meaningful approaches to improve biopharmaceutical PTMs and discuss their applicability as well as future trends in the field.
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Affiliation(s)
- Thomas Amann
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Valerie Schmieder
- acib GmbH-Austrian Centre of Industrial Biotechnology, Graz, Austria.,Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Helene Faustrup Kildegaard
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Nicole Borth
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Mikael Rørdam Andersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
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41
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Boynton PJ. The ecology of killer yeasts: Interference competition in natural habitats. Yeast 2019; 36:473-485. [PMID: 31050852 DOI: 10.1002/yea.3398] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 04/22/2019] [Accepted: 04/23/2019] [Indexed: 12/31/2022] Open
Abstract
Killer yeasts are ubiquitous in the environment: They have been found in diverse habitats ranging from ocean sediment to decaying cacti to insect bodies and on all continents including Antarctica. However, environmental killer yeasts are poorly studied compared with laboratory and domesticated killer yeasts. Killer yeasts secrete so-called killer toxins that inhibit nearby sensitive yeasts, and the toxins are frequently assumed to be tools for interference competition in diverse yeast communities. The diversity and ubiquity of killer yeasts imply that interference competition is crucial for shaping yeast communities. Additionally, these toxins may have ecological functions beyond use in interference competition. This review introduces readers to killer yeasts in environmental systems, with a focus on what is and is not known about their ecology and evolution. It also explores how results from experimental killer systems in laboratories can be extended to understand how competitive strategies shape yeast communities in nature. Overall, killer yeasts are likely to occur everywhere yeasts are found, and the killer phenotype has the potential to radically shape yeast diversity in nature.
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Affiliation(s)
- Primrose J Boynton
- Max-Planck Institute for Evolutionary Biology, Environmental Genomics Group, Plön, Germany
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42
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Ito Y, Watanabe T, Aikawa S, Nishi T, Nishiyama T, Nakamura Y, Hasunuma T, Okubo Y, Ishii J, Kondo A. Deletion of DNA ligase IV homolog confers higher gene targeting efficiency on homologous recombination in Komagataella phaffii. FEMS Yeast Res 2019; 18:5054040. [PMID: 30010892 DOI: 10.1093/femsyr/foy074] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 07/12/2018] [Indexed: 01/24/2023] Open
Abstract
The non-conventional yeast Komagataella phaffii, formerly Pichia pastoris, is a popular host for recombinant protein production. The relatively lower gene targeting efficiency observed in this species occurs due to high levels of non-homologous recombination activity. In the current study, we explored the function of the K. phaffii homolog of DNA ligase IV (Dnl4p) by creating a DNL4-disrupted strain. To assess the roles of non-homologous end joining (NHEJ)-related proteins in this species, strains deleted for either or both genes encoding Dnl4p or the telomeric Ku complex subunit (Ku70p) were generated. These deletions were constructed by either of two distinct marker-recycling methods (yielding either a seamless gene deletion or a Cre-loxP-mediated gene deletion). The resulting dnl4- and/or ku70-deleted K. phaffii strains were used to evaluate gene targeting efficiency in gene knock-out and gene knock-in experiments. The Dnl4p-defective strain showed improved gene targeting efficiency for homologous recombination compared to the wild-type and Ku70p-deffective strains. The dnl4 ku70 double knock-out strain exhibited a further improvement in gene targeting efficiency. Thus, the K. phaffii dnl4 and dnl4 ku70 deletion strains are expected to serve as useful platforms for functional analysis and strain development in this species.
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Affiliation(s)
- Yoichiro Ito
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Toru Watanabe
- Biotechnology Research Laboratories, Kaneka Corporation, 1-8 Miyamae-cho, Takasago-cho, Takasago, Hyogo 676-8688, Japan
| | - Shimpei Aikawa
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Teruyuki Nishi
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
- Biotechnology Research Laboratories, Kaneka Corporation, 1-8 Miyamae-cho, Takasago-cho, Takasago, Hyogo 676-8688, Japan
| | - Tozo Nishiyama
- Biotechnology Research Laboratories, Kaneka Corporation, 1-8 Miyamae-cho, Takasago-cho, Takasago, Hyogo 676-8688, Japan
| | - Yasuyuki Nakamura
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Tomohisa Hasunuma
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Yuji Okubo
- Biotechnology Research Laboratories, Kaneka Corporation, 1-8 Miyamae-cho, Takasago-cho, Takasago, Hyogo 676-8688, Japan
| | - Jun Ishii
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Akihiko Kondo
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
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43
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Kumar R. Simplified protocol for faster transformation of (a large number of) Pichia pastoris strains. Yeast 2019; 36:399-410. [PMID: 30756442 DOI: 10.1002/yea.3383] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 01/16/2019] [Accepted: 02/05/2019] [Indexed: 12/15/2022] Open
Abstract
During the last couple of decades, the methylotrophic yeast, Pichia pastoris, has emerged as an important yeast species owing to its increasing importance both in industry and in basic research. The presently available methods for P. pastoris transformation necessitate the preparation of competent cells, which requires lots of resource, space, time, and efforts. This limits the number of transformations that can be performed by an individual in a given time. This paper is reporting a modification in the available protocols, which makes P. pastoris transformation hassle-free. In the present, modified procedure, cells were grown in patches on YPD plate(s), and the rest of the steps were carried out in small Eppendorf tubes. This modified protocol does not require a big centrifuge and shaker. This modified procedure of P. pastoris transformation with its unique way of competent cells preparation will be helpful for those working with this yeast species.
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Affiliation(s)
- Ravinder Kumar
- Section of Molecular Biology, Division of Biological Science, University of California San Diego, San Diego, California, USA
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Coverage-Versus-Length Plots, a Simple Quality Control Step for de Novo Yeast Genome Sequence Assemblies. G3-GENES GENOMES GENETICS 2019; 9:879-887. [PMID: 30674538 PMCID: PMC6404606 DOI: 10.1534/g3.118.200745] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Illumina sequencing has revolutionized yeast genomics, with prices for commercial draft genome sequencing now below $200. The popular SPAdes assembler makes it simple to generate a de novo genome assembly for any yeast species. However, whereas making genome assemblies has become routine, understanding what they contain is still challenging. Here, we show how graphing the information that SPAdes provides about the length and coverage of each scaffold can be used to investigate the nature of an assembly, and to diagnose possible problems. Scaffolds derived from mitochondrial DNA, ribosomal DNA, and yeast plasmids can be identified by their high coverage. Contaminating data, such as cross-contamination from other samples in a multiplex sequencing run, can be identified by its low coverage. Scaffolds derived from the bacteriophage PhiX174 and Lambda DNAs that are frequently used as molecular standards in Illumina protocols can also be detected. Assemblies of yeast genomes with high heterozygosity, such as interspecies hybrids, often contain two types of scaffold: regions of the genome where the two alleles assembled into two separate scaffolds and each has a coverage level C, and regions where the two alleles co-assembled (collapsed) into a single scaffold that has a coverage level 2C. Visualizing the data with Coverage-vs.-Length (CVL) plots, which can be done using Microsoft Excel or Google Sheets, provides a simple method to understand the structure of a genome assembly and detect aberrant scaffolds or contigs. We provide a Python script that allows assemblies to be filtered to remove contaminants identified in CVL plots.
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Gündüz Ergün B, Hüccetoğulları D, Öztürk S, Çelik E, Çalık P. Established and Upcoming Yeast Expression Systems. Methods Mol Biol 2019; 1923:1-74. [PMID: 30737734 DOI: 10.1007/978-1-4939-9024-5_1] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Yeast was the first microorganism used by mankind for biotransformation of feedstock that laid the foundations of industrial biotechnology. Long historical use, vast amount of data, and experience paved the way for Saccharomyces cerevisiae as a first yeast cell factory, and still it is an important expression platform as being the production host for several large volume products. Continuing special needs of each targeted product and different requirements of bioprocess operations have led to identification of different yeast expression systems. Modern bioprocess engineering and advances in omics technology, i.e., genomics, transcriptomics, proteomics, secretomics, and interactomics, allow the design of novel genetic tools with fine-tuned characteristics to be used for research and industrial applications. This chapter focuses on established and upcoming yeast expression platforms that have exceptional characteristics, such as the ability to utilize a broad range of carbon sources or remarkable resistance to various stress conditions. Besides the conventional yeast S. cerevisiae, established yeast expression systems including the methylotrophic yeasts Pichia pastoris and Hansenula polymorpha, the dimorphic yeasts Arxula adeninivorans and Yarrowia lipolytica, the lactose-utilizing yeast Kluyveromyces lactis, the fission yeast Schizosaccharomyces pombe, and upcoming yeast platforms, namely, Kluyveromyces marxianus, Candida utilis, and Zygosaccharomyces bailii, are compiled with special emphasis on their genetic toolbox for recombinant protein production.
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Affiliation(s)
- Burcu Gündüz Ergün
- Biochemical Reaction Engineering Laboratory, Department of Chemical Engineering, Middle East Technical University, Ankara, Turkey
| | - Damla Hüccetoğulları
- Biochemical Reaction Engineering Laboratory, Department of Chemical Engineering, Middle East Technical University, Ankara, Turkey
| | - Sibel Öztürk
- Biochemical Reaction Engineering Laboratory, Department of Chemical Engineering, Middle East Technical University, Ankara, Turkey
| | - Eda Çelik
- Department of Chemical Engineering, Hacettepe University, Ankara, Turkey
- Bioengineering Division, Institute of Science, Hacettepe University, Ankara, Turkey
| | - Pınar Çalık
- Biochemical Reaction Engineering Laboratory, Department of Chemical Engineering, Middle East Technical University, Ankara, Turkey.
- Industrial Biotechnology and Metabolic Engineering Laboratory, Department of Biotechnology, Graduate School of Natural and Applied Sciences, Middle East Technical University, Ankara, Turkey.
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Rinnofner C, Kerschbaumer B, Weber H, Glieder A, Winkler M. Cytochrome P450 mediated hydroxylation of ibuprofen using Pichia pastoris as biocatalyst. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2019. [DOI: 10.1016/j.bcab.2018.12.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Barrero JJ, Casler JC, Valero F, Ferrer P, Glick BS. An improved secretion signal enhances the secretion of model proteins from Pichia pastoris. Microb Cell Fact 2018; 17:161. [PMID: 30314480 PMCID: PMC6182871 DOI: 10.1186/s12934-018-1009-5] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 10/08/2018] [Indexed: 12/16/2022] Open
Abstract
Background Proteins can be secreted from a host organism with the aid of N-terminal secretion signals. The budding yeast Pichia pastoris (Komagataella sp.) is widely employed to secrete proteins of academic and industrial interest. For this yeast, the most commonly used secretion signal is the N-terminal portion of pre-pro-α-factor from Saccharomyces cerevisiae. However, this secretion signal promotes posttranslational translocation into the endoplasmic reticulum (ER), so proteins that can fold in the cytosol may be inefficiently translocated and thus poorly secreted. In addition, if a protein self-associates, the α-factor pro region can potentially cause aggregation, thereby hampering export from the ER. This study addresses both limitations of the pre-pro-α-factor secretion signal. Results We engineered a hybrid secretion signal consisting of the S. cerevisiae Ost1 signal sequence, which promotes cotranslational translocation into the ER, followed by the α-factor pro region. Secretion and intracellular localization were assessed using as a model protein the tetrameric red fluorescent protein E2-Crimson. When paired with the α-factor pro region, the Ost1 signal sequence yielded much more efficient secretion than the α-factor signal sequence. Moreover, an allelic variant of the α-factor pro region reduced aggregation of the E2-Crimson construct in the ER. The resulting improved secretion signal enhanced secretion of E2-Crimson up to 20-fold compared to the levels obtained with the original α-factor secretion signal. Similar findings were obtained with the lipase BTL2, which exhibited 10-fold enhanced secretion with the improved secretion signal. Conclusions The improved secretion signal confers dramatic benefits for the secretion of certain proteins from P. pastoris. These benefits are likely to be most evident for proteins that can fold in the cytosol and for oligomeric proteins. Electronic supplementary material The online version of this article (10.1186/s12934-018-1009-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Juan J Barrero
- Department of Chemical, Biological and Environmental Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès), 08193, Catalonia, Spain.,Department of Molecular Genetics and Cell Biology, University of Chicago, 920 East 58th Street, Chicago, IL, 60637, USA
| | - Jason C Casler
- Department of Molecular Genetics and Cell Biology, University of Chicago, 920 East 58th Street, Chicago, IL, 60637, USA
| | - Francisco Valero
- Department of Chemical, Biological and Environmental Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès), 08193, Catalonia, Spain
| | - Pau Ferrer
- Department of Chemical, Biological and Environmental Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès), 08193, Catalonia, Spain.,Luxembourg Institute of Science and Technology (LIST), Belvaux, Luxembourg
| | - Benjamin S Glick
- Department of Molecular Genetics and Cell Biology, University of Chicago, 920 East 58th Street, Chicago, IL, 60637, USA.
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The yeast stands alone: the future of protein biologic production. Curr Opin Biotechnol 2018; 53:50-58. [DOI: 10.1016/j.copbio.2017.12.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 12/07/2017] [Accepted: 12/08/2017] [Indexed: 12/13/2022]
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A Stable, Autonomously Replicating Plasmid Vector Containing Pichia pastoris Centromeric DNA. Appl Environ Microbiol 2018; 84:AEM.02882-17. [PMID: 29802190 DOI: 10.1128/aem.02882-17] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 05/20/2018] [Indexed: 01/07/2023] Open
Abstract
The methylotrophic yeast Pichia pastoris is widely used to produce recombinant proteins, taking advantage of this species' high-density cell growth and strong ability to secrete proteins. Circular plasmids containing the P. pastoris-specific autonomously replicating sequence (PARS1) permit transformation of P. pastoris with higher efficiency than obtained following chromosomal integration by linearized DNA. Unfortunately, however, existing autonomously replicating plasmids are known to be inherently unstable. In this study, we used transcriptome sequencing (RNA-seq) data and genome sequence information to independently identify, on each of the four chromosomes, centromeric DNA sequences consisting of long inverted repeat sequences. By examining the chromosome 2 centromeric DNA sequence (Cen2) in detail, we demonstrate that an ∼111-bp region located at one end of the putative centromeric sequence had autonomous replication activity. In addition, the full-length Cen2 sequence, which contains two long inverted repeat sequences and a nonrepetitive central core region, is needed for the accurate replication and distribution of plasmids in P. pastoris Thus, we constructed a new, stable, autonomously replicating plasmid vector that harbors the entire Cen2 sequence; this episome facilitates genetic manipulation in P. pastoris, providing high transformation efficiency and plasmid stability.IMPORTANCE Secretory production of recombinant proteins is the most important application of the methylotrophic yeast Pichia pastoris, a species that permits mass production of heterologous proteins. To date, the genetic engineering of P. pastoris has relied largely on integrative vectors due to the lack of user-friendly tools. Autonomously replicating Pichia plasmids are expected to facilitate genetic manipulation; however, the existing systems, which use autonomously replicating sequences (ARSs) such as the P. pastoris-specific ARS (PARS1), are known to be inherently unstable for plasmid replication and distribution. Recently, the centromeric DNA sequences of P. pastoris were identified in back-to-back studies published by several groups; therefore, a new episomal plasmid vector with centromere DNA as a tool for genetic manipulation of P. pastoris is ready to be developed.
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Evolutionary instability of CUG-Leu in the genetic code of budding yeasts. Nat Commun 2018; 9:1887. [PMID: 29760453 PMCID: PMC5951914 DOI: 10.1038/s41467-018-04374-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 04/12/2018] [Indexed: 11/08/2022] Open
Abstract
The genetic code used in nuclear genes is almost universal, but here we report that it changed three times in parallel during the evolution of budding yeasts. All three changes were reassignments of the codon CUG, which is translated as serine (in 2 yeast clades), alanine (1 clade), or the ‘universal’ leucine (2 clades). The newly discovered Ser2 clade is in the final stages of a genetic code transition. Most species in this clade have genes for both a novel tRNASer(CAG) and an ancestral tRNALeu(CAG) to read CUG, but only tRNASer(CAG) is used in standard growth conditions. The coexistence of these alloacceptor tRNA genes indicates that the genetic code transition occurred via an ambiguous translation phase. We propose that the three parallel reassignments of CUG were not driven by natural selection in favor of their effects on the proteome, but by selection to eliminate the ancestral tRNALeu(CAG). The genetic code for amino acids is nearly universal, and among eukaryotic nuclear genomes the only known reassignments are of codon CUG in yeasts. Here, the authors identify a third independent CUG transition in budding yeasts that is still ongoing with alternative tRNAs present in the genome.
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