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Khalifeh Soltani M, Arjmand S, Ranaei Siadat SO, Bagheri A, Marashi SH. Hansenula polymorpha methanol metabolism genes enhance recombinant protein production in Komagataella phaffi. AMB Express 2024; 14:88. [PMID: 39095661 PMCID: PMC11296995 DOI: 10.1186/s13568-024-01743-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 07/08/2024] [Indexed: 08/04/2024] Open
Abstract
Recombinant protein production in Komagataella phaffi (K. phaffi), a widely utilized host organism, can be optimized by enhancing the metabolic flux in the central carbon metabolism pathways. The methanol utilization pathway (MUT) during methanol-based growth plays a crucial role in providing precursors and energy for cell growth and development. This study investigated the impact of boosting the methanol dissimilation pathway, a branch of MUT that plays a vital role in detoxifying formaldehyde and providing energy in the form of NADH, in K. phaffi. This was achieved by integrating two orthologous genes from Hansenula polymorpha into the K. phaffi genome: formaldehyde dehydrogenase (HpFLD) and formate dehydrogenase (HpFMDH). The HpFLD and HpFMDH genes were isolated from the Hansenula polymorpha genome and inserted under the regulation of the pAOX1 promoter in the genome of recombinant K. phaffi that already contained a single copy of model protein genes (eGFP or EGII). The expression levels of these model proteins were assessed through protein activity assays and gene expression analysis. The findings revealed that while both orthologous genes positively influenced model protein production, HpFMDH exhibited a more pronounced upregulation in expression compared to HpFLD. Co-expression of both orthologous genes demonstrated synergistic effects, resulting in approximately a twofold increase in the levels of the model proteins detected. This study provides valuable insights into enhancing the production capacity of recombinant proteins in K. phaffi.
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Affiliation(s)
- Maryam Khalifeh Soltani
- Department of Biotechnology and Plant Breeding, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Sareh Arjmand
- Protein Research Center, Shahid Beheshti University, Tehran, Iran
| | | | - Abdolreza Bagheri
- Department of Biotechnology and Plant Breeding, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran.
| | - Seyed Hassan Marashi
- Department of Biotechnology and Plant Breeding, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
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2
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Prins RC, Billerbeck S. The signal peptide of yeast killer toxin K2 confers producer self-protection and allows conversion into a modular toxin-immunity system. Cell Rep 2024; 43:114449. [PMID: 38985680 DOI: 10.1016/j.celrep.2024.114449] [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: 03/25/2024] [Revised: 05/30/2024] [Accepted: 06/20/2024] [Indexed: 07/12/2024] Open
Abstract
Some microbial toxins also target the producer species itself, necessitating a means of self-protection. The M2 double-stranded RNA (dsRNA) killer virus in Saccharomyces cerevisiae contains a single open reading frame (ORF) encoding both the secreted pore-forming toxin K2 as well as a cognate immunity factor. Here, we show that expression of a 49-amino acid N-terminal peptide from the K2 precursor is both necessary and sufficient for immunity. This immunity peptide simultaneously functions as a signal peptide for toxin secretion and protects the cell against the cytotoxic K2 α subunit. The K2 toxin and immunity factor can be functionally separated into two ORFs, yielding a modular toxin-immunity system. This case further shows how a (signal) peptide can carry the potential for providing cellular protection against an antimicrobial toxin.
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Affiliation(s)
- Rianne C Prins
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Sonja Billerbeck
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, the Netherlands.
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3
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O’Riordan N, Jurić V, O’Neill SK, Roche AP, Young PW. A Yeast Modular Cloning (MoClo) Toolkit Expansion for Optimization of Heterologous Protein Secretion and Surface Display in Saccharomyces cerevisiae. ACS Synth Biol 2024; 13:1246-1258. [PMID: 38483353 PMCID: PMC11036508 DOI: 10.1021/acssynbio.3c00743] [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: 12/12/2023] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 04/20/2024]
Abstract
Saccharomyces cerevisiae is an attractive host for the expression of secreted proteins in a biotechnology context. Unfortunately, many heterologous proteins fail to enter, or efficiently progress through, the secretory pathway, resulting in poor yields. Similarly, yeast surface display has become a widely used technique in protein engineering but achieving sufficient levels of surface expression of recombinant proteins is often challenging. Signal peptides (SPs) and translational fusion partners (TFPs) can be used to direct heterologous proteins through the yeast secretory pathway, however, selection of the optimal secretion promoting sequence is largely a process of trial and error. The yeast modular cloning (MoClo) toolkit utilizes type IIS restriction enzymes to facilitate an efficient assembly of expression vectors from standardized parts. We have expanded this toolkit to enable the efficient incorporation of a panel of 16 well-characterized SPs and TFPs and five surface display anchor proteins into S. cerevisiae expression cassettes. The secretion promoting signals are validated by using five different proteins of interest. Comparison of intracellular and secreted protein levels reveals the optimal secretion promoting sequence for each individual protein. Large, protein of interest-specific variations in secretion efficiency are observed. SP sequences are also used with the five surface display anchors, and the combination of SP and anchor protein proves critical for efficient surface display. These observations highlight the value of the described panel of MoClo compatible parts to allow facile screening of SPs and TFPs and anchor proteins for optimal secretion and/or surface display of a given protein of interest in S. cerevisiae.
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Affiliation(s)
- Nicola
M. O’Riordan
- School
of Biochemistry and Cell Biology, University
College Cork, Cork T12 YN60, Ireland
| | - Vanja Jurić
- School
of Biochemistry and Cell Biology, University
College Cork, Cork T12 YN60, Ireland
- AMBER
Centre, Environmental Research Institute, University College Cork, Cork T23 XE10, Ireland
| | - Sarah K. O’Neill
- School
of Biochemistry and Cell Biology, University
College Cork, Cork T12 YN60, Ireland
| | - Aoife P. Roche
- School
of Biochemistry and Cell Biology, University
College Cork, Cork T12 YN60, Ireland
| | - Paul W. Young
- School
of Biochemistry and Cell Biology, University
College Cork, Cork T12 YN60, Ireland
- AMBER
Centre, Environmental Research Institute, University College Cork, Cork T23 XE10, Ireland
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4
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Kiribayeva A, Silayev D, Akishev Z, Baltin K, Aktayeva S, Ramankulov Y, Khassenov B. An impact of N-glycosylation on biochemical properties of a recombinant α-amylase from Bacillus licheniformis. Heliyon 2024; 10:e28064. [PMID: 38515717 PMCID: PMC10956057 DOI: 10.1016/j.heliyon.2024.e28064] [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] [Received: 07/04/2023] [Revised: 03/11/2024] [Accepted: 03/11/2024] [Indexed: 03/23/2024] Open
Abstract
Amylases are enzymes that are known to hydrolyze starch. High efficiency of amylolytic enzymes allows them to compete in the industry with the technology of chemical hydrolysis of starch. A Bacillus licheniformis strain with high amylolytic activity was isolated from soil and designated as T5. The gene encoding α-amylase from B. licheniformis T5 was successfully expressed in both Escherichia coli (rAmyT5-E) and Pichia pastoris (as rAmyT5-P). According to the study, the recombinant α-amylases rAmyT5-E and rAmyT5-P exhibited the highest activity at pH 6.0 and temperatures of 70 and 80 °C, respectively. Over 80% of the rAmyT5-E enzyme activity was preserved following incubation within the pH range of 5-9; the same was true for rAmyT5-P after incubation at pH 6-9. N-glycosylation reduced the thermal and pH stability of the enzyme. The specific activity and catalytic efficiency of the recombinant AmyT5 α-amylase were also diminished by N-glycosylation.
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Affiliation(s)
- Assel Kiribayeva
- National Center for Biotechnology, 13/5 Kurgalzhynskoye Road, Astana, 010000, Kazakhstan
| | - Dmitriy Silayev
- National Center for Biotechnology, 13/5 Kurgalzhynskoye Road, Astana, 010000, Kazakhstan
| | - Zhiger Akishev
- National Center for Biotechnology, 13/5 Kurgalzhynskoye Road, Astana, 010000, Kazakhstan
| | - Kairat Baltin
- National Center for Biotechnology, 13/5 Kurgalzhynskoye Road, Astana, 010000, Kazakhstan
| | - Saniya Aktayeva
- National Center for Biotechnology, 13/5 Kurgalzhynskoye Road, Astana, 010000, Kazakhstan
| | - Yerlan Ramankulov
- National Center for Biotechnology, 13/5 Kurgalzhynskoye Road, Astana, 010000, Kazakhstan
| | - Bekbolat Khassenov
- National Center for Biotechnology, 13/5 Kurgalzhynskoye Road, Astana, 010000, Kazakhstan
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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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6
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Pipiya SO, Kudzhaev AM, Mirzoeva NZ, Mokrushina YA, Ziganshin RH, Komlev AS, Petrova PE, Smirnov IV, Gabibov AG, Shamova OV, Terekhov SS. Bioengineering the Antimicrobial Activity of Yeast by Recombinant Thanatin Production. Antibiotics (Basel) 2023; 12:1719. [PMID: 38136753 PMCID: PMC10741026 DOI: 10.3390/antibiotics12121719] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
The global spread of antibiotic resistance marks the end of the era of conventional antibiotics. Mankind desires new molecular tools to fight pathogenic bacteria. In this regard, the development of new antimicrobials based on antimicrobial peptides (AMPs) is again of particular interest. AMPs have various mechanisms of action on bacterial cells. Moreover, AMPs have been reported to be efficient in preclinical studies, demonstrating a low level of resistance formation. Thanatin is a small, beta-hairpin antimicrobial peptide with a bacterial-specific mode of action, predetermining its low cytotoxicity toward eukaryotic cells. This makes thanatin an exceptional candidate for new antibiotic development. Here, a microorganism was bioengineered to produce an antimicrobial agent, providing novel opportunities in antibiotic research through the directed creation of biocontrol agents. The constitutive heterologous production of recombinant thanatin (rThan) in the yeast Pichia pastoris endows the latter with antibacterial properties. Optimized expression and purification conditions enable a high production level, yielding up to 20 mg/L of rThan from the culture medium. rThan shows a wide spectrum of activity against pathogenic bacteria, similarly to its chemically synthesized analogue. The designed approach provides new avenues for AMP engineering and creating live biocontrol agents to fight antibiotic resistance.
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Affiliation(s)
- Sofiya O. Pipiya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (A.M.K.); (N.Z.M.); (Y.A.M.); (R.H.Z.); (I.V.S.); (A.G.G.)
| | - Arsen M. Kudzhaev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (A.M.K.); (N.Z.M.); (Y.A.M.); (R.H.Z.); (I.V.S.); (A.G.G.)
| | - Nisso Z. Mirzoeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (A.M.K.); (N.Z.M.); (Y.A.M.); (R.H.Z.); (I.V.S.); (A.G.G.)
| | - Yuliana A. Mokrushina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (A.M.K.); (N.Z.M.); (Y.A.M.); (R.H.Z.); (I.V.S.); (A.G.G.)
| | - Rustam H. Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (A.M.K.); (N.Z.M.); (Y.A.M.); (R.H.Z.); (I.V.S.); (A.G.G.)
| | - Alexey S. Komlev
- Institute of Experimental Medicine, WCRC “Center for Personalized Medicine”, Saint-Petersburg 197022, Russia; (A.S.K.); (P.E.P.); (O.V.S.)
| | - Polina E. Petrova
- Institute of Experimental Medicine, WCRC “Center for Personalized Medicine”, Saint-Petersburg 197022, Russia; (A.S.K.); (P.E.P.); (O.V.S.)
| | - Ivan V. Smirnov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (A.M.K.); (N.Z.M.); (Y.A.M.); (R.H.Z.); (I.V.S.); (A.G.G.)
- Department of Chemistry, Lomonosov Mscow State University, Moscow 119991, Russia
| | - Alexander G. Gabibov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (A.M.K.); (N.Z.M.); (Y.A.M.); (R.H.Z.); (I.V.S.); (A.G.G.)
- Department of Chemistry, Lomonosov Mscow State University, Moscow 119991, Russia
| | - Olga V. Shamova
- Institute of Experimental Medicine, WCRC “Center for Personalized Medicine”, Saint-Petersburg 197022, Russia; (A.S.K.); (P.E.P.); (O.V.S.)
- Department of Biochemistry, Saint Petersburg State University, Saint-Petersburg 199034, Russia
| | - Stanislav S. Terekhov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (A.M.K.); (N.Z.M.); (Y.A.M.); (R.H.Z.); (I.V.S.); (A.G.G.)
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7
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Eskandari A, Nezhad NG, Leow TC, Rahman MBA, Oslan SN. Current achievements, strategies, obstacles, and overcoming the challenges of the protein engineering in Pichia pastoris expression system. World J Microbiol Biotechnol 2023; 40:39. [PMID: 38062216 DOI: 10.1007/s11274-023-03851-6] [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] [Received: 10/11/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023]
Abstract
Yeasts serve as exceptional hosts in the manufacturing of functional protein engineering and possess industrial or medical utilities. Considerable focus has been directed towards yeast owing to its inherent benefits and recent advancements in this particular cellular host. The Pichia pastoris expression system is widely recognized as a prominent and widely accepted instrument in molecular biology for the purpose of generating recombinant proteins. The advantages of utilizing the P. pastoris system for protein production encompass the proper folding process occurring within the endoplasmic reticulum (ER), as well as the subsequent secretion mediated by Kex2 as a signal peptidase, ultimately leading to the release of recombinant proteins into the extracellular environment of the cell. In addition, within the P. pastoris expression system, the ease of purifying recombinant protein arises from its restricted synthesis of endogenous secretory proteins. Despite its achievements, scientists often encounter persistent challenges when attempting to utilize yeast for the production of recombinant proteins. This review is dedicated to discussing the current achievements in the usage of P. pastoris as an expression host. Furthermore, it sheds light on the strategies employed in the expression system and the optimization and development of the fermentative process of this yeast. Finally, the impediments (such as identifying high expression strains, improving secretion efficiency, and decreasing hyperglycosylation) and successful resolution of certain difficulties are put forth and deliberated upon in order to assist and promote the expression of complex proteins in this prevalent recombinant host.
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Affiliation(s)
- Azadeh Eskandari
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia
| | - Nima Ghahremani Nezhad
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia
| | - Thean Chor Leow
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia
- Enzyme Technology and X-Ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia
| | | | - Siti Nurbaya Oslan
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia.
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia.
- Enzyme Technology and X-Ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia (UPM), 43400, Serdang, Selangor, Malaysia.
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8
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Pyne ME, Bagley JA, Narcross L, Kevvai K, Exley K, Davies M, Wang Q, Whiteway M, Martin VJJ. Screening non-conventional yeasts for acid tolerance and engineering Pichia occidentalis for production of muconic acid. Nat Commun 2023; 14:5294. [PMID: 37652930 PMCID: PMC10471774 DOI: 10.1038/s41467-023-41064-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 08/22/2023] [Indexed: 09/02/2023] Open
Abstract
Saccharomyces cerevisiae is a workhorse of industrial biotechnology owing to the organism's prominence in alcohol fermentation and the suite of sophisticated genetic tools available to manipulate its metabolism. However, S. cerevisiae is not suited to overproduce many bulk bioproducts, as toxicity constrains production at high titers. Here, we employ a high-throughput assay to screen 108 publicly accessible yeast strains for tolerance to 20 g L-1 adipic acid (AA), a nylon precursor. We identify 15 tolerant yeasts and select Pichia occidentalis for production of cis,cis-muconic acid (CCM), the precursor to AA. By developing a genome editing toolkit for P. occidentalis, we demonstrate fed-batch production of CCM with a maximum titer (38.8 g L-1), yield (0.134 g g-1 glucose) and productivity (0.511 g L-1 h-1) that surpasses all metrics achieved using S. cerevisiae. This work brings us closer to the industrial bioproduction of AA and underscores the importance of host selection in bioprocessing.
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Affiliation(s)
- Michael E Pyne
- Department of Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- Department of Biology, University of Western Ontario, Ontario, Canada
| | - James A Bagley
- Department of Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
| | - Lauren Narcross
- Department of Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- Amyris, Inc., Emeryville, CA, USA
| | - Kaspar Kevvai
- Department of Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- Pivot Bio, Berkeley, CA, USA
| | - Kealan Exley
- Department of Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- Novo Nordisk Foundation Center for Biosustainability, Lyngby, Denmark
| | - Meghan Davies
- Department of Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- BenchSci, Toronto, ON, Canada
| | | | - Malcolm Whiteway
- Department of Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
| | - Vincent J J Martin
- Department of Biology, Concordia University, Montréal, QC, H4B 1R6, Canada.
- Centre for Applied Synthetic Biology, Concordia University, Montréal, QC, H4B 1R6, Canada.
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9
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Xiao C, Xue S, Pan Y, Liu X, Huang M. Overexpression of genes by stress-responsive promoters increases protein secretion in Saccharomyces cerevisiae. World J Microbiol Biotechnol 2023; 39:203. [PMID: 37209206 DOI: 10.1007/s11274-023-03646-9] [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: 02/15/2023] [Accepted: 05/10/2023] [Indexed: 05/22/2023]
Abstract
Recombinant proteins produced by cell factories are now widely used in various fields. Many efforts have been made to improve the secretion capacity of cell factories to meet the increasing demand for recombinant proteins. Recombinant protein production usually causes cell stress in the endoplasmic reticulum (ER). The overexpression of key genes possibly removes limitations in protein secretion. However, inappropriate gene expression may have negative effects. There is a need for dynamic control of genes adapted to cellular status. In this study, we constructed and characterized synthetic promoters that were inducible under ER stress conditions in Saccharomyces cerevisiae. The unfolded protein response element UPRE2, responding to stress with a wide dynamic range, was assembled with various promoter core regions, resulting in UPR-responsive promoters. Synthetic responsive promoters regulated gene expression by responding to stress level, which reflected the cellular status. The engineered strain using synthetic responsive promoters P4UPRE2 - TDH3 and P4UPRE2 - TEF1 for co-expression of ERO1 and SLY1 had 95% higher α-amylase production compared with the strain using the native promoters PTDH3 and PTEF1. This work showed that UPR-responsive promoters were useful in the metabolic engineering of yeast strains for tuning genes to support efficient protein production.
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Affiliation(s)
- Chufan Xiao
- School of Food Science and Engineering, South China University of Technology, Guangzhou, 510641, China
| | - Songlyu Xue
- School of Food Science and Engineering, South China University of Technology, Guangzhou, 510641, China
| | - Yuyang Pan
- School of Food Science and Engineering, South China University of Technology, Guangzhou, 510641, China
| | - Xiufang Liu
- School of Food Science and Engineering, South China University of Technology, Guangzhou, 510641, China
| | - Mingtao Huang
- School of Food Science and Engineering, South China University of Technology, Guangzhou, 510641, China.
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10
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Wang X, Wang P, Li W, Zhu C, Fan D. Effect and mechanism of signal peptide and maltose on recombinant type III collagen production in Pichia pastoris. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12579-0. [PMID: 37199749 DOI: 10.1007/s00253-023-12579-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/04/2023] [Accepted: 05/09/2023] [Indexed: 05/19/2023]
Abstract
Recombinant type III collagen plays an important role in cosmetics, wound healing, and tissue engineering. Thus, increasing its production is necessary. After an initial increase in output by modifying the signal peptide, we showed that adding 1% maltose directly to the medium increased the yield and reduced the degradation of recombinant type III collagen. We initially verified that Pichia pastoris GS115 can metabolize and utilize maltose. Interestingly, maltose metabolism-associated proteins in Pichia pastoris GS115 have not yet been identified. RNA sequencing and transmission electron microscopy were performed to clarify the specific mechanism of maltose influence. The results showed that maltose significantly improved the metabolism of methanol, thiamine, riboflavin, arginine, and proline. After adding maltose, the cell microstructures tended more toward the normal. Adding maltose also contributed to yeast homeostasis and methanol tolerance. Finally, adding maltose resulted in the downregulation of aspartic protease YPS1 and a decrease in yeast mortality, thereby slowing down recombinant type III collagen degradation. KEY POINTS: • Co-feeding of maltose improves recombinant type III collagen production. • Maltose incorporation enhances methanol metabolism and antioxidant capacity. • Maltose addition contributes to Pichia pastoris GS115 homeostasis.
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Affiliation(s)
- Xingyin Wang
- Shaanxi Key Laboratory of Degradable Biomedical Materials, School of Chemical Engineering, Northwest University, Xi'an, 710069, Shaanxi, China
- Shaanxi R&D Center of Biomaterials and Fermentation Engineering, School of Chemical Engineering, Northwest University, Xi'an, 710069, Shaanxi, China
- Biotech. & Biomed. Research Institute, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Pan Wang
- Shaanxi Key Laboratory of Degradable Biomedical Materials, School of Chemical Engineering, Northwest University, Xi'an, 710069, Shaanxi, China
- Shaanxi R&D Center of Biomaterials and Fermentation Engineering, School of Chemical Engineering, Northwest University, Xi'an, 710069, Shaanxi, China
- Biotech. & Biomed. Research Institute, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Weina Li
- Shaanxi Key Laboratory of Degradable Biomedical Materials, School of Chemical Engineering, Northwest University, Xi'an, 710069, Shaanxi, China
- Shaanxi R&D Center of Biomaterials and Fermentation Engineering, School of Chemical Engineering, Northwest University, Xi'an, 710069, Shaanxi, China
- Biotech. & Biomed. Research Institute, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Chenhui Zhu
- Shaanxi Key Laboratory of Degradable Biomedical Materials, School of Chemical Engineering, Northwest University, Xi'an, 710069, Shaanxi, China
- Shaanxi R&D Center of Biomaterials and Fermentation Engineering, School of Chemical Engineering, Northwest University, Xi'an, 710069, Shaanxi, China
- Biotech. & Biomed. Research Institute, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Daidi Fan
- Shaanxi Key Laboratory of Degradable Biomedical Materials, School of Chemical Engineering, Northwest University, Xi'an, 710069, Shaanxi, China.
- Shaanxi R&D Center of Biomaterials and Fermentation Engineering, School of Chemical Engineering, Northwest University, Xi'an, 710069, Shaanxi, China.
- Biotech. & Biomed. Research Institute, Northwest University, Xi'an, 710069, Shaanxi, China.
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11
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Shrivastava A, Pal M, Sharma RK. Pichia as Yeast Cell Factory for Production of Industrially Important Bio-Products: Current Trends, Challenges, and Future Prospects. JOURNAL OF BIORESOURCES AND BIOPRODUCTS 2023. [DOI: 10.1016/j.jobab.2023.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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12
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Chow JY, Nguyen GKT. Rational Design of Lipase ROL to Increase Its Thermostability for Production of Structured Tags. Int J Mol Sci 2022; 23:ijms23179515. [PMID: 36076913 PMCID: PMC9455606 DOI: 10.3390/ijms23179515] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/17/2022] [Accepted: 08/20/2022] [Indexed: 12/05/2022] Open
Abstract
1,3-regiospecific lipases are important enzymes that are heavily utilized in the food industries to produce structured triacylglycerols (TAGs). The Rhizopus oryzae lipase (ROL) has recently gained interest because this enzyme possesses high selectivity and catalytic efficiency. However, its low thermostability limits its use towards reactions that work at lower temperature. Most importantly, the enzyme cannot be used for the production of 1,3-dioleoyl-2-palmitoylglycerol (OPO) and 1,3-stearoyl-2-oleoyl-glycerol (SOS) due to the high melting points of the substrates used for the reaction. Despite various engineering efforts used to improve the thermostability of ROL, the enzyme is unable to function at temperatures above 60 °C. Here, we describe the rational design of ROL to identify variants that can retain their activity at temperatures higher than 60 °C. After two rounds of mutagenesis and screening, we were able to identify a mutant ROL_10x that can retain most of its activity at 70 °C. We further demonstrated that this mutant is useful for the synthesis of SOS while minimal product formation was observed with ROL_WT. Our engineered enzyme provides a promising solution for the industrial synthesis of structured lipids at high temperature.
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13
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Gätjen D, Tomszak F, Dettmann JC, Droste M, Nölle V, Wieczorek M. Design of a novel switchable antibody display system in Pichia pastoris. Appl Microbiol Biotechnol 2022; 106:6209-6224. [PMID: 35953606 DOI: 10.1007/s00253-022-12108-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/29/2022] [Indexed: 12/13/2022]
Abstract
Yeast surface display (YSD) has been shown to represent a powerful tool in the field of antibody discovery and engineering as well as for selection of high producer clones. However, YSD is predominantly applied in Saccharomyces cerevisiae, whereas expression of heterologous proteins is generally favored in the non-canonical yeast Pichia pastoris (Komagataella phaffii). Establishment of surface display in P. pastoris would therefore enable antibody selection and expression in a single host. Here we describe the generation of a Pichia surface display (PSD) system based on antibody expression from episomal plasmids. By screening a diverse set of expression vectors using Design of Experiments (DoE), the effect of different genetic elements on the surface expression of antibody fragments was analyzed. Among the tested genetic elements, we found that the combination of P. pastoris formaldehyde dehydrogenase (FLD1) promoter, S. cerevisiae invertase 2 signal peptide (SUC2), and α-agglutinin cell wall protein (SAG1) including an autonomously replicating sequence of Kluyveromyces lactis (panARS) were contributing most strongly to higher display levels of three tested antibody fragments. Employing this combination resulted in the display of antibody fragments for up to 25% of cells. Despite significantly reduced expression levels in PSD compared to well-established YSD in S. cerevisiae, similar fractions of antigen binding single-chain variable fragments (scFvs) were observed (80% vs. 84%). In addition, plasmid stability assays and flow cytometric analysis demonstrated the efficient plasmid clearance of cells and associated loss of antibody fragment display after removal of selective pressure. KEY POINTS: • First report of antibody display in P. pastoris using episomal plasmids. • Identification of genetic elements conferring highest levels of antibody display. • Comparable antigen binding capacity of displayed scFvs for PSD compared to YSD.
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Affiliation(s)
- Dominic Gätjen
- Miltenyi Biotec B.V. & Co. KG, Friedrich-Ebert-Straße 68, 51429, Bergisch, Gladbach, Germany
| | - Florian Tomszak
- Miltenyi Biotec B.V. & Co. KG, Friedrich-Ebert-Straße 68, 51429, Bergisch, Gladbach, Germany
| | | | - Miriam Droste
- Miltenyi Biotec B.V. & Co. KG, Friedrich-Ebert-Straße 68, 51429, Bergisch, Gladbach, Germany
| | - Volker Nölle
- Miltenyi Biotec B.V. & Co. KG, Friedrich-Ebert-Straße 68, 51429, Bergisch, Gladbach, Germany
| | - Marek Wieczorek
- Miltenyi Biotec B.V. & Co. KG, Friedrich-Ebert-Straße 68, 51429, Bergisch, Gladbach, Germany.
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14
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Malcı K, Watts E, Roberts TM, Auxillos JY, Nowrouzi B, Boll HO, Nascimento CZSD, Andreou A, Vegh P, Donovan S, Fragkoudis R, Panke S, Wallace E, Elfick A, Rios-Solis L. Standardization of Synthetic Biology Tools and Assembly Methods for Saccharomyces cerevisiae and Emerging Yeast Species. ACS Synth Biol 2022; 11:2527-2547. [PMID: 35939789 PMCID: PMC9396660 DOI: 10.1021/acssynbio.1c00442] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
![]()
As redesigning organisms using engineering principles
is one of
the purposes of synthetic biology (SynBio), the standardization of
experimental methods and DNA parts is becoming increasingly a necessity.
The synthetic biology community focusing on the engineering of Saccharomyces cerevisiae has been in the foreground in this
area, conceiving several well-characterized SynBio toolkits widely
adopted by the community. In this review, the molecular methods and
toolkits developed for S. cerevisiae are discussed
in terms of their contributions to the required standardization efforts.
In addition, the toolkits designed for emerging nonconventional yeast
species including Yarrowia lipolytica, Komagataella
phaffii, and Kluyveromyces marxianus are
also reviewed. Without a doubt, the characterized DNA parts combined
with the standardized assembly strategies highlighted in these toolkits
have greatly contributed to the rapid development of many metabolic
engineering and diagnostics applications among others. Despite the
growing capacity in deploying synthetic biology for common yeast genome
engineering works, the yeast community has a long journey to go to
exploit it in more sophisticated and delicate applications like bioautomation.
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Affiliation(s)
- Koray Malcı
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Kings Buildings, EH9 3BF Edinburgh, United Kingdom.,Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, EH9 3BD Edinburgh, United Kingdom
| | - Emma Watts
- School of Biological Sciences, University of Edinburgh, Kings Buildings, EH9 3JW Edinburgh, United Kingdom
| | | | - Jamie Yam Auxillos
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, EH9 3BD Edinburgh, United Kingdom.,Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Kings Buildings, EH9 3FF Edinburgh, United Kingdom
| | - Behnaz Nowrouzi
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Kings Buildings, EH9 3BF Edinburgh, United Kingdom.,Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, EH9 3BD Edinburgh, United Kingdom
| | - Heloísa Oss Boll
- Department of Genetics and Morphology, Institute of Biological Sciences, University of Brasília, Brasília, Federal District 70910-900, Brazil
| | | | - Andreas Andreou
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, EH9 3BD Edinburgh, United Kingdom
| | - Peter Vegh
- Edinburgh Genome Foundry, University of Edinburgh, Kings Buildings, Edinburgh EH9 3BF, United Kingdom
| | - Sophie Donovan
- Edinburgh Genome Foundry, University of Edinburgh, Kings Buildings, Edinburgh EH9 3BF, United Kingdom
| | - Rennos Fragkoudis
- Edinburgh Genome Foundry, University of Edinburgh, Kings Buildings, Edinburgh EH9 3BF, United Kingdom
| | - Sven Panke
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - Edward Wallace
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, EH9 3BD Edinburgh, United Kingdom.,Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Kings Buildings, EH9 3FF Edinburgh, United Kingdom
| | - Alistair Elfick
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Kings Buildings, EH9 3BF Edinburgh, United Kingdom.,Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, EH9 3BD Edinburgh, United Kingdom
| | - Leonardo Rios-Solis
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Kings Buildings, EH9 3BF Edinburgh, United Kingdom.,Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, EH9 3BD Edinburgh, United Kingdom.,School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
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15
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Mózsik L, Iacovelli R, Bovenberg RAL, Driessen AJM. Transcriptional Activation of Biosynthetic Gene Clusters in Filamentous Fungi. Front Bioeng Biotechnol 2022; 10:901037. [PMID: 35910033 PMCID: PMC9335490 DOI: 10.3389/fbioe.2022.901037] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/17/2022] [Indexed: 11/13/2022] Open
Abstract
Filamentous fungi are highly productive cell factories, many of which are industrial producers of enzymes, organic acids, and secondary metabolites. The increasing number of sequenced fungal genomes revealed a vast and unexplored biosynthetic potential in the form of transcriptionally silent secondary metabolite biosynthetic gene clusters (BGCs). Various strategies have been carried out to explore and mine this untapped source of bioactive molecules, and with the advent of synthetic biology, novel applications, and tools have been developed for filamentous fungi. Here we summarize approaches aiming for the expression of endogenous or exogenous natural product BGCs, including synthetic transcription factors, assembly of artificial transcription units, gene cluster refactoring, fungal shuttle vectors, and platform strains.
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Affiliation(s)
- László Mózsik
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Riccardo Iacovelli
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Roel A. L. Bovenberg
- DSM Biotechnology Center, Delft, Netherlands
- Department of Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Arnold J. M. Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
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16
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Öling D, Lan-Chow-Wing O, Martella A, Gilberto S, Chi J, Cooper E, Edström T, Peng B, Sumner D, Karlsson F, Volkov P, Webster CI, Roth R. FRAGLER: A Fragment Recycler Application Enabling Rapid and Scalable Modular DNA Assembly. ACS Synth Biol 2022; 11:2229-2237. [PMID: 35797032 DOI: 10.1021/acssynbio.2c00106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Rapid and flexible plasmid construct generation at scale is one of the most limiting first steps in drug discovery projects. These hurdles can partly be overcome by adopting modular DNA design principles, automated sequence fragmentation, and plasmid assembly. To this end we have designed a robust, multimodule golden gate based cloning platform for construct generation with a wide range of applications. The assembly efficiency of the system was validated by splitting sfGFP and sfCherry3C cassettes and expressing them in E. coli followed by fluorometric assessment. To minimize timelines and cost for complex constructs, we developed a software tool named FRAGLER (FRAGment recycLER) that performs codon optimization, multiple sequence alignment, and automated generation of fragments for recycling. To highlight the flexibility and robustness of the platform, we (i) generated plasmids for SarsCoV2 protein reagents, (ii) automated and parallelized assemblies, and (iii) built modular libraries of chimeric antigen receptors (CARs) variants. Applying the new assembly framework, we have greatly streamlined plasmid construction and increased our capacity for rapid generation of complex plasmids.
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Affiliation(s)
- David Öling
- Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, 43183 Gothenburg, Sweden
| | | | - Andrea Martella
- Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, CB2 0AA Cambridge, U.K
| | - Samuel Gilberto
- Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, CB2 0AA Cambridge, U.K
| | - Jordi Chi
- Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, 43183 Gothenburg, Sweden
| | - Emily Cooper
- Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, CB2 0AA Cambridge, U.K
| | - Tora Edström
- Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, 43183 Gothenburg, Sweden
| | - Bo Peng
- Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, 43183 Gothenburg, Sweden
| | - Dean Sumner
- Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, 43183 Gothenburg, Sweden
| | - Fredrik Karlsson
- Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, 43183 Gothenburg, Sweden
| | - Petr Volkov
- Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, 43183 Gothenburg, Sweden
| | - Carl I Webster
- Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, CB2 0AA Cambridge, U.K
| | - Robert Roth
- Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, 43183 Gothenburg, Sweden
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17
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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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18
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Mózsik L, Pohl C, Meyer V, Bovenberg RAL, Nygård Y, Driessen AJM. Modular Synthetic Biology Toolkit for Filamentous Fungi. ACS Synth Biol 2021; 10:2850-2861. [PMID: 34726388 PMCID: PMC8609570 DOI: 10.1021/acssynbio.1c00260] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
![]()
Filamentous fungi
are highly productive cell factories, often used
in industry for the production of enzymes and small bioactive compounds.
Recent years have seen an increasing number of synthetic-biology-based
applications in fungi, emphasizing the need for a synthetic biology
toolkit for these organisms. Here we present a collection of 96 genetic
parts, characterized in Penicillium or Aspergillus species, that are
compatible and interchangeable with the Modular Cloning system. The
toolkit contains natural and synthetic promoters (constitutive and
inducible), terminators, fluorescent reporters, and selection markers.
Furthermore, there are regulatory and DNA-binding domains of transcriptional
regulators and components for implementing different CRISPR-based
technologies. Genetic parts can be assembled into complex multipartite
assemblies and delivered through genomic integration or expressed
from an AMA1-sequence-based, fungal-replicating shuttle vector. With
this toolkit, synthetic transcription units with established promoters,
fusion proteins, or synthetic transcriptional regulation devices can
be more rapidly assembled in a standardized and modular manner for
novel fungal cell factories.
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Affiliation(s)
- László Mózsik
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Carsten Pohl
- Chair of Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany
| | - Vera Meyer
- Chair of Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany
| | - Roel A. L. Bovenberg
- DSM Biotechnology Center, 2613 AX Delft, The Netherlands
- Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Yvonne Nygård
- Department of Biology and Biological Engineering, Division of Industrial Biotechnology, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Arnold J. M. Driessen
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
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19
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Liao X, Li L, Jameel A, Xing XH, Zhang C. A versatile toolbox for CRISPR-based genome engineering in Pichia pastoris. Appl Microbiol Biotechnol 2021; 105:9211-9218. [PMID: 34773154 DOI: 10.1007/s00253-021-11688-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 10/26/2021] [Accepted: 11/07/2021] [Indexed: 10/19/2022]
Abstract
Pichia pastoris has gained much attention as a popular microbial cell factory for the production of recombinant proteins and high-value chemicals from laboratory to industrial scale. However, the lack of convenient and efficient genome engineering tools has impeded further applications of Pichia pastoris towards metabolic engineering and synthetic biology. Here, we report a CRISPR-based toolbox for gene editing and transcriptional regulation in P. pastoris. Based on the previous attempts in P. pastoris, we constructed a CRISPR/Cas9 system for gene editing using the RNA Pol-III-driven expression of sgRNA. The system was used to rapidly recycle the selectable marker with an eliminable episomal plasmid and achieved up to 100% knockout efficiency. Via dCas9 fused with transcriptional repressor (Mix1/RD1152) or activator (VPR), a flexible toolbox for regulation of gene expression was developed. The reporter gene eGFP driven by yeast pGAP or pCYC1 promoter showed strong inhibition (above 70%) and up to ~ 3.5-fold activation. To implement the combinatorial genetic engineering strategy, the CRISPR system contained a single Cas9-VPR protein, and engineered gRNA was introduced in P. pastoris for simultaneous gene activation, repression, and editing (CRISPR-ARE). We demonstrated that CRISPR-ARE was highly efficient for eGFP activation, mCherry repression, and ADE2 disruption, individually or in a combinatorial manner with a stable expression of multiplex sgRNAs. The simple and multifunctional toolkit demonstrated in this study will accelerate the application of P. pastoris in metabolic engineering and synthetic biology. KEY POINTS: • An eliminable CRISPR/Cas9 system yielded a highly efficient knockout of genes. • Simplified CRISPR/dCas9-based tools enabled transcriptional regulation of targeted genes. • CRISPR-ARE system achieved simultaneous gene activation, repression, and editing in P. pastoris.
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Affiliation(s)
- Xihao Liao
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, China.,Center for Synthetic and Systems Biology, Tsinghua University, Beijing, China
| | - Lu Li
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, China.,Center for Synthetic and Systems Biology, Tsinghua University, Beijing, China
| | - Aysha Jameel
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, China.,Center for Synthetic and Systems Biology, Tsinghua University, Beijing, China
| | - Xin-Hui Xing
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, China.,Center for Synthetic and Systems Biology, Tsinghua University, Beijing, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Chong Zhang
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, China. .,Center for Synthetic and Systems Biology, Tsinghua University, Beijing, China. .,National Technology Innovation Center of Synthetic Biology, Tianjin, China.
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20
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Mante J, Roehner N, Keating K, McLaughlin JA, Young E, Beal J, Myers CJ. Curation Principles Derived from the Analysis of the SBOL iGEM Data Set. ACS Synth Biol 2021; 10:2592-2606. [PMID: 34546707 DOI: 10.1021/acssynbio.1c00225] [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] [Indexed: 01/04/2023]
Abstract
As an engineering endeavor, synthetic biology requires effective sharing of genetic design information that can be reused in the construction of new designs. While there are a number of large community repositories of design information, curation of this information has been limited. This in turn limits the ways in which design information can be put to use. The aim of this work was to improve this situation by creating a curated library of parts from the International Genetically Engineered Machines (iGEM) registry data set. To this end, an analysis of the Synthetic Biology Open Language (SBOL) version of the iGEM registry was carried out using four different approaches-simple statistics, SnapGene autoannotation, SYNBICT autoannotation, and expert analysis-the results of which are presented herein. Key challenges encountered include the use of free text, insufficient part provenance, part duplication, lack of part removal, and insufficient continuous curation. On the basis of these analyses, the focus has shifted from the creation of a curated iGEM part library to instead the extraction of a set of lessons, which are presented here. These lessons can be exploited to facilitate the creation and curation of other part libraries using a simpler and less labor intensive process.
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Affiliation(s)
- Jeanet Mante
- University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Nicholas Roehner
- Raytheon BBN Technologies, Cambridge, Massachusetts 02138, United States
| | - Kevin Keating
- Worcester Polytechnic Institute, Worcester, Massachusetts 01609, United States
| | | | - Eric Young
- Worcester Polytechnic Institute, Worcester, Massachusetts 01609, United States
| | - Jacob Beal
- Raytheon BBN Technologies, Cambridge, Massachusetts 02138, United States
| | - Chris J. Myers
- University of Colorado Boulder, Boulder, Colorado 80309, United States
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21
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Mante J, Hao Y, Jett J, Joshi U, Keating K, Lu X, Nakum G, Rodriguez NE, Tang J, Terry L, Wu X, Yu E, Downie JS, McInnes BT, Nguyen MH, Sepulvado B, Young EM, Myers CJ. Synthetic Biology Knowledge System. ACS Synth Biol 2021; 10:2276-2285. [PMID: 34387462 DOI: 10.1021/acssynbio.1c00188] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The Synthetic Biology Knowledge System (SBKS) is an instance of the SynBioHub repository that includes text and data information that has been mined from papers published in ACS Synthetic Biology. This paper describes the SBKS curation framework that is being developed to construct the knowledge stored in this repository. The text mining pipeline performs automatic annotation of the articles using natural language processing techniques to identify salient content such as key terms, relationships between terms, and main topics. The data mining pipeline performs automatic annotation of the sequences extracted from the supplemental documents with the genetic parts used in them. Together these two pipelines link genetic parts to papers describing the context in which they are used. Ultimately, SBKS will reduce the time necessary for synthetic biologists to find the information necessary to complete their designs.
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Affiliation(s)
- Jeanet Mante
- University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Yikai Hao
- University of California San Diego, La Jolla, California 92093, United States
| | - Jacob Jett
- University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Udayan Joshi
- University of California San Diego, La Jolla, California 92093, United States
| | - Kevin Keating
- Worcester Polytechnic Institute, Worcester, Massachusettes 01609, United States
| | - Xiang Lu
- University of California San Diego, La Jolla, California 92093, United States
| | - Gaurav Nakum
- University of California San Diego, La Jolla, California 92093, United States
| | | | - Jiawei Tang
- University of California San Diego, La Jolla, California 92093, United States
| | - Logan Terry
- University of Utah, Salt Lake City, Utah 84112, United States
| | - Xuanyu Wu
- University of California San Diego, La Jolla, California 92093, United States
| | - Eric Yu
- University of Utah, Salt Lake City, Utah 84112, United States
| | - J. Stephen Downie
- University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Bridget T. McInnes
- Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Mai H. Nguyen
- University of California San Diego, La Jolla, California 92093, United States
| | - Brandon Sepulvado
- NORC at the University of Chicago Bethesda, Chicago, Illinois 60637, United States
| | - Eric M. Young
- Worcester Polytechnic Institute, Worcester, Massachusettes 01609, United States
| | - Chris J. Myers
- University of Colorado Boulder, Boulder, Colorado 80309, United States
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22
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de Sá Magalhães S, Keshavarz-Moore E. Pichia pastoris ( Komagataella phaffii) as a Cost-Effective Tool for Vaccine Production for Low- and Middle-Income Countries (LMICs). Bioengineering (Basel) 2021; 8:119. [PMID: 34562941 PMCID: PMC8468848 DOI: 10.3390/bioengineering8090119] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 08/05/2021] [Accepted: 08/24/2021] [Indexed: 01/26/2023] Open
Abstract
Vaccination is of paramount importance to global health. With the advent of the more recent pandemics, the urgency to expand the range has become even more evident. However, the potential limited availability and affordability of vaccines to resource low- and middle-income countries has created a need for solutions that will ensure cost-effective vaccine production methods for these countries. Pichia pastoris (P. pastoris) (also known as Komagataella phaffii) is one of the most promising candidates for expression of heterologous proteins in vaccines development. It combines the speed and ease of highly efficient prokaryotic platforms with some key capabilities of mammalian systems, potentially reducing manufacturing costs. This review will examine the latest developments in P. pastoris from cell engineering and design to industrial production systems with focus on vaccine development and with reference to specific key case studies.
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Affiliation(s)
| | - Eli Keshavarz-Moore
- Department of Biochemical Engineering, University College London, Gower Street, London WC1E 6BT, UK;
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23
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Abstract
The methylotrophic yeast Pichia pastoris is currently one of the most versatile and popular hosts for the production of heterologous proteins, including industrial enzymes. The popularity of P. pastoris stems from its ability to grow to high cell densities, producing high titers of secreted heterologous protein with very low amounts of endogenous proteins. Its ability to express correctly folded proteins with post-translational modifications makes it an excellent candidate for the production of biopharmaceuticals. In addition, production in P. pastoris typically uses the strong, methanol-inducible and tightly regulated promoter (PAOX1), which can result in heterologous protein that constitutes up to 30% of total cell protein upon growth in methanol. In this chapter, we present methodology for the production of secreted recombinant proteins in P. pastoris, and we discuss alternatives to enhance protein production with the desired yield and quality.
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24
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Püllmann P, Weissenborn MJ. Improving the Heterologous Production of Fungal Peroxygenases through an Episomal Pichia pastoris Promoter and Signal Peptide Shuffling System. ACS Synth Biol 2021; 10:1360-1372. [PMID: 34075757 DOI: 10.1021/acssynbio.0c00641] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Fungal peroxygenases (UPOs) have emerged as oxyfunctionalization catalysts of tremendous interest in recent years. However, their widespread use in the field of biocatalysis is still hampered by their challenging heterologous production, substantially limiting the panel of accessible enzymes for investigation and enzyme engineering. Building upon previous work on UPO production in yeast, we have developed a combined promoter and signal peptide shuffling system for episomal high throughput UPO production in the industrially relevant, methylotrophic yeast Pichia pastoris. Eleven endogenous and orthologous promoters were shuffled with a diverse set of 17 signal peptides. Three previously described UPOs were selected as first test set, leading to the identification of beneficial promoter/signal peptide combinations for protein production. We applied the system then successfully to produce two novel UPOs: MfeUPO from Myceliophthora fergusii and MhiUPO from Myceliophthora hinnulea. To demonstrate the feasibility of the developed system to other enzyme classes, it was applied for the industrially relevant lipase CalB and the laccase Mrl2. In total, approximately 3200 transformants of eight diverse enzymes were screened and the best promoter/signal peptide combinations studied at various cofeeding, derepression, and induction conditions. High volumetric production titers were achieved by subsequent creation of stable integration lines and harnessing orthologous promoters from Hansenula polymorpha. In most cases promising yields were also achieved without the addition of methanol under derepressed conditions. To foster the use of the episomal high throughput promoter/signal peptide Pichia pastoris system, we made all plasmids available through Addgene.
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Affiliation(s)
- Pascal Püllmann
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany
| | - Martin J. Weissenborn
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle (Saale), Germany
- Institute of Chemistry, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Straße 2, 06120 Halle (Saale), Germany
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25
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Raschmanová H, Weninger A, Knejzlík Z, Melzoch K, Kovar K. Engineering of the unfolded protein response pathway in Pichia pastoris: enhancing production of secreted recombinant proteins. Appl Microbiol Biotechnol 2021; 105:4397-4414. [PMID: 34037840 PMCID: PMC8195892 DOI: 10.1007/s00253-021-11336-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 04/30/2021] [Accepted: 05/06/2021] [Indexed: 12/14/2022]
Abstract
Folding and processing of proteins in the endoplasmic reticulum (ER) are major impediments in the production and secretion of proteins from Pichia pastoris (Komagataella sp.). Overexpression of recombinant genes can overwhelm the innate secretory machinery of the P. pastoris cell, and incorrectly folded proteins may accumulate inside the ER. To restore proper protein folding, the cell naturally triggers an unfolded protein response (UPR) pathway, which upregulates the expression of genes coding for chaperones and other folding-assisting proteins (e.g., Kar2p, Pdi1, Ero1p) via the transcription activator Hac1p. Unfolded/misfolded proteins that cannot be repaired are degraded via the ER-associated degradation (ERAD) pathway, which decreases productivity. Co-expression of selected UPR genes, along with the recombinant gene of interest, is a common approach to enhance the production of properly folded, secreted proteins. Such an approach, however, is not always successful and sometimes, protein productivity decreases because of an unbalanced UPR. This review summarizes successful chaperone co-expression strategies in P. pastoris that are specifically related to overproduction of foreign proteins and the UPR. In addition, it illustrates possible negative effects on the cell's physiology and productivity resulting from genetic engineering of the UPR pathway. We have focused on Pichia's potential for commercial production of valuable proteins and we aim to optimize molecular designs so that production strains can be tailored to suit a specific heterologous product. KEY POINTS: • Chaperones co-expressed with recombinant genes affect productivity in P. pastoris. • Enhanced UPR may impair strain physiology and promote protein degradation. • Gene copy number of the target gene and the chaperone determine the secretion rate.
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Affiliation(s)
- Hana Raschmanová
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czech Republic.
- Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences ZHAW, Wädenswil, Switzerland.
| | - Astrid Weninger
- Institute of Molecular Biotechnology, Graz University of Technology, Graz, Austria
| | - Zdeněk Knejzlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Karel Melzoch
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Karin Kovar
- Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences ZHAW, Wädenswil, Switzerland
- daspool Association, Wädenswil, Switzerland
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26
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Characterization of Lysozyme-Like Effector TseP Reveals the Dependence of Type VI Secretion System (T6SS) Secretion on Effectors in Aeromonas dhakensis Strain SSU. Appl Environ Microbiol 2021; 87:e0043521. [PMID: 33837015 DOI: 10.1128/aem.00435-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The type VI secretion system (T6SS) is a widespread weapon employed by Gram-negative bacteria for interspecies interaction in complex communities. Analogous to a contractile phage tail, the double-tubular T6SS injects toxic effectors into prokaryotic and eukaryotic neighboring cells. Although effectors dictate T6SS functions, their identities remain elusive in many pathogens. Here, we report the lysozyme-like effector TseP in Aeromonas dhakensis, a waterborne pathogen that can cause severe gastroenteritis and systemic infection. Using secretion, competition, and enzymatic assays, we demonstrate that TseP is a T6SS-dependent effector with cell wall-lysing activities, and TsiP is its cognate immunity protein. Triple deletion of tseP and two known effector genes, tseI and tseC, abolished T6SS-mediated secretion, while complementation with any single effector gene partially restored bacterial killing and Hcp secretion. In contrast to whole-gene deletions, the triple-effector inactivation in the 3effc mutant abolished antibacterial killing but not T6SS secretion. We further demonstrate that the 3effc mutation abolished T6SS-mediated toxicity of SSU to Dictyostelium discoideum amoebae, suggesting that the T6SS physical puncture is nontoxic to eukaryotic cells. These data highlight not only the necessity of possessing functionally diverse effectors for survival in multispecies communities but also that effector inactivation would be an efficient strategy to detoxify the T6SS while preserving its delivery efficiency, converting the T6SS to a platform for protein delivery to a variety of recipient cells. IMPORTANCE Delivery of cargo proteins via protein secretion systems has been shown to be a promising tool in various applications. However, secretion systems are often used by pathogens to cause disease. Thus, strategies are needed to detoxify secretion systems while preserving their efficiency. The T6SS can translocate proteins through physical puncture of target cells without specific surface receptors and can target a broad range of recipients. In this study, we identified a cell wall-lysing effector, and by inactivating it and the other two known effectors, we have built a detoxified T6SS-active strain that may be used for protein delivery to prokaryotic and eukaryotic recipient cells.
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27
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Püllmann P, Knorrscheidt A, Münch J, Palme PR, Hoehenwarter W, Marillonnet S, Alcalde M, Westermann B, Weissenborn MJ. A modular two yeast species secretion system for the production and preparative application of unspecific peroxygenases. Commun Biol 2021; 4:562. [PMID: 33980981 PMCID: PMC8115255 DOI: 10.1038/s42003-021-02076-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 03/31/2021] [Indexed: 01/27/2023] Open
Abstract
Fungal unspecific peroxygenases (UPOs) represent an enzyme class catalysing versatile oxyfunctionalisation reactions on a broad substrate scope. They are occurring as secreted, glycosylated proteins bearing a haem-thiolate active site and rely on hydrogen peroxide as the oxygen source. However, their heterologous production in a fast-growing organism suitable for high throughput screening has only succeeded once-enabled by an intensive directed evolution campaign. We developed and applied a modular Golden Gate-based secretion system, allowing the first production of four active UPOs in yeast, their one-step purification and application in an enantioselective conversion on a preparative scale. The Golden Gate setup was designed to be universally applicable and consists of the three module types: i) signal peptides for secretion, ii) UPO genes, and iii) protein tags for purification and split-GFP detection. The modular episomal system is suitable for use in Saccharomyces cerevisiae and was transferred to episomal and chromosomally integrated expression cassettes in Pichia pastoris. Shake flask productions in Pichia pastoris yielded up to 24 mg/L secreted UPO enzyme, which was employed for the preparative scale conversion of a phenethylamine derivative reaching 98.6 % ee. Our results demonstrate a rapid, modular yeast secretion workflow of UPOs yielding preparative scale enantioselective biotransformations.
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Affiliation(s)
- Pascal Püllmann
- Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | | | - Judith Münch
- Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | - Paul R Palme
- Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | | | | | - Miguel Alcalde
- Department of Biocatalysis, Institute of Catalysis, CSIC, Madrid, Spain
| | - Bernhard Westermann
- Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
- Institute of Chemistry, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Martin J Weissenborn
- Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany.
- Institute of Chemistry, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany.
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28
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Akishev Z, Kiribayeva A, Mussakhmetov A, Baltin K, Ramankulov Y, Khassenov B. Constitutive expression of Camelus bactrianus prochymosin B in Pichia pastoris. Heliyon 2021; 7:e07137. [PMID: 34113734 PMCID: PMC8170492 DOI: 10.1016/j.heliyon.2021.e07137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 04/14/2021] [Accepted: 05/20/2021] [Indexed: 11/30/2022] Open
Abstract
Camel chymosin can be efficiently employed to produce cheese. Traditionally the rennet enzyme produced by the glands of the fourth stomach of ruminant animals (abomassum) is used in cheese making. Full-length Camelus bactrianus (Bactrian camel) prochymosin gene was synthesized and constitutively expressed in Pichia pastoris cells under glyceraldehydes-3-phosphate dehydrogenase (GAP) promoter. It was purified by sequential anion and cation exchange chromatography. SDS-PAGE analysis resulted in two bands, approximately 42 and 35 kDa. The 42 kDa band vanished when the sample was treated with endoglycosidase H, indicating that the recombinant protein is partially glycosylated. Optimal pH for the activity of the highest-purity recombinant chymosin was pH 4.5 for cow's milk and pH 4.0 for mare's milk. The range 45-50 °C and 70 °C for cow's and mare's milk types, respectively, was found to be the most appropriate for maximal relative milk-clotting activity. Concentration of CaCl2 that ensured the stability of the chymosin milk-clotting activity was between 20 and 50 mM with an optimum at 30 mM. Milk-clotting activity of camel recombinant chymosin and ability to make curd was successfully tested on fresh mare's milk. Pichia pastoris strain with integrated camel chymosin gene showed high productivity of submerged fermentation in bioreactor with milk-clotting activity 1412 U/mL and 80 mg/L enzyme yield. These results suggest that the constitutive expression of the camel chymosin Camelus bactrianus in the yeast Pichia pastoris has good prospects for practical applications.
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Affiliation(s)
- Zhiger Akishev
- National Center for Biotechnology, 13/5 Kurgalzhynskoye Road, Nur-Sultan, 010000, Kazakhstan
- L.N.Gumilyov Eurasian National University, 2 Kanysh Satpayev Street, Nur-Sultan, 010008, Kazakhstan
| | - Assel Kiribayeva
- National Center for Biotechnology, 13/5 Kurgalzhynskoye Road, Nur-Sultan, 010000, Kazakhstan
- L.N.Gumilyov Eurasian National University, 2 Kanysh Satpayev Street, Nur-Sultan, 010008, Kazakhstan
| | - Arman Mussakhmetov
- National Center for Biotechnology, 13/5 Kurgalzhynskoye Road, Nur-Sultan, 010000, Kazakhstan
| | - Kairat Baltin
- National Center for Biotechnology, 13/5 Kurgalzhynskoye Road, Nur-Sultan, 010000, Kazakhstan
| | - Yerlan Ramankulov
- National Center for Biotechnology, 13/5 Kurgalzhynskoye Road, Nur-Sultan, 010000, Kazakhstan
| | - Bekbolat Khassenov
- National Center for Biotechnology, 13/5 Kurgalzhynskoye Road, Nur-Sultan, 010000, Kazakhstan
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29
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Collins JH, Keating KW, Jones TR, Balaji S, Marsan CB, Çomo M, Newlon ZJ, Mitchell T, Bartley B, Adler A, Roehner N, Young EM. Engineered yeast genomes accurately assembled from pure and mixed samples. Nat Commun 2021; 12:1485. [PMID: 33674578 PMCID: PMC7935868 DOI: 10.1038/s41467-021-21656-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 02/04/2021] [Indexed: 01/31/2023] Open
Abstract
Yeast whole genome sequencing (WGS) lacks end-to-end workflows that identify genetic engineering. Here we present Prymetime, a tool that assembles yeast plasmids and chromosomes and annotates genetic engineering sequences. It is a hybrid workflow-it uses short and long reads as inputs to perform separate linear and circular assembly steps. This structure is necessary to accurately resolve genetic engineering sequences in plasmids and the genome. We show this by assembling diverse engineered yeasts, in some cases revealing unintended deletions and integrations. Furthermore, the resulting whole genomes are high quality, although the underlying assembly software does not consistently resolve highly repetitive genome features. Finally, we assemble plasmids and genome integrations from metagenomic sequencing, even with 1 engineered cell in 1000. This work is a blueprint for building WGS workflows and establishes WGS-based identification of yeast genetic engineering.
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Affiliation(s)
- Joseph H Collins
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Kevin W Keating
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Trent R Jones
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Shravani Balaji
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Celeste B Marsan
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Marina Çomo
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Zachary J Newlon
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Tom Mitchell
- Synthetic Biology, Raytheon BBN Technologies, Cambridge, MA, USA
| | - Bryan Bartley
- Synthetic Biology, Raytheon BBN Technologies, Cambridge, MA, USA
| | - Aaron Adler
- Synthetic Biology, Raytheon BBN Technologies, Cambridge, MA, USA
| | - Nicholas Roehner
- Synthetic Biology, Raytheon BBN Technologies, Cambridge, MA, USA
| | - Eric M Young
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, USA.
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30
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Lin Y, Guan Y, Dong X, Ma Y, Wang X, Leng Y, Wu F, Ye JW, Chen GQ. Engineering Halomonas bluephagenesis as a chassis for bioproduction from starch. Metab Eng 2021; 64:134-145. [PMID: 33577951 DOI: 10.1016/j.ymben.2021.01.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/22/2020] [Accepted: 01/30/2021] [Indexed: 10/22/2022]
Abstract
Halomonas bluephagenesis has been successfully engineered to produce multiple products under open unsterile conditions utilizing costly glucose as the carbon source. It would be highly interesting to investigate if H. bluephagenesis, a chassis for the Next Generation Industrial Biotechnology (NGIB), can be reconstructed to become an extracellular hydrolytic enzyme producer replacing traditional enzyme producer Bacillus spp. If successful, cost of bulk hydrolytic enzymes such as amylase and protease, can be significantly reduced due to the contamination resistant and robust growth of H. bluephagenesis. This also allows H. bluephagenesis to be able to grow on low cost substrates such as starch. The modularized secretion machinery was constructed and fine-tuned in H. bluephagenesis using codon-optimized gene encoding α-amylase from Bacillus lichenifomis. Screening of suitable signal peptides and linkers based on super-fold green fluorescence protein (sfGFP) for enhanced expression in H. bluephagenesis resulted in a 7-fold enhancement of sfGFP secretion in the recombinant H. bluephagenesis. When the gene encoding sfGFP was replaced by α-amylase encoding gene, recombinant H. bluephagenesis harboring this amylase secretory system was able to produce poly(3-hydroxybutyrate) (PHB), poly(3-hydroxybutyrate-co-4-hydroxybutyrate) (P34HB), poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV), ectoine and L-threonine utilizing starch as the growth substrate, respectively. Recombinant H. bluephagenesis TN04 expressing genes encoding α-amylase and glucosidase on chromosome and plasmid-based systems, respectively, was able to grow on corn starch to approximately 10 g/L cell dry weight containing 51% PHB when grown in shake flasks. H. bluephagenesis was demonstrated to be a chassis for productions of extracellular enzymes and multiple products from low cost corn starch.
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Affiliation(s)
- Yina Lin
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China; Tsinghua-Peking Center for Life Sciences, 100084, China
| | - Yuying Guan
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xu Dong
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yueyuan Ma
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xuan Wang
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China; Tsinghua-Peking Center for Life Sciences, 100084, China
| | - Yuchen Leng
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Fuqing Wu
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China; Tsinghua-Peking Center for Life Sciences, 100084, China; MOE Key Lab of Industrial Biocatalysis, Tsinghua University, Beijing, 100084, China
| | - Jian-Wen Ye
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China; Tsinghua-Peking Center for Life Sciences, 100084, China; Center for Materials Synthetic Biology, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Guo-Qiang Chen
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China; Tsinghua-Peking Center for Life Sciences, 100084, China; MOE Key Lab of Industrial Biocatalysis, Tsinghua University, Beijing, 100084, China.
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31
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Di Blasi R, Zouein A, Ellis T, Ceroni F. Genetic Toolkits to Design and Build Mammalian Synthetic Systems. Trends Biotechnol 2021; 39:1004-1018. [PMID: 33526300 DOI: 10.1016/j.tibtech.2020.12.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 12/14/2020] [Accepted: 12/14/2020] [Indexed: 11/17/2022]
Abstract
Construction of DNA-encoded programs is central to synthetic biology and the chosen method often determines the time required to design and build constructs for testing. Here, we describe and summarise key features of the available toolkits for DNA construction for mammalian cells. We compare the different cloning strategies based on their complexity and the time needed to generate constructs of different sizes, and we reflect on why Golden Gate toolkits now dominate due to their modular design. We look forward to future advances, including accessory packs for cloning toolkits that can facilitate editing, orthogonality, advanced regulation, and integration into synthetic chromosome construction.
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Affiliation(s)
- Roberto Di Blasi
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, UK; Imperial College Centre for Synthetic Biology, South Kensington Campus, London, UK
| | - Annalise Zouein
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, UK; Imperial College Centre for Synthetic Biology, South Kensington Campus, London, UK; Department of Bioengineering, Imperial College London, South Kensington Campus, London, UK
| | - Tom Ellis
- Imperial College Centre for Synthetic Biology, South Kensington Campus, London, UK; Department of Bioengineering, Imperial College London, South Kensington Campus, London, UK; Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Francesca Ceroni
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, UK; Imperial College Centre for Synthetic Biology, South Kensington Campus, London, UK.
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32
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Patra P, Das M, Kundu P, Ghosh A. Recent advances in systems and synthetic biology approaches for developing novel cell-factories in non-conventional yeasts. Biotechnol Adv 2021; 47:107695. [PMID: 33465474 DOI: 10.1016/j.biotechadv.2021.107695] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 12/14/2020] [Accepted: 01/09/2021] [Indexed: 12/14/2022]
Abstract
Microbial bioproduction of chemicals, proteins, and primary metabolites from cheap carbon sources is currently an advancing area in industrial research. The model yeast, Saccharomyces cerevisiae, is a well-established biorefinery host that has been used extensively for commercial manufacturing of bioethanol from myriad carbon sources. However, its Crabtree-positive nature often limits the use of this organism for the biosynthesis of commercial molecules that do not belong in the fermentative pathway. To avoid extensive strain engineering of S. cerevisiae for the production of metabolites other than ethanol, non-conventional yeasts can be selected as hosts based on their natural capacity to produce desired commodity chemicals. Non-conventional yeasts like Kluyveromyces marxianus, K. lactis, Yarrowia lipolytica, Pichia pastoris, Scheffersomyces stipitis, Hansenula polymorpha, and Rhodotorula toruloides have been considered as potential industrial eukaryotic hosts owing to their desirable phenotypes such as thermotolerance, assimilation of a wide range of carbon sources, as well as ability to secrete high titers of protein and lipid. However, the advanced metabolic engineering efforts in these organisms are still lacking due to the limited availability of systems and synthetic biology methods like in silico models, well-characterised genetic parts, and optimized genome engineering tools. This review provides an insight into the recent advances and challenges of systems and synthetic biology as well as metabolic engineering endeavours towards the commercial usage of non-conventional yeasts. Particularly, the approaches in emerging non-conventional yeasts for the production of enzymes, therapeutic proteins, lipids, and metabolites for commercial applications are extensively discussed here. Various attempts to address current limitations in designing novel cell factories have been highlighted that include the advances in the fields of genome-scale metabolic model reconstruction, flux balance analysis, 'omics'-data integration into models, genome-editing toolkit development, and rewiring of cellular metabolisms for desired chemical production. Additionally, the understanding of metabolic networks using 13C-labelling experiments as well as the utilization of metabolomics in deciphering intracellular fluxes and reactions have also been discussed here. Application of cutting-edge nuclease-based genome editing platforms like CRISPR/Cas9, and its optimization towards efficient strain engineering in non-conventional yeasts have also been described. Additionally, the impact of the advances in promising non-conventional yeasts for efficient commercial molecule synthesis has been meticulously reviewed. In the future, a cohesive approach involving systems and synthetic biology will help in widening the horizon of the use of unexplored non-conventional yeast species towards industrial biotechnology.
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Affiliation(s)
- Pradipta Patra
- School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Manali Das
- School of Bioscience, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Pritam Kundu
- School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Amit Ghosh
- School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, West Bengal 721302, India; P.K. Sinha Centre for Bioenergy and Renewables, Indian Institute of Technology Kharagpur, West Bengal 721302, India.
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Dusek J, Plchova H, Cerovska N, Poborilova Z, Navratil O, Kratochvilova K, Gunter C, Jacobs R, Hitzeroth II, Rybicki EP, Moravec T. Extended Set of GoldenBraid Compatible Vectors for Fast Assembly of Multigenic Constructs and Their Use to Create Geminiviral Expression Vectors. FRONTIERS IN PLANT SCIENCE 2020; 11:522059. [PMID: 33193468 PMCID: PMC7641900 DOI: 10.3389/fpls.2020.522059] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 09/15/2020] [Indexed: 06/11/2023]
Abstract
Methods for simple and fast assembly of exchangeable standard DNA parts using Type II S restriction enzymes are becoming more and more popular in plant synthetic and molecular biology. These methods enable routine construction of large and complex multigene DNA structures. Two available frameworks emphasize either high cloning capacity (Modular Cloning, MoClo) or simplicity (GoldenBraid, GB). Here we present a set of novel α-level plasmids compatible with the GB convention that extend the ability of GB to rapidly assemble more complex genetic constructs, while maintaining compatibility with all existing GB parts as well as most MoClo parts and GB modules. With the use of our new plasmids, standard GB parts can be assembled into complex assemblies containing 1, 5, 10 and up to theoretically 50 units in each successive level of infinite loop assembly. Assembled DNA constructs can be also combined with conventional binary GB-assemblies (1, 2, 4, 8… units). We demonstrate the usefulness of our framework on single tube assembly of replicating plant expression constructs based on the geminivirus Bean yellow dwarf virus (BeYDV).
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Affiliation(s)
- Jakub Dusek
- Laboratory of Virology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
- Department of Plant Protection, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Prague, Czechia
| | - Helena Plchova
- Laboratory of Virology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - Noemi Cerovska
- Laboratory of Virology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - Zuzana Poborilova
- Laboratory of Virology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - Oldrich Navratil
- Laboratory of Virology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - Katerina Kratochvilova
- Laboratory of Virology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czechia
| | - Cornelius Gunter
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Raygaana Jacobs
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Inga I. Hitzeroth
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Edward P. Rybicki
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Tomas Moravec
- Laboratory of Virology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
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Pryor JM, Potapov V, Kucera RB, Bilotti K, Cantor EJ, Lohman GJS. Enabling one-pot Golden Gate assemblies of unprecedented complexity using data-optimized assembly design. PLoS One 2020; 15:e0238592. [PMID: 32877448 PMCID: PMC7467295 DOI: 10.1371/journal.pone.0238592] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 08/19/2020] [Indexed: 12/21/2022] Open
Abstract
DNA assembly is an integral part of modern synthetic biology, as intricate genetic engineering projects require robust molecular cloning workflows. Golden Gate assembly is a frequently employed DNA assembly methodology that utilizes a Type IIS restriction enzyme and a DNA ligase to generate recombinant DNA constructs from smaller DNA fragments. However, the utility of this methodology has been limited by a lack of resources to guide experimental design. For example, selection of the DNA sequences at fusion sites between fragments is based on broad assembly guidelines or pre-vetted sets of junctions, rather than being customized for a particular application or cloning project. To facilitate the design of robust assembly reactions, we developed a high-throughput DNA sequencing assay to examine reaction outcomes of Golden Gate assembly with T4 DNA ligase and the most commonly used Type IIS restriction enzymes that generate three-base and four-base overhangs. Next, we incorporated these findings into a suite of webtools that design assembly reactions using the experimental data. These webtools can be used to create customized assemblies from a target DNA sequence or a desired number of fragments. Lastly, we demonstrate how using these tools expands the limits of current assembly systems by carrying out one-pot assemblies of up to 35 DNA fragments. Full implementation of the tools developed here enables direct expansion of existing assembly standards for modular cloning systems (e.g. MoClo) as well as the formation of robust new high-fidelity standards.
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Affiliation(s)
- John M. Pryor
- Research Department, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Vladimir Potapov
- Research Department, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Rebecca B. Kucera
- Applications and Product Development, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Katharina Bilotti
- Research Department, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Eric J. Cantor
- Applications and Product Development, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Gregory J. S. Lohman
- Research Department, New England Biolabs, Ipswich, Massachusetts, United States of America
- * E-mail:
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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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Rahmat E, Kang Y. Yeast metabolic engineering for the production of pharmaceutically important secondary metabolites. Appl Microbiol Biotechnol 2020; 104:4659-4674. [DOI: 10.1007/s00253-020-10587-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 01/30/2020] [Accepted: 03/24/2020] [Indexed: 11/29/2022]
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Thak EJ, Yoo SJ, Moon HY, Kang HA. Yeast synthetic biology for designed cell factories producing secretory recombinant proteins. FEMS Yeast Res 2020; 20:5721243. [DOI: 10.1093/femsyr/foaa009] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 01/30/2020] [Indexed: 12/17/2022] Open
Abstract
ABSTRACT
Yeasts are prominent hosts for the production of recombinant proteins from industrial enzymes to therapeutic proteins. Particularly, the similarity of protein secretion pathways between these unicellular eukaryotic microorganisms and higher eukaryotic organisms has made them a preferential host to produce secretory recombinant proteins. However, there are several bottlenecks, in terms of quality and quantity, restricting their use as secretory recombinant protein production hosts. In this mini-review, we discuss recent developments in synthetic biology approaches to constructing yeast cell factories endowed with enhanced capacities of protein folding and secretion as well as designed targeted post-translational modification process functions. We focus on the new genetic tools for optimizing secretory protein expression, such as codon-optimized synthetic genes, combinatory synthetic signal peptides and copy number-controllable integration systems, and the advanced cellular engineering strategies, including endoplasmic reticulum and protein trafficking pathway engineering, synthetic glycosylation, and cell wall engineering, for improving the quality and yield of secretory recombinant proteins.
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Affiliation(s)
- Eun Jung Thak
- Laboratory of Molecular Systems Biology, Department of Life Science, Chung-Ang University, Seoul 06974, South Korea
| | - Su Jin Yoo
- Laboratory of Molecular Systems Biology, Department of Life Science, Chung-Ang University, Seoul 06974, South Korea
| | - Hye Yun Moon
- Laboratory of Molecular Systems Biology, Department of Life Science, Chung-Ang University, Seoul 06974, South Korea
| | - Hyun Ah Kang
- Laboratory of Molecular Systems Biology, Department of Life Science, Chung-Ang University, Seoul 06974, South Korea
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Huang H, Liang Q, Wang Y, Chen J, Kang Z. High-level constitutive expression of leech hyaluronidase with combined strategies in recombinant Pichia pastoris. Appl Microbiol Biotechnol 2020; 104:1621-1632. [DOI: 10.1007/s00253-019-10282-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 11/19/2019] [Accepted: 11/26/2019] [Indexed: 02/06/2023]
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Nevalainen H. Strategies and Challenges for the Development of Industrial Enzymes Using Fungal Cell Factories. GRAND CHALLENGES IN FUNGAL BIOTECHNOLOGY 2020. [PMCID: PMC7123961 DOI: 10.1007/978-3-030-29541-7_7] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Industrial enzymes have been produced from microorganisms for more than a century. Today, a large share of enzyme products is manufactured using recombinant microorganisms. This chapter focuses on major industrial fungal species belonging to the ascomycetes like Aspergillus niger, A. oryzae, and Trichoderma reesei. Many of the commercially available recombinant enzymes are manufactured using fungi. Examples of fungal enzymes used in food products are described. The enzyme industry is to a large extent cost-driven, so the enzyme product needs to meet strict COGS (cost of goods sold) targets. Therefore, the cell factory must be very efficient to produce the enzyme in high titers and efficiently utilize raw materials. Secondly, it must be designed for a robust and generic fermentation process. When developing fungal hosts for enzyme production, several properties of the system need to be considered relating to efficiency of the cell factory, purity of the product, and safety of both the cell factory and the product. Purity is secured by engineering of the cell factory, and properties related to safety must also be engineered into the fungal host. The methods used for strain improvement are continuously being developed to increase yields and are described herein. More automation using precision tools for modification of the genome (i.e., CRISPR) and low-cost sequencing have vastly expanded the possibilities and enabled fast strain development. Using systems biology approaches, better understanding of cellular processes is now possible enabling advanced engineering of fungal cell factories. Surprisingly, a survey of innovation in the field revealed a decrease in the number of patent applications in recent years. Finally, the requirements for enzyme approval, especially in food and feed, have increased significantly worldwide in the last few years. A description of the regulatory landscape and its challenges in food and feed is included.
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Affiliation(s)
- Helena Nevalainen
- Department of Molecular Sciences, Macquarie University, Sydney, NSW Australia
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40
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Poliner E, Clark E, Cummings C, Benning C, Farre EM. A high-capacity gene stacking toolkit for the oleaginous microalga, Nannochloropsis oceanica CCMP1779. ALGAL RES 2020. [DOI: 10.1016/j.algal.2019.101664] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Pauly M, Gawenda N, Wagner C, Fischbach P, Ramírez V, Axmann IM, Voiniciuc C. The Suitability of Orthogonal Hosts to Study Plant Cell Wall Biosynthesis. PLANTS (BASEL, SWITZERLAND) 2019; 8:E516. [PMID: 31744209 PMCID: PMC6918405 DOI: 10.3390/plants8110516] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/08/2019] [Accepted: 11/15/2019] [Indexed: 12/20/2022]
Abstract
Plant cells are surrounded by an extracellular matrix that consists mainly of polysaccharides. Many molecular components involved in plant cell wall polymer synthesis have been identified, but it remains largely unknown how these molecular players function together to define the length and decoration pattern of a polysaccharide. Synthetic biology can be applied to answer questions beyond individual glycosyltransferases by reconstructing entire biosynthetic machineries required to produce a complete wall polysaccharide. Recently, this approach was successful in establishing the production of heteromannan from several plant species in an orthogonal host-a yeast-illuminating the role of an auxiliary protein in the biosynthetic process. In this review we evaluate to what extent a selection of organisms from three kingdoms of life (Bacteria, Fungi and Animalia) might be suitable for the synthesis of plant cell wall polysaccharides. By identifying their key attributes for glycoengineering as well as analyzing the glycosidic linkages of their native polymers, we present a valuable comparison of their key advantages and limitations for the production of different classes of plant polysaccharides.
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Affiliation(s)
- Markus Pauly
- Institute for Plant Cell Biology and Biotechnology, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (M.P.); (N.G.); (V.R.)
| | - Niklas Gawenda
- Institute for Plant Cell Biology and Biotechnology, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (M.P.); (N.G.); (V.R.)
| | - Christine Wagner
- Independent Junior Research Group–Designer Glycans, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany;
| | - Patrick Fischbach
- Institute of Synthetic Biology, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany;
| | - Vicente Ramírez
- Institute for Plant Cell Biology and Biotechnology, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; (M.P.); (N.G.); (V.R.)
| | - Ilka M. Axmann
- Institute for Synthetic Microbiology, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany;
| | - Cătălin Voiniciuc
- Independent Junior Research Group–Designer Glycans, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany;
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Liu Q, Shi X, Song L, Liu H, Zhou X, Wang Q, Zhang Y, Cai M. CRISPR-Cas9-mediated genomic multiloci integration in Pichia pastoris. Microb Cell Fact 2019; 18:144. [PMID: 31434578 PMCID: PMC6704636 DOI: 10.1186/s12934-019-1194-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/14/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Pichia pastoris (syn. Komagataella phaffii) is a widely used generally recognized as safe host for heterologous expression of proteins in both industry and academia. Recently, it has been shown to be a potentially good chassis host for the production of high-value pharmaceuticals and chemicals. Nevertheless, limited availability of selective markers and low efficiency of homologous recombination make this process difficult and time-consuming, particularly in the case of multistep biosynthetic pathways. Therefore, it is crucial to develop an efficient and marker-free multiloci gene knock-in method in P. pastoris. RESULTS A non-homologous-end-joining defective strain (Δku70) was first constructed using the CRISPR-Cas9 based gene deficiency approach. It was then used as a parent strain for multiloci gene integration. Ten guide RNA (gRNA) targets were designed within 100 bp upstream of the promoters or downstream of terminator, and then tested using an eGFP reporter and confirmed as suitable single-locus integration sites. Three high-efficiency gRNA targets (PAOX1UP-g2, PTEF1UP-g1, and PFLD1UP-g1) were selected for double- and triple-locus co-integration. The integration efficiency ranged from 57.7 to 70% and 12.5 to 32.1% for double-locus and triple-locus integration, respectively. In addition, biosynthetic pathways of 6-methylsalicylic acid and 3-methylcatechol were successfully assembled using the developed method by one-step integration of functional genes. The desired products were obtained, which further established the effectiveness and applicability of the developed CRISPR-Cas9-mediated gene co-integration method in P. pastoris. CONCLUSIONS A CRISPR-Cas9-mediated multiloci gene integration method was developed with efficient gRNA targets in P. pastoris. Using this method, multiple gene cassettes can be simultaneously integrated into the genome without employing selective markers. The multiloci integration strategy is beneficial for pathway assembly of complicated pharmaceuticals and chemicals expressed in P. pastoris.
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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
| | - Xiaona Shi
- 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
| | - Haifeng Liu
- Chinare Resources Angde Biotech Pharmaceutical Co., Ltd., 78 E-jiao Street, Liaocheng, China
| | - Xiangshan Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 China
- Chinare Resources Angde Biotech Pharmaceutical Co., Ltd., 78 E-jiao Street, Liaocheng, 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
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Nora LC, Westmann CA, Guazzaroni ME, Siddaiah C, Gupta VK, Silva-Rocha R. Recent advances in plasmid-based tools for establishing novel microbial chassis. Biotechnol Adv 2019; 37:107433. [PMID: 31437573 DOI: 10.1016/j.biotechadv.2019.107433] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 07/11/2019] [Accepted: 08/16/2019] [Indexed: 12/28/2022]
Abstract
A key challenge for domesticating alternative cultivable microorganisms with biotechnological potential lies in the development of innovative technologies. Within this framework, a myriad of genetic tools has flourished, allowing the design and manipulation of complex synthetic circuits and genomes to become the general rule in many laboratories rather than the exception. More recently, with the development of novel technologies such as DNA automated synthesis/sequencing and powerful computational tools, molecular biology has entered the synthetic biology era. In the beginning, most of these technologies were established in traditional microbial models (known as chassis in the synthetic biology framework) such as Escherichia coli and Saccharomyces cerevisiae, enabling fast advances in the field and the validation of fundamental proofs of concept. However, it soon became clear that these organisms, although extremely useful for prototyping many genetic tools, were not ideal for a wide range of biotechnological tasks due to intrinsic limitations in their molecular/physiological properties. Over the last decade, researchers have been facing the great challenge of shifting from these model systems to non-conventional chassis with endogenous capacities for dealing with specific tasks. The key to address these issues includes the generation of narrow and broad host plasmid-based molecular tools and the development of novel methods for engineering genomes through homologous recombination systems, CRISPR/Cas9 and other alternative methods. Here, we address the most recent advances in plasmid-based tools for the construction of novel cell factories, including a guide for helping with "build-your-own" microbial host.
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Affiliation(s)
- Luísa Czamanski Nora
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil
| | - Cauã Antunes Westmann
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil
| | - María-Eugenia Guazzaroni
- Faculty of Philosophy, Science and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil
| | | | - Vijai Kumar Gupta
- ERA Chair of Green Chemistry, Department of Chemistry and Biotechnology, School of Science, Tallinn University of Technology, 12618 Tallinn, Estonia
| | - Rafael Silva-Rocha
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil.
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Liu S, Xiao H, Zhang F, Lu Z, Zhang Y, Deng A, Li Z, Yang C, Wen T. A seamless and iterative DNA assembly method named PS-Brick and its assisted metabolic engineering for threonine and 1-propanol production. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:180. [PMID: 31338122 PMCID: PMC6628500 DOI: 10.1186/s13068-019-1520-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 07/03/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND DNA assembly is an essential technique enabling metabolic engineering and synthetic biology. Combining novel DNA assembly technologies with rational metabolic engineering can facilitate the construction of microbial cell factories. Amino acids and derived biochemicals are important products in industrial biotechnology with wide application and huge markets. DNA assembly scenarios encountered in metabolic engineering for the construction of amino acid and related compound producers, such as design-build-test-learn cycles, construction of precise genetic circuits and repetitive DNA molecules, usually require for iterative, scarless and repetitive sequence assembly methods, respectively. RESULTS Restriction endonuclease (RE)-assisted strategies constitute one of the major categories of DNA assembly. Here, we developed a Type IIP and IIS RE-assisted method named PS-Brick that comprehensively takes advantage of the properties of PCR fragments and REs for iterative, seamless and repetitive sequence assembly. One round of PS-Brick reaction using purified plasmids and PCR fragments was accomplished within several hours, and transformation of the resultant reaction product from this PS-Brick assembly reaction exhibited high efficiency (104-105 CFUs/µg DNA) and high accuracy (~ 90%). An application of metabolic engineering to threonine production, including the release of feedback regulation, elimination of metabolic bottlenecks, intensification of threonine export and inactivation of threonine catabolism, was stepwise resolved in E. coli by rounds of "design-build-test-learn" cycles through the iterative PS-Brick paradigm, and 45.71 g/L threonine was obtained through fed-batch fermentation. In addition to the value of the iterative character of PS-Brick for sequential strain engineering, seamless cloning enabled precise in-frame fusion for codon saturation mutagenesis and bicistronic design, and the repetitive sequence cloning ability of PS-Brick enabled construction of tandem CRISPR sgRNA arrays for genome editing. Moreover, the heterologous pathway deriving 1-propanol pathway from threonine, composed of Lactococcus lactis kivD and Saccharomyces cerevisiae ADH2, was assembled by one cycle of PS-Brick, resulting in 1.35 g/L 1-propanol in fed-batch fermentation. CONCLUSIONS To the best of our knowledge, the PS-Brick framework is the first RE-assisted DNA assembly method using the strengths of both Type IIP and IIS REs. In this study, PS-Brick was demonstrated to be an efficient DNA assembly method for pathway construction and genome editing and was successfully applied in design-build-test-learn (DBTL) cycles of metabolic engineering for the production of threonine and threonine-derived 1-propanol. The PS-Brick presents a valuable addition to the current toolbox of synthetic biology and metabolic engineering.
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Affiliation(s)
- Shuwen Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Haihan Xiao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Fangfang Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- Institute of Physical Science and Information Technology, Anhui University, Hefei, 230039 China
| | - Zheng Lu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Yun Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Aihua Deng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Zhongcai Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Cui Yang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Tingyi Wen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049 China
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Theron CW, Berrios J, Steels S, Telek S, Lecler R, Rodriguez C, Fickers P. Expression of recombinant enhanced green fluorescent protein provides insight into foreign gene‐expression differences betweenMut+andMutSstrains ofPichia pastoris. Yeast 2019; 36:285-296. [DOI: 10.1002/yea.3388] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 03/04/2019] [Accepted: 03/19/2019] [Indexed: 12/13/2022] Open
Affiliation(s)
- Chrispian W. Theron
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, Gembloux AgroBio TechUniversity of Liège Gembloux Belgium
| | - Julio Berrios
- Escuela de Ingeniería BioquímicaPontificia Universidad Católica de Valparaíso Valparaíso Chile
| | - Sébastien Steels
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, Gembloux AgroBio TechUniversity of Liège Gembloux Belgium
| | - Samuel Telek
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, Gembloux AgroBio TechUniversity of Liège Gembloux Belgium
| | | | | | - Patrick Fickers
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, Gembloux AgroBio TechUniversity of Liège Gembloux Belgium
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Rajkumar AS, Varela JA, Juergens H, Daran JMG, Morrissey JP. Biological Parts for Kluyveromyces marxianus Synthetic Biology. Front Bioeng Biotechnol 2019; 7:97. [PMID: 31134195 PMCID: PMC6515861 DOI: 10.3389/fbioe.2019.00097] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 04/16/2019] [Indexed: 11/13/2022] Open
Abstract
Kluyveromyces marxianus is a non-conventional yeast whose physiology and metabolism lends itself to diverse biotechnological applications. While the wild-type yeast is already in use for producing fragrances and fermented products, the lack of standardised tools for its genetic and metabolic engineering prevent it from being used as a next-generation cell factory for bio-based chemicals. In this paper, we bring together and characterise a set of native K. marxianus parts for the expression of multiple genes for metabolic engineering and synthetic biology. All parts are cloned and stored according to the MoClo/Yeast Tool Kit standard for quick sharing and rapid construction. Using available genomic and transcriptomic data, we have selected promoters and terminators to fine-tune constitutive and inducible gene expression. The collection includes a number of known centromeres and autonomously replication sequences (ARS). We also provide a number of chromosomal integration sites selected for efficiency or visible phenotypes for rapid screening. Finally, we provide a single-plasmid CRISPR/Cas9 platform for genome engineering and facilitated gene targeting, and rationally create auxotrophic strains to expand the common range of selection markers available to K. marxianus. The curated and characterised tools we have provided in this kit will serve as a base to efficiently build next-generation cell factories from this alternative yeast. Plasmids containing all parts are available at Addgene for public distribution.
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Affiliation(s)
- Arun S Rajkumar
- School of Microbiology, Centre for Synthetic Biology and Biotechnology, Environmental Research Institute, APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Javier A Varela
- School of Microbiology, Centre for Synthetic Biology and Biotechnology, Environmental Research Institute, APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Hannes Juergens
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Jean-Marc G Daran
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - John P Morrissey
- School of Microbiology, Centre for Synthetic Biology and Biotechnology, Environmental Research Institute, APC Microbiome Institute, University College Cork, Cork, Ireland
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Velastegui E, Theron C, Berrios J, Fickers P. Downregulation by organic nitrogen of AOX1 promoter used for controlled expression of foreign genes in the yeast Pichia pastoris. Yeast 2019; 36:297-304. [PMID: 30699241 DOI: 10.1002/yea.3381] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 01/14/2019] [Accepted: 01/23/2019] [Indexed: 01/18/2023] Open
Abstract
Pichia pastoris is a well-established cell factory for recombinant protein synthesis. Various optimization strategies of processes based on AOX1 promoter have been investigated, including methanol co-feeding with glycerol or sorbitol during the induction stage. Compared with carbon sources, comparatively little research has been devoted to the effects of nitrogen sources. Several reports have described the benefits of adding casamino acids (CA) to the recombinant protein production medium, however, without considering its effects at the gene expression level. Using enhanced green fluorescent protein as a reporter protein, monitored using flow cytometry, CA was shown to downregulate AOX1 promoter induction. Despite higher growth rates, cultures containing CA exhibited slower transition to the induced state, whereas metabolite analysis revealed that methanol consumption was reduced in the presence of CA compared with its absence. The repressive effect of CA was further confirmed by analysing the synthesis of extracellular recombinant Candida antarctica lipase under control of the AOX1 promoter. These findings highlight nitrogen source selection as an important consideration for AOX1-based protein production.
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Affiliation(s)
- Edgar Velastegui
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Chrispian Theron
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, Gembloux Agro Bio Tech, University of Liege, Gembloux, Belgium
| | - Julio Berrios
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Patrick Fickers
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, Gembloux Agro Bio Tech, University of Liege, Gembloux, Belgium
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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: 18] [Impact Index Per Article: 3.6] [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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Brown AJ, Gibson SJ, Hatton D, Arnall CL, James DC. Whole synthetic pathway engineering of recombinant protein production. Biotechnol Bioeng 2018; 116:375-387. [DOI: 10.1002/bit.26855] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 09/14/2018] [Accepted: 10/18/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Adam J. Brown
- Department of Chemical and Biological EngineeringUniversity of SheffieldSheffield UK
| | | | - Diane Hatton
- Biopharmaceutical Development, MedImmuneCambridge UK
| | - Claire L. Arnall
- Department of Chemical and Biological EngineeringUniversity of SheffieldSheffield UK
| | - David C. James
- Department of Chemical and Biological EngineeringUniversity of SheffieldSheffield UK
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