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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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Wang JY(J, Khmelinskaia A, Sheffler W, Miranda MC, Antanasijevic A, Borst AJ, Torres SV, Shu C, Hsia Y, Nattermann U, Ellis D, Walkey C, Ahlrichs M, Chan S, Kang A, Nguyen H, Sydeman C, Sankaran B, Wu M, Bera AK, Carter L, Fiala B, Murphy M, Baker D, Ward AB, King NP. Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains. Proc Natl Acad Sci U S A 2023; 120:e2214556120. [PMID: 36888664 PMCID: PMC10089191 DOI: 10.1073/pnas.2214556120] [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: 08/26/2022] [Accepted: 02/03/2023] [Indexed: 03/09/2023] Open
Abstract
Computationally designed protein nanoparticles have recently emerged as a promising platform for the development of new vaccines and biologics. For many applications, secretion of designed nanoparticles from eukaryotic cells would be advantageous, but in practice, they often secrete poorly. Here we show that designed hydrophobic interfaces that drive nanoparticle assembly are often predicted to form cryptic transmembrane domains, suggesting that interaction with the membrane insertion machinery could limit efficient secretion. We develop a general computational protocol, the Degreaser, to design away cryptic transmembrane domains without sacrificing protein stability. The retroactive application of the Degreaser to previously designed nanoparticle components and nanoparticles considerably improves secretion, and modular integration of the Degreaser into design pipelines results in new nanoparticles that secrete as robustly as naturally occurring protein assemblies. Both the Degreaser protocol and the nanoparticles we describe may be broadly useful in biotechnological applications.
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Affiliation(s)
- Jing Yang (John) Wang
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA98195
| | - Alena Khmelinskaia
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
- Transdisciplinary Research Area “Building Blocks of Matter and Fundamental Interactions”, University of Bonn, 53113Bonn, Germany
- Life and Medical Sciences Institute, University of Bonn, 53121Bonn, Germany
| | - William Sheffler
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Marcos C. Miranda
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Aleksandar Antanasijevic
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA92037
- Scripps Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA92037
| | - Andrew J. Borst
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Susana V. Torres
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Chelsea Shu
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Yang Hsia
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Una Nattermann
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
- Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA98195
| | - Daniel Ellis
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA98195
| | - Carl Walkey
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Maggie Ahlrichs
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Sidney Chan
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Alex Kang
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Hannah Nguyen
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Claire Sydeman
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley Laboratory, Berkeley, CA94720
- Berkeley Center for Structural Biology, Lawrence Berkeley Laboratory, Berkeley, CA94720
| | - Mengyu Wu
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Asim K. Bera
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Brooke Fiala
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Michael Murphy
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Andrew B. Ward
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA92037
- Scripps Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA92037
| | - Neil P. King
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
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Wu Z, Basu S, Wu X, Kurgan L. qNABpredict: Quick, accurate, and taxonomy-aware sequence-based prediction of content of nucleic acid binding amino acids. Protein Sci 2023; 32:e4544. [PMID: 36519304 PMCID: PMC9798252 DOI: 10.1002/pro.4544] [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: 09/16/2022] [Revised: 12/07/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022]
Abstract
Protein sequence-based predictors of nucleic acid (NA)-binding include methods that predict NA-binding proteins and NA-binding residues. The residue-level tools produce more details but suffer high computational cost since they must predict every amino acid in the input sequence and rely on multiple sequence alignments. We propose an alternative approach that predicts content (fraction) of the NA-binding residues, offering more information than the protein-level prediction and much shorter runtime than the residue-level tools. Our first-of-its-kind content predictor, qNABpredict, relies on a small, rationally designed and fast-to-compute feature set that represents relevant characteristics extracted from the input sequence and a well-parametrized support vector regression model. We provide two versions of qNABpredict, a taxonomy-agnostic model that can be used for proteins of unknown taxonomic origin and more accurate taxonomy-aware models that are tailored to specific taxonomic kingdoms: archaea, bacteria, eukaryota, and viruses. Empirical tests on a low-similarity test dataset show that qNABpredict is 100 times faster and generates statistically more accurate content predictions when compared to the content extracted from results produced by the residue-level predictors. We also show that qNABpredict's content predictions can be used to improve results generated by the residue-level predictors. We release qNABpredict as a convenient webserver and source code at http://biomine.cs.vcu.edu/servers/qNABpredict/. This new tool should be particularly useful to predict details of protein-NA interactions for large protein families and proteomes.
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Affiliation(s)
- Zhonghua Wu
- School of Mathematical Sciences and LPMCNankai UniversityTianjinChina
| | - Sushmita Basu
- Department of Computer ScienceVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Xuantai Wu
- School of Mathematical Sciences and LPMCNankai UniversityTianjinChina
| | - Lukasz Kurgan
- Department of Computer ScienceVirginia Commonwealth UniversityRichmondVirginiaUSA
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Sieow BFL, De Sotto R, Seet ZRD, Hwang IY, Chang MW. Synthetic Biology Meets Machine Learning. Methods Mol Biol 2023; 2553:21-39. [PMID: 36227537 DOI: 10.1007/978-1-0716-2617-7_2] [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: 06/16/2023]
Abstract
This chapter outlines the myriad applications of machine learning (ML) in synthetic biology, specifically in engineering cell and protein activity, and metabolic pathways. Though by no means comprehensive, the chapter highlights several prominent computational tools applied in the field and their potential use cases. The examples detailed reinforce how ML algorithms can enhance synthetic biology research by providing data-driven insights into the behavior of living systems, even without detailed knowledge of their underlying mechanisms. By doing so, ML promises to increase the efficiency of research projects by modeling hypotheses in silico that can then be tested through experiments. While challenges related to training dataset generation and computational costs remain, ongoing improvements in ML tools are paving the way for smarter and more streamlined synthetic biology workflows that can be readily employed to address grand challenges across manufacturing, medicine, engineering, agriculture, and beyond.
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Affiliation(s)
- Brendan Fu-Long Sieow
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Graduate School for Integrative Sciences and Engineering Programme, National University of Singapore, Singapore, Singapore
| | - Ryan De Sotto
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Zhi Ren Darren Seet
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - In Young Hwang
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Matthew Wook Chang
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore.
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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