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Martinusen SG, Slaton EW, Nelson SE, Pulgar MA, Besu JT, Simas CF, Denard CA. Modular and integrative activity reporters enhance biochemical studies in the yeast ER. Protein Eng Des Sel 2024; 37:gzae008. [PMID: 38696722 DOI: 10.1093/protein/gzae008] [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: 07/13/2023] [Revised: 03/31/2024] [Accepted: 05/01/2024] [Indexed: 05/04/2024] Open
Abstract
The yeast endoplasmic reticulum sequestration and screening (YESS) system is a broadly applicable platform to perform high-throughput biochemical studies of post-translational modification enzymes (PTM-enzymes). This system enables researchers to profile and engineer the activity and substrate specificity of PTM-enzymes and to discover inhibitor-resistant enzyme mutants. In this study, we expand the capabilities of YESS by transferring its functional components to integrative plasmids. The YESS integrative system yields uniform protein expression and protease activities in various configurations, allows one to integrate activity reporters at two independent loci and to split the system between integrative and centromeric plasmids. We characterize these integrative reporters with two viral proteases, Tobacco etch virus (TEVp) and 3-chymotrypsin like protease (3CLpro), in terms of coefficient of variance, signal-to-noise ratio and fold-activation. Overall, we provide a framework for chromosomal-based studies that is modular, enabling rigorous high-throughput assays of PTM-enzymes in yeast.
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Affiliation(s)
| | - Ethan W Slaton
- Department of Chemical Engineering, University of Florida, Gainesville, 32611, USA
| | - Sage E Nelson
- Department of Chemical Engineering, University of Florida, Gainesville, 32611, USA
| | - Marian A Pulgar
- Department of Chemical Engineering, University of Florida, Gainesville, 32611, USA
| | - Julia T Besu
- Department of Biology, University of Florida, Gainesville, 32611, USA
| | - Cassidy F Simas
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, 32611, USA
| | - Carl A Denard
- Department of Chemical Engineering, University of Florida, Gainesville, 32611, USA
- UF Health Cancer Center, University of Florida, Gainesville, 32611, USA
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2
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Yogarajah T, Chu JJH. Construction of Infectious Clones for Human Enteroviruses. Methods Mol Biol 2024; 2733:155-174. [PMID: 38064032 DOI: 10.1007/978-1-0716-3533-9_10] [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: 12/18/2023]
Abstract
The infectious clone has been constructed for years via various mechanisms using reverse genetics of viral RNA into cDNA. The mechanism of construction has evolved to DNA-launch plasmids which simplify infectious clone manipulation and expression in mammalian cells. Infectious clones have enormously allowed manipulation of the enterovirus genome to discover antivirals, viral replication mechanisms, and functions of essential viral proteins. Here we will be discussing methods for the production of DNA-launch human enterovirus infectious clones and viral genome engineered with a fluorescent reporter gene.
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Affiliation(s)
- Thinesshwary Yogarajah
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore, Singapore
| | - Justin Jang Hann Chu
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System, Singapore, Singapore.
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3
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Martinusen SG, Slaton EW, Nelson SE, Pulgar MA, Besu JT, Simas CF, Denard CA. Modular and integrative activity reporters enhance biochemical studies in the yeast ER. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.12.548713. [PMID: 37502857 PMCID: PMC10369952 DOI: 10.1101/2023.07.12.548713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The yeast endoplasmic reticulum sequestration and screening (YESS) system is a generalizable platform that has become highly useful to investigate post-translational modification enzymes (PTM-enzymes). This system enables researchers to profile and engineer the activity and substrate specificity of PTM-enzymes and to discover inhibitor-resistant enzyme mutants. In this study, we expand the capabilities of YESS by transferring its functional components to integrative plasmids. The YESS integrative system yields uniform protein expression and protease activities in various configurations, allows one to integrate activity reporters at two independent loci and to split the system between integrative and centromeric plasmids. We characterize these integrative reporters with two viral proteases, Tobacco etch virus (TEVp) and 3-chymotrypsin like protease (3CL pro ), in terms of coefficient of variance, signal-to-noise ratio and fold-activation. Overall, we provide a framework for chromosomal-based studies that is modular, enabling rigorous high-throughput assays of PTM-enzymes in yeast.
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4
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Cleveland JD, Taslimi A, Liu Q, Van Keuren AM, Churchill MEA, Tucker CL. Reprogramming the Cleavage Specificity of Botulinum Neurotoxin Serotype B1. ACS Synth Biol 2022; 11:3318-3329. [PMID: 36153971 PMCID: PMC9907380 DOI: 10.1021/acssynbio.2c00235] [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] [Indexed: 01/24/2023]
Abstract
Proteases with reprogrammed specificity for nonnative substrates are highly desired in synthetic biology and biomedicine. However, generating reprogrammed proteases that are orthogonal and highly specific for a new target has been a major challenge. In this work, we sought to expand the versatility of protease systems by engineering an orthogonal botulinum neurotoxin serotype B (BoNT/B) protease that recognizes an orthogonal substrate. We designed and validated an orthogonal BoNT/B protease system in mammalian cells, combining mutations in the protease with compensatory mutations in the protease substrate and incorporating a truncated target sequence and then demonstrated use of this orthogonal BoNT/B protease-substrate combination to regulate complex transcriptional circuitry in mammalian cells. Transposing this platform into yeast, we demonstrated utility of this approach for in vivo protease evolution. We tested this platform with the newly designed orthogonal protease and then used it in a high-throughput screen to identify novel orthogonal protease/protease substrate combinations. While carrying out this work, we also generated new cleavage reporters that could be used to report botulinum toxin protease activity in mammalian cells using simple fluorescent readouts. We envision that these approaches will expand the applications of botulinum protease in new directions and aid in the development of new reprogrammed proteases.
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Affiliation(s)
- Joseph D. Cleveland
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045 USA
| | - Amir Taslimi
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045 USA
| | - Qi Liu
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045 USA
| | - Anna M. Van Keuren
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045 USA
| | - Mair E. A. Churchill
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045 USA
| | - Chandra L. Tucker
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045 USA
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5
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Dyer RP, Weiss GA. Making the cut with protease engineering. Cell Chem Biol 2021; 29:177-190. [PMID: 34921772 PMCID: PMC9127713 DOI: 10.1016/j.chembiol.2021.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 07/30/2021] [Accepted: 11/29/2021] [Indexed: 12/30/2022]
Abstract
Proteases cut with enviable precision and regulate diverse molecular events in biology. Such qualities drive a seemingly inexhaustible appetite for proteases with new activities and capabilities. Comprising 25% of the total industrial enzyme market, proteases appear in consumer goods, such as detergents, textile processing, and numerous foods; additionally, proteases include 25 US Food and Drug Administration-approved medicines and various research tools. Recent advances in protease engineering strategies address target specificity, catalytic efficiency, and stability. This guide to protease engineering surveys best practices and emerging strategies. We further highlight gaps and flexibilities inherent to each system that suggest opportunities for new technology development along with engineered proteases to solve challenges in proteomics, protein sequencing, and synthetic gene circuits.
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Affiliation(s)
- Rebekah P Dyer
- Department of Molecular Biology and Biochemistry, University of California, Irvine, 1102 NS-2, Irvine, CA 92697-2025, USA
| | - Gregory A Weiss
- Department of Chemistry, University of California, Irvine, 1102 NS-2, Irvine, CA 92697-2025, USA; Department of Molecular Biology and Biochemistry, University of California, Irvine, 1102 NS-2, Irvine, CA 92697-2025, USA; Department of Pharmaceutical Sciences, University of California, Irvine, 1102 NS-2, Irvine, CA 92697-2025, USA.
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7
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Blum TR, Liu H, Packer MS, Xiong X, Lee PG, Zhang S, Richter M, Minasov G, Satchell KJF, Dong M, Liu DR. Phage-assisted evolution of botulinum neurotoxin proteases with reprogrammed specificity. Science 2021; 371:803-810. [PMID: 33602850 DOI: 10.1126/science.abf5972] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 12/24/2020] [Indexed: 12/14/2022]
Abstract
Although bespoke, sequence-specific proteases have the potential to advance biotechnology and medicine, generation of proteases with tailor-made cleavage specificities remains a major challenge. We developed a phage-assisted protease evolution system with simultaneous positive and negative selection and applied it to three botulinum neurotoxin (BoNT) light-chain proteases. We evolved BoNT/X protease into separate variants that preferentially cleave vesicle-associated membrane protein 4 (VAMP4) and Ykt6, evolved BoNT/F protease to selectively cleave the non-native substrate VAMP7, and evolved BoNT/E protease to cleave phosphatase and tensin homolog (PTEN) but not any natural BoNT protease substrate in neurons. The evolved proteases display large changes in specificity (218- to >11,000,000-fold) and can retain their ability to form holotoxins that self-deliver into primary neurons. These findings establish a versatile platform for reprogramming proteases to selectively cleave new targets of therapeutic interest.
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Affiliation(s)
- Travis R Blum
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Hao Liu
- Department of Urology, Boston Children's Hospital, Boston, MA 02115, USA.,Department of Microbiology and Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - Michael S Packer
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Xiaozhe Xiong
- Department of Urology, Boston Children's Hospital, Boston, MA 02115, USA.,Department of Microbiology and Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - Pyung-Gang Lee
- Department of Urology, Boston Children's Hospital, Boston, MA 02115, USA.,Department of Microbiology and Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - Sicai Zhang
- Department of Urology, Boston Children's Hospital, Boston, MA 02115, USA.,Department of Microbiology and Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - Michelle Richter
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - George Minasov
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Karla J F Satchell
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Min Dong
- Department of Urology, Boston Children's Hospital, Boston, MA 02115, USA. .,Department of Microbiology and Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. .,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
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8
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Segreto R, Deigin Y, McCairn K, Sousa A, Sirotkin D, Sirotkin K, Couey JJ, Jones A, Zhang D. Should we discount the laboratory origin of COVID-19? ENVIRONMENTAL CHEMISTRY LETTERS 2021; 19:2743-2757. [PMID: 33786037 PMCID: PMC7993900 DOI: 10.1007/s10311-021-01211-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Affiliation(s)
- Rossana Segreto
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
| | | | | | - Alejandro Sousa
- Regional Hospital of Monforte, Lugo, Spain
- University of Santiago de Compostela, Santiago, Spain
| | | | | | | | - Adrian Jones
- Independent Bioinformatics Researcher, Melbourne, Australia
| | - Daoyu Zhang
- Independent Genetics Researcher, Sydney, Australia
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