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Smith M, Hernández JS, Messing S, Ramakrishnan N, Higgins B, Mehalko J, Perkins S, Wall VE, Grose C, Frank PH, Cregger J, Le PV, Johnson A, Sherekar M, Pagonis M, Drew M, Hong M, Widmeyer SRT, Denson JP, Snead K, Poon I, Waybright T, Champagne A, Esposito D, Jones J, Taylor T, Gillette W. Producing recombinant proteins in Vibrio natriegens. Microb Cell Fact 2024; 23:208. [PMID: 39049057 PMCID: PMC11267860 DOI: 10.1186/s12934-024-02455-5] [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: 03/27/2024] [Accepted: 06/08/2024] [Indexed: 07/27/2024] Open
Abstract
The diversity of chemical and structural attributes of proteins makes it inherently difficult to produce a wide range of proteins in a single recombinant protein production system. The nature of the target proteins themselves, along with cost, ease of use, and speed, are typically cited as major factors to consider in production. Despite a wide variety of alternative expression systems, most recombinant proteins for research and therapeutics are produced in a limited number of systems: Escherichia coli, yeast, insect cells, and the mammalian cell lines HEK293 and CHO. Recent interest in Vibrio natriegens as a new bacterial recombinant protein expression host is due in part to its short doubling time of ≤ 10 min but also stems from the promise of compatibility with techniques and genetic systems developed for E. coli. We successfully incorporated V. natriegens as an additional bacterial expression system for recombinant protein production and report improvements to published protocols as well as new protocols that expand the versatility of the system. While not all proteins benefit from production in V. natriegens, we successfully produced several proteins that were difficult or impossible to produce in E. coli. We also show that in some cases, the increased yield is due to higher levels of properly folded protein. Additionally, we were able to adapt our enhanced isotope incorporation methods for use with V. natriegens. Taken together, these observations and improvements allowed production of proteins for structural biology, biochemistry, assay development, and structure-based drug design in V. natriegens that were impossible and/or unaffordable to produce in E. coli.
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Affiliation(s)
- Matthew Smith
- Protein Expression Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - José Sánchez Hernández
- Protein Expression Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Simon Messing
- Protein Expression Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Nitya Ramakrishnan
- Protein Expression Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Brianna Higgins
- Protein Expression Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Jennifer Mehalko
- Protein Expression Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Shelley Perkins
- Protein Expression Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Vanessa E Wall
- Protein Expression Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Carissa Grose
- Protein Expression Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Peter H Frank
- Protein Expression Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Julia Cregger
- Protein Expression Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Phuong Vi Le
- Protein Expression Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Adam Johnson
- Protein Expression Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Mukul Sherekar
- Protein Expression Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Morgan Pagonis
- Protein Expression Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Matt Drew
- Protein Expression Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Min Hong
- Protein Expression Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Stephanie R T Widmeyer
- Protein Expression Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - John-Paul Denson
- Protein Expression Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Kelly Snead
- Protein Expression Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Ivy Poon
- Protein Expression Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Timothy Waybright
- NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Allison Champagne
- Protein Expression Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Dominic Esposito
- Protein Expression Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Jane Jones
- Protein Expression Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Troy Taylor
- Protein Expression Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - William Gillette
- Protein Expression Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA.
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Li H, Zhang J, Wang Z, Shi P, Shi C. Genetically encoded site-specific 19F unnatural amino acid incorporation in V. natriegens for in-cell NMR analysis. Protein Expr Purif 2024; 219:106461. [PMID: 38460621 DOI: 10.1016/j.pep.2024.106461] [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: 11/25/2023] [Revised: 01/22/2024] [Accepted: 02/29/2024] [Indexed: 03/11/2024]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy NMR is a well-established technique for probing protein structure, dynamics and conformational changes. Taking advantage of the high signal sensitivity and broad chemical shift range of 19F nuclei, 19F NMR has been applied to investigate protein function at atomic resolution. In this report, we extend the unnatural amino acid site-specific incorporation into V. natriegens, an alternate protein expression system. The unnatural amino acid L-4-trifluoromethylphenylalanine (tfmF) was site-specifically introduced into the mitogen-activated protein kinase MEKK3 in V. natriegens using genetically encoded technology, which will be an extensive method for in-cell protein structure and dynamic investigation.
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Affiliation(s)
- Hao Li
- Anhui Vocational and Technical College, Hefei, Anhui, 230011, PR China; Hefei National Research Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, 230027, PR China.
| | - Jin Zhang
- Hefei National Research Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, 230027, PR China
| | - Zilong Wang
- Hefei National Research Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, 230027, PR China
| | - Pan Shi
- Hefei National Research Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, 230027, PR China
| | - Chaowei Shi
- Hefei National Research Center for Interdisciplinary Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, 230027, PR China.
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Schulze C, Hädrich M, Borger J, Rühmann B, Döring M, Sieber V, Thoma F, Blombach B. Investigation of exopolysaccharide formation and its impact on anaerobic succinate production with Vibrio natriegens. Microb Biotechnol 2024; 17:e14277. [PMID: 37256270 PMCID: PMC10832516 DOI: 10.1111/1751-7915.14277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/16/2023] [Indexed: 06/01/2023] Open
Abstract
Vibrio natriegens is an emerging host for biotechnology due to its high growth and substrate consumption rates. In industrial processes typically fed-batch processes are applied to obtain high space-time yields. In this study, we established an aerobic glucose-limited fed-batch fermentation with the wild type (wt) of V. natriegens which yielded biomass concentrations of up to 28.4 gX L-1 . However, we observed that the viscosity of the culture broth increased by a factor of 800 at the end of the cultivation due to the formation of 157 ± 20 mg exopolysaccharides (EPS) L-1 . Analysis of the genomic repertoire revealed several genes and gene clusters associated with EPS formation. Deletion of the transcriptional regulator cpsR in V. natriegens wt did not reduce EPS formation, however, it resulted in a constantly low viscosity of the culture broth and altered the carbohydrate content of the EPS. A mutant lacking the cps cluster secreted two-fold less EPS compared to the wt accompanied by an overall low viscosity and a changed EPS composition. When we cultivated the succinate producer V. natriegens Δlldh Δdldh Δpfl Δald Δdns::pycCg (Succ1) under anaerobic conditions on glucose, we also observed an increased viscosity at the end of the cultivation. Deletion of cpsR and the cps cluster in V. natriegens Succ1 reduced the viscosity five- to six-fold which remained at the same level observed at the start of the cultivation. V. natriegens Succ1 ΔcpsR and V. natriegens Succ1 Δcps achieved final succinate concentrations of 51 and 46 g L-1 with a volumetric productivity of 8.5 and 7.7 gSuc L-1 h-1 , respectively. Both strains showed a product yield of about 1.4 molSuc molGlc -1 , which is 27% higher compared with that of V. natriegens Succ1 and corresponds to 81% of the theoretical maximum.
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Affiliation(s)
- Clarissa Schulze
- Microbial Biotechnology, Campus Straubing for Biotechnology and SustainabilityTechnical University of MunichStraubingGermany
| | - Maurice Hädrich
- Microbial Biotechnology, Campus Straubing for Biotechnology and SustainabilityTechnical University of MunichStraubingGermany
| | - Jennifer Borger
- Microbial Biotechnology, Campus Straubing for Biotechnology and SustainabilityTechnical University of MunichStraubingGermany
| | - Broder Rühmann
- Chemistry of Biogenic Resources, Campus Straubing for Biotechnology and SustainabilityTechnical University of MunichStraubingGermany
| | - Manuel Döring
- Chemistry of Biogenic Resources, Campus Straubing for Biotechnology and SustainabilityTechnical University of MunichStraubingGermany
| | - Volker Sieber
- Chemistry of Biogenic Resources, Campus Straubing for Biotechnology and SustainabilityTechnical University of MunichStraubingGermany
- SynBiofoundry@TUMTechnical University of MunichStraubingGermany
| | - Felix Thoma
- Microbial Biotechnology, Campus Straubing for Biotechnology and SustainabilityTechnical University of MunichStraubingGermany
- SynBiofoundry@TUMTechnical University of MunichStraubingGermany
| | - Bastian Blombach
- Microbial Biotechnology, Campus Straubing for Biotechnology and SustainabilityTechnical University of MunichStraubingGermany
- SynBiofoundry@TUMTechnical University of MunichStraubingGermany
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Brück P, Wasser D, Soppa J. Ploidy in Vibrio natriegens: Very Dynamic and Rapidly Changing Copy Numbers of Both Chromosomes. Genes (Basel) 2023; 14:1437. [PMID: 37510340 PMCID: PMC10379091 DOI: 10.3390/genes14071437] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 07/05/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Vibrio natriegens is the fastest-growing bacterium, with a doubling time of approximately 12-14 min. It has a high potential for basic research and biotechnological applications, e.g., it can be used for the cell-free production of (labeled) heterologous proteins, for synthetic biological applications, and for the production of various compounds. However, the ploidy level in V. natriegens remains unknown. At nine time points throughout the growth curve, we analyzed the numbers of origins and termini of both chromosomes with qPCR and the relative abundances of all genomic sites with marker frequency analyses. During the lag phase until early exponential growth, the origin copy number and origin/terminus ratio of chromosome 1 increased severalfold, but the increase was lower for chromosome 2. This increase was paralleled by an increase in cell volume. During the exponential phase, the origin/terminus ratio and cell volume decreased again. This highly dynamic and fast regulation has not yet been described for any other species. In this study, the gene dosage increase in origin-adjacent genes during the lag phase is discussed together with the nonrandom distribution of genes on the chromosomes of V. natriegens. Taken together, the results of this study provide the first comprehensive overview of the chromosome dynamics in V. natriegens and will guide the optimization of molecular biological characterization and biotechnological applications.
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Affiliation(s)
- Patrik Brück
- Institute for Molecular Biosciences, Goethe University, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany
| | - Daniel Wasser
- Institute for Molecular Biosciences, Goethe University, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany
| | - Jörg Soppa
- Institute for Molecular Biosciences, Goethe University, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany
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