1
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Zhu M, Mori M, Hwa T, Dai X. Distantly related bacteria share a rigid proteome allocation strategy with flexible enzyme kinetics. Proc Natl Acad Sci U S A 2025; 122:e2427091122. [PMID: 40299698 PMCID: PMC12067254 DOI: 10.1073/pnas.2427091122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2024] [Accepted: 03/21/2025] [Indexed: 05/01/2025] Open
Abstract
Bacteria are known to allocate their proteomes according to how fast they grow, and the allocation strategies employed strongly affect bacterial adaptation to different environments. Much of what is currently known about proteome allocation is based on extensive studies of the model organism Escherichia coli. It is not clear how much of E. coli's proteome allocation strategy is applicable to other species, particularly since different species can grow at vastly different rates even in the same growth condition. In this study, we investigate differences in nutrient-dependent proteome allocation programs adopted by several distantly related bacterial species, including Vibrio natriegens, one of the fastest-growing bacteria known. Extensive quantitative proteome characterization across conditions reveals an invariant allocation program in response to changing nutrients despite systemic, species-specific differences in enzyme kinetics. This invariant program is not organized according to the growth rate but is based on a common internal metric of nutrient quality after scaling away species-specific differences in enzyme kinetics, with the faster species behaving as if it is growing under a higher temperature. The flexibility of enzyme kinetics and the rigidity of proteome allocation programs across species defy common notions of evolvability and resource optimization. Our results suggest the existence of a blueprint of proteome allocation shared by diverse bacterial species, with implications on common underlying regulatory strategies. Further knowledge on the existence and organization of such phylogeny-transcending relations also promises to simplify the bottom-up description and understanding of bacterial behaviors in ecological communities.
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Affiliation(s)
- Manlu Zhu
- State Key Laboratory of Green Pesticides, Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Department of Microbiology, School of Life Sciences, Central China Normal University, Wuhan430079, China
| | - Matteo Mori
- Department of Physics, University of California, San Diego, La Jolla, CA92093-0319
| | - Terence Hwa
- Department of Physics, University of California, San Diego, La Jolla, CA92093-0319
| | - Xiongfeng Dai
- State Key Laboratory of Green Pesticides, Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Department of Microbiology, School of Life Sciences, Central China Normal University, Wuhan430079, China
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2
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Pu N, Wang MR, Li Y, Li ZJ. Metabolic engineering of Salinivibrio sp. TGB10 for PHBV biosynthesis with a high 3-hydroxyvalerate fraction from starch and propionate. Int J Biol Macromol 2025; 308:142359. [PMID: 40120916 DOI: 10.1016/j.ijbiomac.2025.142359] [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: 11/05/2024] [Revised: 12/26/2024] [Accepted: 03/19/2025] [Indexed: 03/25/2025]
Abstract
Polyhydroxyalkanoates (PHA) are environmentally friendly biopolymers that have the potential to replace non-degradable plastics, yet large-scale industrial PHA production remains unattainable due to their high costs. Halophilic bacteria capable of growing under high-salt conditions are regarded as novel hosts for the economical production of PHA. Salinivibrio sp. TGB10, a moderately halophilic bacterium, efficiently accumulates poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) using glucose and propionate as substrates. The genetic engineering of Salinivibrio species has not been reported due to the lack of molecular biology tools. Here, Salinivibrio sp. TGB10 was metabolically engineered using bacterial conjugation and gene knockout strategies based on markerless genomic DNA replacement. Through this approach, deletion of the native 2-methylcitrate synthase gene (prpC) increased the 3-hydroxyvalerate (3 HV) monomer content in the PHBV copolymer to nearly 90 mol%. Furthermore, the heterologous expression of a NaCl-tolerant amylase from Vibrio alginolyticus enabled efficient starch utilization, resulting in a PHBV titer of 3.35 g/L with 77.89 mol% 3 HV when starch and propionate were used as carbon sources. To the best of our knowledge, this is the first study to report the metabolic engineering of the Salinivibrio genus. The resulted Salinivibrio strains demonstrate significant potential for industrial production of PHBV with a high 3 HV composition.
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Affiliation(s)
- Nan Pu
- State Key Laboratory of Green Biomanufacturing, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Meng-Ru Wang
- State Key Laboratory of Green Biomanufacturing, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yanjie Li
- State Key Laboratory of Green Biomanufacturing, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Zheng-Jun Li
- State Key Laboratory of Green Biomanufacturing, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.
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3
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Zheng S, Zhao C, Chen Y, Zhang Z, He Y, Wang J, He H, Chen GQ. Engineered Vibrio natriegens with a Toxin-Antitoxin System for High-Productivity Biotransformation of l-Lysine to Cadaverine. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2025; 73:6113-6123. [PMID: 39985470 DOI: 10.1021/acs.jafc.4c12616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2025]
Abstract
Vibrio natriegens, a fast-growing bacterium, is an emerging chassis of next-generation industrial biotechnology capable of thriving under open and continuous culture conditions. Cadaverine, a valuable industrial C5 platform chemical, has various chemical and biological activities. This study found that V. natriegens exhibited superior tolerance to lysine, the substrate of cadaverine production. For the first time, a cadaverine synthesis pathway was introduced into V. natriegens for whole-cell catalysis of cadaverine from lysine. A high-efficiency cadaverine-producing strain harboring a toxin-antitoxin system, V. natriegens (pSEVA341-pTac-ldcC-pHbpBC-hbpBC) with lysE (PN96_RS17440) inactivation, was constructed. In 7 L bioreactors, the cadaverine titer increased from 115 g/L in the original strain to 158 g/L within 11 h of biotransformation, exhibiting a 37% increase in production. Its productivity reached 14.4 g/L/h with a conversion rate as high as 90%. These results confirm V. natriegens as an exceptional chassis for effective cadaverine bioproduction.
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Affiliation(s)
- Shuang Zheng
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Cuihuan Zhao
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yuemeng Chen
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zonghao Zhang
- School of Life Sciences, Tsinghua University, Beijing 100084, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai Academy of Animal and Veterinary Sciences, Qinghai University, Xining 810000, China
| | - Yuhan He
- Key Lab of Industrial Biocatalysts of the Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Jiale Wang
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Hongtao He
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Guo-Qiang Chen
- School of Life Sciences, Tsinghua University, Beijing 100084, China
- Key Lab of Industrial Biocatalysts of the Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
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4
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Bai F, Tian H, Liu S. Sustainable pollution removal and resources recovery from electroplating wastewater by coagulation, advanced oxidation coupling with bioaugmentation. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2025; 377:124661. [PMID: 39983566 DOI: 10.1016/j.jenvman.2025.124661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2024] [Revised: 02/09/2025] [Accepted: 02/18/2025] [Indexed: 02/23/2025]
Abstract
Electroplating wastewater contains high concentrations of dissolved organic matter, heavy metal ions (HMs), refractory organic compounds (ROC), and the complicated composition of effluents. Bioaugmentation presents an efficient strategy for eliminating pollution and recycling resources from electroplating effluent. In this study, simultaneous removal of pollution and sustainable resources recovery from electroplating wastewater were conducted by polyferric sulfate (PFS)-based coagulation, ultraviolet (UV)-activated persulfate (PS) (UV-APS)-based advanced oxidation coupling with bioaugmentation. To reduce carbon emissions and achieve carbon neutrality, genetically engineered Vibrio natriegens with an aerobic sulfate reduction pathway (GeVin) was introduced to remove sulfate, organics, and HMs, which further promoted generation of metal sulfides. The results of coagulation by PFS eliminated 34.68% of chemical oxygen demand (COD), 38.56% of ammonia nitrogen (NH4-N), 36.30% of ROC, and 16.67% of HMs. The rest of refractory contaminants in the effluent of coagulation were oxidatively degraded by UV-APS to improve biodegradability index. The bioaugmentation using immobilized GeVin (IMGevin) coupled with membrane bioreactor (MBR) (IMGevin-MBR) significantly removed 98.25% of COD, 96.23% of NH4-N, 99.42% of biochemical oxygen demand (BOD), 97.85% of sulfate, and 97.68% of HMs. Mechanism analysis indicated that sulfate derived from PFS-based coagulation and UV-APS provided more electron acceptors to generate H2S metabolized by GeVin, contributing to HMs removal via sulfate reduction pathway. Furthermore, IMGeVin-MBR decreased startup phase, hydraulic retention time (HRT), increased the microbial activity, functional microbial community and abundances of genes related to sulfate metabolism, resulting in improvement of systemic stability. Meanwhile, IMGeVin-MBR decreased the total treatment cost, sludge yields, and greenhouse gas (GHG) emissions for treatment of electroplating wastewater. In conclusion, this study provides a sustainable pollution removal and resources recovery strategy for treating electroplating wastewater.
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Affiliation(s)
- Fuliang Bai
- School of Geographical Science, Harbin Normal University, Harbin, 150025, China.
| | - Hui Tian
- Heilongjiang Institute of Drug Control, Harbin, 150088, China
| | - Shuo Liu
- School of Geographical Science, Harbin Normal University, Harbin, 150025, China
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5
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Fryer T, Wolff DS, Overath MD, Schäfer E, Laustsen AH, Jenkins TP, Andersen C. Post-assembly Plasmid Amplification for Increased Transformation Yields in E. coli and S. cerevisiae. CHEM & BIO ENGINEERING 2025; 2:87-96. [PMID: 40041006 PMCID: PMC11873849 DOI: 10.1021/cbe.4c00115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2024] [Revised: 10/30/2024] [Accepted: 11/03/2024] [Indexed: 03/06/2025]
Abstract
Many biological disciplines rely upon the transformation of host cells with heterologous DNA to edit, engineer, or examine biological phenotypes. Transformation of model cell strains (Escherichia coli) under model conditions (electroporation of circular supercoiled plasmid DNA; typically pUC19) can achieve >1010 transformants/μg DNA. Yet outside of these conditions, e.g., work with relaxed plasmid DNA from in vitro assembly reactions (cloned DNA) or nonmodel organisms, the efficiency of transformation can drop by multiple orders of magnitude. Overcoming these inefficiencies requires cost- and time-intensive processes, such as generating large quantities of appropriately formatted input DNA or transforming many aliquots of cells in parallel. We sought to simplify the generation of large quantities of appropriately formatted input cloned DNA by using rolling circle amplification (RCA) and treatment with specific endonucleases to generate an efficiently transformable linear DNA product for in vivo circularization in host cells. We achieved an over 6500-fold increase in the yield of input DNA, and demonstrate that the use of a nicking endonuclease to generate homologous single-stranded ends increases the efficiency of E. coli chemical transformation compared to both linear DNA with double-stranded homologous ends and circular Golden-Gate assembly products. Meanwhile, the use of a restriction endonuclease to generate linear DNA with double-stranded homologous ends increases the efficiency of chemical and electrotransformation of Saccharomyces cerevisiae. Importantly, we also optimized the process such that both RCA and endonuclease treatment occur efficiently in the same buffer, streamlining the workflow and reducing product loss through purification steps. We expect that our approach could have utility beyond E. coli and S. cerevisiae and be applicable to areas such as directed evolution, genome engineering, and the manipulation of alternative organisms with even poorer transformation efficiencies.
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Affiliation(s)
- Thomas Fryer
- Department
of Biotechnology and Biomedicine, Technical
University of Denmark, Søltofts Plads 239, Lyngby, Hovedstaden DK 2800, Denmark
- Department
of Molecular Discovery, R&D, Novozymes
A/S, Bagsvaerd, Hovedstaden DK 2880, Denmark
| | - Darian S. Wolff
- Department
of Biotechnology and Biomedicine, Technical
University of Denmark, Søltofts Plads 239, Lyngby, Hovedstaden DK 2800, Denmark
- Department
of Molecular Discovery, R&D, Novozymes
A/S, Bagsvaerd, Hovedstaden DK 2880, Denmark
| | - Max D. Overath
- Department
of Biotechnology and Biomedicine, Technical
University of Denmark, Søltofts Plads 239, Lyngby, Hovedstaden DK 2800, Denmark
| | - Elena Schäfer
- Department
of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Andreas H. Laustsen
- Department
of Biotechnology and Biomedicine, Technical
University of Denmark, Søltofts Plads 239, Lyngby, Hovedstaden DK 2800, Denmark
| | - Timothy P. Jenkins
- Department
of Biotechnology and Biomedicine, Technical
University of Denmark, Søltofts Plads 239, Lyngby, Hovedstaden DK 2800, Denmark
| | - Carsten Andersen
- Department
of Molecular Discovery, R&D, Novozymes
A/S, Bagsvaerd, Hovedstaden DK 2880, Denmark
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6
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Renteln M. Targeting clonal mutations with synthetic microbes. Crit Rev Oncol Hematol 2025; 206:104572. [PMID: 39613236 DOI: 10.1016/j.critrevonc.2024.104572] [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: 08/29/2024] [Revised: 11/06/2024] [Accepted: 11/19/2024] [Indexed: 12/01/2024] Open
Abstract
Recently concluded, large-scale cancer genomics studies involving multiregion sequencing of primary tumors and paired metastases appear to indicate that many or most cancer patients have one or more "clonal" mutations in their tumors. Clonal mutations are those that are present in all of a patient's cancer cells. Clonally mutated proteins can potentially be targeted by inhibitors or E3 ligase small molecule glues, but developing new small molecule drugs for each patient is not feasible currently. Certain companies are using immunotherapies to target clonal mutations. I have devised another approach for exploiting clonal mutations, which I call "Oncolytic Vector Efficient Replication Contingent on Omnipresent Mutation Engagement" (OVERCOME). The ideal version of OVERCOME would likely employ a bioengineered facultative intracellular bacterium. The bacterium would initially be attenuated, but (transiently) reverse its attenuation upon clonal mutation detection.
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Affiliation(s)
- Michael Renteln
- The University of Southern California Keck School of Medicine, The United States.
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7
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Sun D, Li HH, Wu J, Wu J, Lin WQ, He RL, Liu DF, Li WW. Antibiotics-Free Steady Bioproduction of Valuable Chemicals from Organic Wastes by Engineered Vibrio natriegens through Targeted Gene Integration. ACS Synth Biol 2024; 13:4233-4244. [PMID: 39628126 DOI: 10.1021/acssynbio.4c00669] [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: 12/21/2024]
Abstract
Bioproduction of chemicals by using engineered bacteria is promising for a circular economy but challenged the instability of the introduced plasmid by conventional methods. Here, we developed a two-plasmid INTEGRET system to reliably integrate the targeted gene into the Vibrio natriegens genome, making it a powerful strain for efficient and steady bioproduction without requiring antibiotic addition. The INTEGRET system allows for gene insertion at over 75% inserting efficiency and flexibly controllable gene dosages. Additionally, simultaneous gene insertion at four genomic sites was achieved at 54.3% success rate while maintaining stable inheritance of exogenous sequences across multiple generations. The engineered strain could efficiently synthesize PHB from the fermentation of diverse organic wastes, with an efficiency comparable to those with overexpressed plasmid. When the mixture of seawater and molasses was used as the feedstock, it achieved a high PHB yield of 39.41 wt %. An extended application of the INTEGRET system for imparting the riboflavin production ability to the bacterium was also demonstrated. Our work presents a reliable and efficient genomic editing tool to facilitate the development of sustainable and environmentally benign biological platforms for converting biomass wastes into valuable chemicals.
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Affiliation(s)
- Dan Sun
- School of Life Sciences, University of Science & Technology of China, Hefei 230026, China
| | - Hui-Hui Li
- School of Life Sciences, University of Science & Technology of China, Hefei 230026, China
| | - Jing Wu
- School of Life Sciences, University of Science & Technology of China, Hefei 230026, China
| | - Jie Wu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science & Technology of China, Hefei 230026, China
- Institute of Advanced Technology, University of Science and Technology of China, Hefei 230000, China
| | - Wei-Qiang Lin
- School of Life Sciences, University of Science & Technology of China, Hefei 230026, China
| | - Ru-Li He
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science & Technology of China, Hefei 230026, China
- Institute of Advanced Technology, University of Science and Technology of China, Hefei 230000, China
| | - Dong-Feng Liu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science & Technology of China, Hefei 230026, China
| | - Wen-Wei Li
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science & Technology of China, Hefei 230026, China
- SEEM Innovation Center, Suzhou Institute for Advance Research of USTC, Suzhou 215123, China
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8
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Canellas ALB, de Oliveira Nithack Marques M, Lopes MV, Lage A, Klautau M, Muricy G, de Oliveira BFR, Laport MS. Functional and Genomic Insights into the Biotechnological Potential of Vibrio spp. Isolated from Deeply Polluted and Pristine Environments. Curr Microbiol 2024; 82:36. [PMID: 39661196 DOI: 10.1007/s00284-024-04013-z] [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: 09/13/2024] [Accepted: 11/28/2024] [Indexed: 12/12/2024]
Abstract
Vibrio spp. are remarkably diverse bacteria, being worthy of investigation not only for their antibiotic resistance and virulence, but also for their biotechnological potential. Indeed, there is increasing evidence that these bacteria display industrially relevant traits, particularly as producers of antimicrobial substances, tensioactive/emulsifying compounds, and enzymes. Here, our aim was to investigate the potential of Vibrio strains isolated from two different marine sources to produce such biotechnologically applicable substances. From the eighteen analyzed strains, five were isolated from plastic particles from a heavily polluted urban estuary and 13 from calcareous sponges inhabiting submarine caves in an isolated volcanic archipelago in the Atlantic Ocean. Enzymatic screening revealed that most strains were agarolytic and cellulolytic. Overall, six strains showed antimicrobial activity against Staphylococcus aureus ATCC 29,213, with four of them active towards Escherichia coli ATCC 25,922 as well. Additionally, eight strains were positive for the production of bioemulsifiers. Genomic analyses of four strains further revealed insights regarding the enzymatic arsenal, as shown by the detection of several key gene clusters pertaining to the chitin degradation pathway, and also encoding diverse classes of antimicrobial-active metabolites. Our findings highlight the biotechnological potential of Vibrio spp., evidencing their functional diversity and the need for continued and sustained prospecting of this bacterial genus to uncover its potential high-value-added bioproducts.
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Affiliation(s)
- Anna Luiza Bauer Canellas
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Cidade Universitária, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Matheus de Oliveira Nithack Marques
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Cidade Universitária, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Matheus Vieira Lopes
- TaxoN Laboratory, Departamento de Zoologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 792, Cidade Universitária, Rio de Janeiro, 21941-599, Brazil
| | - Anaíra Lage
- TaxoN Laboratory, Departamento de Zoologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 792, Cidade Universitária, Rio de Janeiro, 21941-599, Brazil
- Departamento de Invertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, s/nº, São Cristóvão, Rio de Janeiro, RJ, 20940-040, Brazil
| | - Michelle Klautau
- TaxoN Laboratory, Departamento de Zoologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 792, Cidade Universitária, Rio de Janeiro, 21941-599, Brazil
| | - Guilherme Muricy
- Departamento de Invertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, s/nº, São Cristóvão, Rio de Janeiro, RJ, 20940-040, Brazil
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro, RJ, 22460-030, Brazil
| | | | - Marinella Silva Laport
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Cidade Universitária, Rio de Janeiro, RJ, 21941-902, Brazil.
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Hädrich M, Schulze C, Hoff J, Blombach B. Vibrio natriegens: Application of a Fast-Growing Halophilic Bacterium. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2024. [PMID: 39527262 DOI: 10.1007/10_2024_271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2024]
Abstract
The fast growth accompanied with high substrate consumption rates and a versatile metabolism paved the way to exploit Vibrio natriegens as unconventional host for biotechnological applications. Meanwhile, a wealth of knowledge on the physiology, the metabolism, and the regulation in this halophilic marine bacterium has been gathered. Sophisticated genetic engineering tools and metabolic models are available and have been applied to engineer production strains and first chassis variants of V. natriegens. In this review, we update the current knowledge on the physiology and the progress in the development of synthetic biology tools and provide an overview of recent advances in metabolic engineering of this promising host. We further discuss future challenges to enhance the application range of V. natriegens.
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Affiliation(s)
- Maurice Hädrich
- Microbial Biotechnology, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Straubing, Germany
- SynBiofoundry@TUM, Technical University of Munich, Straubing, Germany
| | - Clarissa Schulze
- Microbial Biotechnology, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Straubing, Germany
| | - Josef Hoff
- Microbial Biotechnology, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Straubing, Germany
- SynBiofoundry@TUM, Technical University of Munich, Straubing, Germany
- Munich Institute of Integrated Materials, Energy and Process Engineering, Technical University of Munich, Garching, Germany
| | - Bastian Blombach
- Microbial Biotechnology, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Straubing, Germany.
- SynBiofoundry@TUM, Technical University of Munich, Straubing, Germany.
- Munich Institute of Integrated Materials, Energy and Process Engineering, Technical University of Munich, Garching, Germany.
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10
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Woo S, Han YH, Lee HK, Baek D, Noh MH, Han S, Lim HG, Jung GY, Seo SW. Generation of a Vibrio-based platform for efficient conversion of raffinose through Adaptive Laboratory Evolution on a solid medium. Metab Eng 2024; 86:300-307. [PMID: 39489215 DOI: 10.1016/j.ymben.2024.11.001] [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: 08/11/2024] [Revised: 10/07/2024] [Accepted: 11/01/2024] [Indexed: 11/05/2024]
Abstract
Raffinose, a trisaccharide abundantly found in soybeans, is a potential alternative carbon source for biorefineries. Nevertheless, residual intermediate di- or monosaccharides and low catabolic efficiency limit raffinose use through conventional microbial hosts. This study presents a Vibrio-based platform to convert raffinose efficiently. Vibrio sp. dhg was selected as the starting strain for the Adaptive Laboratory Evolution (ALE) strategy to leverage its significantly higher metabolic efficiency. We conducted ALE on a solid minimal medium supplemented with raffinose to prevent the enrichment of undesired phenotypes due to the shared effect of extracellular raffinose hydrolysis among multiple strains. As a result, we generated the VRA10 strain that efficiently utilizes raffinose without leaving behind degraded di- or monosaccharides, achieving a notable growth rate (0.40 h-1) and raffinose consumption rate (1.2 g/gdcw/h). Whole genome sequencing and reverse engineering identified that a missense mutation in the melB gene (encoding a melibiose/raffinose:sodium symporter) and the deletion of the two galR genes (encoding transcriptional repressors for galactose catabolism) facilitated rapid raffinose utilization. The further engineered strain produced 6.2 g/L of citramalate from 20 g/L of raffinose. This study will pave the way for the efficient utilization of diverse raffinose-rich byproducts and the expansion of alternative carbon streams in biorefinery applications.
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Affiliation(s)
- Sunghwa Woo
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea
| | - Yong Hee Han
- Interdisciplinary Program in Bioengineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea; School of Biological Sciences and Technology, Chonnam National University, Yongbong-ro 77, Gwangju, 61186, South Korea
| | - Hye Kyung Lee
- Division of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea
| | - Dongyeop Baek
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea
| | - Myung Hyun Noh
- Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), 406-30, Jonggaro, Junggu, Ulsan, 44429, South Korea
| | - Sukjae Han
- Interdisciplinary Program in Bioengineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Hyun Gyu Lim
- Department of Biological Sciences and Bioengineering, Inha University, Inha-ro 100, Michuhol-gu, Incheon, 22212, South Korea
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea; Division of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea.
| | - Sang Woo Seo
- Interdisciplinary Program in Bioengineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea; School of Chemical and Biological Engineering, South Korea; Institute of Chemical Processes, South Korea; Bio-MAX Institute, South Korea; Institute of Bio Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea.
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11
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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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12
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Shi XC, Wang K, Xue M, Mao W, Xu K, Tremblay PL, Zhang T. Ultrafast removal of toxic Cr(VI) by the marine bacterium Vibrio natriegens. CHEMOSPHERE 2024; 350:141177. [PMID: 38211787 DOI: 10.1016/j.chemosphere.2024.141177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 12/04/2023] [Accepted: 01/08/2024] [Indexed: 01/13/2024]
Abstract
The fastest-growing microbe Vibrio natriegens is an excellent platform for bioproduction processes. Until now, this marine bacterium has not been examined for bioremediation applications, where the production of substantial amounts of biomass would be beneficial. V. natriegens can perform extracellular electron transfer (EET) to Fe(III) via a single porin-cytochrome circuit conserved in Vibrionaceae. Electroactive microbes capable of EET to Fe(III) usually also reduce toxic metals such as carcinogenic Cr(VI), which is converted to Cr(III), thus decreasing its toxicity and mobility. Here, the performance of V. natriegens was explored for the bioremediation of Cr(VI). At a density of 100 mg/mL, V. natriegens removed 5-20 mg/L Cr(VI) within 30 s and 100 mg/L Cr(VI) within 10 min. In comparison, the model bacterium Escherichia coli grown to a comparable cell density removed Cr(VI) 36 times slower. To eliminate Cr(VI), V. natriegens had to be metabolically active, and functional outer-membrane c-type cytochromes were required. At the end of the Cr(VI) removal process, V. natriegens had reduced all of it into Cr(III) while adsorbing more than half of the metallic ions. These results demonstrate that V. natriegens, with its fast metabolism, is a viable option for the rapid treatment of aqueous pollution with Cr.
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Affiliation(s)
- Xiao-Chen Shi
- School of Chemistry, Chemical Engineering, and Life Science, Wuhan University of Technology, Wuhan, 430070, PR China; School of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan, 430070, PR China; Advanced Engineering Technology Research Institute of Zhongshan City, Wuhan University of Technology, Zhongshan, 528437, PR China
| | - Kefan Wang
- School of Chemistry, Chemical Engineering, and Life Science, Wuhan University of Technology, Wuhan, 430070, PR China
| | - Miao Xue
- Institut WUT-AMU, Wuhan University of Technology, Wuhan, 430070, PR China
| | - Weijia Mao
- Institut WUT-AMU, Wuhan University of Technology, Wuhan, 430070, PR China
| | - Kai Xu
- Center for Material Research and Analysis, Wuhan University of Technology, Wuhan, 430070, PR China
| | - Pier-Luc Tremblay
- School of Chemistry, Chemical Engineering, and Life Science, Wuhan University of Technology, Wuhan, 430070, PR China; Institut WUT-AMU, Wuhan University of Technology, Wuhan, 430070, PR China; Shaoxing Institute for Advanced Research, Wuhan University of Technology, Shaoxing, 312300, PR China; Sanya Science and Education Innovation Park, Wuhan University of Technology, Sanya, 572024, PR China.
| | - Tian Zhang
- School of Chemistry, Chemical Engineering, and Life Science, Wuhan University of Technology, Wuhan, 430070, PR China; School of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan, 430070, PR China; Institut WUT-AMU, Wuhan University of Technology, Wuhan, 430070, PR China; Shaoxing Institute for Advanced Research, Wuhan University of Technology, Shaoxing, 312300, PR China; Sanya Science and Education Innovation Park, Wuhan University of Technology, Sanya, 572024, PR China.
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13
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Peng Y, Ma L, Xu P, Tao F. High-Performance Production of N-Acetyl-d-Neuraminic Acid with Whole Cells of Fast-Growing Vibrio natriegens via a Thermal Strategy. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:20198-20209. [PMID: 38051209 DOI: 10.1021/acs.jafc.3c07259] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
High performance is the core objective that biotechnologists pursue, of which low efficiency, low titer, and side products are the chief obstacles. Here, a thermal strategy is proposed for simultaneously addressing the obstacles of whole-cell catalysis that is widely applied in the food industry. The strategy, by combining fast-growing Vibrio natriegens, thermophilic enzymes, and high-temperature whole-cell catalysis, was successfully applied for the high-performance production of N-acetyl-d-neuraminic acid (Neu5Ac) that plays essential roles in the fields of food (infant formulas), healthcare, and medicine. By using this strategy, we realized the highest Neu5Ac titer and productivity of 126.1 g/L and up to 71.6 g/(L h), respectively, 7.2-fold higher than the productivity of Escherichia coli. The major byproduct acetic acid was also eliminated via quenching complex metabolic side reactions enabled by temperature elevation. This study offers a broadly applicable strategy for producing chemicals relevant to the food industry, providing insights for its future development.
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Affiliation(s)
- Yuan Peng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Lina Ma
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Fei Tao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
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14
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Peng Y, Xu P, Tao F. Production of N-acetylglucosamine with Vibrio alginolyticus FA2, an emerging platform for economical unsterile open fermentation. Synth Syst Biotechnol 2023; 8:546-554. [PMID: 37637200 PMCID: PMC10457514 DOI: 10.1016/j.synbio.2023.08.003] [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: 06/20/2023] [Revised: 08/01/2023] [Accepted: 08/09/2023] [Indexed: 08/29/2023] Open
Abstract
Members of the Vibrionaceae family are predominantly fast-growing and halophilic microorganisms that have captured the attention of researchers owing to their potential applications in rapid biotechnology. Among them, Vibrio alginolyticus FA2 is a particularly noteworthy halophilic bacterium that exhibits superior growth capability. It has the potential to serve as a biotechnological platform for sustainable and eco-friendly open fermentation with seawater. To evaluate this hypothesis, we integrated the N-acetylglucosamine (GlcNAc) pathway into V. alginolyticus FA2. Seven nag genes were knocked out to obstruct the utilization of GlcNAc, and then 16 exogenous gna1s co-expressing with EcglmS were introduced to strengthen the flux of GlcNAc pathway, respectively. To further enhance GlcNAc production, we fine-tuned promoter strength of the two genes and inactivated two genes alsS and alsD to prevent the production of acetoin. Furthermore, unsterile open fermentation was carried out using simulated seawater and a chemically defined medium, resulting in the production of 9.2 g/L GlcNAc in 14 h. This is the first report for de-novo synthesizing GlcNAc with a Vibrio strain, facilitated by an unsterile open fermentation process employing seawater as a substitute for fresh water. This development establishes a basis for production of diverse valuable chemicals using Vibrio strains and provides insights into biomanufacture.
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Affiliation(s)
- Yuan Peng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Fei Tao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
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15
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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: 1.0] [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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16
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Shin J, Rychel K, Palsson BO. Systems biology of competency in Vibrio natriegens is revealed by applying novel data analytics to the transcriptome. Cell Rep 2023; 42:112619. [PMID: 37285268 DOI: 10.1016/j.celrep.2023.112619] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 04/27/2023] [Accepted: 05/22/2023] [Indexed: 06/09/2023] Open
Abstract
Vibrio natriegens regulates natural competence through the TfoX and QstR transcription factors, which are involved in external DNA capture and transport. However, the extensive genetic and transcriptional regulatory basis for competency remains unknown. We used a machine-learning approach to decompose Vibrio natriegens's transcriptome into 45 groups of independently modulated sets of genes (iModulons). Our findings show that competency is associated with the repression of two housekeeping iModulons (iron metabolism and translation) and the activation of six iModulons; including TfoX and QstR, a novel iModulon of unknown function, and three housekeeping iModulons (representing motility, polycations, and reactive oxygen species [ROS] responses). Phenotypic screening of 83 gene deletion strains demonstrates that loss of iModulon function reduces or eliminates competency. This database-iModulon-discovery cycle unveils the transcriptomic basis for competency and its relationship to housekeeping functions. These results provide the genetic basis for systems biology of competency in this organism.
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Affiliation(s)
- Jongoh Shin
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Kevin Rychel
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
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17
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Sun Y, Xu J, Zhou H, Zhang H, Wu J, Yang L. Recombinant Protein Expression Chassis Library of Vibrio natriegens by Fine-Tuning the Expression of T7 RNA Polymerase. ACS Synth Biol 2023; 12:555-564. [PMID: 36719178 DOI: 10.1021/acssynbio.2c00562] [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] [Indexed: 02/01/2023]
Abstract
Vibrio natriegens is the fastest-growing bacteria, and its doubling time is less than 10 min. At present, the T7 expression system has been introduced into V. natriegens for heterologous protein expression, including the commercial strain Vmax1 and the variant VnDX,2 which is a backup expression chassis of Escherichia coli BL21(DE3). However, the strength of the existing T7 expression system is not optimal for every recombinant protein. The different expression strengths of T7 RNA polymerase (T7 RNAP) can be obtained by changing the promoter and ribosome binding site (RBS) sequences of T7 RNAP at different transcription and translation levels. In this work, we obtained a robust VnDX variant library with the fine-tuning T7 RNAP using the industrially used enzyme glucose dehydrogenase (GDH) as the reporter protein. Among this library, the variant VnDX-tet, whose promoter of T7 RNAP was changed from PlacUV5 to Ptet, showed that the reporter enzyme GDH activity was increased by 109% by the T7 expression system. Similarly, variants with different T7 RNAP translation levels were obtained by changing RBS sequences upstream of T7 RNAP, and the results showed that the variant VnDX-RBS12/pGDH had the highest GDH activity, which increased by 12.6%. The VnDX variant library constructed in this study with different T7 expression strengths provides a choice for expressing various recombinant proteins, greatly expanding the application of V. natriegens.
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Affiliation(s)
- Yijie Sun
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, China.,ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, China
| | - Jiaqi Xu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, China.,ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, China
| | - Haisheng Zhou
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, China.,ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, China
| | - Hongyu Zhang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, China
| | - Jianping Wu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, China.,ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, China
| | - Lirong Yang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, China.,ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, China
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18
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Gong Z, Xie R, Zhang Y, Wang M, Tan T. Identification of Emerging Industrial Biotechnology Chassis Vibrio natriegens as a Novel High Salt-Tolerant and Feedstock Flexibility Electroactive Microorganism for Microbial Fuel Cell. Microorganisms 2023; 11:microorganisms11020490. [PMID: 36838454 PMCID: PMC9961702 DOI: 10.3390/microorganisms11020490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 02/12/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
The development of MFC using electroactive industrial microorganisms has seen a surge of interest because of the co-generation for bioproduct and electricity production. Vibrio natriegens as a promising next-generation industrial microorganism chassis and its application for microbial fuel cells (MFC) was first studied. Mediated electron transfer was found in V. natriegens MFC (VMFC), but V. natriegens cannot secrete sufficient electron mediators to transfer electrons to the anode. All seven electron mediators supplemented are capable of improving the electronic transfer efficiency of VMFC. The media and carbon sources switching study reveals that VMFCs have excellent bioelectricity generation performance with feedstock flexibility and high salt-tolerance. Among them, 1% glycerol as the sole carbon source produced the highest power density of 111.9 ± 6.7 mW/cm2. The insight of the endogenous electronic mediators found that phenazine-1-carboxamide, phenazine-1-carboxylic acid, and 1-hydroxyphenazine are synthesized by V. natriegens via the shikimate pathway and the phenazine synthesis and modification pathways. This work provides the first proof for emerging industrial biotechnology chassis V. natriegens as a novel high salt-tolerant and feedstock flexibility electroactive microorganism for MFC, and giving insight into the endogenous electron mediator biosynthesis of VMFC, paving the way for the application of V. natriegens in MFC and even microbial electrofermentation (EF).
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Affiliation(s)
- Zhijin Gong
- National Energy R&D Center for Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Rong Xie
- National Energy R&D Center for Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yang Zhang
- National Energy R&D Center for Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Meng Wang
- National Energy R&D Center for Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Tianwei Tan
- National Energy R&D Center for Biorefinery, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
- Correspondence:
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19
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Kang CW, Lim HG, Won J, Cha S, Shin G, Yang JS, Sung J, Jung GY. Circuit-guided population acclimation of a synthetic microbial consortium for improved biochemical production. Nat Commun 2022; 13:6506. [PMID: 36344561 PMCID: PMC9640620 DOI: 10.1038/s41467-022-34190-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 10/14/2022] [Indexed: 11/09/2022] Open
Abstract
Microbial consortia have been considered potential platforms for bioprocessing applications. However, the complexity in process control owing to the use of multiple strains necessitates the use of an efficient population control strategy. Herein, we report circuit-guided synthetic acclimation as a strategy to improve biochemical production by a microbial consortium. We designed a consortium comprising alginate-utilizing Vibrio sp. dhg and 3-hydroxypropionic acid (3-HP)-producing Escherichia coli strains for the direct conversion of alginate to 3-HP. We introduced a genetic circuit, named "Population guider", in the E. coli strain, which degrades ampicillin only when 3-HP is produced. In the presence of ampicillin as a selection pressure, the consortium was successfully acclimated for increased 3-HP production by 4.3-fold compared to that by a simple co-culturing consortium during a 48-h fermentation. We believe this concept is a useful strategy for the development of robust consortium-based bioprocesses.
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Affiliation(s)
- Chae Won Kang
- grid.49100.3c0000 0001 0742 4007Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673 Korea
| | - Hyun Gyu Lim
- grid.49100.3c0000 0001 0742 4007Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673 Korea
| | - Jaehyuk Won
- grid.254224.70000 0001 0789 9563Creative Research Initiative Center for Chemical Dynamics in Living Cells, Chung-Ang University, 84 Heukseok-Ro, Dongjak-gu, Seoul 06974 Republic of Korea ,grid.254224.70000 0001 0789 9563Department of Chemistry, Chung-Ang University, 84 Heukseok-Ro, Dongjak-gu, Seoul 06974 Republic of Korea
| | - Sanghak Cha
- grid.49100.3c0000 0001 0742 4007Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673 Korea
| | - Giyoung Shin
- grid.49100.3c0000 0001 0742 4007School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673 Korea
| | - Jae-Seong Yang
- grid.423637.70000 0004 1763 5862Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, 08193 Spain
| | - Jaeyoung Sung
- grid.254224.70000 0001 0789 9563Creative Research Initiative Center for Chemical Dynamics in Living Cells, Chung-Ang University, 84 Heukseok-Ro, Dongjak-gu, Seoul 06974 Republic of Korea ,grid.254224.70000 0001 0789 9563Department of Chemistry, Chung-Ang University, 84 Heukseok-Ro, Dongjak-gu, Seoul 06974 Republic of Korea
| | - Gyoo Yeol Jung
- grid.49100.3c0000 0001 0742 4007Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673 Korea ,grid.49100.3c0000 0001 0742 4007School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673 Korea
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20
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Stadler KA, Becker W, Darnhofer B, Birner-Gruenberger R, Zangger K. Overexpression of recombinant proteins containing non-canonical amino acids in Vibrio natriegens: p-azido-L-phenylalanine as coupling site for 19F-tags. Amino Acids 2022; 54:1041-1053. [PMID: 35419750 PMCID: PMC9217835 DOI: 10.1007/s00726-022-03148-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 02/27/2022] [Indexed: 11/26/2022]
Abstract
Vibrio natriegens is the fastest growing organism identified so far. The minimum doubling time of only 9.4 min, the ability to utilize over 60 different carbon sources and its non-pathogenic properties make it an interesting alternative to E. coli as a new production host for recombinant proteins. We investigated the ability of the engineered V. natriegens strain, Vmax™ Express, to incorporate the non-canonical amino acid (ncAA) p-azido-L-phenylalanine (AzF) into recombinant proteins for NMR applications. AzF was incorporated into enhanced yellow fluorescent protein (EYFP) and MlaC, an intermembrane transport protein, by stop codon suppression. AzF incorporation into EYFP resulted in an improved suppression efficiency (SE) of up to 35.5 ± 0.8% and a protein titer of 26.7 ± 0.7 mg/L. The expression levels of MlaC-AzF even exceeded those of E. coli BL21 cells. For the recording of 1H-15N and 19F NMR spectra, EYFP-AzF was expressed and isotopically labeled in minimal medium and the newly introduced azido-group was used as coupling site for NMR sensitive 19F-tags. Our findings show that Vmax is a flexible expression host, suitable for the incorporation of ncAAs in recombinant proteins with the potential to surpass protein yields of E. coli. The presented method suggests the implementation of V. natriegens for expression of isotopically labeled proteins containing ncAAs, which can be chemically modified for the application in protein-observed 19F-NMR.
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Affiliation(s)
- Karina A Stadler
- Institute of Chemistry, University of Graz, Heinrichstrasse 28, 8010, Graz, Austria
| | - Walter Becker
- Institute of Chemistry, University of Graz, Heinrichstrasse 28, 8010, Graz, Austria
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavägen 9, 17177, Stockholm, Sweden
| | - Barbara Darnhofer
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Stiftingtalstrasse 6, 8010, Graz, Austria
- Omics Center Graz, BioTechMed-Graz, Stiftingtalstrasse 24, 8010, Graz, Austria
| | - Ruth Birner-Gruenberger
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Stiftingtalstrasse 6, 8010, Graz, Austria
- Omics Center Graz, BioTechMed-Graz, Stiftingtalstrasse 24, 8010, Graz, Austria
- Institute of Chemical Technologies and Analytics, Faculty of Technical Chemistry, Technische Universität Wien, Getreidemarkt 9/164, 1060, Vienna, Austria
| | - Klaus Zangger
- Institute of Chemistry, University of Graz, Heinrichstrasse 28, 8010, Graz, Austria.
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