1
|
Kong J, Miao L, Lu Z, Wang S, Zhao B, Zhang C, Xiao D, Teo D, Leong SSJ, Wong A, Yu A. Enhanced production of amyrin in Yarrowia lipolytica using a combinatorial protein and metabolic engineering approach. Microb Cell Fact 2022; 21:186. [PMID: 36085205 PMCID: PMC9463779 DOI: 10.1186/s12934-022-01915-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 08/26/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Amyrin is an important triterpenoid and precursor to a wide range of cosmetic, pharmaceutical and nutraceutical products. In this study, we metabolically engineered the oleaginous yeast, Yarrowia lipolytica to produce α- and β-amyrin on simple sugar and waste cooking oil. RESULTS We first validated the in vivo enzymatic activity of a multi-functional amyrin synthase (CrMAS) from Catharanthus roseus, by expressing its codon-optimized gene in Y. lipolytica and assayed for amyrins. To increase yield, prevailing genes in the mevalonate pathway, namely HMG1, ERG20, ERG9 and ERG1, were overexpressed singly and in combination to direct flux towards amyrin biosynthesis. By means of a semi-rational protein engineering approach, we augmented the catalytic activity of CrMAS and attained ~ 10-folds higher production level on glucose. When applied together, protein engineering with enhanced precursor supplies resulted in more than 20-folds increase in total amyrins. We also investigated the effects of different fermentation conditions in flask cultures, including temperature, volumetric oxygen mass transfer coefficient and carbon source types. The optimized fermentation condition attained titers of at least 100 mg/L α-amyrin and 20 mg/L β-amyrin. CONCLUSIONS The design workflow demonstrated herein is simple and remarkably effective in amplifying triterpenoid biosynthesis in the yeast Y. lipolytica.
Collapse
Affiliation(s)
- Jing Kong
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No.29 the 13th Street TEDA, Tianjin, 300457, People's Republic of China
| | - Lin Miao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No.29 the 13th Street TEDA, Tianjin, 300457, People's Republic of China
| | - Zhihui Lu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No.29 the 13th Street TEDA, Tianjin, 300457, People's Republic of China
| | - Shuhui Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No.29 the 13th Street TEDA, Tianjin, 300457, People's Republic of China
| | - Baixiang Zhao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No.29 the 13th Street TEDA, Tianjin, 300457, People's Republic of China
| | - Cuiying Zhang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No.29 the 13th Street TEDA, Tianjin, 300457, People's Republic of China
| | - Dongguang Xiao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No.29 the 13th Street TEDA, Tianjin, 300457, People's Republic of China
| | - Desmond Teo
- Food, Chemical and Biotechnology Cluster, Singapore Institute of Technology, Singapore, 138683, Singapore
| | - Susanna Su Jan Leong
- Food, Chemical and Biotechnology Cluster, Singapore Institute of Technology, Singapore, 138683, Singapore
| | - Adison Wong
- Food, Chemical and Biotechnology Cluster, Singapore Institute of Technology, Singapore, 138683, Singapore.
| | - Aiqun Yu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No.29 the 13th Street TEDA, Tianjin, 300457, People's Republic of China.
| |
Collapse
|
2
|
Zibulski DL, Schlichting N, Kabisch J. HyperXpress: Rapid Single Vessel DNA Assembly and Protein Production in Microliterscale. Front Bioeng Biotechnol 2022; 10:832176. [PMID: 35433646 PMCID: PMC9011061 DOI: 10.3389/fbioe.2022.832176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/28/2022] [Indexed: 11/16/2022] Open
Abstract
Rapid prototyping of biological functions has the common aim of generating, screening, and selecting variant libraries as quickly as possible. This approach is now to be extended by the HyperXpress workflow, which connects ligase cycling reaction for DNA assembly, multiply-primed rolling circle amplification for signal amplification, and cell-free protein synthesis to a single vessel reaction in the lower µl scale. After substantial optimization of the method a proof-of-principle demonstrating the high flexibility of HyperXpress for semi-rational protein engineering by expanding, reducing, and replacing β-strands of three different green fluorescent proteins is described. These single-day experiments resulted in six functional, new-to-nature GFP prototypes.
Collapse
Affiliation(s)
| | | | - Johannes Kabisch
- Computer-aided Synthetic Biology, Darmstadt, Germany
- Department of Biotechnology and Food Science, NTNU, Trondheim, Norway
- *Correspondence: Johannes Kabisch,
| |
Collapse
|
3
|
Multitasking Na+/Taurocholate Cotransporting Polypeptide (NTCP) as a Drug Target for HBV Infection: From Protein Engineering to Drug Discovery. Biomedicines 2022; 10:biomedicines10010196. [PMID: 35052874 PMCID: PMC8773476 DOI: 10.3390/biomedicines10010196] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/10/2022] [Accepted: 01/13/2022] [Indexed: 02/05/2023] Open
Abstract
Hepatitis B virus (HBV) infections are among the major public health concerns worldwide with more than 250 million of chronically ill individuals. Many of them are additionally infected with the Hepatitis D virus, a satellite virus to HBV. Chronic infection frequently leads to serious liver diseases including cirrhosis and hepatocellular carcinoma, the most common type of liver cancer. Although current antiviral therapies can control HBV replication and slow down disease progress, there is an unmet medical need to identify therapies to cure this chronic infectious disease. Lately, a noteworthy progress in fighting against HBV has been made by identification of the high-affinity hepatic host receptor for HBV and HDV, namely Na+/taurocholate cotransporting polypeptide (NTCP, gene symbol SLC10A1). Next to its primary function as hepatic uptake transporter for bile acids, NTCP is essential for the cellular entry of HBV and HDV into hepatocytes. Due to this high-ranking discovery, NTCP has become a valuable target for drug development strategies for HBV/HDV-infected patients. In this review, we will focus on a newly predicted three-dimensional NTCP model that was generated using computational approaches and discuss its value in understanding the NTCP’s membrane topology, substrate and virus binding taking place in plasma membranes. We will review existing data on structural, functional, and biological consequences of amino acid residue changes and mutations that lead to loss of NTCP’s transport and virus receptor functions. Finally, we will discuss new directions for future investigations aiming at development of new NTCP-based HBV entry blockers that inhibit HBV tropism in human hepatocytes.
Collapse
|
4
|
Scherer M, Fleishman SJ, Jones PR, Dandekar T, Bencurova E. Computational Enzyme Engineering Pipelines for Optimized Production of Renewable Chemicals. Front Bioeng Biotechnol 2021; 9:673005. [PMID: 34211966 PMCID: PMC8239229 DOI: 10.3389/fbioe.2021.673005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/06/2021] [Indexed: 11/13/2022] Open
Abstract
To enable a sustainable supply of chemicals, novel biotechnological solutions are required that replace the reliance on fossil resources. One potential solution is to utilize tailored biosynthetic modules for the metabolic conversion of CO2 or organic waste to chemicals and fuel by microorganisms. Currently, it is challenging to commercialize biotechnological processes for renewable chemical biomanufacturing because of a lack of highly active and specific biocatalysts. As experimental methods to engineer biocatalysts are time- and cost-intensive, it is important to establish efficient and reliable computational tools that can speed up the identification or optimization of selective, highly active, and stable enzyme variants for utilization in the biotechnological industry. Here, we review and suggest combinations of effective state-of-the-art software and online tools available for computational enzyme engineering pipelines to optimize metabolic pathways for the biosynthesis of renewable chemicals. Using examples relevant for biotechnology, we explain the underlying principles of enzyme engineering and design and illuminate future directions for automated optimization of biocatalysts for the assembly of synthetic metabolic pathways.
Collapse
Affiliation(s)
- Marc Scherer
- Department of Bioinformatics, Julius-Maximilians University of Würzburg, Würzburg, Germany
| | - Sarel J Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Patrik R Jones
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Thomas Dandekar
- Department of Bioinformatics, Julius-Maximilians University of Würzburg, Würzburg, Germany
| | - Elena Bencurova
- Department of Bioinformatics, Julius-Maximilians University of Würzburg, Würzburg, Germany
| |
Collapse
|
5
|
Chen LZ, Huang SL, Hou J, Guo XP, Wang FS, Sheng JZ. Cell-based and cell-free biocatalysis for the production of D-glucaric acid. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:203. [PMID: 33303009 PMCID: PMC7731778 DOI: 10.1186/s13068-020-01847-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 12/02/2020] [Indexed: 05/17/2023]
Abstract
D-Glucaric acid (GA) is a value-added chemical produced from biomass, and has potential applications as a versatile platform chemical, food additive, metal sequestering agent, and therapeutic agent. Marketed GA is currently produced chemically, but increasing demand is driving the search for eco-friendlier and more efficient production approaches. Cell-based production of GA represents an alternative strategy for GA production. A series of synthetic pathways for GA have been ported into Escherichia coli, Saccharomyces cerevisiae and Pichia pastoris, respectively, and these engineered cells show the ability to synthesize GA de novo. Optimization of the GA metabolic pathways in host cells has leapt forward, and the titer and yield have increased rapidly. Meanwhile, cell-free multi-enzyme catalysis, in which the desired pathway is constructed in vitro from enzymes and cofactors involved in GA biosynthesis, has also realized efficient GA bioconversion. This review presents an overview of studies of the development of cell-based GA production, followed by a brief discussion of potential applications of biosensors that respond to GA in these biosynthesis routes.
Collapse
Affiliation(s)
- Lu-Zhou Chen
- Key Laboratory of Chemical Biology of Natural Products (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Si-Ling Huang
- Bloomage BioTechnology Corp., Ltd., Jinan, 250010, China
| | - Jin Hou
- The State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Xue-Ping Guo
- Bloomage BioTechnology Corp., Ltd., Jinan, 250010, China
| | - Feng-Shan Wang
- Key Laboratory of Chemical Biology of Natural Products (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
- National Glycoengineering Research Center, Shandong University, Jinan, 250012, China
| | - Ju-Zheng Sheng
- Key Laboratory of Chemical Biology of Natural Products (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China.
- National Glycoengineering Research Center, Shandong University, Jinan, 250012, China.
| |
Collapse
|
6
|
Synthetic small regulatory RNAs in microbial metabolic engineering. Appl Microbiol Biotechnol 2020; 105:1-12. [PMID: 33201273 DOI: 10.1007/s00253-020-10971-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 10/15/2020] [Accepted: 10/21/2020] [Indexed: 02/06/2023]
Abstract
Small regulatory RNAs (sRNAs) finely control gene expression in prokaryotes and synthetic sRNA has become a useful high-throughput approach to tackle current challenges in metabolic engineering because of its many advantages compared to conventional gene knockouts. In this review, we first focus on the modular structures of sRNAs and rational design strategies of synthetic sRNAs on the basis of their modular structures. The wide applications of synthetic sRNAs in bacterial metabolic engineering, with or without the aid of heterogeneously expressed Hfq protein, were also covered. In addition, we give attention to the improvements in implementing synthetic sRNAs, which make the synthetic sRNA strategy universally applicable in metabolic engineering and synthetic biology. KEY POINTS: • Synthetic sRNAs can be rationally designed based on modular structures of natural sRNAs. • Synthetic sRNAs were widely used for metabolic engineering in various microorganisms. • Several technological improvements made the synthetic sRNA strategy more applicable.
Collapse
|
7
|
Li S, Huang L, Ke C, Pang Z, Liu L. Pathway dissection, regulation, engineering and application: lessons learned from biobutanol production by solventogenic clostridia. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:39. [PMID: 32165923 PMCID: PMC7060580 DOI: 10.1186/s13068-020-01674-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 02/04/2020] [Indexed: 06/01/2023]
Abstract
The global energy crisis and limited supply of petroleum fuels have rekindled the interest in utilizing a sustainable biomass to produce biofuel. Butanol, an advanced biofuel, is a superior renewable resource as it has a high energy content and is less hygroscopic than other candidates. At present, the biobutanol route, employing acetone-butanol-ethanol (ABE) fermentation in Clostridium species, is not economically competitive due to the high cost of feedstocks, low butanol titer, and product inhibition. Based on an analysis of the physiological characteristics of solventogenic clostridia, current advances that enhance ABE fermentation from strain improvement to product separation were systematically reviewed, focusing on: (1) elucidating the metabolic pathway and regulation mechanism of butanol synthesis; (2) enhancing cellular performance and robustness through metabolic engineering, and (3) optimizing the process of ABE fermentation. Finally, perspectives on engineering and exploiting clostridia as cell factories to efficiently produce various chemicals and materials are also discussed.
Collapse
Affiliation(s)
- Shubo Li
- College of Light Industry and Food Engineering, Guangxi University, Nanning, 530004 China
| | - Li Huang
- College of Light Industry and Food Engineering, Guangxi University, Nanning, 530004 China
| | - Chengzhu Ke
- College of Light Industry and Food Engineering, Guangxi University, Nanning, 530004 China
| | - Zongwen Pang
- College of Life Science and Technology, Guangxi University, Nanning, 530005 China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122 China
| |
Collapse
|
8
|
Systems biology based metabolic engineering for non-natural chemicals. Biotechnol Adv 2019; 37:107379. [DOI: 10.1016/j.biotechadv.2019.04.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 02/23/2019] [Accepted: 04/01/2019] [Indexed: 12/17/2022]
|
9
|
Structural Insights into Catalytic Versatility of the Flavin-dependent Hydroxylase (HpaB) from Escherichia coli. Sci Rep 2019; 9:7087. [PMID: 31068633 PMCID: PMC6506529 DOI: 10.1038/s41598-019-43577-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 04/27/2019] [Indexed: 01/07/2023] Open
Abstract
4-Hydroxyphenylacetate 3-hydroxylase (EcHpaB) from Escherichia coli is capable of efficient ortho-hydroxylation of a wide range of phenolic compounds and demonstrates great potential for broad chemoenzymatic applications. To understand the structural and mechanistic basis of its catalytic versatility, we elucidated the crystal structure of EcHpaB by X-ray crystallography, which revealed a unique loop structure covering the active site. We further performed mutagenesis studies of this loop to probe its role in substrate specificity and catalytic activity. Our results not only showed the loop has great plasticity and strong tolerance towards extensive mutagenesis, but also suggested a flexible loop that enables the entrance and stable binding of substrates into the active site is the key factor to the enzyme catalytic versatility. These findings lay the groundwork for editing the loop sequence and structure for generation of EcHpaB mutants with improved performance for broader laboratory and industrial use.
Collapse
|
10
|
Leistra AN, Curtis NC, Contreras LM. Regulatory non-coding sRNAs in bacterial metabolic pathway engineering. Metab Eng 2018; 52:190-214. [PMID: 30513348 DOI: 10.1016/j.ymben.2018.11.013] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 10/31/2018] [Accepted: 11/29/2018] [Indexed: 12/11/2022]
Abstract
Non-coding RNAs (ncRNAs) are versatile and powerful controllers of gene expression that have been increasingly linked to cellular metabolism and phenotype. In bacteria, identified and characterized ncRNAs range from trans-acting, multi-target small non-coding RNAs to dynamic, cis-encoded regulatory untranslated regions and riboswitches. These native regulators have inspired the design and construction of many synthetic RNA devices. In this work, we review the design, characterization, and impact of ncRNAs in engineering both native and exogenous metabolic pathways in bacteria. We also consider the opportunities afforded by recent high-throughput approaches for characterizing sRNA regulators and their corresponding networks to showcase their potential applications and impact in engineering bacterial metabolism.
Collapse
Affiliation(s)
- Abigail N Leistra
- McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keeton Street Stop C0400, Austin, TX 78712, USA
| | - Nicholas C Curtis
- McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keeton Street Stop C0400, Austin, TX 78712, USA
| | - Lydia M Contreras
- McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keeton Street Stop C0400, Austin, TX 78712, USA.
| |
Collapse
|
11
|
Fürst MJLJ, Martin C, Lončar N, Fraaije MW. Experimental Protocols for Generating Focused Mutant Libraries and Screening for Thermostable Proteins. Methods Enzymol 2018; 608:151-187. [PMID: 30173762 DOI: 10.1016/bs.mie.2018.04.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Many proteins are rapidly deactivated when exposed to high or even ambient temperatures. This cannot only impede the study of a particular protein, but also is one of the major reasons why enzyme catalysis is still widely unable to compete with established chemical processes. Furthermore, differences in protein stability are a challenge in synthetic biology, when individual modules prove to be incompatible. The targeted stabilization of proteins can overcome these hurdles, and protein engineering techniques are more and more reliably supported by computational chemistry tools. Accordingly, algorithms to predict the differences in folding energy of a mutant compared to the wild-type, ΔΔGfold, are used in the highly successful FRESCO workflow. The resulting single mutant prediction library consists typically of a few hundred amino acid exchanges, and after combining the most successful hits we so far obtained stabilized mutants which exhibited increases in apparent melting temperature of 20-35°C and showed vastly increased half-lives, as well as resistance to cosolvents. Here, we report a detailed protocol to generate these mutant libraries experimentally, covering the entire workflow from primer design, through mutagenesis, protein production and screening, to mutation combination strategies. The individual parts of the method are furthermore applicable to many other scenarios besides protein stabilization, and these protocols are valuable for any project requiring individual or semi high-throughput site-directed mutagenesis, protein expression and purification, or generation of mutant combination libraries.
Collapse
Affiliation(s)
- Max J L J Fürst
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Caterina Martin
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Nikola Lončar
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Marco W Fraaije
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.
| |
Collapse
|
12
|
Wang X, He Q, Yang Y, Wang J, Haning K, Hu Y, Wu B, He M, Zhang Y, Bao J, Contreras LM, Yang S. Advances and prospects in metabolic engineering of Zymomonas mobilis. Metab Eng 2018; 50:57-73. [PMID: 29627506 DOI: 10.1016/j.ymben.2018.04.001] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/31/2018] [Accepted: 04/01/2018] [Indexed: 12/22/2022]
Abstract
Biorefinery of biomass-based biofuels and biochemicals by microorganisms is a competitive alternative of traditional petroleum refineries. Zymomonas mobilis is a natural ethanologen with many desirable characteristics, which makes it an ideal industrial microbial biocatalyst for commercial production of desirable bioproducts through metabolic engineering. In this review, we summarize the metabolic engineering progress achieved in Z. mobilis to expand its substrate and product ranges as well as to enhance its robustness against stressful conditions such as inhibitory compounds within the lignocellulosic hydrolysates and slurries. We also discuss a few metabolic engineering strategies that can be applied in Z. mobilis to further develop it as a robust workhorse for economic lignocellulosic bioproducts. In addition, we briefly review the progress of metabolic engineering in Z. mobilis related to the classical synthetic biology cycle of "Design-Build-Test-Learn", as well as the progress and potential to develop Z. mobilis as a model chassis for biorefinery practices in the synthetic biology era.
Collapse
Affiliation(s)
- Xia Wang
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 430062, China.
| | - Qiaoning He
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 430062, China.
| | - Yongfu Yang
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 430062, China.
| | - Jingwen Wang
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 430062, China.
| | - Katie Haning
- Institute for Cellular and Molecular Biology, Department of Chemical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX, United States.
| | - Yun Hu
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 430062, China.
| | - Bo Wu
- Key Laboratory of Development and Application of Rural Renewable Energy, Biomass Energy Technology Research Centre, Biogas Institute of Ministry of Agriculture, South Renmin Road, Chengdu 610041, China.
| | - Mingxiong He
- Key Laboratory of Development and Application of Rural Renewable Energy, Biomass Energy Technology Research Centre, Biogas Institute of Ministry of Agriculture, South Renmin Road, Chengdu 610041, China.
| | - Yaoping Zhang
- DOE-Great Lakes Bioenergy Research Center (GLBRC), University of Wisconsin-Madison, Madison, WI, United States.
| | - Jie Bao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China.
| | - Lydia M Contreras
- Institute for Cellular and Molecular Biology, Department of Chemical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX, United States.
| | - Shihui Yang
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 430062, China.
| |
Collapse
|
13
|
Torres-Salas P, Bernal V, López-Gallego F, Martínez-Crespo J, Sánchez-Murcia PA, Barrera V, Morales-Jiménez R, García-Sánchez A, Mañas-Fernández A, Seoane JM, Sagrera Polo M, Miranda JD, Calvo J, Huertas S, Torres JL, Alcalde-Bascones A, González-Barrera S, Gago F, Morreale A, González-Barroso MDM. Engineering Erg10 Thiolase from Saccharomyces cerevisiae as a Synthetic Toolkit for the Production of Branched-Chain Alcohols. Biochemistry 2018; 57:1338-1348. [PMID: 29360348 DOI: 10.1021/acs.biochem.7b01186] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Thiolases catalyze the condensation of acyl-CoA thioesters through the Claisen condensation reaction. The best described enzymes usually yield linear condensation products. Using a combined computational/experimental approach, and guided by structural information, we have studied the potential of thiolases to synthesize branched compounds. We have identified a bulky residue located at the active site that blocks proper accommodation of substrates longer than acetyl-CoA. Amino acid replacements at such a position exert effects on the activity and product selectivity of the enzymes that are highly dependent on a protein scaffold. Among the set of five thiolases studied, Erg10 thiolase from Saccharomyces cerevisiae showed no acetyl-CoA/butyryl-CoA branched condensation activity, but variants at position F293 resulted the most active and selective biocatalysts for this reaction. This is the first time that a thiolase has been engineered to synthesize branched compounds. These novel enzymes enrich the toolbox of combinatorial (bio)chemistry, paving the way for manufacturing a variety of α-substituted synthons. As a proof of concept, we have engineered Clostridium's 1-butanol pathway to obtain 2-ethyl-1-butanol, an alcohol that is interesting as a branched model compound.
Collapse
Affiliation(s)
- Pamela Torres-Salas
- Centro de Tecnología de Repsol, REPSOL S. A. Calle Agustín de Betancourt , s/n, 28935 Móstoles, Madrid, Spain
| | - Vicente Bernal
- Centro de Tecnología de Repsol, REPSOL S. A. Calle Agustín de Betancourt , s/n, 28935 Móstoles, Madrid, Spain
| | - Fernando López-Gallego
- Centro de Tecnología de Repsol, REPSOL S. A. Calle Agustín de Betancourt , s/n, 28935 Móstoles, Madrid, Spain.,CIC biomaGUNE , Paseo de Miramón 182, 20014 San Sebastián, Spain.,ARAID Foundation , Zaragoza, Spain
| | - Javier Martínez-Crespo
- Centro de Tecnología de Repsol, REPSOL S. A. Calle Agustín de Betancourt , s/n, 28935 Móstoles, Madrid, Spain
| | - Pedro A Sánchez-Murcia
- Departamento de Ciencias Biomédicas and "Unidad Asociada IQM-CSIC", Universidad de Alcalá , E-28805 Alcalá de Henares, Madrid, Spain
| | - Victor Barrera
- Centro de Tecnología de Repsol, REPSOL S. A. Calle Agustín de Betancourt , s/n, 28935 Móstoles, Madrid, Spain
| | - Rocío Morales-Jiménez
- Centro de Tecnología de Repsol, REPSOL S. A. Calle Agustín de Betancourt , s/n, 28935 Móstoles, Madrid, Spain
| | - Ana García-Sánchez
- Centro de Tecnología de Repsol, REPSOL S. A. Calle Agustín de Betancourt , s/n, 28935 Móstoles, Madrid, Spain
| | - Aurora Mañas-Fernández
- Centro de Tecnología de Repsol, REPSOL S. A. Calle Agustín de Betancourt , s/n, 28935 Móstoles, Madrid, Spain
| | - José M Seoane
- Centro de Tecnología de Repsol, REPSOL S. A. Calle Agustín de Betancourt , s/n, 28935 Móstoles, Madrid, Spain
| | - Marta Sagrera Polo
- Centro de Investigaciones Biológicas (CSIC) , Calle Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Juande D Miranda
- Centro de Tecnología de Repsol, REPSOL S. A. Calle Agustín de Betancourt , s/n, 28935 Móstoles, Madrid, Spain
| | - Javier Calvo
- CIC biomaGUNE , Paseo de Miramón 182, 20014 San Sebastián, Spain
| | - Sonia Huertas
- Centro de Tecnología de Repsol, REPSOL S. A. Calle Agustín de Betancourt , s/n, 28935 Móstoles, Madrid, Spain
| | - José L Torres
- Centro de Tecnología de Repsol, REPSOL S. A. Calle Agustín de Betancourt , s/n, 28935 Móstoles, Madrid, Spain
| | - Ana Alcalde-Bascones
- Centro de Tecnología de Repsol, REPSOL S. A. Calle Agustín de Betancourt , s/n, 28935 Móstoles, Madrid, Spain
| | - Sergio González-Barrera
- Centro de Tecnología de Repsol, REPSOL S. A. Calle Agustín de Betancourt , s/n, 28935 Móstoles, Madrid, Spain
| | - Federico Gago
- Departamento de Ciencias Biomédicas and "Unidad Asociada IQM-CSIC", Universidad de Alcalá , E-28805 Alcalá de Henares, Madrid, Spain
| | - Antonio Morreale
- Centro de Tecnología de Repsol, REPSOL S. A. Calle Agustín de Betancourt , s/n, 28935 Móstoles, Madrid, Spain
| | | |
Collapse
|
14
|
Wang J, Wu Y, Sun X, Yuan Q, Yan Y. De Novo Biosynthesis of Glutarate via α-Keto Acid Carbon Chain Extension and Decarboxylation Pathway in Escherichia coli. ACS Synth Biol 2017; 6:1922-1930. [PMID: 28618222 DOI: 10.1021/acssynbio.7b00136] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Microbial based bioplastics are promising alternatives to petroleum based synthetic plastics due to their renewability and economic feasibility. Glutarate is one of the most potential building blocks for bioplastics. The recent biosynthetic routes for glutarate were mostly based on the l-lysine degradation pathway from Pseudomonas putida that required lysine either by feeding or lysine overproduction via genetic manipulations. Herein, we established a novel glutarate biosynthetic pathway by incorporation of a "+1" carbon chain extension pathway from α-ketoglutarate (α-KG) in combination with α-keto acid decarboxylation pathway in Escherichia coli. Introduction of homocitrate synthase (HCS), homoaconitase (HA) and homoisocitrate dehydrogenase (HICDH) from Saccharomyces cerevisiae into E. coli enabled "+1" carbon extension from α-KG to α-ketoadipate (α-KA), which was subsequently converted into glutarate by a promiscuous α-keto acid decarboxylase (KivD) and a succinate semialdehyde dehydrogenase (GabD). The recombinant E. coli coexpressing all five genes produced 0.3 g/L glutarate from glucose. To further improve the titers, α-KG was rechanneled into carbon chain extension pathway via the clustered regularly interspersed palindromic repeats system mediated interference (CRISPRi) of essential genes sucA and sucB in tricarboxylic acid (TCA) cycle. The final strain could produce 0.42 g/L glutarate, which was increased by 40% compared with the parental strain.
Collapse
Affiliation(s)
- Jian Wang
- College
of Engineering, The University of Georgia, Athens, Georgia 30602, United States
| | - Yifei Wu
- State
Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
- Beijing
Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xinxiao Sun
- State
Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
- Beijing
Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Qipeng Yuan
- State
Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
- Beijing
Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yajun Yan
- College
of Engineering, The University of Georgia, Athens, Georgia 30602, United States
| |
Collapse
|
15
|
Jansen MLA, Bracher JM, Papapetridis I, Verhoeven MD, de Bruijn H, de Waal PP, van Maris AJA, Klaassen P, Pronk JT. Saccharomyces cerevisiae strains for second-generation ethanol production: from academic exploration to industrial implementation. FEMS Yeast Res 2017; 17:3868933. [PMID: 28899031 PMCID: PMC5812533 DOI: 10.1093/femsyr/fox044] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 06/15/2017] [Indexed: 11/18/2022] Open
Abstract
The recent start-up of several full-scale 'second generation' ethanol plants marks a major milestone in the development of Saccharomyces cerevisiae strains for fermentation of lignocellulosic hydrolysates of agricultural residues and energy crops. After a discussion of the challenges that these novel industrial contexts impose on yeast strains, this minireview describes key metabolic engineering strategies that have been developed to address these challenges. Additionally, it outlines how proof-of-concept studies, often developed in academic settings, can be used for the development of robust strain platforms that meet the requirements for industrial application. Fermentation performance of current engineered industrial S. cerevisiae strains is no longer a bottleneck in efforts to achieve the projected outputs of the first large-scale second-generation ethanol plants. Academic and industrial yeast research will continue to strengthen the economic value position of second-generation ethanol production by further improving fermentation kinetics, product yield and cellular robustness under process conditions.
Collapse
Affiliation(s)
- Mickel L. A. Jansen
- DSM Biotechnology Centre, Alexander Fleminglaan 1, 2613 AX Delft, The
Netherlands
| | - Jasmine M. Bracher
- Department of Biotechnology, Delft University of Technology, Van der Maasweg
9, 2629 HZ Delft, The Netherlands
| | - Ioannis Papapetridis
- Department of Biotechnology, Delft University of Technology, Van der Maasweg
9, 2629 HZ Delft, The Netherlands
| | - Maarten D. Verhoeven
- Department of Biotechnology, Delft University of Technology, Van der Maasweg
9, 2629 HZ Delft, The Netherlands
| | - Hans de Bruijn
- DSM Biotechnology Centre, Alexander Fleminglaan 1, 2613 AX Delft, The
Netherlands
| | - Paul P. de Waal
- DSM Biotechnology Centre, Alexander Fleminglaan 1, 2613 AX Delft, The
Netherlands
| | - Antonius J. A. van Maris
- Department of Biotechnology, Delft University of Technology, Van der Maasweg
9, 2629 HZ Delft, The Netherlands
| | - Paul Klaassen
- DSM Biotechnology Centre, Alexander Fleminglaan 1, 2613 AX Delft, The
Netherlands
| | - Jack T. Pronk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg
9, 2629 HZ Delft, The Netherlands
| |
Collapse
|
16
|
Wang J, Jain R, Shen X, Sun X, Cheng M, Liao JC, Yuan Q, Yan Y. Rational engineering of diol dehydratase enables 1,4-butanediol biosynthesis from xylose. Metab Eng 2017; 40:148-156. [DOI: 10.1016/j.ymben.2017.02.003] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 02/09/2017] [Accepted: 02/10/2017] [Indexed: 11/29/2022]
|
17
|
Cheon S, Kim HM, Gustavsson M, Lee SY. Recent trends in metabolic engineering of microorganisms for the production of advanced biofuels. Curr Opin Chem Biol 2016; 35:10-21. [DOI: 10.1016/j.cbpa.2016.08.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 07/14/2016] [Accepted: 08/07/2016] [Indexed: 10/21/2022]
|
18
|
Case AE, Atsumi S. Cyanobacterial chemical production. J Biotechnol 2016; 231:106-114. [DOI: 10.1016/j.jbiotec.2016.05.023] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 05/19/2016] [Indexed: 01/03/2023]
|
19
|
Meng H, Liu P, Sun H, Cai Z, Zhou J, Lin J, Li Y. Engineering a d-lactate dehydrogenase that can super-efficiently utilize NADPH and NADH as cofactors. Sci Rep 2016; 6:24887. [PMID: 27109778 PMCID: PMC4842997 DOI: 10.1038/srep24887] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 04/06/2016] [Indexed: 11/09/2022] Open
Abstract
Engineering the cofactor specificity of a natural enzyme often results in a significant decrease in its activity on original cofactor. Here we report that a NADH-dependent dehydrogenase (d-LDH) from Lactobacillus delbrueckii 11842 can be rationally engineered to efficiently use both NADH and NADPH as cofactors. Point mutations on three amino acids (D176S, I177R, F178T) predicted by computational analysis resulted in a modified enzyme designated as d-LDH*. The Kcat/Km of the purified d-LDH* on NADPH increased approximately 184-fold while the Kcat/Km on NADH also significantly increased, showing for the first time that a rationally engineered d-LDH could exhibit comparable activity on both NADPH and NADH. Further kinetic analysis revealed that the enhanced affinity with NADH or NADPH and the significant increased Kcat of d-LDH* resulted in the significant increase of d-LDH* activity on both NADPH and NADH. This study thus demonstrated that the cofactor specificity of dehydrogenase can be broadened by using targeted engineering approach, and the engineered enzyme can efficiently function in NADH-rich, or NADPH-rich, or NADH and NADPH-rich environment.
Collapse
Affiliation(s)
- Hengkai Meng
- Department of Cellular Biology, University of Science and Technology of China, Hefei, China.,CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Pi Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Hongbing Sun
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Zhen Cai
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jie Zhou
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jianping Lin
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,College of Pharmacy, Nankai University, Tianjin, China
| | - Yin Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
20
|
Zhou LB, Zeng AP. Exploring lysine riboswitch for metabolic flux control and improvement of L-lysine synthesis in Corynebacterium glutamicum. ACS Synth Biol 2015; 4:729-34. [PMID: 25575181 DOI: 10.1021/sb500332c] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Riboswitch, a regulatory part of an mRNA molecule that can specifically bind a metabolite and regulate gene expression, is attractive for engineering biological systems, especially for the control of metabolic fluxes in industrial microorganisms. Here, we demonstrate the use of lysine riboswitch and intracellular l-lysine as a signal to control the competing but essential metabolic by-pathways of lysine biosynthesis. To this end, we first examined the natural lysine riboswitches of Eschericia coli (ECRS) and Bacillus subtilis (BSRS) to control the expression of citrate synthase (gltA) and thus the metabolic flux in the tricarboxylic acid (TCA) cycle in E. coli. ECRS and BSRS were then successfully used to control the gltA gene and TCA cycle activity in a lysine producing strain Corynebacterium glutamicum LP917, respectively. Compared with the strain LP917, the growth of both lysine riboswitch-gltA mutants was slower, suggesting a reduced TCA cycle activity. The lysine production was 63% higher in the mutant ECRS-gltA and 38% higher in the mutant BSRS-gltA, indicating a higher metabolic flux into the lysine synthesis pathway. This is the first report on using an amino acid riboswitch for improvement of lysine biosynthesis. The lysine riboswitches can be easily adapted to dynamically control other essential but competing metabolic pathways or even be engineered as an "on-switch" to enhance the metabolic fluxes of desired metabolic pathways.
Collapse
Affiliation(s)
- Li-Bang Zhou
- Institute of Bioprocess and
Biosystems Engineering, Hamburg University of Technology Denickestrasse
15, D-21073 Hamburg, Germany
| | - An-Ping Zeng
- Institute of Bioprocess and
Biosystems Engineering, Hamburg University of Technology Denickestrasse
15, D-21073 Hamburg, Germany
| |
Collapse
|
21
|
Pandey N, Nobles CL, Zechiedrich L, Maresso AW, Silberg JJ. Combining random gene fission and rational gene fusion to discover near-infrared fluorescent protein fragments that report on protein-protein interactions. ACS Synth Biol 2015; 4:615-24. [PMID: 25265085 PMCID: PMC4487222 DOI: 10.1021/sb5002938] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Gene fission can convert monomeric proteins into two-piece catalysts, reporters, and transcription factors for systems and synthetic biology. However, some proteins can be challenging to fragment without disrupting function, such as near-infrared fluorescent protein (IFP). We describe a directed evolution strategy that can overcome this challenge by randomly fragmenting proteins and concomitantly fusing the protein fragments to pairs of proteins or peptides that associate. We used this method to create libraries that express fragmented IFP as fusions to a pair of associating peptides (IAAL-E3 and IAAL-K3) and proteins (CheA and CheY) and screened for fragmented IFP with detectable near-infrared fluorescence. Thirteen novel fragmented IFPs were identified, all of which arose from backbone fission proximal to the interdomain linker. Either the IAAL-E3 and IAAL-K3 peptides or CheA and CheY proteins could assist with IFP fragment complementation, although the IAAL-E3 and IAAL-K3 peptides consistently yielded higher fluorescence. These results demonstrate how random gene fission can be coupled to rational gene fusion to create libraries enriched in fragmented proteins with AND gate logic that is dependent upon a protein-protein interaction, and they suggest that these near-infrared fluorescent protein fragments will be suitable as reporters for pairs of promoters and protein-protein interactions within whole animals.
Collapse
Affiliation(s)
- Naresh Pandey
- Department
of Biosciences, Rice University, Houston, Texas 77005, United States
| | | | | | | | - Jonathan J. Silberg
- Department
of Biosciences, Rice University, Houston, Texas 77005, United States
| |
Collapse
|
22
|
Gorai B, Prabhavadhni A, Sivaraman T. Unfolding stabilities of two structurally similar proteins as probed by temperature-induced and force-induced molecular dynamics simulations. J Biomol Struct Dyn 2014; 33:2037-47. [DOI: 10.1080/07391102.2014.986668] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
23
|
Lin Y, Sun X, Yuan Q, Yan Y. Engineering bacterial phenylalanine 4-hydroxylase for microbial synthesis of human neurotransmitter precursor 5-hydroxytryptophan. ACS Synth Biol 2014; 3:497-505. [PMID: 24936877 DOI: 10.1021/sb5002505] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
5-Hydroxytryptophan (5-HTP) is a drug that is clinically effective against depression, insomnia, obesity, chronic headaches, etc. It is only commercially produced by the extraction from the seeds of Griffonia simplicifolia because of a lack of synthetic methods. Here, we report the efficient microbial production of 5-HTP via combinatorial protein and metabolic engineering approaches. First, we reconstituted and screened prokaryotic phenylalanine 4-hydroxylase activity in Escherichia coli. Then, sequence- and structure-based protein engineering dramatically shifted its substrate preference, allowing for efficient conversion of tryptophan to 5-HTP. Importantly, E. coli endogenous tetrahydromonapterin (MH4) could be utilized as the coenzyme, when a foreign MH4 recycling mechanism was introduced. Whole-cell bioconversion allowed the high-level production of 5-HTP (1.1-1.2 g/L) from tryptophan in shake flasks. On this basis, metabolic engineering efforts were further made to achieve the de novo 5-HTP biosynthesis from glucose. This work not only holds great scale-up potential but also demonstrates a strategy for expanding the native metabolism of microorganisms.
Collapse
Affiliation(s)
- Yuheng Lin
- College
of Engineering, University of Georgia, Athens, Georgia 30602, United States
| | - Xinxiao Sun
- State
Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Qipeng Yuan
- State
Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yajun Yan
- BioChemical
Engineering Program, College of Engineering, University of Georgia, Athens, Georgia 30602, United States
| |
Collapse
|
24
|
Recent advances in engineering proteins for biocatalysis. Biotechnol Bioeng 2014; 111:1273-87. [DOI: 10.1002/bit.25240] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 02/10/2014] [Accepted: 03/19/2014] [Indexed: 01/14/2023]
|
25
|
Han L, Liu P, Peng Y, Lin J, Wang Q, Ma Y. Engineering the biosynthesis of novel rhamnolipids in Escherichia coli
for enhanced oil recovery. J Appl Microbiol 2014; 117:139-50. [DOI: 10.1111/jam.12515] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 03/22/2014] [Accepted: 03/31/2014] [Indexed: 11/28/2022]
Affiliation(s)
- L. Han
- Key Laboratory of Systems Microbial Biotechnology; Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; Tianjin China
- College of Life Sciences; University of Chinese Academy of Sciences; Beijing China
| | - P. Liu
- College of Pharmacy; State Key Laboratory of Medicinal Chemical Biology; Nankai University; Tianjin China
| | - Y. Peng
- Key Laboratory of Systems Microbial Biotechnology; Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; Tianjin China
| | - J. Lin
- College of Pharmacy; State Key Laboratory of Medicinal Chemical Biology; Nankai University; Tianjin China
| | - Q. Wang
- Key Laboratory of Systems Microbial Biotechnology; Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; Tianjin China
| | - Y. Ma
- Key Laboratory of Systems Microbial Biotechnology; Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; Tianjin China
| |
Collapse
|
26
|
Coussement P, Maertens J, Beauprez J, Van Bellegem W, De Mey M. One step DNA assembly for combinatorial metabolic engineering. Metab Eng 2014; 23:70-7. [PMID: 24594279 DOI: 10.1016/j.ymben.2014.02.012] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 01/28/2014] [Accepted: 02/24/2014] [Indexed: 11/19/2022]
Abstract
The rapid and efficient assembly of multi-step metabolic pathways for generating microbial strains with desirable phenotypes is a critical procedure for metabolic engineering, and remains a significant challenge in synthetic biology. Although several DNA assembly methods have been developed and applied for metabolic pathway engineering, many of them are limited by their suitability for combinatorial pathway assembly. The introduction of transcriptional (promoters), translational (ribosome binding site (RBS)) and enzyme (mutant genes) variability to modulate pathway expression levels is essential for generating balanced metabolic pathways and maximizing the productivity of a strain. We report a novel, highly reliable and rapid single strand assembly (SSA) method for pathway engineering. The method was successfully optimized and applied to create constructs containing promoter, RBS and/or mutant enzyme libraries. To demonstrate its efficiency and reliability, the method was applied to fine-tune multi-gene pathways. Two promoter libraries were simultaneously introduced in front of two target genes, enabling orthogonal expression as demonstrated by principal component analysis. This shows that SSA will increase our ability to tune multi-gene pathways at all control levels for the biotechnological production of complex metabolites, achievable through the combinatorial modulation of transcription, translation and enzyme activity.
Collapse
Affiliation(s)
- Pieter Coussement
- Centre of Expertise - Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium.
| | - Jo Maertens
- Centre of Expertise - Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium.
| | - Joeri Beauprez
- Centre of Expertise - Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium.
| | - Wouter Van Bellegem
- Centre of Expertise - Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium.
| | - Marjan De Mey
- Centre of Expertise - Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium.
| |
Collapse
|
27
|
Improving d-glucaric acid production from myo-inositol in E. coli by increasing MIOX stability and myo-inositol transport. Metab Eng 2014; 22:22-31. [DOI: 10.1016/j.ymben.2013.12.002] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 11/04/2013] [Accepted: 12/03/2013] [Indexed: 12/17/2022]
|
28
|
Metabolic engineering of Escherichia coli for biosynthesis of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) from glucose. Appl Microbiol Biotechnol 2013; 98:95-104. [PMID: 24113828 DOI: 10.1007/s00253-013-5285-z] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 09/18/2013] [Accepted: 09/19/2013] [Indexed: 01/23/2023]
Abstract
The Escherichia coli XL1-blue strain was metabolically engineered to synthesize poly(3-hydroxybutyrate-co-3-hydroxyvalerate) [P(3HB-co-3HV)] through 2-ketobutyrate, which is generated via citramalate pathway, as a precursor for propionyl-CoA. Two different metabolic pathways were examined for the synthesis of propionyl-CoA from 2-ketobutyrate. The first pathway is composed of the Dickeya dadantii 3937 2-ketobutyrate oxidase or the E. coli pyruvate oxidase mutant (PoxB L253F V380A) for the conversion of 2-ketobutyrate into propionate and the Ralstonia eutropha propionyl-CoA synthetase (PrpE) or the E. coli acetyl-CoA:acetoacetyl-CoA transferase for further conversion of propionate into propionyl-CoA. The second pathway employs pyruvate formate lyase encoded by the E. coli tdcE gene or the Clostridium difficile pflB gene for the direct conversion of 2-ketobutyrate into propionyl-CoA. As the direct conversion of 2-ketobutyrate into propionyl-CoA could not support the efficient production of P(3HB-co-3HV) from glucose, the first metabolic pathway was further examined. When the recombinant E. coli XL1-blue strain equipped with citramalate pathway expressing the E. coli poxB L253F V380A gene and R. eutropha prpE gene together with the R. eutropha PHA biosynthesis genes was cultured in a chemically defined medium containing 20 g/L of glucose as a sole carbon source, P(3HB-co-2.3 mol% 3HV) was produced up to the polymer content of 61.7 wt.%. Moreover, the 3HV monomer fraction in P(3HB-co-3HV) could be increased up to 5.5 mol% by additional deletion of the prpC and scpC genes, which are responsible for the metabolism of propionyl-CoA in host strains.
Collapse
|
29
|
Alper HS, Wittmann C. Editorial: how multiplexed tools and approaches speed up the progress of metabolic engineering. Biotechnol J 2013; 8:506-7. [PMID: 23636973 DOI: 10.1002/biot.201300167] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Systems metabolic engineering is becoming a widely-evoked paradigm for industrial strain design and optimization. Specifically, systems wide experimental and computational analyses of cells and their environments enable guide metabolic engineers to quickly parse the genome and creating desirable overproduction phenotypes.
Collapse
Affiliation(s)
- Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, USA.
| | | |
Collapse
|