1
|
Wu M, Sun Y, Zhu M, Zhu L, Lü J, Geng F. Molecular Dynamics-Based Allosteric Prediction Method to Design Key Residues in Threonine Dehydrogenase for Amino-Acid Production. ACS OMEGA 2021; 6:10975-10983. [PMID: 34056250 PMCID: PMC8153896 DOI: 10.1021/acsomega.1c00798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/01/2021] [Indexed: 06/12/2023]
Abstract
Allosteric proteins are considered as one of the most critical targets to design cell factories via synthetic biology approaches. Here, we proposed a molecular dynamics-based allosteric prediction method (MBAP) to screen indirect-binding sites and potential mutations for protein re-engineering. Using this MBAP method, we have predicted new sites to relieve the allosteric regulation of threonine dehydrogenase (TD) by isoleucine. An obtained mutation P441L has been verified with the ability to significantly reduce the allosteric regulation of TD in vitro assays and with the fermentation application in vivo for amino-acid production. These findings have proved the MBAP method as an effective and efficient predicting tool to find new positions of the allosteric enzymes, thus opening a new path to constructing cell factories in synthetic biology.
Collapse
Affiliation(s)
- Mingyu Wu
- School
of Pharmacy, Binzhou Medical University, No. 346 Guanhai Road, Yantai 264003, China
| | - Yu Sun
- School
of Pharmacy, Binzhou Medical University, No. 346 Guanhai Road, Yantai 264003, China
| | - Meiru Zhu
- School
of Pharmacy, Binzhou Medical University, No. 346 Guanhai Road, Yantai 264003, China
| | - Laiyu Zhu
- School
of Pharmacy, Binzhou Medical University, No. 346 Guanhai Road, Yantai 264003, China
| | - Junhong Lü
- School
of Pharmacy, Binzhou Medical University, No. 346 Guanhai Road, Yantai 264003, China
- Zhangjiang
Laboratory, Shanghai Advanced Research Institute,
Chinese Academy of Sciences, No. 239 Zhangheng Road, Pudong New District, Shanghai 201203, China
| | - Feng Geng
- School
of Pharmacy, Binzhou Medical University, No. 346 Guanhai Road, Yantai 264003, China
| |
Collapse
|
2
|
Mora-Villalobos JA, Zeng AP. Synthetic pathways and processes for effective production of 5-hydroxytryptophan and serotonin from glucose in Escherichia coli. J Biol Eng 2018; 12:3. [PMID: 29568327 PMCID: PMC5856393 DOI: 10.1186/s13036-018-0094-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 01/22/2018] [Indexed: 01/01/2023] Open
Abstract
Background Tryptophan derivatives such as 5-hydroxytryptophan (5HTP) and serotonin are valuable molecules with pharmaceutical interest. 5HTP is presently mainly obtained by extraction from the plant Griffonia simplicifolia and serotonin is produced by chemical synthesis. A simple biotechnological method for the production of these compounds is desired. Results In a first attempt to synthesize serotonin from glucose, we used a single engineered Escherichia coli strain and observed a low production of maximal 0.8 ± 0.2 mg/L of serotonin, probably due to the undesired site-reaction of direct decarboxylation of tryptophan and the consequent decrease of the precursor 5HTP. To circumvent this problem, we have constructed a stepwise system in which the 5HTP production and the serotonin conversion are separated. 962 ± 58 mg/L of 5HTP was produced in the first step using a recombinant strain with a semi-rationally engineered aromatic amino acid hydroxylase, the highest concentration reported so far. In a subsequent step of 5HTP bioconversion using a recombinant strain harboring a tryptophan decarboxylase, 154.3 ± 14.3 mg/L of serotonin was produced. Conclusions We present results of a two-stage fermentation process for the production of 5HTP and serotonin. The first strain is a highly efficient 5HTP producer, and after fermentation the supernatant is separated and used for the production of serotonin. This is the first report for the microbial production of serotonin from glucose.
Collapse
Affiliation(s)
- José-Aníbal Mora-Villalobos
- 1Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Hamburg, Germany.,Centro Nacional de Innovaciones Biotecnológicas, Centro Nacional de Alta Tecnología, San José, Costa Rica
| | - An-Ping Zeng
- 1Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Hamburg, Germany
| |
Collapse
|
3
|
Wu W, Zhang Y, Huang J, Wu Y, Liu D, Chen Z. Discovery of a Potentially New Subfamily of ELFV Dehydrogenases Effective for l
-Arginine Deamination by Enzyme Mining. Biotechnol J 2017; 13. [DOI: 10.1002/biot.201700305] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 09/11/2017] [Accepted: 10/09/2017] [Indexed: 11/05/2022]
Affiliation(s)
- Wenjun Wu
- Institute of Applied Chemistry, Department of Chemical Engineering; Tsinghua University; Beijing 100084 China
| | - Ye Zhang
- Institute of Applied Chemistry, Department of Chemical Engineering; Tsinghua University; Beijing 100084 China
| | - Jinhai Huang
- Institute of Applied Chemistry, Department of Chemical Engineering; Tsinghua University; Beijing 100084 China
| | - Yao Wu
- Institute of Applied Chemistry, Department of Chemical Engineering; Tsinghua University; Beijing 100084 China
| | - Dehua Liu
- Institute of Applied Chemistry, Department of Chemical Engineering; Tsinghua University; Beijing 100084 China
- Tsinghua Innovation Center in Dongguan; Dongguan 523808 China
| | - Zhen Chen
- Institute of Applied Chemistry, Department of Chemical Engineering; Tsinghua University; Beijing 100084 China
- Tsinghua Innovation Center in Dongguan; Dongguan 523808 China
| |
Collapse
|
4
|
Mora-Villalobos JA, Zeng AP. Protein and pathway engineering for the biosynthesis of 5-hydroxytryptophan in Escherichia coli. Eng Life Sci 2017; 17:892-899. [PMID: 32624837 DOI: 10.1002/elsc.201700064] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 05/16/2017] [Accepted: 05/29/2017] [Indexed: 11/06/2022] Open
Abstract
The hydroxylation of tryptophan is an important reaction in the biosynthesis of natural products. 5-Hydroxytryptophan (5HTP) is not only an important compound for its pharmaceutical value but also because it is the precursor of other molecules, such as serotonin. In this study, we have extended the metabolism of an E. coli strain to produce 5HTP. Aromatic amino acid hydroxylase from Cupriavidus taiwanensis (CtAAAH) was selected using an in silico structure-based approach. We have predicted and selected several substrate-determining residues using sequence, phylogenetic and functional divergence analyses; we also did rational design on CtAAAH to shift the enzyme preference from phenylalanine to tryptophan. Whole cell bioconversion assays were used to show the effect of predicted sites. In general, all of them decreased the preference toward phenylalanine and increased the tryptophan synthesis activity. The best performer, CtAAAH-W192F, was transformed into a strain that had the tryptophanase gene disrupted and carried a human tetrahydrobiopterin (BH4) regeneration pathway. The resulting strain was capable of synthesizing 2.5 mM 5HTP after 24 hours. This work demonstrates the application of computational approaches for protein engineering and further coupling with the bacterial metabolism.
Collapse
Affiliation(s)
- José-Aníbal Mora-Villalobos
- Institute of Bioprocess and Biosystems Engineering Hamburg University of Technology Hamburg Germany.,Centro Nacional de Innovaciones Biotecnológicas Centro Nacional de Alta Tecnología San Jose Costa Rica
| | - An-Ping Zeng
- Institute of Bioprocess and Biosystems Engineering Hamburg University of Technology Hamburg Germany
| |
Collapse
|
5
|
Huang J, Wu Y, Wu W, Zhang Y, Liu D, Chen Z. Cofactor recycling for co-production of 1,3-propanediol and glutamate by metabolically engineered Corynebacterium glutamicum. Sci Rep 2017; 7:42246. [PMID: 28176878 PMCID: PMC5296756 DOI: 10.1038/srep42246] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 01/05/2017] [Indexed: 01/03/2023] Open
Abstract
Production of 1,3-propanediol (1,3-PDO) from glycerol is a promising route toward glycerol biorefinery. However, the yield of 1,3-PDO is limited due to the requirement of NADH regeneration via glycerol oxidation process, which generates large amounts of undesired byproducts. Glutamate fermentation by Corynebacterium glutamicum is an important oxidation process generating excess NADH. In this study, we proposed a novel strategy to couple the process of 1,3-PDO synthesis with glutamate production for cofactor regeneration. With the optimization of 1,3-PDO synthesis route, C. glutamicum can efficiently convert glycerol into 1,3-PDO with the yield of ~ 1.0 mol/mol glycerol. Co-production of 1,3-PDO and glutamate was also achieved which increased the yield of glutamate by 18% as compared to the control. Since 1,3-PDO and glutamate can be easily separated in downstream process, this study provides a potential green route for coupled production of 1,3-PDO and glutamate to enhance the economic viability of biorefinery process.
Collapse
Affiliation(s)
- Jinhai Huang
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Yao Wu
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Wenjun Wu
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Ye Zhang
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Dehua Liu
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China.,Tsinghua Innovation Center in Dongguan, Dongguan 523808, China
| | - Zhen Chen
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China.,Tsinghua Innovation Center in Dongguan, Dongguan 523808, China
| |
Collapse
|
6
|
Metabolic engineering of Corynebacterium glutamicum for the production of 3-hydroxypropionic acid from glucose and xylose. Metab Eng 2017; 39:151-158. [DOI: 10.1016/j.ymben.2016.11.009] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 10/21/2016] [Accepted: 11/26/2016] [Indexed: 12/29/2022]
|
7
|
da Luz JA, Hans E, Frank D, Zeng AP. Analysis of intracellular metabolites of Corynebacterium glutamicum at high cell density with automated sampling and filtration and assessment of engineered enzymes for effective l-lysine production. Eng Life Sci 2016; 17:512-522. [PMID: 32624795 DOI: 10.1002/elsc.201600163] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 09/13/2016] [Accepted: 10/27/2016] [Indexed: 01/18/2023] Open
Abstract
Engineering of enzymes and pathways is generally required for the development of efficient strains for bioproduction processes. To this end, quantitative and reliable data of intracellular metabolites are highly desired, but often not available, especially for conditions more close to industrial applications, i.e. at high cell density and product concentration. Here, we investigated the intracellular metabolite profiles of an engineered l-lysine-producing Corynebacterium glutamicum strain and the corresponding wild-type strain to assess the impacts of deregulation of product inhibition of the key enzymes aspartate kinase and phosphoenolpyruvate carboxylase and to identify potentials for their further improvement. A bioreactor system with automated fast-sampling, filtration and on-filter quenching of the metabolism was used for a more reliable determination of intracellular metabolites in batch cultures with optical cell density (OD660) up to 40. The l-lysine-producing strain showed substantially different metabolite profiles in the amino acid metabolism, including increased intracellular pool sizes in the l-lysine-, l-homoserine- and l-threonine pathways and decreased intracellular pool sizes for all other determined amino acids. By comparing data of in vitro inhibition of the engineered enzymes and determined intracellular concentrations of the inhibitors it was found that the inferred in vivo activities of these enzymes are still significantly below their in vitro maximums. This work demonstrates the usefulness of metabolic analysis for assessing the impact of engineered enzymes and identifying targets for further strain development.
Collapse
Affiliation(s)
- Julian A da Luz
- Institute of Bioprocess- and Biosystems Engineering Hamburg University of Technology Hamburg Germany
| | - Enrico Hans
- Institute of Bioprocess- and Biosystems Engineering Hamburg University of Technology Hamburg Germany
| | - Doinita Frank
- Institute of Bioprocess- and Biosystems Engineering Hamburg University of Technology Hamburg Germany
| | - An-Ping Zeng
- Institute of Bioprocess- and Biosystems Engineering Hamburg University of Technology Hamburg Germany
| |
Collapse
|
8
|
Chen Z, Zeng AP. Protein engineering approaches to chemical biotechnology. Curr Opin Biotechnol 2016; 42:198-205. [DOI: 10.1016/j.copbio.2016.07.007] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 06/10/2016] [Accepted: 07/30/2016] [Indexed: 01/09/2023]
|
9
|
Metabolic engineering of Corynebacterium glutamicum for the de novo production of ethylene glycol from glucose. Metab Eng 2016; 33:12-18. [DOI: 10.1016/j.ymben.2015.10.013] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 09/14/2015] [Accepted: 10/30/2015] [Indexed: 11/23/2022]
|
10
|
Abstract
Synthetic biology (SB) is an emerging discipline, which is slowly reorienting the field of drug discovery. For thousands of years, living organisms such as plants were the major source of human medicines. The difficulty in resynthesizing natural products, however, often turned pharmaceutical industries away from this rich source for human medicine. More recently, progress on transformation through genetic manipulation of biosynthetic units in microorganisms has opened the possibility of in-depth exploration of the large chemical space of natural products derivatives. Success of SB in drug synthesis culminated with the bioproduction of artemisinin by microorganisms, a tour de force in protein and metabolic engineering. Today, synthetic cells are not only used as biofactories but also used as cell-based screening platforms for both target-based and phenotypic-based approaches. Engineered genetic circuits in synthetic cells are also used to decipher disease mechanisms or drug mechanism of actions and to study cell-cell communication within bacteria consortia. This review presents latest developments of SB in the field of drug discovery, including some challenging issues such as drug resistance and drug toxicity.
Collapse
Affiliation(s)
| | - Pablo Carbonell
- Faculty of Life Sciences, SYNBIOCHEM Centre, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
- Department of Experimental and Health Sciences (DCEXS), Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Universitat Pompeu Fabra (UPF), Barcelona, Spain
| |
Collapse
|
11
|
Chen Z, Wu Y, Huang J, Liu D. Metabolic engineering of Klebsiella pneumoniae for the de novo production of 2-butanol as a potential biofuel. BIORESOURCE TECHNOLOGY 2015; 197:260-5. [PMID: 26342337 DOI: 10.1016/j.biortech.2015.08.086] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 08/14/2015] [Accepted: 08/17/2015] [Indexed: 05/14/2023]
Abstract
Butanol isomers are important bulk chemicals and promising fuel substitutes. The inevitable toxicity of n-butanol and isobutanol to microbial cells hinders their final titers. In this study, we attempt to engineer Klebsiella pneumoniae for the de novo production of 2-butanol, another butanol isomer which shows lower toxicity than n-butanol and isobutanol. 2-Butanol synthesis was realized by the extension of the native meso-2,3-butanediol synthesis pathway with the introduction of diol dehydratase and secondary alcohol dehydrogenase. By the screening of different secondary alcohol dehydrogenases and diol dehydratases, 320mg/L of 2-butanol was produced by the best engineered K. pneumoniae. The production was increased to 720mg/L by knocking out the ldhA gene and appropriate addition of coenzyme B12. Further improvement of 2-butanol to 1030mg/L was achieved by protein engineering of diol dehydratase. This work lays the basis for the metabolic engineering of microorganism for the production of 2-butanol as potential biofuel.
Collapse
Affiliation(s)
- Zhen Chen
- Institute of Applied Chemistry, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China; Tsinghua Innovation Center in Dongguan, Dongguan 523808, China.
| | - Yao Wu
- Institute of Applied Chemistry, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Jinhai Huang
- Institute of Applied Chemistry, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Dehua Liu
- Institute of Applied Chemistry, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China; Tsinghua Innovation Center in Dongguan, Dongguan 523808, China
| |
Collapse
|
12
|
Chen Z, Sun H, Huang J, Wu Y, Liu D. Metabolic Engineering of Klebsiella pneumoniae for the Production of 2-Butanone from Glucose. PLoS One 2015; 10:e0140508. [PMID: 26465746 PMCID: PMC4605612 DOI: 10.1371/journal.pone.0140508] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 09/25/2015] [Indexed: 11/27/2022] Open
Abstract
2-Butanone is an important commodity chemical of wide application in different areas. In this study, Klebsiella pneumoniae was engineered to directly produce 2-butanone from glucose by extending its native 2, 3-butanediol synthesis pathway. To identify the potential enzyme for the efficient conversion of 2, 3-butanediol to 2-butanone, we screened different glycerol dehydratases and diol dehydratases. By introducing the diol dehydratase from Lactobacillus brevis and deleting the ldhA gene encoding lactate dehydrogenase, the engineered K. pneumoniae was able to accumulate 246 mg/L of 2-butanone in shake flask. With further optimization of culture condition, the titer of 2-butanone was increased to 450 mg/L. This study lays the basis for developing an efficient biological process for 2-butanone production.
Collapse
Affiliation(s)
- Zhen Chen
- Institute of Applied Chemistry, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
- Tsinghua Innovation Center in Dongguan, Dongguan 523808, China
- * E-mail:
| | - He Sun
- Institute of Applied Chemistry, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Jinhai Huang
- Institute of Applied Chemistry, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Yao Wu
- Institute of Applied Chemistry, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Dehua Liu
- Institute of Applied Chemistry, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
- Tsinghua Innovation Center in Dongguan, Dongguan 523808, China
| |
Collapse
|
13
|
Han L, Liu P, Sun J, Wu Y, Zhang Y, Chen W, Lin J, Wang Q, Ma Y. Engineering catechol 1, 2-dioxygenase by design for improving the performance of the cis, cis-muconic acid synthetic pathway in Escherichia coli. Sci Rep 2015; 5:13435. [PMID: 26306712 PMCID: PMC4549619 DOI: 10.1038/srep13435] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 07/27/2015] [Indexed: 11/09/2022] Open
Abstract
Regulating and ameliorating enzyme expression and activity greatly affects the performance of a given synthetic pathway. In this study, a new synthetic pathway for cis, cis-muconic acid (ccMA) production was reconstructed without exogenous induction by regulating the constitutive expression of the important enzyme catechol 1,2-dioxygenase (CatA). Next, new CatAs with significantly improved activities were developed to enhance ccMA production using structure-assisted protein design. Nine mutations were designed, simulated and constructed based on the analysis of the CatA crystal structure. These results showed that mutations at Gly72, Leu73 and/or Pro76 in CatA could improve enzyme activity, and the activity of the most effective mutant was 10-fold greater than that of the wild-type CatA from Acinetobacter sp. ADP1. The most productive synthetic pathway with a mutated CatA increased the titer of ccMA by more than 25%. Molecular dynamic simulation results showed that enlarging the entrance of the substrate-binding pocket in the mutants contributed to their increased enzyme activities and thus improved the performance of the synthetic pathway.
Collapse
Affiliation(s)
- Li Han
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Pi Liu
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin 300071, China
| | - Jixue Sun
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin 300071, China
| | - Yuanqing Wu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yuanyuan Zhang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Wujiu Chen
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Jianping Lin
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin 300071, China
| | - Qinhong Wang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yanhe Ma
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| |
Collapse
|
14
|
Scaife MA, Nguyen GTDT, Rico J, Lambert D, Helliwell KE, Smith AG. Establishing Chlamydomonas reinhardtii as an industrial biotechnology host. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 82:532-546. [PMID: 25641561 PMCID: PMC4515103 DOI: 10.1111/tpj.12781] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 01/19/2015] [Accepted: 01/20/2015] [Indexed: 05/20/2023]
Abstract
Microalgae constitute a diverse group of eukaryotic unicellular organisms that are of interest for pure and applied research. Owing to their natural synthesis of value-added natural products microalgae are emerging as a source of sustainable chemical compounds, proteins and metabolites, including but not limited to those that could replace compounds currently made from fossil fuels. For the model microalga, Chlamydomonas reinhardtii, this has prompted a period of rapid development so that this organism is poised for exploitation as an industrial biotechnology platform. The question now is how best to achieve this? Highly advanced industrial biotechnology systems using bacteria and yeasts were established in a classical metabolic engineering manner over several decades. However, the advent of advanced molecular tools and the rise of synthetic biology provide an opportunity to expedite the development of C. reinhardtii as an industrial biotechnology platform, avoiding the process of incremental improvement. In this review we describe the current status of genetic manipulation of C. reinhardtii for metabolic engineering. We then introduce several concepts that underpin synthetic biology, and show how generic parts are identified and used in a standard manner to achieve predictable outputs. Based on this we suggest that the development of C. reinhardtii as an industrial biotechnology platform can be achieved more efficiently through adoption of a synthetic biology approach.
Collapse
Affiliation(s)
- Mark A Scaife
- Department of Plant Science, University of CambridgeDowning Street, Cambridge, CB2 3EA, UK
- *For correspondence (e-mails or )
| | - Ginnie TDT Nguyen
- Department of Plant Science, University of CambridgeDowning Street, Cambridge, CB2 3EA, UK
| | - Juan Rico
- Department of Plant Science, University of CambridgeDowning Street, Cambridge, CB2 3EA, UK
| | - Devinn Lambert
- Department of Plant Science, University of CambridgeDowning Street, Cambridge, CB2 3EA, UK
| | - Katherine E Helliwell
- Department of Plant Science, University of CambridgeDowning Street, Cambridge, CB2 3EA, UK
| | - Alison G Smith
- Department of Plant Science, University of CambridgeDowning Street, Cambridge, CB2 3EA, UK
- *For correspondence (e-mails or )
| |
Collapse
|
15
|
Brockman IM, Prather KLJ. Dynamic metabolic engineering: New strategies for developing responsive cell factories. Biotechnol J 2015; 10:1360-9. [PMID: 25868062 DOI: 10.1002/biot.201400422] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 02/02/2015] [Accepted: 03/15/2015] [Indexed: 12/22/2022]
Abstract
Metabolic engineering strategies have enabled improvements in yield and titer for a variety of valuable small molecules produced naturally in microorganisms, as well as those produced via heterologous pathways. Typically, the approaches have been focused on up- and downregulation of genes to redistribute steady-state pathway fluxes, but more recently a number of groups have developed strategies for dynamic regulation, which allows rebalancing of fluxes according to changing conditions in the cell or the fermentation medium. This review highlights some of the recently published work related to dynamic metabolic engineering strategies and explores how advances in high-throughput screening and synthetic biology can support development of new dynamic systems. Dynamic gene expression profiles allow trade-offs between growth and production to be better managed and can help avoid build-up of undesired intermediates. The implementation is more complex relative to static control, but advances in screening techniques and DNA synthesis will continue to drive innovation in this field.
Collapse
Affiliation(s)
- Irene M Brockman
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kristala L J Prather
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
| |
Collapse
|
16
|
Chen Z, Rappert S, Zeng AP. Rational design of allosteric regulation of homoserine dehydrogenase by a nonnatural inhibitor L-lysine. ACS Synth Biol 2015; 4:126-31. [PMID: 24344690 DOI: 10.1021/sb400133g] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Allosteric proteins, which can sense different signals, are interesting biological parts for synthetic biology. In particular, the design of an artificial allosteric enzyme to sense an unnatural signal is both challenging and highly desired, for example, for a precise and dynamical control of fluxes of growth-essential but byproduct pathways in metabolic engineering of industrial microorganisms. In this work, we used homoserine dehydrogenase (HSDH) of Corynebacterium glutamicum, which is naturally allosterically regulated by threonine and isoleucine, as an example to demonstrate the feasibility of reengineering an allosteric enzyme to respond to an unnatural inhibitor L-lysine. For this purpose, the natural threonine binding sites of HSD were first predicted and verified by mutagenesis experiments. The threonine binding sites were then engineered to a lysine binding pocket. The reengineered HSD only responds to lysine inhibition but not to threonine. This is a significant step toward the construction of artificial molecular circuits for dynamic control of growth-essential byproduct formation pathway for lysine biosynthesis.
Collapse
Affiliation(s)
- Zhen Chen
- Institute
of Bioprocess and
Biosystems Engineering, Hamburg University of Technology Denickestrasse
15, D-21073 Hamburg, Germany
| | - Sugima Rappert
- 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
|
17
|
Liu Y, Shin HD, Li J, Liu L. Toward metabolic engineering in the context of system biology and synthetic biology: advances and prospects. Appl Microbiol Biotechnol 2014; 99:1109-18. [DOI: 10.1007/s00253-014-6298-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 12/02/2014] [Accepted: 12/04/2014] [Indexed: 12/22/2022]
|
18
|
Chen Z, Geng F, Zeng AP. Protein design and engineering of a de novo pathway for microbial production of 1,3-propanediol from glucose. Biotechnol J 2014; 10:284-9. [DOI: 10.1002/biot.201400235] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 05/25/2014] [Accepted: 06/06/2014] [Indexed: 01/25/2023]
|
19
|
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
|
20
|
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
|
21
|
Marcheschi RJ, Gronenberg LS, Liao JC. Protein engineering for metabolic engineering: current and next-generation tools. Biotechnol J 2013; 8:545-55. [PMID: 23589443 DOI: 10.1002/biot.201200371] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 03/07/2013] [Accepted: 03/20/2013] [Indexed: 11/10/2022]
Abstract
Protein engineering in the context of metabolic engineering is increasingly important to the field of industrial biotechnology. As the demand for biologically produced food, fuels, chemicals, food additives, and pharmaceuticals continues to grow, the ability to design and modify proteins to accomplish new functions will be required to meet the high productivity demands for the metabolism of engineered organisms. We review advances in selecting, modeling, and engineering proteins to improve or alter their activity. Some of the methods have only recently been developed for general use and are just beginning to find greater application in the metabolic engineering community. We also discuss methods of generating random and targeted diversity in proteins to generate mutant libraries for analysis. Recent uses of these techniques to alter cofactor use; produce non-natural amino acids, alcohols, and carboxylic acids; and alter organism phenotypes are presented and discussed as examples of the successful engineering of proteins for metabolic engineering purposes.
Collapse
Affiliation(s)
- Ryan J Marcheschi
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA, USA
| | | | | |
Collapse
|
22
|
Chen Z, Jandt U, Rappert S, Zeng AP. Proteindesign für die Entwicklung von industriellen Mikroorganismen. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/s12268-013-0276-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|