1
|
Yu L, Gao Y, He Y, Liu Y, Shen J, Liang H, Gong R, Duan H, Price NPJ, Song X, Deng Z, Chen W. Developing the E. coli platform for efficient production of UMP-derived chemicals. Metab Eng 2024; 83:61-74. [PMID: 38522576 DOI: 10.1016/j.ymben.2024.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 03/10/2024] [Accepted: 03/21/2024] [Indexed: 03/26/2024]
Abstract
5-Methyluridine (5-MU) is a prominent intermediate for industrial synthesis of several antiviral-drugs, however, its availability over the past decades has overwhelmingly relied on chemical and enzymatic strategies. Here, we have realized efficient production of 5-MU in E. coli, for the first time, via a designer artificial pathway consisting of a two-enzyme cascade (UMP 5-methylase and phosphatase). More importantly, we have engineered the E. coli cell factory to boost 5-MU production by systematic evaluation of multiple strategies, and as a proof of concept, we have further developed an antibiotic-free fermentation strategy to realize 5-MU production (10.71 g/L) in E. coli MB229 (a ΔthyA strain). Remarkably, we have also established a versatile and robust platform with exploitation of the engineered E. coli for efficient production of diversified UMP-derived chemicals. This study paves the way for future engineering of E. coli as a synthetic biology platform for acceleratively accessing UMP-derived chemical diversities.
Collapse
Affiliation(s)
- Le Yu
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Yaojie Gao
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Yuanyuan He
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Yang Liu
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Jianning Shen
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Han Liang
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Rong Gong
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - He Duan
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Neil P J Price
- US Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Peoria, IL, USA
| | - Xuemin Song
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Zixin Deng
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Wenqing Chen
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China.
| |
Collapse
|
2
|
Pang L, Yao D, Gao F, Bian X, Zhang Y, Zhong G. Biosyntheses of azetidine-containing natural products. Org Biomol Chem 2023; 21:7242-7254. [PMID: 37642579 DOI: 10.1039/d3ob01205k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Azetidine is a four-membered polar heterocycle including a basic secondary amine, and is characterized by its high ring-strain energy, strong molecular rigidity and satisfactory stability. As a result, azetidine exhibits great challenges in its chemical synthesis and biosynthesis, which may explain the limited number of azetidine-containing natural products uncovered to date. In particular, the biosynthetic mechanisms of naturally occurring azetidines are poorly understood. Only some of them have been intensively investigated and few reviews have been published for the summarization of azetidine biosynthesis. In this review, we provide a comprehensive description of the biosyntheses of all the azetidine-containing natural products, especially the biosyntheses of azetidine moieties. We hope that this review will draw much attention to the biosynthetic research of the largely unexplored azetidine moieties as well as the discovery of novel azetidine-containing natural products in the near future.
Collapse
Affiliation(s)
- Linlin Pang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China.
| | - Daichen Yao
- School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Fenghui Gao
- School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Xiaoying Bian
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China.
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China.
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology and Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Guannan Zhong
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China.
- Suzhou Research Institute of Shandong University, Suzhou 215123, China
| |
Collapse
|
3
|
McErlean M, Liu X, Cui Z, Gust B, Van Lanen SG. Identification and characterization of enzymes involved in the biosynthesis of pyrimidine nucleoside antibiotics. Nat Prod Rep 2021; 38:1362-1407. [PMID: 33404015 DOI: 10.1039/d0np00064g] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: up to September 2020 Hundreds of nucleoside-based natural products have been isolated from various microorganisms, several of which have been utilized in agriculture as pesticides and herbicides, in medicine as therapeutics for cancer and infectious disease, and as molecular probes to study biological processes. Natural products consisting of structural modifications of each of the canonical nucleosides have been discovered, ranging from simple modifications such as single-step alkylations or acylations to highly elaborate modifications that dramatically alter the nucleoside scaffold and require multiple enzyme-catalyzed reactions. A vast amount of genomic information has been uncovered the past two decades, which has subsequently allowed the first opportunity to interrogate the chemically intriguing enzymatic transformations for the latter type of modifications. This review highlights (i) the discovery and potential applications of structurally complex pyrimidine nucleoside antibiotics for which genetic information is known, (ii) the established reactions that convert the canonical pyrimidine into a new nucleoside scaffold, and (iii) the important tailoring reactions that impart further structural complexity to these molecules.
Collapse
Affiliation(s)
- M McErlean
- Department of Pharmaceutical Science, College of Pharmacy, University of Kentucky, USA.
| | - X Liu
- Department of Pharmaceutical Science, College of Pharmacy, University of Kentucky, USA.
| | - Z Cui
- Department of Pharmaceutical Science, College of Pharmacy, University of Kentucky, USA.
| | - B Gust
- Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, Germany
| | - S G Van Lanen
- Department of Pharmaceutical Science, College of Pharmacy, University of Kentucky, USA.
| |
Collapse
|
4
|
Abstract
Natural nonproteinogenic amino acids vastly outnumber the well-known 22 proteinogenic amino acids. Such amino acids are generated in specialized metabolic pathways. In these pathways, diverse biosynthetic transformations, ranging from isomerizations to the stereospecific functionalization of C-H bonds, are employed to generate structural diversity. The resulting nonproteinogenic amino acids can be integrated into more complex natural products. Here we review recently discovered biosynthetic routes to freestanding nonproteinogenic α-amino acids, with an emphasis on work reported between 2013 and mid-2019.
Collapse
Affiliation(s)
- Jason B Hedges
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Katherine S Ryan
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| |
Collapse
|
8
|
Rudolf JD, Dong LB, Huang T, Shen B. A genetically amenable platensimycin- and platencin-overproducer as a platform for biosynthetic explorations: a showcase of PtmO4, a long-chain acyl-CoA dehydrogenase. MOLECULAR BIOSYSTEMS 2015; 11:2717-26. [PMID: 26055255 PMCID: PMC4573825 DOI: 10.1039/c5mb00303b] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Platensimycin (PTM) and platencin (PTN) are members of a new class of promising drug leads that target bacterial and mammalian fatty acid synthases. We previously cloned and sequenced the PTM and PTN gene clusters, discovered six additional PTM-PTN dual producing strains, and demonstrated the dramatic overproduction of PTM and PTN by inactivating the pathway-specific regulators ptmR1 or ptnR1 in five different strains. Our ability to utilize these PTM-PTN dual overproducing strains was limited by their lack of genetic amenability. Here we report the construction of Streptomyces platensis SB12029, a genetically amenable, in-frame ΔptmR1 dual PTM-PTN overproducing strain. To highlight the potential of this strain for future PTM and PTN biosynthetic studies, we created the ΔptmR1 ΔptmO4 double mutant S. platensis SB12030. Fourteen PTM and PTN congeners, ten of which were new, were isolated from SB12030, shedding new insights into PTM and PTN biosynthesis. PtmO4, a long-chain acyl-CoA dehydrogenase, is strongly implicated to catalyze β-oxidation of the diterpenoid intermediates into the PTM and PTN scaffolds. SB12029 sets the stage for future biosynthetic and bioengineering studies of the PTM and PTN family of natural products.
Collapse
Affiliation(s)
- Jeffrey D Rudolf
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA.
| | | | | | | |
Collapse
|
9
|
Qi J, Liu J, Wan D, Cai YS, Wang Y, Li S, Wu P, Feng X, Qiu G, Yang SP, Chen W, Deng Z. Metabolic engineering of an industrial polyoxin producer for the targeted overproduction of designer nucleoside antibiotics. Biotechnol Bioeng 2015; 112:1865-71. [DOI: 10.1002/bit.25594] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2015] [Accepted: 03/03/2015] [Indexed: 11/07/2022]
Affiliation(s)
- Jianzhao Qi
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences; Wuhan University; Wuhan 430071 China
| | - Jin Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences; Wuhan University; Wuhan 430071 China
| | - Dan Wan
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences; Wuhan University; Wuhan 430071 China
| | - You-sheng Cai
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences; Wuhan University; Wuhan 430071 China
| | - Yinghu Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences; Wuhan University; Wuhan 430071 China
| | - Shunying Li
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences; Wuhan University; Wuhan 430071 China
| | - Pan Wu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences; Wuhan University; Wuhan 430071 China
| | - Xuan Feng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences; Wuhan University; Wuhan 430071 China
| | - Guofu Qiu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences; Wuhan University; Wuhan 430071 China
| | - Sheng-ping Yang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences; Wuhan University; Wuhan 430071 China
| | - Wenqing Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences; Wuhan University; Wuhan 430071 China
- State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology; Shanghai 200237 China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences; Wuhan University; Wuhan 430071 China
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology; Shanghai Jiao Tong University; Shanghai 200030 China
| |
Collapse
|
10
|
Ge Z, Ji Q, Chen C, Liao Q, Wu H, Liu X, Huang Y, Yuan L, Liao F. Synthesis and biological evaluation of novel 3-substituted amino-4-hydroxylcoumarin derivatives as chitin synthase inhibitors and antifungal agents. J Enzyme Inhib Med Chem 2015; 31:219-28. [DOI: 10.3109/14756366.2015.1016511] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Zhiqiang Ge
- Key Laboratory of Applied Chemistry of Chongqing Municipality, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, PR China and
| | - Qinggang Ji
- Key Laboratory of Applied Chemistry of Chongqing Municipality, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, PR China and
| | - Chunyan Chen
- Unit for Analytical Probe and Protein Biotechnology, Key Laboratory of Clinical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, Chongqing, PR China
| | - Qin Liao
- Key Laboratory of Applied Chemistry of Chongqing Municipality, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, PR China and
| | - Hualong Wu
- Key Laboratory of Applied Chemistry of Chongqing Municipality, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, PR China and
| | - Xiaofei Liu
- Key Laboratory of Applied Chemistry of Chongqing Municipality, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, PR China and
| | - Yanrong Huang
- Key Laboratory of Applied Chemistry of Chongqing Municipality, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, PR China and
| | - Lvjiang Yuan
- Key Laboratory of Applied Chemistry of Chongqing Municipality, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, PR China and
| | - Fei Liao
- Unit for Analytical Probe and Protein Biotechnology, Key Laboratory of Clinical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, Chongqing, PR China
| |
Collapse
|