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Holland CK, Jez JM. Fidelity in plant hormone modifications catalyzed by Arabidopsis GH3 acyl acid amido synthetases. J Biol Chem 2024; 300:107421. [PMID: 38815865 PMCID: PMC11253546 DOI: 10.1016/j.jbc.2024.107421] [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: 03/30/2024] [Revised: 05/06/2024] [Accepted: 05/22/2024] [Indexed: 06/01/2024] Open
Abstract
GRETCHEN HAGEN 3 (GH3) acyl acid amido synthetases conjugate amino acids to acyl acid hormones to either activate or inactivate the hormone molecule. The largest subgroup of GH3 proteins modify the growth-promoting hormone auxin (indole-3-acetic acid; IAA) with the second largest class activating the defense hormone jasmonic acid (JA). The two-step reaction mechanism of GH3 proteins provides a potential proofreading mechanism to ensure fidelity of hormone modification. Examining pyrophosphate release in the first-half reaction of Arabidopsis GH3 proteins that modify IAA (AtGH3.2/YDK2, AtGH3.5/WES1, AtGH3.17/VAS2), JA (AtGH3.11/JAR1), and other acyl acids (AtGH3.7, AtGH3.12/PBS3) indicates that acyl acid-AMP intermediates are hydrolyzed into acyl acid and AMP in the absence of the amino acid, a typical feature of pre-transfer editing mechanisms. Single-turnover kinetic analysis of AtGH3.2/YDK2 and AtGH3.5/WES1 shows that non-cognate acyl acid-adenylate intermediates are more rapidly hydrolyzed than the cognate IAA-adenylate. In contrast, AtGH3.11/JAR1 only adenylates JA, not IAA. While some of the auxin-conjugating GH3 proteins in Arabidopsis (i.e., AtGH3.5/WES1) accept multiple acyl acid substrates, others, like AtGH3.2/YDK2, are specific for IAA; however, both these proteins share similar active site residues. Biochemical analysis of chimeric variants of AtGH3.2/YDK2 and AtGH3.5/WES1 indicates that the C-terminal domain contributes to selection of cognate acyl acid substrates. These findings suggest that the hydrolysis of non-cognate acyl acid-adenylate intermediates, or proofreading, proceeds via a slowed structural switch that provides a checkpoint for fidelity before the full reaction proceeds.
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Affiliation(s)
- Cynthia K Holland
- Department of Biology, Williams College, Williamstown, Massachusetts; Department of Biology, Washington University in St Louis, St Louis, Missouri
| | - Joseph M Jez
- Department of Biology, Washington University in St Louis, St Louis, Missouri.
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2
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Ma D, Du G, Fang H, Li R, Zhang D. Advances and prospects in microbial production of biotin. Microb Cell Fact 2024; 23:135. [PMID: 38735926 PMCID: PMC11089781 DOI: 10.1186/s12934-024-02413-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 04/30/2024] [Indexed: 05/14/2024] Open
Abstract
Biotin, serving as a coenzyme in carboxylation reactions, is a vital nutrient crucial for the natural growth, development, and overall well-being of both humans and animals. Consequently, biotin is widely utilized in various industries, including feed, food, and pharmaceuticals. Despite its potential advantages, the chemical synthesis of biotin for commercial production encounters environmental and safety challenges. The burgeoning field of synthetic biology now allows for the creation of microbial cell factories producing bio-based products, offering a cost-effective alternative to chemical synthesis for biotin production. This review outlines the pathway and regulatory mechanism involved in biotin biosynthesis. Then, the strategies to enhance biotin production through both traditional chemical mutagenesis and advanced metabolic engineering are discussed. Finally, the article explores the limitations and future prospects of microbial biotin production. This comprehensive review not only discusses strategies for biotin enhancement but also provides in-depth insights into systematic metabolic engineering approaches aimed at boosting biotin production.
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Affiliation(s)
- Donghan Ma
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Guangqing Du
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Huan Fang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Rong Li
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China.
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China.
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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3
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Zhao JR, Zuo SQ, Xiao F, Guo FZ, Chen LY, Bi K, Cheng DY, Xu ZN. Advances in biotin biosynthesis and biotechnological production in microorganisms. World J Microbiol Biotechnol 2024; 40:163. [PMID: 38613659 DOI: 10.1007/s11274-024-03971-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 03/28/2024] [Indexed: 04/15/2024]
Abstract
Biotin, also known as vitamin H or B7, acts as a crucial cofactor in the central metabolism processes of fatty acids, amino acids, and carbohydrates. Biotin has important applications in food additives, biomedicine, and other fields. While the ability to synthesize biotin de novo is confined to microorganisms and plants, humans and animals require substantial daily intake, primarily through dietary sources and intestinal microflora. Currently, chemical synthesis stands as the primary method for commercial biotin production, although microbial biotin production offers an environmentally sustainable alternative with promising prospects. This review presents a comprehensive overview of the pathways involved in de novo biotin synthesis in various species of microbes and insights into its regulatory and transport systems. Furthermore, diverse strategies are discussed to improve the biotin production here, including mutation breeding, rational metabolic engineering design, artificial genetic modification, and process optimization. The review also presents the potential strategies for addressing current challenges for industrial-scale bioproduction of biotin in the future. This review is very helpful for exploring efficient and sustainable strategies for large-scale biotin production.
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Affiliation(s)
- Jia-Run Zhao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
- Institute of Biological Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Si-Qi Zuo
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
- Institute of Biological Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Feng Xiao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
- Institute of Biological Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310000, China
| | - Feng-Zhu Guo
- Zhejiang Sliver-Elephant Bio-engineering Co., Ltd., Tiantai, 317200, China
| | - Lu-Yi Chen
- Zhejiang Sliver-Elephant Bio-engineering Co., Ltd., Tiantai, 317200, China
| | - Ke Bi
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
- Institute of Biological Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Dong-Yuan Cheng
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
- Institute of Biological Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Zhi-Nan Xu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
- Institute of Biological Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
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4
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Chaudhury D, Torkelson ER, Meyers KA, Acheson JF, Landucci L, Pu Y, Sun Z, Tonelli M, Bingman CA, Smith RA, Karlen SD, Mansfield SD, Ralph J, Fox BG. Rapid Biocatalytic Synthesis of Aromatic Acid CoA Thioesters by Using Microbial Aromatic Acid CoA Ligases. Chembiochem 2023; 24:e202300001. [PMID: 36821718 PMCID: PMC10467583 DOI: 10.1002/cbic.202300001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 02/25/2023]
Abstract
Chemically labile ester linkages can be introduced into lignin by incorporation of monolignol conjugates, which are synthesized in planta by acyltransferases that use a coenzyme A (CoA) thioester donor and a nucleophilic monolignol alcohol acceptor. The presence of these esters facilitates processing and aids in the valorization of renewable biomass feedstocks. However, the effectiveness of this strategy is potentially limited by the low steady-state levels of aromatic acid thioester donors in plants. As part of an effort to overcome this, aromatic acid CoA ligases involved in microbial aromatic degradation were identified and screened against a broad panel of substituted cinnamic and benzoic acids involved in plant lignification. Functional fingerprinting of this ligase library identified four robust, highly active enzymes capable of facile, rapid, and high-yield synthesis of aromatic acid CoA thioesters under mild aqueous reaction conditions mimicking in planta activity.
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Affiliation(s)
- Debayan Chaudhury
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA
| | - Ella R Torkelson
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA
| | - Kaya A Meyers
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA
| | - Justin F Acheson
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA
| | - Leta Landucci
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA
| | - Yucen Pu
- Department of Botany and Department of Wood Science, University of British Columbia, 2424 Main Mall, Vancouver, BC V6T 1Z4, Canada
| | - Zimou Sun
- Department of Botany and Department of Wood Science, University of British Columbia, 2424 Main Mall, Vancouver, BC V6T 1Z4, Canada
| | - Marco Tonelli
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA
| | - Craig A Bingman
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA
| | - Rebecca A Smith
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA
| | - Steven D Karlen
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA
| | - Shawn D Mansfield
- Department of Botany and Department of Wood Science, University of British Columbia, 2424 Main Mall, Vancouver, BC V6T 1Z4, Canada
| | - John Ralph
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA
| | - Brian G Fox
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706, USA
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5
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Shi Y, Cao Q, Sun J, Hu X, Su Z, Xu Y, Zhang H, Lan L, Feng Y. The opportunistic pathogen Pseudomonas aeruginosa exploits bacterial biotin synthesis pathway to benefit its infectivity. PLoS Pathog 2023; 19:e1011110. [PMID: 36689471 PMCID: PMC9894557 DOI: 10.1371/journal.ppat.1011110] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 02/02/2023] [Accepted: 01/09/2023] [Indexed: 01/24/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that predominantly causes nosocomial and community-acquired lung infections. As a member of ESKAPE pathogens, carbapenem-resistant P. aeruginosa (CRPA) compromises the limited therapeutic options, raising an urgent demand for the development of lead compounds against previously-unrecognized drug targets. Biotin is an important cofactor, of which the de novo synthesis is an attractive antimicrobial target in certain recalcitrant infections. Here we report genetic and biochemical definition of P. aeruginosa BioH (PA0502) that functions as a gatekeeper enzyme allowing the product pimeloyl-ACP to exit from fatty acid synthesis cycle and to enter the late stage of biotin synthesis pathway. In relative to Escherichia coli, P. aeruginosa physiologically requires 3-fold higher level of cytosolic biotin, which can be attributed to the occurrence of multiple biotinylated enzymes. The BioH protein enables the in vitro reconstitution of biotin synthesis. The repertoire of biotin abundance is assigned to different mouse tissues and/or organ contents, and the plasma biotin level of mouse is around 6-fold higher than that of human. Removal of bioH renders P. aeruginosa biotin auxotrophic and impairs its intra-phagosome persistence. Based on a model of CD-1 mice mimicking the human environment, lung challenge combined with systemic infection suggested that BioH is necessary for the full virulence of P. aeruginosa. As expected, the biotin synthesis inhibitor MAC13772 is capable of dampening the viability of CRPA. Notably, MAC13772 interferes the production of pyocyanin, an important virulence factor of P. aeruginosa. Our data expands our understanding of P. aeruginosa biotin synthesis relevant to bacterial infectivity. In particular, this study represents the first example of an extracellular pathogen P. aeruginosa that exploits biotin cofactor as a fitness determinant, raising the possibility of biotin synthesis as an anti-CRPA target.
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Affiliation(s)
- Yu Shi
- Department of Microbiology, and Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Qin Cao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Jingdu Sun
- Department of Microbiology, and Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaofang Hu
- Fuzhou Medical College of Nanchang University, Fuzhou, Jiangxi, China
| | - Zhi Su
- Department of Microbiology, and Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Yongchang Xu
- Department of Microbiology, and Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Huimin Zhang
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Lefu Lan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang, China
- * E-mail: (LL); (YF)
| | - Youjun Feng
- Department of Microbiology, and Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
- * E-mail: (LL); (YF)
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6
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Xu Y, Yang J, Li W, Song S, Shi Y, Wu L, Sun J, Hou M, Wang J, Jia X, Zhang H, Huang M, Lu T, Gan J, Feng Y. Three enigmatic BioH isoenzymes are programmed in the early stage of mycobacterial biotin synthesis, an attractive anti-TB drug target. PLoS Pathog 2022; 18:e1010615. [PMID: 35816546 PMCID: PMC9302846 DOI: 10.1371/journal.ppat.1010615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/21/2022] [Accepted: 05/24/2022] [Indexed: 11/19/2022] Open
Abstract
Tuberculosis (TB) is one of the leading infectious diseases of global concern, and one quarter of the world’s population are TB carriers. Biotin metabolism appears to be an attractive anti-TB drug target. However, the first-stage of mycobacterial biotin synthesis is fragmentarily understood. Here we report that three evolutionarily-distinct BioH isoenzymes (BioH1 to BioH3) are programmed in biotin synthesis of Mycobacterium smegmatis. Expression of an individual bioH isoform is sufficient to allow the growth of an Escherichia coli ΔbioH mutant on the non-permissive condition lacking biotin. The enzymatic activity in vitro combined with biotin bioassay in vivo reveals that BioH2 and BioH3 are capable of removing methyl moiety from pimeloyl-ACP methyl ester to give pimeloyl-ACP, a cognate precursor for biotin synthesis. In particular, we determine the crystal structure of dimeric BioH3 at 2.27Å, featuring a unique lid domain. Apart from its catalytic triad, we also dissect the substrate recognition of BioH3 by pimeloyl-ACP methyl ester. The removal of triple bioH isoforms (ΔbioH1/2/3) renders M. smegmatis biotin auxotrophic. Along with the newly-identified Tam/BioC, the discovery of three unusual BioH isoforms defines an atypical ‘BioC-BioH(3)’ paradigm for the first-stage of mycobacterial biotin synthesis. This study solves a long-standing puzzle in mycobacterial nutritional immunity, providing an alternative anti-TB drug target.
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Affiliation(s)
- Yongchang Xu
- Departments of Microbiology, and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, The People’s Republic of China
| | - Jie Yang
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Science, Fudan University, Shanghai, The People’s Republic of China
| | - Weihui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, The People’s Republic of China
| | - Shuaijie Song
- Departments of Microbiology, and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, The People’s Republic of China
| | - Yu Shi
- Departments of Microbiology, and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, The People’s Republic of China
| | - Lihan Wu
- Departments of Microbiology, and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, The People’s Republic of China
| | - Jingdu Sun
- Departments of Microbiology, and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, The People’s Republic of China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, The People’s Republic of China
| | - Mengyun Hou
- Departments of Microbiology, and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, The People’s Republic of China
| | - Jinzi Wang
- Guangxi Key Laboratory of Utilization of Microbial and Botanical Resources & Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning, Guangxi, The People’s Republic of China
| | - Xu Jia
- Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, Sichuan, The People’s Republic of China
| | - Huimin Zhang
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Man Huang
- Departments of Microbiology, and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, The People’s Republic of China
| | - Ting Lu
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Jianhua Gan
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Science, Fudan University, Shanghai, The People’s Republic of China
- * E-mail: (JG); (YF)
| | - Youjun Feng
- Departments of Microbiology, and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, The People’s Republic of China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, The People’s Republic of China
- Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, Sichuan, The People’s Republic of China
- * E-mail: (JG); (YF)
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7
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Richardson SM, Harrison PJ, Herrera MA, Wang M, Verez R, Ortiz GP, Campopiano DJ. BioWF: A naturally-fused, di-domain biocatalyst from biotin biosynthesis displays an unexpectedly broad substrate scope. Chembiochem 2022; 23:e202200171. [PMID: 35695820 PMCID: PMC9544090 DOI: 10.1002/cbic.202200171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/10/2022] [Indexed: 11/30/2022]
Abstract
The carbon backbone of biotin is constructed from the C7 di‐acid pimelate, which is converted to an acyl‐CoA thioester by an ATP‐dependent, pimeloyl‐CoA synthetase (PCAS, encoded by BioW). The acyl‐thioester is condensed with ʟ‐alanine in a decarboxylative, Claisen‐like reaction to form an aminoketone (8‐amino‐7‐oxononanoic acid, AON). This step is catalysed by the pyridoxal 5’‐phosphate (PLP)‐dependent enzyme (AON synthase, AONS, encoded by BioF). Distinct versions of Bacillus subtilis BioW (BsBioW) and E. coli BioF (EcBioF) display strict substrate specificity. In contrast, a BioW‐BioF fusion from Corynebacterium amycolatum (CaBioWF) accepts a wider range of mono‐ and di‐fatty acids. Analysis of the active site of the BsBioW : pimeloyl‐adenylate complex suggested a key role for a Phe (F192) residue in the CaBioW domain; a F192Y mutant restored the substrate specificity to pimelate. This surprising substrate flexibility also extends to the CaBioF domain, which accepts ʟ‐alanine, ʟ‐serine and glycine. Structural models of the CaBioWF fusion provide insight into how both domains interact with each other and suggest the presence of an intra‐domain tunnel. The CaBioWF fusion catalyses conversion of various fatty acids and amino acids to a range of AON derivatives. Such unexpected, natural broad substrate scope suggests that the CaBioWF fusion is a versatile biocatalyst that can be used to prepare a number of aminoketone analogues.
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Affiliation(s)
- Shona M Richardson
- The University of Edinburgh School of Chemistry, Chemistry, David Brewster Road, EH9 3FJ, Edinburgh, UNITED KINGDOM
| | - Peter J Harrison
- The University of Edinburgh School of Chemistry, Chemistry, UNITED KINGDOM
| | - Michael A Herrera
- The University of Edinburgh School of Chemistry, Chemistry, UNITED KINGDOM
| | - Menglu Wang
- The University of Edinburgh School of Chemistry, Chemistry, UNITED KINGDOM
| | - Rebecca Verez
- The University of Edinburgh School of Chemistry, Chemistry, UNITED KINGDOM
| | | | - Dominic James Campopiano
- The Joseph Black Chemistry Building The King's Buildings, School of Chemistry, EastChem, David Brewster Road, EH9 3FJ, Edinburgh, UNITED KINGDOM
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8
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Bao Q, Zhi R, Zhou S, Zhao Y, Mao Y, Li G, Deng YU. Claisen condensation reaction mediated pimelate biosynthesis via the reverse adipate-degradation pathway and its isoenzymes. Chembiochem 2022; 23:e202200098. [PMID: 35352865 DOI: 10.1002/cbic.202200098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/30/2022] [Indexed: 11/11/2022]
Abstract
Pimelic acid is an important seven-carbon dicarboxylic acid, which is broadly applied in various fields. The industrial production of pimelic acid is mainly through chemical method, which is complicated and environment unfriendly. Herein, we found that pimelic acid could be biosynthesized by the reverse adipate-degradation pathway (RADP), a typical Claisen condensation reaction that could be applied to the arrangement of C-C bond. In order to strengthen the supply of glutaryl-CoA precursor, PA5530 protein was used to transport glutaric acid. Subsequently, we discovered that the enzymes in the BIOZ pathway was isoenzymes with the RADP. By combining the isoenzymes of the two pathways, the titer of pimelic acid reached 36.7 mg·L -1 under the optimal combination, which was increased by 382.9% compared with the control strain B-3. It was also the highest titer of pimelic acid biosynthesized by Claisen condensation reaction, laying foundations for further pimelic acid and its derivatives production.
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Affiliation(s)
- Qingqing Bao
- Jiangnan University, National Engineering Laboratory for Cereal Fermentation Technology (NELCF), CHINA
| | - Rui Zhi
- Jiangnan University, National Engineering Laboratory for Cereal Fermentation Technology (NELCF), CHINA
| | - Shenghu Zhou
- Jiangnan University, National Engineering Laboratory for Cereal Fermentation Technology (NELCF), CHINA
| | - Yunying Zhao
- Jiangnan University, National Engineering Laboratory for Cereal Fermentation Technology (NELCF), CHINA
| | - Yin Mao
- Jiangnan University, National Engineering Laboratory for Cereal Fermentation Technology (NELCF), CHINA
| | - Guohui Li
- Jiangnan University, National Engineering Laboratory for Cereal Fermentation Technology (NELCF), CHINA
| | - Y U Deng
- Jiangnan University, School of biotechnology, 1800 LIHU AVENUE, 214122, WUXI, CHINA
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9
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Rajakumara E, Abhishek S, Nitin K, Saniya D, Bajaj P, Schwaneberg U, Davari MD. Structure and Cooperativity in Substrate-Enzyme Interactions: Perspectives on Enzyme Engineering and Inhibitor Design. ACS Chem Biol 2022; 17:266-280. [PMID: 35041385 DOI: 10.1021/acschembio.1c00500] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Enzyme-based synthetic chemistry provides a green way to synthesize industrially important chemical scaffolds and provides incomparable substrate specificity and unmatched stereo-, regio-, and chemoselective product formation. However, using biocatalysts at an industrial scale has its challenges, like their narrow substrate scope, limited stability in large-scale one-pot reactions, and low expression levels. These limitations can be overcome by engineering and fine-tuning these biocatalysts using advanced protein engineering methods. A detailed understanding of the enzyme structure and catalytic mechanism and its structure-function relationship, cooperativity in binding of substrates, and dynamics of substrate-enzyme-cofactor complexes is essential for rational enzyme engineering for a specific purpose. This Review covers all these aspects along with an in-depth categorization of various industrially and pharmaceutically crucial bisubstrate enzymes based on their reaction mechanisms and their active site and substrate/cofactor-binding site structures. As the bisubstrate enzymes constitute around 60% of the known industrially important enzymes, studying their mechanism of actions and structure-activity relationship gives significant insight into deciding the targets for protein engineering for developing industrial biocatalysts. Thus, this Review is focused on providing a comprehensive knowledge of the bisubstrate enzymes' structure, their mechanisms, and protein engineering approaches to develop them into industrial biocatalysts.
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Affiliation(s)
- Eerappa Rajakumara
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Suman Abhishek
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Kulhar Nitin
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Dubey Saniya
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Priyanka Bajaj
- National Institute of Pharmaceutical Education and Research (NIPER), NH-44, Balanagar, Hyderabad 500037, India
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074 Aachen, Germany
| | - Mehdi D. Davari
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
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10
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Mapping the biosynthetic pathway of a hybrid polyketide-nonribosomal peptide in a metazoan. Nat Commun 2021; 12:4912. [PMID: 34389721 PMCID: PMC8363725 DOI: 10.1038/s41467-021-24682-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 06/30/2021] [Indexed: 11/10/2022] Open
Abstract
Polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) hybrid systems typically use complex protein-protein interactions to facilitate direct transfer of intermediates between these multimodular megaenzymes. In the canal-associated neurons (CANs) of Caenorhabditis elegans, PKS-1 and NRPS-1 produce the nemamides, the only known hybrid polyketide-nonribosomal peptides biosynthesized by animals, through a poorly understood mechanism. Here, we use genome editing and mass spectrometry to map the roles of individual PKS-1 and NRPS-1 enzymatic domains in nemamide biosynthesis. Furthermore, we show that nemamide biosynthesis requires at least five additional enzymes expressed in the CANs that are encoded by genes distributed across the worm genome. We identify the roles of these enzymes and discover a mechanism for trafficking intermediates between a PKS and an NRPS. Specifically, the enzyme PKAL-1 activates an advanced polyketide intermediate as an adenylate and directly loads it onto a carrier protein in NRPS-1. This trafficking mechanism provides a means by which a PKS-NRPS system can expand its biosynthetic potential and is likely important for the regulation of nemamide biosynthesis. The only known animal polyketide-nonribosomal peptides, the nemamides, are biosynthesized by two megasynthetases in the canal-associated neurons (CANs) of C. elegans. Here, the authors map the biosynthetic roles of individual megasynthetase domains and identify additional enzymes in the CANs required for nemamide biosynthesis.
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11
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Biochemical and structural characterization of the BioZ enzyme engaged in bacterial biotin synthesis pathway. Nat Commun 2021; 12:2056. [PMID: 33824341 PMCID: PMC8024396 DOI: 10.1038/s41467-021-22360-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/12/2021] [Indexed: 01/07/2023] Open
Abstract
Biotin is an essential micro-nutrient across the three domains of life. The paradigm earlier step of biotin synthesis denotes "BioC-BioH" pathway in Escherichia coli. Here we report that BioZ bypasses the canonical route to begin biotin synthesis. In addition to its origin of Rhizobiales, protein phylogeny infers that BioZ is domesticated to gain an atypical role of β-ketoacyl-ACP synthase III. Genetic and biochemical characterization demonstrates that BioZ catalyzes the condensation of glutaryl-CoA (or ACP) with malonyl-ACP to give 5'-keto-pimeloyl ACP. This intermediate proceeds via type II fatty acid synthesis (FAS II) pathway, to initiate the formation of pimeloyl-ACP, a precursor of biotin synthesis. To further explore molecular basis of BioZ activity, we determine the crystal structure of Agrobacterium tumefaciens BioZ at 1.99 Å, of which the catalytic triad and the substrate-loading tunnel are functionally defined. In particular, we localize that three residues (S84, R147, and S287) at the distant bottom of the tunnel might neutralize the charge of free C-carboxyl group of the primer glutaryl-CoA. Taken together, this study provides molecular insights into the BioZ biotin synthesis pathway.
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12
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Metabolomics reveals biomarkers of opioid use disorder. Transl Psychiatry 2021; 11:103. [PMID: 33542199 PMCID: PMC7862627 DOI: 10.1038/s41398-021-01228-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 01/08/2021] [Accepted: 01/18/2021] [Indexed: 01/30/2023] Open
Abstract
Opioid use disorder (OUD) is diagnosed using the qualitative criteria defined by the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-5). Diagnostic biomarkers for OUD do not currently exist. Our study focused on developing objective biological markers to differentiate chronic opiate users with OUD from chronic opiate users without OUD. Using biospecimens from the Golestan Cohort Study, we compared the metabolomics profiles of high opium users who were diagnosed as OUD positive with high opium users who were diagnosed as OUD negative. High opium use was defined as maximum weekly opium usage greater than or equal to the median usage (2.4 g per week), and OUD was defined as having 2 or more DSM-5 criteria in any 12-month period. Among the 218 high opium users in this study, 80 were diagnosed as OUD negative, while 138 were diagnosed as OUD positive. Seven hundred and twelve peaks differentiated high opium users diagnosed as OUD positive from high opium users diagnosed as OUD negative. Stepwise logistic regression modeling of subject characteristics data together with the 712 differentiating peaks revealed a signature that is 95% predictive of an OUD positive diagnosis, a significant (p < 0.0001) improvement over a 63% accurate prediction based on subject characteristic data for these samples. These results suggest that a metabolic profile can be used to predict an OUD positive diagnosis.
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13
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Sirithanakorn C, Cronan JE. Biotin, a universal and essential cofactor: Synthesis, ligation and regulation. FEMS Microbiol Rev 2021; 45:6081095. [PMID: 33428728 DOI: 10.1093/femsre/fuab003] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/08/2021] [Indexed: 12/22/2022] Open
Abstract
Biotin is a covalently attached enzyme cofactor required for intermediary metabolism in all three domains of life. Several important human pathogens (e.g. Mycobacterium tuberculosis) require biotin synthesis for pathogenesis. Humans lack a biotin synthetic pathway hence bacterial biotin synthesis is a prime target for new therapeutic agents. The biotin synthetic pathway is readily divided into early and late segments. Although pimelate, a seven carbon α,ω-dicarboxylic acid that contributes seven of the ten biotin carbons atoms, was long known to be a biotin precursor, its biosynthetic pathway was a mystery until the E. coli pathway was discovered in 2010. Since then, diverse bacteria encode evolutionarily distinct enzymes that replace enzymes in the E. coli pathway. Two new bacterial pimelate synthesis pathways have been elucidated. In contrast to the early pathway the late pathway, assembly of the fused rings of the cofactor, was long thought settled. However, a new enzyme that bypasses a canonical enzyme was recently discovered as well as homologs of another canonical enzyme that functions in synthesis of another protein-bound coenzyme, lipoic acid. Most bacteria tightly regulate transcription of the biotin synthetic genes in a biotin-responsive manner. The bifunctional biotin ligases which catalyze attachment of biotin to its cognate enzymes and repress biotin gene transcription are best understood regulatory system.
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Affiliation(s)
- Chaiyos Sirithanakorn
- Faculty of Medicine, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand.,Department of Microbiology, University of Illinois, Urbana, IL 61801, USA
| | - John E Cronan
- Department of Microbiology, University of Illinois, Urbana, IL 61801, USA.,Department of Biochemistry, University of Illinois, Urbana, IL 61801, USA
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14
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Driscoll TP, Verhoeve VI, Brockway C, Shrewsberry DL, Plumer M, Sevdalis SE, Beckmann JF, Krueger LM, Macaluso KR, Azad AF, Gillespie JJ. Evolution of Wolbachia mutualism and reproductive parasitism: insight from two novel strains that co-infect cat fleas. PeerJ 2020; 8:e10646. [PMID: 33362982 PMCID: PMC7750005 DOI: 10.7717/peerj.10646] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 12/03/2020] [Indexed: 12/26/2022] Open
Abstract
Wolbachiae are obligate intracellular bacteria that infect arthropods and certain nematodes. Usually maternally inherited, they may provision nutrients to (mutualism) or alter sexual biology of (reproductive parasitism) their invertebrate hosts. We report the assembly of closed genomes for two novel wolbachiae, wCfeT and wCfeJ, found co-infecting cat fleas (Ctenocephalides felis) of the Elward Laboratory colony (Soquel, CA, USA). wCfeT is basal to nearly all described Wolbachia supergroups, while wCfeJ is related to supergroups C, D and F. Both genomes contain laterally transferred genes that inform on the evolution of Wolbachia host associations. wCfeT carries the Biotin synthesis Operon of Obligate intracellular Microbes (BOOM); our analyses reveal five independent acquisitions of BOOM across the Wolbachia tree, indicating parallel evolution towards mutualism. Alternately, wCfeJ harbors a toxin-antidote operon analogous to the wPip cinAB operon recently characterized as an inducer of cytoplasmic incompatibility (CI) in flies. wCfeJ cinB and three adjacent genes are collectively similar to large modular toxins encoded in CI-like operons of certain Wolbachia strains and Rickettsia species, signifying that CI toxins streamline by fission of large modular toxins. Remarkably, the C. felis genome itself contains two CI-like antidote genes, divergent from wCfeJ cinA, revealing episodic reproductive parasitism in cat fleas and evidencing mobility of CI loci independent of WO-phage. Additional screening revealed predominant co-infection (wCfeT/wCfeJ) amongst C. felis colonies, though fleas in wild populations mostly harbor wCfeT alone. Collectively, genomes of wCfeT, wCfeJ, and their cat flea host supply instances of lateral gene transfers that could drive transitions between parasitism and mutualism.
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Affiliation(s)
| | - Victoria I Verhoeve
- Microbiology and Immunology, University of Maryland at Baltimore, Baltimore, MD, USA
| | | | | | - Mariah Plumer
- Microbiology and Immunology, University of Maryland at Baltimore, Baltimore, MD, USA
| | - Spiridon E Sevdalis
- Microbiology and Immunology, University of Maryland at Baltimore, Baltimore, MD, USA
| | - John F Beckmann
- Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
| | - Laura M Krueger
- Orange County Mosquito and Vector Control District, Garden Grove, CA, USA
| | - Kevin R Macaluso
- Microbiology and Immunology, University of South Alabama, Mobile, AL, USA
| | - Abdu F Azad
- Microbiology and Immunology, University of Maryland at Baltimore, Baltimore, MD, USA
| | - Joseph J Gillespie
- Microbiology and Immunology, University of Maryland at Baltimore, Baltimore, MD, USA
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15
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Bockman MR, Mishra N, Aldrich CC. The Biotin Biosynthetic Pathway in Mycobacterium tuberculosis is a Validated Target for the Development of Antibacterial Agents. Curr Med Chem 2020; 27:4194-4232. [PMID: 30663561 DOI: 10.2174/0929867326666190119161551] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 12/14/2018] [Accepted: 01/12/2019] [Indexed: 12/11/2022]
Abstract
Mycobacterium tuberculosis, responsible for Tuberculosis (TB), remains the leading cause of mortality among infectious diseases worldwide from a single infectious agent, with an estimated 1.7 million deaths in 2016. Biotin is an essential cofactor in M. tuberculosis that is required for lipid biosynthesis and gluconeogenesis. M. tuberculosis relies on de novo biotin biosynthesis to obtain this vital cofactor since it cannot scavenge sufficient biotin from a mammalian host. The biotin biosynthetic pathway in M. tuberculosis has been well studied and rigorously genetically validated providing a solid foundation for medicinal chemistry efforts. This review examines the mechanism and structure of the enzymes involved in biotin biosynthesis and ligation, summarizes the reported genetic validation studies of the pathway, and then analyzes the most promising inhibitors and natural products obtained from structure-based drug design and phenotypic screening.
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Affiliation(s)
- Matthew R Bockman
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, United States
| | - Neeraj Mishra
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, United States
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, United States
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16
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Walker PD, Rowe MT, Winter AJ, Weir AN, Akter N, Wang L, Race PR, Williams C, Song Z, Simpson TJ, Willis CL, Crump MP. A Priming Cassette Generates Hydroxylated Acyl Starter Units in Mupirocin and Thiomarinol Biosynthesis. ACS Chem Biol 2020; 15:494-503. [PMID: 31977176 DOI: 10.1021/acschembio.9b00969] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Mupirocin, a commercially available antibiotic produced by Pseudomonas fluorescens NCIMB 10586, and thiomarinol, isolated from the marine bacterium Pseudoalteromonas sp. SANK 73390, both consist of a polyketide-derived monic acid homologue esterified with either 9-hydroxynonanoic acid (mupirocin, 9HN) or 8-hydroxyoctanoic acid (thiomarinol, 8HO). The mechanisms of formation of these deceptively simple 9HN and 8HO fatty acid moieties in mup and tml, respectively, remain unresolved. To define starter unit generation, the purified mupirocin proteins MupQ, MupS, and MacpD and their thiomarinol equivalents (TmlQ, TmlS and TacpD) have been expressed and shown to convert malonyl coenzyme A (CoA) and succinyl CoA to 3-hydroxypropionoyl (3-HP) or 4-hydroxybutyryl (4-HB) fatty acid starter units, respectively, via the MupQ/TmlQ catalyzed generation of an unusual bis-CoA/acyl carrier protein (ACP) thioester, followed by MupS/TmlS catalyzed reduction. Mix and match experiments show MupQ/TmlQ to be highly selective for the correct CoA. MacpD/TacpD were interchangeable but alternate trans-acting ACPs from the mupirocin pathway (MacpA/TacpA) or a heterologous ACP (BatA) were nonfunctional. MupS and TmlS selectivity was more varied, and these reductases differed in their substrate and ACP selectivity. The solution structure of MacpD determined by NMR revealed a C-terminal extension with partial helical character that has been shown to be important for maintaining high titers of mupirocin. We generated a truncated MacpD construct, MacpD_T, which lacks this C-terminal extension but retains an ability to generate 3-HP with MupS and MupQ, suggesting further downstream roles in protein-protein interactions for this region of the ACP.
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Affiliation(s)
- Paul D. Walker
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS, United Kingdom
- College of Medical and Dental Sciences, Institute of Metabolism and Systems Research, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Matthew T. Rowe
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS, United Kingdom
| | - Ashley J. Winter
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS, United Kingdom
| | - Angus N.M. Weir
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS, United Kingdom
| | - Nahida Akter
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS, United Kingdom
| | - Luoyi Wang
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS, United Kingdom
| | - Paul R. Race
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, United Kingdom
| | - Christopher Williams
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS, United Kingdom
| | - Zhongshu Song
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS, United Kingdom
| | - Thomas J. Simpson
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS, United Kingdom
| | - Christine L. Willis
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS, United Kingdom
| | - Matthew P. Crump
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS, United Kingdom
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17
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Harnessing and engineering amide bond forming ligases for the synthesis of amides. Curr Opin Chem Biol 2020; 55:77-85. [PMID: 32058241 DOI: 10.1016/j.cbpa.2019.12.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 12/06/2019] [Accepted: 12/12/2019] [Indexed: 11/21/2022]
Abstract
The amide functional group is ubiquitous in nature and one of the most important motifs in pharmaceuticals, agrochemicals, and other valuable products. While coupling amides and carboxylic acids is a trivial synthetic transformation, it often requires protective group manipulation, along with stoichiometric quantities of expensive and deleterious coupling reagents. Nature has evolved a range of enzymes to construct amide bonds, the vast majority of which utilize adenosine triphosphate to activate the carboxylic acid substrate for amine coupling. Despite the fact that these enzymes operate under mild conditions, as well as possessing chemoselectivity and regioselectivity that obviates the need for protecting groups, their synthetic potential has been largely unexplored. In this review, we discuss recent research into the discovery, characterization, and development of amide bond forming enzymes, with an emphasis on stand-alone ligase enzymes that can generate amides directly from simple carboxylic acid and amine substrates.
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18
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Zeng Q, Yang Q, Jia J, Bi H. A Moraxella Virulence Factor Catalyzes an Essential Esterase Reaction of Biotin Biosynthesis. Front Microbiol 2020; 11:148. [PMID: 32117167 PMCID: PMC7026016 DOI: 10.3389/fmicb.2020.00148] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 01/22/2020] [Indexed: 11/13/2022] Open
Abstract
Pimeloyl-acyl carrier protein (ACP) methyl ester esterase catalyzes the last biosynthetic step of the pimelate moiety of biotin, a key intermediate in biotin biosynthesis. The paradigm pimeloyl-ACP methyl ester esterase is the BioH protein of Escherichia coli that hydrolyses the ester bond of pimeloyl-ACP methyl ester. Biotin synthesis in E. coli also requires the function of the malonyl-ACP methyltransferase gene (bioC) to employ a methylation strategy to allow elongation of a temporarily disguised malonate moiety to a pimelate moiety by the fatty acid synthetic enzymes. However, bioinformatics analyses of the extant bacterial genomes showed that bioH is absent in many bioC-containing bacteria. The genome of the Gram-negative bacterium, Moraxella catarrhalis lacks a gene encoding a homolog of any of the six known pimeloyl-ACP methyl ester esterase isozymes suggesting that this organism encodes a novel pimeloyl-ACP methyl ester esterase isoform. We report that this is the case. The gene encoding the new isoform, called btsA, was isolated by complementation of an E. coli bioH deletion strain. The requirement of BtsA for the biotin biosynthesis in M. catarrhalis was confirmed by a biotin auxotrophic phenotype caused by deletion of btsA in vivo and a reconstituted in vitro desthiobiotin synthesis system. Purified BtsA was shown to cleave the physiological substrate pimeloyl-ACP methyl ester to pimeloyl-ACP by use of a Ser117-His254-Asp287 catalytic triad. The lack of sequence alignment with other isozymes together with phylogenetic analyses revealed BtsA as a new class of pimeloyl-ACP methyl ester esterase. The involvement of BtsA in M. catarrhalis virulence was confirmed by the defect of bacterial invasion to lung epithelial cells and survival within macrophages in the ΔbtsA strains. Identification of the new esterase gene btsA exclusive in Moraxella species that links biotin biosynthesis to bacterial virulence, can reveal a new valuable target for development of drugs against M. catarrhalis.
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Affiliation(s)
- Qi Zeng
- Jiangsu Key Laboratory of Pathogen Biology, Department of Pathogen Biology, Nanjing Medical University, Nanjing, China
| | - Qi Yang
- Jiangsu Key Laboratory of Pathogen Biology, Department of Pathogen Biology, Nanjing Medical University, Nanjing, China
| | - Jia Jia
- Jiangsu Key Laboratory of Pathogen Biology, Department of Pathogen Biology, Nanjing Medical University, Nanjing, China
| | - Hongkai Bi
- Jiangsu Key Laboratory of Pathogen Biology, Department of Pathogen Biology, Nanjing Medical University, Nanjing, China
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19
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Structures of 2-Hydroxyisobutyric Acid-CoA Ligase Reveal Determinants of Substrate Specificity and Describe a Multi-Conformational Catalytic Cycle. J Mol Biol 2019; 431:2747-2761. [DOI: 10.1016/j.jmb.2019.05.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 05/14/2019] [Accepted: 05/16/2019] [Indexed: 02/01/2023]
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20
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Lux MC, Standke LC, Tan DS. Targeting adenylate-forming enzymes with designed sulfonyladenosine inhibitors. J Antibiot (Tokyo) 2019; 72:325-349. [PMID: 30982830 PMCID: PMC6594144 DOI: 10.1038/s41429-019-0171-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/19/2019] [Accepted: 02/26/2019] [Indexed: 02/07/2023]
Abstract
Adenylate-forming enzymes are a mechanistic superfamily that are involved in diverse biochemical pathways. They catalyze ATP-dependent activation of carboxylic acid substrates as reactive acyl adenylate (acyl-AMP) intermediates and subsequent coupling to various nucleophiles to generate ester, thioester, and amide products. Inspired by natural products, acyl sulfonyladenosines (acyl-AMS) that mimic the tightly bound acyl-AMP reaction intermediates have been developed as potent inhibitors of adenylate-forming enzymes. This simple yet powerful inhibitor design platform has provided a wide range of biological probes as well as several therapeutic lead compounds. Herein, we provide an overview of the nine structural classes of adenylate-forming enzymes and examples of acyl-AMS inhibitors that have been developed for each.
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Affiliation(s)
- Michaelyn C Lux
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Lisa C Standke
- Pharmacology Graduate Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Derek S Tan
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA. .,Pharmacology Graduate Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA. .,Chemical Biology Program, Sloan Kettering Institute, and Tri-Institutional Research Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
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21
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Functional Replacement of the BioC and BioH Proteins of Escherichia coli Biotin Precursor Biosynthesis by Ehrlichia chaffeensis Novel Proteins. Curr Microbiol 2019; 76:626-636. [PMID: 30915508 DOI: 10.1007/s00284-019-01669-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 03/05/2019] [Indexed: 01/22/2023]
Abstract
The biosynthesis of the pimelate moiety of biotin in Escherichia coli requires two specialized proteins, BioC and BioH. However, the enzymes that have BioC- or BioH-like activities show remarkable sequence diversity among biotin-producing bacteria. Here, we report that the intracellular rickettsial pathogen Ehrlichia chaffeensis encodes two novel proteins, BioT and BioU, which functionally replace the E. coli BioC and BioH proteins, respectively. The desthiobiotin assays demonstrated that these two proteins make pimeloyl-acyl carrier protein (ACP) from the substrate malonyl-ACP with the aid of the FAS II pathway, through the expected pimeloyl-ACP methyl ester intermediate. BioT and BioU homologues seem restricted to the species of Ehrlichia and its close relative, Anaplasma. Taken together, the synthesis of the biotin precursor in E. chaffeensis appears to be catalyzed by two novel BioC- and BioH-like proteins.
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22
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Cronan JE. Advances in synthesis of biotin and assembly of lipoic acid. Curr Opin Chem Biol 2018; 47:60-66. [PMID: 30236800 PMCID: PMC6289770 DOI: 10.1016/j.cbpa.2018.08.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 08/07/2018] [Indexed: 11/27/2022]
Abstract
Although biotin and lipoic acid are two universally conserved cofactors essential for intermediary metabolism, their synthetic pathways have become known only in recent years. Both pathways have unusual features. Biotin synthesis in Escherichia coli requires a methylation that is later removed whereas lipoic acid is assembled on the enzymes where it is required for activity by two different pathways.
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Affiliation(s)
- John E Cronan
- Department of Microbiology, University of Illinois, Urbana, IL 61801, USA; Department of Biochemistry, University of Illinois, Urbana, IL 61801, USA.
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23
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Fatty Acyl-AMP Ligases as Mechanistic Variants of ANL Superfamily and Molecular Determinants Dictating Substrate Specificities. J Indian Inst Sci 2018. [DOI: 10.1007/s41745-018-0084-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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24
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Carroll CS, Moore MM. Ironing out siderophore biosynthesis: a review of non-ribosomal peptide synthetase (NRPS)-independent siderophore synthetases. Crit Rev Biochem Mol Biol 2018; 53:356-381. [DOI: 10.1080/10409238.2018.1476449] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
| | - Margo M. Moore
- Department of Biological Sciences, Simon Fraser University, Burnaby, Canada
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25
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Natural separation of the acyl-CoA ligase reaction results in a non-adenylating enzyme. Nat Chem Biol 2018; 14:730-737. [PMID: 29867143 PMCID: PMC6008203 DOI: 10.1038/s41589-018-0061-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 03/19/2018] [Indexed: 01/23/2023]
Abstract
Acyl-coenzyme A (CoA) ligases catalyze the activation of carboxylic acids via a two-step reaction of adenylation followed by thioesterification. Here, we report the discovery of a non-adenylating acyl-CoA ligase PtmA2 and the functional separation of an acyl-CoA ligase reaction. Both PtmA1 and PtmA2, two acyl-CoA ligases from the biosynthetic pathway of platensimycin and platencin, are necessary for the two steps of CoA activation. Gene inactivation of ptmA1 and ptmA2 resulted in the accumulation of free acid and adenylate intermediates, respectively. Enzymatic and structural characterization of PtmA2 confirmed its ability to only catalyze thioesterification. Structural characterization of PtmA2 revealed it binds both free acid and adenylate substrates and undergoes the established mechanism of domain alternation. Finally, site-directed mutagenesis restored both the adenylation and complete CoA activation reactions. This study challenges the currently accepted paradigm of adenylating enzymes and inspires future investigations on functionally separated acyl-CoA ligases and their ramifications in biology.
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Hemmerling F, Lebe KE, Wunderlich J, Hahn F. An Unusual Fatty Acyl:Adenylate Ligase (FAAL)-Acyl Carrier Protein (ACP) Didomain in Ambruticin Biosynthesis. Chembiochem 2018. [DOI: 10.1002/cbic.201800084] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Franziska Hemmerling
- Professur für Organische Chemie (Lebensmittelchemie); Fakultät für Biologie, Chemie und Geowissenschaften; Universität Bayreuth; Universitätsstrasse 30 95447 Bayreuth Germany
- Biomolekulares Wirkstoffzentrum; Leibniz Universität Hannover; Schneiderberg 38 30167 Hannover Germany
| | - Karen E. Lebe
- Biomolekulares Wirkstoffzentrum; Leibniz Universität Hannover; Schneiderberg 38 30167 Hannover Germany
| | - Johannes Wunderlich
- Professur für Organische Chemie (Lebensmittelchemie); Fakultät für Biologie, Chemie und Geowissenschaften; Universität Bayreuth; Universitätsstrasse 30 95447 Bayreuth Germany
| | - Frank Hahn
- Professur für Organische Chemie (Lebensmittelchemie); Fakultät für Biologie, Chemie und Geowissenschaften; Universität Bayreuth; Universitätsstrasse 30 95447 Bayreuth Germany
- Biomolekulares Wirkstoffzentrum; Leibniz Universität Hannover; Schneiderberg 38 30167 Hannover Germany
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Manandhar M, Cronan JE. A Canonical Biotin Synthesis Enzyme, 8-Amino-7-Oxononanoate Synthase (BioF), Utilizes Different Acyl Chain Donors in Bacillus subtilis and Escherichia coli. Appl Environ Microbiol 2018; 84:e02084-17. [PMID: 29054876 PMCID: PMC5734022 DOI: 10.1128/aem.02084-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 10/15/2017] [Indexed: 12/24/2022] Open
Abstract
BioF (8-amino-7-oxononanoate synthase) is a strictly conserved enzyme that catalyzes the first step in assembly of the fused heterocyclic rings of biotin. The BioF acyl chain donor has long been thought to be pimeloyl-CoA. Indeed, in vitro the Escherichia coli and Bacillus sphaericus enzymes have been shown to condense pimeloyl-CoA with l-alanine in a pyridoxal 5'-phosphate-dependent reaction with concomitant CoA release and decarboxylation of l-alanine. However, recent in vivo studies of E. coli and Bacillus subtilis suggested that the BioF proteins of the two bacteria could have different specificities for pimelate thioesters in that E. coli BioF may utilize either pimeloyl coenzyme A (CoA) or the pimelate thioester of the acyl carrier protein (ACP) of fatty acid synthesis. In contrast, B. subtilis BioF seemed likely to be specific for pimeloyl-CoA and unable to utilize pimeloyl-ACP. We now report genetic and in vitro data demonstrating that B. subtilis BioF specifically utilizes pimeloyl-CoA.IMPORTANCE Biotin is an essential vitamin required by mammals and birds because, unlike bacteria, plants, and some fungi, these organisms cannot make biotin. Currently, the biotin included in vitamin tablets and animal feeds is made by chemical synthesis. This is partly because the biosynthetic pathways in bacteria are incompletely understood. This paper defines an enzyme of the Bacillus subtilis pathway and shows that it differs from that of Escherichia coli in the ability to utilize specific precursors. These bacteria have been used in biotin production and these data may aid in making biotin produced by biotechnology commercially competitive with that produced by chemical synthesis.
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Affiliation(s)
- Miglena Manandhar
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - John E Cronan
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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Gerlt JA. Genomic Enzymology: Web Tools for Leveraging Protein Family Sequence-Function Space and Genome Context to Discover Novel Functions. Biochemistry 2017; 56:4293-4308. [PMID: 28826221 PMCID: PMC5569362 DOI: 10.1021/acs.biochem.7b00614] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
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The exponentially increasing number
of protein and nucleic acid
sequences provides opportunities to discover novel enzymes, metabolic
pathways, and metabolites/natural products, thereby adding to our
knowledge of biochemistry and biology. The challenge has evolved from
generating sequence information to mining the databases to integrating
and leveraging the available information, i.e., the availability of
“genomic enzymology” web tools. Web tools that allow
identification of biosynthetic gene clusters are widely used by the
natural products/synthetic biology community, thereby facilitating
the discovery of novel natural products and the enzymes responsible
for their biosynthesis. However, many novel enzymes with interesting
mechanisms participate in uncharacterized small-molecule metabolic
pathways; their discovery and functional characterization also can
be accomplished by leveraging information in protein and nucleic acid
databases. This Perspective focuses on two genomic enzymology web
tools that assist the discovery novel metabolic pathways: (1) Enzyme
Function Initiative-Enzyme Similarity Tool (EFI-EST) for generating
sequence similarity networks to visualize and analyze sequence–function
space in protein families and (2) Enzyme Function Initiative-Genome
Neighborhood Tool (EFI-GNT) for generating genome neighborhood networks
to visualize and analyze the genome context in microbial and fungal
genomes. Both tools have been adapted to other applications to facilitate
target selection for enzyme discovery and functional characterization.
As the natural products community has demonstrated, the enzymology
community needs to embrace the essential role of web tools that allow
the protein and genome sequence databases to be leveraged for novel
insights into enzymological problems.
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Affiliation(s)
- John A Gerlt
- Departments of Biochemistry and Chemistry, Institute for Genomic Biology, University of Illinois , Urbana-Champaign Urbana, Illinois 61801, United States
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Manandhar M, Cronan JE. Pimelic acid, the first precursor of the Bacillus subtilis biotin synthesis pathway, exists as the free acid and is assembled by fatty acid synthesis. Mol Microbiol 2017; 104:595-607. [PMID: 28196402 PMCID: PMC5426962 DOI: 10.1111/mmi.13648] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Biotin synthetic pathways are readily separated into two stages, synthesis of the seven carbon α, ω-dicarboxylic acid pimelate moiety and assembly of the fused heterocyclic rings. The biotin pathway genes responsible for pimelate moiety synthesis vary widely among bacteria whereas the ring synthesis genes are highly conserved. Bacillus subtilis seems to have redundant genes, bioI and bioW, for generation of the pimelate intermediate. Largely consistent with previous genetic studies it was found that deletion of bioW caused a biotin auxotrophic phenotype whereas deletion of bioI did not. BioW is a pimeloyl-CoA synthetase that converts pimelic acid to pimeloyl-CoA. The essentiality of BioW for biotin synthesis indicates that the free form of pimelic acid is an intermediate in biotin synthesis although this is not the case in E. coli. Since the origin of pimelic acid in Bacillus subtilis is unknown, 13 C-NMR studies were carried out to decipher the pathway for its generation. The data provided evidence for the role of free pimelate in biotin synthesis and the involvement of fatty acid synthesis in pimelate production. Cerulenin, an inhibitor of the key fatty acid elongation enzyme, FabF, markedly decreased biotin production by B. subtilis resting cells whereas a strain having a cerulenin-resistant FabF mutant produced more biotin. In addition, supplementation with pimelic acid fully restored biotin production in cerulenin-treated cells. These results indicate that pimelic acid originating from fatty acid synthesis pathway is a bona fide precursor of biotin in B. subtilis.
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Affiliation(s)
- Miglena Manandhar
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - John E Cronan
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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