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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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2
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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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3
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Chang MY, Chen PH. Synthesis of 4-sulfonyl-1,7-diesters via K 2CO 3-mediated alkylative debenzoylation of α-sulfonyl o-hydroxyacetophenones with acrylates. Org Biomol Chem 2024; 22:1194-1204. [PMID: 38224195 DOI: 10.1039/d3ob01703f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
The synthesis of 4-sulfonyl-1,7-diesters was well developed, under open-vessel conditions, by K2CO3-mediated double alkylation of α-sulfonyl o-hydroxyacetophenones with acrylates and tandem debenzoylation of the resulting α,α-disubstituted o-hydroxyacetophenones. A plausible mechanism is proposed and discussed here. This high-yielding protocol provides a highly effective intermolecular alkylation and intramolecular debenzoylation via the formation of two carbon-carbon (C-C) single bonds and the cleavage of a carbon-carbon (C-C) single bond.
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Affiliation(s)
- Meng-Yang Chang
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
- NPUST College of Professional Studies, National Pingtung University of Science and Technology, Pingtung 912, Taiwan
| | - Pin-Hsien Chen
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
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4
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de Carvalho CC, Murray IP, Nguyen H, Nguyen T, Cantu DC. Acyltransferase families that act on thioesters: Sequences, structures, and mechanisms. Proteins 2024; 92:157-169. [PMID: 37776148 DOI: 10.1002/prot.26599] [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: 05/09/2023] [Revised: 09/11/2023] [Accepted: 09/19/2023] [Indexed: 10/01/2023]
Abstract
Acyltransferases (AT) are enzymes that catalyze the transfer of acyl group to a receptor molecule. This review focuses on ATs that act on thioester-containing substrates. Although many ATs can recognize a wide variety of substrates, sequence similarity analysis allowed us to classify the ATs into fifteen distinct families. Each AT family is originated from enzymes experimentally characterized to have AT activity, classified according to sequence similarity, and confirmed with tertiary structure similarity for families that have crystallized structures available. All the sequences and structures of the AT families described here are present in the thioester-active enzyme (ThYme) database. The AT sequences and structures classified into families and available in the ThYme database could contribute to enlightening the understanding acyl transfer to thioester-containing substrates, most commonly coenzyme A, which occur in multiple metabolic pathways, mostly with fatty acids.
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Affiliation(s)
- Caio C de Carvalho
- Department of Chemical and Materials Engineering, University of Nevada, Reno, Reno, Nevada, USA
| | - Ian P Murray
- Department of Chemical and Materials Engineering, University of Nevada, Reno, Reno, Nevada, USA
| | - Hung Nguyen
- Department of Computer Science and Software Engineering, Auburn University, Auburn, Alabama, USA
| | - Tin Nguyen
- Department of Chemical and Materials Engineering, University of Nevada, Reno, Reno, Nevada, USA
- Department of Computer Science and Software Engineering, Auburn University, Auburn, Alabama, USA
| | - David C Cantu
- Department of Chemical and Materials Engineering, University of Nevada, Reno, Reno, Nevada, USA
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5
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Li X, Hu X, Zhao X, Wang F, Zhao Y. Pulsed electric field enhanced Bacillus sp. DL4 biodegradation of Triclosan: Focusing on operational performance and metabolomic analysis. ENVIRONMENTAL TECHNOLOGY 2023:1-39. [PMID: 37470412 DOI: 10.1080/09593330.2023.2238930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
Electrochemical-assisted microbial degradation technology was considered a crucial strategy to reduce micropollutants, but the mechanism of the pulsed electric field (PEF) in affecting biodegradation had not been systematically studied. This study aimed to construct a bio-electrochemical system (BES) using PEF to investigate its effect on the degradation of triclosan (TCS) by the aerobic bacterium Bacillus sp. DL4. The operating optimal parameters for the BES (i.e., 0.01 A of the pulsed current, 1000 Hz of the pulse frequency, Fe (+) - C (-) of the plate materials, 4 cm of the plate spacing) were obtained by batch experiments. The maximum biomass (OD600 = 1.0 ± 0.05) was achieved and the removal efficiency of TCS reached above 95% in 24 h under the obtained operating conditions. Meanwhile, a thorough and methodical investigation of the metabolites in strain DL4 stimulated by PEF using untargeted Liquid Chromatography - Mass Spectrometry (LC-MS). In multivariate analysis, the experimental groups showed a notable separation in Principal Components Analysis (PCA) and Orthogonal Partial Least Squares Analysis discriminant analysis (OPLS-DA) score plots. A total of 3181 differential metabolites were obtained, and the up-regulated metabolites were mainly related to "Aminoacyl-tRNA biosynthesis", "Arginine and proline metabolism", "Lysine degradation", "ABC transporters", and "TCA cycle", implying that PEF enhanced the degradation efficiency of TCS by enriching functional genes with transport ability and ion migration ability in cells. This study illuminated how PEF can affect TCS biodegradation and gives insights into the application prospect of electrochemical-assisted biodegradation technology in water environment treatment.
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Affiliation(s)
- Xuejie Li
- Key Laboratory of Ministry of Education on Safe Mining of Deep Metal Mines, Northeastern University, Shenyang 110819, P. R. China
| | - Xiaomin Hu
- Key Laboratory of Ministry of Education on Safe Mining of Deep Metal Mines, Northeastern University, Shenyang 110819, P. R. China
| | - Xin Zhao
- Key Laboratory of Ministry of Education on Safe Mining of Deep Metal Mines, Northeastern University, Shenyang 110819, P. R. China
| | - Fan Wang
- Key Laboratory of Ministry of Education on Safe Mining of Deep Metal Mines, Northeastern University, Shenyang 110819, P. R. China
| | - Yan Zhao
- Key Laboratory of Ministry of Education on Safe Mining of Deep Metal Mines, Northeastern University, Shenyang 110819, P. R. China
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6
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Li R, Tao J, Huang D, Zhou W, Gao L, Wang X, Chen H, Huang H. Investigating the effects of biodegradable microplastics and copper ions on probiotic (Bacillus amyloliquefaciens): Toxicity and application. JOURNAL OF HAZARDOUS MATERIALS 2023; 443:130081. [PMID: 36367472 DOI: 10.1016/j.jhazmat.2022.130081] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/13/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Currently, microplastic pollution is more serious and complicates the toxic effects of other co-existing pollutants in the environment. However, the effect and mechanism of biodegradable plastics on the growth and metabolism of probiotic remain unclear. This work selected Bacillus amyloliquefaciens as model bacterium for a three-day exposure experiment to probe the issues. The results showed that 100 mg/L polylactic acid microplastics (PLA MPs) (3-4 mm, flake shape) caused oxidative damage to cell membranes, disrupted cell wall composition and inhibited cell growth by 21.2-27.5 %. The toxicity was not simply additive or synergistic effects when PLA MPs (100 mg/L) and copper ions (10 mg/L) coexisted. PLA MPs did not significantly increase the toxicity of copper to bacteria, instead triggered some mechanisms to resist the toxicity of copper. The bacteria formed spores to resist PLA MPs, while the copper ions toxicity was weaken by chelation and efflux. It is worth noting that copper ions instead increased the expression of genes related fengycin and iturin then improving the bacteriostatic activity of the probiotic. This paper deeply analyzes the toxicity mechanism of combined pollution on Bacillus amyloliquefacien, and also provides new perspective for helping to inhibit pathogenic bacteria under biodegradable microplastics and metal stress.
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Affiliation(s)
- Ruijin Li
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Jiaxi Tao
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Danlian Huang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China.
| | - Wei Zhou
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Lan Gao
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Xinya Wang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Haojie Chen
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Hai Huang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
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7
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Kairamkonda M, Sharma M, Gupta P, Poluri KM. Overexpression of bacteriophage T4 and T7 endolysins differentially regulate the metabolic fingerprint of host Escherichia coli. Int J Biol Macromol 2022; 221:212-223. [PMID: 36075302 DOI: 10.1016/j.ijbiomac.2022.09.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/26/2022] [Accepted: 09/02/2022] [Indexed: 12/21/2022]
Abstract
Bioactive proteins are often overexpressed in different host systems for biotechnological/biomedical applications. Endolysins are natural bactericidal proteins that cleave the bacterial peptidoglycan membrane, and have the potential to be the next-generation enzybiotics. Therefore, the present study aims to elucidate the impact of two endolysins (T4L, T7L) overexpression on metabolic fingerprint of E. coli using NMR spectroscopy. The 1H NMR-based metabolomics analysis revealed global metabolite profiles of E. coli in response to endolysins. The study has identified nearly 75 metabolites, including organic acids, amino acids, sugars and nucleic acids. RNA Polymerase (RNAP) has been considered as reference protein for marking the specific alterations in metabolic pathways. The data suggested downregulation of central carbon metabolic pathway in both endolysins overexpression, but to a different extent. Also, the endolysin overexpression have highlighted the enhanced metabolic load and stress generation in the host cells, thus leading to the activation of osmoregulatory pathways. The overall changes in metabolic fingerprint of E. coli highlights the enhanced perturbations during the overexpression of T4L as compared to T7L. These untargeted metabolic studies shed light on the regulation of molecular pathways during the heterologous overexpression of these lytic enzymes that are lethal to the host.
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Affiliation(s)
- Manikyaprabhu Kairamkonda
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Meenakshi Sharma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Payal Gupta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Krishna Mohan Poluri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India; Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India.
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8
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Functional Versatility of the Human 2-Oxoadipate Dehydrogenase in the L-Lysine Degradation Pathway toward Its Non-Cognate Substrate 2-Oxopimelic Acid. Int J Mol Sci 2022; 23:ijms23158213. [PMID: 35897808 PMCID: PMC9367764 DOI: 10.3390/ijms23158213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/23/2022] [Accepted: 07/24/2022] [Indexed: 11/17/2022] Open
Abstract
The human 2-oxoadipate dehydrogenase complex (OADHc) in L-lysine catabolism is involved in the oxidative decarboxylation of 2-oxoadipate (OA) to glutaryl-CoA and NADH (+H+). Genetic findings have linked the DHTKD1 encoding 2-oxoadipate dehydrogenase (E1a), the first component of the OADHc, to pathogenesis of AMOXAD, eosinophilic esophagitis (EoE), and several neurodegenerative diseases. A multipronged approach, including circular dichroism spectroscopy, Fourier Transform Mass Spectrometry, and computational approaches, was applied to provide novel insight into the mechanism and functional versatility of the OADHc. The results demonstrate that E1a oxidizes a non-cognate substrate 2-oxopimelate (OP) as well as OA through the decarboxylation step, but the OADHc was 100-times less effective in reactions producing adipoyl-CoA and NADH from the dihydrolipoamide succinyltransferase (E2o) and dihydrolipoamide dehydrogenase (E3). The results revealed that the E2o is capable of producing succinyl-CoA, glutaryl-CoA, and adipoyl-CoA. The important conclusions are the identification of: (i) the functional promiscuity of E1a and (ii) the ability of the E2o to form acyl-CoA products derived from homologous 2-oxo acids with five, six, and even seven carbon atoms. The findings add to our understanding of both the OADHc function in the L-lysine degradative pathway and of the molecular mechanisms leading to the pathogenesis associated with DHTKD1 variants.
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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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10
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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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11
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Hackmann TJ. Redefining the coenzyme A transferase superfamily with a large set of manually-annotated proteins. Protein Sci 2022; 31:864-881. [PMID: 35049101 PMCID: PMC8927868 DOI: 10.1002/pro.4277] [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: 09/14/2021] [Revised: 12/07/2021] [Accepted: 01/13/2022] [Indexed: 10/19/2022]
Abstract
The coenzyme A (CoA) transferases are a superfamily of proteins central to the metabolism of acetyl-CoA and other CoA thioesters. They are diverse group, catalyzing over a hundred biochemical reactions and spanning all three domains of life. A deeply rooted idea, proposed two decades ago, is these enzymes fall into three families (I, II, III). Here we find they fall into different families, which we achieve by analyzing all CoA transferases characterized to date. We manually annotated 94 CoA transferases with functional information (including rates of catalysis for 208 reactions) from 97 publications. This represents all enzymes we could find in the primary literature, and it is double the number annotated in four protein databases (BRENDA, KEGG, MetaCyc, UniProt). We found family I transferases are not closely related to each other in terms of sequence, structure, and reactions catalyzed. This family is not even monophyletic. These problems are solved by regrouping the three families into six, including one family with many non-CoA transferases. The problem (and solution) became apparent only by analyzing our large set of manually-annotated proteins. It would have been missed if we had used the small number of proteins annotated in UniProt and other databases. Our work is important to understanding the biology of CoA transferases. It also warns investigators doing phylogenetic analyses of proteins to go beyond information in databases. This article is protected by copyright. All rights reserved.
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Price DRG, Bartley K, Blake DP, Karp-Tatham E, Nunn F, Burgess STG, Nisbet AJ. A Rickettsiella Endosymbiont Is a Potential Source of Essential B-Vitamins for the Poultry Red Mite, Dermanyssus gallinae. Front Microbiol 2021; 12:695346. [PMID: 34539600 PMCID: PMC8446615 DOI: 10.3389/fmicb.2021.695346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 07/28/2021] [Indexed: 12/27/2022] Open
Abstract
Many obligate blood-sucking arthropods rely on symbiotic bacteria to provision essential B vitamins that are either missing or at sub-optimal levels in their nutritionally challenging blood diet. The poultry red mite Dermanyssus gallinae, an obligate blood-feeding ectoparasite, is a serious threat to the hen egg industry. Poultry red mite infestation has a major impact on hen health and welfare and causes a significant reduction in both egg quality and production. Thus far, the identity and biological role of nutrient provisioning bacterial mutualists from D. gallinae are little understood. Here, we demonstrate that an obligate intracellular bacterium of the Rickettsiella genus is detected in D. gallinae mites collected from 63 sites (from 15 countries) across Europe. In addition, we report the genome sequence of Rickettsiella from D. gallinae (Rickettsiella - D. gallinae endosymbiont; Rickettsiella DGE). Rickettsiella DGE has a circular 1.89Mbp genome that encodes 1,973 proteins. Phylogenetic analysis confirms the placement of Rickettsiella DGE within the Rickettsiella genus, related to a facultative endosymbiont from the pea aphid and Coxiella-like endosymbionts (CLEs) from blood feeding ticks. Analysis of the Rickettsiella DGE genome reveals that many protein-coding sequences are either pseudogenized or lost, but Rickettsiella DGE has retained several B vitamin biosynthesis pathways, suggesting the importance of these pathways in evolution of a nutritional symbiosis with D. gallinae. In silico metabolic pathway reconstruction revealed that Rickettsiella DGE is unable to synthesize protein amino acids and, therefore, amino acids are potentially provisioned by the host. In contrast, Rickettsiella DGE retains biosynthetic pathways for B vitamins: thiamine (vitamin B1) via the salvage pathway; riboflavin (vitamin B2) and pyridoxine (vitamin B6) and the cofactors: flavin adenine dinucleotide (FAD) and coenzyme A (CoA) that likely provision these nutrients to the host.
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Affiliation(s)
| | | | - Damer P Blake
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London, United Kingdom
| | - Eleanor Karp-Tatham
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London, United Kingdom
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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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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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