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Sharma V, Fedoseyenko D, Joshi S, Abdelwahed S, Begley TP. Phosphomethylpyrimidine Synthase (ThiC): Trapping of Five Intermediates Provides Mechanistic Insights on a Complex Radical Cascade Reaction in Thiamin Biosynthesis. ACS CENTRAL SCIENCE 2024; 10:988-1000. [PMID: 38799670 PMCID: PMC11117688 DOI: 10.1021/acscentsci.4c00125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/26/2024] [Accepted: 03/26/2024] [Indexed: 05/29/2024]
Abstract
Phosphomethylpyrimidine synthase (ThiC) catalyzes the conversion of AIR to the thiamin pyrimidine HMP-P. This reaction is the most complex enzyme-catalyzed radical cascade identified to date, and the detailed mechanism has remained elusive. In this paper, we describe the trapping of five new intermediates that provide snapshots of the ThiC reaction coordinate and enable the formulation of a revised mechanism for the ThiC-catalyzed reaction.
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Affiliation(s)
- Vishav Sharma
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Dmytro Fedoseyenko
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Sumedh Joshi
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Sameh Abdelwahed
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Tadhg P. Begley
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
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2
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Kim JH, Ko GP, Son KH, Ku BH, Bang MA, Kang MJ, Park HY. Arazyme in combination with dietary carbohydrolases influences odor emission and gut microbiome in growing-finishing pigs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 848:157735. [PMID: 35926625 DOI: 10.1016/j.scitotenv.2022.157735] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 07/13/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
This study evaluated the effects of supplementing feed with arazyme and dietary carbohydrolases derived from invertebrate gut-associated symbionts on the noxious gas emissions, gut microbiota, and host-microbiome interactions of pigs. Here, 270 and 260 growing pigs were assigned to control and treatment groups, respectively. The tested feed additives contained a mixture of arazyme (2,500,000 Unit/kg) and synergetic enzymes, xylanase (200,000 Unit/kg) and mannanase (200,000 Unit/kg), derived from insect gut-associated symbionts in a 7.5:1:1 ratio. The control group was fed a basal diet and the treatment group was fed the basal diet supplemented with 0.1 % enzyme mixture (v/v) for 2 months. Odorous gases were monitored in ventilated air from tested houses. Fecal samples were collected from steel plate under the cage at the completion of the experiment to determine chemical composition, odor emissions, and bacterial communities. There was a significant decrease in the concentration of NH3 (22.5 vs. 11.2 ppm; P < 0.05), H2S (7.35 vs. 3.74 ppm; P < 0.05), trimethylamine (TMA) (0.066 vs. 0.001 ppm; P < 0.05), and p-cresol (0.004 ppm vs. 0 ppm; P < 0.05) at 56 d in treatment group compared with the control group. Moreover, fecal analysis results showed that exogenous enzyme supplementation caused a reduction in VFAs and indole content with approximately >60 % and 72.7 %, respectively. The result of gas emission analysis showed that NH3 (9.9 vs. 5.3 ppm; P < 0.05) and H2S (5.8 vs. 4.1 ppm; P < 0.05) were significantly reduced in the treatment group compared to the control group. The gut microbiota of the treatment group differed significantly from that of the control group, and the treatment group altered predicted metabolic pathways, including sulfur and nitrogen related metabolism, urea degradation. The results demonstrated that supplementing feed with arazyme with dietary carbohydrolases effectively controls noxious gas emissions and improves health and meat quality of pigs.
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Affiliation(s)
- Jong-Hoon Kim
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Gwang-Pyo Ko
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Kwang-Hee Son
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Bon-Hwan Ku
- Insect Biotech Co. Ltd., Daejeon 34054, Republic of Korea
| | - Mi-Ae Bang
- Department of Animal Science, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Man-Jong Kang
- Department of Food Industry Research Center, Jeonnam Bioindustry Foundation, Naju 58275, Republic of Korea.
| | - Ho-Yong Park
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea.
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Exchange of Vitamin B 1 and Its Biosynthesis Intermediates Shapes the Composition of Synthetic Microbial Cocultures and Reveals Complexities of Nutrient Sharing. J Bacteriol 2022; 204:e0050321. [PMID: 35357164 DOI: 10.1128/jb.00503-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Microbial communities occupy diverse niches in nature, and community members routinely exchange a variety of nutrients among themselves. While large-scale metagenomic and metabolomic studies shed some light on these exchanges, the contribution of individual species and the molecular details of specific interactions are difficult to track. In this study, we follow the exchange of vitamin B1 (thiamin) and its intermediates between microbes within synthetic cocultures of Escherichia coli and Vibrio anguillarum. Thiamin contains two moieties, 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP) and 4-methyl-5-(2-hydroxyethyl)thiazole (THZ), which are synthesized by distinct pathways using enzymes ThiC and ThiG, respectively, and then coupled by ThiE to form thiamin. Even though E. coli ΔthiC, ΔthiE, and ΔthiG mutants are thiamin auxotrophs, we observed that cocultures of ΔthiC-ΔthiE and ΔthiC-ΔthiG mutants are able to grow in a thiamin-deficient medium, whereas the ΔthiE-ΔthiG coculture does not. Further, the exchange of thiamin and its intermediates in V. anguillarum cocultures and in mixed cocultures of V. anguillarum and E. coli revealed that there exist specific patterns for thiamin metabolism and exchange among these microbes. Our findings show that HMP is shared more frequently than THZ, concurrent with previous observations that free HMP and HMP auxotrophy is commonly found in various environments. Furthermore, we observe that the availability of exogenous thiamin in the media affects whether these strains interact with each other or grow independently. These findings collectively underscore the importance of the exchange of essential metabolites as a defining factor in building and modulating synthetic or natural microbial communities. IMPORTANCE Vitamin B1 (thiamin) is an essential nutrient for cellular metabolism. Microorganisms that are unable to synthesize thiamin either fully or in part exogenously obtain it from their environment or via exchanges with other microbial members in their community. In this study, we created synthetic microbial cocultures that rely on sharing thiamin and its biosynthesis intermediates and observed that some of them are preferentially exchanged. We also observed that the coculture composition is dictated by the production and/or availability of thiamin and its intermediates. Our studies with synthetic cocultures provide the molecular basis for understanding thiamin sharing among microorganisms and lay out broad guidelines for setting up synthetic microbial cocultures by using the exchange of an essential metabolite as their foundation.
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4
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Pramastya H, Song Y, Elfahmi EY, Sukrasno S, Quax WJ. Positioning Bacillus subtilis as terpenoid cell factory. J Appl Microbiol 2020; 130:1839-1856. [PMID: 33098223 PMCID: PMC8247319 DOI: 10.1111/jam.14904] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/29/2020] [Accepted: 10/09/2020] [Indexed: 12/16/2022]
Abstract
Increasing demands for bioactive compounds have motivated researchers to employ micro‐organisms to produce complex natural products. Currently, Bacillus subtilis has been attracting lots of attention to be developed into terpenoids cell factories due to its generally recognized safe status and high isoprene precursor biosynthesis capacity by endogenous methylerythritol phosphate (MEP) pathway. In this review, we describe the up‐to‐date knowledge of each enzyme in MEP pathway and the subsequent steps of isomerization and condensation of C5 isoprene precursors. In addition, several representative terpene synthases expressed in B. subtilis and the engineering steps to improve corresponding terpenoids production are systematically discussed. Furthermore, the current available genetic tools are mentioned as along with promising strategies to improve terpenoids in B. subtilis, hoping to inspire future directions in metabolic engineering of B. subtilis for further terpenoid cell factory development.
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Affiliation(s)
- H Pramastya
- University of Groningen, Groningen, The Netherlands.,Pharmaceutical Biology Research Group, School of Pharmacy, Institut Teknologi Bandung, Bandung, Indonesia
| | - Y Song
- University of Groningen, Groningen, The Netherlands
| | - E Y Elfahmi
- Pharmaceutical Biology Research Group, School of Pharmacy, Institut Teknologi Bandung, Bandung, Indonesia
| | - S Sukrasno
- Pharmaceutical Biology Research Group, School of Pharmacy, Institut Teknologi Bandung, Bandung, Indonesia
| | - W J Quax
- University of Groningen, Groningen, The Netherlands
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5
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Annan FJ, Al-Sinawi B, Humphreys CM, Norman R, Winzer K, Köpke M, Simpson SD, Minton NP, Henstra AM. Engineering of vitamin prototrophy in Clostridium ljungdahlii and Clostridium autoethanogenum. Appl Microbiol Biotechnol 2019; 103:4633-4648. [PMID: 30972463 PMCID: PMC6505512 DOI: 10.1007/s00253-019-09763-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 02/19/2019] [Accepted: 03/12/2019] [Indexed: 11/30/2022]
Abstract
Clostridium autoethanogenum and Clostridium ljungdahlii are physiologically and genetically very similar strict anaerobic acetogens capable of growth on carbon monoxide as sole carbon source. While exact nutritional requirements have not been reported, we observed that for growth, the addition of vitamins to media already containing yeast extract was required, an indication that these are fastidious microorganisms. Elimination of complex components and individual vitamins from the medium revealed that the only organic compounds required for growth were pantothenate, biotin and thiamine. Analysis of the genome sequences revealed that three genes were missing from pantothenate and thiamine biosynthetic pathways, and five genes were absent from the pathway for biotin biosynthesis. Prototrophy in C. autoethanogenum and C. ljungdahlii for pantothenate was obtained by the introduction of plasmids carrying the heterologous gene clusters panBCD from Clostridium acetobutylicum, and for thiamine by the introduction of the thiC-purF operon from Clostridium ragsdalei. Integration of panBCD into the chromosome through allele-coupled exchange also conveyed prototrophy. C. autoethanogenum was converted to biotin prototrophy with gene sets bioBDF and bioHCA from Desulfotomaculum nigrificans strain CO-1-SRB, on plasmid and integrated in the chromosome. The genes could be used as auxotrophic selection markers in recombinant DNA technology. Additionally, transformation with a subset of the genes for pantothenate biosynthesis extended selection options with the pantothenate precursors pantolactone and/or beta-alanine. Similarly, growth was obtained with the biotin precursor pimelate combined with genes bioYDA from C. acetobutylicum. The work raises questions whether alternative steps exist in biotin and thiamine biosynthesis pathways in these acetogens.
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Affiliation(s)
- Florence J Annan
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Bakir Al-Sinawi
- University of New-South Wales (UNSW) Sydney, Kensington, Australia
| | - Christopher M Humphreys
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Rupert Norman
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Klaus Winzer
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Michael Köpke
- LanzaTech Inc., 8045 Lamon Avenue, Suite 400, Skokie, IL, USA
| | - Sean D Simpson
- LanzaTech Inc., 8045 Lamon Avenue, Suite 400, Skokie, IL, USA
| | - Nigel P Minton
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Anne M Henstra
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
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Paerl RW, Bertrand EM, Rowland E, Schatt P, Mehiri M, Niehaus TD, Hanson AD, Riemann L, Bouget FY. Carboxythiazole is a key microbial nutrient currency and critical component of thiamin biosynthesis. Sci Rep 2018; 8:5940. [PMID: 29654239 PMCID: PMC5899164 DOI: 10.1038/s41598-018-24321-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 03/28/2018] [Indexed: 11/25/2022] Open
Abstract
Almost all cells require thiamin, vitamin B1 (B1), which is synthesized via the coupling of thiazole and pyrimidine precursors. Here we demonstrate that 5-(2-hydroxyethyl)-4-methyl-1,3-thiazole-2-carboxylic acid (cHET) is a useful in vivo B1 precursor for representatives of ubiquitous marine picoeukaryotic phytoplankton and Escherichia coli – drawing attention to cHET as a valuable exogenous micronutrient for microorganisms with ecological, industrial, and biomedical value. Comparative utilization experiments with the terrestrial plant Arabidopsis thaliana revealed that it can also use exogenous cHET, but notably, picoeukaryotic marine phytoplankton and E. coli were adapted to grow on low (picomolar) concentrations of exogenous cHET. Our results call for the modification of the conventional B1 biosynthesis model to incorporate cHET as a key precursor for B1 biosynthesis in two domains of life, and for consideration of cHET as a microbial micronutrient currency modulating marine primary productivity and community interactions in human gut-hosted microbiomes.
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Affiliation(s)
- Ryan W Paerl
- Department of Marine Earth and Atmospheric Sciences, North Carolina State University, Raleigh, NC, USA 27695, USA. .,Department of Biology, University of Copenhagen, 3000, Helsingør, Denmark.
| | - Erin M Bertrand
- Department of Biology, Dalhousie University, Halifax, NS, Canada
| | - Elden Rowland
- Department of Biology, Dalhousie University, Halifax, NS, Canada
| | - Phillippe Schatt
- Sorbonne Universités, Université Pierre and Marie Curie (Paris 06), UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, F-66650, Banyuls/mer, France
| | - Mohamed Mehiri
- University Nice Côte d'Azur, CNRS, Institute of Chemistry of Nice, UMR 7272, Marine Natural Products Team, Nice, France
| | - Thomas D Niehaus
- Horticultural Sciences Department, University of Florida, Gainesville, FL, USA 32611, USA
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL, USA 32611, USA
| | - Lasse Riemann
- Department of Biology, University of Copenhagen, 3000, Helsingør, Denmark
| | - Francois-Yves Bouget
- University Nice Côte d'Azur, CNRS, Institute of Chemistry of Nice, UMR 7272, Marine Natural Products Team, Nice, France
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7
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Wang Y, Wang J, Yu S, Wang F, Ma H, Yue C, Liu M, Deng Z, Huang Y, Qu X. Identifying the Minimal Enzymes for Unusual Carbon-Sulfur Bond Formation in Thienodolin Biosynthesis. Chembiochem 2016; 17:799-803. [PMID: 26854280 DOI: 10.1002/cbic.201500670] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Indexed: 01/26/2023]
Affiliation(s)
- Yaya Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery; Ministry of Education, School of Pharmaceutical Sciences; Wuhan University; 185 Donghu Road Wuhan 430071 China
| | - Jiali Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery; Ministry of Education, School of Pharmaceutical Sciences; Wuhan University; 185 Donghu Road Wuhan 430071 China
| | - Shuqi Yu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery; Ministry of Education, School of Pharmaceutical Sciences; Wuhan University; 185 Donghu Road Wuhan 430071 China
| | - Fan Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery; Ministry of Education, School of Pharmaceutical Sciences; Wuhan University; 185 Donghu Road Wuhan 430071 China
| | - Hongmin Ma
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery; Ministry of Education, School of Pharmaceutical Sciences; Wuhan University; 185 Donghu Road Wuhan 430071 China
| | - Changwu Yue
- State Key Laboratory of Microbial Resources; Institute of Microbiology; Chinese Academy of Sciences, 1 Beichen West Road; Beijing 100101 China
- Guizhou Key Laboratory of Microbial Resources and Drug Development; Zunyi Medical College, 201 Dalian Road; Zunyi 563003 China
| | - Minghao Liu
- State Key Laboratory of Microbial Resources; Institute of Microbiology; Chinese Academy of Sciences, 1 Beichen West Road; Beijing 100101 China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery; Ministry of Education, School of Pharmaceutical Sciences; Wuhan University; 185 Donghu Road Wuhan 430071 China
| | - Ying Huang
- State Key Laboratory of Microbial Resources; Institute of Microbiology; Chinese Academy of Sciences, 1 Beichen West Road; Beijing 100101 China
| | - Xudong Qu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery; Ministry of Education, School of Pharmaceutical Sciences; Wuhan University; 185 Donghu Road Wuhan 430071 China
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8
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Synthesis, characterization, crystal structures and biological activity of set of Cu(II) benzothiazole complexes: Artificial nucleases with cytotoxic activities. J Inorg Biochem 2014; 137:1-11. [DOI: 10.1016/j.jinorgbio.2014.04.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 04/01/2014] [Accepted: 04/02/2014] [Indexed: 12/20/2022]
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9
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Pourcel L, Moulin M, Fitzpatrick TB. Examining strategies to facilitate vitamin B1 biofortification of plants by genetic engineering. FRONTIERS IN PLANT SCIENCE 2013; 4:160. [PMID: 23755056 PMCID: PMC3665906 DOI: 10.3389/fpls.2013.00160] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Indexed: 05/20/2023]
Abstract
Thiamin (vitamin B1) is made by plants and microorganisms but is an essential micronutrient in the human diet. All organisms require it as a cofactor in its form as thiamin pyrophosphate (TPP) for the activity of key enzymes of central metabolism. In humans, deficiency is widespread particularly in populations where polished rice is a major component of the diet. Considerable progress has been made on the elucidation of the biosynthesis pathway within the last few years enabling concrete strategies for biofortification purposes to be devised, with a particular focus here on genetic engineering. Furthermore, the vitamin has been shown to play a role in both abiotic and biotic stress responses. The precursors for de novo biosynthesis of thiamin differ between microorganisms and plants. Bacteria use intermediates derived from purine and isoprenoid biosynthesis, whereas the pathway in yeast involves the use of compounds from the vitamin B3 and B6 groups. Plants on the other hand use a combination of the bacterial and yeast pathways and there is subcellular partitioning of the biosynthesis steps. Specifically, thiamin biosynthesis occurs in the chloroplast of plants through the separate formation of the pyrimidine and thiazole moieties, which are then coupled to form thiamin monophosphate (TMP). Phosphorylation of thiamin to form TPP occurs in the cytosol. Therefore, thiamin (or TMP) must be exported from the chloroplast to the cytosol for the latter step to be executed. The regulation of biosynthesis is mediated through riboswitches, where binding of the product TPP to the pre-mRNA of a biosynthetic gene modulates expression. Here we examine and hypothesize on genetic engineering approaches attempting to increase the thiamin content employing knowledge gained with the model plant Arabidopsis thaliana. We will discuss the regulatory steps that need to be taken into consideration and can be used a prerequisite for devising such strategies in crop plants.
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Affiliation(s)
| | | | - Teresa B. Fitzpatrick
- *Correspondence: Teresa B. Fitzpatrick, Department of Botany and Plant Biology, University of Geneva, Sciences III, 30 Quai E. Ansermet, 1211 Geneva, Switzerland e-mail:
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Begley TP, Ealick SE, McLafferty FW. Thiamin biosynthesis: still yielding fascinating biological chemistry. Biochem Soc Trans 2012; 40:555-60. [PMID: 22616866 PMCID: PMC3771315 DOI: 10.1042/bst20120084] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The present paper describes the biosynthesis of the thiamin thiazole in Bacillus subtilis and Saccharomyces cerevisiae. The two pathways are quite different: in B. subtilis, the thiazole is formed by an oxidative condensation of glycine, deoxy-D-xylulose 5-phosphate and a protein thiocarboxylate, whereas, in S. cerevisiae, the thiazole is assembled from glycine, NAD and Cys205 of the thiazole synthase.
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Affiliation(s)
- Tadhg P Begley
- Department of Chemistry, Texas A&M University, College Station, TX 77843, U.S.A.
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11
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Fugate CJ, Jarrett JT. Biotin synthase: insights into radical-mediated carbon-sulfur bond formation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1824:1213-22. [PMID: 22326745 DOI: 10.1016/j.bbapap.2012.01.010] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Accepted: 01/17/2012] [Indexed: 10/14/2022]
Abstract
The enzyme cofactor and essential vitamin biotin is biosynthesized in bacteria, fungi, and plants through a pathway that culminates with the addition of a sulfur atom to generate the five-membered thiophane ring. The immediate precursor, dethiobiotin, has methylene and methyl groups at the C6 and C9 positions, respectively, and formation of a thioether bridging these carbon atoms requires cleavage of unactivated CH bonds. Biotin synthase is an S-adenosyl-l-methionine (SAM or AdoMet) radical enzyme that catalyzes reduction of the AdoMet sulfonium to produce 5'-deoxyadenosyl radicals, high-energy carbon radicals that can directly abstract hydrogen atoms from dethiobiotin. The available experimental and structural data suggest that a [2Fe-2S](2+) cluster bound deep within biotin synthase provides a sulfur atom that is added to dethiobiotin in a stepwise reaction, first at the C9 position to generate 9-mercaptodethiobiotin, and then at the C6 position to close the thiophane ring. The formation of sulfur-containing biomolecules through a radical reaction involving an iron-sulfur cluster is an unprecedented reaction in biochemistry; however, recent enzyme discoveries suggest that radical sulfur insertion reactions may be a distinct subgroup within the burgeoning Radical SAM superfamily. This article is part of a Special Issue entitled: Radical SAM enzymes and Radical Enzymology.
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Affiliation(s)
- Corey J Fugate
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, HI 96822, USA
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12
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Hazra AB, Han Y, Chatterjee A, Zhang Y, Lai RY, Ealick SE, Begley TP. A missing enzyme in thiamin thiazole biosynthesis: identification of TenI as a thiazole tautomerase. J Am Chem Soc 2011; 133:9311-9. [PMID: 21534620 PMCID: PMC3116082 DOI: 10.1021/ja1110514] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In many bacteria tenI is found clustered with genes involved in thiamin thiazole biosynthesis. However, while TenI shows high sequence similarity with thiamin phosphate synthase, the purified protein has no thiamin phosphate synthase activity, and the role of this enzyme in thiamin biosynthesis remains unknown. In this contribution, we identify the function of TenI as a thiazole tautomerase, describe the structure of the enzyme complexed with its reaction product, identify the substrates phosphate and histidine 122 as the acid/base residues involved in catalysis, and propose a mechanism for the reaction. The identification of the function of TenI completes the identification of all of the enzymes needed for thiamin biosynthesis by the major bacterial pathway.
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Affiliation(s)
| | - Ying Han
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
| | - Abhishek Chatterjee
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
| | - Yang Zhang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
| | - Rung-Yi Lai
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
| | - Steven E. Ealick
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
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13
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14
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Paul D, Chatterjee A, Begley TP, Ealick SE. Domain organization in Candida glabrata THI6, a bifunctional enzyme required for thiamin biosynthesis in eukaryotes. Biochemistry 2010; 49:9922-34. [PMID: 20968298 PMCID: PMC2996881 DOI: 10.1021/bi101008u] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
THI6 is a bifunctional enzyme found in the thiamin biosynthetic pathway in eukaryotes. The N-terminal domain of THI6 catalyzes the ligation of the thiamin thiazole and pyrimidine moieties to form thiamin phosphate, and the C-terminal domain catalyzes the phosphorylation of 4-methyl-5-hydroxyethylthiazole in a salvage pathway. In prokaryotes, thiamin phosphate synthase and 4-methyl-5-hydroxyethylthiazole kinase are separate gene products. Here we report the first crystal structure of a eukaryotic THI6 along with several complexes that characterize the active sites responsible for the two chemical reactions. THI6 from Candida glabrata is a homohexamer in which the six protomers form a cage-like structure. Each protomer is composed of two domains, which are structurally homologous to their monofunctional bacterial counterparts. Two loop regions not found in the bacterial enzymes provide interactions between the two domains. The structures of different protein-ligand complexes define the thiazole and ATP binding sites of the 4-methyl-5-hydroxyethylthiazole kinase domain and the thiazole phosphate and 4-amino-5-hydroxymethyl-2-methylpyrimidine pyrophosphate binding sites of the thiamin phosphate synthase domain. Our structural studies reveal that the active sites of the two domains are 40 Å apart and are not connected by an obvious channel. Biochemical studies show 4-methyl-5-hydroxyethylthiazole phosphate is a substrate for THI6; however, adenosine diphospho-5β-ethyl-4-methylthiazole-2-carboxylic acid, the product of THI4, is not a substrate for THI6. This suggests that an unidentified enzyme is necessary to produce the substrate for THI6 from the THI4 product.
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Affiliation(s)
- Debamita Paul
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
| | | | - Tadhg P. Begley
- Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - Steven E. Ealick
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
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15
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Challand MR, Martins FT, Roach PL. Catalytic activity of the anaerobic tyrosine lyase required for thiamine biosynthesis in Escherichia coli. J Biol Chem 2009; 285:5240-8. [PMID: 19923213 DOI: 10.1074/jbc.m109.056606] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Thiazole synthase in Escherichia coli is an alphabeta heterodimer of ThiG and ThiH. ThiH is a tyrosine lyase that cleaves the C alpha-C beta bond of tyrosine, generating p-cresol as a by-product, to form dehydroglycine. This reactive intermediate acts as one of three substrates for the thiazole cyclization reaction catalyzed by ThiG. ThiH is a radical S-adenosylmethionine (AdoMet) enzyme that utilizes a [4Fe-4S](+) cluster to reductively cleave AdoMet, forming methionine and a 5'-deoxyadenosyl radical. Analysis of the time-dependent formation of the reaction products 5'-deoxyadenosine (DOA) and p-cresol has demonstrated catalytic behavior of the tyrosine lyase. The kinetics of product formation showed a pre-steady state burst phase, and the involvement of DOA in product inhibition was identified by the addition of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase to activity assays. This hydrolyzed the DOA and changed the rate-determining step but, in addition, substantially increased the uncoupled turnover of AdoMet. Addition of glyoxylate and ammonium inhibited the tyrosine cleavage reaction, but the reductive cleavage of AdoMet continued in an uncoupled manner. Tyrosine analogues were incubated with ThiGH, which showed a strong preference for phenolic substrates. 4-Hydroxyphenylpropionic acid analogues allowed uncoupled AdoMet cleavage but did not result in further reaction (C alpha-C beta bond cleavage). The results of the substrate analogue studies and the product inhibition can be explained by a mechanistic hypothesis involving two reaction pathways, a product-forming pathway and a futile cycle.
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Affiliation(s)
- Martin R Challand
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
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Affiliation(s)
- Edward McDonald
- Cancer Research UK Centre for Cancer Therapeutics, The Institute of Cancer Research, Sutton, Surrey, UK.
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