1
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Barra L, Awakawa T, Abe I. Noncanonical Functions of Enzyme Cofactors as Building Blocks in Natural Product Biosynthesis. JACS AU 2022; 2:1950-1963. [PMID: 36186570 PMCID: PMC9516700 DOI: 10.1021/jacsau.2c00391] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 08/05/2022] [Accepted: 08/05/2022] [Indexed: 06/16/2023]
Abstract
Enzymes involved in secondary metabolite biosynthetic pathways have typically evolutionarily diverged from their counterparts functioning in primary metabolism. They often catalyze diverse and complex chemical transformations and are thus a treasure trove for the discovery of unique enzyme-mediated chemistries. Besides major natural product classes, such as terpenoids, polyketides, and ribosomally or nonribosomally synthesized peptides, biosynthetic investigations of noncanonical natural product biosynthetic pathways often reveal functionally distinct enzyme chemistries. In this Perspective, we aim to highlight challenges and opportunities of biosynthetic investigations on noncanonical natural product pathways that utilize primary metabolites as building blocks, otherwise generally considered as enzyme cofactors. A focus is made on the discovered chemical and enzymological novelties.
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Affiliation(s)
- Lena Barra
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Department
of Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - Takayoshi Awakawa
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative
Research Institute of Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Ikuro Abe
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative
Research Institute of Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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2
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Pardo I, Bednar D, Calero P, Volke DC, Damborský J, Nikel PI. A Nonconventional Archaeal Fluorinase Identified by In Silico Mining for Enhanced Fluorine Biocatalysis. ACS Catal 2022; 12:6570-6577. [PMID: 35692250 PMCID: PMC9173684 DOI: 10.1021/acscatal.2c01184] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/15/2022] [Indexed: 12/28/2022]
Abstract
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Fluorinases, the
only enzymes known to catalyze the transfer of
fluorine to an organic molecule, are essential catalysts for the biological
synthesis of valuable organofluorines. However, the few fluorinases
identified so far have low turnover rates that hamper biotechnological
applications. Here, we isolated and characterized putative fluorinases
retrieved from systematic in silico mining and identified a nonconventional
archaeal enzyme from Methanosaeta sp. that mediates
the fastest SN2 fluorination rate reported to date. Furthermore,
we demonstrate enhanced production of fluoronucleotides in vivo in
a bacterial host engineered with this archaeal fluorinase, paving
the way toward synthetic metabolism for efficient biohalogenation.
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Affiliation(s)
- Isabel Pardo
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 601 77 Brno, Czech Republic
- International Clinical Research Centre, St. Anne’s University Hospital, 656 91 Brno, Czech Republic
| | - Patricia Calero
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Daniel C. Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Jiří Damborský
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 601 77 Brno, Czech Republic
- International Clinical Research Centre, St. Anne’s University Hospital, 656 91 Brno, Czech Republic
| | - Pablo I. Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
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3
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Caswell BT, de Carvalho CC, Nguyen H, Roy M, Nguyen T, Cantu DC. Thioesterase enzyme families: Functions, structures, and mechanisms. Protein Sci 2022; 31:652-676. [PMID: 34921469 PMCID: PMC8862431 DOI: 10.1002/pro.4263] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/11/2021] [Accepted: 12/14/2021] [Indexed: 12/12/2022]
Abstract
Thioesterases are enzymes that hydrolyze thioester bonds in numerous biochemical pathways, for example in fatty acid synthesis. This work reports known functions, structures, and mechanisms of updated thioesterase enzyme families, which are classified into 35 families based on sequence similarity. Each thioesterase family is based on at least one experimentally characterized enzyme, and most families have enzymes that have been crystallized and their tertiary structure resolved. Classifying thioesterases into families allows to predict tertiary structures and infer catalytic residues and mechanisms of all sequences in a family, which is particularly useful because the majority of known protein sequence have no experimental characterization. Phylogenetic analysis of experimentally characterized thioesterases that have structures with the two main structural folds reveal convergent and divergent evolution. Based on tertiary structure superimposition, catalytic residues are predicted.
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Affiliation(s)
- Benjamin T. Caswell
- Department of Chemical and Materials EngineeringUniversity of Nevada, RenoRenoNevadaUSA
| | - Caio C. de Carvalho
- Department of Chemical and Materials EngineeringUniversity of Nevada, RenoRenoNevadaUSA
| | - Hung Nguyen
- Department of Computer Science and EngineeringUniversity of Nevada, RenoRenoNevadaUSA
| | - Monikrishna Roy
- Department of Computer Science and EngineeringUniversity of Nevada, RenoRenoNevadaUSA
| | - Tin Nguyen
- Department of Computer Science and EngineeringUniversity of Nevada, RenoRenoNevadaUSA
| | - David C. Cantu
- Department of Chemical and Materials EngineeringUniversity of Nevada, RenoRenoNevadaUSA
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4
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Villalobos AS, Wiese J, Borchert E, Rahn T, Slaby BM, Steiner LX, Künzel S, Dorador C, Imhoff JF. Micromonospora tarapacensis sp. nov., a bacterium isolated from a hypersaline lake. Int J Syst Evol Microbiol 2021; 71. [PMID: 34787539 DOI: 10.1099/ijsem.0.005109] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain Llam7T was isolated from microbial mat samples from the hypersaline lake Salar de Llamará, located in Taracapá region in the hyper-arid core of the Atacama Desert (Chile). Phenotypic, chemotaxonomic and genomic traits were studied. Phylogenetic analyses based on 16S rRNA gene sequences assigned the strain to the family Micromonosporaceae with affiliation to the genera Micromonospora and Salinispora. Major fatty acids were C17 : 1ω8c, iso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The cell walls contained meso-diaminopimelic acid and ll-2,6 diaminopimelic acid (ll-DAP), while major whole-cell sugars were glucose, mannose, xylose and ribose. The major menaquinones were MK-9(H4) and MK-9(H6). As polar lipids phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and several unidentified lipids, i.e. two glycolipids, one aminolipid, three phospholipids, one aminoglycolipid and one phosphoglycolipid, were detected. Genome sequencing revealed a genome size of 6.894 Mb and a DNA G+C content of 71.4 mol%. Phylogenetic analyses with complete genome sequences positioned strain Llam7T within the family Micromonosporaceae forming a distinct cluster with Micromonospora (former Xiangella) phaseoli DSM 45730T. This cluster is related to Micromonospora pelagivivens KJ-029T, Micromonospora craterilacus NA12T, and Micromonospora craniellae LHW63014T as well as to all members of the former genera Verrucosispora and Jishengella, which were re-classified as members of the genus Micromonospora, forming a clade distinct from the genus Salinispora. Pairwise whole genome average nucleotide identity (ANI) values, digital DNA-DNA hybridization (dDDH) values, the presence of the diamino acid ll-DAP, and the composition of whole sugars and polar lipids indicate that Llam7T represents a novel species, for which the name Micromonospora tarapacensis sp. nov. is proposed, with Llam7T (=DSM 109510T,=LMG 31023T) as the type strain.
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Affiliation(s)
- Alvaro S Villalobos
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Research Unit Marine Symbioses, Kiel, Germany.,Escuela de Ciencias del Mar, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Jutta Wiese
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Research Unit Marine Symbioses, Kiel, Germany
| | - Erik Borchert
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Research Unit Marine Symbioses, Kiel, Germany
| | - Tanja Rahn
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Research Unit Marine Symbioses, Kiel, Germany
| | - Beate M Slaby
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Research Unit Marine Symbioses, Kiel, Germany
| | - Leon X Steiner
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Research Unit Marine Symbioses, Kiel, Germany
| | - Sven Künzel
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional and Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos Universidad de Antofagasta, Antofagasta, Chile
| | - Johannes F Imhoff
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Research Unit Marine Symbioses, Kiel, Germany
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5
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Cheng X, Ma L. Enzymatic synthesis of fluorinated compounds. Appl Microbiol Biotechnol 2021; 105:8033-8058. [PMID: 34625820 PMCID: PMC8500828 DOI: 10.1007/s00253-021-11608-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/16/2021] [Accepted: 09/18/2021] [Indexed: 12/31/2022]
Abstract
Fluorinated compounds are widely used in the fields of molecular imaging, pharmaceuticals, and materials. Fluorinated natural products in nature are rare, and the introduction of fluorine atoms into organic compound molecules can give these compounds new functions and make them have better performance. Therefore, the synthesis of fluorides has attracted more and more attention from biologists and chemists. Even so, achieving selective fluorination is still a huge challenge under mild conditions. In this review, the research progress of enzymatic synthesis of fluorinated compounds is summarized since 2015, including cytochrome P450 enzymes, aldolases, fluoroacetyl coenzyme A thioesterases, lipases, transaminases, reductive aminases, purine nucleoside phosphorylases, polyketide synthases, fluoroacetate dehalogenases, tyrosine phenol-lyases, glycosidases, fluorinases, and multienzyme system. Of all enzyme-catalyzed synthesis methods, the direct formation of the C-F bond by fluorinase is the most effective and promising method. The structure and catalytic mechanism of fluorinase are introduced to understand fluorobiochemistry. Furthermore, the distribution, applications, and future development trends of fluorinated compounds are also outlined. Hopefully, this review will help researchers to understand the significance of enzymatic methods for the synthesis of fluorinated compounds and find or create excellent fluoride synthase in future research.Key points• Fluorinated compounds are distributed in plants and microorganisms, and are used in imaging, medicine, materials science.• Enzyme catalysis is essential for the synthesis of fluorinated compounds.• The loop structure of fluorinase is the key to forming the C-F bond.
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Affiliation(s)
- Xinkuan Cheng
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Laboratory of Metabolic Control Fermentation Technology, College of Biotechnology, Tianjin University of Science & Technology, No. 29, Thirteenth Street, Binhai New District, Tianjin, 300457, China
| | - Long Ma
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Laboratory of Metabolic Control Fermentation Technology, College of Biotechnology, Tianjin University of Science & Technology, No. 29, Thirteenth Street, Binhai New District, Tianjin, 300457, China.
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6
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Peculiarities of promiscuous L-threonine transaldolases for enantioselective synthesis of β-hydroxy-α-amino acids. Appl Microbiol Biotechnol 2021; 105:3507-3520. [PMID: 33900425 PMCID: PMC8072733 DOI: 10.1007/s00253-021-11288-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/31/2021] [Accepted: 04/07/2021] [Indexed: 02/07/2023]
Abstract
The introduction of β-hydroxy-α-amino acids (βHAAs) into organic molecules has received considerable attention as these molecules have often found widespread applications in bioorganic chemistry, medicinal chemistry and biomaterial science. Despite innovation of asymmetric synthesis of βHAAs, stereoselective synthesis to control the two chiral centres at Cα and Cβ positions is still challenging, with poor atomic economy and multi protection and deprotection steps. These syntheses are often operated under harsh conditions. Therefore, a biotransformation approach using biocatalysts is needed to selectively introduce these two chiral centres into structurally diverse molecules. Yet, there are few ways that enable one-step synthesis of βHAAs. One is to extend the substrate scope of the existing enzyme inventory. Threonine aldolases have been explored to produce βHAAs. However, the enzymes have poor controlled installation at Cβ position, often resulting in a mixture of diastereoisomers which are difficult to be separated. In this respect, L-threonine transaldolases (LTTAs) offer an excellent potential as the enzymes often provide controlled stereochemistry at Cα and Cβ positions. Another is to mine LTTA homologues and engineer the enzymes using directed evolution with the aim of finding engineered biocatalysts to accept broad substrates with enhanced conversion and stereoselectivity. Here, we review the development of LTTAs that incorporate various aldehyde acceptors to generate structurally diverse βHAAs and highlight areas for future developments. KEY POINTS: • The general mechanism of the transaldolation reaction catalysed by LTTAs • Recent advances in LTTAs from different biosynthetic pathways • Applications of LTTAs as biocatalysts for production of βHAAs.
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7
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Ngivprom U, Kluaiphanngam S, Ji W, Siriwibool S, Kamkaew A, Ketudat Cairns JR, Zhang Q, Lai RY. Characterization of NucPNP and NucV involved in the early steps of nucleocidin biosynthesis in Streptomyces calvus. RSC Adv 2021; 11:3510-3515. [PMID: 35424298 PMCID: PMC8694150 DOI: 10.1039/d0ra10878b] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 12/28/2020] [Indexed: 12/18/2022] Open
Abstract
Nucleocidin 1 produced by Streptomyces calvus is one of five characterized natural products containing fluorine. It was discovered in 1956, but its biosynthesis is not yet completely resolved. Recently, the biosynthetic gene cluster of 1 was identified. The nucPNP gene, which was initially annotated as orf206 and encodes a putative purine nucleoside phosphorylase, is essential for nucleocidin production. In this study, we performed in vitro assays and showed NucPNP produced adenine 3 from methylthioadenosine (MTA) 2 and adenosine 4. We also showed the downstream enzyme, NucV annotated as adenine phosphoribosyltransferase (APRT), catalyzes AMP formation from adenine 3 and 5-phospho-α-d-ribose-1-diphosphate (PRPP) 5. However, the catalytic efficiency of NucV was much slower than its homolog ScAPRT involved in the biosynthesis of canonical purine nucleoside in the same strain. These results provide new insights in nucleocidin biosynthesis and could guide future research on organofluorine formation.
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Affiliation(s)
- Utumporn Ngivprom
- School of Chemistry, Institute of Science, Suranaree University of Technology Nakhon Ratchasima 30000 Thailand
| | - Surayut Kluaiphanngam
- School of Chemistry, Institute of Science, Suranaree University of Technology Nakhon Ratchasima 30000 Thailand
| | - Wenjuan Ji
- Department of Chemistry, Fudan University Shanghai 200433 China
| | - Siriwalee Siriwibool
- School of Chemistry, Institute of Science, Suranaree University of Technology Nakhon Ratchasima 30000 Thailand
| | - Anyanee Kamkaew
- School of Chemistry, Institute of Science, Suranaree University of Technology Nakhon Ratchasima 30000 Thailand
| | - James R Ketudat Cairns
- School of Chemistry, Institute of Science, Suranaree University of Technology Nakhon Ratchasima 30000 Thailand .,Center for Biomolecular Structure, Function and Application, Suranaree University of Technology Nakhon Ratchasima 30000 Thailand
| | - Qi Zhang
- Department of Chemistry, Fudan University Shanghai 200433 China
| | - Rung-Yi Lai
- School of Chemistry, Institute of Science, Suranaree University of Technology Nakhon Ratchasima 30000 Thailand .,Center for Biomolecular Structure, Function and Application, Suranaree University of Technology Nakhon Ratchasima 30000 Thailand
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8
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Kuzmishin Nagy AB, Bakhtina M, Musier-Forsyth K. Trans-editing by aminoacyl-tRNA synthetase-like editing domains. Enzymes 2020; 48:69-115. [PMID: 33837712 DOI: 10.1016/bs.enz.2020.07.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Aminoacyl-tRNA synthetases (aaRS) are ubiquitous enzymes responsible for aminoacyl-tRNA (aa-tRNA) synthesis. Correctly formed aa-tRNAs are necessary for proper decoding of mRNA and accurate protein synthesis. tRNAs possess specific nucleobases that promote selective recognition by cognate aaRSs. Selecting the cognate amino acid can be more challenging because all amino acids share the same peptide backbone and several are isosteric or have similar side chains. Thus, aaRSs can misactivate non-cognate amino acids and produce mischarged aa-tRNAs. If left uncorrected, mischarged aa-tRNAs deliver their non-cognate amino acid to the ribosome resulting in misincorporation into the nascent polypeptide chain. This changes the primary protein sequence and potentially causes misfolding or formation of non-functional proteins that impair cell survival. A variety of proofreading or editing pathways exist to prevent and correct mistakes in aa-tRNA formation. Editing may occur before the amino acid transfer step of aminoacylation via hydrolysis of the aminoacyl-adenylate. Alternatively, post-transfer editing, which occurs after the mischarged aa-tRNA is formed, may be carried out via a distinct editing site on the aaRS where the mischarged aa-tRNA is deacylated. In recent years, it has become clear that most organisms also encode factors that lack aminoacylation activity but resemble aaRS editing domains and function to clear mischarged aa-tRNAs in trans. This review focuses on these trans-editing factors, which are encoded in all three domains of life and function together with editing domains present within aaRSs to ensure that the accuracy of protein synthesis is sufficient for cell survival.
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Affiliation(s)
- Alexandra B Kuzmishin Nagy
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, OH, United States
| | - Marina Bakhtina
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, OH, United States
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, OH, United States.
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9
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Nieto-Domínguez M, Nikel PI. Intersecting Xenobiology and Neometabolism To Bring Novel Chemistries to Life. Chembiochem 2020; 21:2551-2571. [PMID: 32274875 DOI: 10.1002/cbic.202000091] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/09/2020] [Indexed: 12/19/2022]
Abstract
The diversity of life relies on a handful of chemical elements (carbon, oxygen, hydrogen, nitrogen, sulfur and phosphorus) as part of essential building blocks; some other atoms are needed to a lesser extent, but most of the remaining elements are excluded from biology. This circumstance limits the scope of biochemical reactions in extant metabolism - yet it offers a phenomenal playground for synthetic biology. Xenobiology aims to bring novel bricks to life that could be exploited for (xeno)metabolite synthesis. In particular, the assembly of novel pathways engineered to handle nonbiological elements (neometabolism) will broaden chemical space beyond the reach of natural evolution. In this review, xeno-elements that could be blended into nature's biosynthetic portfolio are discussed together with their physicochemical properties and tools and strategies to incorporate them into biochemistry. We argue that current bioproduction methods can be revolutionized by bridging xenobiology and neometabolism for the synthesis of new-to-nature molecules, such as organohalides.
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Affiliation(s)
- Manuel Nieto-Domínguez
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
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10
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Markakis K, Lowe PT, Davison‐Gates L, O'Hagan D, Rosser SJ, Elfick A. An Engineered
E. coli
Strain for Direct in Vivo Fluorination. Chembiochem 2020; 21:1856-1860. [DOI: 10.1002/cbic.202000051] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Indexed: 02/04/2023]
Affiliation(s)
- Konstantinos Markakis
- Institute for BioengineeringSchool of EngineeringUniversity of Edinburgh Faraday Building King's Buildings Colin Maclaurin Road Edinburgh EH9 3DW UK
| | - Phillip T. Lowe
- School of ChemistryUniversity of St. Andrews Purdie Building North Haugh St. Andrews KY16 9ST UK
| | - Liam Davison‐Gates
- Institute for BioengineeringSchool of EngineeringUniversity of Edinburgh Faraday Building King's Buildings Colin Maclaurin Road Edinburgh EH9 3DW UK
| | - David O'Hagan
- School of ChemistryUniversity of St. Andrews Purdie Building North Haugh St. Andrews KY16 9ST UK
| | - Susan J. Rosser
- School of Biological SciencesThe University of Edinburgh Roger Land Building The King's Buildings Alexander Crum Brown Road Edinburgh EH9 3FF UK
| | - Alistair Elfick
- Institute for BioengineeringSchool of EngineeringUniversity of Edinburgh Faraday Building King's Buildings Colin Maclaurin Road Edinburgh EH9 3DW UK
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11
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Sulzbach M, Kunjapur AM. The Pathway Less Traveled: Engineering Biosynthesis of Nonstandard Functional Groups. Trends Biotechnol 2020; 38:532-545. [PMID: 31954529 DOI: 10.1016/j.tibtech.2019.12.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 12/02/2019] [Accepted: 12/06/2019] [Indexed: 12/12/2022]
Abstract
The field of metabolic engineering has achieved biochemical routes for conversion of renewable inputs to structurally diverse chemicals, but these products contain a limited number of chemical functional groups. In this review, we provide an overview of the progression of uncommon or 'nonstandard' functional groups from the elucidation of their biosynthetic machinery to the pathway optimization framework of metabolic engineering. We highlight exemplary efforts from primarily the last 5 years for biosynthesis of aldehyde, ester, terminal alkyne, terminal alkene, fluoro, epoxide, nitro, nitroso, nitrile, and hydrazine functional groups. These representative nonstandard functional groups vary in development stage and showcase the pipeline of chemical diversity that could soon appear within customized, biologically produced molecules.
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Affiliation(s)
- Morgan Sulzbach
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711, USA
| | - Aditya M Kunjapur
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711, USA.
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12
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Wu L, Deng H. Defluorination of 4-fluorothreonine by threonine deaminase. Org Biomol Chem 2020; 18:6236-6240. [DOI: 10.1039/d0ob01358g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Threonine deaminase from E. coli catalyses defluorination on 4-fluorothreonine.
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Affiliation(s)
- Linrui Wu
- Department of Chemistry
- University of Aberdeen
- Aberdeen AB24 3UE
- UK
| | - Hai Deng
- Department of Chemistry
- University of Aberdeen
- Aberdeen AB24 3UE
- UK
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13
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Entropy drives selective fluorine recognition in the fluoroacetyl-CoA thioesterase from Streptomyces cattleya. Proc Natl Acad Sci U S A 2018; 115:E2193-E2201. [PMID: 29453276 DOI: 10.1073/pnas.1717077115] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fluorinated small molecules play an important role in the design of bioactive compounds for a broad range of applications. As such, there is strong interest in developing a deeper understanding of how fluorine affects the interaction of these ligands with their targets. Given the small number of fluorinated metabolites identified to date, insights into fluorine recognition have been provided almost entirely by synthetic systems. The fluoroacetyl-CoA thioesterase (FlK) from Streptomyces cattleya thus provides a unique opportunity to study an enzyme-ligand pair that has been evolutionarily optimized for a surprisingly high 106 selectivity for a single fluorine substituent. In these studies, we synthesize a series of analogs of fluoroacetyl-CoA and acetyl-CoA to generate nonhydrolyzable ester, amide, and ketone congeners of the thioester substrate to isolate the role of fluorine molecular recognition in FlK selectivity. Using a combination of thermodynamic, kinetic, and protein NMR experiments, we show that fluorine recognition is entropically driven by the interaction of the fluorine substituent with a key residue, Phe-36, on the lid structure that covers the active site, resulting in an ∼5- to 20-fold difference in binding (KD). Although the magnitude of discrimination is similar to that found in designed synthetic ligand-protein complexes where dipolar interactions control fluorine recognition, these studies show that hydrophobic and solvation effects serve as the major determinant of naturally evolved fluorine selectivity.
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14
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Fluorothreonyl-tRNA deacylase prevents mistranslation in the organofluorine producer Streptomyces cattleya. Proc Natl Acad Sci U S A 2017; 114:11920-11925. [PMID: 29078362 DOI: 10.1073/pnas.1711482114] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Fluorine is an element with unusual properties that has found significant utility in the design of synthetic small molecules, ranging from therapeutics to materials. In contrast, only a few fluorinated compounds made by living organisms have been found to date, most of which derive from the fluoroacetate/fluorothreonine biosynthetic pathway first discovered in Streptomyces cattleya While fluoroacetate has long been known to act as an inhibitor of the tricarboxylic acid cycle, the fate of the amino acid fluorothreonine is still not well understood. Here, we show that fluorothreonine can be misincorporated into protein in place of the proteinogenic amino acid threonine. We have identified two conserved proteins from the organofluorine biosynthetic locus, FthB and FthC, that are involved in managing fluorothreonine toxicity. Using a combination of biochemical, genetic, physiological, and proteomic studies, we show that FthB is a trans-acting transfer RNA (tRNA) editing protein, which hydrolyzes fluorothreonyl-tRNA 670-fold more efficiently than threonyl-RNA, and assign a role to FthC in fluorothreonine transport. While trans-acting tRNA editing proteins have been found to counteract the misacylation of tRNA with commonly occurring near-cognate amino acids, their role has yet to be described in the context of secondary metabolism. In this regard, the recruitment of tRNA editing proteins to biosynthetic clusters may have enabled the evolution of pathways to produce specialized amino acids, thereby increasing the diversity of natural product structure while also attenuating the risk of mistranslation that would ensue.
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15
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Leong LEX, Khan S, Davis CK, Denman SE, McSweeney CS. Fluoroacetate in plants - a review of its distribution, toxicity to livestock and microbial detoxification. J Anim Sci Biotechnol 2017; 8:55. [PMID: 28674607 PMCID: PMC5485738 DOI: 10.1186/s40104-017-0180-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 05/11/2017] [Indexed: 02/08/2023] Open
Abstract
Fluoroacetate producing plants grow worldwide and it is believed they produce this toxic compound as a defence mechanism against grazing by herbivores. Ingestion by livestock often results in fatal poisonings, which causes significant economic problems to commercial farmers in many countries such as Australia, Brazil and South Africa. Several approaches have been adopted to protect livestock from the toxicity with limited success including fencing, toxic plant eradication and agents that bind the toxin. Genetically modified bacteria capable of degrading fluoroacetate have been able to protect ruminants from fluoroacetate toxicity under experimental conditions but concerns over the release of these microbes into the environment have prevented the application of this technology. Recently, a native bacterium from an Australian bovine rumen was isolated which can degrade fluoroacetate. This bacterium, strain MFA1, which belongs to the Synergistetes phylum degrades fluoroacetate to fluoride ions and acetate. The discovery and isolation of this bacterium provides a new opportunity to detoxify fluoroacetate in the rumen. This review focuses on fluoroacetate toxicity in ruminant livestock, the mechanism of fluoroacetate toxicity, tolerance of some animals to fluoroaceate, previous attempts to mitigate toxicity, aerobic and anaerobic microbial degradation of fluoroacetate, and future directions to overcome fluoroacetate toxicity.
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Affiliation(s)
- Lex Ee Xiang Leong
- School of Chemistry and Molecular Bioscience, University of Queensland, St Lucia, 4072 QLD Australia
| | - Shahjalal Khan
- School of Agriculture and Food Sciences, University of Queensland, St Lucia, 4072 QLD Australia
| | - Carl K Davis
- School of Chemistry and Molecular Bioscience, University of Queensland, St Lucia, 4072 QLD Australia
| | - Stuart E Denman
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St Lucia, 4072 QLD Australia
| | - Chris S McSweeney
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St Lucia, 4072 QLD Australia
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16
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Carvalho MF, Oliveira RS. Natural production of fluorinated compounds and biotechnological prospects of the fluorinase enzyme. Crit Rev Biotechnol 2017; 37:880-897. [PMID: 28049355 DOI: 10.1080/07388551.2016.1267109] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Fluorinated compounds are finding increasing uses in several applications. They are employed in almost all areas of modern society. These compounds are all produced by chemical synthesis and their abundance highly contrasts with fluorinated molecules of natural origin. To date, only some plants and a handful of actinomycetes species are known to produce a small number of fluorinated compounds that include fluoroacetate (FA), some ω-fluorinated fatty acids, nucleocidin, 4-fluorothreonine (4-FT), and the more recently identified (2R3S4S)-5-fluoro-2,3,4-trihydroxypentanoic acid. This largely differs from other naturally produced halogenated compounds, which totals more than 5000. The mechanisms underlying biological fluorination have been uncovered after discovering the first actinomycete species, Streptomyces cattleya, that is capable of producing FA and 4-FT, and a fluorinase has been identified as the enzyme responsible for the formation of the C-F bond. The discovery of this enzyme has opened new perspectives for the biotechnological production of fluorinated compounds and many advancements have been achieved in its application mainly as a biocatalyst for the synthesis of [18F]-labeled radiotracers for medical imaging. Natural fluorinated compounds may also be derived from abiogenic sources, such as volcanoes and rocks, though their concentrations and production mechanisms are not well known. This review provides an outlook of what is currently known about fluorinated compounds with natural origin. The paucity of these compounds and the biological mechanisms responsible for their production are addressed. Due to its relevance, special emphasis is given to the discovery, characterization and biotechnological potential of the unique fluorinase enzyme.
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Affiliation(s)
- Maria F Carvalho
- a CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto , Porto , Portugal
| | - Rui S Oliveira
- b Centre for Functional Ecology, Department of Life Sciences , University of Coimbra , Coimbra , Portugal.,c Department of Environmental Health , Research Centre on Health and Environment, School of Allied Health Sciences, Polytechnic Institute of Porto , Porto , Portugal
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17
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Walker MC, Chang MCY. Natural and engineered biosynthesis of fluorinated natural products. Chem Soc Rev 2015; 43:6527-36. [PMID: 24776946 DOI: 10.1039/c4cs00027g] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Both natural products and synthetic organofluorines play important roles in the discovery and design of pharmaceuticals. The combination of these two classes of molecules has the potential to be useful in the ongoing search for new bioactive compounds but our ability to produce site-selectively fluorinated natural products remains limited by challenges in compatibility between their high structural complexity and current methods for fluorination. Living systems provide an alternative route to chemical fluorination and could enable the production of organofluorine natural products through synthetic biology approaches. While the identification of biogenic organofluorines has been limited, the study of the native organisms and enzymes that utilize these compounds can help to guide efforts to engineer the incorporation of this unusual element into complex pharmacologically active natural products. This review covers recent advances in understanding both natural and engineered production of organofluorine natural products.
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Affiliation(s)
- Mark C Walker
- Departments of Chemistry and Molecular & Cell Biology, University of California, Berkeley, 125 Lewis, Berkeley, CA 94720-1460, USA.
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18
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Odar C, Winkler M, Wiltschi B. Fluoro amino acids: A rarity in nature, yet a prospect for protein engineering. Biotechnol J 2015; 10:427-46. [DOI: 10.1002/biot.201400587] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 12/08/2014] [Accepted: 01/09/2015] [Indexed: 01/01/2023]
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19
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O'Hagan D, Deng H. Enzymatic fluorination and biotechnological developments of the fluorinase. Chem Rev 2014; 115:634-49. [PMID: 25253234 DOI: 10.1021/cr500209t] [Citation(s) in RCA: 215] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- David O'Hagan
- EaStChem School of Chemistry, University of St Andrews , North Haugh, St Andrews KY169ST, United Kingdom
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20
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Pandya C, Farelli JD, Dunaway-Mariano D, Allen KN. Enzyme promiscuity: engine of evolutionary innovation. J Biol Chem 2014; 289:30229-30236. [PMID: 25210039 DOI: 10.1074/jbc.r114.572990] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Catalytic promiscuity and substrate ambiguity are keys to evolvability, which in turn is pivotal to the successful acquisition of novel biological functions. Action on multiple substrates (substrate ambiguity) can be harnessed for performance of functions in the cell that supersede catalysis of a single metabolite. These functions include proofreading, scavenging of nutrients, removal of antimetabolites, balancing of metabolite pools, and establishing system redundancy. In this review, we present examples of enzymes that perform these cellular roles by leveraging substrate ambiguity and then present the structural features that support both specificity and ambiguity. We focus on the phosphatases of the haloalkanoate dehalogenase superfamily and the thioesterases of the hotdog fold superfamily.
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Affiliation(s)
- Chetanya Pandya
- Bioinformatics Graduate Program and Boston University, Boston, Massachusetts 02215
| | - Jeremiah D Farelli
- Department of Chemistry, Boston University, Boston, Massachusetts 02215 and
| | - Debra Dunaway-Mariano
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131.
| | - Karen N Allen
- Bioinformatics Graduate Program and Boston University, Boston, Massachusetts 02215; Department of Chemistry, Boston University, Boston, Massachusetts 02215 and.
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21
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Weeks AM, Keddie NS, Wadoux RDP, O'Hagan D, Chang MCY. Molecular recognition of fluorine impacts substrate selectivity in the fluoroacetyl-CoA thioesterase FlK. Biochemistry 2014; 53:2053-63. [PMID: 24635371 PMCID: PMC3985765 DOI: 10.1021/bi4015049] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The fluoroacetate-producing bacterium Streptomyces cattleya has evolved a fluoroacetyl-CoA thioesterase
(FlK) that exhibits
a remarkably high level of discrimination for its cognate substrate
compared to the cellularly abundant analogue acetyl-CoA, which differs
only by the absence of the fluorine substitution. A major determinant
of FlK specificity derives from its ability to take advantage of the
unique properties of fluorine to enhance the reaction rate, allowing
fluorine discrimination under physiological conditions where both
substrates are likely to be present at saturating concentrations.
Using a combination of pH–rate profiles, pre-steady-state kinetic
experiments, and Taft analysis of wild-type and mutant FlKs with a
set of substrate analogues, we explore the role of fluorine in controlling
the enzyme acylation and deacylation steps. Further analysis of chiral
(R)- and (S)-[2H1]fluoroacetyl-CoA substrates demonstrates that a kinetic isotope
effect (1.7 ± 0.2) is observed for only the (R)-2H1 isomer, indicating that deacylation requires
recognition of the prochiral fluoromethyl group to position the α-carbon
for proton abstraction. Taken together, the selectivity for the fluoroacetyl-CoA
substrate appears to rely not only on the enhanced polarization provided
by the electronegative fluorine substitution but also on molecular
recognition of fluorine in both formation and breakdown of the acyl-enzyme
intermediate to control active site reactivity. These studies provide
insights into the basis of fluorine selectivity in a naturally occurring
enzyme–substrate pair, with implications for drug design and
the development of fluorine-selective biocatalysts.
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Affiliation(s)
- Amy M Weeks
- Department of Chemistry, University of California , Berkeley, California 94720-1460, United States
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22
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Wang Y, Deng Z, Qu X. Characterization of a SAM-dependent fluorinase from a latent biosynthetic pathway for fluoroacetate and 4-fluorothreonine formation in Nocardia brasiliensis. F1000Res 2014; 3:61. [PMID: 24795808 PMCID: PMC3999930 DOI: 10.12688/f1000research.3-61.v1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/18/2014] [Indexed: 11/20/2022] Open
Abstract
Fluorination has been widely used in chemical synthesis, but is rare in nature. The only known biological fluorination scope is represented by the
fl pathway from
Streptomyces cattleya that produces fluoroacetate (FAc) and 4-fluorothreonine (4-FT). Here we report the identification of a novel pathway for FAc and 4-FT biosynthesis from the actinomycetoma-causing pathogen
Nocardia brasiliensis ATCC 700358. The new pathway shares overall conservation with the
fl pathway in
S. cattleya. Biochemical characterization of the conserved domains revealed a novel fluorinase NobA that can biosynthesize 5’-fluoro-5’-deoxyadenosine (5’-FDA) from inorganic fluoride and
S-adenosyl-l-methionine (SAM). The NobA shows similar halide specificity and characteristics to the fluorination enzyme FlA of the
fl pathway. Kinetic parameters for fluoride (
K
m 4153 μM,
k
cat 0.073 min
-1) and SAM (
K
m 416 μM,
k
cat 0.139 min
-1) have been determined, revealing that NobA is slightly (2.3 fold) slower than FlA. Upon sequence comparison, we finally identified a distinct loop region in the fluorinases that probably accounts for the disparity of fluorination activity.
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Affiliation(s)
- Yaya Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China
| | - Xudong Qu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China
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23
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Deng H, Ma L, Bandaranayaka N, Qin Z, Mann G, Kyeremeh K, Yu Y, Shepherd T, Naismith JH, O'Hagan D. Identification of fluorinases from Streptomyces sp MA37, Norcardia brasiliensis, and Actinoplanes sp N902-109 by genome mining. Chembiochem 2014; 15:364-8. [PMID: 24449539 DOI: 10.1002/cbic.201300732] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Indexed: 11/10/2022]
Abstract
The fluorinase is an enzyme that catalyses the combination of S-adenosyl-L-methionine (SAM) and a fluoride ion to generate 5'-fluorodeoxy adenosine (FDA) and L-methionine through a nucleophilic substitution reaction with a fluoride ion as the nucleophile. It is the only native fluorination enzyme that has been characterised. The fluorinase was isolated in 2002 from Streptomyces cattleya, and, to date, this has been the only source of the fluorinase enzyme. Herein, we report three new fluorinase isolates that have been identified by genome mining. The novel fluorinases from Streptomyces sp. MA37, Nocardia brasiliensis, and an Actinoplanes sp. have high homology (80-87 % identity) to the original S. cattleya enzyme. They all possess a characteristic 21-residue loop. The three newly identified genes were overexpressed in E. coli and shown to be fluorination enzymes. An X-ray crystallographic study of the Streptomyces sp. MA37 enzyme demonstrated that it is almost identical in structure to the original fluorinase. Culturing of the Streptomyces sp. MA37 strain demonstrated that it not only also elaborates the fluorometabolites, fluoroacetate and 4-fluorothreonine, similar to S. cattleya, but this strain also produces a range of unidentified fluorometabolites. These are the first new fluorinases to be reported since the first isolate, over a decade ago, and their identification extends the range of fluorination genes available for fluorination biotechnology.
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Affiliation(s)
- Hai Deng
- UK Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE (UK).
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24
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Huang S, Ma L, Tong MH, Yu Y, O'Hagan D, Deng H. Fluoroacetate biosynthesis from the marine-derived bacterium Streptomyces xinghaiensis NRRL B-24674. Org Biomol Chem 2014; 12:4828-31. [DOI: 10.1039/c4ob00970c] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Streptomyces xinghaiensis is the first fluorometabolite producing microorganism identified from the marine environment.
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Affiliation(s)
- Sheng Huang
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education)
- School of Pharmaceutical Sciences
- Wuhan University
- Wuhan 430071, P. R. China
| | - Long Ma
- School of Chemistry and Biomedical Sciences Research Centre
- University of St Andrews
- St Andrews KY169ST, UK
| | - Ming Him Tong
- Marine Biodiscovery Centre
- Department of Chemistry
- Meston Walk
- University of Aberdeen
- Aberdeen AB24 3UE, UK
| | - Yi Yu
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education)
- School of Pharmaceutical Sciences
- Wuhan University
- Wuhan 430071, P. R. China
| | - David O'Hagan
- School of Chemistry and Biomedical Sciences Research Centre
- University of St Andrews
- St Andrews KY169ST, UK
| | - Hai Deng
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education)
- School of Pharmaceutical Sciences
- Wuhan University
- Wuhan 430071, P. R. China
- Marine Biodiscovery Centre
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25
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Walker MC, Thuronyi BW, Charkoudian LK, Lowry B, Khosla C, Chang MCY. Expanding the fluorine chemistry of living systems using engineered polyketide synthase pathways. Science 2013; 341:1089-94. [PMID: 24009388 PMCID: PMC4057101 DOI: 10.1126/science.1242345] [Citation(s) in RCA: 139] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Organofluorines represent a rapidly expanding proportion of molecules that are used in pharmaceuticals, diagnostics, agrochemicals, and materials. Despite the prevalence of fluorine in synthetic compounds, the known biological scope is limited to a single pathway that produces fluoroacetate. Here, we demonstrate that this pathway can be exploited as a source of fluorinated building blocks for introduction of fluorine into natural-product scaffolds. Specifically, we have constructed pathways involving two polyketide synthase systems, and we show that fluoroacetate can be used to incorporate fluorine into the polyketide backbone in vitro. We further show that fluorine can be inserted site-selectively and introduced into polyketide products in vivo. These results highlight the prospects for the production of complex fluorinated natural products using synthetic biology.
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Affiliation(s)
- Mark C. Walker
- Departments of Chemistry and Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA 94720-1460
| | - Benjamin W. Thuronyi
- Departments of Chemistry and Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA 94720-1460
| | - Louise K. Charkoudian
- Departments of Chemistry, Chemical Engineering, and Biochemistry, Stanford University, Stanford, CA 94305
| | - Brian Lowry
- Departments of Chemistry, Chemical Engineering, and Biochemistry, Stanford University, Stanford, CA 94305
| | - Chaitan Khosla
- Departments of Chemistry, Chemical Engineering, and Biochemistry, Stanford University, Stanford, CA 94305
| | - Michelle C. Y. Chang
- Departments of Chemistry and Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA 94720-1460
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26
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Scope and potential of halogenases in biosynthetic applications. Curr Opin Chem Biol 2013; 17:276-83. [DOI: 10.1016/j.cbpa.2013.01.018] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Revised: 01/22/2013] [Accepted: 01/23/2013] [Indexed: 11/24/2022]
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27
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Abstract
The investigation of unique chemical phenotypes has led to the discovery of enzymes with interesting behaviors that allow us to explore unusual function. The organofluorine-producing microbe Streptomyces cattleya has evolved a fluoroacetyl-CoA thioesterase (FlK) that demonstrates a surprisingly high level of discrimination for a single fluorine substituent on its substrate compared with the cellularly abundant hydrogen analog, acetyl-CoA. In this report, we show that the high selectivity of FlK is achieved through catalysis rather than molecular recognition, where deprotonation at the C(α) position to form a putative ketene intermediate only occurs on the fluorinated substrate, thereby accelerating the rate of hydrolysis 10(4)-fold compared with the nonfluorinated congener. These studies provide insight into mechanisms of catalytic selectivity in a native system where the existence of two reaction pathways determines substrate rather than product selection.
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Affiliation(s)
| | - Michelle C. Y. Chang
- Departments of Chemistry and
- Molecular and Cell Biology, University of California, Berkeley, CA 94720; and
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
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28
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Insights into fluorometabolite biosynthesis in Streptomyces cattleya DSM46488 through genome sequence and knockout mutants. Bioorg Chem 2012; 44:1-7. [PMID: 22858315 DOI: 10.1016/j.bioorg.2012.06.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 06/20/2012] [Indexed: 11/20/2022]
Abstract
Streptomyces cattleya DSM 46488 is unusual in its ability to biosynthesise fluorine containing natural products, where it can produce fluoroacetate and 4-fluorothreonine. The individual enzymes involved in fluorometabolite biosynthesis have already been demonstrated in in vitro investigations. Candidate genes for the individual biosynthetic steps were located from recent genome sequences. In vivo inactivation of individual genes including those encoding the S-adenosyl-l-methionine:fluoride adenosyltransferase (fluorinase, SCATT_41540), 5'-fluoro-5'-deoxyadenosine phosphorylase (SCATT_41550), fluoroacetyl-CoA thioesterase (SCATT_41470), 5-fluoro-5-deoxyribose-1-phosphate isomerase (SCATT_20080) and a 4-fluorothreonine acetaldehyde transaldolase (SCATT_p11780) confirm that they are essential for fluorometabolite production. Notably gene disruption of the transaldolase (SCATT_p11780) resulted in a mutant which could produce fluoroacetate but was blocked in its ability to biosynthesise 4-fluorothreonine, revealing a branchpoint role for the PLP-transaldolase.
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29
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Walker MC, Wen M, Weeks AM, Chang MCY. Temporal and fluoride control of secondary metabolism regulates cellular organofluorine biosynthesis. ACS Chem Biol 2012; 7:1576-85. [PMID: 22769062 DOI: 10.1021/cb3002057] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Elucidating mechanisms of natural organofluorine biosynthesis is essential for a basic understanding of fluorine biochemistry in living systems as well as for expanding biological methods for fluorine incorporation into small molecules of interest. To meet this goal we have combined massively parallel sequencing technologies, genetic knockout, and in vitro biochemical approaches to investigate the fluoride response of the only known genetic host of an organofluorine-producing pathway, Streptomyces cattleya. Interestingly, we have discovered that the major mode of S. cattleya's resistance to the fluorinated toxin it produces, fluoroacetate, may be due to temporal control of production rather than the ability of the host's metabolic machinery to discriminate between fluorinated and non-fluorinated molecules. Indeed, neither the acetate kinase/phosphotransacetylase acetate assimilation pathway nor the TCA cycle enzymes (citrate synthase and aconitase) exclude fluorinated substrates based on in vitro biochemical characterization. Furthermore, disruption of the fluoroacetate resistance gene encoding a fluoroacetyl-CoA thioesterase (FlK) does not appear to lead to an observable growth defect related to organofluorine production. By showing that a switch in central metabolism can mediate and control molecular fluorine incorporation, our findings reveal a new potential strategy toward diversifying simple fluorinated building blocks into more complex products.
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Affiliation(s)
- Mark C. Walker
- Departments of †Chemistry and ‡Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720-1460,
United States
| | - Miao Wen
- Departments of †Chemistry and ‡Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720-1460,
United States
| | - Amy M. Weeks
- Departments of †Chemistry and ‡Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720-1460,
United States
| | - Michelle C. Y. Chang
- Departments of †Chemistry and ‡Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720-1460,
United States
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30
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Song F, Thoden JB, Zhuang Z, Latham J, Trujillo M, Holden HM, Dunaway-Mariano D. The catalytic mechanism of the hotdog-fold enzyme superfamily 4-hydroxybenzoyl-CoA thioesterase from Arthrobacter sp. strain SU. Biochemistry 2012; 51:7000-16. [PMID: 22873756 DOI: 10.1021/bi301059m] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The hotdog-fold enzyme 4-hydroxybenzoyl-coenzyme A (4-HB-CoA) thioesterase from Arthrobacter sp. strain AU catalyzes the hydrolysis of 4-HB-CoA to form 4-hydroxybenzoate (4-HB) and coenzyme A (CoA) in the final step of the 4-chlorobenzoate dehalogenation pathway. Guided by the published X-ray structures of the liganded enzyme (Thoden, J. B., Zhuang, Z., Dunaway-Mariano, D., and Holden H. M. (2003) J. Biol. Chem. 278, 43709-43716), a series of site-directed mutants were prepared for testing the roles of active site residues in substrate binding and catalysis. The mutant thioesterases were subjected to X-ray structure determination to confirm retention of the native fold, and in some cases, to reveal changes in the active site configuration. In parallel, the wild-type and mutant thioesterases were subjected to transient and steady-state kinetic analysis, and to (18)O-solvent labeling experiments. Evidence is provided that suggests that Glu73 functions in nucleophilic catalysis, that Gly65 and Gln58 contribute to transition-state stabilization via hydrogen bond formation with the thioester moiety and that Thr77 orients the water nucleophile for attack at the 4-hydroxybenzoyl carbon of the enzyme-anhydride intermediate. The replacement of Glu73 with Asp was shown to switch the function of the carboxylate residue from nucleophilic catalysis to base catalysis and thus, the reaction from a two-step process involving a covalent enzyme intermediate to a single-step hydrolysis reaction. The E73D/T77A double mutant regained most of the catalytic efficiency lost in the E73D single mutant. The results from (31)P NMR experiments indicate that the substrate nucleotide unit is bound to the enzyme surface. Kinetic analysis of site-directed mutants was carried out to determine the contributions made by Arg102, Arg150, Ser120, and Thr121 in binding the nucleotide unit. Lastly, we show by kinetic and X-ray analyses of Asp31, His64, and Glu78 site-directed mutants that these three active site residues are important for productive binding of the substrate 4-hydroxybenzoyl ring.
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Affiliation(s)
- Feng Song
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131, USA
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31
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Lechner A, Eustáquio AS, Gulder TAM, Hafner M, Moore BS. Selective overproduction of the proteasome inhibitor salinosporamide A via precursor pathway regulation. ACTA ACUST UNITED AC 2012; 18:1527-36. [PMID: 22195555 DOI: 10.1016/j.chembiol.2011.10.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 09/30/2011] [Accepted: 10/11/2011] [Indexed: 12/30/2022]
Abstract
The chlorinated natural product salinosporamide A is a potent 20S proteasome inhibitor currently in clinical trials as an anticancer agent. To deepen our understanding of salinosporamide biosynthesis, we investigated the function of a LuxR-type pathway-specific regulatory gene, salR2, and observed a selective effect on the production of salinosporamide A over its less active aliphatic analogs. SalR2 specifically activates genes involved in the biosynthesis of the halogenated precursor chloroethylmalonyl-CoA, which is a dedicated precursor of salinosporamide A. Specifically, SalR2 activates transcription of two divergent operons-one of which contains the unique S-adenosyl-L-methionine-dependent chlorinase encoding gene salL. By applying this knowledge to rational engineering, we were able to selectively double salinosporamide A production. This study exemplifies the specialized regulation of a polyketide precursor pathway and its application to the selective overproduction of a specific natural product congener.
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Affiliation(s)
- Anna Lechner
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093-0204, USA
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Dalvit C, Vulpetti A. Intermolecular and intramolecular hydrogen bonds involving fluorine atoms: implications for recognition, selectivity, and chemical properties. ChemMedChem 2012; 7:262-72. [PMID: 22262517 DOI: 10.1002/cmdc.201100483] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Revised: 12/02/2011] [Indexed: 11/06/2022]
Abstract
A correlation between 19F NMR isotropic chemical shift and close intermolecular F⋅⋅⋅H-X contacts (with X=N or O) has been identified upon analysis of the X-ray crystal structures of fluorinated molecules listed in the Cambridge Structural Database (CSD). An optimal F⋅⋅⋅X distance involving primary and shielded secondary fluorine atoms in hydrogen-bond formation along with a correlation between F⋅⋅⋅H distance and F⋅⋅⋅H-X angle were also derived from the analysis. The hydrogen bonds involving fluorine are relevant, not only for the recognition mechanism and stabilization of a preferred conformation, but also for improvement in the permeability of the molecules, as shown with examples taken from a proprietary database. Results of an analysis of the small number of fluorine-containing natural products listed in the Protein Data Bank (PDB) appear to strengthen the derived correlation between 19F NMR isotropic chemical shift and interactions involving fluorine (also known as the "rule of shielding") and provides a hypothesis for the recognition mechanism and catalytic activity of specific enzymes. Novel chemical scaffolds, based on the rule of shielding, have been designed for recognizing distinct structural motifs present in proteins. It is envisaged that this approach could find useful applications in drug design for the efficient optimization of chemical fragments or promising compounds by increasing potency and selectivity against the desired biomolecular target.
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Affiliation(s)
- Claudio Dalvit
- Department of Chemistry, University of Neuchâtel, Avenue de Bellevaux 51, 2000 Neuchâtel, Swizerland.
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Complete genome sequence of Streptomyces cattleya NRRL 8057, a producer of antibiotics and fluorometabolites. J Bacteriol 2011; 193:5055-6. [PMID: 21868806 DOI: 10.1128/jb.05583-11] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Streptomyces cattleya, a producer of the antibiotics thienamycin and cephamycin C, is one of the rare bacteria known to synthesize fluorinated metabolites. The genome consists of two linear replicons. The genes involved in fluorine metabolism and in the biosynthesis of the antibiotic thienamycin were mapped on both replicons.
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Gulder TAM, Moore BS. Salinosporamide natural products: Potent 20 S proteasome inhibitors as promising cancer chemotherapeutics. Angew Chem Int Ed Engl 2010; 49:9346-67. [PMID: 20927786 PMCID: PMC3103133 DOI: 10.1002/anie.201000728] [Citation(s) in RCA: 171] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Proteasome inhibitors are rapidly evolving as potent treatment options in cancer therapy. One of the most promising drug candidates of this type is salinosporamide A from the bacterium Salinispora tropica. This marine natural product possesses a complex, densely functionalized γ-lactam-β-lactone pharmacophore, which is responsible for its irreversible binding to its target, the β subunit of the 20S proteasome. Salinosporamide A entered phase I clinical trials for the treatment of multiple myeloma only three years after its discovery. The strong biological activity and the challenging structure of this compound have fueled intense academic and industrial research in recent years, which has led to the development of more than ten syntheses, the elucidation of its biosynthetic pathway, and the generation of promising structure-activity relationships and oncological data. Salinosporamide A thus serves as an intriguing example of the successful interplay of modern drug discovery and biomedical research, medicinal chemistry and pharmacology, natural product synthesis and analysis, as well as biosynthesis and bioengineering.
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Affiliation(s)
- Tobias A. M. Gulder
- Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0204 (USA), Fax: (+1)858-534-1305, , Homepage: http://moorelab.ucsd.edu
| | - Bradley S. Moore
- Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0204 (USA), Fax: (+1)858-534-1305, , Homepage: http://moorelab.ucsd.edu
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Weeks AM, Coyle SM, Jinek M, Doudna JA, Chang MCY. Structural and biochemical studies of a fluoroacetyl-CoA-specific thioesterase reveal a molecular basis for fluorine selectivity. Biochemistry 2010; 49:9269-79. [PMID: 20836570 PMCID: PMC3461317 DOI: 10.1021/bi101102u] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We have initiated a broad-based program aimed at understanding the molecular basis of fluorine specificity in enzymatic systems, and in this context, we report crystallographic and biochemical studies on a fluoroacetyl-coenzyme A (CoA) specific thioesterase (FlK) from Streptomyces cattleya. Our data establish that FlK is competent to protect its host from fluoroacetate toxicity in vivo and demonstrate a 10(6)-fold discrimination between fluoroacetyl-CoA (k(cat)/K(M) = 5 × 10⁷ M⁻¹ s⁻¹) and acetyl-CoA (k(cat)/K(M) = 30 M⁻¹ s⁻¹) based on a single fluorine substitution that originates from differences in both substrate reactivity and binding. We show that Thr 42, Glu 50, and His 76 are key catalytic residues and identify several factors that influence substrate selectivity. We propose that FlK minimizes interaction with the thioester carbonyl, leading to selection against acetyl-CoA binding that can be recovered in part by new C═O interactions in the T42S and T42C mutants. We hypothesize that the loss of these interactions is compensated by the entropic driving force for fluorinated substrate binding in a hydrophobic binding pocket created by a lid structure, containing Val 23, Leu 26, Phe 33, and Phe 36, that is not found in other structurally characterized members of this superfamily. We further suggest that water plays a critical role in fluorine specificity based on biochemical and structural studies focused on the unique Phe 36 "gate" residue, which functions to exclude water from the active site. Taken together, the findings from these studies offer molecular insights into organofluorine recognition and design of fluorine-specific enzymes.
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Affiliation(s)
- Amy M. Weeks
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720-1460
| | - Scott M. Coyle
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720-1460
| | - Martin Jinek
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720-1460
| | - Jennifer A. Doudna
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720-1460
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720-1460
| | - Michelle C. Y. Chang
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720-1460
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720-1460
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Gulder TAM, Moore BS. Salinosporamid-Naturstoffe: potente Inhibitoren des 20S-Proteasoms als vielversprechende Krebs-Chemotherapeutika. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201000728] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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37
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Dias MVB, Huang F, Chirgadze DY, Tosin M, Spiteller D, Dry EFV, Leadlay PF, Spencer JB, Blundell TL. Structural basis for the activity and substrate specificity of fluoroacetyl-CoA thioesterase FlK. J Biol Chem 2010; 285:22495-504. [PMID: 20430898 PMCID: PMC2903362 DOI: 10.1074/jbc.m110.107177] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2010] [Revised: 04/08/2010] [Indexed: 11/29/2022] Open
Abstract
The thioesterase FlK from the fluoroacetate-producing Streptomyces cattleya catalyzes the hydrolysis of fluoroacetyl-coenzyme A. This provides an effective self-defense mechanism, preventing any fluoroacetyl-coenzyme A formed from being further metabolized to 4-hydroxy-trans-aconitate, a lethal inhibitor of the tricarboxylic acid cycle. Remarkably, FlK does not accept acetyl-coenzyme A as a substrate. Crystal structure analysis shows that FlK forms a dimer, in which each subunit adopts a hot dog fold as observed for type II thioesterases. Unlike other type II thioesterases, which invariably utilize either an aspartate or a glutamate as catalytic base, we show by site-directed mutagenesis and crystallography that FlK employs a catalytic triad composed of Thr(42), His(76), and a water molecule, analogous to the Ser/Cys-His-acid triad of type I thioesterases. Structural comparison of FlK complexed with various substrate analogues suggests that the interaction between the fluorine of the substrate and the side chain of Arg(120) located opposite to the catalytic triad is essential for correct coordination of the substrate at the active site and therefore accounts for the substrate specificity.
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Affiliation(s)
| | - Fanglu Huang
- University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | | | - Manuela Tosin
- University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | | | - Emily F. V. Dry
- University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | | | - Jonathan B. Spencer
- University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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Eustáquio AS, O'Hagan D, Moore BS. Engineering fluorometabolite production: fluorinase expression in Salinispora tropica Yields Fluorosalinosporamide. JOURNAL OF NATURAL PRODUCTS 2010; 73:378-82. [PMID: 20085308 PMCID: PMC2846182 DOI: 10.1021/np900719u] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Organofluorine compounds play an important role in medicinal chemistry, where they are responsible for up to 15% of the pharmaceutical products on the market. While natural products are valuable sources of new chemical entities, natural fluorinated molecules are extremely rare and the pharmaceutical industry has not benefited from a microbial source of this class of compounds. Streptomyces cattleya is an unusual bacterium in that it elaborates fluoroacetate and the amino acid 4-fluorothreonine. The discovery in 2002 of the fluorination enzyme FlA responsible for C-F bond formation in S. cattleya, and its subsequent characterization, opened up for the first time the prospect of genetically engineering fluorometabolite production from fluoride ion in host organisms. As a proof of principle, we report here the induced production of fluorosalinosporamide by replacing the chlorinase gene salL from Salinispora tropica with the fluorinase gene flA.
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Affiliation(s)
- Alessandra S. Eustáquio
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, 92093-0204
| | - David O'Hagan
- Centre for Biomolecular Sciences, School of Chemistry, University of St Andrews, KY16 9ST, UK
- To whom correspondence should be addressed. B.S.M. Tel: +1 858 822 6650. Fax: +1 858 558 3702. . D.O'H. Tel: +44 1334 467176. Fax: +44 1334 463808.
| | - Bradley S. Moore
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, 92093-0204
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, 92093-0204
- To whom correspondence should be addressed. B.S.M. Tel: +1 858 822 6650. Fax: +1 858 558 3702. . D.O'H. Tel: +44 1334 467176. Fax: +44 1334 463808.
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39
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Murphy CD. Biodegradation and biotransformation of organofluorine compounds. Biotechnol Lett 2009; 32:351-9. [DOI: 10.1007/s10529-009-0174-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2009] [Revised: 11/06/2009] [Accepted: 11/09/2009] [Indexed: 10/20/2022]
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Biosynthesis of the salinosporamide A polyketide synthase substrate chloroethylmalonyl-coenzyme A from S-adenosyl-L-methionine. Proc Natl Acad Sci U S A 2009; 106:12295-300. [PMID: 19590008 DOI: 10.1073/pnas.0901237106] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Polyketides are among the major classes of bioactive natural products used to treat microbial infections, cancer, and other diseases. Here we describe a pathway to chloroethylmalonyl-CoA as a polyketide synthase building block in the biosynthesis of salinosporamide A, a marine microbial metabolite whose chlorine atom is crucial for potent proteasome inhibition and anticancer activity. S-adenosyl-L-methionine (SAM) is converted to 5'-chloro-5'-deoxyadenosine (5'-ClDA) in a reaction catalyzed by a SAM-dependent chlorinase as previously reported. By using a combination of gene deletions, biochemical analyses, and chemical complementation experiments with putative intermediates, we now provide evidence that 5'-ClDA is converted to chloroethylmalonyl-CoA in a 7-step route via the penultimate intermediate 4-chlorocrotonyl-CoA. Because halogenation often increases the bioactivity of drugs, the availability of a halogenated polyketide building block may be useful in molecular engineering approaches toward polyketide scaffolds.
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41
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Kaysser L, Lutsch L, Siebenberg S, Wemakor E, Kammerer B, Gust B. Identification and manipulation of the caprazamycin gene cluster lead to new simplified liponucleoside antibiotics and give insights into the biosynthetic pathway. J Biol Chem 2009; 284:14987-96. [PMID: 19351877 DOI: 10.1074/jbc.m901258200] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Caprazamycins are potent anti-mycobacterial liponucleoside antibiotics isolated from Streptomyces sp. MK730-62F2 and belong to the translocase I inhibitor family. Their complex structure is derived from 5'-(beta-O-aminoribosyl)-glycyluridine and comprises a unique N-methyldiazepanone ring. The biosynthetic gene cluster has been identified, cloned, and sequenced, representing the first gene cluster of a translocase I inhibitor. Sequence analysis revealed the presence of 23 open reading frames putatively involved in export, resistance, regulation, and biosynthesis of the caprazamycins. Heterologous expression of the gene cluster in Streptomyces coelicolor M512 led to the production of non-glycosylated bioactive caprazamycin derivatives. A set of gene deletions validated the boundaries of the cluster and inactivation of cpz21 resulted in the accumulation of novel simplified liponucleoside antibiotics that lack the 3-methylglutaryl moiety. Therefore, Cpz21 is assigned to act as an acyltransferase in caprazamycin biosynthesis. In vivo and in silico analysis of the caprazamycin biosynthetic gene cluster allows a first proposal of the biosynthetic pathway and provides insights into the biosynthesis of related uridyl-antibiotics.
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Affiliation(s)
- Leonard Kaysser
- Pharmazeutische Biologie, Pharmazeutisches Institut, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 8, 72076 Tübingen
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42
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Abstract
This review covers the biosynthesis of extender units that are utilized for the assembly of polyketides by polyketide synthases. The metabolic origins of each of the currently known polyketide synthase extender units are covered.
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Affiliation(s)
- Yolande A. Chan
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, WI 53706, USA
| | - Angela M. Podevels
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Brian M. Kevany
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Michael G. Thomas
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, WI 53706, USA
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Deng H, Cross SM, McGlinchey RP, Hamilton JT, O'Hagan D. In Vitro Reconstituted Biotransformation of 4-Fluorothreonine from Fluoride Ion: Application of the Fluorinase. ACTA ACUST UNITED AC 2008; 15:1268-76. [DOI: 10.1016/j.chembiol.2008.10.012] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2008] [Revised: 10/13/2008] [Accepted: 10/16/2008] [Indexed: 11/16/2022]
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Hong H, Spiteller D, Spencer JB. Incorporation of fluoroacetate into an aromatic polyketide and its influence on the mode of cyclization. Angew Chem Int Ed Engl 2008; 47:6028-32. [PMID: 18613185 DOI: 10.1002/anie.200801100] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Hui Hong
- University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
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45
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Hong H, Spiteller D, Spencer J. Incorporation of Fluoroacetate into an Aromatic Polyketide and Its Influence on the Mode of Cyclization. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200801100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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46
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Leadlay P. Obituary: Jonathan B. Spencer (1960-2008). CHEMISTRY & BIOLOGY 2008; 15:424-426. [PMID: 18551814 DOI: 10.1016/j.chembiol.2008.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Affiliation(s)
- Peter Leadlay
- Department of Biochemistry, University of Cambridge, Cambridge, UK.
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Chen X, van Pée KH. Catalytic mechanisms, basic roles, and biotechnological and environmental significance of halogenating enzymes. Acta Biochim Biophys Sin (Shanghai) 2008; 40:183-93. [PMID: 18330472 DOI: 10.1111/j.1745-7270.2008.00390.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The understanding of enzymatic incorporation of halogen atoms into organic molecules has increased during the last few years. Two novel types of halogenating enzymes, flavin-dependent halogenases and alpha-ketoglutarate-dependent halogenases, are now known to play a significant role in enzyme-catalyzed halogenation. The recent advances on the halogenating enzymes RebH, SyrB2, and CytC3 have suggested some new mechanisms for enzymatic halogenations. This review concentrates on the occurrence, catalytic mechanisms, and biotechnological applications of the halogenating enzymes that are currently known.
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Affiliation(s)
- Xianping Chen
- Biomedical Engineering Centre, Guilin University of Electronic Technology, Guilin 541004, China
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Eustáquio AS, Pojer F, Noel JP, Moore BS. Discovery and characterization of a marine bacterial SAM-dependent chlorinase. Nat Chem Biol 2007; 4:69-74. [PMID: 18059261 PMCID: PMC2762381 DOI: 10.1038/nchembio.2007.56] [Citation(s) in RCA: 160] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2007] [Accepted: 10/25/2007] [Indexed: 11/09/2022]
Abstract
Halogen atom incorporation into a scaffold of bioactive compounds often amplifies biological activity, as is the case for the anticancer agent salinosporamide A (1), a chlorinated natural product from the marine bacterium Salinispora tropica. Significant effort in understanding enzymatic chlorination shows that oxidative routes predominate to form reactive electrophilic or radical chlorine species. Here we report the genetic, biochemical and structural characterization of the chlorinase SalL, which halogenates S-adenosyl-L-methionine (2) with chloride to generate 5'-chloro-5'-deoxyadenosine (3) and L-methionine (4) in a rarely observed nucleophilic substitution strategy analogous to that of Streptomyces cattleya fluorinase. Further metabolic tailoring produces a halogenated polyketide synthase substrate specific for salinosporamide A biosynthesis. SalL also accepts bromide and iodide as substrates, but not fluoride. High-resolution crystal structures of SalL and active site mutants complexed with substrates and products support the S(N)2 nucleophilic substitution mechanism and further illuminate halide specificity in this newly discovered halogenase family.
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Affiliation(s)
- Alessandra S Eustáquio
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA.
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Onega M, McGlinchey RP, Deng H, Hamilton JTG, O'Hagan D. The identification of (3R,4S)-5-fluoro-5-deoxy-d-ribulose-1-phosphate as an intermediate in fluorometabolite biosynthesis in Streptomyces cattleya. Bioorg Chem 2007; 35:375-85. [PMID: 17574646 DOI: 10.1016/j.bioorg.2007.04.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2007] [Revised: 04/17/2007] [Accepted: 04/18/2007] [Indexed: 11/22/2022]
Abstract
(3R,4S)-5-Fluoro-5-deoxy-D-ribulose-1-phosphate (5-FDRulP) has been identified as the third fluorinated intermediate on the biosynthetic pathway to fluoroacetate and 4-fluorothreonine in Streptomyces cattleya. 5-FDRulP is generated after formation of 5'-fluoro-5'-deoxyadenosine (5'-FDA) and then phosphorolysis of 5'-FDA to 5-fluoro-5-deoxy-D-ribose-1-phosphate (5-FDRP) by the action of a purine nucleoside phosphorylase. An isomerase mediates the conversion of 5-FDRP to 5-FDRulP. The identity of the (3R,4S) diastereoisomer of 5-FDRulP was established by comparative (19)F{(1)H} NMR studies whereby 5-FDRulP that accumulated in a cell free extract of S. cattleya, was treated with a phytase to generate the non-phosphorylated sugar, 5-fluoro-5-deoxy-D-ribulose (5-FDRul). This S. cattleya product was compared to the product of an in-vitro biotransformation where separately 5-fluoro-5-deoxy-D-ribose and 5-fluoro-5-deoxy-D-xylose were converted to 5-fluoro-5-deoxy-D-ribulose and 5-fluoro-5-deoxy-D-xylulose respectively by the action of glucose isomerase. It was demonstrated that 5-fluoro-5-deoxy-D-ribose gave the identical diastereoisomer to that observed from 5-FDRulP.
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Affiliation(s)
- Mayca Onega
- School of Chemistry and Centre for Biomolecular Science, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK
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50
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