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Schroeter KL, Rolfe N, Forrester TJB, Kimber MS, Seah SYK. Shy is a proteobacterial steroid hydratase which catalyzes steroid side chain degradation without requiring a catalytically inert partner domain. J Biol Chem 2024; 300:107509. [PMID: 38944126 PMCID: PMC11321319 DOI: 10.1016/j.jbc.2024.107509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 06/17/2024] [Accepted: 06/20/2024] [Indexed: 07/01/2024] Open
Abstract
Shy (side chain hydratase) and Sal (side chain aldolase), are involved in successive reactions in the pathway of bile acid side chain catabolism in Proteobacteria. Untagged Shy copurified with His-tagged Sal indicating that the two enzymes form a complex. Shy contains a MaoC and a DUF35 domain. When coexpressed with Sal, the DUF35 domain but not the MaoC domain of Shy was observed to copurify with Sal, indicating Sal interacts with Shy through its DUF35 domain. The MaoC domain of Shy (ShyMaoC) remained catalytically viable and could hydrate cholyl-enoyl-CoA with similar catalytic efficiency as in the Shy-Sal complex. Sal expressed with the DUF35 domain of Shy (Sal-ShyDUF35) was similarly competent for the retro-aldol cleavage of cholyl-3-OH-CoA. ShyMaoC showed a preference for C5 side chain bile acid substrates, exhibiting low activity toward C3 side chain substrates. The ShyMaoC structure was determined by X-ray crystallography, showing a hot dog fold with a short central helix surrounded by a twisted antiparallel β-sheet. Modeling and mutagenesis studies suggest that the bile acid substrate occupies the large open cleft formed by the truncated central helix and repositioning of the active site housing. ShyMaoC therefore contains two substrate binding sites per homodimer, making it distinct from previously characterized MaoC steroid hydratases that are (pseudo) heterodimers with one substrate binding site per dimer. The characterization of Shy provides insight into how MaoC family hydratases have adapted to accommodate large polycyclic substrates that can facilitate future engineering of these enzymes to produce novel steroid pharmaceuticals.
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Affiliation(s)
- Kurt L Schroeter
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Nicolas Rolfe
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Taylor J B Forrester
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Matthew S Kimber
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Stephen Y K Seah
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.
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2
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Bai L, Yang P, Han B, Kong L. Progress of the acyl-Coenzyme A thioester hydrolase family in cancer. Front Oncol 2024; 14:1374094. [PMID: 38562172 PMCID: PMC10982514 DOI: 10.3389/fonc.2024.1374094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 02/26/2024] [Indexed: 04/04/2024] Open
Abstract
In recent years, the acyl-Coenzyme A thioester hydrolase family (ACOTs) has received wide attention as a key link in lipid metabolism. This family is a class of enzymes that catalyze the hydrolysis of fatty acyl-Coenzyme A, disrupting the thioester bond present within acyl-CoA ester molecules to produce free fatty acids (FFA) and the corresponding coenzyme A (CoA). Such enzymes play a very important role in lipid metabolism through maintaining appropriate levels of intracellular FFA and fatty acyl-CoA as well as CoA. It is broadly divided into two distinct subgroups, the type-I α/β-hydrolase fold enzyme superfamily and the type-II 'hot dog' fold superfamily. There are currently four human type-I genes and eight human type-II genes. Although the two subgroups catalyze the same reaction, they are not structurally similar, do not share the same sequence homology, and differ greatly in protein executive functions. This review summarizes the classification of the acyl-CoA thioester hydrolase family, an overview of the structural sequences, and advances in digestive, respiratory, and urinary systemic tumors. In order to explore potential specific drug targets and effective interventions, to provide new strategies for tumor prevention and treatment.
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Affiliation(s)
- Lu Bai
- Inner Mongolia Medical University, Hohhot, China
- Department of Pathology, Peking University Cancer Hospital & Affiliated Cancer Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Pengjie Yang
- Thoracic Surgery Department, Peking University Cancer Hospital & Affiliated Cancer Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Bater Han
- Thoracic Surgery Department, Peking University Cancer Hospital & Affiliated Cancer Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Linghui Kong
- Department of Pathology, Peking University Cancer Hospital & Affiliated Cancer Hospital of Inner Mongolia Medical University, Hohhot, China
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3
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de Dios SMR, Hass JL, Graham DL, Kumar N, Antony AE, Morton MD, Berkowitz DB. Information-Rich, Dual-Function 13C/ 2H-Isotopic Crosstalk NMR Assay for Human Serine Racemase (hSR) Provides a PLP-Enzyme "Partitioning Fingerprint" and Reveals Disparate Chemotypes for hSR Inhibition. J Am Chem Soc 2023; 145:3158-3174. [PMID: 36696670 PMCID: PMC11103274 DOI: 10.1021/jacs.2c12774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The first dual-function assay for human serine racemase (hSR), the only bona fide racemase in human biology, is reported. The hSR racemization function is essential for neuronal signaling, as the product, d-serine (d-Ser), is a potent N-methyl d-aspartate (NMDA) coagonist, important for learning and memory, with dysfunctional d-Ser-signaling being observed in some neuronal disorders. The second hSR function is β-elimination and gives pyruvate; this activity is elevated in colorectal cancer. This new NMR-based assay allows one to monitor both α-proton-exchange chemistry and β-elimination using only the native l-Ser substrate and hSR and is the most sensitive such assay. The assay judiciously employs segregated dual 13C-labeling and 13C/2H crosstalk, exploiting both the splitting and shielding effects of deuterium. The assay is deployed to screen a 1020-compound library and identifies an indolo-chroman-2,4-dione inhibitor family that displays allosteric site binding behavior (noncompetitive inhibition vs l-Ser substrate; competitive inhibition vs adenosine 5'-triphosphate (ATP)). This assay also reveals important mechanistic information for hSR; namely, that H/D exchange is ∼13-fold faster than racemization, implying that K56 protonates the carbanionic intermediate on the si-face much faster than does S84 on the re-face. Moreover, the 13C NMR peak pattern seen is suggestive of internal return, pointing to K56 as the likely enamine-protonating residue for β-elimination. The 13C/2H-isotopic crosstalk assay has also been applied to the enzyme tryptophan synthase and reveals a dramatically different partition ratio in this active site (β-replacement: si-face protonation ∼6:1 vs β-elimination: si-face protonation ∼1:3.6 for hSR), highlighting the value of this approach for fingerprinting the pyridoxal phosphate (PLP) enzyme mechanism.
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Affiliation(s)
| | | | | | - Nivesh Kumar
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588 USA
| | - Aina E. Antony
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588 USA
| | - Martha D. Morton
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588 USA
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4
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Hobson C, Jenner M, Jian X, Griffiths D, Roberts DM, Rey-Carrizo M, Challis GL. Diene incorporation by a dehydratase domain variant in modular polyketide synthases. Nat Chem Biol 2022; 18:1410-1416. [PMID: 36109649 PMCID: PMC7613849 DOI: 10.1038/s41589-022-01127-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/27/2022] [Indexed: 11/09/2022]
Abstract
Modular polyketide synthases (PKSs) are biosynthetic assembly lines that construct structurally diverse natural products with wide-ranging applications in medicine and agriculture. Various mechanisms contribute to structural diversification during PKS-mediated chain assembly, including dehydratase (DH) domain-mediated elimination of water from R and S-configured 3-hydroxy-thioesters to introduce E- and Z-configured carbon-carbon double bonds, respectively. Here we report the discovery of a DH domain variant that catalyzes the sequential elimination of two molecules of water from a (3R, 5S)-3,5-dihydroxy thioester during polyketide chain assembly, introducing a conjugated E,Z-diene into various modular PKS products. We show that the reaction proceeds via a (2E, 5S)-2-enoyl-5-hydroxy-thioester intermediate and involves an additional universally conserved histidine residue that is absent from the active site of most conventional DH domains. These findings expand the diverse range of chemistries mediated by DH-like domains in modular PKSs, highlighting the catalytic versatility of the double hotdog fold.
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Affiliation(s)
- Christian Hobson
- Department of Chemistry, University of Warwick, Coventry, UK.,Willow Biosciences Inc., Vancouver, British Columbia, Canada
| | - Matthew Jenner
- Department of Chemistry, University of Warwick, Coventry, UK.,Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, UK
| | - Xinyun Jian
- Department of Chemistry, University of Warwick, Coventry, UK.,Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, UK.,Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Daniel Griffiths
- Department of Chemistry, University of Warwick, Coventry, UK.,Monash University Accident Research Centre, Clayton, Victoria, Australia
| | | | - Matias Rey-Carrizo
- Department of Chemistry, University of Warwick, Coventry, UK.,BCN Medical Writing, Sabadell, Spain
| | - Gregory L Challis
- Department of Chemistry, University of Warwick, Coventry, UK. .,Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, UK. .,Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia. .,ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, Victoria, Australia.
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5
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Tittes YU, Herbst DA, Martin SFX, Munoz-Hernandez H, Jakob RP, Maier T. The structure of a polyketide synthase bimodule core. SCIENCE ADVANCES 2022; 8:eabo6918. [PMID: 36129979 PMCID: PMC9491710 DOI: 10.1126/sciadv.abo6918] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 08/04/2022] [Indexed: 06/15/2023]
Abstract
Polyketide synthases (PKSs) are predominantly microbial biosynthetic enzymes. They assemble highly potent bioactive natural products from simple carboxylic acid precursors. The most versatile families of PKSs are organized as assembly lines of functional modules. Each module performs one round of precursor extension and optional modification, followed by directed transfer of the intermediate to the next module. While enzymatic domains and even modules of PKSs are well understood, the higher-order modular architecture of PKS assembly lines remains elusive. Here, we visualize a PKS bimodule core using cryo-electron microscopy and resolve a two-dimensional meshwork of the bimodule core formed by homotypic interactions between modules. The sheet-like organization provides the framework for efficient substrate transfer and for sequestration of trans-acting enzymes required for polyketide production.
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Bacterial Hydratases Involved in Steroid Side Chain Degradation Have Distinct Substrate Specificities. J Bacteriol 2022; 204:e0023622. [PMID: 36000836 PMCID: PMC9491828 DOI: 10.1128/jb.00236-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Actinobacterial MaoC family enoyl coenzyme A (CoA) hydratases catalyze the addition of water across the double bond of CoA esters during steroid side chain catabolism. We determined that heteromeric MaoC type hydratases, exemplified by ChsH1-ChsH2Mtb of Mycobacterium tuberculosis and CasM-CasORjost from Rhodococcus jostii RHA1, are specific toward a 3-carbon side chain steroid metabolite, consistent with their roles in the last β-oxidation cycle of steroid side chain degradation. Hydratases containing two fused MaoC domains are responsible for the degradation of longer steroid side chains. These hydratases, encoded in the cholesterol degradation gene clusters of M. tuberculosis and R. jostii RHA1, have broad specificity and were able to catalyze the hydration of the 5-carbon side chain of both cholesterol and bile acid metabolites. Surprisingly, the homologous hydratases from the bile acid degradation pathway have low catalytic efficiencies or no activity toward the 5-carbon side chain bile acid metabolites, cholyl-enoyl-CoA, lithocholyl-enoyl-CoA, and chenodeoxycholyl-enoyl-CoA. Instead, these hydratases preferred a cholate metabolite with oxidized steroid rings and a planar ring structure. Together, the results suggest that ring oxidation occurs prior to side chain degradation in the actinobacterial bile acid degradation pathway. IMPORTANCE Characterization of the substrate specificity of hydratases described here will facilitate the development of specific inhibitors that may be useful as novel therapeutics against M. tuberculosis and to metabolically engineer bacteria to produce steroid pharmaceuticals with desired steroid rings and side chain structures.
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Singh BK, Biswas R, Bhattacharyya S, Basak A, Das AK. The C‐terminal end of mycobacterial HadBC regulates AcpM interaction during the FAS‐II pathway: a structural perspective. FEBS J 2022; 289:4963-4980. [DOI: 10.1111/febs.16405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 01/22/2022] [Accepted: 02/15/2022] [Indexed: 11/26/2022]
Affiliation(s)
- Bina Kumari Singh
- School of Biosciences Indian Institute of Technology Kharagpur India
| | - Rupam Biswas
- Department of Biotechnology Indian Institute of Technology Kharagpur India
| | - Sudipta Bhattacharyya
- Department of Bioscience & Bioengineering Indian Institute of Technology Jodhpur India
| | - Amit Basak
- Department of Chemistry Indian Institute of Technology Kharagpur India
| | - Amit K. Das
- Department of Biotechnology Indian Institute of Technology Kharagpur India
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Johnen P, Zimmermann S, Betz M, Hendriks J, Zimmermann A, Marnet M, De I, Zimmermann G, Kibat C, Cornaciu I, Mariaule V, Pica A, Clavel D, Márquez JA, Witschel M. Inhibition of acyl-ACP thioesterase as site of action of the commercial herbicides cumyluron, oxaziclomefone, bromobutide, methyldymron and tebutam. PEST MANAGEMENT SCIENCE 2022; 78:3620-3629. [PMID: 35604014 DOI: 10.1002/ps.7004] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 05/18/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Understanding the mode and site of action of a herbicide is key for its efficient development, the evaluation of its toxicological risk, efficient weed control and resistance management. Recently, the mode of action (MoA) of the herbicide cinmethylin was identified in lipid biosynthesis with acyl-ACP thioesterase (FAT) as the site of action (SoA). Cinmethylin was registered for selective use in cereal crops for the control of grass weeds in 2020. RESULTS Here, we present a high-resolution co-crystal structure of FAT in complex with cumyluron identified by a high throughput crystallization screen. We show binding to and inhibition of FAT by cumyluron. Furthermore, in an array of experiments consisting of FAT binding assays, FAT inhibition assays, physiological and metabolic profiling, we tested compounds that are structurally related to cumyluron and identified the commercial herbicides oxaziclomefone, methyldymron, tebutam and bromobutide, with so far unknown sites of action, as FAT inhibitors. Additionally, we show that the previously described FAT inhibitors cinmethylin and methiozolin bind to FAT in a nanomolar range, inhibit FAT enzymatic activity and lead to similar metabolic changes. CONCLUSION Based on presented data, we corroborate cinmethylin and methiozolin as potent FAT inhibitors and identify FAT as the SoA of the herbicides cumyluron, oxaziclomefone, bromobutide, methyldymron and tebutam. © 2022 Society of Chemical Industry.
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9
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Whaley SG, Radka CD, Subramanian C, Frank MW, Rock CO. Malonyl-acyl carrier protein decarboxylase activity promotes fatty acid and cell envelope biosynthesis in Proteobacteria. J Biol Chem 2021; 297:101434. [PMID: 34801557 PMCID: PMC8666670 DOI: 10.1016/j.jbc.2021.101434] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/02/2021] [Accepted: 11/09/2021] [Indexed: 11/20/2022] Open
Abstract
Bacterial fatty acid synthesis in Escherichia coli is initiated by the condensation of an acetyl-CoA with a malonyl-acyl carrier protein (ACP) by the β-ketoacyl-ACP synthase III enzyme, FabH. E. coli ΔfabH knockout strains are viable because of the yiiD gene that allows FabH-independent fatty acid synthesis initiation. However, the molecular function of the yiiD gene product is not known. Here, we show the yiiD gene product is a malonyl-ACP decarboxylase (MadA). MadA has two independently folded domains: an amino-terminal N-acetyl transferase (GNAT) domain (MadAN) and a carboxy-terminal hot dog dimerization domain (MadAC) that encodes the malonyl-ACP decarboxylase function. Members of the proteobacterial Mad protein family are either two domain MadA (GNAT-hot dog) or standalone MadB (hot dog) decarboxylases. Using structure-guided, site-directed mutagenesis of MadB from Shewanella oneidensis, we identified Asn45 on a conserved catalytic loop as critical for decarboxylase activity. We also found that MadA, MadAC, or MadB expression all restored normal cell size and growth rates to an E. coli ΔfabH strain, whereas the expression of MadAN did not. Finally, we verified that GlmU, a bifunctional glucosamine-1-phosphate N-acetyl transferase/N-acetyl-glucosamine-1-phosphate uridylyltransferase that synthesizes the key intermediate UDP-GlcNAc, is an ACP binding protein. Acetyl-ACP is the preferred glucosamine-1-phosphate N-acetyl transferase/N-acetyl-glucosamine-1-phosphate uridylyltransferase substrate, in addition to being the substrate for the elongation-condensing enzymes FabB and FabF. Thus, we conclude that the Mad family of malonyl-ACP decarboxylases supplies acetyl-ACP to support the initiation of fatty acid, lipopolysaccharide, peptidoglycan, and enterobacterial common antigen biosynthesis in Proteobacteria.
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Affiliation(s)
- Sarah G Whaley
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Christopher D Radka
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Chitra Subramanian
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Matthew W Frank
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Charles O Rock
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee, USA.
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Little RF, Hertweck C. Chain release mechanisms in polyketide and non-ribosomal peptide biosynthesis. Nat Prod Rep 2021; 39:163-205. [PMID: 34622896 DOI: 10.1039/d1np00035g] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Review covering up to mid-2021The structure of polyketide and non-ribosomal peptide natural products is strongly influenced by how they are released from their biosynthetic enzymes. As such, Nature has evolved a diverse range of release mechanisms, leading to the formation of bioactive chemical scaffolds such as lactones, lactams, diketopiperazines, and tetronates. Here, we review the enzymes and mechanisms used for chain release in polyketide and non-ribosomal peptide biosynthesis, how these mechanisms affect natural product structure, and how they could be utilised to introduce structural diversity into the products of engineered biosynthetic pathways.
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Affiliation(s)
- Rory F Little
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Germany.
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Germany.
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11
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Paiva P, Medina FE, Viegas M, Ferreira P, Neves RPP, Sousa JPM, Ramos MJ, Fernandes PA. Animal Fatty Acid Synthase: A Chemical Nanofactory. Chem Rev 2021; 121:9502-9553. [PMID: 34156235 DOI: 10.1021/acs.chemrev.1c00147] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Fatty acids are crucial molecules for most living beings, very well spread and conserved across species. These molecules play a role in energy storage, cell membrane architecture, and cell signaling, the latter through their derivative metabolites. De novo synthesis of fatty acids is a complex chemical process that can be achieved either by a metabolic pathway built by a sequence of individual enzymes, such as in most bacteria, or by a single, large multi-enzyme, which incorporates all the chemical capabilities of the metabolic pathway, such as in animals and fungi, and in some bacteria. Here we focus on the multi-enzymes, specifically in the animal fatty acid synthase (FAS). We start by providing a historical overview of this vast field of research. We follow by describing the extraordinary architecture of animal FAS, a homodimeric multi-enzyme with seven different active sites per dimer, including a carrier protein that carries the intermediates from one active site to the next. We then delve into this multi-enzyme's detailed chemistry and critically discuss the current knowledge on the chemical mechanism of each of the steps necessary to synthesize a single fatty acid molecule with atomic detail. In line with this, we discuss the potential and achieved FAS applications in biotechnology, as biosynthetic machines, and compare them with their homologous polyketide synthases, which are also finding wide applications in the same field. Finally, we discuss some open questions on the architecture of FAS, such as their peculiar substrate-shuttling arm, and describe possible reasons for the emergence of large megasynthases during evolution, questions that have fascinated biochemists from long ago but are still far from answered and understood.
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Affiliation(s)
- Pedro Paiva
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Fabiola E Medina
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Autopista Concepción-Talcahuano, 7100 Talcahuano, Chile
| | - Matilde Viegas
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro Ferreira
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Rui P P Neves
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - João P M Sousa
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Maria J Ramos
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro A Fernandes
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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Suharti, Mahardika G, Raissa, Dewi L, Yohandini H, Widhiastuty MP, Sakti RAW, Wahyudi ST, Akhmaloka. Cloning, heterologous expression, and characterization of a novel thioesterase from natural sample. Heliyon 2021; 7:e06542. [PMID: 33851045 PMCID: PMC8024609 DOI: 10.1016/j.heliyon.2021.e06542] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 11/24/2020] [Accepted: 03/15/2021] [Indexed: 11/30/2022] Open
Abstract
A novel thioesterse gene was successfully cloned and sequenced directly from natural sample of Domas Hot Spring, West Java, Indonesia. Homological analysis of the sequence showed that the gene appeared high homology to thioesterase genes with the highest to a putative thioesterase gene from uncultured Acidilobus sp. JCHS at 66% identity. However, phylogenetic analysis showed that the protein was separated from the branch with other known thioesterases. The size of the gene is around 500 base pairs, lied into 2 kb DNA fragment from a random PCR amplicon. The gene was overexpressed in Escherichia coli, a dominant band appeared at 17 kDa in SDS-PAGE with expression level at around 32% of total proteins. The activity of the purified protein using acetyl-CoA as substrate showed that the protein exhibited thioesterase activity. Furthermore, the enzyme also showed esterase activity on p-nitrophenyl ester as substrate. Detail characterization of esterolytic activity showed that the enzyme preferred p-nitrophenyl decanoate as substrate. The optimum activity of the enzyme was at 80 °C and pH 8. Activity of the enzyme was maintained after incubation at 80 °C up to 24 h. In addition, the enzyme was favorable on polar organic solvents. All the data obtained suggested that the enzyme is a novel alkaline thermostable thioesterase.
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Affiliation(s)
- Suharti
- Biochemistry Research Group, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung, Indonesia
- Department of Chemistry, Faculty of Science and Computer, Universitas Pertamina, Jl. Teuku Nyak Arief, Simprug Kebayoran, South Jakarta, Indonesia
| | - Gita Mahardika
- Biochemistry Research Group, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung, Indonesia
| | - Raissa
- Department of Chemistry, Faculty of Science and Computer, Universitas Pertamina, Jl. Teuku Nyak Arief, Simprug Kebayoran, South Jakarta, Indonesia
| | - Laksmi Dewi
- Department of Chemical Engineering, Faculty of Industrial Engineering, Universitas Pertamina, Jl. Teuku Nyak Arief, Simprug Kebayoran, South Jakarta, Indonesia
| | - Heni Yohandini
- Biochemistry Research Group, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung, Indonesia
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Sriwijaya, Jl. Raya Palembang Prabumulih KM 32, Indralaya-Ogan Ilir, Indonesia
| | - Made Puspasari Widhiastuty
- Biochemistry Research Group, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung, Indonesia
| | - Raden Aditya Wibawa Sakti
- Department of Chemistry, Faculty of Science and Computer, Universitas Pertamina, Jl. Teuku Nyak Arief, Simprug Kebayoran, South Jakarta, Indonesia
| | - Setyanto Tri Wahyudi
- Biochemistry Research Group, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung, Indonesia
- Department of Physics, IPB University, Bogor, 16680, Indonesia
| | - Akhmaloka
- Biochemistry Research Group, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung, Indonesia
- Department of Chemistry, Faculty of Science and Computer, Universitas Pertamina, Jl. Teuku Nyak Arief, Simprug Kebayoran, South Jakarta, Indonesia
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13
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Deng Z, Liu J, Li T, Li H, Liu Z, Dong Y, Li W. An Unusual Type II Polyketide Synthase System Involved in Cinnamoyl Lipid Biosynthesis. Angew Chem Int Ed Engl 2020; 60:153-158. [PMID: 32860295 DOI: 10.1002/anie.202007777] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 08/13/2020] [Indexed: 12/13/2022]
Abstract
As a unique structural moiety in natural products, cinnamoyl lipids (CLs), are proposed to be assembled by unusual type II polyketide synthases (PKSs). Herein, we demonstrate that the assembly of the CL compounds youssoufenes is accomplished by a PKS system that uniquely harbors three phylogenetically different ketosynthase/chain length factor (KS/CLF) complexes (YsfB/C, YsfD/E, and YsfJ/K). Through in vivo gene inactivation and in vitro reconstitution, as well as an intracellular tagged carrier-protein tracking (ITCT) strategy developed in this study, we successfully elucidated the isomerase-dependent ACP-tethered polyunsaturated chain elongation process. The three KS/CLFs were revealed to modularly assemble different parts of the youssoufene skeleton, during which benzene ring closure happens right after the formation of an ACP-tethered C18 polyene. Of note, the ITCT strategy could significantly contribute to the elucidation of other carrier-protein-dependent biosynthetic machineries.
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Affiliation(s)
- Zirong Deng
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Jing Liu
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Tong Li
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Huayue Li
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Zengzhi Liu
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Yujing Dong
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Wenli Li
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
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14
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Deng Z, Liu J, Li T, Li H, Liu Z, Dong Y, Li W. An Unusual Type II Polyketide Synthase System Involved in Cinnamoyl Lipid Biosynthesis. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202007777] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Zirong Deng
- Key Laboratory of Marine Drugs Ministry of Education School of Medicine and Pharmacy Ocean University of China Qingdao 266003 China
| | - Jing Liu
- Key Laboratory of Marine Drugs Ministry of Education School of Medicine and Pharmacy Ocean University of China Qingdao 266003 China
| | - Tong Li
- Key Laboratory of Marine Drugs Ministry of Education School of Medicine and Pharmacy Ocean University of China Qingdao 266003 China
| | - Huayue Li
- Key Laboratory of Marine Drugs Ministry of Education School of Medicine and Pharmacy Ocean University of China Qingdao 266003 China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology Qingdao 266237 China
| | - Zengzhi Liu
- Key Laboratory of Marine Drugs Ministry of Education School of Medicine and Pharmacy Ocean University of China Qingdao 266003 China
| | - Yujing Dong
- Key Laboratory of Marine Drugs Ministry of Education School of Medicine and Pharmacy Ocean University of China Qingdao 266003 China
| | - Wenli Li
- Key Laboratory of Marine Drugs Ministry of Education School of Medicine and Pharmacy Ocean University of China Qingdao 266003 China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology Qingdao 266237 China
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15
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Niehs SP, Dose B, Richter S, Pidot SJ, Dahse H, Stinear TP, Hertweck C. Mining Symbionts of a Spider‐Transmitted Fungus Illuminates Uncharted Biosynthetic Pathways to Cytotoxic Benzolactones. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201916007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Sarah P. Niehs
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI) Beutenbergstr. 11a 07745 Jena Germany
| | - Benjamin Dose
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI) Beutenbergstr. 11a 07745 Jena Germany
| | - Sophie Richter
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI) Beutenbergstr. 11a 07745 Jena Germany
| | - Sacha J. Pidot
- Department of Microbiology and Immunology Doherty Institute 792 Elizabeth Street Melbourne 3000 Australia
| | | | - Timothy P. Stinear
- Department of Microbiology and Immunology Doherty Institute 792 Elizabeth Street Melbourne 3000 Australia
| | - Christian Hertweck
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI) Beutenbergstr. 11a 07745 Jena Germany
- Faculty of Biological Sciences Friedrich Schiller University Jena 07743 Jena Germany
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16
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Niehs SP, Dose B, Richter S, Pidot SJ, Dahse H, Stinear TP, Hertweck C. Mining Symbionts of a Spider-Transmitted Fungus Illuminates Uncharted Biosynthetic Pathways to Cytotoxic Benzolactones. Angew Chem Int Ed Engl 2020; 59:7766-7771. [PMID: 32040253 PMCID: PMC7318616 DOI: 10.1002/anie.201916007] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Indexed: 11/17/2022]
Abstract
A spider-transmitted fungus (Rhizopus microsporus) that was isolated from necrotic human tissue was found to harbor endofungal bacteria (Burkholderia sp.). Metabolic profiling of the symbionts revealed a complex of cytotoxic agents (necroximes). Their structures were characterized as oxime-substituted benzolactone enamides with a peptidic side chain. The potently cytotoxic necroximes are also formed in symbiosis with the fungal host and could have contributed to the necrosis. Genome sequencing and computational analyses revealed a novel modular PKS/NRPS assembly line equipped with several non-canonical domains. Based on gene-deletion mutants, we propose a biosynthetic model for bacterial benzolactones. We identified specific traits that serve as genetic handles to find related salicylate macrolide pathways (lobatamide, oximidine, apicularen) in various other bacterial genera. Knowledge of the biosynthetic pathway enables biosynthetic engineering and genome-mining approaches.
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Affiliation(s)
- Sarah P. Niehs
- Department of Biomolecular ChemistryLeibniz Institute for Natural Product Chemistry and Infection Biology (HKI)Beutenbergstr. 11a07745JenaGermany
| | - Benjamin Dose
- Department of Biomolecular ChemistryLeibniz Institute for Natural Product Chemistry and Infection Biology (HKI)Beutenbergstr. 11a07745JenaGermany
| | - Sophie Richter
- Department of Biomolecular ChemistryLeibniz Institute for Natural Product Chemistry and Infection Biology (HKI)Beutenbergstr. 11a07745JenaGermany
| | - Sacha J. Pidot
- Department of Microbiology and ImmunologyDoherty Institute792 Elizabeth StreetMelbourne3000Australia
| | | | - Timothy P. Stinear
- Department of Microbiology and ImmunologyDoherty Institute792 Elizabeth StreetMelbourne3000Australia
| | - Christian Hertweck
- Department of Biomolecular ChemistryLeibniz Institute for Natural Product Chemistry and Infection Biology (HKI)Beutenbergstr. 11a07745JenaGermany
- Faculty of Biological SciencesFriedrich Schiller University Jena07743JenaGermany
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17
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Liu LL, Chen ZF, Liu Y, Tang D, Gao HH, Zhang Q, Gao JM. Molecular networking-based for the target discovery of potent antiproliferative polycyclic macrolactam ansamycins from Streptomyces cacaoi subsp. asoensis. Org Chem Front 2020. [DOI: 10.1039/d0qo00557f] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Molecular networking-based for the target discovery of potent antiproliferative polycyclic macrolactam ansamycins.
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Affiliation(s)
- Ling-Li Liu
- Shaanxi Key Laboratory of Natural Products & Chemical Biology
- College of Chemistry & Pharmacy
- Northwest A&F University
- Yangling 712100
- People's Republic of China
| | - Zhi-Fan Chen
- Shaanxi Key Laboratory of Natural Products & Chemical Biology
- College of Chemistry & Pharmacy
- Northwest A&F University
- Yangling 712100
- People's Republic of China
| | - Yao Liu
- Shaanxi Key Laboratory of Natural Products & Chemical Biology
- College of Chemistry & Pharmacy
- Northwest A&F University
- Yangling 712100
- People's Republic of China
| | - Dan Tang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology
- College of Chemistry & Pharmacy
- Northwest A&F University
- Yangling 712100
- People's Republic of China
| | - Hua-Hua Gao
- Shaanxi Key Laboratory of Natural Products & Chemical Biology
- College of Chemistry & Pharmacy
- Northwest A&F University
- Yangling 712100
- People's Republic of China
| | - Qiang Zhang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology
- College of Chemistry & Pharmacy
- Northwest A&F University
- Yangling 712100
- People's Republic of China
| | - Jin-Ming Gao
- Shaanxi Key Laboratory of Natural Products & Chemical Biology
- College of Chemistry & Pharmacy
- Northwest A&F University
- Yangling 712100
- People's Republic of China
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18
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Kornfuehrer T, Eustáquio AS. Diversification of polyketide structures via synthase engineering. MEDCHEMCOMM 2019; 10:1256-1272. [PMID: 32180918 PMCID: PMC7053703 DOI: 10.1039/c9md00141g] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 05/09/2019] [Indexed: 12/16/2022]
Abstract
Polyketide natural products possess diverse biological activities including antibiotic, anticancer, and immunosuppressive. Their equally varied and complex structures arise from head-to-tail condensation of simple carboxyacyl monomers. Since the seminal discovery that biosynthesis of polyketides such as the macrolide erythromycin is catalyzed by uncharacteristically large, multifunctional enzymes, termed modular type I polyketide synthases, chemists and biologists alike have been inspired to harness the apparent modularity of the synthases to further diversify polyketide structures. Yet, initial attempts to perform "combinatorial biosynthesis" failed due to challenges associated with maintaining the structural and catalytic integrity of large, chimeric synthases. Fast forward nearly 30 years, and advancements in our understanding of polyketide synthase structure and function have allowed the field to make significant progress toward effecting desired modifications to polyketide scaffolds in addition to engineering small, chiral fragments. This review highlights selected examples of polyketide diversification via control of monomer selection, oxidation state, stereochemistry, and cyclization. We conclude with a perspective on the present and future of polyketide structure diversification and hope that the examples presented here will encourage medicinal chemists to embrace polyketide synthetic biology as a means to revitalize polyketide drug discovery.
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Affiliation(s)
- Taylor Kornfuehrer
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences , College of Pharmacy , University of Illinois at Chicago , Chicago , Illinois 60607 , USA . ; Tel: +1 3124137082
| | - Alessandra S Eustáquio
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences , College of Pharmacy , University of Illinois at Chicago , Chicago , Illinois 60607 , USA . ; Tel: +1 3124137082
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19
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Mutagenesis separates ATPase and thioesterase activities of the peroxisomal ABC transporter, Comatose. Sci Rep 2019; 9:10502. [PMID: 31324846 PMCID: PMC6642094 DOI: 10.1038/s41598-019-46685-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 06/27/2019] [Indexed: 01/11/2023] Open
Abstract
The peroxisomal ABC transporter, Comatose (CTS), a full length transporter from Arabidopsis has intrinsic acyl-CoA thioesterase (ACOT) activity, important for physiological function. We used molecular modelling, mutagenesis and biochemical analysis to identify amino acid residues important for ACOT activity. D863, Q864 and T867 lie within transmembrane helix 9. These residues are orientated such that they might plausibly contribute to a catalytic triad similar to type II Hotdog fold thioesterases. When expressed in Saccharomyces cerevisiae, mutation of these residues to alanine resulted in defective of β-oxidation. All CTS mutants were expressed and targeted to peroxisomes and retained substrate-stimulated ATPase activity. When expressed in insect cell membranes, Q864A and S810N had similar ATPase activity to wild type but greatly reduced ACOT activity, whereas the Walker A mutant K487A had greatly reduced ATPase and no ATP-dependent ACOT activity. In wild type CTS, ATPase but not ACOT was stimulated by non-cleavable C14 ether-CoA. ACOT activity was stimulated by ATP but not by non-hydrolysable AMPPNP. Thus, ACOT activity depends on functional ATPase activity but not vice versa, and these two activities can be separated by mutagenesis. Whether D863, Q864 and T867 have a catalytic role or play a more indirect role in NBD-TMD communication is discussed.
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20
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Tang MC, Fischer CR, Chari JV, Tan D, Suresh S, Chu A, Miranda M, Smith J, Zhang Z, Garg NK, St Onge RP, Tang Y. Thioesterase-Catalyzed Aminoacylation and Thiolation of Polyketides in Fungi. J Am Chem Soc 2019; 141:8198-8206. [PMID: 31051070 DOI: 10.1021/jacs.9b01083] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Fungal highly reducing polyketide synthases (HRPKSs) biosynthesize polyketides using a single set of domains iteratively. Product release is a critical step in HRPKS function to ensure timely termination and enzyme turnover. Nearly all of the HRPKSs characterized to date employ a separate thioesterase (TE) or acyltransferase enzyme for product release. In this study, we characterized two fungal HRPKSs that have fused C-terminal TE domains, a new domain architecture for fungal HRPKSs. We showed that both HRPKS-TEs synthesize aminoacylated polyketides in an ATP-independent fashion. The KU42 TE domain selects cysteine and homocysteine and catalyzes transthioesterification using the side-chain thiol group as the nucleophile. In contrast, the KU43 TE domain selects leucine methyl ester and performs a direct amidation of the polyketide, a reaction typically catalyzed by nonribosomal peptide synthetase (NRPS) domains. The characterization of these HRPKS-TE enzymes showcases the functional diversity of HRPKS enzymes and provides potential TE domains as biocatalytic tools to diversify HRPKS structures.
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21
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Medina FE, Neves RPP, Ramos MJ, Fernandes PA. QM/MM Study of the Reaction Mechanism of the Dehydratase Domain from Mammalian Fatty Acid Synthase. ACS Catal 2018. [DOI: 10.1021/acscatal.8b02616] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Fabiola E. Medina
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Rui P. P. Neves
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Maria J. Ramos
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro A. Fernandes
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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22
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Meoded RA, Ueoka R, Helfrich EJN, Jensen K, Magnus N, Piechulla B, Piel J. A Polyketide Synthase Component for Oxygen Insertion into Polyketide Backbones. Angew Chem Int Ed Engl 2018; 57:11644-11648. [PMID: 29898240 PMCID: PMC6174933 DOI: 10.1002/anie.201805363] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 06/08/2018] [Indexed: 12/31/2022]
Abstract
Enzymatic core components from trans-acyltransferase polyketide synthases (trans-AT PKSs) catalyze exceptionally diverse biosynthetic transformations to generate structurally complex bioactive compounds. Here we focus on a group of oxygenases identified in various trans-AT PKS pathways, including those for pederin, oocydins, and toblerols. Using the oocydin pathway homologue (OocK) from Serratia plymuthica 4Rx13 and N-acetylcysteamine (SNAC) thioesters as test surrogates for acyl carrier protein (ACP)-tethered intermediates, we show that the enzyme inserts oxygen into β-ketoacyl moieties to yield malonyl ester SNAC products. Based on these data and the identification of a non-hydrolyzed oocydin congener with retained ester moiety, we propose a unified biosynthetic pathway of oocydins, haterumalides, and biselides. By providing access to internal ester, carboxylate pseudostarter, and terminal hydroxyl functions, oxygen insertion into polyketide backbones greatly expands the biosynthetic scope of PKSs.
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Affiliation(s)
- Roy A. Meoded
- Institute of MicrobiologyEigenössische Technische Hochschule (ETH) ZurichVladimir-Prelog-Weg 48093ZurichSwitzerland
| | - Reiko Ueoka
- Institute of MicrobiologyEigenössische Technische Hochschule (ETH) ZurichVladimir-Prelog-Weg 48093ZurichSwitzerland
| | - Eric J. N. Helfrich
- Institute of MicrobiologyEigenössische Technische Hochschule (ETH) ZurichVladimir-Prelog-Weg 48093ZurichSwitzerland
| | - Katja Jensen
- Institute of MicrobiologyEigenössische Technische Hochschule (ETH) ZurichVladimir-Prelog-Weg 48093ZurichSwitzerland
| | - Nancy Magnus
- Institute for Biological SciencesUniversity of RostockAlbert-Einstein-Straße 318059RostockGermany
| | - Birgit Piechulla
- Institute for Biological SciencesUniversity of RostockAlbert-Einstein-Straße 318059RostockGermany
| | - Jörn Piel
- Institute of MicrobiologyEigenössische Technische Hochschule (ETH) ZurichVladimir-Prelog-Weg 48093ZurichSwitzerland
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23
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Meoded RA, Ueoka R, Helfrich EJN, Jensen K, Magnus N, Piechulla B, Piel J. A Polyketide Synthase Component for Oxygen Insertion into Polyketide Backbones. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201805363] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Roy A. Meoded
- Institute of Microbiology; Eigenössische Technische Hochschule (ETH) Zurich; Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Reiko Ueoka
- Institute of Microbiology; Eigenössische Technische Hochschule (ETH) Zurich; Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Eric J. N. Helfrich
- Institute of Microbiology; Eigenössische Technische Hochschule (ETH) Zurich; Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Katja Jensen
- Institute of Microbiology; Eigenössische Technische Hochschule (ETH) Zurich; Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Nancy Magnus
- Institute for Biological Sciences; University of Rostock; Albert-Einstein-Straße 3 18059 Rostock Germany
| | - Birgit Piechulla
- Institute for Biological Sciences; University of Rostock; Albert-Einstein-Straße 3 18059 Rostock Germany
| | - Jörn Piel
- Institute of Microbiology; Eigenössische Technische Hochschule (ETH) Zurich; Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
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24
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Shehata HR, Raizada MN. A Burkholderia endophyte of the ancient maize landrace Chapalote utilizes c-di-GMP-dependent and independent signaling to suppress diverse plant fungal pathogen targets. FEMS Microbiol Lett 2018; 364:3898815. [PMID: 28679171 DOI: 10.1093/femsle/fnx138] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 06/29/2017] [Indexed: 12/19/2022] Open
Abstract
Chapalote is a maize (corn) landrace grown continuously by subsistence farmers in the Americas since 1000 BC, valued in part for its broad-spectrum pathogen resistance. Previously, we showed that Chapalote possesses a bacterial endophyte, Burkholderia gladioli strain 3A12, which suppresses growth of Sclerotinia homoeocarpa, a fungal pathogen of a maize relative, used as a model system. Ten mutants that lost the anti-pathogen activities were identified, corresponding to five genes. However, S. homoeocarpa is not a known maize pathogen; hence, the relevance of these anti-fungal mechanisms to its ancient host has not been clear. Here, the strain 3A12 mutants were tested against a known pathogen of maize and many crops, Rhizoctonia solani. Microscopy established that wild-type 3A12 swarms towards, and attaches onto, the pathogen, forming microcolonies, resulting in hyphal cleavage. Analysis of the mutants revealed that 3A12 uses common downstream gene products (e.g. fungicides) to suppress the growth of both S. homoeocarpa and R. solani, but apparently different upstream regulatory machinery, with the former, but not latter pathogen, requiring YajQ, a receptor for the secondary messenger c-di-GMP. We conclude that B. gladioli strain 3A12, an endophyte of an ancient maize, employs both c-di-GMP-dependent and independent signaling to target diverse fungal pathogens.
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Affiliation(s)
- Hanan R Shehata
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada.,Department of Microbiology, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Manish N Raizada
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada
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25
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Khandokar YB, Srivastava P, Cowieson N, Sarker S, Aragao D, Das S, Smith KM, Raidal SR, Forwood JK. Structural insights into GDP-mediated regulation of a bacterial acyl-CoA thioesterase. J Biol Chem 2017; 292:20461-20471. [PMID: 28972175 DOI: 10.1074/jbc.m117.800227] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Revised: 09/12/2017] [Indexed: 11/06/2022] Open
Abstract
Thioesterases catalyze the cleavage of thioester bonds within many activated fatty acids and acyl-CoA substrates. They are expressed ubiquitously in both prokaryotes and eukaryotes and are subdivided into 25 thioesterase families according to their catalytic active site, protein oligomerization, and substrate specificity. Although many of these enzyme families are well-characterized in terms of function and substrate specificity, regulation across most thioesterase families is poorly understood. Here, we characterized a TE6 thioesterase from the bacterium Neisseria meningitidis Structural analysis with X-ray crystallographic diffraction data to 2.0-Å revealed that each protein subunit harbors a hot dog-fold and that the TE6 enzyme forms a hexamer with D3 symmetry. An assessment of thioesterase activity against a range of acyl-CoA substrates revealed the greatest activity against acetyl-CoA, and structure-guided mutagenesis of putative active site residues identified Asn24 and Asp39 as being essential for activity. Our structural analysis revealed that six GDP nucleotides bound the enzyme in close proximity to an intersubunit disulfide bond interactions that covalently link thioesterase domains in a double hot dog dimer. Structure-guided mutagenesis of residues within the GDP-binding pocket identified Arg93 as playing a key role in the nucleotide interaction and revealed that GDP is required for activity. All mutations were confirmed to be specific and not to have resulted from structural perturbations by X-ray crystallography. This is the first report of a bacterial GDP-regulated thioesterase and of covalent linkage of thioesterase domains through a disulfide bond, revealing structural similarities with ADP regulation in the human ACOT12 thioesterase.
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Affiliation(s)
| | | | - Nathan Cowieson
- the Life Sciences Division, Diamond Light Source, Didcot OX11 0DE, United Kingdom
| | - Subir Sarker
- the Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Melbourne, Victoria 3086, Australia, and
| | - David Aragao
- the Australian National Synchrotron, Melbourne, Victoria 3168, Australia
| | - Shubagata Das
- School of Animal and Veterinary Sciences, Charles Sturt University, Boorooma Street, Wagga Wagga, New South Wales 2678, Australia
| | | | - Shane R Raidal
- School of Animal and Veterinary Sciences, Charles Sturt University, Boorooma Street, Wagga Wagga, New South Wales 2678, Australia
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26
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Chisuga T, Miyanaga A, Kudo F, Eguchi T. Structural analysis of the dual-function thioesterase SAV606 unravels the mechanism of Michael addition of glycine to an α,β-unsaturated thioester. J Biol Chem 2017; 292:10926-10937. [PMID: 28522606 PMCID: PMC5491777 DOI: 10.1074/jbc.m117.792549] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 05/11/2017] [Indexed: 01/14/2023] Open
Abstract
Thioesterases catalyze hydrolysis of acyl thioesters to release carboxylic acid or macrocyclization to produce the corresponding macrocycle in the biosynthesis of fatty acids, polyketides, or nonribosomal peptides. Recently, we reported that the thioesterase CmiS1 from Streptomyces sp. MJ635-86F5 catalyzes the Michael addition of glycine to an α,β-unsaturated fatty acyl thioester followed by thioester hydrolysis in the biosynthesis of the macrolactam antibiotic cremimycin. However, the molecular mechanisms of CmiS1-catalyzed reactions are unclear. Here, we report on the functional and structural characterization of the CmiS1 homolog SAV606 from Streptomyces avermitilis MA-4680. In vitro analysis indicated that SAV606 catalyzes the Michael addition of glycine to crotonic acid thioester and subsequent hydrolysis yielding (R)-N-carboxymethyl-3-aminobutyric acid. We also determined the crystal structures of SAV606 both in ligand-free form at 2.4 Å resolution and in complex with (R)-N-carboxymethyl-3-aminobutyric acid at 2.0 Å resolution. We found that SAV606 adopts an α/β hotdog fold and has an active site at the dimeric interface. Examining the complexed structure, we noted that the substrate-binding loop comprising Tyr-53-Asn-61 recognizes the glycine moiety of (R)-N-carboxymethyl-3-aminobutyric acid. Moreover, we found that SAV606 does not contain an acidic residue at the active site, which is distinct from canonical hotdog thioesterases. Site-directed mutagenesis experiments revealed that His-59 plays a crucial role in both the Michael addition and hydrolysis via a water molecule. These results allow us to propose the reaction mechanism of the SAV606-catalyzed Michael addition and thioester hydrolysis and provide new insight into the multiple functions of a thioesterase family enzyme.
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Affiliation(s)
- Taichi Chisuga
- From the Department of Chemistry and Materials Science and
| | - Akimasa Miyanaga
- Department of Chemistry, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Tadashi Eguchi
- From the Department of Chemistry and Materials Science and
- Department of Chemistry, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan
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27
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Faille A, Gavalda S, Slama N, Lherbet C, Maveyraud L, Guillet V, Laval F, Quémard A, Mourey L, Pedelacq JD. Insights into Substrate Modification by Dehydratases from Type I Polyketide Synthases. J Mol Biol 2017; 429:1554-1569. [PMID: 28377293 DOI: 10.1016/j.jmb.2017.03.026] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 03/21/2017] [Accepted: 03/27/2017] [Indexed: 02/04/2023]
Abstract
Dehydration reactions play a crucial role in the de novo biosynthesis of fatty acids and a wide range of pharmacologically active polyketide natural products with strong emphasis on human medicine. The type I polyketide synthase PpsC from Mycobacterium tuberculosis catalyzes key biosynthetic steps of lipid virulence factors phthiocerol dimycocerosates and phenolic glycolipids. Given the insolubility of the natural C28-C30 fatty acyl substrate of the PpsC dehydratase (DH) domain, we investigated its structure-function relationships in the presence of shorter surrogate substrates. Since most enzymes belonging to the (R)-specific enoyl hydratase/hydroxyacyl dehydratase family conduct the reverse hydration reaction in vitro, we have determined the X-ray structures of the PpsC DH domain, both unliganded (apo) and in complex with trans-but-2-enoyl-CoA or trans-dodec-2-enoyl-CoA derivatives. This study provides for the first time a snapshot of dehydratase-ligand interactions following a hydration reaction. Our structural analysis allowed us to identify residues essential for substrate binding and activity. The structural comparison of the two complexes also sheds light on the need for long acyl chains for this dehydratase to carry out its function, consistent with both its in vitro catalytic behavior and the physiological role of the PpsC enzyme.
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Affiliation(s)
- Alexandre Faille
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31077 Toulouse Cedex 04, France
| | - Sabine Gavalda
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31077 Toulouse Cedex 04, France
| | - Nawel Slama
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31077 Toulouse Cedex 04, France
| | | | - Laurent Maveyraud
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31077 Toulouse Cedex 04, France
| | - Valérie Guillet
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31077 Toulouse Cedex 04, France
| | - Françoise Laval
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31077 Toulouse Cedex 04, France
| | - Annaïk Quémard
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31077 Toulouse Cedex 04, France
| | - Lionel Mourey
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31077 Toulouse Cedex 04, France.
| | - Jean-Denis Pedelacq
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31077 Toulouse Cedex 04, France.
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28
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Sánchez-Reyez A, Batista-García RA, Valdés-García G, Ortiz E, Perezgasga L, Zárate-Romero A, Pastor N, Folch-Mallol JL. A family 13 thioesterase isolated from an activated sludge metagenome: Insights into aromatic compounds metabolism. Proteins 2017; 85:1222-1237. [DOI: 10.1002/prot.25282] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 02/21/2017] [Accepted: 02/27/2017] [Indexed: 12/23/2022]
Affiliation(s)
- Ayixon Sánchez-Reyez
- Centro de Investigación en Dinámica Celular, IICBA, Universidad Autónoma del Estado de Morelos (UAEM), Colonia Chamilpa; CP 62209 Cuernavaca, Morelos Mexico
- Centro de Investigación en Biotecnología UAEM; CP 62209 Cuernavaca Morelos Mexico
| | - Ramón Alberto Batista-García
- Centro de Investigación en Dinámica Celular, IICBA, Universidad Autónoma del Estado de Morelos (UAEM), Colonia Chamilpa; CP 62209 Cuernavaca, Morelos Mexico
| | - Gilberto Valdés-García
- Centro de Investigación en Dinámica Celular, IICBA, Universidad Autónoma del Estado de Morelos (UAEM), Colonia Chamilpa; CP 62209 Cuernavaca, Morelos Mexico
| | - Ernesto Ortiz
- Instituto de Biotecnología. Universidad Nacional Autónoma de México; CP 62210 Cuernavaca Morelos Mexico
| | - Lucía Perezgasga
- Instituto de Biotecnología. Universidad Nacional Autónoma de México; CP 62210 Cuernavaca Morelos Mexico
| | - Andrés Zárate-Romero
- Centro de Investigación en Biotecnología UAEM; CP 62209 Cuernavaca Morelos Mexico
| | - Nina Pastor
- Centro de Investigación en Dinámica Celular, IICBA, Universidad Autónoma del Estado de Morelos (UAEM), Colonia Chamilpa; CP 62209 Cuernavaca, Morelos Mexico
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29
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Weissman KJ. Polyketide stereocontrol: a study in chemical biology. Beilstein J Org Chem 2017; 13:348-371. [PMID: 28326145 PMCID: PMC5331325 DOI: 10.3762/bjoc.13.39] [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: 11/04/2016] [Accepted: 02/01/2017] [Indexed: 11/23/2022] Open
Abstract
The biosynthesis of reduced polyketides in bacteria by modular polyketide synthases (PKSs) proceeds with exquisite stereocontrol. As the stereochemistry is intimately linked to the strong bioactivity of these molecules, the origins of stereochemical control are of significant interest in attempts to create derivatives of these compounds by genetic engineering. In this review, we discuss the current state of knowledge regarding this key aspect of the biosynthetic pathways. Given that much of this information has been obtained using chemical biology tools, work in this area serves as a showcase for the power of this approach to provide answers to fundamental biological questions.
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Affiliation(s)
- Kira J Weissman
- UMR 7365, Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), CNRS-Université de Lorraine, Biopôle de l’Université de Lorraine, Campus Biologie Santé, Avenue de la Forêt de Haye, BP 50184, 54505 Vandœuvre-lès-Nancy Cedex, France
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30
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Bayly CL, Yadav VG. Towards Precision Engineering of Canonical Polyketide Synthase Domains: Recent Advances and Future Prospects. Molecules 2017; 22:molecules22020235. [PMID: 28165430 PMCID: PMC6155766 DOI: 10.3390/molecules22020235] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 01/10/2017] [Accepted: 01/11/2017] [Indexed: 01/09/2023] Open
Abstract
Modular polyketide synthases (mPKSs) build functionalized polymeric chains, some of which have become blockbuster therapeutics. Organized into repeating clusters (modules) of independently-folding domains, these assembly-line-like megasynthases can be engineered by introducing non-native components. However, poor introduction points and incompatible domain combinations can cause both unintended products and dramatically reduced activity. This limits the engineering and combinatorial potential of mPKSs, precluding access to further potential therapeutics. Different regions on a given mPKS domain determine how it interacts both with its substrate and with other domains. Within the assembly line, these interactions are crucial to the proper ordering of reactions and efficient polyketide construction. Achieving control over these domain functions, through precision engineering at key regions, would greatly expand our catalogue of accessible polyketide products. Canonical mPKS domains, given that they are among the most well-characterized, are excellent candidates for such fine-tuning. The current minireview summarizes recent advances in the mechanistic understanding and subsequent precision engineering of canonical mPKS domains, focusing largely on developments in the past year.
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Affiliation(s)
- Carmen L Bayly
- Department of Genome Sciences & Technology, The University of British Columbia, Vancouver, BC V5Z 4S6, Canada.
- Department of Chemical & Biological Engineering, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
| | - Vikramaditya G Yadav
- Department of Chemical & Biological Engineering, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
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31
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Liddle E, Scott A, Han LC, Ivison D, Simpson TJ, Willis CL, Cox RJ. In vitro kinetic study of the squalestatin tetraketide synthase dehydratase reveals the stereochemical course of a fungal highly reducing polyketide synthase. Chem Commun (Camb) 2017; 53:1727-1730. [PMID: 28106181 DOI: 10.1039/c6cc10172k] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Six potential diketide substrates for the squalestatin tetraketide synthase (SQTKS) dehydratase (DH) domain were synthesised as N-acetyl cysteamine thiolesters (SNAC) and tested in kinetic assays as substrates with an isolated DH domain. 3R-3-hydroxybutyryl SNAC 3R-16 was turned over by the enzyme, but its enantiomer was not. Of the four 2-methyl substrates only 2R,3R-2-methyl-3-hydroxybutyryl SNAC 2R,3R-8 was a substrate. Combined with stereochemical information from the isolated SQTKS enoyl reductase (ER) domain, our results provide a near complete stereochemical description of the first cycle of beta-modification reactions of a fungal highly reducing polyketide synthase (HR-PKS). The results emphasise the close relationship between fungal HR-PKS and vertebrate fatty acid synthases (vFAS).
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Affiliation(s)
- Emma Liddle
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
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32
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Sheehan J, Murphy CD, Caffrey P. New insights into polyene macrolide biosynthesis in Couchioplanes caeruleus. MOLECULAR BIOSYSTEMS 2017; 13:866-873. [DOI: 10.1039/c7mb00112f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Analysis of 67–121 biosynthesis reveals how aromatic heptaene producers impose double bond geometry and avoid interference with folate biosynthesis.
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Affiliation(s)
- J. Sheehan
- School of Biomolecular and Biomedical Science
- University College Dublin
- Belfield
- Ireland
| | - C. D. Murphy
- School of Biomolecular and Biomedical Science
- University College Dublin
- Belfield
- Ireland
| | - P. Caffrey
- School of Biomolecular and Biomedical Science
- University College Dublin
- Belfield
- Ireland
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33
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Shehata HR, Ettinger CL, Eisen JA, Raizada MN. Genes Required for the Anti-fungal Activity of a Bacterial Endophyte Isolated from a Corn Landrace Grown Continuously by Subsistence Farmers Since 1000 BC. Front Microbiol 2016; 7:1548. [PMID: 27757101 PMCID: PMC5047915 DOI: 10.3389/fmicb.2016.01548] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 09/15/2016] [Indexed: 12/14/2022] Open
Abstract
Endophytes are microbes that inhabit internal plant tissues without causing disease. Some endophytes are known to combat pathogens. The corn (maize) landrace Chapalote has been grown continuously by subsistence farmers in the Americas since 1000 BC, without the use of fungicides, and the crop remains highly valued by farmers, in part for its natural tolerance to pests. We hypothesized that the pathogen tolerance of Chapalote may, in part, be due to assistance from its endophytes. We previously identified a bacterial endophyte from Chapalote seeds, Burkholderia gladioli strain 3A12, for its ability to combat a diversity of crop pathogens, including Sclerotinia homoeocarpa, the most important fungal disease of creeping bentgrass, a relative of maize used here as a model system. Strain 3A12 represents a unique opportunity to understand the anti-fungal activities of an endophyte associated with a crop variety grown by subsistence farmers since ancient times. Here, microscopy combined with Tn5-mutagenesis demonstrates that the anti-fungal mode of action of 3A12 involves flagella-dependent swarming toward its pathogen target, attachment and biofilm-mediated microcolony formation. The mutant screen revealed that YajQ, a receptor for the secondary messenger c-di-GMP, is a critical signaling system that mediates this endophytic mobility-based defense for its host. Microbes from the traditional seeds of farmers may represent a new frontier in elucidating host-microbe mutualistic interactions.
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Affiliation(s)
- Hanan R. Shehata
- Department of Plant Agriculture, University of Guelph, GuelphON, Canada
- Department of Microbiology, School of Pharmacy, Mansoura UniversityMansoura, Egypt
| | - Cassandra L. Ettinger
- Genome Center, University of California Davis, DavisCA, USA
- Department of Evolution and Ecology, University of California Davis, DavisCA, USA
| | - Jonathan A. Eisen
- Genome Center, University of California Davis, DavisCA, USA
- Department of Evolution and Ecology, University of California Davis, DavisCA, USA
- Department of Medical Microbiology and Immunology, University of California Davis, DavisCA, USA
| | - Manish N. Raizada
- Department of Plant Agriculture, University of Guelph, GuelphON, Canada
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34
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Caffrey P, De Poire E, Sheehan J, Sweeney P. Polyene macrolide biosynthesis in streptomycetes and related bacteria: recent advances from genome sequencing and experimental studies. Appl Microbiol Biotechnol 2016; 100:3893-908. [PMID: 27023916 DOI: 10.1007/s00253-016-7474-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/13/2016] [Accepted: 03/15/2016] [Indexed: 02/07/2023]
Abstract
The polyene macrolide group includes important antifungal drugs, to which resistance does not arise readily. Chemical and biological methods have been used in attempts to make polyene antibiotics with fewer toxic side effects. Genome sequencing of producer organisms is contributing to this endeavour, by providing access to new compounds and by enabling yield improvement for polyene analogues obtained by engineered biosynthesis. This recent work is also enhancing bioinformatic methods for deducing the structures of cryptic natural products from their biosynthetic enzymes. The stereostructure of candicidin D has recently been determined by NMR spectroscopy. Genes for the corresponding polyketide synthase have been uncovered in several different genomes. Analysis of this new information strengthens the view that protein sequence motifs can be used to predict double bond geometry in many polyketides.Chemical studies have shown that improved polyenes can be obtained by modifying the mycosamine sugar that is common to most of these compounds. Glycoengineered analogues might be produced by biosynthetic methods, but polyene glycosyltransferases show little tolerance for donors other than GDP-α-D-mycosamine. Genome sequencing has revealed extending glycosyltransferases that add a second sugar to the mycosamine of some polyenes. NppY of Pseudonocardia autotrophica uses UDP-N-acetyl-α-D-glucosamine as donor whereas PegA from Actinoplanes caeruleus uses GDP-α-D-mannose. These two enzymes show 51 % sequence identity and are also closely related to mycosaminyltransferases. These findings will assist attempts to construct glycosyltransferases that transfer alternative UDP- or (d)TDP-linked sugars to polyene macrolactones.
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Affiliation(s)
- Patrick Caffrey
- School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Eimear De Poire
- School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - James Sheehan
- School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Paul Sweeney
- School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
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35
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Dong Y, Qiu X, Shaw N, Xu Y, Sun Y, Li X, Li J, Rao Z. Molecular basis for the inhibition of β-hydroxyacyl-ACP dehydratase HadAB complex from Mycobacterium tuberculosis by flavonoid inhibitors. Protein Cell 2015; 6:504-17. [PMID: 26081470 PMCID: PMC4491049 DOI: 10.1007/s13238-015-0181-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 05/08/2015] [Indexed: 11/28/2022] Open
Abstract
Dehydration is one of the key steps in the biosynthesis of mycolic acids and is vital to the growth of Mycobacterium tuberculosis (Mtb). Consequently, stalling dehydration cures tuberculosis (TB). Clinically used anti-TB drugs like thiacetazone (TAC) and isoxyl (ISO) as well as flavonoids inhibit the enzyme activity of the β-hydroxyacyl-ACP dehydratase HadAB complex. How this inhibition is exerted, has remained an enigma for years. Here, we describe the first crystal structures of the MtbHadAB complex bound with flavonoid inhibitor butein, 2',4,4'-trihydroxychalcone or fisetin. Despite sharing no sequence identity from Blast, HadA and HadB adopt a very similar hotdog fold. HadA forms a tight dimer with HadB in which the proteins are sitting side-by-side, but are oriented anti-parallel. While HadB contributes the catalytically critical His-Asp dyad, HadA binds the fatty acid substrate in a long channel. The atypical double hotdog fold with a single active site formed by MtbHadAB gives rise to a long, narrow cavity that vertically traverses the fatty acid binding channel. At the base of this cavity lies Cys61, which upon mutation to Ser confers drug-resistance in TB patients. We show that inhibitors bind in this cavity and protrude into the substrate binding channel. Thus, inhibitors of MtbHadAB exert their effect by occluding substrate from the active site. The unveiling of this mechanism of inhibition paves the way for accelerating development of next generation of anti-TB drugs.
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Affiliation(s)
- Yu Dong
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
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36
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Biswas R, Dutta A, Dutta D, Hazra D, Banerjee DR, Basak A, Das AK. Crystal structure of dehydratase component HadAB complex of mycobacterial FAS-II pathway. Biochem Biophys Res Commun 2015; 458:369-74. [DOI: 10.1016/j.bbrc.2015.01.119] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 01/25/2015] [Indexed: 10/24/2022]
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37
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He HY, Yuan H, Tang MC, Tang GL. An Unusual Dehydratase Acting on Glycerate and a Ketoreducatse Stereoselectively Reducing α-Ketone in Polyketide Starter Unit Biosynthesis. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201406602] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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38
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He HY, Yuan H, Tang MC, Tang GL. An unusual dehydratase acting on glycerate and a ketoreducatse stereoselectively reducing α-ketone in polyketide starter unit biosynthesis. Angew Chem Int Ed Engl 2014; 53:11315-9. [PMID: 25160004 DOI: 10.1002/anie.201406602] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Indexed: 11/06/2022]
Abstract
Polyketide synthases (PKSs) usually employ a ketoreductase (KR) to catalyze the reduction of a β-keto group, followed by a dehydratase (DH) that drives the dehydration to form a double bond between the α- and β-carbon atoms. Herein, a DH*-KR* involved in FR901464 biosynthesis was characterized: DH* acts on glyceryl-S-acyl carrier protein (ACP) to yield ACP-linked pyruvate; subsequently KR* reduces α-ketone that yields L-lactyl-S-ACP as starter unit for polyketide biosynthesis. Genetic and biochemical evidence was found to support a similar pathway that is involved in the biosynthesis of lankacidins. These results not only identified new PKS domains acting on different substrates, but also provided additional options for engineering the PKS starter pathway or biocatalysis.
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Affiliation(s)
- Hai-Yan He
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032 (China)
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39
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He HY, Tang MC, Zhang F, Tang GL. Cis-Double Bond Formation by Thioesterase and Transfer by Ketosynthase in FR901464 Biosynthesis. J Am Chem Soc 2014; 136:4488-91. [DOI: 10.1021/ja500942y] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hai-Yan He
- State
Key Laboratory of Bio-organic
and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Man-Cheng Tang
- State
Key Laboratory of Bio-organic
and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Feng Zhang
- State
Key Laboratory of Bio-organic
and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Gong-Li Tang
- State
Key Laboratory of Bio-organic
and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
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40
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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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41
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Salem SM, Kancharla P, Florova G, Gupta S, Lu W, Reynolds KA. Elucidation of final steps of the marineosins biosynthetic pathway through identification and characterization of the corresponding gene cluster. J Am Chem Soc 2014; 136:4565-74. [PMID: 24575817 PMCID: PMC3985843 DOI: 10.1021/ja411544w] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The
marine Streptomyces sp. CNQ-617 produces two
diastereomers, marineosins A and B. These are structurally related
to alkyl prodiginines, but with a more complex cyclization and an
unusual spiroaminal skeleton. We report the identification of the mar biosynthetic gene cluster and demonstrate production
of marineosins through heterologous expression in a S. venezuelae host named JND2. The mar cluster shares the same
gene organization and has high homology to the genes of the red cluster (which directs the biosynthesis of undecylprodiginine)
but contains an additional gene, named marA. Replacement
of marA in the JND2 strain leads to the accumulation
of premarineosin, which is identical to marineosin with the exception
that the middle pyrrole (Ring B) has not been reduced. The final step
of the marineosin pathway is thus a MarA catalyzed reduction of this
ring. Replacement of marG (a homologue of redG that directs undecylprodiginine cyclization to give
streptorubin B) in the JND2 strain leads to the loss of all spiroaminal
products and the accumulation of 23-hydroxyundecylprodiginine and
a shunt product, 23-ketoundecylprodiginine. MarG thus catalyzes the
penultimate step of the marineosin pathway catalyzing conversion of
23-hydroxyundecylprodiginine to premarineosin. The preceding steps
of the biosynthetic marineosin pathway likely mirror that in the red-directed biosynthetic process, with the exception of
the introduction of the hydroxyl functionality required for spiroaminal
formation. This work presents the first experimentally supported scheme
for biosynthesis of marineosin and provides a new biologically active
molecule, premarineosin.
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Affiliation(s)
- Shaimaa M Salem
- Department of Chemistry, Portland State University , Portland, Oregon, 97201-3203, United States
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