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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: 24] [Impact Index Per Article: 8.0] [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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2
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Stegemann F, Grininger M. Transacylation Kinetics in Fatty Acid and Polyketide Synthases and its Sensitivity to Point Mutations**. ChemCatChem 2021. [DOI: 10.1002/cctc.202002077] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Franziska Stegemann
- Institute of Organic Chemistry and Chemical Biology Buchmann Institute for Molecular Life Sciences Goethe University Frankfurt Max-von-Laue-Str. 15 60438 Frankfurt am Main Germany
| | - Martin Grininger
- Institute of Organic Chemistry and Chemical Biology Buchmann Institute for Molecular Life Sciences Goethe University Frankfurt Max-von-Laue-Str. 15 60438 Frankfurt am Main Germany
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3
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Interfacial plasticity facilitates high reaction rate of E. coli FAS malonyl-CoA:ACP transacylase, FabD. Proc Natl Acad Sci U S A 2020; 117:24224-24233. [PMID: 32929027 DOI: 10.1073/pnas.2009805117] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fatty acid synthases (FASs) and polyketide synthases (PKSs) iteratively elongate and often reduce two-carbon ketide units in de novo fatty acid and polyketide biosynthesis. Cycles of chain extensions in FAS and PKS are initiated by an acyltransferase (AT), which loads monomer units onto acyl carrier proteins (ACPs), small, flexible proteins that shuttle covalently linked intermediates between catalytic partners. Formation of productive ACP-AT interactions is required for catalysis and specificity within primary and secondary FAS and PKS pathways. Here, we use the Escherichia coli FAS AT, FabD, and its cognate ACP, AcpP, to interrogate type II FAS ACP-AT interactions. We utilize a covalent crosslinking probe to trap transient interactions between AcpP and FabD to elucidate the X-ray crystal structure of a type II ACP-AT complex. Our structural data are supported using a combination of mutational, crosslinking, and kinetic analyses, and long-timescale molecular dynamics (MD) simulations. Together, these complementary approaches reveal key catalytic features of FAS ACP-AT interactions. These mechanistic inferences suggest that AcpP adopts multiple, productive conformations at the AT binding interface, allowing the complex to sustain high transacylation rates. Furthermore, MD simulations support rigid body subdomain motions within the FabD structure that may play a key role in AT activity and substrate selectivity.
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4
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Siroli L, Braschi G, Rossi S, Gottardi D, Patrignani F, Lanciotti R. Lactobacillus paracasei A13 and High-Pressure Homogenization Stress Response. Microorganisms 2020; 8:E439. [PMID: 32244939 PMCID: PMC7143770 DOI: 10.3390/microorganisms8030439] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/14/2020] [Accepted: 03/19/2020] [Indexed: 11/17/2022] Open
Abstract
Sub-lethal high-pressure homogenization treatments applied to Lactobacillus paracasei A13 demonstrated to be a useful strategy to enhance technological and functional properties without detrimental effects on the viability of this strain. Modification of membrane fatty acid composition is reported to be the main regulatory mechanisms adopted by probiotic lactobacilli to counteract high-pressure stress. This work is aimed to clarify and understand the relationship between the modification of membrane fatty acid composition and the expression of genes involved in fatty acid biosynthesis in Lactobacillus paracasei A13, before and after the application of different sub-lethal hyperbaric treatments. Our results showed that Lactobacillus paracasei A13 activated a series of reactions aimed to control and stabilize membrane fluidity in response to high-pressure homogenization treatments. In fact, the production of cyclic fatty acids was counterbalanced by the unsaturation and elongation of fatty acids. The gene expression data indicate an up-regulation of the genes accA, accC, fabD, fabH and fabZ after high-pressure homogenization treatment at 150 and 200 MPa, and of fabK and fabZ after a treatment at 200 MPa suggesting this regulation of the genes involved in fatty acids biosynthesis as an immediate response mechanism adopted by Lactobacillus paracasei A13 to high-pressure homogenization treatments to balance the membrane fluidity. Although further studies should be performed to clarify the modulation of phospholipids and glycoproteins biosynthesis since they play a crucial role in the functional properties of the probiotic strains, this study represents an important step towards understanding the response mechanisms of Lactobacillus paracasei A13 to sub-lethal high-pressure homogenization treatments.
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Affiliation(s)
- Lorenzo Siroli
- Department of Agricultural and Food Sciences, University of Bologna, p.zza Goidanich 60, 47521 Cesena, Italy; (L.S.); (G.B.); (S.R.); (D.G.); (R.L.)
| | - Giacomo Braschi
- Department of Agricultural and Food Sciences, University of Bologna, p.zza Goidanich 60, 47521 Cesena, Italy; (L.S.); (G.B.); (S.R.); (D.G.); (R.L.)
| | - Samantha Rossi
- Department of Agricultural and Food Sciences, University of Bologna, p.zza Goidanich 60, 47521 Cesena, Italy; (L.S.); (G.B.); (S.R.); (D.G.); (R.L.)
| | - Davide Gottardi
- Department of Agricultural and Food Sciences, University of Bologna, p.zza Goidanich 60, 47521 Cesena, Italy; (L.S.); (G.B.); (S.R.); (D.G.); (R.L.)
| | - Francesca Patrignani
- Department of Agricultural and Food Sciences, University of Bologna, p.zza Goidanich 60, 47521 Cesena, Italy; (L.S.); (G.B.); (S.R.); (D.G.); (R.L.)
- Interdepartmental Center for Industrial Agri-food Research, University of Bologna, Piazza Goidanich 60, 47521 Cesena, Italy
| | - Rosalba Lanciotti
- Department of Agricultural and Food Sciences, University of Bologna, p.zza Goidanich 60, 47521 Cesena, Italy; (L.S.); (G.B.); (S.R.); (D.G.); (R.L.)
- Interdepartmental Center for Industrial Agri-food Research, University of Bologna, Piazza Goidanich 60, 47521 Cesena, Italy
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5
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Kumar V, Sharma A, Pratap S, Kumar P. Biochemical and biophysical characterization of 1,4-naphthoquinone as a dual inhibitor of two key enzymes of type II fatty acid biosynthesis from Moraxella catarrhalis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:1131-1142. [PMID: 30282611 DOI: 10.1016/j.bbapap.2018.08.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 08/17/2018] [Accepted: 08/20/2018] [Indexed: 02/03/2023]
Abstract
The fatty acid biosynthesis (FAS II) is a vital process in bacteria and regarded as an attractive pathway for the development of potential antimicrobial agents. In this study, we report 1,4-naphthoquinone (NPQ) as a dual inhibitor of two key enzymes of FAS II pathway, namely FabD (Malonyl-CoA:ACP transacylase) and FabZ (β-hydroxyacyl-ACP dehydratase). Mode of inhibition of NPQ was found to be non-competitive for both enzymes with IC50 of 26.67 μΜ and 23.18 μΜ against McFabZ and McFabD respectively. Conformational changes in secondary and tertiary structures marked by the loss of helical contents were observed in both enzymes upon NPQ binding. The fluorescence quenching was found to be static with a stable ground state complex formation. ITC based studies have shown that NPQ is binding to McFabZ with a stronger affinity (~1.5×) as compared to McFabD. Molecular docking studies have found that NPQ interacts with key residues of both McFabD (Ser209, Arg126, and Leu102) and McFabZ (His74 and Tyr112) enzymes. Both complexes have shown the structural stability during the 20 ns run of molecular dynamics based simulations. Altogether, the present study suggests that NPQ scaffold can be exploited as a multi-targeted inhibitor of FAS II pathway, and these biochemical and biophysical findings will further help in the development of potent antibacterial agents targeting FAS II pathway.
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Affiliation(s)
- Vijay Kumar
- Department of Biotechnology, Indian Institute of Technology Roorkee, India
| | - Anchal Sharma
- Department of Biotechnology, Indian Institute of Technology Roorkee, India
| | - Shivendra Pratap
- Department of Biotechnology, Indian Institute of Technology Roorkee, India
| | - Pravindra Kumar
- Department of Biotechnology, Indian Institute of Technology Roorkee, India.
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6
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Tsai SC(S. The Structural Enzymology of Iterative Aromatic Polyketide Synthases: A Critical Comparison with Fatty Acid Synthases. Annu Rev Biochem 2018; 87:503-531. [DOI: 10.1146/annurev-biochem-063011-164509] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Polyketides are a large family of structurally complex natural products including compounds with important bioactivities. Polyketides are biosynthesized by polyketide synthases (PKSs), multienzyme complexes derived evolutionarily from fatty acid synthases (FASs). The focus of this review is to critically compare the properties of FASs with iterative aromatic PKSs, including type II PKSs and fungal type I nonreducing PKSs whose chemical logic is distinct from that of modular PKSs. This review focuses on structural and enzymological studies that reveal both similarities and striking differences between FASs and aromatic PKSs. The potential application of FAS and aromatic PKS structures for bioengineering future drugs and biofuels is highlighted.
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Affiliation(s)
- Shiou-Chuan (Sheryl) Tsai
- Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, California 92697, USA
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7
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Marcella AM, Barb AW. Acyl-coenzyme A:(holo-acyl carrier protein) transacylase enzymes as templates for engineering. Appl Microbiol Biotechnol 2018; 102:6333-6341. [PMID: 29858956 DOI: 10.1007/s00253-018-9114-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 05/16/2018] [Accepted: 05/17/2018] [Indexed: 01/18/2023]
Abstract
This review will cover the structure, enzymology, and related aspects that are important for structure-based engineering of the transacylase enzymes from fatty acid biosynthesis and polyketide synthesis. Furthermore, this review will focus on in vitro characteristics and not cover engineering of the upstream or downstream reactions or strategies to manipulate metabolic flux in vivo. The malonyl-coenzyme A(CoA)-holo-acyl-carrier protein (holo-ACP) transacylase (FabD) from Escherichia coli serves as a model for this enzyme with thorough descriptions of structure, enzyme mechanism, and effects of mutation on substrate binding presented in the literature. Here, we discuss multiple practical and theoretical considerations regarding engineering transacylase enzymes to accept non-cognate substrates and form novel acyl-ACPs for downstream reactions.
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Affiliation(s)
- Aaron M Marcella
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, 2437 Pammel Drive, Molecular Biology Building, rm 4210, Ames, IA, 50011, USA
| | - Adam W Barb
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, 2437 Pammel Drive, Molecular Biology Building, rm 4210, Ames, IA, 50011, USA.
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8
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Diouf B, Lin W, Goktug A, Grace CRR, Waddell MB, Bao J, Shao Y, Heath RJ, Zheng JJ, Shelat AA, Relling MV, Chen T, Evans WE. Alteration of RNA Splicing by Small-Molecule Inhibitors of the Interaction between NHP2L1 and U4. SLAS DISCOVERY 2017; 23:164-173. [PMID: 28985478 DOI: 10.1177/2472555217735035] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Splicing is an important eukaryotic mechanism for expanding the transcriptome and proteome, influencing a number of biological processes. Understanding its regulation and identifying small molecules that modulate this process remain a challenge. We developed an assay based on time-resolved fluorescence resonance energy transfer (TR-FRET) to detect the interaction between the protein NHP2L1 and U4 RNA, which are two key components of the spliceosome. We used this assay to identify small molecules that interfere with this interaction in a high-throughput screening (HTS) campaign. Topotecan and other camptothecin derivatives were among the top hits. We confirmed that topotecan disrupts the interaction between NHP2L1 and U4 by binding to U4 and inhibits RNA splicing. Our data reveal new functions of known drugs that could facilitate the development of therapeutic strategies to modify splicing and alter gene function.
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Affiliation(s)
- Barthelemy Diouf
- 1 Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, USA.,2 Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wenwei Lin
- 3 Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Asli Goktug
- 3 Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Christy R R Grace
- 4 Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael Brett Waddell
- 5 Molecular Interaction Analysis Shared Resource, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ju Bao
- 1 Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, USA.,2 Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Youming Shao
- 6 Protein Production Facility, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Richard J Heath
- 6 Protein Production Facility, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jie J Zheng
- 7 Stein Eye Institute and Department of Ophthalmology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Anang A Shelat
- 3 Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mary V Relling
- 1 Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, USA.,2 Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Taosheng Chen
- 3 Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - William E Evans
- 1 Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN, USA.,2 Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
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9
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Xia K, Zang N, Zhang J, Zhang H, Li Y, Liu Y, Feng W, Liang X. New insights into the mechanisms of acetic acid resistance in Acetobacter pasteurianus using iTRAQ-dependent quantitative proteomic analysis. Int J Food Microbiol 2016; 238:241-251. [PMID: 27681379 DOI: 10.1016/j.ijfoodmicro.2016.09.016] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 09/20/2016] [Accepted: 09/21/2016] [Indexed: 12/01/2022]
Abstract
Acetobacter pasteurianus is the main starter in rice vinegar manufacturing due to its remarkable abilities to resist and produce acetic acid. Although several mechanisms of acetic acid resistance have been proposed and only a few effector proteins have been identified, a comprehensive depiction of the biological processes involved in acetic acid resistance is needed. In this study, iTRAQ-based quantitative proteomic analysis was adopted to investigate the whole proteome of different acidic titers (3.6, 7.1 and 9.3%, w/v) of Acetobacter pasteurianus Ab3 during the vinegar fermentation process. Consequently, 1386 proteins, including 318 differentially expressed proteins (p<0.05), were identified. Compared to that in the low titer circumstance, cells conducted distinct biological processes under high acetic acid stress, where >150 proteins were differentially expressed. Specifically, proteins involved in amino acid metabolic processes and fatty acid biosynthesis were differentially expressed, which may contribute to the acetic acid resistance of Acetobacter. Transcription factors, two component systems and toxin-antitoxin systems were implicated in the modulatory network at multiple levels. In addition, the identification of proteins involved in redox homeostasis, protein metabolism, and the cell envelope suggested that the whole cellular system is mobilized in response to acid stress. These findings provide a differential proteomic profile of acetic acid resistance in Acetobacter pasteurianus and have potential application to highly acidic rice vinegar manufacturing.
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Affiliation(s)
- Kai Xia
- Department of Biochemical Engineering, School of Food Science and Biochemical Engineering, Zhejiang Gongshang University, Hangzhou 310025, China
| | - Ning Zang
- Medical Scientific Research Center, Guangxi Medical University, Nanning 530021, China
| | - Junmei Zhang
- Department of Biochemical Engineering, School of Food Science and Biochemical Engineering, Zhejiang Gongshang University, Hangzhou 310025, China
| | - Hong Zhang
- Department of Biochemical Engineering, School of Food Science and Biochemical Engineering, Zhejiang Gongshang University, Hangzhou 310025, China
| | - Yudong Li
- Department of Biochemical Engineering, School of Food Science and Biochemical Engineering, Zhejiang Gongshang University, Hangzhou 310025, China
| | - Ye Liu
- Zhejiang Wuweihe Food Co. Ltd., Huzhou 313213, China
| | - Wei Feng
- Zhejiang Wuweihe Food Co. Ltd., Huzhou 313213, China
| | - Xinle Liang
- Department of Biochemical Engineering, School of Food Science and Biochemical Engineering, Zhejiang Gongshang University, Hangzhou 310025, China.
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10
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Sun J, Ye X, Xie M, Ye J. Induction of triglyceride accumulation and mitochondrial maintenance in muscle cells by lactate. Sci Rep 2016; 6:33732. [PMID: 27645401 PMCID: PMC5028732 DOI: 10.1038/srep33732] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 09/01/2016] [Indexed: 11/02/2022] Open
Abstract
Muscle exercise induces intramuscular triglyceride (TG) accumulation and promotes mitochondrial maintenance in myotubes. However, the mechanism underlying exercise effects remains unknown. In this study, lactic acid was tested as a signaling molecule in C2C12 myotubes to understand the mechanism. Intracellular TG storage was induced in the cells by sodium lactate. The lactate activity was observed with an inhibition of the cAMP-PKA pathway as indicated by a reduction in the phosphorylation status of CREB (pCREB). Induction of pCREB signal by forskolin was blocked by pretreatment of cells with lactate. The impact of lactate on mitochondrial function was examined with a focus on the activities of two enzymes, MCAT (malonylCoA:ACP transferase) and PDH (pyruvate dehydrogenase). The enzyme activities were induced in the cells by lactate. Expression of the lactate receptor (GPR81) and lactate transporters (MCT1/4) were induced as well by lactate. The lactate activities were observed at concentrations between 4-64 mM, and were not dependent on the increase in intracellular pyruvate. Pyruvate treatment did not generate the same effects in the cells. Those results suggest that lactate may induce intramuscular TG storage and mitochondrial maintenance in myotubes through inhibition of the cAMP pathway by activation of GPR81 in a positive feedback manner.
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Affiliation(s)
- Jingquan Sun
- Sport Science College of Beijing Sport University, Beijing, China.,Antioxidant and Gene Regulation Laboratory, Pennington Biomedical Research Center, Louisiana State University, Louisiana, USA
| | - Xin Ye
- Antioxidant and Gene Regulation Laboratory, Pennington Biomedical Research Center, Louisiana State University, Louisiana, USA
| | - Minhao Xie
- China Institute of Sports Medicine, Beijing, China
| | - Jianping Ye
- Antioxidant and Gene Regulation Laboratory, Pennington Biomedical Research Center, Louisiana State University, Louisiana, USA
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11
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Marcella AM, Barb AW. A rapid fluorometric assay for the S-malonyltransacylase FabD and other sulfhydryl utilizing enzymes. J Biol Methods 2016; 3. [PMID: 27642613 PMCID: PMC5023282 DOI: 10.14440/jbm.2016.144] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The development of biorenewable chemicals will support green chemistry initiatives and supplement the catalog of starting materials available to the chemical industry. Bacterial fatty acid biosynthesis is being pursued as a source of protein catalysts to synthesize novel reduced carbon molecules in fermentation systems. The availability of methods to measure enzyme catalysis for native and engineered enzymes from this pathway remains a bottleneck because a simple quantitative enzyme assay for numerous enzymes does not exist. Here we present two variations of a fluorescence assay that is readily extendable to high-throughput screening and is appropriate for thiol consuming and generating enzymes including the E. coli enzymes malonyl-coenzyme A transacylase (FabD) and keto-acylsynthase III (FabH). We measured KM values of 60 ± 20 µM (acetyl-CoA) and 20 ± 10 µM (malonyl-ACP) and a kcat of 7.4–9.0 s-1 with FabH. Assays of FabD included a precipitation step to remove the thiol-containing substrate holo-ACP from the reaction product coenzyme-A to estimate reaction rates. Analysis of initial velocity measurements revealed KM values of 60 ± 20 µM (malonyl-CoA) and 40 ± 10 µM (holo-ACP) and a kcat of 2100–2600 s-1 for the FabD enzyme. Our data show similar results when compared to existing radioactive and continuous coupled assays in terms of sensitivity while providing the benefit of simplicity, scalability and repeatability. Fluorescence detection also eliminates the need for radioactive substrates traditionally used to assay these enzymes.
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Affiliation(s)
- Aaron M Marcella
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Molecular Biology Building, Room 4210, 2437 Pammel Drive, Iowa State University, Ames, IA 50011, USA
| | - Adam W Barb
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Molecular Biology Building, Room 4210, 2437 Pammel Drive, Iowa State University, Ames, IA 50011, USA
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12
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Beld J, Lee DJ, Burkart MD. Fatty acid biosynthesis revisited: structure elucidation and metabolic engineering. MOLECULAR BIOSYSTEMS 2015; 11:38-59. [PMID: 25360565 PMCID: PMC4276719 DOI: 10.1039/c4mb00443d] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Fatty acids are primary metabolites synthesized by complex, elegant, and essential biosynthetic machinery. Fatty acid synthases resemble an iterative assembly line, with an acyl carrier protein conveying the growing fatty acid to necessary enzymatic domains for modification. Each catalytic domain is a unique enzyme spanning a wide range of folds and structures. Although they harbor the same enzymatic activities, two different types of fatty acid synthase architectures are observed in nature. During recent years, strained petroleum supplies have driven interest in engineering organisms to either produce more fatty acids or specific high value products. Such efforts require a fundamental understanding of the enzymatic activities and regulation of fatty acid synthases. Despite more than one hundred years of research, we continue to learn new lessons about fatty acid synthases' many intricate structural and regulatory elements. In this review, we summarize each enzymatic domain and discuss efforts to engineer fatty acid synthases, providing some clues to important challenges and opportunities in the field.
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Affiliation(s)
- Joris Beld
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA.
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13
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Poust S, Yoon I, Adams PD, Katz L, Petzold CJ, Keasling JD. Understanding the role of histidine in the GHSxG acyltransferase active site motif: evidence for histidine stabilization of the malonyl-enzyme intermediate. PLoS One 2014; 9:e109421. [PMID: 25286165 PMCID: PMC4186864 DOI: 10.1371/journal.pone.0109421] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 08/30/2014] [Indexed: 11/18/2022] Open
Abstract
Acyltransferases determine which extender units are incorporated into polyketide and fatty acid products. The ping-pong acyltransferase mechanism utilizes a serine in a conserved GHSxG motif. However, the role of the conserved histidine in this motif is poorly understood. We observed that a histidine to alanine mutation (H640A) in the GHSxG motif of the malonyl-CoA specific yersiniabactin acyltransferase results in an approximately seven-fold higher hydrolysis rate over the wildtype enzyme, while retaining transacylation activity. We propose two possibilities for the reduction in hydrolysis rate: either H640 structurally stabilizes the protein by hydrogen bonding with a conserved asparagine in the ferredoxin-like subdomain of the protein, or a water-mediated hydrogen bond between H640 and the malonyl moiety stabilizes the malonyl-O-AT ester intermediate.
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Affiliation(s)
- Sean Poust
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, United States of America
| | - Isu Yoon
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, United States of America
| | - Paul D. Adams
- Joint BioEnergy Institute, Emeryville, California, United States of America
- Physical Bioscience division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Leonard Katz
- Synthetic Biology Engineering Research Center, Emeryville, California, United States of America
- Joint BioEnergy Institute, Emeryville, California, United States of America
| | - Christopher J. Petzold
- Joint BioEnergy Institute, Emeryville, California, United States of America
- Physical Bioscience division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Jay D. Keasling
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, United States of America
- QB3 Institute, University of California, Berkeley, California, United States of America
- Synthetic Biology Engineering Research Center, Emeryville, California, United States of America
- Joint BioEnergy Institute, Emeryville, California, United States of America
- Physical Bioscience division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- * E-mail:
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14
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Xi Y, Zhao Y, Wang L, Wang F. Comparison on extreme pathways reveals nature of different biological processes. BMC SYSTEMS BIOLOGY 2014; 8 Suppl 1:S10. [PMID: 24565046 PMCID: PMC4080357 DOI: 10.1186/1752-0509-8-s1-s10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Background Constraint-based reconstruction and analysis (COBRA) is used for modeling genome-scale metabolic networks (MNs). In a COBRA model, extreme pathways (ExPas) are the edges of its conical solution space, which is formed by all viable steady-state flux distributions. ExPa analysis has been successfully applied to MNs to reveal their phenotypic capabilities and properties. Recently, the COBRA framework has been extended to transcriptional regulatory networks (TRNs) and transcriptional and translational networks (TTNs), so efforts are needed to determine whether ExPa analysis is also effective on these two types of networks. Results In this paper, the ExPas resulting from the COBRA models of E.coli's MN, TRN and TTN were horizontally compared from 5 aspects: (1) Total number and the ratio of their amount to reaction amount; (2) Length distribution; (3) Reaction participation; (4) Correlated reaction sets (CoSets); (5) interconnectivity degree. Significant discrepancies in above properties were observed during the comparison, which reveals the biological natures of different biological processes. Besides, by demonstrating the application of ExPa analysis on E.coli, we provide a practical guidance of an improved approach to compute ExPas on COBRA models of TRNs. Conclusions ExPas of E.coli's MN, TRN and TTN have different properties, which are strongly connected with various biological natures of biochemical networks, such as topological structure, specificity and redundancy. Our study shows that ExPas are biologically meaningful on the newborn models and suggests the effectiveness of ExPa analysis on them.
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15
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Crosby J, Crump MP. The structural role of the carrier protein--active controller or passive carrier. Nat Prod Rep 2012; 29:1111-37. [PMID: 22930263 DOI: 10.1039/c2np20062g] [Citation(s) in RCA: 132] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Common to all FASs, PKSs and NRPSs is a remarkable component, the acyl or peptidyl carrier protein (A/PCP). These take the form of small individual proteins in type II systems or discrete folded domains in the multi-domain type I systems and are characterized by a fold consisting of three major α-helices and between 60-100 amino acids. This protein is central to these biosynthetic systems and it must bind and transport a wide variety of functionalized ligands as well as mediate numerous protein-protein interactions, all of which contribute to efficient enzyme turnover. This review covers the structural and biochemical characterization of carrier proteins, as well as assessing their interactions with different ligands, and other synthase components. Finally, their role as an emerging tool in biotechnology is discussed.
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Affiliation(s)
- John Crosby
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
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16
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Musiol EM, Weber T. Discrete acyltransferases involved in polyketide biosynthesis. MEDCHEMCOMM 2012. [DOI: 10.1039/c2md20048a] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Shepherd MD, Kharel MK, Zhu LL, van Lanen SG, Rohr J. Delineating the earliest steps of gilvocarcin biosynthesis: role of GilP and GilQ in starter unit specificity. Org Biomol Chem 2010; 8:3851-6. [PMID: 20617244 DOI: 10.1039/c0ob00036a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In vivo and in vitro investigations of GilP and GilQ, two acyltransferases encoded by the gilvocarcin gene cluster, show that GilQ confers unique starter unit specificity when catalyzing an early as well as rate limiting step of gilvocarcin biosynthesis.
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Affiliation(s)
- Micah D Shepherd
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536-0596, USA
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18
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Hiltunen JK, Chen Z, Haapalainen AM, Wierenga RK, Kastaniotis AJ. Mitochondrial fatty acid synthesis – An adopted set of enzymes making a pathway of major importance for the cellular metabolism. Prog Lipid Res 2010; 49:27-45. [DOI: 10.1016/j.plipres.2009.08.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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19
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Arthur CJ, Williams C, Pottage K, Płoskoń E, Findlow SC, Burston SG, Simpson TJ, Crump MP, Crosby J. Structure and malonyl CoA-ACP transacylase binding of streptomyces coelicolor fatty acid synthase acyl carrier protein. ACS Chem Biol 2009; 4:625-36. [PMID: 19555075 DOI: 10.1021/cb900099e] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Malonylation of an acyl carrier protein (ACP) by malonyl Coenzyme A-ACP transacylase (MCAT) is fundamental to bacterial fatty acid biosynthesis. Here, we report the structure of the Steptomyces coelicolor (Sc) fatty acid synthase (FAS) ACP and studies of its binding to MCAT. The carrier protein adopts an alpha-helical bundle structure common to other known carrier proteins. The Sc FAS ACP shows close structural homology with other fatty acid ACPs and less similarity with Sc actinorhodin (act) polyketide synthase (PKS) ACP where the orientation of helix I differs. NMR experiments were used to map the binding of ACP to MCAT. This data suggests that Sc FAS ACP interacts with MCAT through the negatively charged helix II of ACP, consistent with proposed models for ACP recognition by other FAS enzymes. Differential roles for residues at the interface are demonstrated using site-directed mutagenesis and in vitro assays. MCAT has been suggested, moreover, to participate in bacterial polyketide synthesis in vivo. We demonstrate that the affinity of the polyketide synthase ACP for MCAT is lower than that of the FAS ACP. Mutagenesis of homologous helix II residues on the polyketide synthase ACP suggests that the PKS ACP may bind to MCAT in a different manner than the FAS counterpart.
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Affiliation(s)
| | - Christopher Williams
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Katherine Pottage
- School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, U.K
| | - Eliza Płoskoń
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Stuart C. Findlow
- School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, U.K
| | - Steven G. Burston
- Department of Biochemistry, University of Bristol, School of Medical Sciences, University Walk, Bristol BS8 1TD, U.K
| | - Thomas J. Simpson
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Matthew P. Crump
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - John Crosby
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
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20
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Cheng YQ, Coughlin JM, Lim SK, Shen B. Type I polyketide synthases that require discrete acyltransferases. Methods Enzymol 2009; 459:165-86. [PMID: 19362640 DOI: 10.1016/s0076-6879(09)04608-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
The diverse structures of polyketide natural products are reflected by the equally diverse polyketide biosynthetic enzymes, namely polyketide synthases (PKSs). Three major classes of PKSs are known-noniterative type I PKSs, iterative type II PKSs and acyl carrier protein-independent type III PKSs, each of which consists of additional variants. One such variant is the noniterative type I PKS in which each PKS module lacks the cognate acyltransferase (AT) domain. The essential AT activity is instead provided by a discrete AT in trans. Termed "AT-less" type I PKSs, the loading of the malonate extender units by the discrete AT enzyme LnmG to each of the AT-less PKS modules of LnmI and LnmJ was confirmed experimentally for biosynthesis of the anticancer antibiotic leinamycin (LNM). The LNM PKS has since served as a model for the continuous discovery of numerous additional AT-less type I PKSs incorporating variable extender units. However, biochemical characterization of AT-less type I PKSs remains very limited, and the mechanism by which AT-less type I PKSs accommodate multiple extender units is unknown. This chapter provides the protocols used to establish and characterize the LNM PKS. Application of these methods to other AT-less type I PKSs should aid the biochemical characterization and hence possible exploitation of these unique PKSs for polyketide natural product structural diversity by combinatorial biosynthetic methods.
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Affiliation(s)
- Yi-Qiang Cheng
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
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21
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Misra A, Surolia N, Surolia A. Catalysis and mechanism of malonyl transferase activity in type II fatty acid biosynthesis acyl carrier proteins. MOLECULAR BIOSYSTEMS 2009; 5:651-9. [PMID: 19462023 DOI: 10.1039/b820420a] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
One of the unexplored, yet important aspects of the biology of acyl carrier proteins (ACPs) is the self-acylation and malonyl transferase activities dedicated to ACPs in polyketide synthesis. Our studies demonstrate the existence of malonyl transferase activity in ACPs involved in type II fatty acid biosynthesis from Plasmodium falciparum and Escherichia coli. We also show that the catalytic malonyl transferase activity is intrinsic to an individual ACP. Mutational analysis implicates an arginine/lysine in loop II and an arginine/glutamine in helix III as the catalytic residues for transferase function. The hydrogen bonding properties of these residues appears to be indispensable for the transferase reaction. Complementation of fabD(Ts) E. coli highlights the putative physiological role of this process. Our studies thus shed light on a key aspect of ACP biology and provide insights into the mechanism involved therein.
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Affiliation(s)
- Ashish Misra
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
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22
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Beltran-Alvarez P, Arthur CJ, Cox RJ, Crosby J, Crump MP, Simpson TJ. Preliminary kinetic analysis of acyl carrier protein–ketoacylsynthase interactions in the actinorhodin minimal polyketide synthase. MOLECULAR BIOSYSTEMS 2009; 5:511-8. [DOI: 10.1039/b821844g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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23
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Abstract
This chapter describes structural and associated enzymological studies of polyketide synthases, including isolated single domains and multidomain fragments. The sequence-structure-function relationship of polyketide biosynthesis, compared with homologous fatty acid synthesis, is discussed in detail. Structural enzymology sheds light on sequence and structural motifs that are important for the precise timing, substrate recognition, enzyme catalysis, and protein-protein interactions leading to the extraordinary structural diversity of naturally occurring polyketides.
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24
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Lopanik NB, Shields JA, Buchholz TJ, Rath CM, Hothersall J, Haygood MG, Håkansson K, Thomas CM, Sherman DH. In vivo and in vitro trans-acylation by BryP, the putative bryostatin pathway acyltransferase derived from an uncultured marine symbiont. CHEMISTRY & BIOLOGY 2008; 15:1175-86. [PMID: 19022178 PMCID: PMC2861360 DOI: 10.1016/j.chembiol.2008.09.013] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2008] [Revised: 09/18/2008] [Accepted: 09/24/2008] [Indexed: 01/14/2023]
Abstract
The putative modular polyketide synthase (PKS) that prescribes biosynthesis of the bryostatin natural products from the uncultured bacterial symbiont of the marine bryozoan Bugula neritina possesses a discrete open reading frame (ORF) (bryP) that encodes a protein containing tandem acyltransferase (AT) domains upstream of the PKS ORFs. BryP is hypothesized to catalyze in trans acylation of the PKS modules for polyketide chain elongation. To verify conservation of function, bryP was introduced into AT-deletion mutant strains of a heterologous host containing a PKS cluster with similar architecture, and polyketide production was partially rescued. Biochemical characterization demonstrated that BryP catalyzes selective malonyl-CoA acylation of native and heterologous acyl carrier proteins and complete PKS modules in vitro. The results support the hypothesis that BryP loads malonyl-CoA onto Bry PKS modules, and provide the first biochemical evidence of the functionality of the bry cluster.
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Affiliation(s)
- Nicole B. Lopanik
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, United States
| | - Jennifer A. Shields
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Tonia J. Buchholz
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, United States
| | - Christopher M. Rath
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, United States
| | - Joanne Hothersall
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Margo G. Haygood
- Department of Environmental and Biomolecular Systems, Oregon Health and Science University, Beaverton, OR 97006, United States
| | - Kristina Håkansson
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, United States
| | - Christopher M. Thomas
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - David H. Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Microbiology & Immunology, University of Michigan, Ann Arbor, MI 48109, United States
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25
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Misra A, Sharma SK, Surolia N, Surolia A. Self-acylation properties of type II fatty acid biosynthesis acyl carrier protein. ACTA ACUST UNITED AC 2007; 14:775-83. [PMID: 17656314 DOI: 10.1016/j.chembiol.2007.05.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2007] [Revised: 05/21/2007] [Accepted: 05/25/2007] [Indexed: 11/15/2022]
Abstract
Acyl carrier protein (ACP) plays a central role in many metabolic processes inside the cell, and almost 4% of the total enzymes inside the cell require it as a cofactor. Here, we report self-acylation properties in ACPs from Plasmodium falciparum and Brassica napus that are essential components of type II fatty acid biosynthesis (FAS II), disproving the existing notion that this phenomenon is restricted only to ACPs involved in polyketide biosynthesis. We also provide strong evidence to suggest that catalytic self-acylation is intrinsic to the individual ACP. Mutational analysis of these ACPs revealed the key residue(s) involved in this phenomenon. We also demonstrate that these FAS II ACPs exhibit a high degree of selectivity for self-acylation employing only dicarboxylic acids as substrates. A plausible mechanism for the self-acylation reaction is also proposed.
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Affiliation(s)
- Ashish Misra
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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26
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Aron ZD, Fortin PD, Calderone CT, Walsh CT. FenF: Servicing the Mycosubtilin Synthetase Assembly Linein trans. Chembiochem 2007; 8:613-6. [PMID: 17330903 DOI: 10.1002/cbic.200600575] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Zachary D Aron
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
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27
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Ma Y, Smith LH, Cox RJ, Beltran-Alvarez P, Arthur CJ, Simpson F R S TJ. Catalytic relationships between type I and type II iterative polyketide synthases: The Aspergillus parasiticus norsolorinic acid synthase. Chembiochem 2007; 7:1951-8. [PMID: 17086560 DOI: 10.1002/cbic.200600341] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Norsolorinic acid synthase (NSAS) is a type I iterative polyketide synthase that occurs in the filamentous fungus Aspergillus parasiticus. PCR was used to clone fragments of NSAS corresponding to the acyl carrier protein (ACP), acyl transferase (AT) and beta-ketoacyl-ACP synthase (KS) catalytic domains. Expression of these gene fragments in Escherichia coli led to the production of soluble ACP and AT proteins. Coexpression of ACP with E. coli holo-ACP synthase (ACPS) let to production of NSAS holo-ACP, which could also be formed in vitro by using Streptomyces coelicolor ACPS. Analysis by mass spectrometry showed that, as with other type I carrier proteins, self-malonylation is not observed in the presence of malonyl CoA alone. However, the NSAS holo-ACP serves as substrate for S. coelicolor MCAT, S. coelicolor actinorhodin holo-ACP and NSAS AT domain-catalysed malonate transfer from malonyl CoA. The AT domain could transfer malonate from malonyl CoA to NSAS holo-ACP, but not hexanoate or acetate from either the cognate CoA or FAS ACP species to NSAS holo-ACP. The NSAS holo-ACP was also active in actinorhodin minimal PKS assays, but only in the presence of exogenous malonyl transferases.
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Affiliation(s)
- Yue Ma
- School of Chemistry, University of Bristol, Cantock's Close, Clifton, Bristol, BS8 1TS, UK
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28
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Liu W, Du L, Zhang L, Chen J, Shen X, Jiang H. Helicobacter pylori acyl carrier protein: expression, purification, and its interaction with beta-hydroxyacyl-ACP dehydratase. Protein Expr Purif 2006; 52:74-81. [PMID: 17049879 DOI: 10.1016/j.pep.2006.09.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2006] [Revised: 09/04/2006] [Accepted: 09/06/2006] [Indexed: 11/21/2022]
Abstract
Acyl carrier protein (ACP) is an essential component in the type II fatty acid biosynthesis (FAS II) process and is responsible for the acyl group transfer within a series of related enzymes. In this work, the ACP from Helicobacter pylori strain SS1 was cloned and the gene sequence of Hpacp was deposited in the GenBank database (Accession No.: AY904356). Two forms of HpACP (apo, holo) were successfully purified and characterized. The thermal stability of these two forms was quantitatively investigated by CD spectral analyses. The results revealed that the holo-HpACP was more stable than apo-HpACP according to the transition midpoint temperature(Tm). Moreover, the interaction of HpACP with the related enzyme (beta-hydroxyacyl-ACP dehydratase, HpFabZ) was determined by GST-pull down assay and surface plasmon resonance (SPR) technique in vitro, the results showed that HpACP displays a strong binding affinity to HpFabZ (KD=1.2 x 10(-8)M). This current work is hoped to supply useful information for better understanding the ACP features of Helicobacter pylori SS1 strain.
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Affiliation(s)
- Weizhi Liu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
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29
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Arthur CJ, Szafranska AE, Long J, Mills J, Cox RJ, Findlow SC, Simpson TJ, Crump MP, Crosby J. The malonyl transferase activity of type II polyketide synthase acyl carrier proteins. ACTA ACUST UNITED AC 2006; 13:587-96. [PMID: 16793516 DOI: 10.1016/j.chembiol.2006.03.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2006] [Revised: 03/13/2006] [Accepted: 03/24/2006] [Indexed: 11/21/2022]
Abstract
Acyl carrier proteins (ACPs) play a fundamental role in directing intermediates among the enzyme active sites of fatty acid and polyketide synthases (PKSs). In this paper, we demonstrate that the Streptomyces coelicolor (S. coelicolor) actinorhodin (act) PKS ACP can catalyze transfer of malonate to type II S. coelicolor fatty acid synthase (FAS) and other PKS ACPs in vitro. The reciprocal transfer from S. coelicolor FAS ACP to a PKS ACP was not observed. Several mutations in both act ACP and S. coelicolor FAS ACP could be classified by their participation in either donation or acceptance of this malonyl group. These mutations indicated that self-malonylation and malonyl transfer could be completely decoupled, implying that they were separate processes and that a FAS ACP could be converted from a non-malonyl-transferring protein to one with malonyl transferase activity.
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Affiliation(s)
- Christopher J Arthur
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
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30
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Liu W, Han C, Hu L, Chen K, Shen X, Jiang H. Characterization and inhibitor discovery of one novel malonyl-CoA: Acyl carrier protein transacylase (MCAT) fromHelicobacter pylori. FEBS Lett 2006; 580:697-702. [PMID: 16413022 DOI: 10.1016/j.febslet.2005.12.085] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2005] [Revised: 12/27/2005] [Accepted: 12/27/2005] [Indexed: 10/25/2022]
Abstract
Type II fatty acid synthesis (FAS II) is an essential process for bacteria survival, and malonyl-CoA:acyl carrier protein transacylase (MCAT) is a key enzyme in FAS II pathway, which is responsible for transferring the malonyl group from malonyl-CoA to the holo-ACP by forming malonyl-ACP. In this work, we described the cloning, characterization and enzymatic inhibition of a new MCAT from Helicobacter pylori strain SS1 (HpMCAT), and the gene sequence of HpfabD was deposited in the GenBank database (Accession No. AY738332 ). Enzymatic characterization of HpMCAT showed that the K(m) value for malonyl-CoA was 21.01+/-2.3 microM, and the thermal- and guanidinium hydrochloride-induced unfolding processes for HpMCAT were quantitatively investigated by circular dichroism spectral analyses. Moreover, a natural product, corytuberine, was discovered to demonstrate inhibitory activity against HpMCAT with IC(50) value at 33.1+/-3.29 microM. Further enzymatic assay results indicated that corytuberine inhibits HpMCAT in an uncompetitive manner. To our knowledge, this is the firstly reported MCAT inhibitor to date. This current work is hoped to supply useful information for better understanding the MCAT features of H. pylori strain, and corytuberine might be used as a potential lead compound in the discovery of the antibacterial agents using HpMCAT as target.
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Affiliation(s)
- Weizhi Liu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Graduate School of the Chinese Academy of Sciences, Shanghai 201203, China
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Abstract
The type II fatty acid synthetic pathway is the principal route for the production of membrane phospholipid acyl chains in bacteria and plants. The reaction sequence is carried out by a series of individual soluble proteins that are each encoded by a discrete gene, and the pathway intermediates are shuttled between the enzymes as thioesters of an acyl carrier protein. The Escherichia coli system is the paradigm for the study of this system, and high-resolution X-ray and/or NMR structures of representative members of every enzyme in the type II pathway are now available. The structural biology of these proteins reveals the specific three-dimensional features of the enzymes that explain substrate recognition, chain length specificity, and the catalytic mechanisms that define their roles in producing the multitude of products generated by the type II system. These structures are also a valuable resource to guide antibacterial drug discovery.
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Affiliation(s)
- Stephen W White
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA.
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Abstract
Combinatorial biosynthesis involves the genetic manipulation of natural product biosynthetic enzymes to produce potential new drug candidates that would otherwise be difficult to obtain. In either a theoretical or practical sense, the number of combinations possible from different types of natural product pathways ranges widely. Enzymes that have been the most amenable to this technology synthesize the polyketides, nonribosomal peptides, and hybrids of the two. The number of polyketide or peptide natural products theoretically possible is huge, but considerable work remains before these large numbers can be realized. Nevertheless, many analogs have been created by this technology, providing useful structure-activity relationship data and leading to a few compounds that may reach the clinic in the next few years. In this review the focus is on recent advances in our understanding of how different enzymes for natural product biosynthesis can be used successfully in this technology.
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Keatinge-Clay AT, Shelat AA, Savage DF, Tsai SC, Miercke LJW, O'Connell JD, Khosla C, Stroud RM. Catalysis, specificity, and ACP docking site of Streptomyces coelicolor malonyl-CoA:ACP transacylase. Structure 2003; 11:147-54. [PMID: 12575934 DOI: 10.1016/s0969-2126(03)00004-2] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Malonyl-CoA:ACP transacylase (MAT), the fabD gene product of Streptomyces coelicolor A3(2), participates in both fatty acid and polyketide synthesis pathways, transferring malonyl groups that are used as extender units in chain growth from malonyl-CoA to pathway-specific acyl carrier proteins (ACPs). Here, the 2.0 A structure reveals an invariant arginine bound to an acetate that mimics the malonyl carboxylate and helps define the extender unit binding site. Catalysis may only occur when the oxyanion hole is formed through substrate binding, preventing hydrolysis of the acyl-enzyme intermediate. Macromolecular docking simulations with actinorhodin ACP suggest that the majority of the ACP docking surface is formed by a helical flap. These results should help to engineer polyketide synthases (PKSs) that produce novel polyketides.
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Affiliation(s)
- Adrian T Keatinge-Clay
- Graduate Group in Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
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