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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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3
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Wlodek A, Kendrew SG, Coates NJ, Hold A, Pogwizd J, Rudder S, Sheehan LS, Higginbotham SJ, Stanley-Smith AE, Warneck T, Nur-E-Alam M, Radzom M, Martin CJ, Overvoorde L, Samborskyy M, Alt S, Heine D, Carter GT, Graziani EI, Koehn FE, McDonald L, Alanine A, Rodríguez Sarmiento RM, Chao SK, Ratni H, Steward L, Norville IH, Sarkar-Tyson M, Moss SJ, Leadlay PF, Wilkinson B, Gregory MA. Diversity oriented biosynthesis via accelerated evolution of modular gene clusters. Nat Commun 2017; 8:1206. [PMID: 29089518 PMCID: PMC5663706 DOI: 10.1038/s41467-017-01344-3] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 09/08/2017] [Indexed: 11/09/2022] Open
Abstract
Erythromycin, avermectin and rapamycin are clinically useful polyketide natural products produced on modular polyketide synthase multienzymes by an assembly-line process in which each module of enzymes in turn specifies attachment of a particular chemical unit. Although polyketide synthase encoding genes have been successfully engineered to produce novel analogues, the process can be relatively slow, inefficient, and frequently low-yielding. We now describe a method for rapidly recombining polyketide synthase gene clusters to replace, add or remove modules that, with high frequency, generates diverse and highly productive assembly lines. The method is exemplified in the rapamycin biosynthetic gene cluster where, in a single experiment, multiple strains were isolated producing new members of a rapamycin-related family of polyketides. The process mimics, but significantly accelerates, a plausible mechanism of natural evolution for modular polyketide synthases. Detailed sequence analysis of the recombinant genes provides unique insight into the design principles for constructing useful synthetic assembly-line multienzymes. Reengineering polyketide synthase encoding genes to produce analogues of natural products can be slow and low-yielding. Here the authors use accelerated evolution to recombine the gene cluster for rapid production of rapamycin-related products.
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Affiliation(s)
- Aleksandra Wlodek
- Isomerase Therapeutics Ltd., Chesterford Research Park, Cambridge, CB10 1XL, UK
| | - Steve G Kendrew
- Biotica Technology Ltd., Chesterford Research Park, Cambridge, CB10 1XL, UK.,Engineered Biodesign Limited, Cambridge, CB22 3GN, UK
| | - Nigel J Coates
- Isomerase Therapeutics Ltd., Chesterford Research Park, Cambridge, CB10 1XL, UK.,Biotica Technology Ltd., Chesterford Research Park, Cambridge, CB10 1XL, UK
| | - Adam Hold
- Isomerase Therapeutics Ltd., Chesterford Research Park, Cambridge, CB10 1XL, UK
| | - Joanna Pogwizd
- Isomerase Therapeutics Ltd., Chesterford Research Park, Cambridge, CB10 1XL, UK
| | - Steven Rudder
- Isomerase Therapeutics Ltd., Chesterford Research Park, Cambridge, CB10 1XL, UK
| | - Lesley S Sheehan
- Isomerase Therapeutics Ltd., Chesterford Research Park, Cambridge, CB10 1XL, UK.,Biotica Technology Ltd., Chesterford Research Park, Cambridge, CB10 1XL, UK
| | | | - Anna E Stanley-Smith
- Isomerase Therapeutics Ltd., Chesterford Research Park, Cambridge, CB10 1XL, UK.,Biotica Technology Ltd., Chesterford Research Park, Cambridge, CB10 1XL, UK
| | - Tony Warneck
- Biotica Technology Ltd., Chesterford Research Park, Cambridge, CB10 1XL, UK
| | - Mohammad Nur-E-Alam
- Biotica Technology Ltd., Chesterford Research Park, Cambridge, CB10 1XL, UK.,Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, 12372, Saudi Arabia
| | - Markus Radzom
- Biotica Technology Ltd., Chesterford Research Park, Cambridge, CB10 1XL, UK.,BASF SE, Speyerer Str. 2, Limburgerhof, 67117, Germany
| | - Christine J Martin
- Biotica Technology Ltd., Chesterford Research Park, Cambridge, CB10 1XL, UK
| | - Lois Overvoorde
- Isomerase Therapeutics Ltd., Chesterford Research Park, Cambridge, CB10 1XL, UK
| | - Markiyan Samborskyy
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Silke Alt
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Daniel Heine
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Guy T Carter
- Chemical and Screening Sciences, Wyeth Pharmaceuticals, 401 North Middletown Road, Pearl River, NY, 10965, USA
| | - Edmund I Graziani
- Chemical and Screening Sciences, Wyeth Pharmaceuticals, 401 North Middletown Road, Pearl River, NY, 10965, USA.,Medicine Discovery Network-Synthetic Biology, Pfizer Worldwide R&D, 445 Eastern Point Rd., Groton, CT, 06340, USA
| | - Frank E Koehn
- Chemical and Screening Sciences, Wyeth Pharmaceuticals, 401 North Middletown Road, Pearl River, NY, 10965, USA
| | - Leonard McDonald
- Chemical and Screening Sciences, Wyeth Pharmaceuticals, 401 North Middletown Road, Pearl River, NY, 10965, USA
| | - Alexander Alanine
- Roche Innovation Center Basel, Pharmaceutical Research and Early Development (PRED), Basel, CH-4070, Switzerland
| | | | - Suzan Keen Chao
- Roche Innovation Center Basel, Pharmaceutical Research and Early Development (PRED), Basel, CH-4070, Switzerland
| | - Hasane Ratni
- Roche Innovation Center Basel, Pharmaceutical Research and Early Development (PRED), Basel, CH-4070, Switzerland
| | - Lucinda Steward
- Roche Innovation Center Basel, Pharmaceutical Research and Early Development (PRED), Basel, CH-4070, Switzerland
| | - Isobel H Norville
- Defence Science and Technology Laboratory, Porton Down, PO17 6AD, UK
| | - Mitali Sarkar-Tyson
- Defence Science and Technology Laboratory, Porton Down, PO17 6AD, UK.,Marshall Centre for Infectious Diseases, School of Biomedical Sciences, University of Western Australia, Monash Avenue, Nedlands, WA, 6009, Australia
| | - Steven J Moss
- Isomerase Therapeutics Ltd., Chesterford Research Park, Cambridge, CB10 1XL, UK.,Biotica Technology Ltd., Chesterford Research Park, Cambridge, CB10 1XL, UK
| | - Peter F Leadlay
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Barrie Wilkinson
- Isomerase Therapeutics Ltd., Chesterford Research Park, Cambridge, CB10 1XL, UK. .,Biotica Technology Ltd., Chesterford Research Park, Cambridge, CB10 1XL, UK. .,Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
| | - Matthew A Gregory
- Isomerase Therapeutics Ltd., Chesterford Research Park, Cambridge, CB10 1XL, UK. .,Biotica Technology Ltd., Chesterford Research Park, Cambridge, CB10 1XL, UK.
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Noinaj N, Bosserman MA, Schickli MA, Piszczek G, Kharel MK, Pahari P, Buchanan SK, Rohr J. The crystal structure and mechanism of an unusual oxidoreductase, GilR, involved in gilvocarcin V biosynthesis. J Biol Chem 2011; 286:23533-43. [PMID: 21561854 PMCID: PMC3123116 DOI: 10.1074/jbc.m111.247833] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Revised: 04/29/2011] [Indexed: 01/04/2023] Open
Abstract
GilR is a recently identified oxidoreductase that catalyzes the terminal step of gilvocarcin V biosynthesis and is a unique enzyme that establishes the lactone core of the polyketide-derived gilvocarcin chromophore. Gilvocarcin-type compounds form a small distinct family of anticancer agents that are involved in both photo-activated DNA-alkylation and histone H3 cross-linking. High resolution crystal structures of apoGilR and GilR in complex with its substrate pregilvocarcin V reveals that GilR belongs to the small group of a relatively new type of the vanillyl-alcohol oxidase flavoprotein family characterized by bicovalently tethered cofactors. GilR was found as a dimer, with the bicovalently attached FAD cofactor mediated through His-65 and Cys-125. Subsequent mutagenesis and functional assays indicate that Tyr-445 may be involved in reaction catalysis and in mediating the covalent attachment of FAD, whereas Tyr-448 serves as an essential residue initiating the catalysis by swinging away from the active site to accommodate binding of the 6R-configured substrate and consequently abstracting the proton of the hydroxyl residue of the substrate hemiacetal 6-OH group. These studies lay the groundwork for future enzyme engineering to broaden the substrate specificity of this bottleneck enzyme of the gilvocarcin biosynthetic pathway for the development of novel anti-cancer therapeutics.
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Affiliation(s)
| | - Mary A. Bosserman
- From the Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536-0596 and
| | - M. Alexandra Schickli
- From the Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536-0596 and
| | | | - Madan K. Kharel
- From the Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536-0596 and
| | - Pallab Pahari
- From the Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536-0596 and
| | | | - Jürgen Rohr
- From the Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536-0596 and
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