1
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Zhao C, Slocum ST, Sherman DH, Ruotolo BT. Time-Resolved Ion Mobility-Mass Spectrometry Reveals Structural Transitions in the Disassembly of Modular Polyketide Syntheses. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:2136-2142. [PMID: 39038158 DOI: 10.1021/jasms.4c00181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
The type 1 polyketide synthase (PKS) assembly line uses its modular structure to produce polyketide natural products that form the basis of many pharmaceuticals. Currently, several cryoelectron microscopy (cryo-EM) structures of a multidomain PKS module have been constructed, but much remains to be learned. Here we utilize ion-mobility mass spectrometry (IM-MS) to record size and shape information and detect different conformational states of a 207 kDa didomain dimer comprised of ketosynthase (KS) and acyl transferase (AT), excised from full-length module. Furthermore, gas-phase stability differences between these different conformations are captured by collision induced unfolding (CIU) technology. Additionally, through tracking these forms as a function of time, we elucidate a detailed disassembly pathway for KS-AT dimers for the first time.
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Affiliation(s)
- Chunyi Zhao
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Samuel T Slocum
- Life Science Institute, Departments of Medicinal Chemistry, Chemistry and Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - David H Sherman
- Life Science Institute, Departments of Medicinal Chemistry, Chemistry and Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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2
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Ray KA, Lutgens JD, Bista R, Zhang J, Desai RR, Hirsch M, Miyazawa T, Cordova A, Keatinge-Clay AT. Assessing and harnessing updated polyketide synthase modules through combinatorial engineering. Nat Commun 2024; 15:6485. [PMID: 39090122 PMCID: PMC11294587 DOI: 10.1038/s41467-024-50844-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 07/23/2024] [Indexed: 08/04/2024] Open
Abstract
The modular nature of polyketide assembly lines and the significance of their products make them prime targets for combinatorial engineering. The recently updated module boundary has been successful for engineering short synthases, yet larger synthases constructed using the updated boundary have not been investigated. Here we describe our design and implementation of a BioBricks-like platform to rapidly construct 5 triketide, 25 tetraketide, and 125 pentaketide synthases to test every module combination of the pikromycin synthase. Anticipated products are detected from 60% of the triketide synthases, 32% of the tetraketide synthases, and 6.4% of the pentaketide synthases. We determine ketosynthase gatekeeping and module-skipping are the principal impediments to obtaining functional synthases. The platform is also employed to construct active hybrid synthases by incorporating modules from the erythromycin, spinosyn, and rapamycin assembly lines. The relaxed gatekeeping of a ketosynthase in the rapamycin synthase is especially encouraging in the quest to produce designer polyketides.
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Affiliation(s)
- Katherine A Ray
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Joshua D Lutgens
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Ramesh Bista
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Jie Zhang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Ronak R Desai
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Melissa Hirsch
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Takeshi Miyazawa
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Antonio Cordova
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Adrian T Keatinge-Clay
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
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3
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Hirsch M, Desai RR, Annaswamy S, Keatinge-Clay AT. Mutagenesis Supports AlphaFold Prediction of How Modular Polyketide Synthase Acyl Carrier Proteins Dock With Downstream Ketosynthases. Proteins 2024. [PMID: 39078105 DOI: 10.1002/prot.26733] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 06/07/2024] [Accepted: 07/05/2024] [Indexed: 07/31/2024]
Abstract
The docking of an acyl carrier protein (ACP) domain with a downstream ketosynthase (KS) domain in each module of a polyketide synthase (PKS) helps ensure accurate biosynthesis. If the polyketide chain bound to the ACP has been properly modified by upstream processing enzymes and is compatible with gatekeeping residues in the KS tunnel, a transacylation reaction can transfer it from the 18.1-Å phosphopantetheinyl arm of the ACP to the reactive cysteine of the KS. AlphaFold-Multimer predicts a general interface for these transacylation checkpoints. Half of the solutions obtained for 50 ACP/KS pairs show the KS motif TxLGDP forming the first turn of an α-helix, as in reported structures, while half show it forming a type I β-turn not previously observed. Solutions with the latter conformation may represent how these domains are relatively positioned during the transacylation reaction, as the entrance to the KS active site is relatively open and the phosphopantetheinylated ACP serine and the reactive KS cysteine are relatively closer-17.2 versus 20.9 Å, on average. To probe the predicted interface, 20 mutations were made to KS surface residues within the model triketide lactone synthase P1-P6-P7. The activities of these mutants are consistent with the proposed interface.
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Affiliation(s)
- Melissa Hirsch
- Department of Chemistry, The University of Texas at Austin, Austin, Texas, USA
| | - Ronak R Desai
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Shreyas Annaswamy
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Adrian T Keatinge-Clay
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
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4
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Zhao C, Borotto NB, Schmidt J, Srivastava K, Lowell A, Hakansson K, Sherman DH, Ruotolo BT. Gas-Phase Unfolding Reveals Stability Shifts Associated with Substrate Binding in Modular Polyketide Synthases. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024. [PMID: 39052932 DOI: 10.1021/jasms.4c00179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
Native mass spectrometry (MS), ion mobility (IM), and collision-induced unfolding (CIU) have all been widely used to study the binding of small molecules to proteins and their complexes. Despite many successes in detecting subtle gas-phase stability differences in smaller systems dominated by single-domain subunits, studies targeting complexes comprised of large, multidomain subunits still face many challenges. For example, polyketide synthases (PKSs) are multiprotein enzymes that use their modular architecture to produce polyketide natural products and form the basis for nearly one-third of pharmaceuticals. Here, we describe the development of CIU methods capable of extracting information from these multiprotein complexes and demonstrate the current limits of quantitative CIU technology by probing the stabilities ∼280 kDa PKS dimer protein complexes. Our approach detects the evidence of the stability shifts associated with substrate binding that accounts for <0.1% of the mass for the intact assembly.
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Affiliation(s)
- Chunyi Zhao
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Nicholas B Borotto
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jennifer Schmidt
- Life Science Institute, Departments of Medicinal Chemistry, Chemistry, and Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kinshuk Srivastava
- Life Science Institute, Departments of Medicinal Chemistry, Chemistry, and Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Andrew Lowell
- Life Science Institute, Departments of Medicinal Chemistry, Chemistry, and Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kristina Hakansson
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - David H Sherman
- Life Science Institute, Departments of Medicinal Chemistry, Chemistry, and Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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5
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Scat S, Weissman KJ, Chagot B. Insights into docking in megasynthases from the investigation of the toblerol trans-AT polyketide synthase: many α-helical means to an end. RSC Chem Biol 2024; 5:669-683. [PMID: 38966669 PMCID: PMC11221535 DOI: 10.1039/d4cb00075g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 05/16/2024] [Indexed: 07/06/2024] Open
Abstract
The fidelity of biosynthesis by modular polyketide synthases (PKSs) depends on specific moderate affinity interactions between successive polypeptide subunits mediated by docking domains (DDs). These sequence elements are notably portable, allowing their transplantation into alternative biosynthetic and metabolic contexts. Herein, we use integrative structural biology to characterize a pair of DDs from the toblerol trans-AT PKS. Both are intrinsically disordered regions (IDRs) that fold into a 3 α-helix docking complex of unprecedented topology. The C-terminal docking domain (CDD) resembles the 4 α-helix type (4HB) CDDs, which shows that the same type of DD can be redeployed to form complexes of distinct geometry. By carefully re-examining known DD structures, we further extend this observation to type 2 docking domains, establishing previously unsuspected structural relations between DD types. Taken together, these data illustrate the plasticity of α-helical DDs, which allow the formation of a diverse topological spectrum of docked complexes. The newly identified DDs should also find utility in modular PKS genetic engineering.
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Affiliation(s)
- Serge Scat
- Université de Lorraine, CNRS, IMoPA F-54000 Nancy France
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6
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Nava A, Roberts J, Haushalter RW, Wang Z, Keasling JD. Module-Based Polyketide Synthase Engineering for de Novo Polyketide Biosynthesis. ACS Synth Biol 2023; 12:3148-3155. [PMID: 37871264 PMCID: PMC10661043 DOI: 10.1021/acssynbio.3c00282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Indexed: 10/25/2023]
Abstract
Polyketide retrobiosynthesis, where the biosynthetic pathway of a given polyketide can be reversibly engineered due to the colinearity of the polyketide synthase (PKS) structure and function, has the potential to produce millions of organic molecules. Mixing and matching modules from natural PKSs is one of the routes to produce many of these molecules. Evolutionary analysis of PKSs suggests that traditionally used module boundaries may not lead to the most productive hybrid PKSs and that new boundaries around and within the ketosynthase domain may be more active when constructing hybrid PKSs. As this is still a nascent area of research, the generality of these design principles based on existing engineering efforts remains inconclusive. Recent advances in structural modeling and synthetic biology present an opportunity to accelerate PKS engineering by re-evaluating insights gained from previous engineering efforts with cutting edge tools.
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Affiliation(s)
- Alberto
A. Nava
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Jacob Roberts
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Bioengineering, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Robert W. Haushalter
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Zilong Wang
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jay D. Keasling
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
- Department
of Bioengineering, University of California,
Berkeley, Berkeley, California 94720, United States
- Center
for Synthetic Biochemistry, Shenzhen Institutes
for Advanced Technologies, Shenzhen 518055, P.R. China
- The
Novo
Nordisk Foundation Center for Biosustainability, Technical University Denmark, Kemitorvet, Building 220, Kongens Lyngby 2800, Denmark
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7
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Ray KA, Lutgens JD, Bista R, Zhang J, Desai RR, Hirsch M, Miyazawa T, Cordova A, Keatinge-Clay AT. Assessing and harnessing updated polyketide synthase modules through combinatorial engineering. RESEARCH SQUARE 2023:rs.3.rs-3157617. [PMID: 37546965 PMCID: PMC10402262 DOI: 10.21203/rs.3.rs-3157617/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The modular nature of polyketide assembly lines and the significance of their products make them prime targets for combinatorial engineering. While short synthases constructed using the recently updated module boundary have been shown to outperform those using the traditional boundary, larger synthases constructed using the updated boundary have not been investigated. Here we describe our design and implementation of a BioBricks-like platform to rapidly construct 5 triketide, 25 tetraketide, and 125 pentaketide synthases from the updated modules of the Pikromycin synthase. Every combinatorial possibility of modules 2-6 inserted between the first and last modules of the native synthase was constructed and assayed. Anticipated products were observed from 60% of the triketide synthases, 32% of the tetraketide synthases, and 6.4% of the pentaketide synthases. Ketosynthase gatekeeping and module-skipping were determined to be the principal impediments to obtaining functional synthases. The platform was also used to create functional hybrid synthases through the incorporation of modules from the Erythromycin, Spinosyn, and Rapamycin assembly lines. The relaxed gatekeeping observed from a ketosynthase in the Rapamycin synthase is especially encouraging in the quest to produce designer polyketides.
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Affiliation(s)
- Katherine A. Ray
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX
| | - Joshua D. Lutgens
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX
| | - Ramesh Bista
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX
| | - Jie Zhang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX
| | - Ronak R. Desai
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX
| | - Melissa Hirsch
- Department of Chemistry, The University of Texas at Austin, Austin, TX
| | - Takeshi Miyazawa
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX
| | - Antonio Cordova
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX
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8
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Enzymology of assembly line synthesis by modular polyketide synthases. Nat Chem Biol 2023; 19:401-415. [PMID: 36914860 DOI: 10.1038/s41589-023-01277-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 01/31/2023] [Indexed: 03/16/2023]
Abstract
Modular polyketide synthases (PKSs) run catalytic reactions over dozens of steps in a highly orchestrated manner. To accomplish this synthetic feat, they form megadalton multienzyme complexes that are among the most intricate proteins on earth. Polyketide products are of elaborate chemistry with molecular weights of usually several hundred daltons and include clinically important drugs such as erythromycin (antibiotic), rapamycin (immunosuppressant) and epothilone (anticancer drug). The term 'modular' refers to a hierarchical structuring of modules and domains within an overall assembly line arrangement, in which PKS organization is colinearly translated into the polyketide structure. New structural information obtained during the past few years provides substantial direct insight into the orchestration of catalytic events within a PKS module and leads to plausible models for synthetic progress along assembly lines. In light of these structural insights, the PKS engineering field is poised to enter a new era of engineering.
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9
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Keatinge-Clay AT, Miyazawa T, Zhang J, Ray KA, Lutgens JD, Bista R, Lin SN. Crystal structures reveal the framework of cis -acyltransferase modular polyketide synthases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.11.528132. [PMID: 36798387 PMCID: PMC9934609 DOI: 10.1101/2023.02.11.528132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
Although the domains of cis -acyltransferase ( cis -AT) modular polyketide synthases (PKS's) have been understood at atomic resolution for over a decade, the domain-domain interactions responsible for the architectures and activities of these giant molecular assembly lines remain largely uncharacterized. The multimeric structure of the α 6 β 6 fungal fatty acid synthase (FAS) provides 6 equivalent reaction chambers for its acyl carrier protein (ACP) domains to shuttle carbon building blocks and the growing acyl chain between surrounding, oriented enzymatic domains. The presumed homodimeric oligomerization of cis -AT assembly lines is insufficient to provide similar reaction chambers; however, the crystal structure of a ketosynthase (KS)+AT didomain presented here and three already reported show an interaction between the AT domains appropriate for lateral multimerization. This interaction was used to construct a framework for the pikromycin PKS from its KS, AT, and docking domains that contains highly-ordered reaction chambers. Its AT domains also mediate vertical interactions, both with upstream KS domains and downstream docking domains.
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10
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Zhai G, Zhu Y, Sun G, Zhou F, Sun Y, Hong Z, Dong C, Leadlay PF, Hong K, Deng Z, Zhou F, Sun Y. Insights into azalomycin F assembly-line contribute to evolution-guided polyketide synthase engineering and identification of intermodular recognition. Nat Commun 2023; 14:612. [PMID: 36739290 PMCID: PMC9899208 DOI: 10.1038/s41467-023-36213-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 01/20/2023] [Indexed: 02/06/2023] Open
Abstract
Modular polyketide synthase (PKS) is an ingenious core machine that catalyzes abundant polyketides in nature. Exploring interactions among modules in PKS is very important for understanding the overall biosynthetic process and for engineering PKS assembly-lines. Here, we show that intermodular recognition between the enoylreductase domain ER1/2 inside module 1/2 and the ketosynthase domain KS3 inside module 3 is required for the cross-module enoylreduction in azalomycin F (AZL) biosynthesis. We also show that KS4 of module 4 acts as a gatekeeper facilitating cross-module enoylreduction. Additionally, evidence is provided that module 3 and module 6 in the AZL PKS are evolutionarily homologous, which makes evolution-oriented PKS engineering possible. These results reveal intermodular recognition, furthering understanding of the mechanism of the PKS assembly-line, thus providing different insights into PKS engineering. This also reveals that gene duplication/conversion and subsequent combinations may be a neofunctionalization process in modular PKS assembly-lines, hence providing a different case for supporting the investigation of modular PKS evolution.
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Affiliation(s)
- Guifa Zhai
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, People's Republic of China.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, 430071, Wuhan, People's Republic of China
| | - Yan Zhu
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, People's Republic of China.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, 430071, Wuhan, People's Republic of China
| | - Guo Sun
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, People's Republic of China.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, 430071, Wuhan, People's Republic of China
| | - Fan Zhou
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, People's Republic of China.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, 430071, Wuhan, People's Republic of China
| | - Yangning Sun
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, People's Republic of China.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, 430071, Wuhan, People's Republic of China
| | - Zhou Hong
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, People's Republic of China.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, 430071, Wuhan, People's Republic of China
| | - Chuan Dong
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, People's Republic of China.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, 430071, Wuhan, People's Republic of China
| | - Peter F Leadlay
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, United Kingdom
| | - Kui Hong
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, People's Republic of China.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, 430071, Wuhan, People's Republic of China
| | - Zixin Deng
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, People's Republic of China.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, 430071, Wuhan, People's Republic of China
| | - Fuling Zhou
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, People's Republic of China
| | - Yuhui Sun
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, People's Republic of China. .,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, 430071, Wuhan, People's Republic of China. .,Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, 430071, Wuhan, People's Republic of China.
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11
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Yan M, Cao L, Zhao L, Zhou W, Liu X, Zhang W, Rao Z. The Key Roles of Mycobacterium tuberculosis FadD23 C-terminal Domain in Catalytic Mechanisms. Front Microbiol 2023; 14:1090534. [PMID: 36896429 PMCID: PMC9989471 DOI: 10.3389/fmicb.2023.1090534] [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: 11/07/2022] [Accepted: 01/31/2023] [Indexed: 02/23/2023] Open
Abstract
Sulfolipid-1 (SL-1) is located in the Mycobacterium tuberculosis (M. tb) cell wall, and is essential for pathogen virulence and intracellular growth. Multiple proteins (e.g., Pks2, FadD23, PapA1, and MmpL8) in the SL-1 synthesis pathway can be treated as drug targets, but, to date, their structures have not been solved. The crystal structures of FadD23 bound to ATP or hexadecanoyl adenylate was determined in this study. We have also investigated long-chain saturated fatty acids as biological substrates of FadD23 through structural, biological, and chemical analyses. The mutation at the active site of FadD23 greatly influences enzymatic activity. Meanwhile, the FadD23 N-terminal domain alone cannot bind palmitic acid without C-terminal domain facilitation since it is almost inactive after removing the C-terminal domain. FadD23 is the first protein in the SL-1 synthesis pathway whose structure has been solved. These results reveal the importance of the C-terminal domain in the catalytic mechanism.
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Affiliation(s)
- Mengrong Yan
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, China
| | - Lin Cao
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, China
| | - Li Zhao
- Innovative Center for Pathogen Research, Guangzhou Laboratory, Guangzhou, China
| | - Weihong Zhou
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, China
| | - Xiang Liu
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, China
| | - Wei Zhang
- Innovative Center for Pathogen Research, Guangzhou Laboratory, Guangzhou, China
| | - Zihe Rao
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, China.,Innovative Center for Pathogen Research, Guangzhou Laboratory, Guangzhou, China.,Shanghai Institute for Advanced Immunochemical Studies and School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China.,Laboratory of Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, China
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12
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Armstrong FA, Cheng B, Herold RA, Megarity CF, Siritanaratkul B. From Protein Film Electrochemistry to Nanoconfined Enzyme Cascades and the Electrochemical Leaf. Chem Rev 2022; 123:5421-5458. [PMID: 36573907 PMCID: PMC10176485 DOI: 10.1021/acs.chemrev.2c00397] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Protein film electrochemistry (PFE) has given unrivalled insight into the properties of redox proteins and many electron-transferring enzymes, allowing investigations of otherwise ill-defined or intractable topics such as unstable Fe-S centers and the catalytic bias of enzymes. Many enzymes have been established to be reversible electrocatalysts when attached to an electrode, and further investigations have revealed how unusual dependences of catalytic rates on electrode potential have stark similarities with electronics. A special case, the reversible electrochemistry of a photosynthetic enzyme, ferredoxin-NADP+ reductase (FNR), loaded at very high concentrations in the 3D nanopores of a conducting metal oxide layer, is leading to a new technology that brings PFE to myriad enzymes of other classes, the activities of which become controlled by the primary electron exchange. This extension is possible because FNR-based recycling of NADP(H) can be coupled to a dehydrogenase, and thence to other enzymes linked in tandem by the tight channelling of cofactors and intermediates within the nanopores of the material. The earlier interpretations of catalytic wave-shapes and various analogies with electronics are thus extended to initiate a field perhaps aptly named "cascade-tronics", in which the flow of reactions along an enzyme cascade is monitored and controlled through an electrochemical analyzer. Unlike in photosynthesis where FNR transduces electron transfer and hydride transfer through the unidirectional recycling of NADPH, the "electrochemical leaf" (e-Leaf) can be used to drive reactions in both oxidizing and reducing directions. The e-Leaf offers a natural way to study how enzymes are affected by nanoconfinement and crowding, mimicking the physical conditions under which enzyme cascades operate in living cells. The reactions of the trapped enzymes, often at very high local concentration, are thus studied electrochemically, exploiting the potential domain to control rates and direction and the current-rate analogy to derive kinetic data. Localized NADP(H) recycling is very efficient, resulting in very high cofactor turnover numbers and new opportunities for controlling and exploiting biocatalysis.
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Affiliation(s)
- Fraser A. Armstrong
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Beichen Cheng
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Ryan A. Herold
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Clare F. Megarity
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Bhavin Siritanaratkul
- Stephenson Institute for Renewable Energy and the Department of Chemistry, University of Liverpool, Liverpool L69 7ZF, United Kingdom
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13
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Metabolic pathway assembly using docking domains from type I cis-AT polyketide synthases. Nat Commun 2022; 13:5541. [PMID: 36130947 PMCID: PMC9492657 DOI: 10.1038/s41467-022-33272-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 09/09/2022] [Indexed: 11/21/2022] Open
Abstract
Engineered metabolic pathways in microbial cell factories often have no natural organization and have challenging flux imbalances, leading to low biocatalytic efficiency. Modular polyketide synthases (PKSs) are multienzyme complexes that synthesize polyketide products via an assembly line thiotemplate mechanism. Here, we develop a strategy named mimic PKS enzyme assembly line (mPKSeal) that assembles key cascade enzymes to enhance biocatalytic efficiency and increase target production by recruiting cascade enzymes tagged with docking domains from type I cis-AT PKS. We apply this strategy to the astaxanthin biosynthetic pathway in engineered Escherichia coli for multienzyme assembly to increase astaxanthin production by 2.4-fold. The docking pairs, from the same PKSs or those from different cis-AT PKSs evidently belonging to distinct classes, are effective enzyme assembly tools for increasing astaxanthin production. This study addresses the challenge of cascade catalytic efficiency and highlights the potential for engineering enzyme assembly. Assembly artificial pathway in design connecting media can increase biosynthetic efficiency, but the choice of connecting media is limited. Here, the authors develop a new protein assembly strategy using a pool of docking peptides from polyketide synthase and show its application in astaxanthin biosynthesis in E. coli.
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14
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Chisuga T, Miyanaga A, Eguchi T. Protein-protein Recognition Involved in the Intermodular Transacylation Reaction in Modular Polyketide Synthase in the Biosynthesis of Vicenistatin. Chembiochem 2022; 23:e202200200. [PMID: 35501288 PMCID: PMC9401018 DOI: 10.1002/cbic.202200200] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 04/29/2022] [Indexed: 11/25/2022]
Abstract
The ketosynthase (KS) domain is a core domain found in modular polyketide synthases (PKSs). To maintain the polyketide biosynthetic fidelity, the KS domain must only accept an acyl group from the acyl carrier protein (ACP) domain of the immediate upstream module even when they are separated into different polypeptides. Although it was reported that both the docking domain‐based interactions and KS‐ACP compatibility are important for the interpolypeptide transacylation reaction in 6‐deoxyerythronolide B synthase, it is not clear whether these findings are broadly applied to other modular PKSs. Herein, we describe the importance of protein‐protein recognition in the intermodular transacylation between VinP1 module 3 and VinP2 module 4 in vicenistatin biosynthesis. We compared the transacylation activity and crosslinking efficiency of VinP2 KS4 against the cognate VinP1 ACP3 with the noncognate one. As a result, it appeared that VinP2 KS4 distinguishes the cognate ACP3 from other ACPs.
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Affiliation(s)
- Taichi Chisuga
- Tokyo Institute of Technology - Ookayama Campus: Tokyo Kogyo Daigaku, Chemistry, JAPAN
| | - Akimasa Miyanaga
- Tokyo Institute of Technology - Ookayama Campus: Tokyo Kogyo Daigaku, Chemistry, JAPAN
| | - Tadashi Eguchi
- Tokyo Institute of Technology, Chemistry, O-okayama, Meguro-ku, 1528551, Tokyo, JAPAN
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15
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Engineering the stambomycin modular polyketide synthase yields 37-membered mini-stambomycins. Nat Commun 2022; 13:515. [PMID: 35082289 PMCID: PMC8792006 DOI: 10.1038/s41467-022-27955-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 12/21/2021] [Indexed: 12/14/2022] Open
Abstract
The modular organization of the type I polyketide synthases (PKSs) would seem propitious for rational engineering of desirable analogous. However, despite decades of efforts, such experiments remain largely inefficient. Here, we combine multiple, state-of-the-art approaches to reprogram the stambomycin PKS by deleting seven internal modules. One system produces the target 37-membered mini-stambomycin metabolites − a reduction in chain length of 14 carbons relative to the 51-membered parental compounds − but also substantial quantities of shunt metabolites. Our data also support an unprecedented off-loading mechanism of such stalled intermediates involving the C-terminal thioesterase domain of the PKS. The mini-stambomycin yields are reduced relative to wild type, likely reflecting the poor tolerance of the modules downstream of the modified interfaces to the non-native substrates. Overall, we identify factors contributing to the productivity of engineered whole assembly lines, but our findings also highlight the need for further research to increase production titers. Genetic engineering of the type I polyketide synthases (PKSs) to produce desirable analogous remains largely inefficient. Here, the authors leverage multiple approaches to delete seven internal modules from the stambomycin PKS and generate 37-membered mini-stambomycin macrolactones.
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16
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Klaus M, Rossini E, Linden A, Paithankar KS, Zeug M, Ignatova Z, Urlaub H, Khosla C, Köfinger J, Hummer G, Grininger M. Solution Structure and Conformational Flexibility of a Polyketide Synthase Module. JACS AU 2021; 1:2162-2171. [PMID: 34977887 PMCID: PMC8717363 DOI: 10.1021/jacsau.1c00043] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Indexed: 05/28/2023]
Abstract
Polyketide synthases (PKSs) are versatile C-C bond-forming enzymes that are broadly distributed in bacteria and fungi. The polyketide compound family includes many clinically useful drugs such as the antibiotic erythromycin, the antineoplastic epothilone, and the cholesterol-lowering lovastatin. Harnessing PKSs for custom compound synthesis remains an open challenge, largely because of the lack of knowledge about key structural properties. Particularly, the domains-well characterized on their own-are poorly understood in their arrangement, conformational dynamics, and interplay in the intricate quaternary structure of modular PKSs. Here, we characterize module 2 from the 6-deoxyerythronolide B synthase by small-angle X-ray scattering and cross-linking mass spectrometry with coarse-grained structural modeling. The results of this hybrid approach shed light on the solution structure of a cis-AT type PKS module as well as its inherent conformational dynamics. Supported by a directed evolution approach, we also find that acyl carrier protein (ACP)-mediated substrate shuttling appears to be steered by a nonspecific electrostatic interaction network.
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Affiliation(s)
- Maja Klaus
- Institute
of Organic Chemistry and Chemical Biology, Buchmann Institute for
Molecular Life Sciences, Goethe University
Frankfurt, Max-von-Laue Strasse 15, Frankfurt am Main 60438, Germany
| | - Emanuele Rossini
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue
Strasse 3, Frankfurt am Main 60438, Germany
| | - Andreas Linden
- Max
Planck Institute for Biophysical Chemistry, Am Fassberg 11, Goettingen 37077, Germany
- Institute
for Clinical Chemistry, University Medical
Center Göttingen, Robert Koch Strasse 40, Goettingen 37075, Germany
| | - Karthik S. Paithankar
- Institute
of Organic Chemistry and Chemical Biology, Buchmann Institute for
Molecular Life Sciences, Goethe University
Frankfurt, Max-von-Laue Strasse 15, Frankfurt am Main 60438, Germany
| | - Matthias Zeug
- Institute
of Organic Chemistry and Chemical Biology, Buchmann Institute for
Molecular Life Sciences, Goethe University
Frankfurt, Max-von-Laue Strasse 15, Frankfurt am Main 60438, Germany
| | - Zoya Ignatova
- Institute
for Biochemistry and Molecular Biology, University of Hamburg, Notkestrasse 85, Hamburg 22607, Germany
| | - Henning Urlaub
- Max
Planck Institute for Biophysical Chemistry, Am Fassberg 11, Goettingen 37077, Germany
- Institute
for Clinical Chemistry, University Medical
Center Göttingen, Robert Koch Strasse 40, Goettingen 37075, Germany
| | - Chaitan Khosla
- Department
of Chemistry, Stanford ChEM-H, Department of Chemical Engineering Stanford University, Stanford, California 94305, United States
| | - Jürgen Köfinger
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue
Strasse 3, Frankfurt am Main 60438, Germany
| | - Gerhard Hummer
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue
Strasse 3, Frankfurt am Main 60438, Germany
- Institute
of Biophysics, Goethe University Frankfurt, Max-von-Laue Strasse 1, Frankfurt am Main 60438, Germany
| | - Martin Grininger
- Institute
of Organic Chemistry and Chemical Biology, Buchmann Institute for
Molecular Life Sciences, Goethe University
Frankfurt, Max-von-Laue Strasse 15, Frankfurt am Main 60438, Germany
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17
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Hirsch M, Fitzgerald BJ, Keatinge-Clay AT. How cis-Acyltransferase Assembly-Line Ketosynthases Gatekeep for Processed Polyketide Intermediates. ACS Chem Biol 2021; 16:2515-2526. [PMID: 34590822 PMCID: PMC9879353 DOI: 10.1021/acschembio.1c00598] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
With the redefinition of polyketide synthase (PKS) modules, a new appreciation of their most downstream domain, the ketosynthase (KS), is emerging. In addition to performing its well-established role of generating a carbon-carbon bond between an acyl-CoA building block and a growing polyketide, it may gatekeep against incompletely processed intermediates. Here, we investigate 739 KSs from 92 primarily actinomycete, cis-acyltransferase assembly lines. When KSs were separated into 16 families based on the chemistries at the α- and β-carbons of their polyketide substrates, a comparison of 32 substrate tunnel residues revealed unique sequence fingerprints. Surprisingly, additional fingerprints were detected when the chemistry at the γ-carbon was considered. Representative KSs were modeled bound to their natural polyketide substrates to better understand observed patterns, such as the substitution of a tryptophan by a smaller residue to accommodate an l-α-methyl group or the substitution of four smaller residues by larger ones to make better contact with a primer unit or diketide. Mutagenesis of a conserved glutamine in a KS within a model triketide synthase indicates that the substrate tunnel is sensitive to alteration and that engineering this KS to accept unnatural substrates may require several mutations.
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Affiliation(s)
- Melissa Hirsch
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Brendan J. Fitzgerald
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Adrian T. Keatinge-Clay
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
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18
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Miyazawa T, Fitzgerald BJ, Keatinge-Clay AT. Preparative production of an enantiomeric pair by engineered polyketide synthases. Chem Commun (Camb) 2021; 57:8762-8765. [PMID: 34378565 DOI: 10.1039/d1cc03073f] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Using the updated module boundary of polyketide assembly lines, modules from the pikromycin synthase were recombined into engineered synthases that furnish an enantiomeric pair of 2-stereocenter triketide lactones at >99% ee with yields up to 0.39 g per liter of E. coli K207-3 in shake flasks.
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Affiliation(s)
- Takeshi Miyazawa
- Department of Molecular Biosciences, The University of Texas at Austin, 100 E. 24th St., Austin, TX 78712, USA.
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19
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Fage CD, Kosol S, Jenner M, Öster C, Gallo A, Kaniusaite M, Steinbach R, Staniforth M, Stavros VG, Marahiel MA, Cryle MJ, Lewandowski JR. Communication Breakdown: Dissecting the COM Interfaces between the Subunits of Nonribosomal Peptide Synthetases. ACS Catal 2021. [DOI: 10.1021/acscatal.1c02113] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Christopher D. Fage
- Department of Chemistry/Biochemistry, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry CV4 7AL, U.K
| | - Simone Kosol
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry CV4 7AL, U.K
| | - Matthew Jenner
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry CV4 7AL, U.K
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, U.K
| | - Carl Öster
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry CV4 7AL, U.K
| | - Angelo Gallo
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry CV4 7AL, U.K
| | - Milda Kaniusaite
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- EMBL Australia, Monash University, Clayton, Victoria 3800, Australia
| | - Roman Steinbach
- Department of Chemistry/Biochemistry, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
| | - Michael Staniforth
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry CV4 7AL, U.K
| | - Vasilios G. Stavros
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry CV4 7AL, U.K
| | - Mohamed A. Marahiel
- Department of Chemistry/Biochemistry, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
| | - Max J. Cryle
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- EMBL Australia, Monash University, Clayton, Victoria 3800, Australia
| | - Józef R. Lewandowski
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry CV4 7AL, U.K
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20
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Bozhueyuek KAJ, Watzel J, Abbood N, Bode HB. Synthetic Zippers as an Enabling Tool for Engineering of Non-Ribosomal Peptide Synthetases*. Angew Chem Int Ed Engl 2021; 60:17531-17538. [PMID: 34015175 PMCID: PMC8362031 DOI: 10.1002/anie.202102859] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/31/2021] [Indexed: 12/29/2022]
Abstract
Non‐ribosomal peptide synthetases (NRPSs) are the origin of a wide range of natural products, including many clinically used drugs. Efficient engineering of these often giant biosynthetic machineries to produce novel non‐ribosomal peptides (NRPs) is an ongoing challenge. Here we describe a cloning and co‐expression strategy to functionally combine NRPS fragments of Gram‐negative and ‐positive origin, synthesising novel peptides at titres up to 220 mg L−1. Extending from the recently introduced definition of eXchange Units (XUs), we inserted synthetic zippers (SZs) to split single protein NRPSs into independently expressed and translated polypeptide chains. These synthetic type of NRPS (type S) enables easier access to engineering, overcomes cloning limitations, and provides a simple and rapid approach to building peptide libraries via the combination of different NRPS subunits.
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Affiliation(s)
- Kenan A J Bozhueyuek
- Molecular Biotechnology, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Jonas Watzel
- Molecular Biotechnology, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Nadya Abbood
- Molecular Biotechnology, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.,Max-Planck-Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043, Marburg, Germany
| | - Helge B Bode
- Molecular Biotechnology, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.,Max-Planck-Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043, Marburg, Germany.,Senckenberg Gesellschaft für Naturforschung, 60325, Frankfurt am Main, Germany
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21
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Bozhueyuek KAJ, Watzel J, Abbood N, Bode HB. Synthetic Zippers as an Enabling Tool for Engineering of Non‐Ribosomal Peptide Synthetases**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Kenan A. J. Bozhueyuek
- Molecular Biotechnology Institute of Molecular Biosciences Goethe University Frankfurt 60438 Frankfurt am Main Germany
| | - Jonas Watzel
- Molecular Biotechnology Institute of Molecular Biosciences Goethe University Frankfurt 60438 Frankfurt am Main Germany
| | - Nadya Abbood
- Molecular Biotechnology Institute of Molecular Biosciences Goethe University Frankfurt 60438 Frankfurt am Main Germany
- Max-Planck-Institute for Terrestrial Microbiology Department of Natural Products in Organismic Interactions 35043 Marburg Germany
| | - Helge B. Bode
- Molecular Biotechnology Institute of Molecular Biosciences Goethe University Frankfurt 60438 Frankfurt am Main Germany
- Max-Planck-Institute for Terrestrial Microbiology Department of Natural Products in Organismic Interactions 35043 Marburg Germany
- Senckenberg Gesellschaft für Naturforschung 60325 Frankfurt am Main Germany
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22
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Watzel J, Duchardt-Ferner E, Sarawi S, Bode HB, Wöhnert J. Cooperation between a T Domain and a Minimal C-Terminal Docking Domain to Enable Specific Assembly in a Multiprotein NRPS. Angew Chem Int Ed Engl 2021; 60:14171-14178. [PMID: 33876501 PMCID: PMC8251938 DOI: 10.1002/anie.202103498] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Indexed: 01/27/2023]
Abstract
Non-ribosomal peptide synthetases (NRPS) produce natural products from amino acid building blocks. They often consist of multiple polypeptide chains which assemble in a specific linear order via specialized N- and C-terminal docking domains (N/C DDs). Typically, docking domains function independently from other domains in NRPS assembly. Thus, docking domain replacements enable the assembly of "designer" NRPS from proteins that normally do not interact. The multiprotein "peptide-antimicrobial-Xenorhabdus" (PAX) peptide-producing PaxS NRPS is assembled from the three proteins PaxA, PaxB and PaxC. Herein, we show that the small C DD of PaxA cooperates with its preceding thiolation (T1 ) domain to bind the N DD of PaxB with very high affinity, establishing a structural and thermodynamical basis for this unprecedented docking interaction, and we test its functional importance in vivo in a truncated PaxS assembly line. Similar docking interactions are apparently present in other NRPS systems.
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Affiliation(s)
- Jonas Watzel
- Molecular Biotechnology, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Elke Duchardt-Ferner
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Sepas Sarawi
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.,Molecular Biotechnology, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Helge B Bode
- Department of Natural Products in Organismic Interactions, Max-Planck-Institute for Terrestrial Microbiology, 35043, Marburg, Germany.,Senckenberg Gesellschaft für Naturforschung, 60325, Frankfurt am Main, Germany.,Molecular Biotechnology, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Jens Wöhnert
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
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23
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Watzel J, Duchardt‐Ferner E, Sarawi S, Bode HB, Wöhnert J. Kooperation zwischen T‐Domäne und minimaler C‐terminaler Docking‐Domäne für funktionelle Proteininteraktionen in Multiprotein‐NRPS. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Jonas Watzel
- Molekulare Biotechnologie Institut für Molekulare Biowissenschaften Goethe-Universität Frankfurt 60438 Frankfurt am Main Deutschland
| | - Elke Duchardt‐Ferner
- Institut für Molekulare Biowissenschaften und Biomolekulares Magnetresonanz Zentrum (BMRZ) Goethe-Universität Frankfurt 60438 Frankfurt am Main Deutschland
| | - Sepas Sarawi
- Institut für Molekulare Biowissenschaften und Biomolekulares Magnetresonanz Zentrum (BMRZ) Goethe-Universität Frankfurt 60438 Frankfurt am Main Deutschland
- Molekulare Biotechnologie Institut für Molekulare Biowissenschaften Goethe-Universität Frankfurt 60438 Frankfurt am Main Deutschland
| | - Helge B. Bode
- Abteilung Naturstoffe in organismischen Interaktionen Max-Planck-Institut für terrestrische Mikrobiologie 35043 Marburg Deutschland
- Senckenberg Gesellschaft für Naturforschung 60325 Frankfurt am Main Deutschland
- Molekulare Biotechnologie Institut für Molekulare Biowissenschaften Goethe-Universität Frankfurt 60438 Frankfurt am Main Deutschland
| | - Jens Wöhnert
- Institut für Molekulare Biowissenschaften und Biomolekulares Magnetresonanz Zentrum (BMRZ) Goethe-Universität Frankfurt 60438 Frankfurt am Main Deutschland
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24
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Watzel J, Sarawi S, Duchardt-Ferner E, Bode HB, Wöhnert J. NMR resonance assignments for a docking domain pair with an attached thiolation domain from the PAX peptide-producing NRPS from Xenorhabdus cabanillasii. BIOMOLECULAR NMR ASSIGNMENTS 2021; 15:229-234. [PMID: 33675014 PMCID: PMC7973640 DOI: 10.1007/s12104-021-10010-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 02/16/2021] [Indexed: 05/09/2023]
Abstract
Non-ribosomal peptide synthetases (NRPSs) are large multienzyme machineries. They synthesize numerous important natural products starting from amino acids. For peptide synthesis functionally specialized NRPS modules interact in a defined manner. Individual modules are either located on a single or on multiple different polypeptide chains. The "peptide-antimicrobial-Xenorhabdus" (PAX) peptide producing NRPS PaxS from Xenorhabdus bacteria consists of the three proteins PaxA, PaxB and PaxC. Different docking domains (DDs) located at the N-termini of PaxB and PaxC and at the C-termini of PaxA and BaxB mediate specific non-covalent interactions between them. The N-terminal docking domains precede condensation domains while the C-terminal docking domains follow thiolation domains. The binding specificity of individual DDs is important for the correct assembly of multi-protein NRPS systems. In many multi-protein NRPS systems the docking domains are sufficient to mediate the necessary interactions between individual protein chains. However, it remains unclear if this is a general feature for all types of structurally different docking domains or if the neighboring domains in some cases support the function of the docking domains. Here, we report the 1H, 13C and 15 N NMR resonance assignments for a C-terminal di-domain construct containing a thiolation (T) domain followed by a C-terminal docking domain (CDD) from PaxA and for its binding partner - the N-terminal docking domain (NDD) from PaxB from the Gram-negative entomopathogenic bacterium Xenorhabdus cabanillasii JM26 in their free states and for a 1:1 complex formed by the two proteins. These NMR resonance assignments will facilitate further structural and dynamic studies of this protein complex.
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Affiliation(s)
- Jonas Watzel
- Molecular Biotechnology, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.
| | - Sepas Sarawi
- Molecular Biotechnology, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Elke Duchardt-Ferner
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Helge B Bode
- Molecular Biotechnology, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
- Senckenberg Gesellschaft Für Naturforschung, 60325, Frankfurt am Main, Germany
- Department of Natural Products in Organismic Interactions, Max-Planck-Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Jens Wöhnert
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.
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25
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Wang Y, Correa Marrero M, Medema MH, van Dijk ADJ. Coevolution-based prediction of protein-protein interactions in polyketide biosynthetic assembly lines. Bioinformatics 2021; 36:4846-4853. [PMID: 32592463 DOI: 10.1093/bioinformatics/btaa595] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 05/20/2020] [Accepted: 06/19/2020] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Polyketide synthases (PKSs) are enzymes that generate diverse molecules of great pharmaceutical importance, including a range of clinically used antimicrobials and antitumor agents. Many polyketides are synthesized by cis-AT modular PKSs, which are organized in assembly lines, in which multiple enzymes line up in a specific order. This order is defined by specific protein-protein interactions (PPIs). The unique modular structure and catalyzing mechanism of these assembly lines makes their products predictable and also spurred combinatorial biosynthesis studies to produce novel polyketides using synthetic biology. However, predicting the interactions of PKSs, and thereby inferring the order of their assembly line, is still challenging, especially for cases in which this order is not reflected by the ordering of the PKS-encoding genes in the genome. RESULTS Here, we introduce PKSpop, which uses a coevolution-based PPI algorithm to infer protein order in PKS assembly lines. Our method accurately predicts protein orders (93% accuracy). Additionally, we identify new residue pairs that are key in determining interaction specificity, and show that coevolution of N- and C-terminal docking domains of PKSs is significantly more predictive for PPIs than coevolution between ketosynthase and acyl carrier protein domains. AVAILABILITY AND IMPLEMENTATION The code is available on http://www.bif.wur.nl/ (under 'Software'). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | | | | | - Aalt D J van Dijk
- Bioinformatics Group.,Department of Plant Sciences Biometris, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
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26
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Smith HG, Beech MJ, Lewandowski JR, Challis GL, Jenner M. Docking domain-mediated subunit interactions in natural product megasynth(et)ases. J Ind Microbiol Biotechnol 2021; 48:6152290. [PMID: 33640957 PMCID: PMC9113145 DOI: 10.1093/jimb/kuab018] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 02/24/2021] [Indexed: 12/19/2022]
Abstract
Polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) multienzymes produce numerous high value metabolites. The protein subunits which constitute these megasynth(et)ases must undergo ordered self-assembly to ensure correct organisation of catalytic domains for the biosynthesis of a given natural product. Short amino acid regions at the N- and C-termini of each subunit, termed docking domains (DDs), often occur in complementary pairs, which interact to facilitate substrate transfer and maintain pathway fidelity. This review details all structurally characterised examples of NRPS and PKS DDs to date and summarises efforts to utilise DDs for the engineering of biosynthetic pathways.
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Affiliation(s)
- Helen G Smith
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Matthew J Beech
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | | | - Gregory L Challis
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, UK
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, VIC 3800, Australia
| | - Matthew Jenner
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, UK
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Sulpizio A, Crawford CEW, Koweek RS, Charkoudian LK. Probing the structure and function of acyl carrier proteins to unlock the strategic redesign of type II polyketide biosynthetic pathways. J Biol Chem 2021; 296:100328. [PMID: 33493513 PMCID: PMC7949117 DOI: 10.1016/j.jbc.2021.100328] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 02/04/2023] Open
Abstract
Type II polyketide synthases (PKSs) are protein assemblies, encoded by biosynthetic gene clusters in microorganisms, that manufacture structurally complex and pharmacologically relevant molecules. Acyl carrier proteins (ACPs) play a central role in biosynthesis by shuttling malonyl-based building blocks and polyketide intermediates to catalytic partners for chemical transformations. Because ACPs serve as central hubs in type II PKSs, they can also represent roadblocks to successfully engineering synthases capable of manufacturing 'unnatural natural products.' Therefore, understanding ACP conformational dynamics and protein interactions is essential to enable the strategic redesign of type II PKSs. However, the inherent flexibility and transience of ACP interactions pose challenges to gaining insight into ACP structure and function. In this review, we summarize how the application of chemical probes and molecular dynamic simulations has increased our understanding of the structure and function of type II PKS ACPs. We also share how integrating these advances in type II PKS ACP research with newfound access to key enzyme partners, such as the ketosynthase-chain length factor, sets the stage to unlock new biosynthetic potential.
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Affiliation(s)
- Ariana Sulpizio
- Department of Chemistry, Haverford College, Haverford, Pennsylvania, USA
| | | | - Rebecca S Koweek
- Department of Chemistry, Haverford College, Haverford, Pennsylvania, USA
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Drufva EE, Spengler NR, Hix EG, Bailey CB. Site-Directed Mutagenesis of Modular Polyketide Synthase Ketoreductase Domains for Altered Stereochemical Control. Chembiochem 2020; 22:1122-1150. [PMID: 33185924 DOI: 10.1002/cbic.202000613] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/12/2020] [Indexed: 12/18/2022]
Abstract
Bacterial modular type I polyketide synthases (PKSs) are complex multidomain assembly line proteins that produce a range of pharmaceutically relevant molecules with a high degree of stereochemical control. Due to their colinear properties, they have been considerable targets for rational biosynthetic pathway engineering. Among the domains harbored within these complex assembly lines, ketoreductase (KR) domains have been extensively studied with the goal of altering their stereoselectivity by site-directed mutagenesis, as they confer much of the stereochemical complexity present in pharmaceutically active reduced polyketide scaffolds. Here we review all efforts to date to perform site-directed mutagenesis on PKS KRs, most of which have been done in the context of excised KR domains on model diffusible substrates such as β-keto N-acetyl cysteamine thioesters. We also discuss the challenges around translating the findings of these studies to alter stereocontrol in the context of a complex multidomain enzymatic assembly line.
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Affiliation(s)
- Erin E Drufva
- Department of Chemistry, University of Tennessee, Knoxville, Knoxville, TN 37996, USA
| | - Nolan R Spengler
- Department of Chemistry, University of Tennessee, Knoxville, Knoxville, TN 37996, USA
| | - Elijah G Hix
- Department of Chemistry, University of Tennessee, Knoxville, Knoxville, TN 37996, USA
| | - Constance B Bailey
- Department of Chemistry, University of Tennessee, Knoxville, Knoxville, TN 37996, USA
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29
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Risser F, Collin S, Dos Santos-Morais R, Gruez A, Chagot B, Weissman KJ. Towards improved understanding of intersubunit interactions in modular polyketide biosynthesis: Docking in the enacyloxin IIa polyketide synthase. J Struct Biol 2020; 212:107581. [DOI: 10.1016/j.jsb.2020.107581] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 07/14/2020] [Accepted: 07/16/2020] [Indexed: 12/26/2022]
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30
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Klaus M, Buyachuihan L, Grininger M. Ketosynthase Domain Constrains the Design of Polyketide Synthases. ACS Chem Biol 2020; 15:2422-2432. [PMID: 32786257 DOI: 10.1021/acschembio.0c00405] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Modular polyketide synthases (PKSs) produce complex, bioactive secondary metabolites in assembly line-like multistep reactions. Longstanding efforts to produce novel, biologically active compounds by recombining intact modules to new modular PKSs have mostly resulted in poorly active chimeras and decreased product yields. Recent findings demonstrate that the low efficiencies of modular chimeric PKSs also result from rate limitations in the transfer of the growing polyketide chain across the noncognate module:module interface and further processing of the non-native polyketide substrate by the ketosynthase (KS) domain. In this study, we aim at disclosing and understanding the low efficiency of chimeric modular PKSs and at establishing guidelines for modular PKSs engineering. To do so, we work with a bimodular PKS testbed and systematically vary substrate specificity, substrate identity, and domain:domain interfaces of the KS involved reactions. We observe that KS domains employed in our chimeric bimodular PKSs are bottlenecks with regards to both substrate specificity as well as interaction with the acyl carrier protein (ACP). Overall, our systematic study can explain in quantitative terms why early oversimplified engineering strategies based on the plain shuffling of modules mostly failed and why more recent approaches show improved success rates. We moreover identify two mutations of the KS domain that significantly increased turnover rates in chimeric systems and interpret this finding in mechanistic detail.
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Affiliation(s)
- Maja Klaus
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany
| | - Lynn Buyachuihan
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany
| | - Martin Grininger
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main 60438, Germany
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31
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Drufva EE, Hix EG, Bailey CB. Site directed mutagenesis as a precision tool to enable synthetic biology with engineered modular polyketide synthases. Synth Syst Biotechnol 2020; 5:62-80. [PMID: 32637664 PMCID: PMC7327777 DOI: 10.1016/j.synbio.2020.04.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/01/2020] [Accepted: 04/06/2020] [Indexed: 12/04/2022] Open
Abstract
Modular polyketide synthases (PKSs) are a multidomain megasynthase class of biosynthetic enzymes that have great promise for the development of new compounds, from new pharmaceuticals to high value commodity and specialty chemicals. Their colinear biosynthetic logic has been viewed as a promising platform for synthetic biology for decades. Due to this colinearity, domain swapping has long been used as a strategy to introduce molecular diversity. However, domain swapping often fails because it perturbs critical protein-protein interactions within the PKS. With our increased level of structural elucidation of PKSs, using judicious targeted mutations of individual residues is a more precise way to introduce molecular diversity with less potential for global disruption of the protein architecture. Here we review examples of targeted point mutagenesis to one or a few residues harbored within the PKS that alter domain specificity or selectivity, affect protein stability and interdomain communication, and promote more complex catalytic reactivity.
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Key Words
- ACP, acyl carrier protein
- AT, acyltransferase
- DEBS, 6-deoxyerthronolide B synthase
- DH, dehydratase
- EI, enoylisomerase
- ER, enoylreductase
- KR, ketoreductase
- KS, ketosynthase
- LM, loading module
- MT, methyltransferase
- Mod, module
- PKS, polyketide synthase
- PS, pyran synthase
- Polyketide synthase
- Protein engineering
- Rational design
- SNAC, N-acetyl cysteamine
- Saturation mutagenesis
- Site directed mutagenesis
- Synthetic biology
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Affiliation(s)
- Erin E. Drufva
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN, 37996, USA
| | - Elijah G. Hix
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN, 37996, USA
| | - Constance B. Bailey
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN, 37996, USA
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32
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Hwang S, Lee N, Cho S, Palsson B, Cho BK. Repurposing Modular Polyketide Synthases and Non-ribosomal Peptide Synthetases for Novel Chemical Biosynthesis. Front Mol Biosci 2020; 7:87. [PMID: 32500080 PMCID: PMC7242659 DOI: 10.3389/fmolb.2020.00087] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 04/16/2020] [Indexed: 12/16/2022] Open
Abstract
In nature, various enzymes govern diverse biochemical reactions through their specific three-dimensional structures, which have been harnessed to produce many useful bioactive compounds including clinical agents and commodity chemicals. Polyketide synthases (PKSs) and non-ribosomal peptide synthetases (NRPSs) are particularly unique multifunctional enzymes that display modular organization. Individual modules incorporate their own specific substrates and collaborate to assemble complex polyketides or non-ribosomal polypeptides in a linear fashion. Due to the modular properties of PKSs and NRPSs, they have been attractive rational engineering targets for novel chemical production through the predictable modification of each moiety of the complex chemical through engineering of the cognate module. Thus, individual reactions of each module could be separated as a retro-biosynthetic biopart and repurposed to new biosynthetic pathways for the production of biofuels or commodity chemicals. Despite these potentials, repurposing attempts have often failed owing to impaired catalytic activity or the production of unintended products due to incompatible protein–protein interactions between the modules and structural perturbation of the enzyme. Recent advances in the structural, computational, and synthetic tools provide more opportunities for successful repurposing. In this review, we focused on the representative strategies and examples for the repurposing of modular PKSs and NRPSs, along with their advantages and current limitations. Thereafter, synthetic biology tools and perspectives were suggested for potential further advancement, including the rational and large-scale high-throughput approaches. Ultimately, the potential diverse reactions from modular PKSs and NRPSs would be leveraged to expand the reservoir of useful chemicals.
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Affiliation(s)
- Soonkyu Hwang
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Namil Lee
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Suhyung Cho
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Bernhard Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States.,Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States.,The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Byung-Kwan Cho
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,Intelligent Synthetic Biology Center, Daejeon, South Korea
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33
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Watzel J, Hacker C, Duchardt-Ferner E, Bode HB, Wöhnert J. A New Docking Domain Type in the Peptide-Antimicrobial-Xenorhabdus Peptide Producing Nonribosomal Peptide Synthetase from Xenorhabdus bovienii. ACS Chem Biol 2020; 15:982-989. [DOI: 10.1021/acschembio.9b01022] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jonas Watzel
- Molecular Biotechnology, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Carolin Hacker
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Elke Duchardt-Ferner
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Helge B. Bode
- Molecular Biotechnology, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
- Senckenberg Gesellschaft für Naturforschung, 60325 Frankfurt am Main, Germany
| | - Jens Wöhnert
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
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34
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An in vitro platform for engineering and harnessing modular polyketide synthases. Nat Commun 2020; 11:80. [PMID: 31900404 PMCID: PMC6941969 DOI: 10.1038/s41467-019-13811-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 11/21/2019] [Indexed: 11/15/2022] Open
Abstract
To harness the synthetic power of modular polyketide synthases (PKSs), many aspects of their biochemistry must be elucidated. A robust platform to study these megadalton assembly lines has not yet been described. Here, we in vitro reconstitute the venemycin PKS, a short assembly line that generates an aromatic product. Incubating its polypeptides, VemG and VemH, with 3,5-dihydroxybenzoic acid, ATP, malonate, coenzyme A, and the malonyl-CoA ligase MatB, venemycin production can be monitored by HPLC and NMR. Multi-milligram quantities of venemycin are isolable from dialysis-based reactors without chromatography, and the enzymes can be recycled. Assembly line engineering is performed using pikromycin modules, with synthases designed using the updated module boundaries outperforming those using the traditional module boundaries by over an order of magnitude. Using combinations of VemG, VemH, and their engineered derivatives, as well as the alternate starter unit 3-hydroxybenzoic acid, a combinatorial library of six polyketide products is readily accessed. A robust platform to study modular polyketide synthases (PKSs) in vitro is still unavailable. Here, the authors report the reconstitution of the venemycin PKS, engineer hybrid venemycin/pikromycin PKSs, and obtain much improved yields through employing the updated module boundaries.
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35
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Emulating evolutionary processes to morph aureothin-type modular polyketide synthases and associated oxygenases. Nat Commun 2019; 10:3918. [PMID: 31477708 PMCID: PMC6718629 DOI: 10.1038/s41467-019-11896-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 08/12/2019] [Indexed: 12/17/2022] Open
Abstract
Polyketides produced by modular type I polyketide synthases (PKSs) play eminent roles in the development of medicines. Yet, the production of structural analogs by genetic engineering poses a major challenge. We report an evolution-guided morphing of modular PKSs inspired by recombination processes that lead to structural diversity in nature. By deletion and insertion of PKS modules we interconvert the assembly lines for related antibiotic and antifungal agents, aureothin (aur) and neoaureothin (nor) (aka spectinabilin), in both directions. Mutational and functional analyses of the polyketide-tailoring cytochrome P450 monooxygenases, and PKS phylogenies give contradictory clues on potential evolutionary scenarios (generalist-to-specialist enzyme evolution vs. most parsimonious ancestor). The KS-AT linker proves to be well suited as fusion site for both excision and insertion of modules, which supports a model for alternative module boundaries in some PKS systems. This study teaches important lessons on the evolution of PKSs, which may guide future engineering approaches. The wealth of complex polyketides is an essential source for drug discovery. Here, the authors report an evolution-guided rational morphing of modular polyketide synthases (PKSs) for aurothin and neoaurothin biosynthesis, and reveal engineering site suitable for diversifying PKS systems.
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36
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Kosol S, Jenner M, Lewandowski JR, Challis GL. Protein-protein interactions in trans-AT polyketide synthases. Nat Prod Rep 2019; 35:1097-1109. [PMID: 30280735 DOI: 10.1039/c8np00066b] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: up to 2018 The construction of polyketide natural products by type I modular polyketide synthases (PKSs) requires the coordinated action of several protein subunits to ensure biosynthetic fidelity. This is particularly the case for trans-AT PKSs, which in contrast to most cis-AT PKSs, contain split modules and employ several trans-acting catalytic domains. This article summarises recent advances in understanding the protein-protein interactions underpinning subunit assembly and intra-subunit communication in such systems and highlights potential avenues and approaches for future research.
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Affiliation(s)
- Simone Kosol
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
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37
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Feng Y, Yu Z, Zhang S, Xue Z, Huang J, Zhang H, Wan X, Chen A, Wang J. Isolation and Characterization of New 16-Membered Macrolides from the aveA3 Gene Replacement Mutant Strain Streptomyces avermitilis TM24 with Acaricidal and Nematicidal Activities. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:4782-4792. [PMID: 30973721 DOI: 10.1021/acs.jafc.9b00079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Polyketides represent an important class of biologically active and structurally diverse compounds found in nature. They are biosynthesized from acyl CoA precursors by polyketide synthases (PKSs). The use of combinatorial biosynthesis to form hybrid PKSs is considered to be an excellent approach for the development of novel polyketides. Here, 10 new 16-membered macrolide compounds were isolated from the broth of the genetically engineered strain Streptomyces avermitilis TM24, in which the PKS gene aveA3 was seamlessly replaced by the milbemycin PKS gene milA3. Their structures were elucidated on the basis of NMR and MS spectroscopic analyses. The acaricidal and nematicidal activities of them against Tetranychus cinnabarinus and Bursaphelenchus xylophilus were tested. The results indicated that compound 1 had potent acaricidal activity against adult mites with an LC50 value of 0.0022 mg L-1, while compounds 5 and 7 possessed potent nematicidal activity with LC50 values of 4.56 and 4.30 mg L-1, respectively.
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Affiliation(s)
- Youling Feng
- Provincial Joint Engineering Laboratory of Biopesticide Preparation, School of Forestry & Biotechnology , Zhejiang Agricultural and Forestry University , Lin'An 311300 , People's Republic of China
| | - Zhen Yu
- Zhejiang Key Laboratory of Antifungal Drugs , Zhejiang Hisun Pharmaceutical Co., Ltd. , Taizhou 318000 , People's Republic of China
| | - Shaoyong Zhang
- Zhejiang Key Laboratory of Antifungal Drugs , Zhejiang Hisun Pharmaceutical Co., Ltd. , Taizhou 318000 , People's Republic of China
| | - Zhenglian Xue
- College of Biochemical Engineering , Anhui Polytechnic University , Wuhu 241000 , People's Republic of China
| | - Jun Huang
- Zhejiang Key Laboratory of Antifungal Drugs , Zhejiang Hisun Pharmaceutical Co., Ltd. , Taizhou 318000 , People's Republic of China
- Zhejiang Makohs Biotech Co., Ltd. , Taizhou 318000 , People's Republic of China
| | - Hui Zhang
- Zhejiang Key Laboratory of Antifungal Drugs , Zhejiang Hisun Pharmaceutical Co., Ltd. , Taizhou 318000 , People's Republic of China
| | - Xu Wan
- Provincial Joint Engineering Laboratory of Biopesticide Preparation, School of Forestry & Biotechnology , Zhejiang Agricultural and Forestry University , Lin'An 311300 , People's Republic of China
| | - Anliang Chen
- Provincial Joint Engineering Laboratory of Biopesticide Preparation, School of Forestry & Biotechnology , Zhejiang Agricultural and Forestry University , Lin'An 311300 , People's Republic of China
| | - Jidong Wang
- Zhejiang Key Laboratory of Antifungal Drugs , Zhejiang Hisun Pharmaceutical Co., Ltd. , Taizhou 318000 , People's Republic of China
- College of Biochemical Engineering , Anhui Polytechnic University , Wuhu 241000 , People's Republic of China
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38
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Lin GM, Warden-Rothman R, Voigt CA. Retrosynthetic design of metabolic pathways to chemicals not found in nature. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.coisb.2019.04.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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39
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Klaus M, D’Souza AD, Nivina A, Khosla C, Grininger M. Engineering of Chimeric Polyketide Synthases Using SYNZIP Docking Domains. ACS Chem Biol 2019; 14:426-433. [PMID: 30682239 DOI: 10.1021/acschembio.8b01060] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Engineering of assembly line polyketide synthases (PKSs) to produce novel bioactive compounds has been a goal for over 20 years. The apparent modularity of PKSs has inspired many engineering attempts in which entire modules or single domains were exchanged. In recent years, it has become evident that certain domain-domain interactions are evolutionarily optimized and, if disrupted, cause a decrease of the overall turnover rate of the chimeric PKS. In this study, we compared different types of chimeric PKSs in order to define the least invasive interface and to expand the toolbox for PKS engineering. We generated bimodular chimeric PKSs in which entire modules were exchanged, while either retaining a covalent linker between heterologous modules or introducing a noncovalent docking domain, or SYNZIP domain, mediated interface. These chimeric systems exhibited non-native domain-domain interactions during intermodular polyketide chain translocation. They were compared to otherwise equivalent bimodular PKSs in which a noncovalent interface was introduced between the condensing and processing parts of a module, resulting in non-native domain interactions during the extender unit acylation and polyketide chain elongation steps of their catalytic cycles. We show that the natural PKS docking domains can be efficiently substituted with SYNZIP domains and that the newly introduced noncovalent interface between the condensing and processing parts of a module can be harnessed for PKS engineering. Additionally, we established SYNZIP domains as a new tool for engineering PKSs by efficiently bridging non-native interfaces without perturbing PKS activity.
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Affiliation(s)
- Maja Klaus
- 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
- Departments of Chemistry and Chemical Engineering and Stanford ChEM-H, Stanford University, Stanford, California 94305, United States
| | - Alicia D. D’Souza
- Departments of Chemistry and Chemical Engineering and Stanford ChEM-H, Stanford University, Stanford, California 94305, United States
| | - Aleksandra Nivina
- Departments of Chemistry and Chemical Engineering and Stanford ChEM-H, Stanford University, Stanford, California 94305, United States
| | - Chaitan Khosla
- Departments of Chemistry and Chemical Engineering and Stanford ChEM-H, Stanford University, Stanford, California 94305, United States
| | - 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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40
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Hacker C, Cai X, Kegler C, Zhao L, Weickhmann AK, Wurm JP, Bode HB, Wöhnert J. Structure-based redesign of docking domain interactions modulates the product spectrum of a rhabdopeptide-synthesizing NRPS. Nat Commun 2018; 9:4366. [PMID: 30341296 PMCID: PMC6195595 DOI: 10.1038/s41467-018-06712-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 09/21/2018] [Indexed: 12/18/2022] Open
Abstract
Several peptides in clinical use are derived from non-ribosomal peptide synthetases (NRPS). In these systems multiple NRPS subunits interact with each other in a specific linear order mediated by specific docking domains (DDs), whose structures are not known yet, to synthesize well-defined peptide products. In contrast to classical NRPSs, single-module NRPS subunits responsible for the generation of rhabdopeptide/xenortide-like peptides (RXPs) can act in different order depending on subunit stoichiometry thereby producing peptide libraries. To define the basis for their unusual interaction patterns, we determine the structures of all N-terminal DDs (NDDs) as well as of an NDD-CDD complex and characterize all putative DD interactions thermodynamically for such a system. Key amino acid residues for DD interactions are identified that upon their exchange change the DD affinity and result in predictable changes in peptide production. Recognition rules for DD interactions are identified that also operate in other megasynthase complexes. Rhabdopeptides are synthesized by non-ribosomal peptide synthetases (NRPSs) and the multiple NRPS subunits interact through docking domains (DD). Here the authors provide insights into DD interaction patterns and present the structures of three N-terminal docking domains (NDD) and a NDD-CDD complex and derive a set of recognition rules for DD interactions.
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Affiliation(s)
- Carolin Hacker
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Xiaofeng Cai
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Carsten Kegler
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Lei Zhao
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - A Katharina Weickhmann
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Jan Philip Wurm
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.,Institute of Biophysics and Physical Biochemistry, University of Regensburg, 93053, Regensburg, Germany
| | - Helge B Bode
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany. .,Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.
| | - Jens Wöhnert
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.
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41
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Dodge GJ, Maloney FP, Smith JL. Protein-protein interactions in "cis-AT" polyketide synthases. Nat Prod Rep 2018; 35:1082-1096. [PMID: 30188553 PMCID: PMC6207950 DOI: 10.1039/c8np00058a] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: up to the end of 2018 Polyketides are a valuable source of bioactive and clinically important molecules. The biosynthesis of these chemically complex molecules has led to the discovery of equally complex polyketide synthase (PKS) pathways. Crystallography has yielded snapshots of individual catalytic domains, di-domains, and multi-domains from a variety of PKS megasynthases, and cryo-EM studies have provided initial views of a PKS module in a series of defined biochemical states. Here, we review the structural and biochemical results that shed light on the protein-protein interactions critical to catalysis by PKS systems with an embedded acyltransferase. Interactions include those that occur both within and between PKS modules, as well as with accessory enzymes.
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Affiliation(s)
- Greg J Dodge
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA 48109.
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42
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Abstract
Covering: up to mid of 2018 Type I fatty acid synthases (FASs) are giant multienzymes catalyzing all steps of the biosynthesis of fatty acids from acetyl- and malonyl-CoA by iterative precursor extension. Two strikingly different architectures of FAS evolved in yeast (as well as in other fungi and some bacteria) and metazoans. Yeast-type FAS (yFAS) assembles into a barrel-shaped structure of more than 2 MDa molecular weight. Catalytic domains of yFAS are embedded in an extensive scaffolding matrix and arranged around two enclosed reaction chambers. Metazoan FAS (mFAS) is a 540 kDa X-shaped dimer, with lateral reaction clefts, minimal scaffolding and pronounced conformational variability. All naturally occurring yFAS are strictly specialized for the production of saturated fatty acids. The yFAS architecture is not used for the biosynthesis of any other secondary metabolite. On the contrary, mFAS is related at the domain organization level to major classes of polyketide synthases (PKSs). PKSs produce a variety of complex and potent secondary metabolites; they either act iteratively (iPKS), or are linked via directed substrate transfer into modular assembly lines (modPKSs). Here, we review the architectures of yFAS, mFAS, and iPKSs. We rationalize the evolution of the yFAS assembly, and provide examples for re-engineering of yFAS. Recent studies have provided novel insights into the organization of iPKS. A hybrid crystallographic model of a mycocerosic acid synthase-like Pks5 yielded a comprehensive visualization of the organization and dynamics of fully-reducing iPKS. Deconstruction experiments, structural and functional studies of specialized enzymatic domains, such as the product template (PT) and the starter-unit acyltransferase (SAT) domain have revealed functional principles of non-reducing iterative PKS (NR-PKSs). Most recently, a six-domain loading region of an NR-PKS has been visualized at high-resolution together with cryo-EM studies of a trapped loading intermediate. Altogether, these data reveal the related, yet divergent architectures of mFAS, iPKS and also modPKSs. The new insights highlight extensive dynamics, and conformational coupling as key features of mFAS and iPKS and are an important step towards collection of a comprehensive series of snapshots of PKS action.
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Affiliation(s)
- Dominik A Herbst
- Department Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland.
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43
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Skiba MA, Maloney FP, Dan Q, Fraley AE, Aldrich CC, Smith JL, Brown WC. PKS-NRPS Enzymology and Structural Biology: Considerations in Protein Production. Methods Enzymol 2018; 604:45-88. [PMID: 29779664 PMCID: PMC5992914 DOI: 10.1016/bs.mie.2018.01.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The structural diversity and complexity of marine natural products have made them a rich and productive source of new bioactive molecules for drug development. The identification of these new compounds has led to extensive study of the protein constituents of the biosynthetic pathways from the producing microbes. Essential processes in the dissection of biosynthesis have been the elucidation of catalytic functions and the determination of 3D structures for enzymes of the polyketide synthases and nonribosomal peptide synthetases that carry out individual reactions. The size and complexity of these proteins present numerous difficulties in the process of going from gene to structure. Here, we review the problems that may be encountered at the various steps of this process and discuss some of the solutions devised in our and other labs for the cloning, production, purification, and structure solution of complex proteins using Escherichia coli as a heterologous host.
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Affiliation(s)
| | | | - Qingyun Dan
- University of Michigan, Ann Arbor, MI, United States
| | - Amy E Fraley
- University of Michigan, Ann Arbor, MI, United States
| | | | - Janet L Smith
- University of Michigan, Ann Arbor, MI, United States.
| | - W Clay Brown
- University of Michigan, Ann Arbor, MI, United States.
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44
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Jenner M, Kosol S, Griffiths D, Prasongpholchai P, Manzi L, Barrow AS, Moses JE, Oldham NJ, Lewandowski JR, Challis GL. Mechanism of intersubunit ketosynthase-dehydratase interaction in polyketide synthases. Nat Chem Biol 2018; 14:270-275. [PMID: 29309054 PMCID: PMC5846730 DOI: 10.1038/nchembio.2549] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 11/15/2017] [Indexed: 12/16/2022]
Abstract
Modular polyketide synthases (PKSs) produce numerous structurally complex natural products that have diverse applications in medicine and agriculture. PKSs typically consist of several multienzyme subunits that utilize structurally defined docking domains (DDs) at their N and C termini to ensure correct assembly into functional multiprotein complexes. Here we report a fundamentally different mechanism for subunit assembly in trans-acyltransferase (trans-AT) modular PKSs at the junction between ketosynthase (KS) and dehydratase (DH) domains. This mechanism involves direct interaction of a largely unstructured docking domain (DD) at the C terminus of the KS with the surface of the downstream DH. Acyl transfer assays and mechanism-based crosslinking established that the DD is required for the KS to communicate with the acyl carrier protein appended to the DH. Two distinct regions for binding of the DD to the DH were identified using NMR spectroscopy, carbene footprinting, and mutagenesis, providing a foundation for future elucidation of the molecular basis for interaction specificity.
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Affiliation(s)
- Matthew Jenner
- Department of Chemistry and Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, UK
| | - Simone Kosol
- Department of Chemistry and Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, UK
| | - Daniel Griffiths
- Department of Chemistry and Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, UK
| | - Panward Prasongpholchai
- Department of Chemistry and Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, UK
| | - Lucio Manzi
- School of Chemistry, University of Nottingham, Nottingham NG7 2RD, UK
| | - Andrew S. Barrow
- School of Chemistry, University of Nottingham, Nottingham NG7 2RD, UK
| | - John E. Moses
- School of Chemistry, University of Nottingham, Nottingham NG7 2RD, UK
| | - Neil J. Oldham
- School of Chemistry, University of Nottingham, Nottingham NG7 2RD, UK
| | - Józef R. Lewandowski
- Department of Chemistry and Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, UK
| | - Gregory L. Challis
- Department of Chemistry and Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, UK
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45
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Identification of a biosynthetic gene cluster for the polyene macrolactam sceliphrolactam in a Streptomyces strain isolated from mangrove sediment. Sci Rep 2018; 8:1594. [PMID: 29371699 PMCID: PMC5785472 DOI: 10.1038/s41598-018-20018-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 01/11/2018] [Indexed: 11/25/2022] Open
Abstract
Streptomyces are a genus of Actinobacteria capable of producing structurally diverse natural products. Here we report the isolation and characterization of a biosynthetically talented Streptomyces (Streptomyces sp. SD85) from tropical mangrove sediments. Whole-genome sequencing revealed that Streptomyces sp. SD85 harbors at least 52 biosynthetic gene clusters (BGCs), which constitute 21.2% of the 8.6-Mb genome. When cultivated under lab conditions, Streptomyces sp. SD85 produces sceliphrolactam, a 26-membered polyene macrolactam with unknown biosynthetic origin. Genome mining yielded a putative sceliphrolactam BGC (sce) that encodes a type I modular polyketide synthase (PKS) system, several β-amino acid starter biosynthetic enzymes, transporters, and transcriptional regulators. Using the CRISPR/Cas9–based gene knockout method, we demonstrated that the sce BGC is essential for sceliphrolactam biosynthesis. Unexpectedly, the PKS system encoded by sce is short of one module required for assembling the 26-membered macrolactam skeleton according to the collinearity rule. With experimental data disfavoring the involvement of a trans-PKS module, the biosynthesis of sceliphrolactam seems to be best rationalized by invoking a mechanism whereby the PKS system employs an iterative module to catalyze two successive chain extensions with different outcomes. The potential violation of the collinearity rule makes the mechanism distinct from those of other polyene macrolactams.
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46
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Miyanaga A, Kudo F, Eguchi T. Protein–protein interactions in polyketide synthase–nonribosomal peptide synthetase hybrid assembly lines. Nat Prod Rep 2018; 35:1185-1209. [DOI: 10.1039/c8np00022k] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The protein–protein interactions in polyketide synthase–nonribosomal peptide synthetase hybrids are summarized and discussed.
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Affiliation(s)
- Akimasa Miyanaga
- Department of Chemistry
- Tokyo Institute of Technology
- Tokyo 152-8551
- Japan
| | - Fumitaka Kudo
- Department of Chemistry
- Tokyo Institute of Technology
- Tokyo 152-8551
- Japan
| | - Tadashi Eguchi
- Department of Chemistry
- Tokyo Institute of Technology
- Tokyo 152-8551
- Japan
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47
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Klaus M, Grininger M. Engineering strategies for rational polyketide synthase design. Nat Prod Rep 2018; 35:1070-1081. [DOI: 10.1039/c8np00030a] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
In this review, we highlight strategies in engineering polyketide synthases (PKSs). We focus on important protein–protein interactions that constitute an intact PKS assembly line.
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Affiliation(s)
- Maja Klaus
- Institute of Organic Chemistry and Chemical Biology
- Buchmann Institute for Molecular Life Sciences
- Cluster of Excellence for Macromolecular Complexes
- Goethe University Frankfurt
- 60438 Frankfurt am Main
| | - Martin Grininger
- Institute of Organic Chemistry and Chemical Biology
- Buchmann Institute for Molecular Life Sciences
- Cluster of Excellence for Macromolecular Complexes
- Goethe University Frankfurt
- 60438 Frankfurt am Main
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48
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Cai W, Zhang W. Engineering modular polyketide synthases for production of biofuels and industrial chemicals. Curr Opin Biotechnol 2017; 50:32-38. [PMID: 28946011 DOI: 10.1016/j.copbio.2017.08.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 08/30/2017] [Accepted: 08/31/2017] [Indexed: 10/18/2022]
Abstract
Polyketide synthases (PKSs) are one of the most profound biosynthetic factories for producing polyketides with diverse structures and biological activities. These enzymes have been historically studied and engineered to make un-natural polyketides for drug discovery, and have also recently been explored for synthesizing biofuels and industrial chemicals due to their versatility and customizability. Here, we review recent advances in the mechanistic understanding and engineering of modular PKSs for producing polyketide-derived chemicals, and provide perspectives on this relatively new application of PKSs.
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Affiliation(s)
- Wenlong Cai
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA 94720, United States
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA 94720, United States; Chan Zuckerberg Biohub, San Francisco, CA 94158, United States.
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49
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Barajas JF, Blake-Hedges JM, Bailey CB, Curran S, Keasling JD. Engineered polyketides: Synergy between protein and host level engineering. Synth Syst Biotechnol 2017; 2:147-166. [PMID: 29318196 PMCID: PMC5655351 DOI: 10.1016/j.synbio.2017.08.005] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 08/26/2017] [Accepted: 08/26/2017] [Indexed: 01/01/2023] Open
Abstract
Metabolic engineering efforts toward rewiring metabolism of cells to produce new compounds often require the utilization of non-native enzymatic machinery that is capable of producing a broad range of chemical functionalities. Polyketides encompass one of the largest classes of chemically diverse natural products. With thousands of known polyketides, modular polyketide synthases (PKSs) share a particularly attractive biosynthetic logic for generating chemical diversity. The engineering of modular PKSs could open access to the deliberate production of both existing and novel compounds. In this review, we discuss PKS engineering efforts applied at both the protein and cellular level for the generation of a diverse range of chemical structures, and we examine future applications of PKSs in the production of medicines, fuels and other industrially relevant chemicals.
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Key Words
- ACP, Acyl carrier protein
- AT, Acyltransferase
- CoL, CoA-Ligase
- Commodity chemical
- DE, Dimerization element
- DEBS, 6-deoxyerythronolide B synthase
- DH, Dehydratase
- ER, Enoylreductase
- FAS, Fatty acid synthases
- KR, Ketoreductase
- KS, Ketosynthase
- LM, Loading module
- LTTR, LysR-type transcriptional regulator
- Metabolic engineering
- Natural products
- PCC, Propionyl-CoA carboxylase
- PDB, Precursor directed biosynthesis
- PK, Polyketide
- PKS, Polyketide synthase
- Polyketide
- Polyketide synthase
- R, Reductase domain
- SARP, Streptomyces antibiotic regulatory protein
- SNAC, N-acetylcysteamine
- Synthetic biology
- TE, Thioesterase
- TKL, Triketide lactone
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Affiliation(s)
| | | | - Constance B. Bailey
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Samuel Curran
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Comparative Biochemistry Graduate Group, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jay. D. Keasling
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- QB3 Institute, University of California, Berkeley, Emeryville, CA 94608, USA
- Department of Chemical & Biomolecular Engineering, Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University Denmark, DK2970 Horsholm, Denmark
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50
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Lowell AN, DeMars MD, Slocum ST, Yu F, Anand K, Chemler JA, Korakavi N, Priessnitz JK, Park SR, Koch AA, Schultz PJ, Sherman DH. Chemoenzymatic Total Synthesis and Structural Diversification of Tylactone-Based Macrolide Antibiotics through Late-Stage Polyketide Assembly, Tailoring, and C-H Functionalization. J Am Chem Soc 2017; 139:7913-7920. [PMID: 28525276 PMCID: PMC5532807 DOI: 10.1021/jacs.7b02875] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Polyketide synthases (PKSs) represent a powerful catalytic platform capable of effecting multiple carbon-carbon bond forming reactions and oxidation state adjustments. We explored the functionality of two terminal PKS modules that produce the 16-membered tylosin macrocycle, using them as biocatalysts in the chemoenzymatic synthesis of tylactone and its subsequent elaboration to complete the first total synthesis of the juvenimicin, M-4365, and rosamicin classes of macrolide antibiotics via late-stage diversification. Synthetic chemistry was employed to generate the tylactone hexaketide chain elongation intermediate that was accepted by the juvenimicin (Juv) ketosynthase of the penultimate JuvEIV PKS module. The hexaketide is processed through two complete modules (JuvEIV and JuvEV) in vitro, which catalyze elongation and functionalization of two ketide units followed by cyclization of the resulting octaketide into tylactone. After macrolactonization, a combination of in vivo glycosylation, selective in vitro cytochrome P450-mediated oxidation, and chemical oxidation was used to complete the scalable construction of a series of macrolide natural products in as few as 15 linear steps (21 total) with an overall yield of 4.6%.
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Affiliation(s)
- Andrew N. Lowell
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Matthew D. DeMars
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Samuel T. Slocum
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Fengan Yu
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Krithika Anand
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Joseph A. Chemler
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Nisha Korakavi
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jennifer K. Priessnitz
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Sung Ryeol Park
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Aaron A. Koch
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Pamela J. Schultz
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - David H. Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan 48109, United States
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