1
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Huang S, Ji H, Zheng J. Structural and computational insights into the substrate specificity of acyltransferase domains from modular polyketide synthases. FEBS J 2024. [PMID: 38922792 DOI: 10.1111/febs.17206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/19/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024]
Abstract
Polyketides are natural products synthesized by polyketide synthases (PKSs), where acyltransferase (AT) domains play a crucial role in selection of extender units. Engineering of AT domains enables the site-specific incorporation of non-natural extender units, leading to generation of novel derivatives. Here, we determined the crystal structures of AT domains from the fifth module of tylosin PKS (TylAT5) derived from Streptomyces fradiae and the eighth module of spinosad PKS (SpnAT8) derived from Saccharopolyspora spinosa, and combined them with molecular dynamics simulations and enzyme kinetic studies to elucidate the molecular basis of substrate selection. The ethylmalonyl-CoA-specific conserved motif TAGH of TylAT5 and the MMCoA-specific conserved motif YASH of SpnAT8 were identified within the substrate-binding pocket, and several key residues close to the substrate acyl moiety were located. Through site-directed mutagenesis of four residues near the active site, we successfully reprogrammed the specificity of these two AT domains toward malonyl-CoA. Mutations in TylAT5 enhanced its catalytic activity 2.6-fold toward malonyl-CoA, and mutations in SpnAT8 eliminated the substrate promiscuity. These results extend our understanding of AT substrate specificity and would benefit the engineering of PKSs.
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Affiliation(s)
- Shuxin Huang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, China
| | - Huining Ji
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, China
| | - Jianting Zheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, China
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2
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Liao Y, Wang XJ, Ma GL, Candra H, Qiu En SL, Khandelwal S, Liang ZX. Biosynthesis of Octacosamicin A: Uncommon Starter/extender Units and Product Releasing via Intermolecular Amidation. Chembiochem 2024; 25:e202300590. [PMID: 37908177 DOI: 10.1002/cbic.202300590] [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: 08/22/2023] [Revised: 10/28/2023] [Accepted: 10/31/2023] [Indexed: 11/02/2023]
Abstract
Octacosamicin A is an antifungal metabolite featuring a linear polyene-polyol chain flanked by N-hydroxyguanidine and glycine moieties. We report here that sub-inhibitory concentrations of streptomycin elicited the production of octacosamicin A in Amycolatopsis azurea DSM 43854T . We identified the biosynthetic gene cluster (oca BGC) that encodes a modular polyketide synthase (PKS) system for assembling the polyene-polyol chain of octacosamicin A. Our analysis suggested that the N-hydroxyguanidine unit originates from a 4-guanidinobutyryl-CoA starter unit, while the PKS incorporates an α-hydroxyketone moiety using a (2R)-hydroxymalonyl-CoA extender unit. The modular PKS system contains a non-canonical terminal module that lacks thioesterase (TE) and acyl carrier protein (ACP) domains, indicating the biosynthesis is likely to employ an unconventional and cryptic off-loading mechanism that attaches glycine to the polyene-polyol chain via an intermolecular amidation reaction.
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Affiliation(s)
- Yanghui Liao
- School of Biological Sciences, Nanyang Technological University, Singapore, 67551, Singapore
| | - Xue-Jiao Wang
- School of Biological Sciences, Nanyang Technological University, Singapore, 67551, Singapore
| | - Guang-Lei Ma
- Future Health Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314102, China
| | - Hartono Candra
- School of Biological Sciences, Nanyang Technological University, Singapore, 67551, Singapore
| | - Sean Lee Qiu En
- School of Biological Sciences, Nanyang Technological University, Singapore, 67551, Singapore
| | - Srashti Khandelwal
- School of Biological Sciences, Nanyang Technological University, Singapore, 67551, Singapore
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, Singapore, 67551, Singapore
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3
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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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4
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D’Ambrosio HK, Ganley JG, Keeler AM, Derbyshire ER. A single amino acid residue controls acyltransferase activity in a polyketide synthase from Toxoplasma gondii. iScience 2022; 25:104443. [PMID: 35874921 PMCID: PMC9301873 DOI: 10.1016/j.isci.2022.104443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 04/12/2022] [Accepted: 05/16/2022] [Indexed: 11/17/2022] Open
Abstract
Type I polyketide synthases (PKSs) are multidomain, multimodule enzymes capable of producing complex polyketide metabolites. These modules contain an acyltransferase (AT) domain, which selects acyl-CoA substrates to be incorporated into the metabolite scaffold. Herein, we reveal the sequences of three AT domains from a polyketide synthase (TgPKS2) from the apicomplexan parasite Toxoplasma gondii. Phylogenic analysis indicates these ATs (AT1, AT2, and AT3) are distinct from domains in well-characterized microbial biosynthetic gene clusters. Biochemical investigations revealed that AT1 and AT2 hydrolyze malonyl-CoA but the terminal AT3 domain is non-functional. We further identify an "on-off switch" residue that controls activity such that a single amino acid change in AT3 confers hydrolysis activity while the analogous mutation in AT2 eliminates activity. This biochemical analysis of AT domains from an apicomplexan PKS lays the foundation for further molecular and structural studies on PKSs from T. gondii and other protists.
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Affiliation(s)
- Hannah K. D’Ambrosio
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708, USA
| | - Jack G. Ganley
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708, USA
| | - Aaron M. Keeler
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708, USA
| | - Emily R. Derbyshire
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708, USA
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, 213 Research Drive, Durham, NC 27710, USA
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5
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Interfacial plasticity facilitates high reaction rate of E. coli FAS malonyl-CoA:ACP transacylase, FabD. Proc Natl Acad Sci U S A 2020; 117:24224-24233. [PMID: 32929027 DOI: 10.1073/pnas.2009805117] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fatty acid synthases (FASs) and polyketide synthases (PKSs) iteratively elongate and often reduce two-carbon ketide units in de novo fatty acid and polyketide biosynthesis. Cycles of chain extensions in FAS and PKS are initiated by an acyltransferase (AT), which loads monomer units onto acyl carrier proteins (ACPs), small, flexible proteins that shuttle covalently linked intermediates between catalytic partners. Formation of productive ACP-AT interactions is required for catalysis and specificity within primary and secondary FAS and PKS pathways. Here, we use the Escherichia coli FAS AT, FabD, and its cognate ACP, AcpP, to interrogate type II FAS ACP-AT interactions. We utilize a covalent crosslinking probe to trap transient interactions between AcpP and FabD to elucidate the X-ray crystal structure of a type II ACP-AT complex. Our structural data are supported using a combination of mutational, crosslinking, and kinetic analyses, and long-timescale molecular dynamics (MD) simulations. Together, these complementary approaches reveal key catalytic features of FAS ACP-AT interactions. These mechanistic inferences suggest that AcpP adopts multiple, productive conformations at the AT binding interface, allowing the complex to sustain high transacylation rates. Furthermore, MD simulations support rigid body subdomain motions within the FabD structure that may play a key role in AT activity and substrate selectivity.
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6
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Davis TD, Michaud JM, Burkart MD. Active site labeling of fatty acid and polyketide acyl-carrier protein transacylases. Org Biomol Chem 2020; 17:4720-4724. [PMID: 31044196 DOI: 10.1039/c8ob03229g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Metabolic engineering of fatty acids and polyketides remains challenging due to unresolved protein-protein interactions that are essential to synthase activity. While several chemical probes have been developed to capture and visualize protein interfaces in these systems, acyl carrier protein (ACP) transacylase (AT) domains remain elusive. Herein, we combine a mutational strategy with fluorescent probe design to expedite the study of AT domains from fatty acid and polyketide synthases. We describe the design and evaluation of inhibitor-inspired and substrate-mimetic reporters containing sulfonyl fluoride and β-lactone warheads. Moreover, specific active-site labeling occurs by optimizing pH, time, and probe concentration, and selective labeling is achieved in the presence of inhibitors of competing domains. These findings provide a panel of AT-targeting probes and set the stage for future combinatorial biosynthetic and drug discovery initiatives.
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Affiliation(s)
- Tony D Davis
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA.
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7
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Zhang F, Ji H, Ali I, Deng Z, Bai L, Zheng J. Structural and Biochemical Insight into the Recruitment of Acyl Carrier Protein-Linked Extender Units in Ansamitocin Biosynthesis. Chembiochem 2020; 21:1309-1314. [PMID: 31777147 DOI: 10.1002/cbic.201900628] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Indexed: 01/17/2023]
Abstract
A few acyltransferase (AT) domains of modular polyketide synthases (PKSs) recruit acyl carrier protein (ACP)-linked extender units with unusual C2 substituents to confer functionalities that are not available in coenzyme A (CoA)-linked ones. In this study, an AT specific for methoxymalonyl (MOM)-ACP in the third module of the ansamitocin PKS was structurally and biochemically characterized. The AT uses a conserved tryptophan residue at the entrance of the substrate binding tunnel to discriminate between different carriers. A W275R mutation switches its carrier specificity from the ACP to the CoA molecule. The acyl-AT complex structures clearly show that the MOM-ACP accepted by the AT has the 2S instead of the opposite 2R stereochemistry that is predicted according to the biosynthetic derivation from a d-glycolytic intermediate. Together, these results reveal the structural basis of ATs recognizing ACP-linked extender units in polyketide biosynthesis.
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Affiliation(s)
- Fa Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, 200240, Shanghai, P. R. China
| | - Huining Ji
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, 200240, Shanghai, P. R. China
| | - Imtiaz Ali
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, 200240, Shanghai, P. R. China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, 200240, Shanghai, P. R. China
| | - Linquan Bai
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, 200240, Shanghai, P. R. China
| | - Jianting Zheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, 200240, Shanghai, P. R. China
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8
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Zhang W, Zhou L, Li C, Deng Z, Qu X. Rational engineering acyltransferase domain of modular polyketide synthase for expanding substrate specificity. Methods Enzymol 2019; 622:271-292. [DOI: 10.1016/bs.mie.2019.02.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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9
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Carpenter SM, Williams GJ. Extender Unit Promiscuity and Orthogonal Protein Interactions of an Aminomalonyl-ACP Utilizing Trans-Acyltransferase from Zwittermicin Biosynthesis. ACS Chem Biol 2018; 13:3361-3373. [PMID: 30484625 DOI: 10.1021/acschembio.8b00867] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Trans-acting acyltransferases (trans-ATs) are standalone enzymes that select and deliver extender units to polyketide synthase assembly lines. Accordingly, there is interest in leveraging trans-ATs as tools to regioselectively diversify polyketide structures. Yet, little is known regarding the extender unit and acyl carrier protein (ACP) specificity of trans-ATs, particularly those that utilize unusual ACP-linked extender units. For example, the biosynthesis of the antibiotic zwittermicin involves the trans-AT ZmaF, which is responsible for installing a rare ACP-linked aminomalonyl extender unit. Here, we developed a method to access a panel of non-natural and non-native ACP-linked extender units and used it to probe the promiscuity of ZmaF, revealing one of the most promiscuous ATs characterized to date. Furthermore, we demonstrated that ZmaF is highly orthogonal with respect to its ACP specificity, and the ability of ZmaF to trans-complement noncognate PKS modules was also explored. Together, these results set the stage for further engineering ZmaF as a tool for polyketide diversification.
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Affiliation(s)
- Samantha M. Carpenter
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, United States
| | - Gavin J. Williams
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, United States
- Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina 27695-8204, United States
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10
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Musiol-Kroll EM, Wohlleben W. Acyltransferases as Tools for Polyketide Synthase Engineering. Antibiotics (Basel) 2018; 7:antibiotics7030062. [PMID: 30022008 PMCID: PMC6164871 DOI: 10.3390/antibiotics7030062] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 07/14/2018] [Accepted: 07/16/2018] [Indexed: 12/16/2022] Open
Abstract
Polyketides belong to the most valuable natural products, including diverse bioactive compounds, such as antibiotics, anticancer drugs, antifungal agents, immunosuppressants and others. Their structures are assembled by polyketide synthases (PKSs). Modular PKSs are composed of modules, which involve sets of domains catalysing the stepwise polyketide biosynthesis. The acyltransferase (AT) domains and their “partners”, the acyl carrier proteins (ACPs), thereby play an essential role. The AT loads the building blocks onto the “substrate acceptor”, the ACP. Thus, the AT dictates which building blocks are incorporated into the polyketide structure. The precursor- and occasionally the ACP-specificity of the ATs differ across the polyketide pathways and therefore, the ATs contribute to the structural diversity within this group of complex natural products. Those features make the AT enzymes one of the most promising tools for manipulation of polyketide assembly lines and generation of new polyketide compounds. However, the AT-based PKS engineering is still not straightforward and thus, rational design of functional PKSs requires detailed understanding of the complex machineries. This review summarizes the attempts of PKS engineering by exploiting the AT attributes for the modification of polyketide structures. The article includes 253 references and covers the most relevant literature published until May 2018.
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Affiliation(s)
- Ewa Maria Musiol-Kroll
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.
| | - Wolfgang Wohlleben
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.
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11
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Li Y, Zhang W, Zhang H, Tian W, Wu L, Wang S, Zheng M, Zhang J, Sun C, Deng Z, Sun Y, Qu X, Zhou J. Structural Basis of a Broadly Selective Acyltransferase from the Polyketide Synthase of Splenocin. Angew Chem Int Ed Engl 2018. [PMID: 29536601 DOI: 10.1002/anie.201802805] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Polyketides are a large family of pharmaceutically important natural products, and the structural modification of their scaffolds is significant for drug development. Herein, we report high-resolution X-ray crystal structures of the broadly selective acyltransferase (AT) from the splenocin polyketide synthase (SpnD-AT) in the apo form and in complex with benzylmalonyl and pentynylmalonyl extender unit mimics. These structures revealed the molecular basis for the stereoselectivity and substrate specificity of SpnD-AT, and enabled the engineering of the industrially important Ery-AT6 to broaden its substrate scope to include three new types of extender units.
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Affiliation(s)
- Yuan Li
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road., Wuhan, 430071, China
| | - Wan Zhang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road., Wuhan, 430071, China
| | - Hui Zhang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road., Wuhan, 430071, China
| | - Wenya Tian
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road., Wuhan, 430071, China
| | - Lian Wu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry and Pharmacy, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, Shaanxi, China
| | - Shuwen Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road., Wuhan, 430071, China
| | - Mengmeng Zheng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road., Wuhan, 430071, China
| | - Jinru Zhang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry and Pharmacy, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, Shaanxi, China
| | - Chenghai Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road., Wuhan, 430071, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road., Wuhan, 430071, China
| | - Yuhui Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road., Wuhan, 430071, China
| | - Xudong Qu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road., Wuhan, 430071, China
| | - Jiahai Zhou
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry and Pharmacy, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, Shaanxi, China
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12
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Li Y, Zhang W, Zhang H, Tian W, Wu L, Wang S, Zheng M, Zhang J, Sun C, Deng Z, Sun Y, Qu X, Zhou J. Structural Basis of a Broadly Selective Acyltransferase from the Polyketide Synthase of Splenocin. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201802805] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Yuan Li
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University); Ministry of Education; Wuhan University School of Pharmaceutical Sciences; 185 Donghu Road. Wuhan 430071 China
| | - Wan Zhang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University); Ministry of Education; Wuhan University School of Pharmaceutical Sciences; 185 Donghu Road. Wuhan 430071 China
| | - Hui Zhang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University); Ministry of Education; Wuhan University School of Pharmaceutical Sciences; 185 Donghu Road. Wuhan 430071 China
| | - Wenya Tian
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University); Ministry of Education; Wuhan University School of Pharmaceutical Sciences; 185 Donghu Road. Wuhan 430071 China
| | - Lian Wu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
- Shaanxi Key Laboratory of Natural Products & Chemical Biology; College of Chemistry and Pharmacy; Northwest A&F University; 3 Taicheng Road, Yangling 712100 Shaanxi China
| | - Shuwen Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University); Ministry of Education; Wuhan University School of Pharmaceutical Sciences; 185 Donghu Road. Wuhan 430071 China
| | - Mengmeng Zheng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University); Ministry of Education; Wuhan University School of Pharmaceutical Sciences; 185 Donghu Road. Wuhan 430071 China
| | - Jinru Zhang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
- Shaanxi Key Laboratory of Natural Products & Chemical Biology; College of Chemistry and Pharmacy; Northwest A&F University; 3 Taicheng Road, Yangling 712100 Shaanxi China
| | - Chenghai Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University); Ministry of Education; Wuhan University School of Pharmaceutical Sciences; 185 Donghu Road. Wuhan 430071 China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University); Ministry of Education; Wuhan University School of Pharmaceutical Sciences; 185 Donghu Road. Wuhan 430071 China
| | - Yuhui Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University); Ministry of Education; Wuhan University School of Pharmaceutical Sciences; 185 Donghu Road. Wuhan 430071 China
| | - Xudong Qu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University); Ministry of Education; Wuhan University School of Pharmaceutical Sciences; 185 Donghu Road. Wuhan 430071 China
| | - Jiahai Zhou
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
- Shaanxi Key Laboratory of Natural Products & Chemical Biology; College of Chemistry and Pharmacy; Northwest A&F University; 3 Taicheng Road, Yangling 712100 Shaanxi China
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13
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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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14
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Miyanaga A. Structure and function of polyketide biosynthetic enzymes: various strategies for production of structurally diverse polyketides. Biosci Biotechnol Biochem 2017; 81:2227-2236. [DOI: 10.1080/09168451.2017.1391687] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Abstract
Polyketides constitute a large family of natural products that display various biological activities. Polyketides exhibit a high degree of structural diversity, although they are synthesized from simple acyl building blocks. Recent biochemical and structural studies provide a better understanding of the biosynthetic logic of polyketide diversity. This review highlights the biosynthetic mechanisms of structurally unique polyketides, β-amino acid-containing macrolactams, enterocin, and phenolic lipids. Functional and structural studies of macrolactam biosynthetic enzymes have revealed the unique biosynthetic machinery used for selective incorporation of a rare β-amino acid starter unit into the polyketide skeleton. Biochemical and structural studies of cyclization enzymes involved in the biosynthesis of enterocin and phenolic lipids provide mechanistic insights into how these enzymes diversify the carbon skeletons of their products.
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Affiliation(s)
- Akimasa Miyanaga
- Department of Chemistry, Tokyo Institute of Technology, Tokyo, Japan
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15
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Harunari E, Komaki H, Igarashi Y. Biosynthetic origin of butyrolactol A, an antifungal polyketide produced by a marine-derived Streptomyces. Beilstein J Org Chem 2017; 13:441-450. [PMID: 28382182 PMCID: PMC5355916 DOI: 10.3762/bjoc.13.47] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 02/20/2017] [Indexed: 11/23/2022] Open
Abstract
Butyrolactol A is an antifungal polyketide of Streptomyces bearing an uncommon tert-butyl starter unit and a polyol system in which eight hydroxy/acyloxy carbons are contiguously connected. Except for its congener butyrolactol B, there exist no structurally related natural products to date. In this study, inspired by our previous genomic analysis, incorporation of 13C- and 2H-labeled precursors into butyrolactol A was investigated. Based on the labeling pattern and sequencing analytical data, we confirmed that the tert-butyl group is derived from valine and its C-methylation with methionine and the polyol carbons are derived from a glycolysis intermediate, possibly hydroxymalonyl-ACP.
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Affiliation(s)
- Enjuro Harunari
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Hisayuki Komaki
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Yasuhiro Igarashi
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
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16
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Weissman KJ. Polyketide stereocontrol: a study in chemical biology. Beilstein J Org Chem 2017; 13:348-371. [PMID: 28326145 PMCID: PMC5331325 DOI: 10.3762/bjoc.13.39] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 02/01/2017] [Indexed: 11/23/2022] Open
Abstract
The biosynthesis of reduced polyketides in bacteria by modular polyketide synthases (PKSs) proceeds with exquisite stereocontrol. As the stereochemistry is intimately linked to the strong bioactivity of these molecules, the origins of stereochemical control are of significant interest in attempts to create derivatives of these compounds by genetic engineering. In this review, we discuss the current state of knowledge regarding this key aspect of the biosynthetic pathways. Given that much of this information has been obtained using chemical biology tools, work in this area serves as a showcase for the power of this approach to provide answers to fundamental biological questions.
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Affiliation(s)
- Kira J Weissman
- UMR 7365, Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), CNRS-Université de Lorraine, Biopôle de l’Université de Lorraine, Campus Biologie Santé, Avenue de la Forêt de Haye, BP 50184, 54505 Vandœuvre-lès-Nancy Cedex, France
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17
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Abstract
Polyketides are a diverse group of natural products that form the basis of many important drugs. The engineering of the polyketide synthase (PKS) enzymes responsible for the formation of these compounds has long been considered to have great potential for producing new bioactive molecules. Recent advances in this field have contributed to the understanding of this powerful and complex enzymatic machinery, particularly with regard to domain activity and engineering, unique building block formation and incorporation, and programming rules and limitations. New developments in tools for
in vitro biochemical analysis, full-length megasynthase structural studies, and
in vivo heterologous expression will continue to improve our fundamental understanding of polyketide synthesis as well as our ability to engineer the production of polyketides.
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Affiliation(s)
- Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA
| | - Joyce Liu
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA
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18
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Abstract
This highlight provides an overview of recent advances in understanding the diversity of polyketide synthase (PKS) substrate building blocks. Substrates functioning as starter units and extender units contribute significantly to the chemical complexity and structural diversity exhibited by this class of natural products. This article complements and extends upon the current comprehensive reviews that have been published on these two topics (Moore and Hertweck, Nat. Prod. Rep., 2002, 19, 70; Chan et al., Nat. Prod. Rep., 2009, 1, 90; Wilson and Moore, Nat. Prod. Rep., 2012, 29, 72).
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Affiliation(s)
- Lauren Ray
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093-0204, USA.
| | - Bradley S Moore
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093-0204, USA. and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California 92093-0204, USA
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19
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Structure-based analysis of the molecular interactions between acyltransferase and acyl carrier protein in vicenistatin biosynthesis. Proc Natl Acad Sci U S A 2016; 113:1802-7. [PMID: 26831085 DOI: 10.1073/pnas.1520042113] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Acyltransferases (ATs) are key determinants of building block specificity in polyketide biosynthesis. Despite the importance of protein-protein interactions between AT and acyl carrier protein (ACP) during the acyltransfer reaction, the mechanism of ACP recognition by AT is not understood in detail. Herein, we report the crystal structure of AT VinK, which transfers a dipeptide group between two ACPs, VinL and VinP1LdACP, in vicenistatin biosynthesis. The isolated VinK structure showed a unique substrate-binding pocket for the dipeptide group linked to ACP. To gain greater insight into the mechanism of ACP recognition, we attempted to crystallize the VinK-ACP complexes. Because transient enzyme-ACP complexes are difficult to crystallize, we developed a covalent cross-linking strategy using a bifunctional maleimide reagent to trap the VinK-ACP complexes, allowing the determination of the crystal structure of the VinK-VinL complex. In the complex structure, Arg-153, Met-206, and Arg-299 of VinK interact with the negatively charged helix II region of VinL. The VinK-VinL complex structure allows, to our knowledge, the first visualization of the interaction between AT and ACP and provides detailed mechanistic insights into ACP recognition by AT.
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20
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Abstract
Polyketides are a structurally and functionally diverse family of bioactive natural products that have found widespread application as pharmaceuticals, agrochemicals, and veterinary medicines. In bacteria complex polyketides are biosynthesized by giant multifunctional megaenzymes, termed modular polyketide synthases (PKSs), which construct their products in a highly coordinated assembly line-like fashion from a pool of simple precursor substrates. Not only is the multifaceted enzymology of PKSs a fascinating target for study, but it also presents considerable opportunities for the reengineering of these systems affording access to functionally optimized unnatural natural products. Here we provide an introductory primer to modular polyketide synthase structure and function, and highlight recent advances in the characterization and exploitation of these systems.
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Affiliation(s)
- Marisa Till
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol, BS8 1TD, UK
- BrisSynBio Synthetic Biology Research Centre, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Paul R Race
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol, BS8 1TD, UK
- BrisSynBio Synthetic Biology Research Centre, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, UK
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21
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Winter JM, Cascio D, Dietrich D, Sato M, Watanabe K, Sawaya MR, Vederas JC, Tang Y. Biochemical and Structural Basis for Controlling Chemical Modularity in Fungal Polyketide Biosynthesis. J Am Chem Soc 2015; 137:9885-93. [PMID: 26172141 DOI: 10.1021/jacs.5b04520] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Modular collaboration between iterative fungal polyketide synthases (IPKSs) is an important mechanism for generating structural diversity of polyketide natural products. Inter-PKS communication and substrate channeling are controlled in large by the starter unit acyl carrier protein transacylase (SAT) domain found in the accepting IPKS module. Here, we reconstituted the modular biosynthesis of the benzaldehyde core of the chaetoviridin and chaetomugilin azaphilone natural products using the IPKSs CazF and CazM. Our studies revealed a critical role of CazM's SAT domain in selectively transferring a highly reduced triketide product from CazF. In contrast, a more oxidized triketide that is also produced by CazF and required in later stages of biosynthesis of the final product is not recognized by the SAT domain. The structural basis for the acyl unit selectivity was uncovered by the first X-ray structure of a fungal SAT domain, highlighted by a covalent hexanoyl thioester intermediate in the SAT active site. The crystal structure of SAT domain will enable protein engineering efforts aimed at mixing and matching different IPKS modules for the biosynthesis of new compounds.
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Affiliation(s)
- Jaclyn M Winter
- †Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90095, United States
| | - Duilio Cascio
- §Department of Energy (DOE) Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095, United States
| | - David Dietrich
- ∥Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Michio Sato
- ⊥Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Kenji Watanabe
- ⊥Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Michael R Sawaya
- §Department of Energy (DOE) Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095, United States
| | - John C Vederas
- ∥Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Yi Tang
- †Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90095, United States.,‡Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
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22
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Architecture of the polyketide synthase module: surprises from electron cryo-microscopy. Curr Opin Struct Biol 2015; 31:9-19. [PMID: 25791608 DOI: 10.1016/j.sbi.2015.02.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 02/18/2015] [Accepted: 02/23/2015] [Indexed: 01/16/2023]
Abstract
Modular polyketide synthases (PKS) produce a vast array of bioactive molecules that are the basis of many highly valued pharmaceuticals. The biosynthesis of these compounds is based on ordered assembly lines of multi-domain modules, each extending and modifying a specific chain-elongation intermediate before transfer to the next module for further processing. The first 3D structures of a full polyketide synthase module in different functional states were obtained recently by electron cryo-microscopy. The unexpected module architecture revealed a striking evolutionary divergence of the polyketide synthase compared to its metazoan fatty acid synthase homolog, as well as remarkable conformational rearrangements dependent on its biochemical state during the full catalytic cycle. The design and dynamics of the module are highly optimized for both catalysis and fidelity in the construction of complex, biologically active natural products.
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