1
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Fage CD, Passmore M, Tatman BP, Smith HG, Jian X, Dissanayake UC, Andrés Cisneros G, Challis GL, Lewandowski JR, Jenner M. Molecular basis for short-chain thioester hydrolysis by acyl hydrolase domains in trans -acyltransferase polyketide synthases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.11.552765. [PMID: 37609184 PMCID: PMC10441421 DOI: 10.1101/2023.08.11.552765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Polyketide synthases (PKSs) are multi-domain enzymatic assembly lines that biosynthesise a wide selection of bioactive natural products from simple building blocks. In contrast to their cis -acyltransferase (AT) counterparts, trans -AT PKSs rely on stand-alone AT domains to load extender units onto acyl carrier protein (ACP) domains embedded in the core PKS machinery. Trans -AT PKS gene clusters also encode acyl hydrolase (AH) domains, which are predicted to share the overall fold of AT domains, but hydrolyse aberrant acyl chains from ACP domains, thus ensuring efficient polyketide biosynthesis. How such domains specifically target short acyl chains, in particular acetyl groups, tethered as thioesters to the substrate-shuttling ACP domains, with hydrolytic rather than acyl transfer activity, has remained unclear. To answer these questions, we solved the first structure of an AH domain and performed structure-guided activity assays on active site variants. Our results offer key insights into chain length control and selection against coenzyme A-tethered substrates, and clarify how the interaction interface between AH and ACP domains contributes to recognition of cognate and non-cognate ACP domains. Combining our experimental findings with molecular dynamics simulations allowed for the production of a data-driven model of an AH:ACP domain complex. Our results advance the currently incomplete understanding of polyketide biosynthesis by trans -AT PKSs, and provide foundations for future bioengineering efforts.
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2
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Kudo F, Kishikawa K, Tsuboi K, Kido T, Usui T, Hashimoto J, Shin-Ya K, Miyanaga A, Eguchi T. Acyltransferase Domain Exchange between Two Independent Type I Polyketide Synthases in the Same Producer Strain of Macrolide Antibiotics. Chembiochem 2023; 24:e202200670. [PMID: 36602093 DOI: 10.1002/cbic.202200670] [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: 11/16/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 01/06/2023]
Abstract
Streptomyces graminofaciens A-8890 produces two macrolide antibiotics, FD-891 and virustomycin A, both of which show significant biological activity. In this study, we identified the virustomycin A biosynthetic gene cluster, which encodes type I polyketide synthases (PKSs), ethylmalonyl-CoA biosynthetic enzymes, methoxymalony-acyl carrier protein biosynthetic enzymes, and post-PKS modification enzymes. Next, we demonstrated that the acyltransferase domain can be exchanged between the Vsm PKSs and the PKSs involved in FD-891 biosynthesis (Gfs PKSs), without any supply problems of the unique extender units. We exchanged the malonyltransferase domain in the loading module of Gfs PKS with the ethylmalonyltransferase domain and the methoxymalonyltransferase domain of Vsm PKSs. Consequently, the expected two-carbon-elongated analog 26-ethyl-FD-891 was successfully produced with a titer comparable to FD-891 production by the wild type; however, exchange with the methoxymalonyltransferase domain did not produce any FD-891 analogs. Furthermore, 26-ethyl-FD-891 showed potent cytotoxic activity against HeLa cells, like natural FD-891.
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Affiliation(s)
- Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Meguro-ku, O-okayama, Tokyo, 152-8551, Japan
| | - Kosuke Kishikawa
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Meguro-ku, O-okayama, Tokyo, 152-8551, Japan
| | - Kazuma Tsuboi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Meguro-ku, O-okayama, Tokyo, 152-8551, Japan
| | - Takafusa Kido
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Meguro-ku, O-okayama, Tokyo, 152-8551, Japan
| | - Takeo Usui
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8572, Ibaraki, Japan
| | - Junko Hashimoto
- Japan Biological Informatics Consortium (JBIC), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Akimasa Miyanaga
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Meguro-ku, O-okayama, Tokyo, 152-8551, Japan
| | - Tadashi Eguchi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Meguro-ku, O-okayama, Tokyo, 152-8551, Japan
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3
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Wang J, Wang X, Li X, Kong L, Du Z, Li D, Gou L, Wu H, Cao W, Wang X, Lin S, Shi T, Deng Z, Wang Z, Liang J. C-N bond formation by a polyketide synthase. Nat Commun 2023; 14:1319. [PMID: 36899013 PMCID: PMC10006239 DOI: 10.1038/s41467-023-36989-w] [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: 06/15/2022] [Accepted: 02/28/2023] [Indexed: 03/12/2023] Open
Abstract
Assembly-line polyketide synthases (PKSs) are molecular factories that produce diverse metabolites with wide-ranging biological activities. PKSs usually work by constructing and modifying the polyketide backbone successively. Here, we present the cryo-EM structure of CalA3, a chain release PKS module without an ACP domain, and its structures with amidation or hydrolysis products. The domain organization reveals a unique "∞"-shaped dimeric architecture with five connected domains. The catalytic region tightly contacts the structural region, resulting in two stabilized chambers with nearly perfect symmetry while the N-terminal docking domain is flexible. The structures of the ketosynthase (KS) domain illustrate how the conserved key residues that canonically catalyze C-C bond formation can be tweaked to mediate C-N bond formation, revealing the engineering adaptability of assembly-line polyketide synthases for the production of novel pharmaceutical agents.
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Affiliation(s)
- Jialiang Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaojie Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,Department of Molecular Biology, Shanghai Jikaixing Biotech Inc., Shanghai, 200131, China
| | - Xixi Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - LiangLiang Kong
- National Facility for Protein Science in Shanghai, Chinese Academy of Sciences, Shanghai, 201204, China
| | - Zeqian Du
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Dandan Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Lixia Gou
- School of Life Science, North China University of Science and Technology, Tangshan, Hebei, China
| | - Hao Wu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Wei Cao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaozheng Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Ting Shi
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Zhijun Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Jingdan Liang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
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4
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Feng Y, Zhang F, Huang S, Deng Z, Bai L, Zheng J. Structural visualization of transient interactions between the cis-acting acyltransferase and acyl carrier protein of the salinomycin modular polyketide synthase. ACTA CRYSTALLOGRAPHICA SECTION D STRUCTURAL BIOLOGY 2022; 78:779-791. [DOI: 10.1107/s2059798322004612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 05/02/2022] [Indexed: 11/10/2022]
Abstract
Transient protein–protein interactions between cis-acting acyltransferase (AT) and acyl carrier protein (ACP) domains are critical for the catalysis and processivity of modular polyketide synthases (mPKSs), but are challenging for structural characterization due to the intrinsically weak binding affinity. Here, a stable complex of cis-acting AT and ACP domains from the ninth module of the salinomycin mPKS was obtained using a maleimide cross-linker and the structure of the complex was determined at 2.6 Å resolution. The crystal structure shows that the AT in combination with the ketosynthase (KS)-to-AT linker forms a C-shaped architecture to embrace the ACP. The large hydrolase subdomain of the AT serves as a major binding platform for the ACP, while the small ferredoxin-like subdomain of the AT and the KS-to-AT linker cooperate with each other to constrain binding of the ACP. The importance of interface residues in cis-acting AT–ACP interactions was confirmed by mutagenesis assays. The interaction mode observed in the cis-acting AT–ACP complex is completely different from those observed in trans-acting AT–ACP complexes, where the ACP primarily contacts the small domain of the AT. The complex structure provides detailed mechanistic insights into AT–ACP recognition in cis-AT mPKSs.
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5
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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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6
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Passmore M, Gallo A, Lewandowski JR, Jenner M. Molecular basis for acyl carrier protein-ketoreductase interaction in trans-acyltransferase polyketide synthases. Chem Sci 2021; 12:13676-13685. [PMID: 34760152 PMCID: PMC8549798 DOI: 10.1039/d1sc03478b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 09/29/2021] [Indexed: 12/29/2022] Open
Abstract
The biosynthesis of polyketides by type I modular polyketide synthases (PKS) relies on co-ordinated interactions between acyl carrier protein (ACP) domains and catalytic domains within the megasynthase. Despite the importance of these interactions, and their implications for biosynthetic engineering efforts, they remain poorly understood. Here, we report the molecular details of the interaction interface between an ACP domain and a ketoreductase (KR) domain from a trans-acyltransferase (trans-AT) PKS. Using a high-throughput mass spectrometry (MS)-based assay in combination with scanning alanine mutagenesis, residues contributing to the KR-binding epitope of the ACP domain were identified. Application of carbene footprinting revealed the ACP-binding site on the KR domain surface, and molecular docking simulations driven by experimental data allowed production of an accurate model of the complex. Interactions between ACP and KR domains from trans-AT PKSs were found to be specific for their cognate partner, indicating highly optimised interaction interfaces driven by evolutionary processes. Using detailed knowledge of the ACP:KR interaction epitope, an ACP domain was engineered to interact with a non-cognate KR domain partner. The results provide novel, high resolution insights into the ACP:KR interface and offer valuable rules for future engineering efforts of biosynthetic assembly lines. The interaction epitope between a cognate KR–ACP domain pairing from a trans-AT polyketide synthase is elucidated in molecular detail, providing unique insights into recognition and specificity of the interface.![]()
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Affiliation(s)
- Munro Passmore
- Department of Chemistry, University of Warwick Coventry CV4 7AL UK
| | - Angelo Gallo
- Department of Chemistry, University of Warwick Coventry CV4 7AL UK
| | | | - Matthew Jenner
- Department of Chemistry, University of Warwick Coventry CV4 7AL UK .,Warwick Integrative Synthetic Biology Centre (WISB), University of Warwick Coventry CV4 7AL UK
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7
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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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8
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Sigrist R, Luhavaya H, McKinnie SMK, Ferreira da Silva A, Jurberg ID, Moore BS, Gonzaga de Oliveira L. Nonlinear Biosynthetic Assembly of Alpiniamide by a Hybrid cis/ trans-AT PKS-NRPS. ACS Chem Biol 2020; 15:1067-1077. [PMID: 32195572 DOI: 10.1021/acschembio.0c00081] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Alpiniamide A is a linear polyketide produced by Streptomyces endophytic bacteria. Despite its relatively simple chemical structure suggestive of a linear assembly line biosynthetic construction involving a hybrid polyketide synthase-nonribosomal peptide synthetase enzymatic protein machine, we report an unexpected nonlinear synthesis of this bacterial natural product. Using a combination of genomics, heterologous expression, mutagenesis, isotope-labeling, and chain terminator experiments, we propose that alpiniamide A is assembled in two halves and then ligated into the mature molecule. We show that each polyketide half is constructed using orthogonal biosynthetic strategies, employing either cis- or trans-acyl transferase mechanisms, thus prompting an alternative proposal for the operation of this PKS-NRPS.
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Affiliation(s)
- Renata Sigrist
- Department of Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, São Paulo 13083-970, Brazil
| | - Hanna Luhavaya
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Shaun M. K. McKinnie
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Amanda Ferreira da Silva
- Department of Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, São Paulo 13083-970, Brazil
| | - Igor D. Jurberg
- Department of Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, São Paulo 13083-970, Brazil
| | - Bradley S. Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Luciana Gonzaga de Oliveira
- Department of Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, São Paulo 13083-970, Brazil
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9
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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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10
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Yeo WL, Heng E, Tan LL, Lim YW, Ching KC, Tsai DJ, Jhang YW, Lauderdale TL, Shia KS, Zhao H, Ang EL, Zhang MM, Lim YH, Wong FT. Biosynthetic engineering of the antifungal, anti-MRSA auroramycin. Microb Cell Fact 2020; 19:3. [PMID: 31906943 PMCID: PMC6943886 DOI: 10.1186/s12934-019-1274-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 12/21/2019] [Indexed: 12/12/2022] Open
Abstract
Using an established CRISPR-Cas mediated genome editing technique for streptomycetes, we explored the combinatorial biosynthesis potential of the auroramycin biosynthetic gene cluster in Streptomyces roseosporous. Auroramycin is a potent anti-MRSA polyene macrolactam. In addition, auroramycin has antifungal activities, which is unique among structurally similar polyene macrolactams, such as incednine and silvalactam. In this work, we employed different engineering strategies to target glycosylation and acylation biosynthetic machineries within its recently elucidated biosynthetic pathway. Auroramycin analogs with variations in C-, N- methylation, hydroxylation and extender units incorporation were produced and characterized. By comparing the bioactivity profiles of five of these analogs, we determined that unique disaccharide motif of auroramycin is essential for its antimicrobial bioactivity. We further demonstrated that C-methylation of the 3, 5-epi-lemonose unit, which is unique among structurally similar polyene macrolactams, is key to its antifungal activity.
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Affiliation(s)
- Wan Lin Yeo
- Metabolic Engineering, Functional Molecules & Polymers, Institute of Chemical and Engineering Sciences, A*STAR, Biopolis, Singapore
| | - Elena Heng
- Molecular Engineering Laboratory, Institute of Bioengineering and Nanotechnology, A*STAR, Biopolis, Singapore
| | - Lee Ling Tan
- Molecular Engineering Laboratory, Institute of Bioengineering and Nanotechnology, A*STAR, Biopolis, Singapore
| | - Yi Wee Lim
- Integrated Bio & Organic Chemistry, Functional Molecules & Polymers, Institute of Chemical and Engineering Sciences, A*STAR, Biopolis, Singapore
| | - Kuan Chieh Ching
- Integrated Bio & Organic Chemistry, Functional Molecules & Polymers, Institute of Chemical and Engineering Sciences, A*STAR, Biopolis, Singapore
| | - De-Juin Tsai
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes (NHRI), Zhunan, Miaoli, Taiwan
| | - Yi Wun Jhang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes (NHRI), Zhunan, Miaoli, Taiwan
| | - Tsai-Ling Lauderdale
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes (NHRI), Zhunan, Miaoli, Taiwan
| | - Kak-Shan Shia
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes (NHRI), Zhunan, Miaoli, Taiwan
| | - Huimin Zhao
- Departments of Chemical and Biomolecular Engineering, Chemistry, Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Ee Lui Ang
- Metabolic Engineering, Functional Molecules & Polymers, Institute of Chemical and Engineering Sciences, A*STAR, Biopolis, Singapore
| | - Mingzi M Zhang
- Metabolic Engineering, Functional Molecules & Polymers, Institute of Chemical and Engineering Sciences, A*STAR, Biopolis, Singapore.,Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Yee Hwee Lim
- Integrated Bio & Organic Chemistry, Functional Molecules & Polymers, Institute of Chemical and Engineering Sciences, A*STAR, Biopolis, Singapore.
| | - Fong T Wong
- Molecular Engineering Laboratory, Institute of Bioengineering and Nanotechnology, A*STAR, Biopolis, Singapore.
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11
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Morrison RJ, van der Mei FW, Romiti F, Hoveyda AH. A Catalytic Approach for Enantioselective Synthesis of Homoallylic Alcohols Bearing a Z-Alkenyl Chloride or Trifluoromethyl Group. A Concise and Protecting Group-Free Synthesis of Mycothiazole. J Am Chem Soc 2019; 142:436-447. [PMID: 31873000 DOI: 10.1021/jacs.9b11178] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A protecting group-free strategy is presented for diastereo- and enantioselective routes that can be used to prepare a wide variety of Z-homoallylic alcohols with significantly higher efficiency than is otherwise feasible. The approach entails the merger of several catalytic processes and is expected to facilitate the preparation of bioactive organic molecules. More specifically, Z-chloro-substituted allylic pinacolatoboronate is first obtained through stereoretentive cross-metathesis between Z-crotyl-B(pin) (pin = pinacolato) and Z-dichloroethene, both of which are commercially available. The organoboron compound may be used in the central transformation of the entire approach, an α- and enantioselective addition to an aldehyde, catalyzed by a proton-activated, chiral aminophenol-boryl catalyst. Catalytic cross-coupling can then furnish the desired Z-homoallylic alcohol in high enantiomeric purity. The olefin metathesis step can be carried out with substrates and a Mo-based complex that can be purchased. The aminophenol compound that is needed for the second catalytic step can be prepared in multigram quantities from inexpensive starting materials. A significant assortment of homoallylic alcohols bearing a Z-F3C-substituted alkene can also be prepared with similar high efficiency and regio-, diastereo-, and enantioselectivity. What is more, trisubstituted Z-alkenyl chloride moiety can be accessed with similar efficiency albeit with somewhat lower α-selectivity and enantioselectivity. The general utility of the approach is underscored by a succinct, protecting group-free, and enantioselective total synthesis of mycothiazole, a naturally occurring anticancer agent through a sequence that contains a longest linear sequence of nine steps (12 steps total), seven of which are catalytic, generating mycothiazole in 14.5% overall yield.
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Affiliation(s)
- Ryan J Morrison
- Department of Chemistry, Merkert Chemistry Center , Boston College , Chestnut Hill , Massachusetts 02467 , United States
| | - Farid W van der Mei
- Department of Chemistry, Merkert Chemistry Center , Boston College , Chestnut Hill , Massachusetts 02467 , United States
| | - Filippo Romiti
- Department of Chemistry, Merkert Chemistry Center , Boston College , Chestnut Hill , Massachusetts 02467 , United States.,Supramolecular Science and Engineering Institute , University of Strasbourg, CNRS , Strasbourg 67000 , France
| | - Amir H Hoveyda
- Department of Chemistry, Merkert Chemistry Center , Boston College , Chestnut Hill , Massachusetts 02467 , United States.,Supramolecular Science and Engineering Institute , University of Strasbourg, CNRS , Strasbourg 67000 , France
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12
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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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13
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Chen H, Bian Z, Ravichandran V, Li R, Sun Y, Huo L, Fu J, Bian X, Xia L, Tu Q, Zhang Y. Biosynthesis of polyketides by trans-AT polyketide synthases in Burkholderiales. Crit Rev Microbiol 2019; 45:162-181. [PMID: 31218924 DOI: 10.1080/1040841x.2018.1514365] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Widely used as drugs and agrochemicals, polyketides are a family of bioactive natural products, with diverse structures and functions. Polyketides are produced by megaenzymes termed as polyketide synthases (PKSs). PKS biosynthetic pathways are divided into the cis-AT PKSs and trans-AT PKSs; a division based mainly on the absence of an acyltransferase (AT) domain in the trans-AT PKS modules. In trans-AT biosynthesis, the AT activity is contributed via one or several independent proteins, and there are few other characteristics that distinguish trans-AT PKSs from cis-AT PKSs, especially in the formation of the β-branch. The trans-AT PKSs constitute a major PKS pathway, and many are found in Burkholderia species, which are prevalent in the environment and prolific sources of polyketides. This review summarizes studies from 1973 to 2017 on the biosynthesis of natural products by trans-AT PKSs from Burkholderia species.
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Affiliation(s)
- Hanna Chen
- a Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Sciences , Shandong University , Qingdao , People's Republic of China.,b State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science , Hunan Normal University , Changsha , People's Republic of China
| | - Zhilong Bian
- a Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Sciences , Shandong University , Qingdao , People's Republic of China
| | - Vinothkannan Ravichandran
- a Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Sciences , Shandong University , Qingdao , People's Republic of China
| | - Ruijuan Li
- a Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Sciences , Shandong University , Qingdao , People's Republic of China
| | - Yi Sun
- c Institute of Chinese Materia Medica , China Academy of Chinese Medical Sciences , Beijing , People's Republic of China
| | - Liujie Huo
- a Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Sciences , Shandong University , Qingdao , People's Republic of China
| | - Jun Fu
- a Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Sciences , Shandong University , Qingdao , People's Republic of China
| | - Xiaoying Bian
- a Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Sciences , Shandong University , Qingdao , People's Republic of China
| | - Liqiu Xia
- b State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science , Hunan Normal University , Changsha , People's Republic of China
| | - Qiang Tu
- a Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Sciences , Shandong University , Qingdao , People's Republic of China
| | - Youming Zhang
- a Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Sciences , Shandong University , Qingdao , People's Republic of China.,b State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science , Hunan Normal University , Changsha , People's Republic of China
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14
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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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15
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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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16
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Shen JJ, Chen F, Wang XX, Liu XF, Chen XA, Mao XM, Li YQ. Substrate Specificity of Acyltransferase Domains for Efficient Transfer of Acyl Groups. Front Microbiol 2018; 9:1840. [PMID: 30131798 PMCID: PMC6090053 DOI: 10.3389/fmicb.2018.01840] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 07/23/2018] [Indexed: 11/13/2022] Open
Abstract
Acyltransferase domains (ATs) of polyketide synthases (PKSs) are critical for loading of acyl groups on acyl carrier protein domains (A) via self- and trans-acylation reactions, to produce structurally diverse polyketides. However, the interaction specificity between ATs and unusual acyl units is rarely documented. In Streptomycestsukubaensis YN06, we found that AT4FkbB [an AT in the fourth module of tacrolimus (FK506) PKS] transferred both allylmalonyl (allmal) and emthylmalonyl (ethmal) units to ACPs, which was supposed responsible for the production of both FK506 and its analog FK520, respectively. Mutations of five residues in AT4FkbB (Q119A, L185I-V186D-V187T, and F203L) caused decreased efficiency of allmal transfer, but a higher ratio of ethmal transfer, supposedly due to less nucleophilic attacks between Ser599 in the active site of AT4FkbB and the carbonyl carbon in the allmal unit, as observed from molecular dynamics simulations. Furthermore, reverse mutations of these five residues in ethmal-specific ATs to the corresponding residues of AT4FkbB increased its binding affinity to allmal-CoA. Among these residues, Val187 of AT4FkbB mainly contributed to allmal recognition, and V187K mutant produced less FK520 than wild type. Our findings thus suggested that five critical residues within AT4FkbB were important for AT functionality in polyketide extension and potentially for targeting biosynthesis by generating desirable products and eliminating undesirable analogs.
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Affiliation(s)
- Jie-Jie Shen
- Institute of Pharmaceutical Biotechnology, Zhejiang University, Hangzhou, China
| | - Fu Chen
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China
| | - Xiao-Xuan Wang
- Institute of Pharmaceutical Biotechnology, Zhejiang University, Hangzhou, China
| | - Xiao-Fang Liu
- Institute of Pharmaceutical Biotechnology, Zhejiang University, Hangzhou, China
| | - Xin-Ai Chen
- Institute of Pharmaceutical Biotechnology, Zhejiang University, Hangzhou, China.,Key Laboratory of Microbial Biochemistry and Metabolism Engineering of Zhejiang Province, Hangzhou, China
| | - Xu-Ming Mao
- Institute of Pharmaceutical Biotechnology, Zhejiang University, Hangzhou, China.,Key Laboratory of Microbial Biochemistry and Metabolism Engineering of Zhejiang Province, Hangzhou, China
| | - Yong-Quan Li
- Institute of Pharmaceutical Biotechnology, Zhejiang University, Hangzhou, China.,Key Laboratory of Microbial Biochemistry and Metabolism Engineering of Zhejiang Province, Hangzhou, China
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17
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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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18
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Miyanaga A, Ouchi R, Ishikawa F, Goto E, Tanabe G, Kudo F, Eguchi T. Structural Basis of Protein–Protein Interactions between a trans-Acting Acyltransferase and Acyl Carrier Protein in Polyketide Disorazole Biosynthesis. J Am Chem Soc 2018; 140:7970-7978. [DOI: 10.1021/jacs.8b04162] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Akimasa Miyanaga
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1, O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Risako Ouchi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1, O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Fumihiro Ishikawa
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Ena Goto
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1, O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Genzoh Tanabe
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1, O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Tadashi Eguchi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1, O-okayama, Meguro-ku, Tokyo 152-8551, Japan
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19
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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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20
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Cooke TF, Fischer CR, Wu P, Jiang TX, Xie KT, Kuo J, Doctorov E, Zehnder A, Khosla C, Chuong CM, Bustamante CD. Genetic Mapping and Biochemical Basis of Yellow Feather Pigmentation in Budgerigars. Cell 2017; 171:427-439.e21. [PMID: 28985565 PMCID: PMC5951300 DOI: 10.1016/j.cell.2017.08.016] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 07/14/2017] [Accepted: 08/08/2017] [Indexed: 12/31/2022]
Abstract
Parrot feathers contain red, orange, and yellow polyene pigments called psittacofulvins. Budgerigars are parrots that have been extensively bred for plumage traits during the last century, but the underlying genes are unknown. Here we use genome-wide association mapping and gene-expression analysis to map the Mendelian blue locus, which abolishes yellow pigmentation in the budgerigar. We find that the blue trait maps to a single amino acid substitution (R644W) in an uncharacterized polyketide synthase (MuPKS). When we expressed MuPKS heterologously in yeast, yellow pigments accumulated. Mass spectrometry confirmed that these yellow pigments match those found in feathers. The R644W substitution abolished MuPKS activity. Furthermore, gene-expression data from feathers of different bird species suggest that parrots acquired their colors through regulatory changes that drive high expression of MuPKS in feather epithelia. Our data also help formulate biochemical models that may explain natural color variation in parrots. VIDEO ABSTRACT.
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Affiliation(s)
- Thomas F Cooke
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Curt R Fischer
- ChEM-H, Stanford University, Stanford, CA 94305, USA; Stanford Genome Technology Center, Stanford University, Stanford, CA 94305, USA
| | - Ping Wu
- Department of Pathology, University of Southern California, Los Angeles, CA 90033, USA
| | - Ting-Xin Jiang
- Department of Pathology, University of Southern California, Los Angeles, CA 90033, USA
| | - Kathleen T Xie
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - James Kuo
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Elizabeth Doctorov
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ashley Zehnder
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Chaitan Khosla
- ChEM-H, Stanford University, Stanford, CA 94305, USA; Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA; Departments of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Cheng-Ming Chuong
- Department of Pathology, University of Southern California, Los Angeles, CA 90033, USA; Integrative Stem Cell Center, China Medical University, Taichung 404, Taiwan; Center for the Integrative and Evolutionary Galliformes Genomics, National Chung Hsing University, Taichung 402, Taiwan
| | - Carlos D Bustamante
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA.
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21
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Mathews II, Allison K, Robbins T, Lyubimov AY, Uervirojnangkoorn M, Brunger AT, Khosla C, DeMirci H, McPhillips SE, Hollenbeck M, Soltis M, Cohen AE. The Conformational Flexibility of the Acyltransferase from the Disorazole Polyketide Synthase Is Revealed by an X-ray Free-Electron Laser Using a Room-Temperature Sample Delivery Method for Serial Crystallography. Biochemistry 2017; 56:4751-4756. [PMID: 28832129 PMCID: PMC5721673 DOI: 10.1021/acs.biochem.7b00711] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The crystal structure of the trans-acyltransferase (AT) from the disorazole polyketide synthase (PKS) was determined at room temperature to a resolution of 2.5 Å using a new method for the direct delivery of the sample into an X-ray free-electron laser. A novel sample extractor efficiently delivered limited quantities of microcrystals directly from the native crystallization solution into the X-ray beam at room temperature. The AT structure revealed important catalytic features of this core PKS enzyme, including the occurrence of conformational changes around the active site. The implications of these conformational changes for polyketide synthase reaction dynamics are discussed.
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Affiliation(s)
- Irimpan I Mathews
- Stanford Synchrotron Radiation Lightsource , 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Kim Allison
- Stanford Synchrotron Radiation Lightsource , 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | | | - Artem Y Lyubimov
- Stanford Synchrotron Radiation Lightsource , 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | | | | | | | - Hasan DeMirci
- Stanford Synchrotron Radiation Lightsource , 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Scott E McPhillips
- Stanford Synchrotron Radiation Lightsource , 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Michael Hollenbeck
- Stanford Synchrotron Radiation Lightsource , 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Michael Soltis
- Stanford Synchrotron Radiation Lightsource , 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Aina E Cohen
- Stanford Synchrotron Radiation Lightsource , 2575 Sand Hill Road, Menlo Park, California 94025, United States
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22
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Fu C, Auerbach D, Li Y, Scheid U, Luxenburger E, Garcia R, Irschik H, Müller R. Die Lösung des Rätsels um den Verlust eines Kohlenstoffatoms in der Ripostatin-Biosynthese. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201609950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Chengzhang Fu
- Helmholtz-Institut für Pharmazeutische Forschung Saarland (HIPS); Helmholtz-Zentrum für Infektionsforschung (HZI); Universität des Saarlandes; Campus Gebäude E8.1 66123 Saarbrücken Deutschland
| | - David Auerbach
- Helmholtz-Institut für Pharmazeutische Forschung Saarland (HIPS); Helmholtz-Zentrum für Infektionsforschung (HZI); Universität des Saarlandes; Campus Gebäude E8.1 66123 Saarbrücken Deutschland
| | - Yanyan Li
- Helmholtz-Institut für Pharmazeutische Forschung Saarland (HIPS); Helmholtz-Zentrum für Infektionsforschung (HZI); Universität des Saarlandes; Campus Gebäude E8.1 66123 Saarbrücken Deutschland
- Laboratory Molecules of Communication and Adaptation o Microorganisms (MCAM, UMR 7245 CNRS-MNHN); Sorbonne Universités; Muséum National d'Histoire Naturelle; Centre National de la Recherche Scientifique, CP 54; 57 rue Cuvier 75005 Paris Frankreich
| | - Ullrich Scheid
- Helmholtz-Institut für Pharmazeutische Forschung Saarland (HIPS); Helmholtz-Zentrum für Infektionsforschung (HZI); Universität des Saarlandes; Campus Gebäude E8.1 66123 Saarbrücken Deutschland
- Deutsches Zentrum für Infektionsforschung; Inhoffenstraße 7 38124 Braunschweig Deutschland
| | - Eva Luxenburger
- Helmholtz-Institut für Pharmazeutische Forschung Saarland (HIPS); Helmholtz-Zentrum für Infektionsforschung (HZI); Universität des Saarlandes; Campus Gebäude E8.1 66123 Saarbrücken Deutschland
- Deutsches Zentrum für Infektionsforschung; Inhoffenstraße 7 38124 Braunschweig Deutschland
| | - Ronald Garcia
- Helmholtz-Institut für Pharmazeutische Forschung Saarland (HIPS); Helmholtz-Zentrum für Infektionsforschung (HZI); Universität des Saarlandes; Campus Gebäude E8.1 66123 Saarbrücken Deutschland
- Deutsches Zentrum für Infektionsforschung; Inhoffenstraße 7 38124 Braunschweig Deutschland
| | - Herbert Irschik
- Helmholtz-Zentrum für Infektionsforschung (HZI); Inhoffenstraße 7 38124 Braunschweig Deutschland
| | - Rolf Müller
- Helmholtz-Institut für Pharmazeutische Forschung Saarland (HIPS); Helmholtz-Zentrum für Infektionsforschung (HZI); Universität des Saarlandes; Campus Gebäude E8.1 66123 Saarbrücken Deutschland
- Deutsches Zentrum für Infektionsforschung; Inhoffenstraße 7 38124 Braunschweig Deutschland
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23
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Ad O, Thuronyi BW, Chang MCY. Elucidating the mechanism of fluorinated extender unit loading for improved production of fluorine-containing polyketides. Proc Natl Acad Sci U S A 2017; 114:E660-E668. [PMID: 28096394 PMCID: PMC5293041 DOI: 10.1073/pnas.1614196114] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Polyketides are a large family of bioactive natural products synthesized by polyketide synthase (PKS) enzyme complexes predominantly from acetate and propionate. Given the structural diversity of compounds produced using these two simple building blocks, there has been longstanding interest in engineering the incorporation of alternative extender units. We have been investigating the mechanism of fluorinated monomer insertion by three of the six different modules of the PKS involved in erythromycin biosynthesis (6-deoxyerythronolide B synthase, DEBS) to begin understanding the contribution of different steps, such as enzyme acylation, transacylation, C-C bond formation, and chain transfer, to the overall selectivity and efficiency of this process. In these studies, we observe that inactivation of a cis-acyltransferase (AT) domain to circumvent its native extender unit preference leads concurrently to a change of mechanism in which chain extension with fluorine-substituted extender units switches largely to an acyl carrier protein (ACP)-independent mode. This result suggests that the covalent linkage between the growing polyketide chain and the enzyme is lost in these cases, which would limit efficient chain elongation after insertion of a fluorinated monomer. However, use of a standalone trans-acting AT to complement modules with catalytically deficient AT domains leads to enzyme acylation with the fluoromalonyl-CoA extender unit. Formation of the canonical ACP-linked intermediate with fluoromalonyl-CoA allows insertion of fluorinated extender units at 43% of the yield of the wild-type system while also amplifying product yield in single chain-extension experiments and enabling multiple chain extensions to form multiply fluorinated products.
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Affiliation(s)
- Omer Ad
- Department of Chemistry, University of California, Berkeley, CA 94720-1460
| | - B W Thuronyi
- Department of Chemistry, University of California, Berkeley, CA 94720-1460
| | - Michelle C Y Chang
- Department of Chemistry, University of California, Berkeley, CA 94720-1460;
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-1460
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24
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Koryakina I, Kasey C, McArthur JB, Lowell AN, Chemler JA, Li S, Hansen DA, Sherman DH, Williams GJ. Inversion of Extender Unit Selectivity in the Erythromycin Polyketide Synthase by Acyltransferase Domain Engineering. ACS Chem Biol 2017; 12:114-123. [PMID: 28103677 DOI: 10.1021/acschembio.6b00732] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Acyltransferase (AT) domains of polyketide synthases (PKSs) select extender units for incorporation into polyketides and dictate large portions of the structures of clinically relevant natural products. Accordingly, there is significant interest in engineering the substrate specificity of PKS ATs in order to site-selectively manipulate polyketide structure. However, previous attempts to engineer ATs have yielded mutant PKSs with relaxed extender unit specificity, rather than an inversion of selectivity from one substrate to another. Here, by directly screening the extender unit selectivity of mutants from active site saturation libraries of an AT from the prototypical PKS, 6-deoxyerythronolide B synthase, a set of single amino acid substitutions was discovered that dramatically impact the selectivity of the PKS with only modest reductions of product yields. One particular substitution (Tyr189Arg) inverted the selectivity of the wild-type PKS from its natural substrate toward a non-natural alkynyl-modified extender unit while maintaining more than twice the activity of the wild-type PKS with its natural substrate. The strategy and mutations described herein form a platform for combinatorial biosynthesis of site-selectively modified polyketide analogues that are modified with non-natural and non-native chemical functionality.
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Affiliation(s)
- Irina Koryakina
- Department
of Chemistry, NC State University, Raleigh, North Carolina 27695-8204, United States
| | - Christian Kasey
- Department
of Chemistry, NC State University, Raleigh, North Carolina 27695-8204, United States
| | | | - Andrew N. Lowell
- Life
Sciences Institute, Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Joseph A. Chemler
- Life
Sciences Institute, Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Shasha Li
- Life
Sciences Institute, Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Douglas A. Hansen
- Life
Sciences Institute, Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - David H. Sherman
- Life
Sciences Institute, Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, Department of Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Gavin J. Williams
- Department
of Chemistry, NC State University, Raleigh, North Carolina 27695-8204, United States
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25
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Fu C, Auerbach D, Li Y, Scheid U, Luxenburger E, Garcia R, Irschik H, Müller R. Solving the Puzzle of One-Carbon Loss in Ripostatin Biosynthesis. Angew Chem Int Ed Engl 2017; 56:2192-2197. [DOI: 10.1002/anie.201609950] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Indexed: 01/19/2023]
Affiliation(s)
- Chengzhang Fu
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS); Helmholtz Centre for Infection Research (HZI); Saarland University; Campus Building E8.1 66123 Saarbrücken Germany
| | - David Auerbach
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS); Helmholtz Centre for Infection Research (HZI); Saarland University; Campus Building E8.1 66123 Saarbrücken Germany
| | - Yanyan Li
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS); Helmholtz Centre for Infection Research (HZI); Saarland University; Campus Building E8.1 66123 Saarbrücken Germany
- Current address: Laboratory Molecules of Communication and Adaptation of Microorganisms (MCAM, UMR 7245 CNRS-MNHN); Sorbonne Universités; Muséum National d'Histoire Naturelle; Centre National de la Recherche Scientifique, CP 54; 57 rue Cuvier 75005 Paris France
| | - Ullrich Scheid
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS); Helmholtz Centre for Infection Research (HZI); Saarland University; Campus Building E8.1 66123 Saarbrücken Germany
- German Centre for Infection Research (DZIF); partner site Hannover-Braunschweig; Braunschweig Germany
| | - Eva Luxenburger
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS); Helmholtz Centre for Infection Research (HZI); Saarland University; Campus Building E8.1 66123 Saarbrücken Germany
- German Centre for Infection Research (DZIF); partner site Hannover-Braunschweig; Braunschweig Germany
| | - Ronald Garcia
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS); Helmholtz Centre for Infection Research (HZI); Saarland University; Campus Building E8.1 66123 Saarbrücken Germany
- German Centre for Infection Research (DZIF); partner site Hannover-Braunschweig; Braunschweig Germany
| | - Herbert Irschik
- Helmholtz Centre for Infection Research (HZI); Inhoffenstrasse 7 38124 Braunschweig Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS); Helmholtz Centre for Infection Research (HZI); Saarland University; Campus Building E8.1 66123 Saarbrücken Germany
- German Centre for Infection Research (DZIF); partner site Hannover-Braunschweig; Braunschweig Germany
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26
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Robbins T, Liu YC, Cane DE, Khosla C. Structure and mechanism of assembly line polyketide synthases. Curr Opin Struct Biol 2016; 41:10-18. [PMID: 27266330 PMCID: PMC5136517 DOI: 10.1016/j.sbi.2016.05.009] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 05/19/2016] [Accepted: 05/20/2016] [Indexed: 11/16/2022]
Abstract
Assembly line polyketide synthases (PKSs) are remarkable biosynthetic machines with considerable potential for structure-based engineering. Several types of protein-protein interactions, both within and between PKS modules, play important roles in the catalytic cycle of a multimodular PKS. Additionally, vectorial biosynthesis is enabled by the energetic coupling of polyketide chain elongation to the channeling of intermediates between successive modules. A combination of high-resolution analysis of smaller PKS components and lower resolution characterization of intact modules and bimodules has yielded insights into the structure and organization of a prototypical assembly line PKS. This review discusses our understanding of key structure-function relationships in this family of megasynthases, along with a recap of key unanswered questions in the field.
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Affiliation(s)
- Thomas Robbins
- Department of Chemistry, Stanford University, Stanford, CA 94305, United States
| | - Yu-Chen Liu
- Department of Chemistry, Stanford University, Stanford, CA 94305, United States
| | - David E Cane
- Department of Chemistry, Brown University, Providence, RI 02912-9108, United States
| | - Chaitan Khosla
- Department of Chemistry, Stanford University, Stanford, CA 94305, United States; Department of Chemical Engineering, Stanford University, Stanford, CA 94305, United States.
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27
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Uytterhoeven B, Lathouwers T, Voet M, Michiels CW, Lavigne R. A Protein Interaction Map of the Kalimantacin Biosynthesis Assembly Line. Front Microbiol 2016; 7:1726. [PMID: 27853452 PMCID: PMC5089993 DOI: 10.3389/fmicb.2016.01726] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 10/17/2016] [Indexed: 12/04/2022] Open
Abstract
The antimicrobial secondary metabolite kalimantacin (also called batumin) is produced by a hybrid polyketide/non-ribosomal peptide system in Pseudomonas fluorescens BCCM_ID9359. In this study, the kalimantacin biosynthesis gene cluster is analyzed by yeast two-hybrid analysis, creating a protein–protein interaction map of the entire assembly line. In total, 28 potential interactions were identified, of which 13 could be confirmed further. These interactions include the dimerization of ketosynthase domains, a link between assembly line modules 9 and 10, and a specific interaction between the trans-acting enoyl reductase BatK and the carrier proteins of modules 8 and 10. These interactions reveal fundamental insight into the biosynthesis of secondary metabolites. This study is the first to reveal interactions in a complete biosynthetic pathway. Similar future studies could build a strong basis for engineering strategies in such clusters.
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Affiliation(s)
- Birgit Uytterhoeven
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven Leuven, Belgium
| | - Thomas Lathouwers
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven Leuven, Belgium
| | - Marleen Voet
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven Leuven, Belgium
| | - Chris W Michiels
- Centre for Food and Microbial Technology, Department of Microbial and Molecular Systems, KU Leuven Leuven, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven Leuven, Belgium
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28
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Jenner M, Afonso JP, Kohlhaas C, Karbaum P, Frank S, Piel J, Oldham NJ. Acyl hydrolases from trans-AT polyketide synthases target acetyl units on acyl carrier proteins. Chem Commun (Camb) 2016; 52:5262-5. [PMID: 27003309 DOI: 10.1039/c6cc01453d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Acyl hydrolase (AH) domains are a common feature of trans-AT PKSs. They have been hypothesised to perform a proofreading function by removing acyl chains from stalled sites. This study determines the substrate tolerance of the AH PedC for a range of acyl-ACPs. Clear preference towards short, linear acyl-ACPs is shown, with acetyl-ACP the best substrate. These results imply a more targeted housekeeping role for PedC: namely the removal of unwanted acetyl groups from ACP domains caused by erroneous transfer of acetyl-CoA, or possibly by decarboxylation of malonyl-ACP.
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Affiliation(s)
- Matthew Jenner
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
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29
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Genetic engineering and heterologous expression of the disorazol biosynthetic gene cluster via Red/ET recombineering. Sci Rep 2016; 6:21066. [PMID: 26875499 PMCID: PMC4753468 DOI: 10.1038/srep21066] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 01/18/2016] [Indexed: 11/08/2022] Open
Abstract
Disorazol, a macrocyclic polykitide produced by the myxobacterium Sorangium cellulosum So ce12 and it is reported to have potential cytotoxic activity towards several cancer cell lines, including multi-drug resistant cells. The disorazol biosynthetic gene cluster (dis) from Sorangium cellulosum (So ce12) was identified by transposon mutagenesis and cloned in a bacterial artificial chromosome (BAC) library. The 58-kb dis core gene cluster was reconstituted from BACs via Red/ET recombineering and expressed in Myxococcus xanthus DK1622. For the first time ever, a myxobacterial trans-AT polyketide synthase has been expressed heterologously in this study. Expression in M. xanthus allowed us to optimize the yield of several biosynthetic products using promoter engineering. The insertion of an artificial synthetic promoter upstream of the disD gene encoding a discrete acyl transferase (AT), together with an oxidoreductase (Or), resulted in 7-fold increase in disorazol production. The successful reconstitution and expression of the genetic sequences encoding for these promising cytotoxic compounds will allow combinatorial biosynthesis to generate novel disorazol derivatives for further bioactivity evaluation.
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30
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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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31
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Helfrich EJN, Piel J. Biosynthesis of polyketides by trans-AT polyketide synthases. Nat Prod Rep 2016; 33:231-316. [DOI: 10.1039/c5np00125k] [Citation(s) in RCA: 230] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This review discusses the biosynthesis of natural products that are generated bytrans-AT polyketide synthases, a family of catalytically versatile enzymes that represents one of the major group of proteins involved in the production of bioactive polyketides.
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Affiliation(s)
- Eric J. N. Helfrich
- Institute of Microbiology
- Eidgenössische Technische Hochschule (ETH) Zurich
- 8093 Zurich
- Switzerland
| | - Jörn Piel
- Institute of Microbiology
- Eidgenössische Technische Hochschule (ETH) Zurich
- 8093 Zurich
- Switzerland
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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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33
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The LINKS motif zippers trans-acyltransferase polyketide synthase assembly lines into a biosynthetic megacomplex. J Struct Biol 2015; 193:196-205. [PMID: 26724270 DOI: 10.1016/j.jsb.2015.12.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 12/04/2015] [Accepted: 12/22/2015] [Indexed: 11/21/2022]
Abstract
Polyketides such as the clinically-valuable antibacterial agent mupirocin are constructed by architecturally-sophisticated assembly lines known as trans-acyltransferase polyketide synthases. Organelle-sized megacomplexes composed of several copies of trans-acyltransferase polyketide synthase assembly lines have been observed by others through transmission electron microscopy to be located at the Bacillus subtilis plasma membrane, where the synthesis and export of the antibacterial polyketide bacillaene takes place. In this work we analyze ten crystal structures of trans-acyltransferase polyketide synthases ketosynthase domains, seven of which are reported here for the first time, to characterize a motif capable of zippering assembly lines into a megacomplex. While each of the three-helix LINKS (Laterally-INteracting Ketosynthase Sequence) motifs is observed to similarly dock with a spatially-reversed copy of itself through hydrophobic and ionic interactions, the amino acid sequences of this motif are not conserved. Such a code is appropriate for mediating homotypic contacts between assembly lines to ensure the ordered self-assembly of a noncovalent, yet tightly-knit, enzymatic network. LINKS-mediated lateral interactions would also have the effect of bolstering the vertical association of the polypeptides that comprise a polyketide synthase assembly line.
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34
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The structural biology of biosynthetic megaenzymes. Nat Chem Biol 2015; 11:660-70. [PMID: 26284673 DOI: 10.1038/nchembio.1883] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 07/02/2015] [Indexed: 01/27/2023]
Abstract
The modular polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs) are among the largest and most complicated enzymes in nature. In these biosynthetic systems, independently folding protein domains, which are organized into units called 'modules', operate in assembly-line fashion to construct polymeric chains and tailor their functionalities. Products of PKSs and NRPSs include a number of blockbuster medicines, and this has motivated researchers to understand how they operate so that they can be modified by genetic engineering. Beginning in the 1990s, structural biology has provided a number of key insights. The emerging picture is one of remarkable dynamics and conformational programming in which the chemical states of individual catalytic domains are communicated to the others, configuring the modules for the next stage in the biosynthesis. This unexpected level of complexity most likely accounts for the low success rate of empirical genetic engineering experiments and suggests ways forward for productive megaenzyme synthetic biology.
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35
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Harnessing natural product assembly lines: structure, promiscuity, and engineering. J Ind Microbiol Biotechnol 2015; 43:371-87. [PMID: 26527577 DOI: 10.1007/s10295-015-1704-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 10/18/2015] [Indexed: 10/22/2022]
Abstract
Many therapeutically relevant natural products are biosynthesized by the action of giant mega-enzyme assembly lines. By leveraging the specificity, promiscuity, and modularity of assembly lines, a variety of strategies has been developed that enables the biosynthesis of modified natural products. This review briefly summarizes recent structural advances related to natural product assembly lines, discusses chemical approaches to probing assembly line structures in the absence of traditional biophysical data, and surveys efforts that harness the inherent or engineered promiscuity of assembly lines for the synthesis of non-natural polyketides and non-ribosomal peptide analogues.
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36
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Matilla MA, Leeper FJ, Salmond GPC. Biosynthesis of the antifungal haterumalide, oocydin A, in Serratia, and its regulation by quorum sensing, RpoS and Hfq. Environ Microbiol 2015; 17:2993-3008. [PMID: 25753587 PMCID: PMC4552970 DOI: 10.1111/1462-2920.12839] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 02/27/2015] [Accepted: 03/02/2015] [Indexed: 02/02/2023]
Abstract
Polyketides represent an important class of bioactive natural products with a broad range of biological activities. We identified recently a large trans-acyltransferase (AT) polyketide synthase gene cluster responsible for the biosynthesis of the antifungal, anti-oomycete and antitumor haterumalide, oocydin A (ooc). Using genome sequencing and comparative genomics, we show that the ooc gene cluster is widespread within biocontrol and phytopathogenic strains of the enterobacteria, Serratia and Dickeya. The analysis of in frame deletion mutants confirmed the role of a hydroxymethylglutaryl-coenzyme A synthase cassette, three flavin-dependent tailoring enzymes, a free-standing acyl carrier protein and two hypothetical proteins in oocydin A biosynthesis. The requirement of the three trans-acting AT domains for the biosynthesis of the macrolide was also demonstrated. Expression of the ooc gene cluster was shown to be positively regulated by an N-acyl-L-homoserine lactone-based quorum sensing system, but operating in a strain-dependent manner. At a post-transcriptional level, the RNA chaperone, Hfq, plays a key role in oocydin A biosynthesis. The Hfq-dependent regulation is partially mediated by the stationary phase sigma factor, RpoS, which was also shown to positively regulate the synthesis of the macrolide. Our results reveal differential regulation of the divergently transcribed ooc transcriptional units, highlighting the complexity of oocydin A production.
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Affiliation(s)
- Miguel A Matilla
- Department of Biochemistry, University of CambridgeTennis Court Road, Cambridge, CB2 1QW, UK
| | - Finian J Leeper
- Department of Chemistry, University of CambridgeLensfield Road, Cambridge, CB2 1EW, UK
| | - George P C Salmond
- Department of Biochemistry, University of CambridgeTennis Court Road, Cambridge, CB2 1QW, UK,*For correspondence. E-mail ; Tel. +44 (0)1223 333650; Fax +44 (0)1223 766108
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37
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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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38
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Wang F, Wang Y, Ji J, Zhou Z, Yu J, Zhu H, Su Z, Zhang L, Zheng J. Structural and functional analysis of the loading acyltransferase from avermectin modular polyketide synthase. ACS Chem Biol 2015; 10:1017-25. [PMID: 25581064 DOI: 10.1021/cb500873k] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The loading acyltransferase (AT) domains of modular polyketide synthases (PKSs) control the choice of starter units incorporated into polyketides and are therefore attractive targets for the engineering of modular PKSs. Here, we report the structural and biochemical characterizations of the loading AT from avermectin modular PKS, which accepts more than 40 carboxylic acids as alternative starter units for the biosynthesis of a series of congeners. This first structural analysis of loading ATs from modular PKSs revealed the molecular basis for the relaxed substrate specificity. Residues important for substrate binding and discrimination were predicted by modeling a substrate into the active site. A mutant with altered specificity toward a panel of synthetic substrate mimics was generated by site-directed mutagenesis of the active site residues. The hydrolysis of the N-acetylcysteamine thioesters of racemic 2-methylbutyric acid confirmed the stereospecificity of the avermectin loading AT for an S configuration at the C-2 position of the substrate. Together, these results set the stage for region-specific modification of polyketides through active site engineering of loading AT domains of modular PKSs.
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Affiliation(s)
- Fen Wang
- National
Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, P.R. China
| | - Yanjie Wang
- National
Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, P.R. China
| | - Junjie Ji
- National
Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, P.R. China
| | - Zhan Zhou
- National
Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, P.R. China
| | - Jingkai Yu
- National
Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, P.R. China
| | - Hua Zhu
- CAS
Key Laboratory of Pathogenic Microbiology and Immunology, Institute
of Microbiology, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Zhiguo Su
- National
Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, P.R. China
| | - Lixin Zhang
- CAS
Key Laboratory of Pathogenic Microbiology and Immunology, Institute
of Microbiology, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Jianting Zheng
- National
Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, P.R. China
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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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40
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Abstract
This review covers a breakthrough in the structural biology of the gigantic modular polyketide synthases (PKS): the structural characterization of intact modules by single-particle cryo-electron microscopy and small-angle X-ray scattering.
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Affiliation(s)
- Kira J. Weissman
- Molecular and Structural Enzymology Group
- Université de Lorraine
- IMoPA
- UMR 7365
- Vandœuvre-lès-Nancy
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41
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Randall SM, Koryakina I, Williams GJ, Muddiman DC. Evaluating nonpolar surface area and liquid chromatography/mass spectrometry response: an application for site occupancy measurements for enzyme intermediates in polyketide biosynthesis. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2014; 28:2511-2522. [PMID: 25366398 PMCID: PMC4230892 DOI: 10.1002/rcm.7051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 08/22/2014] [Accepted: 09/09/2014] [Indexed: 05/31/2023]
Abstract
RATIONALE Site occupancy measurements using liquid chromatography/mass spectrometry (LC/MS) are reported throughout the literature. However, site occupancy quantification suffers from ionization bias between modified and unmodified peptides containing the active site. In this study, we explore the MS signal as a function of nonpolar surface area (NPSA) in order to better understand this bias in electrospray response. The correlation between hydrophobicity and LC/MS response was evaluated and applied to study enzyme intermediates in polyketide synthases. METHODS Site occupancy methods were developed to study acyltransferase activity. To further evaluate these methods, several standard peptides containing one cysteine residue were modified with alkylation reagents of increasing hydrophobicity to study the MS signal as a function of NPSA. RESULTS A consistent trend in MS response was observed which is dependent on the NPSA of the analyte. An optimal NPSA zone was observed for the peptides studied. CONCLUSIONS Nonpolar surface area can be used as metric to determine relative LC/MS response for peptides and evaluate site occupancy measurements.
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Affiliation(s)
- Shan M. Randall
- W.M. Keck Fourier Transform Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Irina Koryakina
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Gavin J. Williams
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - David C. Muddiman
- W.M. Keck Fourier Transform Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
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42
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Park H, Kevany BM, Dyer DH, Thomas MG, Forest KT. A polyketide synthase acyltransferase domain structure suggests a recognition mechanism for its hydroxymalonyl-acyl carrier protein substrate. PLoS One 2014; 9:e110965. [PMID: 25340352 PMCID: PMC4207774 DOI: 10.1371/journal.pone.0110965] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 09/27/2014] [Indexed: 11/20/2022] Open
Abstract
We have previously shown that the acyl transferase domain of ZmaA (ZmaA-AT) is involved in the biosynthesis of the aminopolyol polyketide/nonribosomal peptide hybrid molecule zwittermicin A from cereus UW85, and that it specifically recognizes the precursor hydroxymalonyl-acyl carrier protein (ACP) and transfers the hydroxymalonyl extender unit to a downstream second ACP via a transacylated AT domain intermediate. We now present the X-ray crystal structure of ZmaA-AT at a resolution of 1.7 Å. The structure shows a patch of solvent-exposed hydrophobic residues in the area where the AT is proposed to interact with the precursor ACP. We addressed the significance of the AT/ACP interaction in precursor specificity of the AT by testing whether malonyl- or methylmalonyl-ACP can be recognized by ZmaA-AT. We found that the ACP itself biases extender unit selection. Until now, structural information for ATs has been limited to ATs specific for the CoA-linked precursors malonyl-CoA and (2S)-methylmalonyl-CoA. This work contributes to polyketide synthase engineering efforts by expanding our knowledge of AT/substrate interactions with the structure of an AT domain that recognizes an ACP-linked substrate, the rare hydroxymalonate. Our structure suggests a model in which ACP interaction with a hydrophobic motif promotes secondary structure formation at the binding site, and opening of the adjacent substrate pocket lid to allow extender unit binding in the AT active site.
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Affiliation(s)
- Hyunjun Park
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Brian M. Kevany
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - David H. Dyer
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Michael G. Thomas
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail: (MGT); (KTF)
| | - Katrina T. Forest
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail: (MGT); (KTF)
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43
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Piasecki SK, Zheng J, Axelrod AJ, Detelich M, Keatinge-Clay AT. Structural and functional studies of a trans-acyltransferase polyketide assembly line enzyme that catalyzes stereoselective α- and β-ketoreduction. Proteins 2014; 82:2067-77. [PMID: 24634061 PMCID: PMC4142079 DOI: 10.1002/prot.24561] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 02/19/2014] [Accepted: 03/06/2014] [Indexed: 11/06/2022]
Abstract
While the cis-acyltransferase modular polyketide synthase assembly lines have largely been structurally dissected, enzymes from within the recently discovered trans-acyltransferase polyketide synthase assembly lines are just starting to be observed crystallographically. Here we examine the ketoreductase (KR) from the first polyketide synthase module of the bacillaene nonribosomal peptide synthetase/polyketide synthase at 2.35-Å resolution. This KR naturally reduces both α- and β-keto groups and is the only KR known to do so during the biosynthesis of a polyketide. The isolated KR not only reduced an N-acetylcysteamine-bound β-keto substrate to a D-β-hydroxy product, but also an N-acetylcysteamine-bound α-keto substrate to an L-α-hydroxy product. That the substrates must enter the active site from opposite directions to generate these stereochemistries suggests that the acyl-phosphopantetheine moiety is capable of accessing very different conformations despite being anchored to a serine residue of a docked acyl carrier protein. The features enabling stereocontrolled α-ketoreduction may not be extensive since a KR that naturally reduces a β-keto group within a cis-acyltransferase polyketide synthase was identified that performs a completely stereoselective reduction of the same α-keto substrate to generate the D-α-hydroxy product. A sequence analysis of trans-acyltransferase KRs reveals that a single residue, rather than a three-residue motif found in cis-acyltransferase KRs, is predictive of the orientation of the resulting β-hydroxyl group.
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Affiliation(s)
- Shawn K. Piasecki
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
| | - Jianting Zheng
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
| | - Abram J. Axelrod
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
| | - Madeline Detelich
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
| | - Adrian T. Keatinge-Clay
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
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44
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Dunn BJ, Watts KR, Robbins T, Cane DE, Khosla C. Comparative analysis of the substrate specificity of trans- versus cis-acyltransferases of assembly line polyketide synthases. Biochemistry 2014; 53:3796-806. [PMID: 24871074 PMCID: PMC4067149 DOI: 10.1021/bi5004316] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Due
to their pivotal role in extender unit selection during polyketide
biosynthesis, acyltransferase (AT) domains are important engineering
targets. A subset of assembly line polyketide synthases (PKSs) are
serviced by discrete, trans-acting ATs. Theoretically,
these trans-ATs can complement an inactivated cis-AT, promoting introduction of a noncognate extender
unit. This approach requires a better understanding of the substrate
specificity and catalytic mechanism of naturally occurring trans-ATs. We kinetically analyzed trans-ATs from the disorazole and kirromycin synthases and compared them
to a representative cis-AT from the 6-deoxyerythronolide
B synthase (DEBS). During transacylation, the disorazole AT favored
malonyl-CoA over methylmalonyl-CoA by >40000-fold, whereas the
kirromycin
AT favored ethylmalonyl-CoA over methylmalonyl-CoA by 20-fold. Conversely,
the disorazole AT had broader specificity than its kirromycin counterpart
for acyl carrier protein (ACP) substrates. The presence of the ACP
had little effect on the specificity (kcat/KM) of the cis-AT domain
for carboxyacyl-CoA substrates but had a marked influence on the corresponding
specificity parameters for the trans-ATs, suggesting
that these enzymes do not act strictly by a canonical ping-pong mechanism.
To investigate the relevance of the kinetic analysis of isolated ATs
in the context of intact PKSs, we complemented an in vitro AT-null DEBS assembly line with either trans-AT.
Whereas the disorazole AT efficiently complemented the mutant PKS
at substoichiometric protein ratios, the kirromycin AT was considerably
less effective. Our findings suggest that knowledge of both carboxyacyl-CoA
and ACP specificity is critical to the choice of a trans-AT in combination with a mutant PKS to generate novel polyketides.
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Affiliation(s)
- Briana J Dunn
- Department of Chemical Engineering, ‡Department of Chemistry, and ∥Department of Biochemistry, Stanford University , Stanford, California 94305, United States
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45
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Use of transmission electron microscopy to identify nanocrystals of challenging protein targets. Proc Natl Acad Sci U S A 2014; 111:8470-5. [PMID: 24872454 DOI: 10.1073/pnas.1400240111] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The current practice for identifying crystal hits for X-ray crystallography relies on optical microscopy techniques that are limited to detecting crystals no smaller than 5 μm. Because of these limitations, nanometer-sized protein crystals cannot be distinguished from common amorphous precipitates, and therefore go unnoticed during screening. These crystals would be ideal candidates for further optimization or for femtosecond X-ray protein nanocrystallography. The latter technique offers the possibility to solve high-resolution structures using submicron crystals. Transmission electron microscopy (TEM) was used to visualize nanocrystals (NCs) found in crystallization drops that would classically not be considered as "hits." We found that protein NCs were readily detected in all samples tested, including multiprotein complexes and membrane proteins. NC quality was evaluated by TEM visualization of lattices, and diffraction quality was validated by experiments in an X-ray free electron laser.
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46
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Ye Z, Musiol EM, Weber T, Williams GJ. Reprogramming acyl carrier protein interactions of an Acyl-CoA promiscuous trans-acyltransferase. ACTA ACUST UNITED AC 2014; 21:636-46. [PMID: 24726832 DOI: 10.1016/j.chembiol.2014.02.019] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 01/27/2014] [Accepted: 02/06/2014] [Indexed: 11/29/2022]
Abstract
Protein interactions between acyl carrier proteins (ACPs) and trans-acting acyltransferase domains (trans-ATs) are critical for regioselective extender unit installation by many polyketide synthases, yet little is known regarding the specificity of these interactions, particularly for trans-ATs with unusual extender unit specificities. Currently, the best-studied trans-AT with nonmalonyl specificity is KirCII from kirromycin biosynthesis. Here, we developed an assay to probe ACP interactions based on leveraging the extender unit promiscuity of KirCII. The assay allows us to identify residues on the ACP surface that contribute to specific recognition by KirCII. This information proved sufficient to modify a noncognate ACP from a different biosynthetic system to be a substrate for KirCII. The findings form a foundation for further understanding the specificity of trans-AT:ACP protein interactions and for engineering modular polyketide synthases to produce analogs.
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Affiliation(s)
- Zhixia Ye
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA
| | - Ewa M Musiol
- Interfaculty Institute of Microbiology and Infection Medicine, Eberhard Karls University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany; German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Tilmann Weber
- Interfaculty Institute of Microbiology and Infection Medicine, Eberhard Karls University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany; German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Gavin J Williams
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA.
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47
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Till M, Race PR. Progress challenges and opportunities for the re-engineering of trans-AT polyketide synthases. Biotechnol Lett 2014; 36:877-88. [PMID: 24557077 DOI: 10.1007/s10529-013-1449-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2013] [Accepted: 12/23/2013] [Indexed: 12/13/2022]
Abstract
Polyketides are a structurally and functionally diverse family of bioactive natural products that are used extensively as pharmaceuticals and agrochemicals. In bacteria these molecules are biosynthesized by giant, multi-functional enzymatic complexes, termed modular polyketide synthases (PKSs), that function in assembly-line like fashion to fuse and tailor simple carboxylic acid monomers into a vast array of elaborate chemical scaffolds. Modifying PKSs through targeted synthase re-engineering is a promising approach for accessing functionally-optimized polyketides. Due to their highly mosaic architectures the recently identified trans-AT family of modular synthases appear inherently more amenable to re-engineering than their well studied cis-AT counterparts. Here, we review recent progress in the re-engineering of trans-AT PKSs, summarize opportunities for harnessing the biosynthetic potential of these systems, and highlight challenges that such re-engineering approaches present.
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Affiliation(s)
- M Till
- School of Biochemistry, Medical Sciences, University of Bristol, Bristol, BS8 1TD, UK
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48
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Gay DC, Gay G, Axelrod AJ, Jenner M, Kohlhaas C, Kampa A, Oldham NJ, Piel J, Keatinge-Clay AT. A close look at a ketosynthase from a trans-acyltransferase modular polyketide synthase. Structure 2014; 22:444-51. [PMID: 24508341 DOI: 10.1016/j.str.2013.12.016] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2013] [Revised: 12/15/2013] [Accepted: 12/16/2013] [Indexed: 10/25/2022]
Abstract
The recently discovered trans-acyltransferase modular polyketide synthases catalyze the biosynthesis of a wide range of bioactive natural products in bacteria. Here we report the structure of the second ketosynthase from the bacillaene trans-acyltransferase polyketide synthase. This 1.95 Å resolution structure provides the highest resolution view available of a modular polyketide synthase ketosynthase and reveals a flanking subdomain that is homologous to an ordered linker in cis-acyltransferase modular polyketide synthases. The structure of the cysteine-to-serine mutant of the ketosynthase acylated by its natural substrate provides high-resolution details of how a native polyketide intermediate is bound and helps explain the basis of ketosynthase substrate specificity. The substrate range of the ketosynthase was further investigated by mass spectrometry.
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Affiliation(s)
- Darren C Gay
- Department of Molecular Biosciences, The University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
| | - Glen Gay
- Department of Molecular Biosciences, The University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
| | - Abram J Axelrod
- Department of Chemistry, The University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA
| | - Matthew Jenner
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Christoph Kohlhaas
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Annette Kampa
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Neil J Oldham
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Jörn Piel
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany; Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Adrian T Keatinge-Clay
- Department of Molecular Biosciences, The University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA; Department of Chemistry, The University of Texas at Austin, 1 University Station A5300, Austin, TX 78712, USA.
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49
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Davison J, Dorival J, Rabeharindranto H, Mazon H, Chagot B, Gruez A, Weissman KJ. Insights into the function of trans-acyl transferase polyketide synthases from the SAXS structure of a complete module. Chem Sci 2014. [DOI: 10.1039/c3sc53511h] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Combined analysis by SAXS, NMR and homology modeling reveals the structure of an apo module from a trans-acyltransferase polyketide synthase.
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Affiliation(s)
- Jack Davison
- Molecular and Structural Enzymology Group
- Université de Lorraine
- Vandœuvre-Lès-Nancy, France
| | - Jonathan Dorival
- Molecular and Structural Enzymology Group
- Université de Lorraine
- Vandœuvre-Lès-Nancy, France
| | - Hery Rabeharindranto
- Molecular and Structural Enzymology Group
- Université de Lorraine
- Vandœuvre-Lès-Nancy, France
| | - Hortense Mazon
- Molecular and Structural Enzymology Group
- Université de Lorraine
- Vandœuvre-Lès-Nancy, France
| | - Benjamin Chagot
- Molecular and Structural Enzymology Group
- Université de Lorraine
- Vandœuvre-Lès-Nancy, France
| | - Arnaud Gruez
- Molecular and Structural Enzymology Group
- Université de Lorraine
- Vandœuvre-Lès-Nancy, France
| | - Kira J. Weissman
- Molecular and Structural Enzymology Group
- Université de Lorraine
- Vandœuvre-Lès-Nancy, France
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50
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Walker MC, Thuronyi BW, Charkoudian LK, Lowry B, Khosla C, Chang MCY. Expanding the fluorine chemistry of living systems using engineered polyketide synthase pathways. Science 2013; 341:1089-94. [PMID: 24009388 PMCID: PMC4057101 DOI: 10.1126/science.1242345] [Citation(s) in RCA: 139] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Organofluorines represent a rapidly expanding proportion of molecules that are used in pharmaceuticals, diagnostics, agrochemicals, and materials. Despite the prevalence of fluorine in synthetic compounds, the known biological scope is limited to a single pathway that produces fluoroacetate. Here, we demonstrate that this pathway can be exploited as a source of fluorinated building blocks for introduction of fluorine into natural-product scaffolds. Specifically, we have constructed pathways involving two polyketide synthase systems, and we show that fluoroacetate can be used to incorporate fluorine into the polyketide backbone in vitro. We further show that fluorine can be inserted site-selectively and introduced into polyketide products in vivo. These results highlight the prospects for the production of complex fluorinated natural products using synthetic biology.
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Affiliation(s)
- Mark C. Walker
- Departments of Chemistry and Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA 94720-1460
| | - Benjamin W. Thuronyi
- Departments of Chemistry and Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA 94720-1460
| | - Louise K. Charkoudian
- Departments of Chemistry, Chemical Engineering, and Biochemistry, Stanford University, Stanford, CA 94305
| | - Brian Lowry
- Departments of Chemistry, Chemical Engineering, and Biochemistry, Stanford University, Stanford, CA 94305
| | - Chaitan Khosla
- Departments of Chemistry, Chemical Engineering, and Biochemistry, Stanford University, Stanford, CA 94305
| | - Michelle C. Y. Chang
- Departments of Chemistry and Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA 94720-1460
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