1
|
Zhao C, Slocum ST, Sherman DH, Ruotolo BT. Time-Resolved Ion Mobility-Mass Spectrometry Reveals Structural Transitions in the Disassembly of Modular Polyketide Syntheses. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:2136-2142. [PMID: 39038158 DOI: 10.1021/jasms.4c00181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
The type 1 polyketide synthase (PKS) assembly line uses its modular structure to produce polyketide natural products that form the basis of many pharmaceuticals. Currently, several cryoelectron microscopy (cryo-EM) structures of a multidomain PKS module have been constructed, but much remains to be learned. Here we utilize ion-mobility mass spectrometry (IM-MS) to record size and shape information and detect different conformational states of a 207 kDa didomain dimer comprised of ketosynthase (KS) and acyl transferase (AT), excised from full-length module. Furthermore, gas-phase stability differences between these different conformations are captured by collision induced unfolding (CIU) technology. Additionally, through tracking these forms as a function of time, we elucidate a detailed disassembly pathway for KS-AT dimers for the first time.
Collapse
Affiliation(s)
- Chunyi Zhao
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Samuel T Slocum
- Life Science Institute, Departments of Medicinal Chemistry, Chemistry and Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - David H Sherman
- Life Science Institute, Departments of Medicinal Chemistry, Chemistry and Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| |
Collapse
|
2
|
Xiang C, Yao S, Wang R, Zhang L. Bioinformatic prediction of the stereoselectivity of modular polyketide synthase: an update of the sequence motifs in ketoreductase domain. Beilstein J Org Chem 2024; 20:1476-1485. [PMID: 38978744 PMCID: PMC11228615 DOI: 10.3762/bjoc.20.131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 06/21/2024] [Indexed: 07/10/2024] Open
Abstract
Polyketides are a major class of natural products, including bioactive medicines such as erythromycin and rapamycin. They are often rich in stereocenters biosynthesized by the ketoreductase (KR) domain within the polyketide synthase (PKS) assembly line. Previous studies have identified conserved motifs in KR sequences that enable the bioinformatic prediction of product stereochemistry. However, the reliability and applicability of these prediction methods have not been thoroughly assessed. In this study, we conducted a comprehensive bioinformatic analysis of 1,762 KR sequences from cis-AT PKSs to reevaluate the residues involved in conferring stereoselectivity. Our findings indicate that the previously identified fingerprint motifs remain valid for KRs in β-modules from actinobacteria, but their reliability diminishes for KRs from other module types or taxonomic origins. Additionally, we have identified several new motifs that exhibit a strong correlation with the stereochemical outcomes of KRs. These updated fingerprint motifs for stereochemical prediction not only enhance our understanding of the enzymatic mechanisms governing stereocontrol but also facilitate accurate stereochemical prediction and genome mining of polyketides derived from modular cis-AT PKSs.
Collapse
Affiliation(s)
- Changjun Xiang
- Department of Chemistry, Fudan University, Shanghai 200433, China
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, Hangzhou 310030, China
| | - Shunyu Yao
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, Hangzhou 310030, China
| | - Ruoyu Wang
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, Hangzhou 310030, China
| | - Lihan Zhang
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, Hangzhou 310030, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310030, China
| |
Collapse
|
3
|
Fergusson CH, Saulog J, Paulo BS, Wilson DM, Liu DY, Morehouse NJ, Waterworth S, Barkei J, Gray CA, Kwan JC, Eustaquio AS, Linington RG. Discovery of a lagriamide polyketide by integrated genome mining, isotopic labeling, and untargeted metabolomics. Chem Sci 2024; 15:8089-8096. [PMID: 38817573 PMCID: PMC11134395 DOI: 10.1039/d4sc00825a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 04/18/2024] [Indexed: 06/01/2024] Open
Abstract
Microorganisms from the order Burkholderiales have been the source of a number of important classes of natural products in recent years. For example, study of the beetle-associated symbiont Burkholderia gladioli led to the discovery of the antifungal polyketide lagriamide; an important molecule from the perspectives of both biotechnology and chemical ecology. As part of a wider project to sequence Burkholderiales genomes from our in-house Burkholderiales library we identified a strain containing a biosynthetic gene cluster (BGC) similar to the original lagriamide BGC. Structure prediction failed to identify any candidate masses for the products of this BGC from untargeted metabolomics mass spectrometry data. However, genome mining from publicly available databases identified fragments of this BGC from a culture collection strain of Paraburkholderia. Whole genome sequencing of this strain revealed the presence of a homologue of this BGC with very high sequence identity. Stable isotope feeding of the two strains in parallel using our newly developed IsoAnalyst platform identified the product of this lagriamide-like BGC directly from the crude fermentation extracts, affording a culturable supply of this interesting compound class. Using a combination of bioinformatic, computational and spectroscopic methods we defined the absolute configurations for all 11 chiral centers in this new metabolite, which we named lagriamide B. Biological testing of lagriamide B against a panel of 21 bacterial and fungal pathogens revealed antifungal activity against the opportunistic human pathogen Aspergillus niger, while image-based Cell Painting analysis indicated that lagriamide B also causes actin filament disruption in U2-OS osteosarcoma cells.
Collapse
Affiliation(s)
- Claire H Fergusson
- Department of Chemistry, Simon Fraser University 8888 University Drive Burnaby BC V5A 1S6 Canada
| | - Julia Saulog
- Department of Chemistry, Simon Fraser University 8888 University Drive Burnaby BC V5A 1S6 Canada
| | - Bruno S Paulo
- Department of Pharmaceutical Sciences and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago Chicago IL 60607 USA
| | - Darryl M Wilson
- Department of Chemistry, Simon Fraser University 8888 University Drive Burnaby BC V5A 1S6 Canada
| | - Dennis Y Liu
- Department of Chemistry, Simon Fraser University 8888 University Drive Burnaby BC V5A 1S6 Canada
| | - Nicholas J Morehouse
- Department of Biological Sciences, University of New Brunswick Saint John NB Canada
| | - Samantha Waterworth
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin Madison WI 53705 USA
| | - John Barkei
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin Madison WI 53705 USA
| | - Christopher A Gray
- Department of Biological Sciences, University of New Brunswick Saint John NB Canada
| | - Jason C Kwan
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin Madison WI 53705 USA
| | - Alessandra S Eustaquio
- Department of Pharmaceutical Sciences and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago Chicago IL 60607 USA
| | - Roger G Linington
- Department of Chemistry, Simon Fraser University 8888 University Drive Burnaby BC V5A 1S6 Canada
| |
Collapse
|
4
|
Kudo K, Nishimura T, Izumikawa M, Kozone I, Hashimoto J, Fujie M, Suenaga H, Ikeda H, Satoh N, Shin-Ya K. Capability of a large bacterial artificial chromosome clone harboring multiple biosynthetic gene clusters for the production of diverse compounds. J Antibiot (Tokyo) 2024; 77:288-298. [PMID: 38438499 DOI: 10.1038/s41429-024-00711-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 02/02/2024] [Accepted: 02/12/2024] [Indexed: 03/06/2024]
Abstract
The biosynthetic gene clusters (BGCs) for the macrocyclic lactone-based polyketide compounds are extremely large-sized because the polyketide synthases that generate the polyketide chains of the basic backbone are of very high molecular weight. In developing a heterologous expression system for the large BGCs amenable to the production of such natural products, we selected concanamycin as an appropriate target. We obtained a bacterial artificial chromosome (BAC) clone with a 211-kb insert harboring the entire BGC responsible for the biosynthesis of concanamycin. Heterologous expression of this clone in a host strain, Streptomyces avermitilis SUKA32, permitted the production of concanamycin, as well as that of two additional aromatic polyketides. Structural elucidation identified these additional products as ent-gephyromycin and a novel compound that was designated JBIR-157. We describe herein sequencing and expression studies performed on these BGCs, demonstrating the utility of large BAC clones for the heterologous expression of cryptic or near-silent loci.
Collapse
Affiliation(s)
- Kei Kudo
- Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Takehiro Nishimura
- Technology Research Association for Next Generation Natural Products Chemistry, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
- Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo, 105-8512, Japan
| | - Miho Izumikawa
- Japan Biological Informatics Consortium (JBIC), 2-4-32 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Ikuko Kozone
- Japan Biological Informatics Consortium (JBIC), 2-4-32 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Junko Hashimoto
- Japan Biological Informatics Consortium (JBIC), 2-4-32 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Manabu Fujie
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Hikaru Suenaga
- Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Haruo Ikeda
- Kitasato Institute for Life Sciences, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
- Technology Research Association for Next Generation Natural Products Chemistry, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Nori Satoh
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Kazuo Shin-Ya
- Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan.
- Technology Research Association for Next Generation Natural Products Chemistry, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan.
| |
Collapse
|
5
|
Nava A, Roberts J, Haushalter RW, Wang Z, Keasling JD. Module-Based Polyketide Synthase Engineering for de Novo Polyketide Biosynthesis. ACS Synth Biol 2023; 12:3148-3155. [PMID: 37871264 PMCID: PMC10661043 DOI: 10.1021/acssynbio.3c00282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Indexed: 10/25/2023]
Abstract
Polyketide retrobiosynthesis, where the biosynthetic pathway of a given polyketide can be reversibly engineered due to the colinearity of the polyketide synthase (PKS) structure and function, has the potential to produce millions of organic molecules. Mixing and matching modules from natural PKSs is one of the routes to produce many of these molecules. Evolutionary analysis of PKSs suggests that traditionally used module boundaries may not lead to the most productive hybrid PKSs and that new boundaries around and within the ketosynthase domain may be more active when constructing hybrid PKSs. As this is still a nascent area of research, the generality of these design principles based on existing engineering efforts remains inconclusive. Recent advances in structural modeling and synthetic biology present an opportunity to accelerate PKS engineering by re-evaluating insights gained from previous engineering efforts with cutting edge tools.
Collapse
Affiliation(s)
- Alberto
A. Nava
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Jacob Roberts
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Bioengineering, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Robert W. Haushalter
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Zilong Wang
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jay D. Keasling
- Joint
BioEnergy Institute, Lawrence Berkeley National
Laboratory, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
- Department
of Bioengineering, University of California,
Berkeley, Berkeley, California 94720, United States
- Center
for Synthetic Biochemistry, Shenzhen Institutes
for Advanced Technologies, Shenzhen 518055, P.R. China
- The
Novo
Nordisk Foundation Center for Biosustainability, Technical University Denmark, Kemitorvet, Building 220, Kongens Lyngby 2800, Denmark
| |
Collapse
|
6
|
Wang J, Deng Z, Liang J, Wang Z. Structural enzymology of iterative type I polyketide synthases: various routes to catalytic programming. Nat Prod Rep 2023; 40:1498-1520. [PMID: 37581222 DOI: 10.1039/d3np00015j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
Time span of literature covered: up to mid-2023Iterative type I polyketide synthases (iPKSs) are outstanding natural chemists: megaenzymes that repeatedly utilize their catalytic domains to synthesize complex natural products with diverse bioactivities. Perhaps the most fascinating but least understood question about type I iPKSs is how they perform the iterative yet programmed reactions in which the usage of domain combinations varies during the synthetic cycle. The programmed patterns are fulfilled by multiple factors, and strongly influence the complexity of the resulting natural products. This article reviews selected reports on the structural enzymology of iPKSs, focusing on the individual domain structures followed by highlighting the representative programming activities that each domain may contribute.
Collapse
Affiliation(s)
- Jialiang Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Jingdan Liang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Zhijun Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| |
Collapse
|
7
|
McCullough TM, Dhar A, Akey DL, Konwerski JR, Sherman DH, Smith JL. Structure of a modular polyketide synthase reducing region. Structure 2023; 31:1109-1120.e3. [PMID: 37348494 PMCID: PMC10527585 DOI: 10.1016/j.str.2023.05.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/04/2023] [Accepted: 05/26/2023] [Indexed: 06/24/2023]
Abstract
The chemical scaffolds of numerous therapeutics are polyketide natural products, many formed by bacterial modular polyketide synthases (PKS). The large and flexible dimeric PKS modules have distinct extension and reducing regions. Structures are known for all individual enzyme domains and several extension regions. Here, we report the structure of the full reducing region from a modular PKS, the ketoreductase (KR), dehydratase (DH), and enoylreductase (ER) domains of module 5 of the juvenimicin PKS. The modular PKS-reducing region has a different architecture than the homologous fatty acid synthase (FAS) and iterative PKS systems in its arrangement of domains and dimer interface. The structure reveals a critical role for linker peptides in the domain interfaces, leading to discovery of key differences in KR domains dependent on module composition. Finally, our studies provide insight into the mechanism underlying modular PKS intermediate shuttling by carrier protein (ACP) domains.
Collapse
Affiliation(s)
- Tyler M McCullough
- Life Sciences Institute, University of Michigan, Ann Arbor MI 48109, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Anya Dhar
- Life Sciences Institute, University of Michigan, Ann Arbor MI 48109, USA
| | - David L Akey
- Life Sciences Institute, University of Michigan, Ann Arbor MI 48109, USA; Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jamie R Konwerski
- Life Sciences Institute, University of Michigan, Ann Arbor MI 48109, USA
| | - David H Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor MI 48109, USA; Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, USA; Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Janet L Smith
- Life Sciences Institute, University of Michigan, Ann Arbor MI 48109, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
| |
Collapse
|
8
|
Kim MC, Winter JM, Cullum R, Smith AJ, Fenical W. Expanding the Utility of Bioinformatic Data for the Full Stereostructural Assignments of Marinolides A and B, 24- and 26-Membered Macrolactones Produced by a Chemically Exceptional Marine-Derived Bacterium. Mar Drugs 2023; 21:367. [PMID: 37367692 DOI: 10.3390/md21060367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 06/15/2023] [Accepted: 06/16/2023] [Indexed: 06/28/2023] Open
Abstract
Marinolides A and B, two new 24- and 26-membered bacterial macrolactones, were isolated from the marine-derived actinobacterium AJS-327 and their stereostructures initially assigned by bioinformatic data analysis. Macrolactones typically possess complex stereochemistry, the assignments of which have been one of the most difficult undertakings in natural products chemistry, and in most cases, the use of X-ray diffraction methods and total synthesis have been the major methods of assigning their absolute configurations. More recently, however, it has become apparent that the integration of bioinformatic data is growing in utility to assign absolute configurations. Genome mining and bioinformatic analysis identified the 97 kb mld biosynthetic cluster harboring seven type I polyketide synthases. A detailed bioinformatic investigation of the ketoreductase and enoylreductase domains within the multimodular polyketide synthases, coupled with NMR and X-ray diffraction data, allowed for the absolute configurations of marinolides A and B to be determined. While using bioinformatics to assign the relative and absolute configurations of natural products has high potential, this method must be coupled with full NMR-based analysis to both confirm bioinformatic assignments as well as any additional modifications that occur during biosynthesis.
Collapse
Affiliation(s)
- Min Cheol Kim
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, Skaggs School of Pharmacy and Pharmaceutical Sciences, Moores Comprehensive Cancer Center, University of California, La Jolla, San Diego, CA 92093, USA
| | - Jaclyn M Winter
- Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, UT 84112, USA
| | - Reiko Cullum
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, Skaggs School of Pharmacy and Pharmaceutical Sciences, Moores Comprehensive Cancer Center, University of California, La Jolla, San Diego, CA 92093, USA
| | - Alexander J Smith
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, Skaggs School of Pharmacy and Pharmaceutical Sciences, Moores Comprehensive Cancer Center, University of California, La Jolla, San Diego, CA 92093, USA
| | - William Fenical
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, Skaggs School of Pharmacy and Pharmaceutical Sciences, Moores Comprehensive Cancer Center, University of California, La Jolla, San Diego, CA 92093, USA
| |
Collapse
|
9
|
Enzymology of assembly line synthesis by modular polyketide synthases. Nat Chem Biol 2023; 19:401-415. [PMID: 36914860 DOI: 10.1038/s41589-023-01277-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 01/31/2023] [Indexed: 03/16/2023]
Abstract
Modular polyketide synthases (PKSs) run catalytic reactions over dozens of steps in a highly orchestrated manner. To accomplish this synthetic feat, they form megadalton multienzyme complexes that are among the most intricate proteins on earth. Polyketide products are of elaborate chemistry with molecular weights of usually several hundred daltons and include clinically important drugs such as erythromycin (antibiotic), rapamycin (immunosuppressant) and epothilone (anticancer drug). The term 'modular' refers to a hierarchical structuring of modules and domains within an overall assembly line arrangement, in which PKS organization is colinearly translated into the polyketide structure. New structural information obtained during the past few years provides substantial direct insight into the orchestration of catalytic events within a PKS module and leads to plausible models for synthetic progress along assembly lines. In light of these structural insights, the PKS engineering field is poised to enter a new era of engineering.
Collapse
|
10
|
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.
Collapse
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.
| |
Collapse
|
11
|
Du Z, Li Y, Liu Y, Shi T. Molecular Insights into Bifunctional Ambruticin DH3 for Substrate Specificity and Catalytic Mechanism. Chemistry 2023; 29:e202203420. [PMID: 36464909 DOI: 10.1002/chem.202203420] [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: 11/03/2022] [Revised: 11/30/2022] [Accepted: 11/30/2022] [Indexed: 12/11/2022]
Abstract
Dehydratase (DH), a domain located at polyketide synthase (PKS) modules, commonly catalyzes the dehydration of β-hydroxy to an α,β-unsaturated acyl intermediate. As a unique bifunctional dehydratase, AmbDH3 (the DH domain of module 3 of the ambruticin PKS) is verified to be responsible for both dehydration and the following pyran-forming cyclization. Besides, in vitro studies showed that its catalytic efficiency varies with different chiral substrates. However, the detailed molecular mechanism of AmbDH3 remains unclear. In this work, the structural rationale for the substrate specificity (2R/2S- and 6R/6S-substrates) in AmbDH3 was elucidated and the complete reaction pathways including dehydration and cyclization were presented. Both MD simulations and binding free energy calculations indicated AmbDH3 had a stronger preference for 2R-substrates (2R6R-2, 2R6S-3) than 2S-substrates (2S6R-1), and residue H51 and G61 around the catalytic pocket were emphasized by forming stable hydrogen bonds with 2R-substrates. In addition, AmbDH3's mild tolerance at C6 was explained by comparison of substrate conformation and hydrogen bond network in 6S- and 6R-substrate systems. The QM/MM results supported a consecutive one-base dehydration and cyclization mechanism for 2R6S-3 substrate with the energy barrier of 25.2 kcal mol-1 and 24.5 kcal mol-1 , respectively. Our computational results uncover the substrate recognition and catalytic process of the first bifunctional dehydratase-cyclase AmbDH3, which will shed light on the application of multifunctional DH domains in PKSs for diverse natural product analogs and benefit the chemoenzymatic synthesis of stereoselective pyran-containing products.
Collapse
Affiliation(s)
- Zeqian Du
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Yongzhen Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Yihan Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Ting Shi
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, No. 800 Dongchuan Rd., Shanghai, 200240, P. R. China
| |
Collapse
|
12
|
Oves-Costales D, Gren T, Sterndorff EB, Martín J, Ortiz-López FJ, Jørgensen TS, Jiang X, Román-Hurtado F, Reyes F, Genilloud O, Weber T. Identification and heterologous expression of the globomycin biosynthetic gene cluster. Synth Syst Biotechnol 2023; 8:206-212. [PMID: 36844473 PMCID: PMC9943842 DOI: 10.1016/j.synbio.2023.02.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/30/2023] [Accepted: 02/02/2023] [Indexed: 02/10/2023] Open
Abstract
Globomycin is a cyclic lipodepsipeptide originally isolated from several Streptomyces species which displays strong and selective antibacterial activity against Gram-negative pathogens. Its mode of action is based on the competitive inhibition of the lipoprotein signal peptidase II (LspA), which is absent in eukaryotes and considered an attractive target for the development of new antibiotics. Despite its interesting biological properties, the gene cluster encoding its biosynthesis has not yet been identified. In this study we employed a genome-mining approach in the globomycin-producing Streptomyces sp. CA-278952 to identify a candidate gene cluster responsible for its biosynthesis. A null mutant was constructed using CRISPR base editing where production was abolished, strongly suggesting its involvement in the biosynthesis. The putative gene cluster was then cloned and heterologously expressed in Streptomyces albus J1074 and Streptomyces coelicolor M1146, therefore unambiguously linking globomycin and its biosynthetic gene cluster. Our work paves the way for the biosynthesis of new globomycin derivatives with improved pharmacological properties.
Collapse
Affiliation(s)
- Daniel Oves-Costales
- Fundacion MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda del Conocimiento 34, 18016, Armilla, Granada, Spain,Corresponding author.
| | - Tetiana Gren
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, building 220, 2800 Kgs. Lyngby, Denmark
| | - Eva Baggesgaard Sterndorff
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, building 220, 2800 Kgs. Lyngby, Denmark
| | - Jesús Martín
- Fundacion MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda del Conocimiento 34, 18016, Armilla, Granada, Spain
| | - Francisco Javier Ortiz-López
- Fundacion MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda del Conocimiento 34, 18016, Armilla, Granada, Spain
| | - Tue S. Jørgensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, building 220, 2800 Kgs. Lyngby, Denmark
| | - Xinglin Jiang
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, building 220, 2800 Kgs. Lyngby, Denmark
| | - Fernando Román-Hurtado
- Fundacion MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda del Conocimiento 34, 18016, Armilla, Granada, Spain
| | - Fernando Reyes
- Fundacion MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda del Conocimiento 34, 18016, Armilla, Granada, Spain
| | - Olga Genilloud
- Fundacion MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda del Conocimiento 34, 18016, Armilla, Granada, Spain,Corresponding author.
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, building 220, 2800 Kgs. Lyngby, Denmark,Corresponding author.
| |
Collapse
|
13
|
Magar RT, Pham VTT, Poudel PB, Nguyen HT, Bridget AF, Sohng JK. Biosynthetic pathway of peucemycin and identification of its derivative from Streptomyces peucetius. Appl Microbiol Biotechnol 2023; 107:1217-1231. [PMID: 36680588 DOI: 10.1007/s00253-023-12385-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/08/2023] [Accepted: 01/10/2023] [Indexed: 01/22/2023]
Abstract
Streptomyces peucetius ATCC 27952 is a well-known producer of important anticancer compounds, daunorubicin and doxorubicin. In this study, we successfully identified a new macrolide, 25-hydroxy peucemycin, that exhibited an antibacterial effect on some pathogens. Based on the structure of a newly identified compound and through the inactivation of a polyketide synthase gene, we successfully identified its biosynthetic gene cluster which was considered to be the cryptic biosynthetic gene cluster. The biosynthetic gene cluster spans 51 kb with 16 open reading frames. Five type I polyketide synthase (PKS) genes encode eight modules that synthesize the polyketide chain of peucemycin before undergoing post-PKS tailoring steps. In addition to the regular starter and extender units, some modules have specificity towards ethylmalonyl-CoA and unusual butylmalonyl-CoA. A credible explanation for the specificity of the unusual extender unit has been searched for. Moreover, the enzyme responsible for the final tailoring pathway was also identified. Based on all findings, a plausible biosynthetic pathway is here proposed. KEY POINTS: • Identification of a new macrolide, 25-hydroxy peucemycin. • An FMN-dependent monooxygenase is responsible for the hydroxylation of peucemycin. • The module encoded by peuC is unique to accept the butylmalonyl-CoA as an unusual extender unit.
Collapse
Affiliation(s)
- Rubin Thapa Magar
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sun Moon-Ro 221, Tangjeong-Myeon, Asan-Si, Chungnam, 31460, South Korea
| | - Van Thuy Thi Pham
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sun Moon-Ro 221, Tangjeong-Myeon, Asan-Si, Chungnam, 31460, South Korea
| | - Purna Bahadur Poudel
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sun Moon-Ro 221, Tangjeong-Myeon, Asan-Si, Chungnam, 31460, South Korea
| | - Hue Thi Nguyen
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sun Moon-Ro 221, Tangjeong-Myeon, Asan-Si, Chungnam, 31460, South Korea
| | - Adzemye Fovennso Bridget
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sun Moon-Ro 221, Tangjeong-Myeon, Asan-Si, Chungnam, 31460, South Korea
| | - Jae Kyung Sohng
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sun Moon-Ro 221, Tangjeong-Myeon, Asan-Si, Chungnam, 31460, South Korea.
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, 70 Sun Moon-Ro 221, Tangjeong-Myeon, Asan-Si, Chungnam, 31460, South Korea.
| |
Collapse
|
14
|
Dashti Y, Tajabadi FM, Wu LJ, Sumang FA, Escasinas A, Ellis Allenby NE, Errington J. Discovery of Demurilactone A: A Specific Growth Inhibitor of L-Form Bacillus subtilis. ACS Infect Dis 2022; 8:2253-2258. [PMID: 36268971 PMCID: PMC9673147 DOI: 10.1021/acsinfecdis.2c00220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Metabolic profiling of the extracts from a library of actinobacteria led to the identification of a novel polyketide, demurilactone A, produced by Streptomyces strain DEM21308. The structure of the compound was assigned based on a detailed investigation of 1D/2D NMR spectra and HR-MS. Whole genome DNA sequencing, followed by bioinformatics analysis and insertional mutagenesis, identified type I polyketide synthases encoded by the dml gene cluster to direct the biosynthesis of this polyene macrolide. While the number of modules is consistent with the carbon backbone of the assigned structure, some discrepancies were identified in the domain organization of five modules. Close investigation of the amino acid sequences identified several mutations in the conserved motifs of nonfunctional domains. Furthermore, the absolute configuration of hydroxy-bearing stereocenters was proposed based on analyses of the ketoreductase domains. Remarkably, although demurilactone A has little detectable activity against normal-walled bacteria, it specifically inhibits the growth of cell wall-deficient "L-form" Bacillus subtilis at a minimum inhibitory concentration value of 16 μg/mL. Time-lapse microscopy analyses revealed that demurilactone affects membrane dynamics, probably by reducing membrane fluidity. This compound could be a powerful reagent for studying long-standing questions about the involvement of L-forms in recurrent infection.
Collapse
Affiliation(s)
- Yousef Dashti
- The
Centre for Bacterial Cell Biology, Biosciences Institute, Medical School, Newcastle University, Newcastle Upon Tyne NE2
4AX, U.K.,,
| | - Fatemeh Mazraati Tajabadi
- Odyssey
Therapeutics Inc, The Biosphere, Draymans Way, Newcastle Helix, Newcastle
Upon Tyne NE4 5BX, U.K.
| | - Ling Juan Wu
- The
Centre for Bacterial Cell Biology, Biosciences Institute, Medical School, Newcastle University, Newcastle Upon Tyne NE2
4AX, U.K.
| | - Felaine Anne Sumang
- The
Centre for Bacterial Cell Biology, Biosciences Institute, Medical School, Newcastle University, Newcastle Upon Tyne NE2
4AX, U.K.
| | - Alexander Escasinas
- Odyssey
Therapeutics Inc, The Biosphere, Draymans Way, Newcastle Helix, Newcastle
Upon Tyne NE4 5BX, U.K.
| | | | - Jeff Errington
- The
Centre for Bacterial Cell Biology, Biosciences Institute, Medical School, Newcastle University, Newcastle Upon Tyne NE2
4AX, U.K.,Odyssey
Therapeutics Inc, The Biosphere, Draymans Way, Newcastle Helix, Newcastle
Upon Tyne NE4 5BX, U.K.,
| |
Collapse
|
15
|
Al Fahad AJ. Putative Biosynthesis of Talarodioxadione & Talarooxime from Talaromyces stipitatus. Molecules 2022; 27:molecules27144473. [PMID: 35889347 PMCID: PMC9318984 DOI: 10.3390/molecules27144473] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/06/2022] [Accepted: 07/08/2022] [Indexed: 02/01/2023] Open
Abstract
Polyesters containing 2,4-dihydroxy-6-(2-hydroxypropyl)benzoate and 3-hydroxybutyrate moieties have been isolated from many fungal species. Talaromyces stipitatus was previously reported to produce a similar polyester, talapolyester G. The complete genome sequence and the development of bioinformatics tools have enabled the discovery of the biosynthetic potential of this microorganism. Here, a putative biosynthetic gene cluster (BGC) of the polyesters encoding a highly reducing polyketide synthase (HR-PKS) and nonreducing polyketide synthase (NR-PKS), a cytochrome P450 and a regulator, was identified. Although talapolyester G does not require an oxidative step for its biosynthesis, further investigation into the secondary metabolite production of T. stipitatus resulted in isolating two new metabolites called talarodioxadione and talarooxime, in addition to three known compounds, namely 6-hydroxymellein, 15G256α and transtorine that have never been reported from this organism. Interestingly, the biosynthesis of the cyclic polyester 15G256α requires hydroxylation of an inactive methyl group and thus could be a product of the identified gene cluster. The two compounds, talarooxime and transtorine, are probably the catabolic metabolites of tryptophan through the kynurenine pathway. Tryptophan metabolism exists in almost all organisms and has been of interest to many researchers. The biosynthesis of the new oxime is proposed to involve two subsequent N-hydroxylation of 2-aminoacetophenone.
Collapse
Affiliation(s)
- Ahmed J Al Fahad
- National Center for Biotechnology, Life Science & Environment Research Institute, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia
| |
Collapse
|
16
|
An JS, Lim HJ, Lee JY, Jang YJ, Nam SJ, Lee SK, Oh DC. Hamuramicin C, a Cytotoxic Bicyclic Macrolide Isolated from a Wasp Gut Bacterium. JOURNAL OF NATURAL PRODUCTS 2022; 85:936-942. [PMID: 35362983 DOI: 10.1021/acs.jnatprod.1c01075] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A new bicyclic macrolide, hamuramicin C (1), was isolated from Streptomyces sp. MBP16, a gut bacterial strain of the wasp Vespa crabro flavofasciata. Its 22-membered macrocyclic lactone structure was determined by NMR and mass spectrometry. The relative configurations of hamuramicin C (1) were assigned by J-based configuration analysis utilizing 1H rotating frame Overhauser effect spectroscopy and heteronuclear long-range coupling NMR spectroscopy. Genomic and bioinformatic analyses of the bacterial strain enabled identification of the type-I polyketide synthase pathway, which employs a trans-acyltransferase system. The absolute configurations of 1 were proposed based on the analysis of the sequences of ketoreductases in the modular gene cluster. Moreover, hamuramicin C (1) demonstrated significant inhibitory activity against diverse human cancer cell lines (HCT116, A549, SNU-638, SK-HEP-1, and MDA-MB-231).
Collapse
Affiliation(s)
- Joon Soo An
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyung-Ju Lim
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Ji Yun Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Yong-Joon Jang
- Natura Center of Life and Environment, Seoul 08826, Republic of Korea
| | - Sang-Jip Nam
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| |
Collapse
|
17
|
Aris P, Yan L, Wei Y, Chang Y, Shi B, Xia X. Conservation of griseofulvin genes in the gsf gene cluster among fungal genomes. G3 (BETHESDA, MD.) 2022; 12:jkab399. [PMID: 34792561 PMCID: PMC9210304 DOI: 10.1093/g3journal/jkab399] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 11/08/2021] [Indexed: 11/12/2022]
Abstract
The polyketide griseofulvin is a natural antifungal compound and research in griseofulvin has been key in establishing our current understanding of polyketide biosynthesis. Nevertheless, the griseofulvin gsf biosynthetic gene cluster (BGC) remains poorly understood in most fungal species, including Penicillium griseofulvum where griseofulvin was first isolated. To elucidate essential genes involved in griseofulvin biosynthesis, we performed third-generation sequencing to obtain the genome of P. griseofulvum strain D-756. Furthermore, we gathered publicly available genome of 11 other fungal species in which gsf gene cluster was identified. In a comparative genome analysis, we annotated and compared the gsf BGC of all 12 fungal genomes. Our findings show no gene rearrangements at the gsf BGC. Furthermore, seven gsf genes are conserved by most genomes surveyed whereas the remaining six were poorly conserved. This study provides new insights into differences between gsf BGC and suggests that seven gsf genes are essential in griseofulvin production.
Collapse
Affiliation(s)
- Parisa Aris
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Lihong Yan
- National Joint Engineering Research Center of Industrial Microbiology and Fermentation Technology, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China
- Department of Bioengineering, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Yulong Wei
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Ying Chang
- National Joint Engineering Research Center of Industrial Microbiology and Fermentation Technology, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China
- Department of Bioengineering, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Bihong Shi
- National Joint Engineering Research Center of Industrial Microbiology and Fermentation Technology, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China
- Department of Bioengineering, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Xuhua Xia
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Ottawa Institute of Systems Biology, Ottawa, ON K1H 8M5, Canada
| |
Collapse
|
18
|
Carretero-Molina D, Ortiz-López FJ, Gren T, Oves-Costales D, Martín J, Román-Hurtado F, Sparholt Jørgensen T, de la Cruz M, Díaz C, Vicente F, Blin K, Reyes F, Weber T, Genilloud O. Discovery of gargantulides B and C, new 52-membered macrolactones from Amycolatopsis sp. Complete absolute stereochemistry of the gargantulide family. Org Chem Front 2022. [DOI: 10.1039/d1qo01480c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Gargantulides B and C are among the most complex bacterial polyketides discovered so far. A combination of NMR and genome-based bioinformatics analyses allowed us to complete and revise the absolute stereochemistry of the entire gargantulide family.
Collapse
Affiliation(s)
- Daniel Carretero-Molina
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain
| | - Francisco Javier Ortiz-López
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain
| | - Tetiana Gren
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, building 220, 2800 Kgs. Lyngby, Denmark
| | - Daniel Oves-Costales
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain
| | - Jesús Martín
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain
| | - Fernando Román-Hurtado
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain
| | - Tue Sparholt Jørgensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, building 220, 2800 Kgs. Lyngby, Denmark
| | - Mercedes de la Cruz
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain
| | - Caridad Díaz
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain
| | - Francisca Vicente
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain
| | - Kai Blin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, building 220, 2800 Kgs. Lyngby, Denmark
| | - Fernando Reyes
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, building 220, 2800 Kgs. Lyngby, Denmark
| | - Olga Genilloud
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain
| |
Collapse
|
19
|
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.
Collapse
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
| |
Collapse
|
20
|
Tsutsumi H, Katsuyama Y, Tezuka T, Miyano R, Inahashi Y, Takahashi Y, Nakashima T, Ohnishi Y. Identification and Analysis of the Biosynthetic Gene Cluster for the Indolizidine Alkaloid Iminimycin in Streptomyces griseus. Chembiochem 2021; 23:e202100517. [PMID: 34767291 DOI: 10.1002/cbic.202100517] [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: 09/27/2021] [Revised: 10/27/2021] [Indexed: 11/06/2022]
Abstract
Indolizidine alkaloids, which have versatile bioactivities, are produced by various organisms. Although the biosynthesis of some indolizidine alkaloids has been studied, the enzymatic machinery for their biosynthesis in Streptomyces remains elusive. Here, we report the identification and analysis of the biosynthetic gene cluster for iminimycin, an indolizidine alkaloid with a 6-5-3 tricyclic system containing an iminium cation from Streptomyces griseus. The gene cluster has 22 genes, including four genes encoding polyketide synthases (PKSs), which consist of eight modules in total. In vitro analysis of the first module revealed that its acyltransferase domain selects malonyl-CoA, although predicted to select methylmalonyl-CoA. Inactivation of seven tailoring enzyme-encoding genes and structural elucidation of four compounds accumulated in mutants provided important insights into iminimycin biosynthesis, although some of these compounds appeared to be shunt products. This study expands our knowledge of the biosynthetic machinery of indolizidine alkaloids and the enzymatic chemistry of PKS.
Collapse
Affiliation(s)
- Hayama Tsutsumi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yohei Katsuyama
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Takeaki Tezuka
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Rei Miyano
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1, Minato-ku, Tokyo, 108-8641, Japan
| | - Yuki Inahashi
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1, Minato-ku, Tokyo, 108-8641, Japan.,Kitasato Institute for Life Sciences, Present: Ōmura Satoshi Memorial Institute), Kitasato University, 5-9-1, Minato-ku, Tokyo, 108-8641, Japan
| | - Yoko Takahashi
- Kitasato Institute for Life Sciences, Present: Ōmura Satoshi Memorial Institute), Kitasato University, 5-9-1, Minato-ku, Tokyo, 108-8641, Japan
| | - Takuji Nakashima
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1, Minato-ku, Tokyo, 108-8641, Japan.,Kitasato Institute for Life Sciences, Present: Ōmura Satoshi Memorial Institute), Kitasato University, 5-9-1, Minato-ku, Tokyo, 108-8641, Japan
| | - Yasuo Ohnishi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| |
Collapse
|
21
|
Kontou EE, Gren T, Ortiz-López FJ, Thomsen E, Oves-Costales D, Díaz C, de la Cruz M, Jiang X, Jørgensen TS, Blin K, Charusanti P, Reyes F, Genilloud O, Weber T. Discovery and Characterization of Epemicins A and B, New 30-Membered Macrolides from Kutzneria sp. CA-103260. ACS Chem Biol 2021; 16:1456-1468. [PMID: 34279911 DOI: 10.1021/acschembio.1c00318] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Actinobacteria have been a rich source of novel, structurally complex natural products for many decades. Although the largest genus is Streptomyces, from which the majority of antibiotics in current and past clinical use were originally isolated, other less common genera also have the potential to produce a wealth of novel secondary metabolites. One example is the Kutzneria genus, which currently contains only five reported species. One of these species is Kutzneria albida DSM 43870T, which has 46 predicted biosynthetic gene clusters and is known to produce the macrolide antibiotic aculeximycin. Here, we report the isolation and structural characterization of two novel 30-membered glycosylated macrolides, epemicins A and B, that are structurally related to aculeximycin, from a rare Kutzneria sp. The absolute configuration for all chiral centers in the two compounds is proposed based on extensive 1D and 2D NMR studies and bioinformatics analysis of the gene cluster. Through heterologous expression and genetic inactivation, we have confirmed the link between the biosynthetic gene cluster and the new molecules. These findings show the potential of rare Actinobacteria to produce new, structurally diverse metabolites. Furthermore, the gene inactivation represents the first published report to genetically manipulate a representative of the Kutzneria genus.
Collapse
Affiliation(s)
- Eftychia Eva Kontou
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Tetiana Gren
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Francisco Javier Ortiz-López
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento, 34 Parque Tecnológico de Ciencias de la Salud, 18016 Armilla, Granada, Spain
| | - Emil Thomsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Daniel Oves-Costales
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento, 34 Parque Tecnológico de Ciencias de la Salud, 18016 Armilla, Granada, Spain
| | - Caridad Díaz
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento, 34 Parque Tecnológico de Ciencias de la Salud, 18016 Armilla, Granada, Spain
| | - Mercedes de la Cruz
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento, 34 Parque Tecnológico de Ciencias de la Salud, 18016 Armilla, Granada, Spain
| | - Xinglin Jiang
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Tue Sparholt Jørgensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Kai Blin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Pep Charusanti
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet bygning 220, 2800 Kgs. Lyngby, Denmark
| | - Fernando Reyes
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento, 34 Parque Tecnológico de Ciencias de la Salud, 18016 Armilla, Granada, Spain
| | - Olga Genilloud
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento, 34 Parque Tecnológico de Ciencias de la Salud, 18016 Armilla, Granada, Spain
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet bygning 220, 2800 Kgs. Lyngby, Denmark
| |
Collapse
|
22
|
Shi P, Li Y, Zhu J, Shen Y, Wang H. Targeted Discovery of the Polyene Macrolide Hexacosalactone A from Streptomyces by Reporter-Guided Selection of Fermentation Media. JOURNAL OF NATURAL PRODUCTS 2021; 84:1924-1929. [PMID: 34170140 DOI: 10.1021/acs.jnatprod.1c00144] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
New approaches are still needed to fully explore the biosynthetic potential of microbes. We recently devised a melC reporter-guided fermentation media screening approach for targeted activation of cryptic gene clusters. Using this approach, we successfully activated the expression of the hcl gene cluster in Streptomyces sp. LZ35 and discovered a novel polyene macrolide hexacosalactone A (1).
Collapse
Affiliation(s)
- Peng Shi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, People's Republic of China
| | - Yaoyao Li
- Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, People's Republic of China
| | - Jing Zhu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, People's Republic of China
| | - Yuemao Shen
- Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, People's Republic of China
| | - Haoxin Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, People's Republic of China
| |
Collapse
|
23
|
Kahlert L, Villanueva M, Cox RJ, Skellam EJ. Biosynthesis of 6-Hydroxymellein Requires a Collaborating Polyketide Synthase-like Enzyme. Angew Chem Int Ed Engl 2021; 60:11423-11429. [PMID: 33661567 PMCID: PMC8251887 DOI: 10.1002/anie.202100969] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/22/2021] [Indexed: 12/12/2022]
Abstract
The polyketide synthase (PKS)-like protein TerB, consisting of inactive dehydratase, inactive C-methyltransferase, and functional ketoreductase domains collaborates with the iterative non reducing PKS TerA to produce 6-hydroxymellein, a key pathway intermediate during the biosynthesis of various fungal natural products. The catalytically inactive dehydratase domain of TerB appears to mediate productive interactions with TerA, demonstrating a new mode of trans-interaction between iterative PKS components.
Collapse
Affiliation(s)
- Lukas Kahlert
- Institute for Organic Chemistry and BMWZLeibniz Universität HannoverSchneiderberg 3830167HannoverGermany
| | - Miranda Villanueva
- Institute for Organic Chemistry and BMWZLeibniz Universität HannoverSchneiderberg 3830167HannoverGermany
- Current address: The Molecular Biology InstituteUCLALos AngelesCA90095-1570USA
| | - Russell J. Cox
- Institute for Organic Chemistry and BMWZLeibniz Universität HannoverSchneiderberg 3830167HannoverGermany
| | - Elizabeth J. Skellam
- Institute for Organic Chemistry and BMWZLeibniz Universität HannoverSchneiderberg 3830167HannoverGermany
- Current address: Department of Chemistry & BioDiscovery InstituteUniversity of North Texas1155 Union Circle 305220DentonTX76203USA
| |
Collapse
|
24
|
Kahlert L, Villanueva M, Cox RJ, Skellam EJ. Biosynthesis of 6‐Hydroxymellein Requires a Collaborating Polyketide Synthase‐like Enzyme. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202100969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Lukas Kahlert
- Institute for Organic Chemistry and BMWZ Leibniz Universität Hannover Schneiderberg 38 30167 Hannover Germany
| | - Miranda Villanueva
- Institute for Organic Chemistry and BMWZ Leibniz Universität Hannover Schneiderberg 38 30167 Hannover Germany
- Current address: The Molecular Biology Institute UCLA Los Angeles CA 90095-1570 USA
| | - Russell J. Cox
- Institute for Organic Chemistry and BMWZ Leibniz Universität Hannover Schneiderberg 38 30167 Hannover Germany
| | - Elizabeth J. Skellam
- Institute for Organic Chemistry and BMWZ Leibniz Universität Hannover Schneiderberg 38 30167 Hannover Germany
- Current address: Department of Chemistry & BioDiscovery Institute University of North Texas 1155 Union Circle 305220 Denton TX 76203 USA
| |
Collapse
|
25
|
Adrover-Castellano ML, Schmidt JJ, Sherman DH. Biosynthetic Cyclization Catalysts for the Assembly of Peptide and Polyketide Natural Products. ChemCatChem 2021; 13:2095-2116. [PMID: 34335987 PMCID: PMC8320681 DOI: 10.1002/cctc.202001886] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Indexed: 12/13/2022]
Abstract
Many biologically active natural products are synthesized by nonribosomal peptide synthetases (NRPSs), polyketide synthases (PKSs) and their hybrids. These megasynthetases contain modules possessing distinct catalytic domains that allow for substrate initiation, chain extension, processing and termination. At the end of a module, a terminal domain, usually a thioesterase (TE), is responsible for catalyzing the release of the NRPS or PKS as a linear or cyclized product. In this review, we address the general cyclization mechanism of the TE domain, including oligomerization and the fungal C-C bond forming Claisen-like cyclases (CLCs). Additionally, we include examples of cyclization catalysts acting within or at the end of a module. Furthermore, condensation-like (CT) domains, terminal reductase (R) domains, reductase-like domains that catalyze Dieckmann condensation (RD), thioesterase-like Dieckmann cyclases, trans-acting TEs from the penicillin binding protein (PBP) enzyme family, product template (PT) domains and others will also be reviewed. The studies summarized here highlight the remarkable diversity of NRPS and PKS cyclization catalysts for the production of biologically relevant, complex cyclic natural products and related compounds.
Collapse
Affiliation(s)
| | - Jennifer J Schmidt
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109-2216 (USA)
| | - David H Sherman
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109-2216 (USA)
| |
Collapse
|
26
|
An JS, Shin B, Kim TH, Hwang S, Shin YH, Cui J, Du YE, Yi J, Nam SJ, Hong S, Shin J, Jang J, Yoon YJ, Oh DC. Dumulmycin, an Antitubercular Bicyclic Macrolide from a Riverine Sediment-Derived Streptomyces sp. Org Lett 2021; 23:3359-3363. [DOI: 10.1021/acs.orglett.1c00847] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Joon Soo An
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Bora Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Tae Ho Kim
- Molecular Mechanism of Antibiotics, Division of Life Science, Division of Bio & Medical Big Data Department (BK4 Program), Research Institute of Life Science, Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea
| | - Sunghoon Hwang
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Yern-Hyerk Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Jinsheng Cui
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Young Eun Du
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Jungwoo Yi
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sang-Jip Nam
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Suckchang Hong
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Jongheon Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Jichan Jang
- Molecular Mechanism of Antibiotics, Division of Life Science, Division of Bio & Medical Big Data Department (BK4 Program), Research Institute of Life Science, Gyeongsang National University, Jinju, Gyeongnam 52828, Republic of Korea
| | - Yeo Joon Yoon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| |
Collapse
|
27
|
Quantitative Proteomics Analysis Reveals the Function of the Putative Ester Cyclase UvEC1 in the Pathogenicity of the Rice False Smut Fungus Ustilaginoidea virens. Int J Mol Sci 2021; 22:ijms22084069. [PMID: 33920773 PMCID: PMC8071170 DOI: 10.3390/ijms22084069] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/13/2021] [Accepted: 04/13/2021] [Indexed: 02/06/2023] Open
Abstract
Rice false smut is a fungal disease distributed worldwide and caused by Ustilaginoidea virens. In this study, we identified a putative ester cyclase (named as UvEC1) as being significantly upregulated during U. virens infection. UvEC1 contained a SnoaL-like polyketide cyclase domain, but the functions of ketone cyclases such as SnoaL in plant fungal pathogens remain unclear. Deletion of UvEC1 caused defects in vegetative growth and conidiation. UvEC1 was also required for response to hyperosmotic and oxidative stresses and for maintenance of cell wall integrity. Importantly, ΔUvEC1 mutants exhibited reduced virulence. We performed a tandem mass tag (TMT)-based quantitative proteomic analysis to identify differentially accumulating proteins (DAPs) between the ΔUvEC1-1 mutant and the wild-type isolate HWD-2. Proteomics data revealed that UvEC1 has a variety of effects on metabolism, protein localization, catalytic activity, binding, toxin biosynthesis and the spliceosome. Taken together, our findings suggest that UvEC1 is critical for the development and virulence of U. virens.
Collapse
|
28
|
Hirsch M, Kumru K, Desai RR, Fitzgerald BJ, Miyazawa T, Ray KA, Saif N, Spears S, Keatinge-Clay AT. Insights into modular polyketide synthase loops aided by repetitive sequences. Proteins 2021; 89:1099-1110. [PMID: 33843112 DOI: 10.1002/prot.26083] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 02/05/2021] [Accepted: 04/02/2021] [Indexed: 11/08/2022]
Abstract
The loops of modular polyketide synthases (PKSs) serve diverse functions but are largely uncharacterized. They frequently contain amino acid repeats resulting from genetic events such as slipped-strand mispairing. Determining the tolerance of loops to amino acid changes would aid in understanding and engineering these multidomain molecule factories. Here, tandem repeats in the DNA encoding 949 modules within 129 cis-acyltransferase PKSs were cataloged, and the locations of the corresponding amino acids within the module were identified. The most frequently inserted interdomain loop corresponds with the updated module boundary immediately downstream of the ketosynthase (KS), while the loops bordering the dehydratase are nearly intolerant to such insertions. From the 949 modules, no repetitive sequence loop insertions are located within ACP, and only 2 reside within KS, indicating the sensitivity of these domains to alteration.
Collapse
Affiliation(s)
- Melissa Hirsch
- Department of Chemistry, The University of Texas at Austin, Austin, Texas, USA
| | - Kaan Kumru
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Ronak R Desai
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Brendan J Fitzgerald
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Takeshi Miyazawa
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Katherine A Ray
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Nisha Saif
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Samantha Spears
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Adrian T Keatinge-Clay
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| |
Collapse
|
29
|
Antileishmanial macrolides from ant-associated Streptomyces sp. ISID311. Bioorg Med Chem 2021; 32:116016. [PMID: 33493972 DOI: 10.1016/j.bmc.2021.116016] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 01/04/2021] [Accepted: 01/07/2021] [Indexed: 02/08/2023]
Abstract
Three antifungal macrolides cyphomycin (1), caniferolide C (2) and GT-35 (3) were isolated from Streptomyces sp. ISID311, a bacterial symbiont associated with Cyphomyrmex fungus-growing ants. The planar structures of these compounds were established by 1 and 2D NMR data and MS analysis. The relative configurations of 1-3 were established using Kishi's universal NMR database method, NOE/ROE analysis and coupling constants analysis assisted by comparisons with NMR data of related compounds. Detailed bioinformatic analysis of cyphomycin biosynthetic gene cluster confirmed the stereochemical assignments. Compounds 1-3 displayed high antagonism against different strains of Escovopsis sp., pathogen fungi specialized to the fungus-growing ant system. Compounds 1-3 also exhibited potent antiprotozoal activity against intracellular amastigotes of the human parasite Leishmania donovani with IC50 values of 2.32, 0.091 and 0.073 µM, respectively, with high selectivity indexes.
Collapse
|
30
|
Liu L, Yu Q, Zhang H, Tao W, Wang R, Bai L, Zhao YL, Shi T. Theoretical study on substrate recognition and catalytic mechanisms of gephyronic acid dehydratase DH1. Catal Sci Technol 2021. [DOI: 10.1039/d0cy01776k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The bifunctional dehydratase GphF DH1 catalyzes both the dehydration of β-hydroxy and the double bond isomerization with the energy barrier of 27.0 kcal mol−1 and 17.2 kcal mol−1 respectively.
Collapse
Affiliation(s)
- Lei Liu
- State Key Laboratory of Microbial Metabolism
- Joint International Research Laboratory of Metabolic and Developmental Sciences
- School of Life Sciences and Biotechnology
- Shanghai Jiao Tong University
- Shanghai 200240
| | - Qian Yu
- State Key Laboratory of Microbial Metabolism
- Joint International Research Laboratory of Metabolic and Developmental Sciences
- School of Life Sciences and Biotechnology
- Shanghai Jiao Tong University
- Shanghai 200240
| | - Haoqing Zhang
- State Key Laboratory of Microbial Metabolism
- Joint International Research Laboratory of Metabolic and Developmental Sciences
- School of Life Sciences and Biotechnology
- Shanghai Jiao Tong University
- Shanghai 200240
| | - Wentao Tao
- State Key Laboratory of Microbial Metabolism
- Joint International Research Laboratory of Metabolic and Developmental Sciences
- School of Life Sciences and Biotechnology
- Shanghai Jiao Tong University
- Shanghai 200240
| | - Rufan Wang
- State Key Laboratory of Microbial Metabolism
- Joint International Research Laboratory of Metabolic and Developmental Sciences
- School of Life Sciences and Biotechnology
- Shanghai Jiao Tong University
- Shanghai 200240
| | - Linquan Bai
- State Key Laboratory of Microbial Metabolism
- Joint International Research Laboratory of Metabolic and Developmental Sciences
- School of Life Sciences and Biotechnology
- Shanghai Jiao Tong University
- Shanghai 200240
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism
- Joint International Research Laboratory of Metabolic and Developmental Sciences
- School of Life Sciences and Biotechnology
- Shanghai Jiao Tong University
- Shanghai 200240
| | - Ting Shi
- State Key Laboratory of Microbial Metabolism
- Joint International Research Laboratory of Metabolic and Developmental Sciences
- School of Life Sciences and Biotechnology
- Shanghai Jiao Tong University
- Shanghai 200240
| |
Collapse
|
31
|
Drufva EE, Hix EG, Bailey CB. Site directed mutagenesis as a precision tool to enable synthetic biology with engineered modular polyketide synthases. Synth Syst Biotechnol 2020; 5:62-80. [PMID: 32637664 PMCID: PMC7327777 DOI: 10.1016/j.synbio.2020.04.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/01/2020] [Accepted: 04/06/2020] [Indexed: 12/04/2022] Open
Abstract
Modular polyketide synthases (PKSs) are a multidomain megasynthase class of biosynthetic enzymes that have great promise for the development of new compounds, from new pharmaceuticals to high value commodity and specialty chemicals. Their colinear biosynthetic logic has been viewed as a promising platform for synthetic biology for decades. Due to this colinearity, domain swapping has long been used as a strategy to introduce molecular diversity. However, domain swapping often fails because it perturbs critical protein-protein interactions within the PKS. With our increased level of structural elucidation of PKSs, using judicious targeted mutations of individual residues is a more precise way to introduce molecular diversity with less potential for global disruption of the protein architecture. Here we review examples of targeted point mutagenesis to one or a few residues harbored within the PKS that alter domain specificity or selectivity, affect protein stability and interdomain communication, and promote more complex catalytic reactivity.
Collapse
Key Words
- ACP, acyl carrier protein
- AT, acyltransferase
- DEBS, 6-deoxyerthronolide B synthase
- DH, dehydratase
- EI, enoylisomerase
- ER, enoylreductase
- KR, ketoreductase
- KS, ketosynthase
- LM, loading module
- MT, methyltransferase
- Mod, module
- PKS, polyketide synthase
- PS, pyran synthase
- Polyketide synthase
- Protein engineering
- Rational design
- SNAC, N-acetyl cysteamine
- Saturation mutagenesis
- Site directed mutagenesis
- Synthetic biology
Collapse
Affiliation(s)
- Erin E. Drufva
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN, 37996, USA
| | - Elijah G. Hix
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN, 37996, USA
| | - Constance B. Bailey
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN, 37996, USA
| |
Collapse
|
32
|
Zargar A, Lal R, Valencia L, Wang J, Backman TWH, Cruz-Morales P, Kothari A, Werts M, Wong AR, Bailey CB, Loubat A, Liu Y, Chen Y, Chang S, Benites VT, Hernández AC, Barajas JF, Thompson MG, Barcelos C, Anayah R, Martin HG, Mukhopadhyay A, Petzold CJ, Baidoo EEK, Katz L, Keasling JD. Chemoinformatic-Guided Engineering of Polyketide Synthases. J Am Chem Soc 2020; 142:9896-9901. [DOI: 10.1021/jacs.0c02549] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Amin Zargar
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
- QB3 Institute, University of California−Berkeley, 5885 Hollis Street, Fourth Floor, Emeryville, California 94608, United States
| | - Ravi Lal
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
| | - Luis Valencia
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
| | - Jessica Wang
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
| | - Tyler William H. Backman
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
| | - Pablo Cruz-Morales
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
| | - Ankita Kothari
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
| | - Miranda Werts
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
| | - Andrew R. Wong
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
| | - Constance B. Bailey
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
- QB3 Institute, University of California−Berkeley, 5885 Hollis Street, Fourth Floor, Emeryville, California 94608, United States
| | - Arthur Loubat
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
| | - Yuzhong Liu
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
| | - Yan Chen
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
| | - Samantha Chang
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
| | - Veronica T. Benites
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
- Department of Energy, Agile BioFoundry, Emeryville, California 94608, United States
| | - Amanda C. Hernández
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
| | - Jesus F. Barajas
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
- Department of Energy, Agile BioFoundry, Emeryville, California 94608, United States
| | - Mitchell G. Thompson
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
| | - Carolina Barcelos
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
| | - Rasha Anayah
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
| | - Hector Garcia Martin
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
- Department of Energy, Agile BioFoundry, Emeryville, California 94608, United States
- BCAM, Basque Center for Applied Mathematics, 48009 Bilbao, Spain
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
| | - Christopher J. Petzold
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
- Department of Energy, Agile BioFoundry, Emeryville, California 94608, United States
| | - Edward E. K. Baidoo
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
- Department of Energy, Agile BioFoundry, Emeryville, California 94608, United States
| | - Leonard Katz
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- QB3 Institute, University of California−Berkeley, 5885 Hollis Street, Fourth Floor, Emeryville, California 94608, United States
| | - Jay D. Keasling
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94608, United States
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94710, United States
- QB3 Institute, University of California−Berkeley, 5885 Hollis Street, Fourth Floor, Emeryville, California 94608, United States
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- Department of Bioengineering, University of California, Berkeley, California 94720, United States
| |
Collapse
|
33
|
Hjerrild P, Tørring T, Poulsen TB. Dehydration reactions in polyfunctional natural products. Nat Prod Rep 2020; 37:1043-1064. [DOI: 10.1039/d0np00009d] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Here, we review methods for chemical dehydration of alcohols to alkenes and discuss the potential of late-stage functionalization by direct, site- and chemo-selective dehydration of complex molecular substrates.
Collapse
Affiliation(s)
- Per Hjerrild
- Department of Chemistry
- Aarhus University
- DK-8000 Aarhus C
- Denmark
| | - Thomas Tørring
- Department of Engineering – Microbial Biosynthesis
- Aarhus University
- Aarhus C
- Denmark
| | | |
Collapse
|
34
|
Low ZJ, Xiong J, Xie Y, Ma GL, Saw H, Thi Tran H, Wong SL, Pang LM, Fong J, Lu P, Hu JF, Yang L, Miao Y, Liang ZX. Discovery, biosynthesis and antifungal mechanism of the polyene-polyol meijiemycin. Chem Commun (Camb) 2019; 56:822-825. [PMID: 31848534 DOI: 10.1039/c9cc08908j] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Produced by a newly isolated Streptomycetes strain, meijiemycin is a gigantic linear polyene-polyol that exhibits structural features not seen in other members of the polyene-polyol family. We propose a biosynthetic mechanism and demonstrate that meijiemycin inhibits hyphal growth by inducing the aggregation of ergosterol and restructuring of the fungal plasma membrane.
Collapse
Affiliation(s)
- Zhen Jie Low
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
| | - Juan Xiong
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore. and School of Pharmacy, Fudan University, Shanghai, China
| | - Ying Xie
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
| | - Guang-Lei Ma
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
| | - Howard Saw
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
| | - Hoa Thi Tran
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
| | - Soo Lin Wong
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
| | - Li Mei Pang
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
| | - July Fong
- The Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 637551, Singapore
| | - Peng Lu
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
| | - Jin-Feng Hu
- School of Pharmacy, Fudan University, Shanghai, China
| | - Liang Yang
- School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Yansong Miao
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore. and The Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 637551, Singapore
| |
Collapse
|
35
|
Kawasaki D, Miyanaga A, Chisuga T, Kudo F, Eguchi T. Functional and Structural Analyses of the Split-Dehydratase Domain in the Biosynthesis of Macrolactam Polyketide Cremimycin. Biochemistry 2019; 58:4799-4803. [DOI: 10.1021/acs.biochem.9b00897] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Daisuke Kawasaki
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Akimasa Miyanaga
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Taichi Chisuga
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551, 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
| |
Collapse
|
36
|
Pass-back chain extension expands multimodular assembly line biosynthesis. Nat Chem Biol 2019; 16:42-49. [PMID: 31636431 PMCID: PMC6917876 DOI: 10.1038/s41589-019-0385-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 09/06/2019] [Indexed: 11/26/2022]
Abstract
Modular nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) enzymatic assembly lines are large and dynamic protein machines that generally effect a linear sequence of catalytic cycles. Here we report the heterologous reconstitution and comprehensive characterization of two hybrid NRPS-PKS assembly lines that defy many standard rules of assembly line biosynthesis to generate a large combinatorial library of cyclic lipodepsipeptide protease inhibitors called thalassospiramides. We generate a series of precise domain-inactivating mutations in thalassospiramide assembly lines and present evidence for an unprecedented biosynthetic model that invokes inter-module substrate activation and tailoring, module skipping, and pass-back chain extension, whereby the ability to pass the growing chain back to a preceding module is flexible and substrate-driven. Expanding bidirectional inter-module domain interactions could represent a viable mechanism for generating chemical diversity without increasing the size of biosynthetic assembly lines and challenges our understanding of the potential elasticity of multi-modular megaenzymes.
Collapse
|
37
|
Dhakal D, Sohng JK, Pandey RP. Engineering actinomycetes for biosynthesis of macrolactone polyketides. Microb Cell Fact 2019; 18:137. [PMID: 31409353 PMCID: PMC6693128 DOI: 10.1186/s12934-019-1184-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 08/02/2019] [Indexed: 12/18/2022] Open
Abstract
Actinobacteria are characterized as the most prominent producer of natural products (NPs) with pharmaceutical importance. The production of NPs from these actinobacteria is associated with particular biosynthetic gene clusters (BGCs) in these microorganisms. The majority of these BGCs include polyketide synthase (PKS) or non-ribosomal peptide synthase (NRPS) or a combination of both PKS and NRPS. Macrolides compounds contain a core macro-lactone ring (aglycone) decorated with diverse functional groups in their chemical structures. The aglycon is generated by megaenzyme polyketide synthases (PKSs) from diverse acyl-CoA as precursor substrates. Further, post-PKS enzymes are responsible for allocating the structural diversity and functional characteristics for their biological activities. Macrolides are biologically important for their uses in therapeutics as antibiotics, anti-tumor agents, immunosuppressants, anti-parasites and many more. Thus, precise genetic/metabolic engineering of actinobacteria along with the application of various chemical/biological approaches have made it plausible for production of macrolides in industrial scale or generation of their novel derivatives with more effective biological properties. In this review, we have discussed versatile approaches for generating a wide range of macrolide structures by engineering the PKS and post-PKS cascades at either enzyme or cellular level in actinobacteria species, either the native or heterologous producer strains.
Collapse
Affiliation(s)
- Dipesh Dhakal
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, 31460 Chungnam Republic of Korea
| | - Jae Kyung Sohng
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, 31460 Chungnam Republic of Korea
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, 31460 Chungnam Republic of Korea
| | - Ramesh Prasad Pandey
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, 31460 Chungnam Republic of Korea
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, 31460 Chungnam Republic of Korea
| |
Collapse
|
38
|
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.
Collapse
Affiliation(s)
- Simone Kosol
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
| | | | | | | |
Collapse
|
39
|
Pogorevc D, Panter F, Schillinger C, Jansen R, Wenzel SC, Müller R. Production optimization and biosynthesis revision of corallopyronin A, a potent anti-filarial antibiotic. Metab Eng 2019; 55:201-211. [PMID: 31340171 DOI: 10.1016/j.ymben.2019.07.010] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 07/16/2019] [Accepted: 07/20/2019] [Indexed: 10/26/2022]
Abstract
Corallopyronins (COR) are α-pyrone antibiotics from myxobacteria representing highly promising lead structures for the development of antibacterial therapeutic agents. Their ability to inhibit RNA polymerase through interaction with the "switch region", a novel target, distant from binding sites of previously characterized RNA polymerase inhibitors (e.g. rifampicin), makes them particularly promising as antibiotic candidates. Corallopyronin A is currently also investigated as a lead compound for the treatment of lymphatic filariasis because of its superb activity against the nematode symbiont Wolbachia. As total synthesis is not a valid production option biotechnological optimization of compound supply is of utmost importance to further develop this highly potent compound class. Here we describe decisive improvements of the previously reported heterologous COR production and engineering platform yielding production of ~100 mg/L COR A. Furthermore, we provide a revised model of COR biosynthesis shedding light on the function of several biosynthetic proteins, including an unusual ECH-like enzyme providing dehydration functionality in trans and an uncharacterized protein conferring COR self-resistance in the myxobacterial heterologous host Myxococcus xanthus DK1622. We also report two new COR derivatives, COR D and oxyCOR A discovered in genetically engineered strains.
Collapse
Affiliation(s)
- Domen Pogorevc
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) / Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, 66123, Saarbrücken, Germany; German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Germany
| | - Fabian Panter
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) / Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, 66123, Saarbrücken, Germany; German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Germany
| | - Carolina Schillinger
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) / Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, 66123, Saarbrücken, Germany
| | - Rolf Jansen
- Department Microbial Drugs, Helmholtz Centre for Infection Research (HZI), Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Silke C Wenzel
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) / Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, 66123, Saarbrücken, Germany
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) / Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, 66123, Saarbrücken, Germany; German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Germany.
| |
Collapse
|
40
|
Structural insights into dehydratase substrate selection for the borrelidin and fluvirucin polyketide synthases. J Ind Microbiol Biotechnol 2019; 46:1225-1235. [PMID: 31115703 PMCID: PMC6697708 DOI: 10.1007/s10295-019-02189-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Accepted: 05/16/2019] [Indexed: 12/28/2022]
Abstract
Engineered polyketide synthases (PKSs) are promising synthetic biology platforms for the production of chemicals with diverse applications. The dehydratase (DH) domain within modular type I PKSs generates an α,β-unsaturated bond in nascent polyketide intermediates through a dehydration reaction. Several crystal structures of DH domains have been solved, providing important structural insights into substrate selection and dehydration. Here, we present two DH domain structures from two chemically diverse PKSs. The first DH domain, isolated from the third module in the borrelidin PKS, is specific towards a trans-cyclopentane-carboxylate-containing polyketide substrate. The second DH domain, isolated from the first module in the fluvirucin B1 PKS, accepts an amide-containing polyketide intermediate. Sequence-structure analysis of these domains, in addition to previously published DH structures, display many significant similarities and key differences pertaining to substrate selection. The two major differences between BorA DH M3, FluA DH M1 and other DH domains are found in regions of unmodeled residues or residues containing high B-factors. These two regions are located between α3–β11 and β7–α2. From the catalytic Asp located in α3 to a conserved Pro in β11, the residues between them form part of the bottom of the substrate-binding cavity responsible for binding to acyl-ACP intermediates.
Collapse
|
41
|
Bilyk O, Samborskyy M, Leadlay PF. The biosynthetic pathway to ossamycin, a macrocyclic polyketide bearing a spiroacetal moiety. PLoS One 2019; 14:e0215958. [PMID: 31039188 PMCID: PMC6490886 DOI: 10.1371/journal.pone.0215958] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 04/11/2019] [Indexed: 01/08/2023] Open
Abstract
Ossamycin from Streptomyces hygroscopicus var. ossamyceticus is an antifungal and cytotoxic polyketide and a potent inhibitor of the mitochondrial ATPase. Analysis of a near-complete genome sequence of the ossamycin producer has allowed the identification of the 127-kbp ossamycin biosynthetic gene cluster. The presence in the cluster of a specific crotonyl-CoA carboxylase/reductase homologue suggests that the 5-methylhexanoate extension unit used in construction of the macrocyclic core is incorporated intact from the unusual precursor isobutyrylmalonyl-CoA. Surprisingly, the modular polyketide synthase uses only 14 extension modules to accomplish 15 cycles of polyketide chain extension, a rare example of programmed iteration on a modular polyketide synthase. Specific deletion of genes encoding cytochrome P450 enzymes has given insight into the late-stage tailoring of the ossamycin macrocycle required for the attachment of the unusual 2,3,4,6-deoxyaminohexose sugar l-ossamine to C-8 of the ossamycin macrocycle. The ossamycin cluster also encodes a putative spirocyclase enzyme, OssO, which may play a role in establishing the characteristic spiroketal moiety of the natural product.
Collapse
Affiliation(s)
- Oksana Bilyk
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
| | - Markiyan Samborskyy
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Peter F. Leadlay
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| |
Collapse
|
42
|
Xie X, Cane DE. pH-Rate profiles establish that polyketide synthase dehydratase domains utilize a single-base mechanism. Org Biomol Chem 2019; 16:9165-9170. [PMID: 30457629 DOI: 10.1039/c8ob02637h] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
FosDH1 from module 1 of the fostriecin polyketide synthase (PKS) catalyzes the dehydration of a 3-hydroxybutyryl-SACP to the (E)-3-butenoyl-SACP. The steady-state kinetic parameters, kcat and kcat/Km, were determined over the pH range 3.0 to 9.2 for the FosDH1-catalyzed dehydration of the N-acetycsteamine thioester, 3-hydroxybutyryl-SNAC (3), to (E)-3-butenoyl-SNAC (4). The pH rate profiles for both log(kcat) and log(kcat/Km) each corresponded to a single pH-dependent ionization to give an active site general base, with a calculated pKa 6.1 ± 0.2 for kcat and pKa 5.7 ± 0.1 for kcat/Km. These results are inconsistent with the commonly suggested "two-base" (base-acid) mechanism for the dehydratases of PKS and fatty acid biosynthesis and support a simple one-base mechanism in which the universally conserved active site His residue acts as the base to deprotonate C-2 of the substrate, then redonates the proton to the C-3 hydroxyl group to promote C-O bond-cleavage and elimination of water. The carboxylate of the paired Asp or Glu residue is thought to bind and orient the hydroxyl group of the substrate in the stereoelectonically favored conformation.
Collapse
Affiliation(s)
- Xinqiang Xie
- Department of Chemistry, Box H, Brown University, Providence, Rhode Island 02912-9108, USA.
| | | |
Collapse
|
43
|
Hayashi S, Satoh Y, Ogasawara Y, Maruyama C, Hamano Y, Ujihara T, Dairi T. Control Mechanism for cis
Double-Bond Formation by Polyunsaturated Fatty-Acid Synthases. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201812623] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Shohei Hayashi
- Graduate School of Chemical Sciences and Engineering; Hokkaido University; N13-W8, Kita-ku Sapporo 060-8628 Japan
| | - Yasuharu Satoh
- Graduate School of Engineering; Hokkaido University; N13-W8, Kita-ku Sapporo 060-8628 Japan
| | - Yasushi Ogasawara
- Graduate School of Engineering; Hokkaido University; N13-W8, Kita-ku Sapporo 060-8628 Japan
| | - Chitose Maruyama
- Department of Bioscience; Fukui Prefectural University; Fukui 910-1195 Japan
| | - Yoshimitsu Hamano
- Department of Bioscience; Fukui Prefectural University; Fukui 910-1195 Japan
| | - Tetsuro Ujihara
- Kyowa Hakko Bio Co. Ltd.; 1-6-1, Ohtemachi, Chiyoda-ku Tokyo 100-8185 Japan
| | - Tohru Dairi
- Graduate School of Engineering; Hokkaido University; N13-W8, Kita-ku Sapporo 060-8628 Japan
| |
Collapse
|
44
|
Hayashi S, Satoh Y, Ogasawara Y, Maruyama C, Hamano Y, Ujihara T, Dairi T. Control Mechanism for cis Double-Bond Formation by Polyunsaturated Fatty-Acid Synthases. Angew Chem Int Ed Engl 2019; 58:2326-2330. [PMID: 30623559 DOI: 10.1002/anie.201812623] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 11/30/2018] [Indexed: 11/06/2022]
Abstract
Polyunsaturated fatty acids (PUFAs) such as docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA), and arachidonic acid (ARA) are essential fatty acids for humans. Some microorganisms biosynthesize these PUFAs through PUFA synthases composed of four subunits with multiple catalytic domains. These PUFA synthases each create a specific PUFA without undesirable byproducts, even though the multiple catalytic domains in each large subunit are very similar. However, the detailed biosynthetic pathways and mechanisms for controlling final-product profiles are still obscure. In this study, the FabA-type dehydratase domain (DHFabA ) in the C-subunit and the polyketide synthase-type dehydratase domain (DHPKS ) in the B-subunit of ARA synthase were revealed to be essential for ARA biosynthesis by in vivo gene exchange assays. Furthermore, in vitro analysis with truncated recombinant enzymes and C4 - to C8 -acyl ACP substrates showed that ARA and EPA synthases utilized two types of DH domains, DHPKS and DHFabA , depending on the carbon-chain length, to introduce either saturation or cis double bonds to growing acyl chains.
Collapse
Affiliation(s)
- Shohei Hayashi
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, N13-W8, Kita-ku, Sapporo, 060-8628, Japan
| | - Yasuharu Satoh
- Graduate School of Engineering, Hokkaido University, N13-W8, Kita-ku, Sapporo, 060-8628, Japan
| | - Yasushi Ogasawara
- Graduate School of Engineering, Hokkaido University, N13-W8, Kita-ku, Sapporo, 060-8628, Japan
| | - Chitose Maruyama
- Department of Bioscience, Fukui Prefectural University, Fukui, 910-1195, Japan
| | - Yoshimitsu Hamano
- Department of Bioscience, Fukui Prefectural University, Fukui, 910-1195, Japan
| | - Tetsuro Ujihara
- Kyowa Hakko Bio Co. Ltd., 1-6-1, Ohtemachi, Chiyoda-ku, Tokyo, 100-8185, Japan
| | - Tohru Dairi
- Graduate School of Engineering, Hokkaido University, N13-W8, Kita-ku, Sapporo, 060-8628, Japan
| |
Collapse
|
45
|
Bunnak W, Wonnapinij P, Sriboonlert A, Lazarus CM, Wattana-Amorn P. Heterologous biosynthesis of a fungal macrocyclic polylactone requires only two iterative polyketide synthases. Org Biomol Chem 2019; 17:374-379. [DOI: 10.1039/c8ob02773k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Formation of macrocyclic polylactone catalysed by only reducing and non-reducing polyketide synthases.
Collapse
Affiliation(s)
- Waraporn Bunnak
- Department of Chemistry
- Special Research Unit for Advanced Magnetic Resonance and Center of Excellence for Innovation in Chemistry
- Faculty of Science
- Kasetsart University
- Bangkok
| | - Passorn Wonnapinij
- Department of Genetics
- Faculty of Science
- Kasetsart University
- Bangkok
- Thailand
| | | | | | - Pakorn Wattana-Amorn
- Department of Chemistry
- Special Research Unit for Advanced Magnetic Resonance and Center of Excellence for Innovation in Chemistry
- Faculty of Science
- Kasetsart University
- Bangkok
| |
Collapse
|
46
|
Konno S, La Clair JJ, Burkart MD. Trapping the Complex Molecular Machinery of Polyketide and Fatty Acid Synthases with Tunable Silylcyanohydrin Crosslinkers. Angew Chem Int Ed Engl 2018; 57:17009-17013. [PMID: 30379389 PMCID: PMC6407627 DOI: 10.1002/anie.201806865] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/19/2018] [Indexed: 12/14/2022]
Abstract
Many families of natural products are synthesized by large multidomain biological machines commonly referred to as megasynthases. While the advance of mechanism-based tools has opened new windows into the structural features within the protein-protein interfaces guiding carrier protein dependent enzymes, there is an immediate need for tools that can be engaged to link co-translated domains in a site-selective manner. Now, the use of silylcyanohydrins is demonstrated in a two-step, two-site selective crosslinking for the trapping of carrier-protein interactions within megasynthases. This advance provides a new tool to trap intermediate states within multimodular systems, a key step toward understanding the specificities within fatty acid (FAS) and polyketide (PKS) synthases.
Collapse
Affiliation(s)
- Sho Konno
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - James J La Clair
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| |
Collapse
|
47
|
Konno S, La Clair JJ, Burkart MD. Trapping the Complex Molecular Machinery of Polyketide and Fatty Acid Synthases with Tunable Silylcyanohydrin Crosslinkers. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806865] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Sho Konno
- Department of Chemistry and Biochemistry University of California, San Diego 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - James J. La Clair
- Department of Chemistry and Biochemistry University of California, San Diego 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry University of California, San Diego 9500 Gilman Drive La Jolla CA 92093-0358 USA
| |
Collapse
|
48
|
Shin D, Byun WS, Moon K, Kwon Y, Bae M, Um S, Lee SK, Oh DC. Coculture of Marine Streptomyces sp. With Bacillus sp. Produces a New Piperazic Acid-Bearing Cyclic Peptide. Front Chem 2018; 6:498. [PMID: 30406080 PMCID: PMC6201156 DOI: 10.3389/fchem.2018.00498] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 10/01/2018] [Indexed: 11/30/2022] Open
Abstract
Microbial culture conditions in the laboratory, which conventionally involve the cultivation of one strain in one culture vessel, are vastly different from natural microbial environments. Even though perfectly mimicking natural microbial interactions is virtually impossible, the cocultivation of multiple microbial strains is a reasonable strategy to induce the production of secondary metabolites, which enables the discovery of new bioactive natural products. Our coculture of marine Streptomyces and Bacillus strains isolated together from an intertidal mudflat led to discover a new metabolite, dentigerumycin E (1). Dentigerumycin E was determined to be a new cyclic hexapeptide incorporating three piperazic acids, N-OH-Thr, N-OH-Gly, β-OH-Leu, and a pyran-bearing polyketide acyl chain mainly by analysis of its NMR and MS spectroscopic data. The putative PKS-NRPS biosynthetic gene cluster for dentigerumycin E was found in the Streptomyces strain, providing clear evidence that this cyclic peptide is produced by the Streptomyces strain. The absolute configuration of dentigerumycin E was established based on the advanced Marfey's method, ROESY NMR correlations, and analysis of the amino acid sequence of the ketoreductase domain in the biosynthetic gene cluster. In biological evaluation of dentigerumycin E (1) and its chemical derivatives [2-N,16-N-deoxydenteigerumycin E (2) and dentigerumycin methyl ester (3)], only dentigerumycin E exhibited antiproliferative and antimetastatic activities against human cancer cells, indicating that N-OH and carboxylic acid functional groups are essential for the biological activity.
Collapse
Affiliation(s)
- Daniel Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Woong Sub Byun
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Kyuho Moon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Yun Kwon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Munhyung Bae
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Soohyun Um
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, South Korea
| |
Collapse
|
49
|
Dodge GJ, Maloney FP, Smith JL. Protein-protein interactions in "cis-AT" polyketide synthases. Nat Prod Rep 2018; 35:1082-1096. [PMID: 30188553 PMCID: PMC6207950 DOI: 10.1039/c8np00058a] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: up to the end of 2018 Polyketides are a valuable source of bioactive and clinically important molecules. The biosynthesis of these chemically complex molecules has led to the discovery of equally complex polyketide synthase (PKS) pathways. Crystallography has yielded snapshots of individual catalytic domains, di-domains, and multi-domains from a variety of PKS megasynthases, and cryo-EM studies have provided initial views of a PKS module in a series of defined biochemical states. Here, we review the structural and biochemical results that shed light on the protein-protein interactions critical to catalysis by PKS systems with an embedded acyltransferase. Interactions include those that occur both within and between PKS modules, as well as with accessory enzymes.
Collapse
Affiliation(s)
- Greg J Dodge
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA 48109.
| | | | | |
Collapse
|
50
|
Abstract
Covering: up to mid of 2018 Type I fatty acid synthases (FASs) are giant multienzymes catalyzing all steps of the biosynthesis of fatty acids from acetyl- and malonyl-CoA by iterative precursor extension. Two strikingly different architectures of FAS evolved in yeast (as well as in other fungi and some bacteria) and metazoans. Yeast-type FAS (yFAS) assembles into a barrel-shaped structure of more than 2 MDa molecular weight. Catalytic domains of yFAS are embedded in an extensive scaffolding matrix and arranged around two enclosed reaction chambers. Metazoan FAS (mFAS) is a 540 kDa X-shaped dimer, with lateral reaction clefts, minimal scaffolding and pronounced conformational variability. All naturally occurring yFAS are strictly specialized for the production of saturated fatty acids. The yFAS architecture is not used for the biosynthesis of any other secondary metabolite. On the contrary, mFAS is related at the domain organization level to major classes of polyketide synthases (PKSs). PKSs produce a variety of complex and potent secondary metabolites; they either act iteratively (iPKS), or are linked via directed substrate transfer into modular assembly lines (modPKSs). Here, we review the architectures of yFAS, mFAS, and iPKSs. We rationalize the evolution of the yFAS assembly, and provide examples for re-engineering of yFAS. Recent studies have provided novel insights into the organization of iPKS. A hybrid crystallographic model of a mycocerosic acid synthase-like Pks5 yielded a comprehensive visualization of the organization and dynamics of fully-reducing iPKS. Deconstruction experiments, structural and functional studies of specialized enzymatic domains, such as the product template (PT) and the starter-unit acyltransferase (SAT) domain have revealed functional principles of non-reducing iterative PKS (NR-PKSs). Most recently, a six-domain loading region of an NR-PKS has been visualized at high-resolution together with cryo-EM studies of a trapped loading intermediate. Altogether, these data reveal the related, yet divergent architectures of mFAS, iPKS and also modPKSs. The new insights highlight extensive dynamics, and conformational coupling as key features of mFAS and iPKS and are an important step towards collection of a comprehensive series of snapshots of PKS action.
Collapse
Affiliation(s)
- Dominik A Herbst
- Department Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland.
| | | | | |
Collapse
|