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Vijayanathan M, Vadakkepat AK, Mahendran KR, Sharaf A, Frandsen KEH, Bandyopadhyay D, Pillai MR, Soniya EV. Structural and mechanistic insights into Quinolone Synthase to address its functional promiscuity. Commun Biol 2024; 7:566. [PMID: 38745065 PMCID: PMC11093982 DOI: 10.1038/s42003-024-06152-2] [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: 12/29/2021] [Accepted: 04/07/2024] [Indexed: 05/16/2024] Open
Abstract
Quinolone synthase from Aegle marmelos (AmQNS) is a type III polyketide synthase that yields therapeutically effective quinolone and acridone compounds. Addressing the structural and molecular underpinnings of AmQNS and its substrate interaction in terms of its high selectivity and specificity can aid in the development of numerous novel compounds. This paper presents a high-resolution AmQNS crystal structure and explains its mechanistic role in synthetic selectivity. Additionally, we provide a model framework to comprehend structural constraints on ketide insertion and postulate that AmQNS's steric and electrostatic selectivity plays a role in its ability to bind to various core substrates, resulting in its synthetic diversity. AmQNS prefers quinolone synthesis and can accommodate large substrates because of its wide active site entrance. However, our research suggests that acridone is exclusively synthesized in the presence of high malonyl-CoA concentrations. Potential implications of functionally relevant residue mutations were also investigated, which will assist in harnessing the benefits of mutations for targeted polyketide production. The pharmaceutical industry stands to gain from these findings as they expand the pool of potential drug candidates, and these methodologies can also be applied to additional promising enzymes.
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Affiliation(s)
- Mallika Vijayanathan
- Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India
- Department of Plant and Environment Sciences, University of Copenhagen, 1871, Frederiksberg C, Denmark
| | - Abhinav Koyamangalath Vadakkepat
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
- Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester, LE17HB, UK
| | - Kozhinjampara R Mahendran
- Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India
| | - Abdoallah Sharaf
- SequAna Core Facility, Department of Biology, University of Konstanz, Konstanz, Germany
- Genetic Department, Faculty of Agriculture, Ain Shams University, Cairo, 11241, Egypt
| | - Kristian E H Frandsen
- Department of Plant and Environment Sciences, University of Copenhagen, 1871, Frederiksberg C, Denmark
| | - Debashree Bandyopadhyay
- Department of Biological Sciences, Birla Institute of Technology and Science, Hyderabad, India
| | - M Radhakrishna Pillai
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India
| | - Eppurath Vasudevan Soniya
- Transdisciplinary Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India.
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2
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Mohamed H, Child SA, Doherty DZ, Bruning JB, Bell SG. Structural determination and characterisation of the CYP105Q4 cytochrome P450 enzyme from Mycobacterium marinum. Arch Biochem Biophys 2024; 754:109950. [PMID: 38430969 DOI: 10.1016/j.abb.2024.109950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/16/2024] [Accepted: 02/28/2024] [Indexed: 03/05/2024]
Abstract
The cytochrome P450 family of heme metalloenzymes (CYPs) catalyse important biological monooxygenation reactions. Mycobacterium marinum contains a gene encoding a CYP105Q4 enzyme of unknown function. Other members of the CYP105 CYP family have key roles in bacterial metabolism including the synthesis of secondary metabolites. We produced and purified the cytochrome P450 enzyme CYP105Q4 to enable its characterization. Several nitrogen-donor atom-containing ligands were found to bind to CYP105Q4 generating type II changes in the UV-vis absorbance spectrum. Based on the UV-vis absorbance spectra none of the potential substrate ligands we tested with CYP105Q4 were able to displace the sixth distal aqua ligand from the heme, though there was evidence for binding of oleic acid and amphotericin B. The crystal structure of CYP105Q4 in the substrate-free form was determined in an open conformation. A computational structural similarity search (Dali) was used to find the most closely related characterized relatives within the CYP105 family. The structure of CYP105Q4 enzyme was compared to the GfsF CYP enzyme from Streptomyces graminofaciens which is involved in the biosynthesis of a macrolide polyketide. This structural comparison to GfsF revealed conformational changes in the helices and loops near the entrance to the substrate access channel. A disordered B/C loop region, usually involved in substrate recognition, was also observed.
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Affiliation(s)
- Hebatalla Mohamed
- Department of Chemistry, University of Adelaide, SA, 5005, Australia
| | - Stella A Child
- Department of Chemistry, University of Adelaide, SA, 5005, Australia
| | - Daniel Z Doherty
- Department of Chemistry, University of Adelaide, SA, 5005, Australia
| | - John B Bruning
- School of Biological Sciences, University of Adelaide, SA, 5005, Australia
| | - Stephen G Bell
- Department of Chemistry, University of Adelaide, SA, 5005, Australia.
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3
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Thenmozhi Kulasekaran N, Sankara Subramanian SH, Thilakam ML, Gopal D, Lee JK, Marimuthu J. Functional analysis of a putative type III polyketide synthase from deep-sea sediment metagenome. J Biosci Bioeng 2024; 137:239-244. [PMID: 38307768 DOI: 10.1016/j.jbiosc.2023.12.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 12/22/2023] [Accepted: 12/29/2023] [Indexed: 02/04/2024]
Abstract
Type III polyketide synthases (type III PKSs) are single homodimeric enzymes that produce diverse products such as phloroglucinol, pyrones, resorcinols and chalcones which are biotechnologically important molecules. In an attempt to identify new type III PKS from extreme environments, the deep-sea sediment metagenome from Bay of Bengal was screened for type III PKS genes. BLASTX analyses of Nanopore sequence derived metagenome with the in-house created PKS database revealed a full length type III PKS from a 5 kb fragment. The annotated full length type III PKS, S9PKS showed 25-30 % sequence identity towards previously characterized enzymes. To functionally characterize the gene, it was synthesized, cloned into pET28a and pColdI vectors under T7 and csp promoters, respectively, and expressed in Escherichia coli Rosetta(DE3) pLysS. The optimized PKS (OptiPKS) was expressed as inclusion bodies under both promoters. The inclusion bodies were successfully solubilised using low concentration of urea, refolded and purified using Ni-NTA Agarose resin. The purified OptiPKS was tested for functionality using fatty acyl-CoA substrates at various temperatures. High performance liquid chromatography (HPLC) analyses revealed that OptiPKS produced tri and tetraketide pyrones using C4 to C10 acyl-CoA starter substrates. Further characterization and mutation of the enzyme would reveal its functional significance. Thus, the study could be a lead for the annotation and functional characterization of putative type III PKS from environmental metagenome data.
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Affiliation(s)
| | | | - Mary Leema Thilakam
- Marine Biotechnology Division, National Institute of Ocean Technology, Pallikaranai, Chennai-600100, Tamilnadu, India
| | - Dharani Gopal
- Marine Biotechnology Division, National Institute of Ocean Technology, Pallikaranai, Chennai-600100, Tamilnadu, India
| | - Jung Kul Lee
- Department of Chemical Engineering, Konkuk University, Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Jeya Marimuthu
- Marine Biotechnology Division, National Institute of Ocean Technology, Pallikaranai, Chennai-600100, Tamilnadu, India.
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4
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Mehdiratta K, Nain S, Sharma M, Singh S, Srivastava S, Dhamale BD, Mohanty D, Kamat SS, Natarajan VT, Sharma R, Gokhale RS. Respiratory Quinone Switches from Menaquinone to Polyketide Quinone during the Development Cycle in Streptomyces sp. Strain MNU77. Microbiol Spectr 2023; 11:e0259722. [PMID: 36507669 PMCID: PMC9927152 DOI: 10.1128/spectrum.02597-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 11/14/2022] [Indexed: 12/14/2022] Open
Abstract
Type III polyketide synthases (PKSs) found across Streptomyces species are primarily known for synthesis of a vast repertoire of clinically and industrially relevant secondary metabolites. However, our understanding of the functional relevance of these bioactive metabolites in Streptomyces physiology is still limited. Recently, a role of type III PKS harboring gene cluster in producing alternate electron carrier, polyketide quinone (PkQ) was established in a related member of the Actinobacteria, Mycobacteria, highlighting the critical role these secondary metabolites play in primary cellular metabolism of the producer organism. Here, we report the developmental stage-specific transcriptional regulation of homologous type III PKS containing gene cluster in freshwater Streptomyces sp. strain MNU77. Gene expression analysis revealed the type III PKS gene cluster to be stringently regulated, with significant upregulation observed during the dormant sporulation stage of Streptomyces sp. MNU77. In contrast, the expression levels of only known electron carrier, menaquinone biosynthetic genes were interestingly found to be downregulated. Our liquid chromatography-high-resolution mass spectrometry (LC-HRMS) analysis of a metabolite extract from the Streptomyces sp. MNU77 spores also showed 10 times more metabolic abundance of PkQs than menaquinones. Furthermore, through heterologous complementation studies, we demonstrate that Streptomyces sp. MNU77 type III PKS rescues a respiratory defect of the Mycobacterium smegmatis type III PKS deletion mutant. Together, our studies reveal that freshwater Streptomyces sp. MNU77 robustly produces novel PkQs during the sporulation stage, suggesting utilization of PkQs as alternate electron carriers across Actinobacteria during dormant hypoxic conditions. IMPORTANCE The complex developmental life cycle of Streptomyces sp. mandates efficient cellular respiratory reconfiguration for a smooth transition from aerated nutrient-rich vegetative hyphal growth to the hypoxic-dormant sporulation stage. Polyketide quinones (PkQs) have recently been identified as a class of alternate electron carriers from a related member of the Actinobacteria, Mycobacteria, that facilitates maintenance of membrane potential in oxygen-deficient niches. Our studies with the newly identified freshwater Streptomyces sp. strain MNU77 show conditional transcriptional upregulation and metabolic abundance of PkQs in the spore state of the Streptomyces life cycle. In parallel, the levels of menaquinones, the only known Streptomyces electron carrier, were downregulated, suggesting deployment of PkQs as universal electron carriers in low-oxygen, unfavorable conditions across the Actinobacteria family.
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Affiliation(s)
- Kritee Mehdiratta
- National Institute of Immunology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sonam Nain
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Meenakshi Sharma
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Shubham Singh
- Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra, India
| | | | | | | | - Siddhesh S. Kamat
- Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra, India
| | - Vivek T. Natarajan
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Rakesh Sharma
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Rajesh S. Gokhale
- National Institute of Immunology, New Delhi, India
- Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra, India
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5
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Bredy F, Ishida K, Hertweck C. A Type III Polyketide Synthase Specific for Sporulating Negativicutes is Responsible for Alkylpyrone Biosynthesis. Chembiochem 2022; 23:e202200431. [PMID: 35997218 PMCID: PMC9827899 DOI: 10.1002/cbic.202200431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/22/2022] [Indexed: 01/12/2023]
Abstract
Genomic analyses indicate that anaerobic bacteria represent a neglected source of natural products. Whereas a limited number of polyketides have been reported from anaerobes, products of type III polyketide synthases (PKSs) have remained unknown. We found a highly conserved biosynthetic gene cluster (BGC) comprising genes putatively encoding a type III PKS and a methyltransferase in genomes of the Negativicutes, strictly anaerobic, diderm bacteria. By in vivo and in vitro expression of a type III PKS gene, dquA from the oak-associated Dendrosporobacter quercicolus in E. coli we show production of long-chain alkylpyrones. Intriguingly, this BGC is specific for sporulating Sporomusaceae but absent in related Negativicutes that do not sporulate, thus suggesting a physiological role.
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Affiliation(s)
- Florian Bredy
- Dept. of Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection Biology HKIBeutenbergstr. 11a07745JenaGermany
| | - Keishi Ishida
- Dept. of Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection Biology HKIBeutenbergstr. 11a07745JenaGermany
| | - Christian Hertweck
- Dept. of Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection Biology HKIBeutenbergstr. 11a07745JenaGermany,Institute for MicrobiologyFaculty of Biological SciencesFriedrich Schiller University Jena07743JenaGermany
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6
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Enzymatic assembly of the salinosporamide γ-lactam-β-lactone anticancer warhead. Nat Chem Biol 2022; 18:538-546. [PMID: 35314816 PMCID: PMC9058210 DOI: 10.1038/s41589-022-00993-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 02/04/2022] [Indexed: 12/25/2022]
Abstract
The marine microbial natural product salinosporamide A (Marizomib) is a potent proteasome inhibitor currently in clinical trials for the treatment of brain cancer. Salinosporamide A is characterized by a complex and densely functionalized γ-lactam-β-lactone bicyclic warhead, the assembly of which has long remained a biosynthetic mystery. Here, we report an enzymatic route to the salinosporamide core catalyzed by a standalone ketosynthase, SalC. Chemoenzymatic synthesis of carrier protein-tethered substrates, as well as intact proteomics, allowed us to probe the reactivity of SalC and understand its role as an intramolecular aldolase/β-lactone synthase with roles in both transacylation and bond forming reactions. Additionally, we present the 2.85 Å SalC crystal structure that, combined with site-directed mutagenesis, allowed us to propose a bicyclization reaction mechanism. This work challenges our current understanding of the role of ketosynthase enzymes and establishes a basis for future efforts towards streamlined production of a clinically relevant chemotherapeutic.
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7
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Larsen JS, Pearson LA, Neilan BA. Genome Mining and Evolutionary Analysis Reveal Diverse Type III Polyketide Synthase Pathways in Cyanobacteria. Genome Biol Evol 2021; 13:6178795. [PMID: 33739400 PMCID: PMC8086630 DOI: 10.1093/gbe/evab056] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2021] [Indexed: 11/30/2022] Open
Abstract
Cyanobacteria are prolific producers of natural products, including polyketides and hybrid compounds thereof. Type III polyketide synthases (PKSs) are of particular interest, due to their wide substrate specificity and simple reaction mechanism, compared with both type I and type II PKSs. Surprisingly, only two type III PKS products, hierridins, and (7.7)paracyclophanes, have been isolated from cyanobacteria. Here, we report the mining of 517 cyanobacterial genomes for type III PKS biosynthesis gene clusters. Approximately 17% of the genomes analyzed encoded one or more type III PKSs. Together with already characterized type III PKSs, the phylogeny of this group of enzymes was investigated. Our analysis showed that type III PKSs in cyanobacteria evolved into three major lineages, including enzymes associated with 1) (7.7)paracyclophane-like biosynthesis gene clusters, 2) hierridin-like biosynthesis gene clusters, and 3) cytochrome b5 genes. The evolutionary history of these enzymes is complex, with some sequences partitioning primarily according to speciation and others putatively according to their reaction type. Protein modeling showed that cyanobacterial type III PKSs generally have a smaller active site cavity (mean = 109.035 Å3) compared with enzymes from other organisms. The size of the active site did not correlate well with substrate size, however, the “Gatekeeper” amino acid residues within the active site were strongly correlated to enzyme phylogeny. Our study provides unprecedented insight into the distribution, diversity, and molecular evolution of cyanobacterial type III PKSs, which could facilitate the discovery, characterization, and exploitation of novel enzymes, biochemical pathways, and specialized metabolites from this biosynthetically talented clade of microorganisms.
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Affiliation(s)
- Joachim Steen Larsen
- School of Environmental and Life Sciences, University of Newcastle, Newcastle, New South Wales, Australia
| | - Leanne Andrea Pearson
- School of Environmental and Life Sciences, University of Newcastle, Newcastle, New South Wales, Australia
| | - Brett Anthony Neilan
- School of Environmental and Life Sciences, University of Newcastle, Newcastle, New South Wales, Australia
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8
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Songsiriritthigul C, Nualkaew N, Ketudat-Cairns J, Chen CJ. The crystal structure of benzophenone synthase from Garcinia mangostana L. pericarps reveals the basis for substrate specificity and catalysis. Acta Crystallogr F Struct Biol Commun 2020; 76:597-603. [PMID: 33263571 PMCID: PMC7716263 DOI: 10.1107/s2053230x20014818] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 11/09/2020] [Indexed: 11/10/2022] Open
Abstract
Benzophenone synthase (BPS) catalyzes the production of 2,4,6-trihydroxybenzophenone via the condensation of benzoyl-CoA and three units of malonyl-CoA. The biosynthetic pathway proceeds with the formation of the prenylated xanthone α-mangostin from 2,4,6-trihydroxybenzophenone. Structural elucidation was performed to gain a better understanding of the structural basis of the function of Garcinia mangostana L. (mangosteen) BPS (GmBPS). The structure reveals the common core consisting of a five-layer αβαβα fold as found in other type III polyketide synthase enzymes. The three residues Met264, Tyr266 and Gly339 are proposed to have a significant impact on the substrate-binding specificity of the active site. Crystallographic and docking studies indicate why benzoyl-CoA is preferred over 4-coumaroyl-CoA as the substrate for GmBPS. Met264 and Tyr266 in GmBPS are properly oriented for accommodation of the 2,4,6-trihydroxybenzophenone product but not of naringenin. Gly339 offers a minimal steric hindrance to accommodate the extended substrate. Moreover, the structural arrangement of Thr133 provides the elongation activity and consequently facilitates extension of the polyketide chain. In addition to its impact on the substrate selectivity, Ala257 expands the horizontal cavity and might serve to facilitate the initiation/cyclization reaction. The detailed structure of GmBPS explains its catalytic function, facilitating further structure-based engineering to alter its substrate specificity and obtain the desired products.
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Affiliation(s)
- Chomphunuch Songsiriritthigul
- Synchrotron Light Research Institute (Public Organization), 111 University Avenue, Nakhon Ratchasima 30000, Thailand
- Center for Biomolecular Structure, Function and Application, Suranaree University of Technology, 111 University Avenue, Nakhon Ratchasima 30000, Thailand
| | - Natsajee Nualkaew
- Faculty of Pharmaceutical Sciences, Khon Kaen University, 123 Mittrapap Road, Khon Kaen 40002, Thailand
| | - James Ketudat-Cairns
- Center for Biomolecular Structure, Function and Application, Suranaree University of Technology, 111 University Avenue, Nakhon Ratchasima 30000, Thailand
- School of Chemistry, Institute of Science, Suranaree University of Technology, 111 University Avenue, Nakhon Ratchasima 30000, Thailand
| | - Chun-Jung Chen
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu 30076, Taiwan
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9
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Transcriptional heterologous expression of two type III PKS from the lichen Cladonia uncialis. Mycol Prog 2019. [DOI: 10.1007/s11557-019-01539-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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10
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Reiter S, Cahn JKB, Wiebach V, Ueoka R, Piel J. Characterization of an Orphan Type III Polyketide Synthase Conserved in Uncultivated "Entotheonella" Sponge Symbionts. Chembiochem 2019; 21:564-571. [PMID: 31430416 PMCID: PMC7064976 DOI: 10.1002/cbic.201900352] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 08/19/2019] [Indexed: 02/06/2023]
Abstract
Uncultivated bacterial symbionts from the candidate genus "Entotheonella" have been shown to produce diverse natural products previously attributed to their sponge hosts. In addition to these known compounds, "Entotheonella" genomes contain rich sets of biosynthetic gene clusters that lack identified natural products. Among these is a small type III polyketide synthase (PKS) cluster, one of only three clusters present in all known "Entotheonella" genomes. This conserved "Entotheonella" PKS (cep) cluster encodes the type III PKS CepA and the putative methyltransferase CepB. Herein, the characterization of CepA as an enzyme involved in phenolic lipid biosynthesis is reported. In vitro analysis showed a specificity for alkyl starter substrates and the production of tri- and tetraketide pyrones and tetraketide resorcinols. The conserved distribution of the cep cluster suggests an important role for the phenolic lipid polyketides produced in "Entotheonella" variants.
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Affiliation(s)
- Silke Reiter
- Department of Microbiology, Swiss Federal Institute of Technology, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland.,Institute for Insect Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Jackson K B Cahn
- Department of Microbiology, Swiss Federal Institute of Technology, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Vincent Wiebach
- Department of Microbiology, Swiss Federal Institute of Technology, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Reiko Ueoka
- Department of Microbiology, Swiss Federal Institute of Technology, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Jörn Piel
- Department of Microbiology, Swiss Federal Institute of Technology, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
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11
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Abstract
Enzymes that catalyze a Michael-type addition in polyketide biosynthesis are summarized and discussed.
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Affiliation(s)
- Akimasa Miyanaga
- Department of Chemistry
- Tokyo Institute of Technology
- Tokyo 152-8551
- Japan
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12
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Genome mining reveals uncommon alkylpyrones as type III PKS products from myxobacteria. J Ind Microbiol Biotechnol 2018; 46:319-334. [PMID: 30506464 DOI: 10.1007/s10295-018-2105-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 10/31/2018] [Indexed: 12/13/2022]
Abstract
Type III polyketide synthases (PKSs) are comparatively small homodimeric enzymes affording natural products with diverse structures and functions. While type III PKS biosynthetic pathways have been studied thoroughly in plants, their counterparts from bacteria and fungi are to date scarcely characterized. This gap is exemplified by myxobacteria from which no type III PKS-derived small molecule has previously been isolated. In this study, we conducted a genomic survey of myxobacterial type III PKSs and report the identification of uncommon alkylpyrones as the products of type III PKS biosynthesis from the myxobacterial model strain Myxococcus xanthus DK1622 through a self-resistance-guided screening approach focusing on genes encoding pentapetide repeat proteins, proficient to confer resistance to topoisomerase inhibitors. Using promoter-induced gene expression in the native host as well as heterologous expression of biosynthetic type III PKS genes, sufficient amounts of material could be obtained for structural elucidation and bioactivity testing, revealing potent topoisomerase activity in vitro.
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13
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Parvez A, Giri S, Bisht R, Saxena P. New Insights on Cyclization Specificity of Fungal Type III Polyketide Synthase, PKSIII Nc in Neurospora crassa. Indian J Microbiol 2018; 58:268-277. [PMID: 30013270 PMCID: PMC6023819 DOI: 10.1007/s12088-018-0738-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 05/03/2018] [Indexed: 12/13/2022] Open
Abstract
Type III polyketide synthases (PKSs) biosynthesize varied classes of metabolites with diverse bio-functionalities. Inherent promiscuous substrate specificity, multiple elongations of reaction intermediates and several modes of ring-closure, confer the proteins with the ability to generate unique scaffolds from limited substrate pools. Structural studies have identified crucial amino acid residues that dictate type III PKS functioning, though cyclization specific residues need further investigation. PKSIIINc, a functionally and structurally characterized type III PKS from the fungus, Neurospora crassa, is known to biosynthesize alkyl-resorcinol, alkyl-triketide- and alkyl-tetraketide-α-pyrone products. In this study, we attempted to identify residue positions governing cyclization specificity in PKSIIINc through comparative structural analysis. Structural comparisons with other type III PKSs revealed a motif with conserved hydroxyl/thiol groups that could dictate PKSIIINc catalysis. Site-directed mutagenesis of Cys120 and Ser186 to Ser and Cys, respectively, altered product profiles of mutant proteins. While both C120S and S186C proteins retained wild-type PKSIIINc product activity, S186C favoured lactonization and yielded higher amounts of the α-pyrone products. Notably, C120S gained new cyclization capability and biosynthesized acyl-phloroglucinol in addition to wild-type PKSIIINc products. Generation of alkyl-resorcinol and acyl-phloroglucinol by a single protein is a unique observation in fungal type III PKS family. Mutation of Cys120 to bulky Phe side-chain abrogated formation of tetraketide products and adversely affected overall protein stability as revealed by molecular dynamics simulation studies. Our investigations identify residue positions governing cyclization programming in PKSIIINc protein and provide insights on how subtle variations in protein cores dictate product profiles in type III PKS family.
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Affiliation(s)
- Amreesh Parvez
- Chemical Biology Group, Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, 110021 India
| | - Samir Giri
- Chemical Biology Group, Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, 110021 India
- Present Address: Department of Ecology, School of Biology, University of Osnabrück, Osnabrück, 49076 Germany
| | - Renu Bisht
- Chemical Biology Group, Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, 110021 India
| | - Priti Saxena
- Chemical Biology Group, Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, 110021 India
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14
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Parvez A, Giri S, Giri GR, Kumari M, Bisht R, Saxena P. Novel Type III Polyketide Synthases Biosynthesize Methylated Polyketides in Mycobacterium marinum. Sci Rep 2018; 8:6529. [PMID: 29695799 PMCID: PMC5916927 DOI: 10.1038/s41598-018-24980-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 04/12/2018] [Indexed: 01/09/2023] Open
Abstract
Mycobacterial pathogenesis is hallmarked by lipidic polyketides that decorate the cell envelope and mediate infection. However, factors mediating persistence remain largely unknown. Dynamic cell wall remodeling could facilitate the different pathogenic phases. Recent studies have implicated type III polyketide synthases (PKSs) in cell wall alterations in several bacteria. Comparative genome analysis revealed several type III pks gene clusters in mycobacteria. In this study, we report the functional characterization of two novel type III PKSs, MMAR_2470 and MMAR_2474, in Mycobacterium marinum. These type III pkss belong to a unique pks genomic cluster conserved exclusively in pathogenic mycobacteria. Cell-free reconstitution assays and high-resolution mass spectrometric analyses revealed methylated polyketide products in independent reactions of both proteins. MMAR_2474 protein exceptionally biosynthesized methylated alkyl-resorcinol and methylated acyl-phloroglucinol products from the same catalytic core. Structure-based homology modeling, product docking, and mutational studies identified residues that could facilitate the distinctive catalysis of these proteins. Functional investigations in heterologous mycobacterial strain implicated MMAR_2474 protein to be vital for mycobacterial survival in stationary biofilms. Our investigations provide new insights into type III PKSs conserved in pathogenic mycobacterial species.
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Affiliation(s)
- Amreesh Parvez
- Chemical Biology Group, Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, 110021, India
| | - Samir Giri
- Chemical Biology Group, Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, 110021, India.,Department of Ecology, School of Biology, University of Osnabrück, Osnabrück, 49076, Germany
| | - Gorkha Raj Giri
- Chemical Biology Group, Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, 110021, India
| | - Monika Kumari
- Chemical Biology Group, Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, 110021, India.,Department of Biochemistry, University College of Medical Sciences, Delhi, 110095, India
| | - Renu Bisht
- Chemical Biology Group, Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, 110021, India
| | - Priti Saxena
- Chemical Biology Group, Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, 110021, India.
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15
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Xu J, Liu P, Li X, Gan L, Wang P. Novel Stemphol Derivatives from a marine fungus Pleospora sp. Nat Prod Res 2018; 33:367-373. [DOI: 10.1080/14786419.2018.1452005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Jinzhong Xu
- Institute of Marine Biology, Ocean College, Zhejiang University, Zhoushan, China
| | - Peng Liu
- Institute of Marine Biology, Ocean College, Zhejiang University, Zhoushan, China
| | - Xinyang Li
- Institute of Marine Biology, Ocean College, Zhejiang University, Zhoushan, China
| | - Lishe Gan
- College of Pharmaceutical Science, Zhejiang University, Hangzhou, China
| | - Pinmei Wang
- Institute of Marine Biology, Ocean College, Zhejiang University, Zhoushan, China
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16
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Miyanaga A. Structure and function of polyketide biosynthetic enzymes: various strategies for production of structurally diverse polyketides. Biosci Biotechnol Biochem 2017; 81:2227-2236. [DOI: 10.1080/09168451.2017.1391687] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Abstract
Polyketides constitute a large family of natural products that display various biological activities. Polyketides exhibit a high degree of structural diversity, although they are synthesized from simple acyl building blocks. Recent biochemical and structural studies provide a better understanding of the biosynthetic logic of polyketide diversity. This review highlights the biosynthetic mechanisms of structurally unique polyketides, β-amino acid-containing macrolactams, enterocin, and phenolic lipids. Functional and structural studies of macrolactam biosynthetic enzymes have revealed the unique biosynthetic machinery used for selective incorporation of a rare β-amino acid starter unit into the polyketide skeleton. Biochemical and structural studies of cyclization enzymes involved in the biosynthesis of enterocin and phenolic lipids provide mechanistic insights into how these enzymes diversify the carbon skeletons of their products.
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Affiliation(s)
- Akimasa Miyanaga
- Department of Chemistry, Tokyo Institute of Technology, Tokyo, Japan
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17
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Miyanaga A, Takayanagi R, Furuya T, Kawamata A, Itagaki T, Iwabuchi Y, Kanoh N, Kudo F, Eguchi T. Substrate Recognition by a Dual-Function P450 Monooxygenase GfsF Involved in FD-891 Biosynthesis. Chembiochem 2017; 18:2179-2187. [PMID: 28869713 DOI: 10.1002/cbic.201700429] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Indexed: 12/22/2022]
Abstract
GfsF is a multifunctional P450 monooxygenase that catalyzes epoxidation and subsequent hydroxylation in the biosynthesis of macrolide polyketide FD-891. Here, we describe the biochemical and structural analysis of GfsF. To obtain the structural basis of a dual-function reaction, we determined the crystal structure of ligand-free GfsF, which revealed GfsF to have a predominantly hydrophobic substrate binding pocket. The docking models, in conjunction with the results of the enzymatic assay with substrate analogues and site-directed mutagenesis suggested two distinct substrate binding modes for epoxidation and hydroxylation reactions, which explained how GfsF regulates the order of two oxidative reactions. These findings provide new insights into the reaction mechanism of multifunctional P450 monooxygenases.
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Affiliation(s)
- Akimasa Miyanaga
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo, 152-8551, Japan
| | - Ryuichi Takayanagi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo, 152-8551, Japan
| | - Takashi Furuya
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo, 152-8551, Japan
| | - Ayano Kawamata
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Tomohiro Itagaki
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Yoshiharu Iwabuchi
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Naoki Kanoh
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo, 152-8551, Japan
| | - Tadashi Eguchi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo, 152-8551, Japan
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18
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Mori T, Awakawa T, Shimomura K, Saito Y, Yang D, Morita H, Abe I. Structural Insight into the Enzymatic Formation of Bacterial Stilbene. Cell Chem Biol 2016; 23:1468-1479. [DOI: 10.1016/j.chembiol.2016.10.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Revised: 09/26/2016] [Accepted: 10/21/2016] [Indexed: 02/07/2023]
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19
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Exploiting the Biosynthetic Potential of Type III Polyketide Synthases. Molecules 2016; 21:molecules21060806. [PMID: 27338328 PMCID: PMC6274091 DOI: 10.3390/molecules21060806] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 06/15/2016] [Accepted: 06/17/2016] [Indexed: 11/17/2022] Open
Abstract
Polyketides are structurally and functionally diverse secondary metabolites that are biosynthesized by polyketide synthases (PKSs) using acyl-CoA precursors. Recent studies in the engineering and structural characterization of PKSs have facilitated the use of target enzymes as biocatalysts to produce novel functionally optimized polyketides. These compounds may serve as potential drug leads. This review summarizes the insights gained from research on type III PKSs, from the discovery of chalcone synthase in plants to novel PKSs in bacteria and fungi. To date, at least 15 families of type III PKSs have been characterized, highlighting the utility of PKSs in the development of natural product libraries for therapeutic development.
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20
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Anand A, Verma P, Singh AK, Kaushik S, Pandey R, Shi C, Kaur H, Chawla M, Elechalawar CK, Kumar D, Yang Y, Bhavesh NS, Banerjee R, Dash D, Singh A, Natarajan VT, Ojha AK, Aldrich CC, Gokhale RS. Polyketide Quinones Are Alternate Intermediate Electron Carriers during Mycobacterial Respiration in Oxygen-Deficient Niches. Mol Cell 2015; 60:637-50. [PMID: 26585386 DOI: 10.1016/j.molcel.2015.10.016] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 08/24/2015] [Accepted: 10/08/2015] [Indexed: 11/16/2022]
Abstract
Mycobacterium tuberculosis (Mtb) adaptation to hypoxia is considered crucial to its prolonged latent persistence in humans. Mtb lesions are known to contain physiologically heterogeneous microenvironments that bring about differential responses from bacteria. Here we exploit metabolic variability within biofilm cells to identify alternate respiratory polyketide quinones (PkQs) from both Mycobacterium smegmatis (Msmeg) and Mtb. PkQs are specifically expressed in biofilms and other oxygen-deficient niches to maintain cellular bioenergetics. Under such conditions, these metabolites function as mobile electron carriers in the respiratory electron transport chain. In the absence of PkQs, mycobacteria escape from the hypoxic core of biofilms and prefer oxygen-rich conditions. Unlike the ubiquitous isoprenoid pathway for the biosynthesis of respiratory quinones, PkQs are produced by type III polyketide synthases using fatty acyl-CoA precursors. The biosynthetic pathway is conserved in several other bacterial genomes, and our study reveals a redox-balancing chemicocellular process in microbial physiology.
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Affiliation(s)
- Amitesh Anand
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110020, India; Academy of Scientific and Innovative Research, Rafi Marg, New Delhi 110001, India
| | - Priyanka Verma
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Anil Kumar Singh
- CSIR-North East Institute of Science and Technology, Jorhat 785006, India
| | - Sandeep Kaushik
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110020, India
| | - Rajesh Pandey
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110020, India
| | - Ce Shi
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Harneet Kaur
- Center for Drug Design, University of Minnesota, Minneapolis, MN 55455, USA
| | - Manbeena Chawla
- Department of Microbiology and Cell Biology, Centre for Infectious Disease and Research, Indian Institute of Science, Bangalore 560012, India
| | - Chandra Kumar Elechalawar
- Academy of Scientific and Innovative Research, Rafi Marg, New Delhi 110001, India; CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, India
| | - Dhirendra Kumar
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110020, India
| | - Yong Yang
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA
| | - Neel S Bhavesh
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Rajkumar Banerjee
- Academy of Scientific and Innovative Research, Rafi Marg, New Delhi 110001, India; CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, India
| | - Debasis Dash
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110020, India
| | - Amit Singh
- Department of Microbiology and Cell Biology, Centre for Infectious Disease and Research, Indian Institute of Science, Bangalore 560012, India
| | - Vivek T Natarajan
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110020, India
| | - Anil K Ojha
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA; Center for Drug Design, University of Minnesota, Minneapolis, MN 55455, USA
| | - Rajesh S Gokhale
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110020, India; Academy of Scientific and Innovative Research, Rafi Marg, New Delhi 110001, India; National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India.
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Biosynthesis and function of bacterial dialkylresorcinol compounds. Appl Microbiol Biotechnol 2015; 99:8323-8. [DOI: 10.1007/s00253-015-6905-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 07/29/2015] [Accepted: 07/31/2015] [Indexed: 10/23/2022]
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22
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Tandem expression in E. coli of type III PKS and P450 genes from marine Streptomyces olivaceus FXJ 7.023 gives production of phenol and indole. World J Microbiol Biotechnol 2015; 31:541-8. [PMID: 25697286 DOI: 10.1007/s11274-015-1825-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Accepted: 02/16/2015] [Indexed: 01/10/2023]
Abstract
The draft genome sequence of marine Streptomyces olivaceus strain FXJ 7.023 contains a cryptic Type III polyketide synthase (type III PKS) gene cluster, which is similar to the Streptomyces coelicolor THN biosynthesis gene cluster. A putative type III PKS (SoRppA) gene and its adjacent gene for cytochrome P450 158A2 (SoCYP158A2) of this gene cluster were cloned by PCR screening through a fosmid genomic library of S. olivaceus FXJ 7.023. Tandem expression of SoRppA and SoCYP158A2 in Escherichia coli strain BL21 (DE3) plysS resulted in obvious biosynthesis of phenol and indole, while heterologous expression of SoRppA or SoCYP158A2 alone did not. The engineered strain sorppAcyp158a2BL21 showed tolerance to phenol concentration up to 0.75 g/L. Continuous biosynthesis of phenol and indole by the immobilized engineered strain on macroporousresin was achieved, and the productivities of phenol and indole in extractant-free culture in 102 h were 0.08 and 1.525 g/L/h, respectively, with the highest production reached 0.67 and 14.48 g/L, respectively. These results suggest that the engineered strain and immobilized continuous fermentation process may provide potential for "green" production of phenol and indole.
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