1
|
Sword TT, Dinglasan JLN, Abbas GSK, Barker JW, Spradley ME, Greene ER, Gooden DS, Emrich SJ, Gilchrist MA, Doktycz MJ, Bailey CB. Profiling expression strategies for a type III polyketide synthase in a lysate-based, cell-free system. Sci Rep 2024; 14:12983. [PMID: 38839808 PMCID: PMC11153635 DOI: 10.1038/s41598-024-61376-w] [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: 12/16/2023] [Accepted: 05/06/2024] [Indexed: 06/07/2024] Open
Abstract
Some of the most metabolically diverse species of bacteria (e.g., Actinobacteria) have higher GC content in their DNA, differ substantially in codon usage, and have distinct protein folding environments compared to tractable expression hosts like Escherichia coli. Consequentially, expressing biosynthetic gene clusters (BGCs) from these bacteria in E. coli often results in a myriad of unpredictable issues with regard to protein expression and folding, delaying the biochemical characterization of new natural products. Current strategies to achieve soluble, active expression of these enzymes in tractable hosts can be a lengthy trial-and-error process. Cell-free expression (CFE) has emerged as a valuable expression platform as a testbed for rapid prototyping expression parameters. Here, we use a type III polyketide synthase from Streptomyces griseus, RppA, which catalyzes the formation of the red pigment flaviolin, as a reporter to investigate BGC refactoring techniques. We applied a library of constructs with different combinations of promoters and rppA coding sequences to investigate the synergies between promoter and codon usage. Subsequently, we assess the utility of cell-free systems for prototyping these refactoring tactics prior to their implementation in cells. Overall, codon harmonization improves natural product synthesis more than traditional codon optimization across cell-free and cellular environments. More importantly, the choice of coding sequences and promoters impact protein expression synergistically, which should be considered for future efforts to use CFE for high-yield protein expression. The promoter strategy when applied to RppA was not completely correlated with that observed with GFP, indicating that different promoter strategies should be applied for different proteins. In vivo experiments suggest that there is correlation, but not complete alignment between expressing in cell free and in vivo. Refactoring promoters and/or coding sequences via CFE can be a valuable strategy to rapidly screen for catalytically functional production of enzymes from BCGs, which advances CFE as a tool for natural product research.
Collapse
Affiliation(s)
- Tien T Sword
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN, USA
| | - Jaime Lorenzo N Dinglasan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN, USA
| | - Ghaeath S K Abbas
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN, USA
- School of Chemistry, University of Sydney, Sydney, NSW, Australia
| | - J William Barker
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN, USA
| | - Madeline E Spradley
- Department of Biochemistry, Cellular, and Molecular Biology, University of Tennessee-Knoxville, Knoxville, TN, USA
| | - Elijah R Greene
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN, USA
| | - Damian S Gooden
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN, USA
| | - Scott J Emrich
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN, USA
- Department of Electrical Engineering and Computer Science, University of Tennessee-Knoxville, Knoxville, TN, USA
- Department of Ecology and Evolutionary Biology, University of Tennessee-Knoxville, Knoxville, TN, USA
| | - Michael A Gilchrist
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN, USA
- Department of Ecology and Evolutionary Biology, University of Tennessee-Knoxville, Knoxville, TN, USA
| | - Mitchel J Doktycz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN, USA.
| | - Constance B Bailey
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN, USA.
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN, USA.
- School of Chemistry, University of Sydney, Sydney, NSW, Australia.
| |
Collapse
|
2
|
Zhao F, Moriwaki Y, Noguchi T, Shimizu K, Kuzuyama T, Terada T. QM/MM Study of the Catalytic Mechanism and Substrate Specificity of the Aromatic Substrate C-Methyltransferase Fur6. Biochemistry 2024; 63:806-814. [PMID: 38422553 DOI: 10.1021/acs.biochem.3c00556] [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: 03/02/2024]
Abstract
In the field of medical chemistry and other organic chemistry, introducing a methyl group into a designed position has been difficult to achieve. However, owing to the vigorous developments in the field of enzymology, methyltransferases are considered potential tools for addressing this problem. Within the methyltransferase family, Fur6 catalyzes the methylation of C3 of 1,2,4,5,7-pentahydroxynaphthalene (PHN) using S-adenosyl-l-methionine (SAM) as the methyl donor. Here, we report the catalytic mechanism and substrate specificity of Fur6 based on computational studies. Our molecular dynamics (MD) simulation studies reveal the reactive form of PHN and its interactions with the enzyme. Our hybrid quantum mechanics/molecular mechanics (QM/MM) calculations suggest the reaction pathway of the methyl transfer step in which the energy barrier is 8.6 kcal mol-1. Our free-energy calculations with a polarizable continuum model (PCM) indicate that the final deprotonation step of the methylated intermediate occurs after it is ejected into the water solvent from the active center pocket of Fur6. Additionally, our studies on the protonation states, the highest occupied molecular orbital (HOMOs), and the energy barriers of the methylation reaction for the analogs of PHN demonstrate the mechanism of the specificity to PHN. Our study provides valuable insights into Fur6 chemistry, contributing to a deeper understanding of molecular mechanisms and offering an opportunity to engineer the enzyme to achieve high yields of the desired product(s).
Collapse
Affiliation(s)
- Fan Zhao
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yoshitaka Moriwaki
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
- Graduate School of Agricultural and Life Sciences and Collaborative Research Institute for Innovative Microbiology (CRIIM), The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Tomohiro Noguchi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kentaro Shimizu
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Tomohisa Kuzuyama
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
- Graduate School of Agricultural and Life Sciences and Collaborative Research Institute for Innovative Microbiology (CRIIM), The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Tohru Terada
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
- Graduate School of Agricultural and Life Sciences and Collaborative Research Institute for Innovative Microbiology (CRIIM), The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| |
Collapse
|
3
|
Sweeney D, Chase AB, Bogdanov A, Jensen PR. MAR4 Streptomyces: A Unique Resource for Natural Product Discovery. JOURNAL OF NATURAL PRODUCTS 2024; 87:439-452. [PMID: 38353658 PMCID: PMC10897937 DOI: 10.1021/acs.jnatprod.3c01007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/22/2024] [Accepted: 01/22/2024] [Indexed: 02/24/2024]
Abstract
Marine-derived Streptomyces have long been recognized as a source of novel, pharmaceutically relevant natural products. Among these bacteria, the MAR4 clade within the genus Streptomyces has been identified as metabolically rich, yielding over 93 different compounds to date. MAR4 strains are particularly noteworthy for the production of halogenated hybrid isoprenoid natural products, a relatively rare class of bacterial metabolites that possess a wide range of biological activities. MAR4 genomes are enriched in vanadium haloperoxidase and prenyltransferase genes, thus accounting for the production of these compounds. Functional characterization of the enzymes encoded in MAR4 genomes has advanced our understanding of halogenated, hybrid isoprenoid biosynthesis. Despite the exceptional biosynthetic capabilities of MAR4 bacteria, the large body of research they have stimulated has yet to be compiled. Here we review 35 years of natural product research on MAR4 strains and update the molecular diversity of this unique group of bacteria.
Collapse
Affiliation(s)
- Douglas Sweeney
- Scripps
Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Alexander B. Chase
- Department
of Earth Sciences, Southern Methodist University, Dallas, Texas 75275, United States
| | - Alexander Bogdanov
- Scripps
Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Paul R. Jensen
- Scripps
Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| |
Collapse
|
4
|
Michael HSR, Subiramanian SR, Thyagarajan D, Mohammed NB, Saravanakumar VK, Govindaraj M, Maheswari KM, Karthikeyan N, Ramesh Kumar C. Melanin biopolymers from microbial world with future perspectives-a review. Arch Microbiol 2023; 205:306. [PMID: 37580645 DOI: 10.1007/s00203-023-03642-5] [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: 05/30/2023] [Revised: 07/10/2023] [Accepted: 07/27/2023] [Indexed: 08/16/2023]
Abstract
Melanin is an amorphous polymer made of heterogeneous functional groups synthesized by diverse organisms including fungi, bacteria, animals, and plants. It was widely acknowledged for its biological processes and its key role in the protection of organisms from environmental stress. Recently, melanin clutches attention in the field of nanobiotechnology, drug delivery, organic semiconductors and bioelectronics, environmental bioremediation, photoprotection, etc., Furthermore, melanin from natural sources like microbial community shows antimicrobial, fighting cancer, radical scavenging, cosmeceuticals, and many therapeutic areas as well. Though the multipotentiality nature of melanin has been put forth, real-world applications still flag fall behind, which might be anticipated to the inadequate and high price essence of natural melanin. However, current bioprocess technologies have paved for the large-scale or industrial production of microbial melanin, which could help in the replacement of synthetic melanin. Thus, this review emphasizes the various sources for melanin, i.e., types-based on its pathways and its chemical structures, functional efficiency, physical properties, and conventional and modern methods of both extraction and characterization. Moreover, an outlook on how it works in the field of medicine, bioremediation, and other related areas provides perspectives on the complete exploitation of melanin in practical applications of medicine and the environment.
Collapse
Affiliation(s)
| | - Shri Ranjani Subiramanian
- Department of Biotechnology, Sri Ramakrishna College of Arts & Science, Nava India, Coimbatore, India
| | - Divyavaahini Thyagarajan
- Department of Biotechnology, Sri Ramakrishna College of Arts & Science, Nava India, Coimbatore, India
| | - Nazneen Bobby Mohammed
- Department of Biotechnology, Vignan's Foundation for Science Technology and Research, Vadlamudi, Guntur Dist, Andhra Pradesh, India
| | | | - Mageswari Govindaraj
- Department of Biotechnology, Sri Ramakrishna College of Arts & Science, Nava India, Coimbatore, India
| | | | - Naresh Karthikeyan
- Department of Biotechnology, Sri Ramakrishna College of Arts & Science, Nava India, Coimbatore, India
| | - Charu Ramesh Kumar
- Department of Biotechnology, Sri Ramakrishna College of Arts & Science, Nava India, Coimbatore, India
| |
Collapse
|
5
|
Lin P, Fu Z, Liu X, Liu C, Bai Z, Yang Y, Li Y. Direct Utilization of Peroxisomal Acetyl-CoA for the Synthesis of Polyketide Compounds in Saccharomyces cerevisiae. ACS Synth Biol 2023; 12:1599-1607. [PMID: 37172280 DOI: 10.1021/acssynbio.2c00678] [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] [Indexed: 05/14/2023]
Abstract
Polyketides are a class of natural products with many applications but are mainly appealing as pharmaceuticals. Heterologous production of polyketides in the yeast Saccharomyces cerevisiae has been widely explored because of the many merits of this model eukaryotic microorganism. Although acetyl-CoA and malonyl-CoA, the precursors for polyketide synthesis, are distributed in several yeast subcellular organelles, only cytosolic synthesis of polyketides has been pursued in previous studies. In this study, we investigate polyketide synthesis by directly using acetyl-CoA in the peroxisomes of yeast strain CEN.PK2-1D. We first demonstrate that the polyketide flaviolin can be synthesized in this organelle upon peroxisomal colocalization of native acetyl-CoA carboxylase and 1,3,6,8-tetrahydroxynaphthalene synthase (a type III polyketide synthase). Next, using the synthesis of the polyketide triacetic acid lactone as an example, we show that (1) a new peroxisome targeting sequence, pPTS1, is more effective than the previously reported ePTS1 for peroxisomal polyketide synthesis; (2) engineering peroxisome proliferation is effective to boost polyketide production; and (3) peroxisomes provide an additional acetyl-CoA reservoir and extra space to accommodate enzymes so that utilizing the peroxisomal pathway plus the cytosolic pathway produces more polyketide than the cytosolic pathway alone. This research lays the groundwork for more efficient heterologous polyketide biosynthesis using acetyl-CoA pools in subcellular organelles.
Collapse
Affiliation(s)
- Pingxin Lin
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214112, China
| | - Zhenhao Fu
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214112, China
| | - Xiuxia Liu
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214112, China
| | - Chunli Liu
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214112, China
| | - Zhonghu Bai
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214112, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yankun Yang
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214112, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Ye Li
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214112, China
| |
Collapse
|
6
|
Schwanemann T, Otto M, Wynands B, Marienhagen J, Wierckx N. A Pseudomonas taiwanensis malonyl-CoA platform strain for polyketide synthesis. Metab Eng 2023; 77:219-230. [PMID: 37031949 DOI: 10.1016/j.ymben.2023.04.001] [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: 02/15/2023] [Revised: 03/31/2023] [Accepted: 04/02/2023] [Indexed: 04/11/2023]
Abstract
Malonyl-CoA is a central precursor for biosynthesis of a wide range of complex secondary metabolites. The development of platform strains with increased malonyl-CoA supply can contribute to the efficient production of secondary metabolites, especially if such strains exhibit high tolerance towards these chemicals. In this study, Pseudomonas taiwanensis VLB120 was engineered for increased malonyl-CoA availability to produce bacterial and plant-derived polyketides. A multi-target metabolic engineering strategy focusing on decreasing the malonyl-CoA drain and increasing malonyl-CoA precursor availability, led to an increased production of various malonyl-CoA-derived products, including pinosylvin, resveratrol and flaviolin. The production of flaviolin, a molecule deriving from five malonyl-CoA molecules, was doubled compared to the parental strain by this malonyl-CoA increasing strategy. Additionally, the engineered platform strain enabled production of up to 84 mg L-1 resveratrol from supplemented p-coumarate. One key finding of this study was that acetyl-CoA carboxylase overexpression majorly contributed to an increased malonyl-CoA availability for polyketide production in dependence on the used strain-background and whether downstream fatty acid synthesis was impaired, reflecting its complexity in metabolism. Hence, malonyl-CoA availability is primarily determined by competition of the production pathway with downstream fatty acid synthesis, while supply reactions are of secondary importance for compounds that derive directly from malonyl-CoA in Pseudomonas.
Collapse
Affiliation(s)
- Tobias Schwanemann
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Maike Otto
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Benedikt Wynands
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Jan Marienhagen
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany; Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, D-52074, Aachen, Germany
| | - Nick Wierckx
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.
| |
Collapse
|
7
|
Guo L, Li W, Gu Z, Wang L, Guo L, Ma S, Li C, Sun J, Han B, Chang J. Recent Advances and Progress on Melanin: From Source to Application. Int J Mol Sci 2023; 24:ijms24054360. [PMID: 36901791 PMCID: PMC10002160 DOI: 10.3390/ijms24054360] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 02/15/2023] [Accepted: 02/17/2023] [Indexed: 02/25/2023] Open
Abstract
Melanin is a biological pigment formed by indoles and phenolic compounds. It is widely found in living organisms and has a variety of unique properties. Due to its diverse characteristics and good biocompatibility, melanin has become the focus in the fields of biomedicine, agriculture, the food industry, etc. However, due to the wide range of melanin sources, complex polymerization properties, and low solubility of specific solvents, the specific macromolecular structure and polymerization mechanism of melanin remain unclear, which significantly limits the further study and application of melanin. Its synthesis and degradation pathways are also controversial. In addition, new properties and applications of melanin are constantly being discovered. In this review, we focus on the recent advances in the research of melanin in all aspects. Firstly, the classification, source, and degradation of melanin are summarized. Secondly, a detailed description of the structure, characterization, and properties of melanin is followed. The novel biological activity of melanin and its application is described at the end.
Collapse
Affiliation(s)
- Lili Guo
- College of Marine Life Science, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao 266235, China
| | - Wenya Li
- College of Marine Life Science, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao 266235, China
| | - Zhiyang Gu
- College of Marine Life Science, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao 266235, China
| | - Litong Wang
- College of Marine Life Science, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao 266235, China
| | - Lan Guo
- College of Marine Life Science, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao 266235, China
| | - Saibo Ma
- College of Marine Life Science, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao 266235, China
| | - Cuiyao Li
- College of Marine Life Science, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao 266235, China
| | - Jishang Sun
- College of Marine Life Science, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao 266235, China
| | - Baoqin Han
- College of Marine Life Science, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao 266235, China
| | - Jing Chang
- College of Marine Life Science, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao 266235, China
- Correspondence:
| |
Collapse
|
8
|
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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [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.
Collapse
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
| |
Collapse
|
9
|
Novel Plant-Associated Brevibacillus and Lysinibacillus Genomospecies Harbor a Rich Biosynthetic Potential of Antimicrobial Compounds. Microorganisms 2023; 11:microorganisms11010168. [PMID: 36677460 PMCID: PMC9867215 DOI: 10.3390/microorganisms11010168] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 01/03/2023] [Accepted: 01/06/2023] [Indexed: 01/12/2023] Open
Abstract
We have previously reported the draft genome sequences of 59 endospore-forming Gram-positive bacterial strains isolated from Vietnamese crop plants due to their ability to suppress plant pathogens. Based on their draft genome sequence, eleven of them were assigned to the Brevibacillus and one to the Lysinibacillus genus. Further analysis including full genome sequencing revealed that several of these strains represent novel genomospecies. In vitro and in vivo assays demonstrated their ability to promote plant growth, as well as the strong biocontrol potential of Brevibacilli directed against phytopathogenic bacteria, fungi, and nematodes. Genome mining identified 157 natural product biosynthesis gene clusters (BGCs), including 36 novel BGCs not present in the MIBiG data bank. Our findings indicate that plant-associated Brevibacilli are a rich source of putative antimicrobial compounds and might serve as a valuable starting point for the development of novel biocontrol agents.
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
Lin Z, Qu X. Emerging diversity in polyketide synthase. Tetrahedron Lett 2022. [DOI: 10.1016/j.tetlet.2022.154183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
12
|
Liu RZ, Chen S, Zhang L. A Streptomyces P450 enzyme dimerizes isoflavones from plants. Beilstein J Org Chem 2022; 18:1107-1115. [PMID: 36105730 PMCID: PMC9443421 DOI: 10.3762/bjoc.18.113] [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: 05/31/2022] [Accepted: 08/11/2022] [Indexed: 11/23/2022] Open
Abstract
Dimerization is a widespread natural strategy that enables rapid structural diversification of natural products. However, our understanding of the dimerization enzymes involved in this biotransformation is still limited compared to the numerous reported dimeric natural products. Here, we report the characterization of three new isoflavone dimers from Streptomyces cattleya cultured on an isoflavone-containing agar plate. We further identified a cytochrome P450 monooxygenase, CYP158C1, which is able to catalyze the dimerization of isoflavones. CYP158C1 can also dimerize plant-derived polyketides, such as flavonoids and stilbenes. Our work represents a unique bacterial P450 that can dimerize plant polyphenols, which extends the insights into P450-mediated biaryl coupling reactions in biosynthesis.
Collapse
Affiliation(s)
- Run-Zhou Liu
- 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, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Shanchong Chen
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Lihan Zhang
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| |
Collapse
|
13
|
Genome-Wide Analysis of Type-III Polyketide Synthases in Wheat and Possible Roles in Wheat Sheath-Blight Resistance. Int J Mol Sci 2022; 23:ijms23137187. [PMID: 35806194 PMCID: PMC9266324 DOI: 10.3390/ijms23137187] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/17/2022] [Accepted: 06/23/2022] [Indexed: 02/04/2023] Open
Abstract
The enzymes in the chalcone synthase family, also known as type-III polyketide synthases (PKSs), play important roles in the biosynthesis of various plant secondary metabolites and plant adaptation to environmental stresses. There have been few detailed reports regarding the gene and tissue expression profiles of the PKS (TaPKS) family members in wheat (Triticum aestivum L.). In this study, 81 candidate TaPKS genes were identified in the wheat genome, which were designated as TaPKS1–81. Phylogenetic analysis divided the TaPKS genes into two groups. TaPKS gene family expansion mainly occurred via tandem duplication and fragment duplication. In addition, we analyzed the physical and chemical properties, gene structures, and cis-acting elements of TaPKS gene family members. RNA-seq analysis showed that the expression of TaPKS genes was tissue-specific, and their expression levels differed before and after infection with Rhizoctonia cerealis. The expression levels of four TaPKS genes were also analyzed via qRT-PCR after treatment with methyl jasmonate, salicylic acid, abscisic acid, and ethylene. In the present study, we systematically identified and analyzed TaPKS gene family members in wheat, and our findings may facilitate the cloning of candidate genes associated with resistance to sheath blight in wheat.
Collapse
|
14
|
Natural Melanin: Current Trends, and Future Approaches, with Especial Reference to Microbial Source. Polymers (Basel) 2022; 14:polym14071339. [PMID: 35406213 PMCID: PMC9002885 DOI: 10.3390/polym14071339] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/09/2022] [Accepted: 02/24/2022] [Indexed: 02/04/2023] Open
Abstract
Melanin is a universal natural dark polymeric pigment, arising in microorganisms, animals, and plants. There is a couple of pieces of literature on melanin, each focusing on a different issue, the goal of the present review is to focus on microbial melanin. It has numerous benefits with very few drawbacks. The current situation and expected trends are discussed. Intriguing, numerous studies have provoked a serious necessity for a comprehensive assessment of microbial melanin pigments. So that, such review would help scholars from diverse backgrounds to realize the importance of melanin pigments isolated from microorganisms, with this aim in mind, information, and hypothesis from this review could be the paradigm for studies on melanin in the next era.
Collapse
|
15
|
Zhu Q, Cheng W, Song Y, He Q, Ju J, Li Q. Complete genome sequence of the deep South China Sea-derived Streptomyces niveus SCSIO 3406, the producer of cytotoxic and antibacterial marfuraquinocins. PLoS One 2021; 16:e0248404. [PMID: 33755698 PMCID: PMC7987185 DOI: 10.1371/journal.pone.0248404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 02/25/2021] [Indexed: 12/01/2022] Open
Abstract
Streptomyces niveus SCSIO 3406 was isolated from a sediment sample collected from South China Sea at a depth of 3536 m. Four new sesquiterpenoid naphthoquinones, marfuraquinocins A-D, and two new geranylated phenazines, i. e. phenaziterpenes A and B, were isolated from the fermentation broth of the strain. Here, we present its genome sequence, which contains 7,990,492 bp with a G+C content of 70.46% and harbors 7088 protein-encoding genes. The genome sequence analysis revealed the presence of a 28,787 bp gene cluster encoding for 24 open reading frames including 1,3,6,8-tetrahydroxynaphthalene synthase and monooxygenase, seven phenazine biosynthesis proteins, two prenyltransferases and a squalene-hopene cyclase. These genes are known to be necessary for the biosynthesis of both marfuraquinocins and phenaziterpenes. Outside the gene cluster (and scattered around the genome), there are seven genes belonging to the methylerythritol phosphate pathway for the biosynthesis of the essential primary metabolite, isopentenyl diphosphate, as well as six geranyl diphosphate/farnesyl diphosphate synthase genes. The strain S. niveus SCSIO 3406 showed type I PKS, type III PKS and nonribosomal peptide synthetase cluster. The sequence will provide the genetic basis for better understanding of biosynthesis mechanism of the above mentioned six compounds and for the construction of improved strain for the industrial production of antimicrobial agents.
Collapse
Affiliation(s)
- Qinghua Zhu
- College of Life Science, Dezhou University, Dezhou, China
| | - Weige Cheng
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Yongxiang Song
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Qing He
- College of Life Science, Dezhou University, Dezhou, China
| | - Jianhua Ju
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- * E-mail: (QL); (JJ)
| | - Qinglian Li
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- * E-mail: (QL); (JJ)
| |
Collapse
|
16
|
Pothiraj R, Ravikumar MJ, Suthanthiram B, Subbaraya U, Krishnamurthy P. Genome-scale analyses of polyketide synthases in banana: Phylogenetics and expression profiling forecast their candidacy in specialized metabolism. Gene 2021; 778:145472. [PMID: 33549715 DOI: 10.1016/j.gene.2021.145472] [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: 09/16/2020] [Revised: 01/24/2021] [Accepted: 01/28/2021] [Indexed: 11/27/2022]
Abstract
Plant type III polyketide synthases (PKSs) are associated with various functions in plant growth, development and defense by providing a multitude of polyketide scaffolds for diverse specialized metabolic pathways (SMPs). To decipher banana PKSs involved in specialized metabolism, genome-wide comparative analyses were conducted with A (Musa acuminata) and B (Musa balbisiana) genomes of banana. Both genomes retained eight chalcone synthases (CHSs), seven curcumin synthases (CURSs), three diketidyl-CoA synthases (DCSs) and one anther specific CHS (ASC). Segmental (42%) and tandem (37%) duplication events majorly flourished the banana PKS family. Six of 19 PKSs of A genome (designated as MaPKSs) showed relatively a higher expression in the root, corm, sheath, leaf and embryogenic cell suspension (ECS) of banana. To determine the defense response of MaPKSs and to highlight their candidacy in various SMPs, expression profiling was conducted by qPCR in ECSs treated with 100/200 μM of jasmonic acid (JA) and salicylic acid (SA) at 24/48 h. Maximum and subordinate expression induction of MaPKSs was apparent respectively against JA and SA treatments. Notably, most MaPKSs achieved their peak expression within 24 h of JA and the total flavonoid content was reached maximum within 24 h of JA/SA elicitations. Considering the homology, phylogeny, and expression levels in each analyzed sample (n = 13), three CHSs, three DCSs along with three CURSs and one ASC were selected as most promising candidates respectively for flavonoids, phenylphenalenones and sporopollenin biosynthesis in banana. Our findings provide a first-line resource to disclose the functions of banana PKSs involved in distinct SMPs.
Collapse
Affiliation(s)
- Ramanujam Pothiraj
- Crop Improvement Division, ICAR National Research Centre for Banana, Tiruchirappalli 620-102, India
| | | | - Backiyarani Suthanthiram
- Crop Improvement Division, ICAR National Research Centre for Banana, Tiruchirappalli 620-102, India
| | - Uma Subbaraya
- Crop Improvement Division, ICAR National Research Centre for Banana, Tiruchirappalli 620-102, India
| | | |
Collapse
|
17
|
Jeandet P, Vannozzi A, Sobarzo-Sánchez E, Uddin MS, Bru R, Martínez-Márquez A, Clément C, Cordelier S, Manayi A, Nabavi SF, Rasekhian M, El-Saber Batiha G, Khan H, Morkunas I, Belwal T, Jiang J, Koffas M, Nabavi SM. Phytostilbenes as agrochemicals: biosynthesis, bioactivity, metabolic engineering and biotechnology. Nat Prod Rep 2021; 38:1282-1329. [PMID: 33351014 DOI: 10.1039/d0np00030b] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: 1976 to 2020. Although constituting a limited chemical family, phytostilbenes represent an emblematic group of molecules among natural compounds. Ever since their discovery as antifungal compounds in plants and their ascribed role in human health and disease, phytostilbenes have never ceased to arouse interest for researchers, leading to a huge development of the literature in this field. Owing to this, the number of references to this class of compounds has reached the tens of thousands. The objective of this article is thus to offer an overview of the different aspects of these compounds through a large bibliography analysis of more than 500 articles. All the aspects regarding phytostilbenes will be covered including their chemistry and biochemistry, regulation of their biosynthesis, biological activities in plants, molecular engineering of stilbene pathways in plants and microbes as well as their biotechnological production by plant cell systems.
Collapse
Affiliation(s)
- Philippe Jeandet
- Research Unit "Induced Resistance and Plant Bioprotection", EA 4707, SFR Condorcet FR CNRS 3417, Faculty of Sciences, University of Reims Champagne-Ardenne, PO Box 1039, 51687 Reims Cedex 2, France.
| | - Alessandro Vannozzi
- Department of Agronomy, Food, Natural Resources, Animals, and Environment (DAFNAE), University of Padova, 35020 Legnaro, PD, Italy
| | - Eduardo Sobarzo-Sánchez
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, Campus Vida, 15782 Santiago de Compostela, Spain and Instituto de Investigación e Innovación en Salud, Facultad de Ciencias de la Salud, Universidad Central de Chile, Chile
| | - Md Sahab Uddin
- Department of Pharmacy, Southeast University, Dhaka, Bangladesh and Neuroscience Research Network, Dhaka, Bangladesh
| | - Roque Bru
- Plant Proteomics and Functional Genomics Group, Department of Agrochemistry and Biochemistry, Faculty of Science, University of Alicante, Alicante, Spain
| | - Ascension Martínez-Márquez
- Plant Proteomics and Functional Genomics Group, Department of Agrochemistry and Biochemistry, Faculty of Science, University of Alicante, Alicante, Spain
| | - Christophe Clément
- Research Unit "Induced Resistance and Plant Bioprotection", EA 4707, SFR Condorcet FR CNRS 3417, Faculty of Sciences, University of Reims Champagne-Ardenne, PO Box 1039, 51687 Reims Cedex 2, France.
| | - Sylvain Cordelier
- Research Unit "Induced Resistance and Plant Bioprotection", EA 4707, SFR Condorcet FR CNRS 3417, Faculty of Sciences, University of Reims Champagne-Ardenne, PO Box 1039, 51687 Reims Cedex 2, France.
| | - Azadeh Manayi
- Medicinal Plants Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, 1417614411 Tehran, Iran
| | - Seyed Fazel Nabavi
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran 14359-16471, Iran
| | - Mahsa Rasekhian
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Damanhour University, Damanhour, 22511, AlBeheira, Egypt
| | - Haroon Khan
- Department of Pharmacy, Faculty of Chemical and Life Sciences, Abdul Wali Khan University Mardan, 23200, Pakistan
| | - Iwona Morkunas
- Department of Plant Physiology, Poznań University of Life Sciences, Wołyńska 35, 60-637 Poznań, Poland
| | - Tarun Belwal
- Zhejiang University, College of Biosystems Engineering and Food Science, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Zhejiang Key Laboratory for Agri-Food Processing, Hangzhou 310058, The People's Republic of China
| | - Jingjie Jiang
- Dorothy and Fred Chau '71 Constellation Professor, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Room 4005D, 110 8th Street, Troy, NY 12180, USA
| | - Mattheos Koffas
- Dorothy and Fred Chau '71 Constellation Professor, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Room 4005D, 110 8th Street, Troy, NY 12180, USA
| | - Seyed Mohammad Nabavi
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran 14359-16471, Iran
| |
Collapse
|
18
|
Martinelli L, Redou V, Cochereau B, Delage L, Hymery N, Poirier E, Le Meur C, Le Foch G, Cladiere L, Mehiri M, Demont-Caulet N, Meslet-Cladiere L. Identification and Characterization of a New Type III Polyketide Synthase from a Marine Yeast, Naganishia uzbekistanensis. Mar Drugs 2020; 18:md18120637. [PMID: 33322429 PMCID: PMC7763939 DOI: 10.3390/md18120637] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/02/2020] [Accepted: 12/09/2020] [Indexed: 01/22/2023] Open
Abstract
A putative Type III Polyketide synthase (PKSIII) encoding gene was identified from a marine yeast, Naganishia uzbekistanensis strain Mo29 (UBOCC-A-208024) (formerly named as Cryptococcus sp.) isolated from deep-sea hydrothermal vents. This gene is part of a distinct phylogenetic branch compared to all known terrestrial fungal sequences. This new gene encodes a C-terminus extension of 74 amino acids compared to other known PKSIII proteins like Neurospora crassa. Full-length and reduced versions of this PKSIII were successfully cloned and overexpressed in a bacterial host, Escherichia coli BL21 (DE3). Both proteins showed the same activity, suggesting that additional amino acid residues at the C-terminus are probably not required for biochemical functions. We demonstrated by LC-ESI-MS/MS that these two recombinant PKSIII proteins could only produce tri- and tetraketide pyrones and alkylresorcinols using only long fatty acid chain from C8 to C16 acyl-CoAs as starter units, in presence of malonyl-CoA. In addition, we showed that some of these molecules exhibit cytotoxic activities against several cancer cell lines.
Collapse
Affiliation(s)
- Laure Martinelli
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, University Brest, F-29280 Plouzané, France; (L.M.); (V.R.); (B.C.); (N.H.); (E.P.); (C.L.M.); (G.L.F.)
| | - Vanessa Redou
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, University Brest, F-29280 Plouzané, France; (L.M.); (V.R.); (B.C.); (N.H.); (E.P.); (C.L.M.); (G.L.F.)
| | - Bastien Cochereau
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, University Brest, F-29280 Plouzané, France; (L.M.); (V.R.); (B.C.); (N.H.); (E.P.); (C.L.M.); (G.L.F.)
| | - Ludovic Delage
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR),CNRS, UMR8227, Sorbonne Université, 29680 Roscoff, France; (L.D.); (L.C.)
| | - Nolwenn Hymery
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, University Brest, F-29280 Plouzané, France; (L.M.); (V.R.); (B.C.); (N.H.); (E.P.); (C.L.M.); (G.L.F.)
| | - Elisabeth Poirier
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, University Brest, F-29280 Plouzané, France; (L.M.); (V.R.); (B.C.); (N.H.); (E.P.); (C.L.M.); (G.L.F.)
| | - Christophe Le Meur
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, University Brest, F-29280 Plouzané, France; (L.M.); (V.R.); (B.C.); (N.H.); (E.P.); (C.L.M.); (G.L.F.)
| | - Gaetan Le Foch
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, University Brest, F-29280 Plouzané, France; (L.M.); (V.R.); (B.C.); (N.H.); (E.P.); (C.L.M.); (G.L.F.)
| | - Lionel Cladiere
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR),CNRS, UMR8227, Sorbonne Université, 29680 Roscoff, France; (L.D.); (L.C.)
| | - Mohamed Mehiri
- Marine Natural Products Team, CNRS, UMR 7272, Institut de Chimie de Nice, Université Côte d’Azur, 06108 Nice, France;
| | - Nathalie Demont-Caulet
- UMR ECOSYS, INRAE, INRAE, University of Paris, 78026 Versailles, France;
- AgroParisTech, Université Paris-Saclay, 78026 Versailles, France
| | - Laurence Meslet-Cladiere
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, University Brest, F-29280 Plouzané, France; (L.M.); (V.R.); (B.C.); (N.H.); (E.P.); (C.L.M.); (G.L.F.)
- Correspondence: ; Tel.: +33-2-90-91-51-10
| |
Collapse
|
19
|
Murray LAM, McKinnie SMK, Moore BS, George JH. Meroterpenoid natural products from Streptomyces bacteria - the evolution of chemoenzymatic syntheses. Nat Prod Rep 2020; 37:1334-1366. [PMID: 32602506 PMCID: PMC7578067 DOI: 10.1039/d0np00018c] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Covering: Up to January 2020Meroterpenoids derived from the polyketide 1,3,6,8-tetrahydroxynaphthalene (THN) are complex natural products produced exclusively by Streptomyces bacteria. These antibacterial compounds include the napyradiomycins, merochlorins, marinones, and furaquinocins and have inspired many attempts at their chemical synthesis. In this review, we highlight the role played by biosynthetic studies in the stimulation of biomimetic and, ultimately, chemoenzymatic total syntheses of these natural products. In particular, the application of genome mining techniques to marine Streptomyces bacteria led to the discovery of unique prenyltransferase and vanadium-dependent haloperoxidase enzymes that can be used as highly selective biocatalysts in fully enzymatic total syntheses, thus overcoming the limitations of purely chemical reagents.
Collapse
Affiliation(s)
- Lauren A M Murray
- Department of Chemistry, The University of Adelaide, Adelaide, South Australia 5005, Australia.
| | | | | | | |
Collapse
|
20
|
Sang X, Yang M, Su J. Research on endophytic fungi for producing huperzine A on a large-scale. Crit Rev Microbiol 2020; 46:654-664. [PMID: 32970952 DOI: 10.1080/1040841x.2020.1819771] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Huperzine A (HupA) is an effective inhibitor of acetylcholinesterase and has attracted great interest as a therapeutic candidate for Alzheimer's disease. However, the use of HupA is limited by resource scarcity as well as by its low yields from Huperzia serrata, its primary plant source. Recent studies have shown that this compound is produced by various endophytic fungi, thereby providing a promising alternative source, as fungi are much more amenable than plants owing to their simpler genetics and the ease of manipulation. In this review, we summarize the progress in research on the methods to increase HupA production, including fermentation conditions, fungal elicitors, gene expression, and the activation of key enzymes. This review provides guidance for further studies on HupA-producing endophytic fungi aimed at efficient HupA synthesis and accumulation, and offers new approaches for studies on the regulation of high-value bioactive secondary metabolites.
Collapse
Affiliation(s)
- Xiao Sang
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University, Fuzhou, Fujian, PR China
| | - Minhe Yang
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University, Fuzhou, Fujian, PR China
| | - Jingqian Su
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University, Fuzhou, Fujian, PR China
| |
Collapse
|
21
|
Shen X, Wang X, Huang T, Deng Z, Lin S. Naphthoquinone-Based Meroterpenoids from Marine-Derived Streptomyces sp. B9173. Biomolecules 2020; 10:biom10081187. [PMID: 32824158 PMCID: PMC7463872 DOI: 10.3390/biom10081187] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/12/2020] [Accepted: 08/14/2020] [Indexed: 12/19/2022] Open
Abstract
Naphthoquinone-based meroterpenoids are hybrid polyketide-terpenoid natural products with chemical diversity and a broad range of biological activities. Here, we report the isolation of a group of naphthoquinone-containing compounds from Streptomyces sp. B9173, and their structures were elucidated by using a combination of spectroscopic techniques, including 1D, 2D NMR, and high-resolution mass (HRMS) analysis. Seven flaviogeranin congeners or intermediates, three of which were new, have been derived from common naphthoquinone backbone and subsequent oxidation, methylation, prenylation, and amino group incorporation. Both flaviogeranin B1 (1) and B (2) contain an amino group which was incorporated into the C8 of 1,3,6,8-terhydroxynaphthalene (THN). Flaviogeranin D (3) contains an intact C-geranylgeranyl residue attached to the C2 of THN, while the O-geranylgeranyl group of 2 links with the hydroxyl on the C2 site of THN. Four compounds were selected and tested for antibacterial activity and cytotoxicity, with 3 and flaviogeranin C2 (5) displaying potent activity against selected bacteria and cancer cell lines. In light of the structure features of isolated compounds and the biosynthetic genes, a biosynthetic pathway of naphthoquinone-based flaviogeranins has been proposed. These isolated compounds not only extend the structural diversity but also represent new insights into the biosynthesis of naphthoquinone-based meroterpenoids.
Collapse
Affiliation(s)
- Xinqian Shen
- State Key Laboratory of Microbial Metabolism, and Joint International Research Laboratory on Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University; 800 Dongchuan Rd, Shanghai 200240, China
| | - Xiaozheng Wang
- State Key Laboratory of Microbial Metabolism, and Joint International Research Laboratory on Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University; 800 Dongchuan Rd, Shanghai 200240, China
| | - Tingting Huang
- State Key Laboratory of Microbial Metabolism, and Joint International Research Laboratory on Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University; 800 Dongchuan Rd, Shanghai 200240, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, and Joint International Research Laboratory on Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University; 800 Dongchuan Rd, Shanghai 200240, China
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, and Joint International Research Laboratory on Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University; 800 Dongchuan Rd, Shanghai 200240, China
| |
Collapse
|
22
|
Corretto E, Antonielli L, Sessitsch A, Höfer C, Puschenreiter M, Widhalm S, Swarnalakshmi K, Brader G. Comparative Genomics of Microbacterium Species to Reveal Diversity, Potential for Secondary Metabolites and Heavy Metal Resistance. Front Microbiol 2020; 11:1869. [PMID: 32903828 PMCID: PMC7438953 DOI: 10.3389/fmicb.2020.01869] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 07/16/2020] [Indexed: 12/11/2022] Open
Abstract
Microbacterium species have been isolated from a wide range of hosts and environments, including heavy metal-contaminated sites. Here, we present a comprehensive analysis on the phylogenetic distribution and the genetic potential of 70 Microbacterium belonging to 20 different species isolated from heavy metal-contaminated and non-contaminated sites with particular attention to secondary metabolites gene clusters. The analyzed Microbacterium species are divided in three main functional clades. They share a small core genome (331 gene families covering basic functions) pointing to high genetic diversity. The most common secondary metabolite gene clusters encode pathways for the production of terpenoids, type III polyketide synthases and non-ribosomal peptide synthetases, potentially responsible of the synthesis of siderophore-like compounds. In vitro tests showed that many Microbacterium strains produce siderophores, ACC deaminase, auxins (IAA) and are able to solubilize phosphate. Microbacterium isolates from heavy metal contaminated sites are on average more resistant to heavy metals and harbor more genes related to metal homeostasis (e.g., metalloregulators). On the other hand, the ability to increase the metal mobility in a contaminated soil through the secretion of specific molecules seems to be widespread among all. Despite the widespread capacity of strains to mobilize several metals, plants inoculated with selected Microbacterium isolates showed only slightly increased iron concentrations, whereas concentrations of zinc, cadmium and lead were decreased.
Collapse
Affiliation(s)
- Erika Corretto
- Bioresouces Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Livio Antonielli
- Bioresouces Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Angela Sessitsch
- Bioresouces Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Christoph Höfer
- Institute of Soil Research, Department of Forest- and Soil Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Markus Puschenreiter
- Institute of Soil Research, Department of Forest- and Soil Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Siegrid Widhalm
- Bioresouces Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | | | - Günter Brader
- Bioresouces Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| |
Collapse
|
23
|
Husain SM, Präg A, Linnenbrink A, Bechthold A, Müller M. Insights into the Role of Ketoreductases in the Biosynthesis of Partially Reduced Bacterial Aromatic Polyketides. Chembiochem 2020; 21:780-784. [PMID: 31507033 PMCID: PMC7154522 DOI: 10.1002/cbic.201900357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 09/09/2019] [Indexed: 12/20/2022]
Abstract
Partially reduced aromatic polyketides are bioactive secondary metabolites or intermediates in the biosynthesis of deoxygenated aromatics. For the antibiotic GTRI‐02 (mensalone) in different Streptomyces spp., biosynthesis involving the reduction of a fully aromatized acetyltrihydroxynaphthalene by a naphthol reductase has been proposed and shown in vitro with a fungal enzyme. However, more recently, GTRI‐02 has been identified as a product of the ActIII biosynthetic gene cluster from Streptomyces coelicolor A3(2), for which the reduction of a linear polyketide precursor by ActIII ketoreductase, prior to cyclization and aromatization, has been suggested. We have examined three different ketoreductases from bacterial producer strains of GTRI‐02 for their ability to reduce mono‐, bi‐, and tricyclic aromatic substrates. The enzymes reduced 1‐ and 2‐tetralone but not other aromatic substrates. This strongly suggests a reduction of a cyclized but not yet aromatic polyketide intermediate in the biosynthesis of GTRI‐02. Implications of the results for the biosynthesis of other secondary polyketidic metabolites are discussed.
Collapse
Affiliation(s)
- Syed Masood Husain
- Centre of Biomedical Research, SGPGIMS Campus, Raebareli Road, Lucknow, 226014, Uttar Pradesh, India
| | - Andreas Präg
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Anton Linnenbrink
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Stefan-Meier-Strasse 19, 79104, Freiburg, Germany
| | - Andreas Bechthold
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Stefan-Meier-Strasse 19, 79104, Freiburg, Germany
| | - Michael Müller
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| |
Collapse
|
24
|
Fäseke VC, Raps FC, Sparr C. Polyketide Cyclizations for the Synthesis of Polyaromatics. Angew Chem Int Ed Engl 2020; 59:6975-6983. [DOI: 10.1002/anie.201911255] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 11/05/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Vincent C. Fäseke
- Department of Chemistry University of Basel St. Johanns-Ring 19 4056 Basel Switzerland
| | - Felix C. Raps
- Department of Chemistry University of Basel St. Johanns-Ring 19 4056 Basel Switzerland
| | - Christof Sparr
- Department of Chemistry University of Basel St. Johanns-Ring 19 4056 Basel Switzerland
| |
Collapse
|
25
|
Fäseke VC, Raps FC, Sparr C. Polyketide Cyclizations for the Synthesis of Polyaromatics. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201911255] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Vincent C. Fäseke
- Department of Chemistry University of Basel St. Johanns-Ring 19 4056 Basel Switzerland
| | - Felix C. Raps
- Department of Chemistry University of Basel St. Johanns-Ring 19 4056 Basel Switzerland
| | - Christof Sparr
- Department of Chemistry University of Basel St. Johanns-Ring 19 4056 Basel Switzerland
| |
Collapse
|
26
|
Navarro-Muñoz JC, Collemare J. Evolutionary Histories of Type III Polyketide Synthases in Fungi. Front Microbiol 2020; 10:3018. [PMID: 32038517 PMCID: PMC6985275 DOI: 10.3389/fmicb.2019.03018] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 12/16/2019] [Indexed: 12/30/2022] Open
Abstract
Type III polyketide synthases (PKSs) produce secondary metabolites with diverse biological activities, including antimicrobials. While they have been extensively studied in plants and bacteria, only a handful of type III PKSs from fungi has been characterized in the last 15 years. The exploitation of fungal type III PKSs to produce novel bioactive compounds requires understanding the diversity of these enzymes, as well as of their biosynthetic pathways. Here, phylogenetic and reconciliation analyses of 522 type III PKSs from 1,193 fungal genomes revealed complex evolutionary histories with massive gene duplications and losses, explaining their discontinuous distribution in the fungal tree of life. In addition, horizontal gene transfer events from bacteria to fungi and, to a lower extent, between fungi, could be inferred. Ancestral gene duplication events have resulted in the divergence of eight phylogenetic clades. Especially, two clades show ancestral linkage and functional co-evolution between a type III PKS and a reducing PKS genes. Investigation of the occurrence of protein domains in fungal type III PKS predicted gene clusters highlighted the diversity of biosynthetic pathways, likely reflecting a large chemical landscape. Type III PKS genes are most often located next to genes encoding cytochrome P450s, MFS transporters and transcription factors, defining ancestral core gene clusters. This analysis also allowed predicting gene clusters for the characterized fungal type III PKSs and provides working hypotheses for the elucidation of the full biosynthetic pathways. Altogether, our analyses provide the fundamental knowledge to motivate further characterization and exploitation of fungal type III PKS biosynthetic pathways.
Collapse
|
27
|
Kaneko A, Morishita Y, Tsukada K, Taniguchi T, Asai T. Post-genomic approach based discovery of alkylresorcinols from a cricket-associated fungus, Penicillium soppi. Org Biomol Chem 2019; 17:5239-5243. [PMID: 31086874 DOI: 10.1039/c9ob00807a] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Polyketide synthase (PKS) gene-guided genome mining in a cricket-associated fungus, Penicillium soppi, revealed a cryptic biosynthetic gene cluster that contained a highly reducing PKS (HR-PKS), a type III PKS, and a P450 gene. Heterologous expression of the cluster in Aspergillus oryzae led to the isolation of novel alkylresorcinols with a unique Z,E,Z-triene motif. This study displays an unusual biosynthetic mechanism of an HR-PKS and a new releasing mechanism via a type III PKS in fungi.
Collapse
Affiliation(s)
- Akiho Kaneko
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 komaba, meguro-ku, Tokyo 153-8902, Japan.
| | | | | | | | | |
Collapse
|
28
|
Pavan ME, López NI, Pettinari MJ. Melanin biosynthesis in bacteria, regulation and production perspectives. Appl Microbiol Biotechnol 2019; 104:1357-1370. [PMID: 31811318 DOI: 10.1007/s00253-019-10245-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/25/2019] [Accepted: 11/04/2019] [Indexed: 12/26/2022]
Abstract
The production of black pigments in bacteria was discovered more than a century ago and related to tyrosine metabolism. However, their diverse biological roles and the control of melanin synthesis in different bacteria have only recently been investigated. The broad distribution of these pigments suggests that they have an important role in a variety of organisms. Melanins protect microorganisms from many environmental stress conditions, ranging from ultraviolet radiation and toxic heavy metals to oxidative stress. Melanins can also affect bacterial interactions with other organisms and are important in pathogenesis and survival in many environments. Bacteria produce several types of melanin through dedicated pathways or as a result of enzymatic imbalances in altered metabolic routes. The control of the melanin synthesis in bacteria involves metabolic and transcriptional regulation, but many aspects remain still largely unknown. The diverse properties of melanins have spurred a large number of applications, and recent efforts have been done to produce the pigment at biotechnologically relevant scales.
Collapse
Affiliation(s)
- María Elisa Pavan
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Nancy I López
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina. .,IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.
| | - M Julia Pettinari
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina. .,IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.
| |
Collapse
|
29
|
Pandith SA, Ramazan S, Khan MI, Reshi ZA, Shah MA. Chalcone synthases (CHSs): the symbolic type III polyketide synthases. PLANTA 2019; 251:15. [PMID: 31776718 DOI: 10.1007/s00425-019-03307-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 11/02/2019] [Indexed: 05/08/2023]
Abstract
Present review provides a thorough insight on some significant aspects of CHSs over a period of about past three decades with a better outlook for future studies toward comprehending the structural and mechanistic intricacy of this symbolic enzyme. Polyketide synthases (PKSs) form a large family of iteratively acting multifunctional proteins that are involved in the biosynthesis of spectrum of natural products. They exhibit remarkable versatility in the structural configuration and functional organization with an incredible ability to generate different classes of compounds other than the characteristic secondary metabolite constituents. Architecturally, chalcone synthase (CHS) is considered to be the simplest representative of Type III PKSs. The enzyme is pivotal for phenylpropanoid biosynthesis and is also well known for catalyzing the initial step of the flavonoid/isoflavonoid pathway. Being the first Type III enzyme to be discovered, CHS has been subjected to ample investigations which, to a greater extent, have tried to understand its structural complexity and promiscuous functional behavior. In this context, we vehemently tried to collect the fragmented information entirely focussed on this symbolic enzyme from about past three-four decades. The aim of this review is to selectively summarize data on some of the fundamental aspects of CHSs viz, its history and distribution, localization, structure and analogs in non-plant hosts, promoter analyses, and role in defense, with an emphasis on mechanistic studies in different species and vis-à-vis mutation-led changes, and evolutionary significance which has been discussed in detail. The present review gives an insight with a better perspective for the scientific community for future studies devoted towards delimiting the mechanistic and structural basis of polyketide biosynthetic machinery vis-à-vis CHS.
Collapse
Affiliation(s)
- Shahzad A Pandith
- Department of Botany, University of Kashmir, Srinagar, Jammu and Kashmir, 190006, India.
| | - Salika Ramazan
- Department of Botany, University of Kashmir, Srinagar, Jammu and Kashmir, 190006, India
| | - Mohd Ishfaq Khan
- Department of Botany, University of Kashmir, Srinagar, Jammu and Kashmir, 190006, India
| | - Zafar A Reshi
- Department of Botany, University of Kashmir, Srinagar, Jammu and Kashmir, 190006, India
| | - Manzoor A Shah
- Department of Botany, University of Kashmir, Srinagar, Jammu and Kashmir, 190006, India.
| |
Collapse
|
30
|
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.
Collapse
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
| |
Collapse
|
31
|
Dutta S, Yu SM, Jeong SC, Lee YH. High-throughput analysis of genes involved in biocontrol performance of Pseudomonas fluorescens NBC275 against Gray mold. J Appl Microbiol 2019; 128:265-279. [PMID: 31574191 DOI: 10.1111/jam.14475] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 09/01/2019] [Accepted: 09/17/2019] [Indexed: 01/16/2023]
Abstract
AIMS Many physiological and microbial characteristics influence the biocontrol performance of the biological control agents (BCAs) in agricultural fields. To implement effective biocontrol, the contribution of specific genes, mechanisms and traits to the biocontrol performance of BCAs need to be characterized and explored in greater detail. METHODS AND RESULTS In this study, a transposon (Tn) mutant library using the BCA Pseudomonas fluorescens NBC275 (Pf275) was generated to explore genes and bacterial characteristics involved in antifungal activity and biocontrol performance. Among the Tn mutants, 205 strains showing variations in antifungal activity compared to wild-type (WT) were selected and further analysed for biocontrol efficacy against gray mold in pepper fruits. The genes involved in pyoverdine biosynthesis (pvdI and pvdD) and chitin-binding protein (gbpA) played essential roles in the antifungal activity and biocontrol capacity of Pf275. In addition, a mutation in phlD completely abolished the antifungal activity and significantly suppressed the biocontrol ability of the strain. Genes affecting antifungal activity of Pf275 significantly influenced swimming motility, which was identified as an important trait for the biocontrol ability of the bacterial strain. CONCLUSIONS Overall, our results suggest that antifungal compound production, siderophore biosynthesis and swimming motility synergistically contribute to Pf275 biocontrol performance. The utility of this library was demonstrated by identifying genes for antagonism and biocontrol ability in this BCA strain. The functional roles of many genes identified as contributing to antagonism and in vivo biocontrol activity require further study. SIGNIFICANCE AND IMPACT OF THIS STUDY Genes contributing to antifungal activity and biocontrol performance of P. fluorescens were identified and highlighted by Tn mutagenesis, which will give insight to improve the biocontrol performance of this BCA.
Collapse
Affiliation(s)
- S Dutta
- Division of Biotechnology, Chonbuk National University, Iksan-si, Jeollabuk-do, Republic of Korea
| | - S-M Yu
- Freshwater Bioresources Utilization Division, Nakdonggang National Institute of Biological Resources, Sangju-si, Gyeongsangbuk-do, Republic of Korea
| | - S C Jeong
- Freshwater Bioresources Utilization Division, Nakdonggang National Institute of Biological Resources, Sangju-si, Gyeongsangbuk-do, Republic of Korea
| | - Y H Lee
- Division of Biotechnology, Chonbuk National University, Iksan-si, Jeollabuk-do, Republic of Korea.,Advanced Institute of Environment and Bioscience, Plant Medical Research Center, and Institute of Bio-industry, Chonbuk National University, Ikansi-si, Jeollabuk-do, Republic of Korea
| |
Collapse
|
32
|
Manoharan G, Sairam T, Thangamani R, Ramakrishnan D, K Tiwari M, Lee JK, Marimuthu J. Identification and characterization of type III polyketide synthase genes from culturable endophytes of ethnomedicinal plants. Enzyme Microb Technol 2019; 131:109396. [PMID: 31615679 DOI: 10.1016/j.enzmictec.2019.109396] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/19/2019] [Accepted: 08/06/2019] [Indexed: 11/27/2022]
Abstract
Endophytic fungi provide benefits to host plants by producing a diverse class of secondary metabolites (natural products). Arrays of polyketide natural products are synthesized by specific classes of polyketide synthases (PKS I, II and III) in host organisms. In the present study, we attempt to screen and identify type III PKSs in culturable fungal endophytes isolated from the ethno medicinal plants including Arbus precatorius, Bacopa monnieri,Citrus aurantifolia and Datura metel to detect the genetic potential of endophytic fungi in producing bioactive compounds. A total of seventeen endophytic fungal strains belonging to eight genera were identified using fungal morphology and rDNA-ITS phylogenetic analyses. A CODEHOP-PCR based strategy was followed to design degenerate primers for the screening of type III PKS genes from fungal endophytes. We had successfully amplified partial PKS genes from eight endophytes. The amplified PKS sequences showed 60-99% identity to already characterized/putative PKS genes. From the partial sequence of FiPKS from Fusarium incarnatum BMER1, a full-length gene was amplified, cloned and characterized. FiPKScDNA was cloned and expressed in E. coli Lemo21 (DE3) and the purified protein was shown to produce pyrones and resorcinols using acyl-CoA thioesters as substrates. FiPKS showed the highest catalytic efficiency of 7.6 × 104 s-1 M-1 with stearoyl CoA as a starter unit. This study reports the identification and characterization of type III PKS from endophytes of medicinal plants by CODEHOP PCR.
Collapse
Affiliation(s)
- Gomathi Manoharan
- PSG Centre for Molecular Medicine and Therapeutics, PSG Institute of Medical Sciences and Research, Coimbatore, 641004, India
| | - Thiagarajan Sairam
- PSG Centre for Molecular Medicine and Therapeutics, PSG Institute of Medical Sciences and Research, Coimbatore, 641004, India
| | - Rajesh Thangamani
- Biotechnology Division, CSIR- National Engineering and Environmental Research Institute, CMC, Chennai 600113, India
| | - Dhivya Ramakrishnan
- PSG Centre for Molecular Medicine and Therapeutics, PSG Institute of Medical Sciences and Research, Coimbatore, 641004, India
| | - Manish K Tiwari
- Department of Chemistry, University of Copenhagen, Universitesparken 5, DK-2100, Copenhagen, Denmark
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Jeya Marimuthu
- PSG Centre for Molecular Medicine and Therapeutics, PSG Institute of Medical Sciences and Research, Coimbatore, 641004, India.
| |
Collapse
|
33
|
Ryu MJ, Hwang S, Kim S, Yang I, Oh DC, Nam SJ, Fenical W. Meroindenon and Merochlorins E and F, Antibacterial Meroterpenoids from a Marine-Derived Sediment Bacterium of the Genus Streptomyces. Org Lett 2019; 21:5779-5783. [PMID: 31298867 DOI: 10.1021/acs.orglett.9b01440] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Meroterpenoids, meroindenon (1) and merochlorins E (2) and F (3), were isolated from a marine-derived bacterium belonging to the genus Streptomyces. Their chemical structures were established using extensive analysis of MS, UV, ECD, and NMR spectroscopic data. Compounds 1-3 possess a tetrahydroxynaphthalene core and a C15-isoprene unit. Compounds 2 and 3 exhibited strong antibacterial activities against B. subtilis, K. rhizophila, and S. aureus, with a range of MIC values from 1 to 2 μg/mL.
Collapse
Affiliation(s)
- Min-Ji Ryu
- Department of Chemistry and Nanoscience , Ewha Womans University , Seoul 03760 , Republic of Korea
| | - Sunghoon Hwang
- Natural Products Research Institute, College of Pharmacy , Seoul National University , Seoul 08826 , Republic of Korea
| | - Sojeong Kim
- Graduate School of Industrial Pharmaceutical Sciences , Ewha Womans University , Seoul 03760 , Republic of Korea
| | - Inho Yang
- Department of Convergence Study on the Ocean Science and Technology , Korea Maritime and Ocean University , Busan 49112 , Republic of Korea
| | - Dong-Chan Oh
- 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
| | - William Fenical
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California San Diego , La Jolla , California 92093-0204 , United States
| |
Collapse
|
34
|
Zhou ZZ, Zhu HJ, Lin LP, Zhang X, Ge HM, Jiao RH, Tan RX. Dalmanol biosyntheses require coupling of two separate polyketide gene clusters. Chem Sci 2018; 10:73-82. [PMID: 30746075 PMCID: PMC6335865 DOI: 10.1039/c8sc03697g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Accepted: 11/21/2018] [Indexed: 11/29/2022] Open
Abstract
Polyketide–polyketide hybrids are unique natural products with promising bioactivity, but the hybridization processes remain poorly understood.
Polyketide–polyketide hybrids are unique natural products with promising bioactivity, but the hybridization processes remain poorly understood. Herein, we present that the biosynthetic pathways of two immunosuppressants, dalmanol A and acetodalmanol A, result from an unspecific monooxygenase triggered hybridization of two distinct polyketide (naphthalene and chromane) biosynthetic gene clusters. The orchestration of the functional dimorphism of the polyketide synthase (ChrA) ketoreductase (KR) domain (shortened as ChrA KR) with that of the KR partner (ChrB) in the bioassembly line increases the polyketide diversity and allows the fungal generation of plant chromanes (e.g., noreugenin) and phloroglucinols (e.g., 2,4,6-trihydroxyacetophenone). The simultaneous fungal biosynthesis of 1,3,6,8- and 2-acetyl-1,3,6,8-tetrahydroxynaphthalenes was addressed as well. Collectively, the work may symbolize a movement in understanding the multiple-gene-cluster involved natural product biosynthesis, and highlights the possible fungal generations of some chromane- and phloroglucinol-based phytochemicals.
Collapse
Affiliation(s)
- Zhen Zhen Zhou
- State Key Laboratory of Pharmaceutical Biotechnology , Institute of Functional Biomolecules , Nanjing University , Nanjing 210023 , China .
| | - Hong Jie Zhu
- State Key Laboratory of Pharmaceutical Biotechnology , Institute of Functional Biomolecules , Nanjing University , Nanjing 210023 , China .
| | - Li Ping Lin
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy , Nanjing University of Chinese Medicine , Nanjing 210023 , China.,State Key Laboratory Elemento-Organic Chemistry , Nankai University , Tianjin 300071 , China
| | - Xuan Zhang
- State Key Laboratory of Pharmaceutical Biotechnology , Institute of Functional Biomolecules , Nanjing University , Nanjing 210023 , China .
| | - Hui Ming Ge
- State Key Laboratory of Pharmaceutical Biotechnology , Institute of Functional Biomolecules , Nanjing University , Nanjing 210023 , China .
| | - Rui Hua Jiao
- State Key Laboratory of Pharmaceutical Biotechnology , Institute of Functional Biomolecules , Nanjing University , Nanjing 210023 , China .
| | - Ren Xiang Tan
- State Key Laboratory of Pharmaceutical Biotechnology , Institute of Functional Biomolecules , Nanjing University , Nanjing 210023 , China . .,State Key Laboratory Cultivation Base for TCM Quality and Efficacy , Nanjing University of Chinese Medicine , Nanjing 210023 , China
| |
Collapse
|
35
|
Navigating genetic diversity by painting the bacteria red. Proc Natl Acad Sci U S A 2018; 115:10824-10826. [PMID: 30309959 DOI: 10.1073/pnas.1815763115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
36
|
Repurposing type III polyketide synthase as a malonyl-CoA biosensor for metabolic engineering in bacteria. Proc Natl Acad Sci U S A 2018; 115:9835-9844. [PMID: 30232266 DOI: 10.1073/pnas.1808567115] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Malonyl-CoA is an important central metabolite for the production of diverse valuable chemicals including natural products, but its intracellular availability is often limited due to the competition with essential cellular metabolism. Several malonyl-CoA biosensors have been developed for high-throughput screening of targets increasing the malonyl-CoA pool. However, they are limited for use only in Escherichia coli and Saccharomyces cerevisiae and require multiple signal transduction steps. Here we report development of a colorimetric malonyl-CoA biosensor applicable in three industrially important bacteria: E. coli, Pseudomonas putida, and Corynebacterium glutamicum RppA, a type III polyketide synthase producing red-colored flaviolin, was repurposed as a malonyl-CoA biosensor in E. coli Strains with enhanced malonyl-CoA accumulation were identifiable by the colorimetric screening of cells showing increased red color. Other type III polyketide synthases could also be repurposed as malonyl-CoA biosensors. For target screening, a 1,858 synthetic small regulatory RNA library was constructed and applied to find 14 knockdown gene targets that generally enhanced malonyl-CoA level in E. coli These knockdown targets were applied to produce two polyketide (6-methylsalicylic acid and aloesone) and two phenylpropanoid (resveratrol and naringenin) compounds. Knocking down these genes alone or in combination, and also in multiple different E. coli strains for two polyketide cases, allowed rapid development of engineered strains capable of enhanced production of 6-methylsalicylic acid, aloesone, resveratrol, and naringenin to 440.3, 30.9, 51.8, and 103.8 mg/L, respectively. The malonyl-CoA biosensor developed here is a simple tool generally applicable to metabolic engineering of microorganisms to achieve enhanced production of malonyl-CoA-derived chemicals.
Collapse
|
37
|
Murray LAM, McKinnie SMK, Pepper HP, Erni R, Miles ZD, Cruickshank MC, López-Pérez B, Moore BS, George JH. Total Synthesis Establishes the Biosynthetic Pathway to the Naphterpin and Marinone Natural Products. Angew Chem Int Ed Engl 2018; 57:11009-11014. [PMID: 29935040 PMCID: PMC6248334 DOI: 10.1002/anie.201804351] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Indexed: 01/18/2023]
Abstract
The naphterpins and marinones are naphthoquinone meroterpenoids with an unusual aromatic oxidation pattern that is biosynthesized from 1,3,6,8-tetrahydroxynaphthalene (THN). We propose that cryptic halogenation of THN derivatives by vanadium-dependent chloroperoxidase (VCPO) enzymes is key to this biosynthetic pathway, despite the absence of chlorine in these natural products. This speculation inspired a total synthesis to mimic the naphterpin/marinone biosynthetic pathway. In validation of this biogenetic hypothesis, two VCPOs were discovered that interconvert several of the proposed biosynthetic intermediates.
Collapse
Affiliation(s)
- Lauren A. M. Murray
- Department of Chemistry, University of Adelaide Adelaide, SA 5005 (Australia)
| | - Shaun M. K. McKinnie
- Center for Marine Biotechnology and Biomedicine Scripps Institution of Oceanograph, University of California, San Diego, La Jolla, CA 92093 (USA) and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093 (USA)
| | - Henry P. Pepper
- Department of Chemistry, University of Adelaide Adelaide, SA 5005 (Australia)
| | - Reto Erni
- Center for Marine Biotechnology and Biomedicine Scripps Institution of Oceanograph, University of California, San Diego, La Jolla, CA 92093 (USA) and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093 (USA)
| | - Zachary D. Miles
- Center for Marine Biotechnology and Biomedicine Scripps Institution of Oceanograph, University of California, San Diego, La Jolla, CA 92093 (USA) and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093 (USA)
| | | | - Borja López-Pérez
- Department of Chemistry, University of Adelaide Adelaide, SA 5005 (Australia)
| | - Bradley S. Moore
- Center for Marine Biotechnology and Biomedicine Scripps Institution of Oceanograph, University of California, San Diego, La Jolla, CA 92093 (USA) and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093 (USA)
| | - Jonathan H. George
- Department of Chemistry, University of Adelaide Adelaide, SA 5005 (Australia)
| |
Collapse
|
38
|
Murray LAM, McKinnie SMK, Pepper HP, Erni R, Miles ZD, Cruickshank MC, López‐Pérez B, Moore BS, George JH. Total Synthesis Establishes the Biosynthetic Pathway to the Naphterpin and Marinone Natural Products. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804351] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
| | - Shaun M. K. McKinnie
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanograph University of California, San Diego La Jolla CA 92093 USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences University of California, San Diego La Jolla CA 92093 USA
| | - Henry P. Pepper
- Department of Chemistry University of Adelaide Adelaide SA 5005 Australia
| | - Reto Erni
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanograph University of California, San Diego La Jolla CA 92093 USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences University of California, San Diego La Jolla CA 92093 USA
| | - Zachary D. Miles
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanograph University of California, San Diego La Jolla CA 92093 USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences University of California, San Diego La Jolla CA 92093 USA
| | | | - Borja López‐Pérez
- Department of Chemistry University of Adelaide Adelaide SA 5005 Australia
| | - Bradley S. Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanograph University of California, San Diego La Jolla CA 92093 USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences University of California, San Diego La Jolla CA 92093 USA
| | - Jonathan H. George
- Department of Chemistry University of Adelaide Adelaide SA 5005 Australia
| |
Collapse
|
39
|
Castro JF, Nouioui I, Sangal V, Choi S, Yang SJ, Kim BY, Trujillo ME, Riesco R, Montero-Calasanz MDC, Rahmani TPD, Bull AT, Sutcliffe IC, Asenjo JA, Andrews B, Goodfellow M. Blastococcus atacamensis sp. nov., a novel strain adapted to life in the Yungay core region of the Atacama Desert. Int J Syst Evol Microbiol 2018; 68:2712-2721. [PMID: 29969090 DOI: 10.1099/ijsem.0.002828] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
A polyphasic study was undertaken to establish the taxonomic status of a Blastococcus strain isolated from an extreme hyper-arid Atacama Desert soil. The isolate, strain P6T, was found to have chemotaxonomic and morphological properties consistent with its classification in the genus Blastococcus. It was shown to form a well-supported branch in the Blastococcus 16S rRNA gene tree together with the type strains of Blastococcus capsensis and Blastococcus saxobsidens and was distinguished from the latter, its close phylogenetic neighbour, by a broad range of phenotypic properties. The draft genome sequence of isolate P6T showed 84.6 % average nucleotide identity, 83.0 % average amino acid identity and a digital DNA-DNA hybridisation value of 27.8 % in comparison with the genome sequence of B. saxobsidens DSM 44509T, values consistent with its assignment to a separate species. Based on these data it is proposed that isolate P6T (NCIMB 15090T=NRRL B-65468T) be assigned to the genus Blastococcus as Blastococcus atacamensis sp. nov. Analysis of the whole genome sequence of B. atacamensis P6T, with 3778 open reading frames and a genome size of 3.9 Mb showed the presence of genes and gene clusters that encode for properties that reflect its adaptation to the extreme environmental conditions that prevail in Atacama Desert soils.
Collapse
Affiliation(s)
- Jean Franco Castro
- 1School of Natural and Environmental Sciences, Ridley Building 2, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
- 2Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, University of Chile, Beauchef 851, Santiago, Chile
| | - Imen Nouioui
- 1School of Natural and Environmental Sciences, Ridley Building 2, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Vartul Sangal
- 3Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, UK
| | - Seonbin Choi
- 4ChunLab, Inc., 1, Gwanaka-ro, Gwanak-gu, Seoul 151015, Republic of Korea
| | - Seung-Jo Yang
- 4ChunLab, Inc., 1, Gwanaka-ro, Gwanak-gu, Seoul 151015, Republic of Korea
| | - Byung-Yong Kim
- 4ChunLab, Inc., 1, Gwanaka-ro, Gwanak-gu, Seoul 151015, Republic of Korea
| | - Martha E Trujillo
- 5Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - Raul Riesco
- 4ChunLab, Inc., 1, Gwanaka-ro, Gwanak-gu, Seoul 151015, Republic of Korea
| | | | - Tara P D Rahmani
- 1School of Natural and Environmental Sciences, Ridley Building 2, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Alan T Bull
- 6School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| | - Iain C Sutcliffe
- 3Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, UK
| | - Juan A Asenjo
- 2Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, University of Chile, Beauchef 851, Santiago, Chile
| | - Barbara Andrews
- 2Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, University of Chile, Beauchef 851, Santiago, Chile
| | - Michael Goodfellow
- 1School of Natural and Environmental Sciences, Ridley Building 2, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| |
Collapse
|
40
|
Huang L, Liu M, Huang H, Wen Y, Zhang X, Wei Y. Recent Advances and Progress on Melanin-like Materials and Their Biomedical Applications. Biomacromolecules 2018; 19:1858-1868. [DOI: 10.1021/acs.biomac.8b00437] [Citation(s) in RCA: 174] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Long Huang
- Department of Chemistry, Nanchang University, 999 Xuefu Avenue, Nanchang 330031, China
| | - Meiying Liu
- Department of Chemistry, Nanchang University, 999 Xuefu Avenue, Nanchang 330031, China
| | - Hongye Huang
- Department of Chemistry, Nanchang University, 999 Xuefu Avenue, Nanchang 330031, China
| | - Yuanqing Wen
- Department of Chemistry, Nanchang University, 999 Xuefu Avenue, Nanchang 330031, China
| | - Xiaoyong Zhang
- Department of Chemistry, Nanchang University, 999 Xuefu Avenue, Nanchang 330031, China
| | - Yen Wei
- Department of Chemistry and the Tsinghua Center for Frontier Polymer Research, Tsinghua University, Beijing 100084, P.R. China
- Department of Chemistry and Center for Nanotechnology, Chung-Yuan Christian University, Chung-Li 32023, Taiwan
| |
Collapse
|
41
|
Komaki H, Sakurai K, Hosoyama A, Kimura A, Igarashi Y, Tamura T. Diversity of nonribosomal peptide synthetase and polyketide synthase gene clusters among taxonomically close Streptomyces strains. Sci Rep 2018; 8:6888. [PMID: 29720592 PMCID: PMC5932044 DOI: 10.1038/s41598-018-24921-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 03/26/2018] [Indexed: 11/23/2022] Open
Abstract
To identify the species of butyrolactol-producing Streptomyces strain TP-A0882, whole genome-sequencing of three type strains in a close taxonomic relationship was performed. In silico DNA-DNA hybridization using the genome sequences suggested that Streptomyces sp. TP-A0882 is classified as Streptomyces diastaticus subsp. ardesiacus. Strain TP-A0882, S. diastaticus subsp. ardesiacus NBRC 15402T, Streptomyces coelicoflavus NBRC 15399T, and Streptomyces rubrogriseus NBRC 15455T harbor at least 14, 14, 10, and 12 biosynthetic gene clusters (BGCs), respectively, coding for nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs). All 14 gene clusters were shared by S. diastaticus subsp. ardesiacus strains TP-A0882 and NBRC 15402T, while only four gene clusters were shared by the three distinct species. Although BGCs for bacteriocin, ectoine, indole, melanine, siderophores such as deferrioxamine, terpenes such as albaflavenone, hopene, carotenoid and geosmin are shared by the three species, many BGCs for secondary metabolites such as butyrolactone, lantipeptides, oligosaccharide, some terpenes are species-specific. These results indicate the possibility that strains belonging to the same species possess the same set of secondary metabolite-biosynthetic pathways, whereas strains belonging to distinct species have species-specific pathways, in addition to some common pathways, even if the strains are taxonomically close.
Collapse
Affiliation(s)
- Hisayuki Komaki
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), Chiba, 292-0818, Japan.
| | | | | | | | - Yasuhiro Igarashi
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Toyama, 939-0398, Japan
| | - Tomohiko Tamura
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), Chiba, 292-0818, Japan
| |
Collapse
|
42
|
Iterative genome editing of Escherichia coli for 3-hydroxypropionic acid production. Metab Eng 2018; 47:303-313. [DOI: 10.1016/j.ymben.2018.04.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 04/09/2018] [Accepted: 04/11/2018] [Indexed: 11/21/2022]
|
43
|
Bacterial Enzymes Catalyzing the Synthesis of 1,8-Dihydroxynaphthalene, a Key Precursor of Dihydroxynaphthalene Melanin, from Sorangium cellulosum. Appl Environ Microbiol 2018; 84:AEM.00258-18. [PMID: 29500263 DOI: 10.1128/aem.00258-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 02/21/2018] [Indexed: 12/27/2022] Open
Abstract
1,8-Dihydroxynaphthalene (1,8-DHN) is a key intermediate in the biosynthesis of DHN melanin, which is specific to fungi. In this study, we characterized the enzymatic properties of the gene products of an operon consisting of soceCHS1, bdsA, and bdsB from the Gram-negative bacterium Sorangium cellulosum Heterologous expression of soceCHS1, bdsA, and bdsB in Streptomyces coelicolor caused secretion of a dark-brown pigment into the broth. High-performance liquid chromatography (HPLC) analysis of the broth revealed that the recombinant strain produced 1,8-DHN, indicating that the operon encoded a novel enzymatic system for the synthesis of 1,8-DHN. Simultaneous incubation of the recombinant SoceCHS1, BdsA, and BdsB with malonyl-coenzyme A (malonyl-CoA) and NADPH resulted in the synthesis of 1,8-DHN. SoceCHS1, a type III polyketide synthase (PKS), catalyzed the synthesis of 1,3,6,8-tetrahydroxynaphthalene (T4HN) in vitro T4HN was in turn converted to 1,8-DHN by successive steps of reduction and dehydration, which were catalyzed by BdsA and BdsB. BdsA, which is a member of the aldo-keto reductase (AKR) superfamily, catalyzed the reduction of T4HN and 1,3,8-tetrahydroxynaphthalene (T3HN) to scytalone and vermelone, respectively. The stereoselectivity of T4HN reduction by BdsA occurred on the si-face to give (R)-scytalone with more than 99% optical purity. BdsB, a SnoaL2-like protein, catalyzed the dehydration of scytalone and vermelone to T3HN and 1,8-DHN, respectively. The fungal pathway for the synthesis of 1,8-DHN is composed of a type I PKS, naphthol reductases of the short-chain dehydrogenase/reductase (SDR) superfamily, and scytalone dehydratase (SD). These findings demonstrated 1,8-DHN synthesis by novel enzymes of bacterial origin.IMPORTANCE Although the DHN biosynthetic pathway was thought to be specific to fungi, we discovered novel DHN synthesis enzymes of bacterial origin. The biosynthesis of bacterial DHN utilized a type III PKS for polyketide synthesis, an AKR superfamily for reduction, and a SnoaL2-like NTF2 superfamily for dehydration, whereas the biosynthesis of fungal DHN utilized a type I PKS, SDR superfamily enzyme, and SD-like NTF2 superfamily. Surprisingly, the enzyme systems comprising the pathway were significantly different from each other, suggesting independent, parallel evolution leading to the same biosynthesis. DHN melanin plays roles in host invasion and adaptation to stress in pathogenic fungi and is therefore important to study. However, it is unclear whether DHN biosynthesis occurs in bacteria. Importantly, we did find that bacterial DHN biosynthetic enzymes were conserved among pathogenic bacteria.
Collapse
|
44
|
Castro JF, Nouioui I, Sangal V, Trujillo ME, Montero-Calasanz MDC, Rahmani T, Bull AT, Asenjo JA, Andrews BA, Goodfellow M. Geodermatophilus chilensis sp. nov., from soil of the Yungay core-region of the Atacama Desert, Chile. Syst Appl Microbiol 2018; 41:427-436. [PMID: 29789182 DOI: 10.1016/j.syapm.2018.03.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 03/14/2018] [Accepted: 03/22/2018] [Indexed: 01/20/2023]
Abstract
A polyphasic study was undertaken to establish the taxonomic status of three representative Geodermatophilus strains isolated from an extreme hyper-arid Atacama Desert soil. The strains, isolates B12T, B20 and B25, were found to have chemotaxonomic and morphological properties characteristic of the genus Geodermatophilus. The isolates shared a broad range of chemotaxonomic, cultural and physiological features, formed a well-supported branch in the Geodermatophilus 16S rRNA gene tree in which they were most closely associated with the type strain of Geodermatophilus obscurus. They were distinguished from the latter by BOX-PCR fingerprint patterns and by chemotaxonomic and other phenotypic properties. Average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between the whole genome sequences of isolate B12T and G. obscurus DSM 43160T were 89.28%, 87.27% and 37.4%, respectively, metrics consistent with its classification as a separate species. On the basis of these data, it is proposed that the isolates be assigned to the genus Geodermatophilus as Geodermatophilus chilensis sp. nov. with isolate B12T (CECT 9483T=NCIMB 15089T) as the type strain. Analysis of the whole genome sequence of G. chilensis B12T with 5341 open reading frames and a genome size of 5.5Mb highlighted genes and gene clusters that encode for properties relevant to its adaptation to extreme environmental conditions prevalent in extreme hyper-arid Atacama Desert soils.
Collapse
Affiliation(s)
- Jean Franco Castro
- School of Natural and Environmental Sciences, Ridley Building, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom; Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, University of Chile, Beauchef 851, Santiago, Chile
| | - Imen Nouioui
- School of Natural and Environmental Sciences, Ridley Building, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Vartul Sangal
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, United Kingdom
| | - Martha E Trujillo
- Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | | | - Tara Rahmani
- School of Natural and Environmental Sciences, Ridley Building, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Alan T Bull
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, Kent, United Kingdom
| | - Juan A Asenjo
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, University of Chile, Beauchef 851, Santiago, Chile
| | - Barbara A Andrews
- Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, University of Chile, Beauchef 851, Santiago, Chile
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Ridley Building, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom.
| |
Collapse
|
45
|
Khalid A, Takagi H, Panthee S, Muroi M, Chappell J, Osada H, Takahashi S. Development of a Terpenoid-Production Platform in Streptomyces reveromyceticus SN-593. ACS Synth Biol 2017; 6:2339-2349. [PMID: 29019653 DOI: 10.1021/acssynbio.7b00249] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Terpenoids represent the largest class of natural products, some of which are resources for pharmaceuticals, fragrances, and fuels. Generally, mass production of valuable terpenoid compounds is hampered by their low production levels in organisms and difficulty of chemical synthesis. Therefore, the development of microbial biosynthetic platforms represents an alternative approach. Although microbial terpenoid-production platforms have been established in Escherichia coli and yeast, an optimal platform has not been developed for Streptomyces species, despite the large capacity to produce secondary metabolites, such as polyketide compounds. To explore this potential, we constructed a terpenoid-biosynthetic platform in Streptomyces reveromyceticus SN-593. This strain is unique in that it harbors the mevalonate gene cluster enabling the production of furaquinocin, which can be controlled by the pathway specific regulator Fur22. We simultaneously expressed the mevalonate gene cluster and subsequent terpenoid-biosynthetic genes under the control of Fur22. To achieve improved fur22 gene expression, we screened promoters from S. reveromyceticus SN-593. Our results showed that the promoter associated with rvr2030 gene enabled production of 212 ± 20 mg/L botryococcene to levels comparable to those previously reported for other microbial hosts. Given that the rvr2030 gene encodes for an enzyme involved in the primary metabolism, these results suggest that optimized expression of terpenoid-biosynthetic genes with primary and secondary metabolism might be as important for high yields of terpenoid compounds as is the absolute expression level of a target gene(s).
Collapse
Affiliation(s)
- Ammara Khalid
- Chemical
Biology Research Group, RIKEN Centre for Sustainable Resource Science, Hirosawa, 2-1, Wako, Saitama 351-0198, Japan
- Graduate
School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Hiroshi Takagi
- Natural
Product Biosynthesis Research Unit, RIKEN Centre for Sustainable Resource Science, Hirosawa 2-1, Wako, Saitama 351-0198, Japan
| | - Suresh Panthee
- Natural
Product Biosynthesis Research Unit, RIKEN Centre for Sustainable Resource Science, Hirosawa 2-1, Wako, Saitama 351-0198, Japan
| | - Makoto Muroi
- Chemical
Biology Research Group, RIKEN Centre for Sustainable Resource Science, Hirosawa, 2-1, Wako, Saitama 351-0198, Japan
| | - Joe Chappell
- Pharmaceutical
Sciences, University of Kentucky, 789 S Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Hiroyuki Osada
- Chemical
Biology Research Group, RIKEN Centre for Sustainable Resource Science, Hirosawa, 2-1, Wako, Saitama 351-0198, Japan
- Graduate
School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Shunji Takahashi
- Natural
Product Biosynthesis Research Unit, RIKEN Centre for Sustainable Resource Science, Hirosawa 2-1, Wako, Saitama 351-0198, Japan
| |
Collapse
|
46
|
Park SY, Yang D, Ha SH, Lee SY. Metabolic Engineering of Microorganisms for the Production of Natural Compounds. ACTA ACUST UNITED AC 2017. [DOI: 10.1002/adbi.201700190] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Seon Young Park
- Metabolic and Biomolecular Engineering National Research Laboratory; Department of Chemical and Biomolecular Engineering (BK21 Plus Program); Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon 34141 Republic of Korea
| | - Dongsoo Yang
- Metabolic and Biomolecular Engineering National Research Laboratory; Department of Chemical and Biomolecular Engineering (BK21 Plus Program); Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon 34141 Republic of Korea
| | - Shin Hee Ha
- Metabolic and Biomolecular Engineering National Research Laboratory; Department of Chemical and Biomolecular Engineering (BK21 Plus Program); Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon 34141 Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory; Department of Chemical and Biomolecular Engineering (BK21 Plus Program); Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon 34141 Republic of Korea
- BioProcess Engineering Research Center; KAIST; Daejeon 34141 Republic of Korea
- BioInformatics Research Center; KAIST; Daejeon 34141 Republic of Korea
| |
Collapse
|
47
|
Čihák M, Kameník Z, Šmídová K, Bergman N, Benada O, Kofroňová O, Petříčková K, Bobek J. Secondary Metabolites Produced during the Germination of Streptomyces coelicolor. Front Microbiol 2017; 8:2495. [PMID: 29326665 PMCID: PMC5733532 DOI: 10.3389/fmicb.2017.02495] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 11/30/2017] [Indexed: 11/16/2022] Open
Abstract
Spore awakening is a series of actions that starts with purely physical processes and continues via the launching of gene expression and metabolic activities, eventually achieving a vegetative phase of growth. In spore-forming microorganisms, the germination process is controlled by intra- and inter-species communication. However, in the Streptomyces clade, which is capable of developing a plethora of valuable compounds, the chemical signals produced during germination have not been systematically studied before. Our previously published data revealed that several secondary metabolite biosynthetic genes are expressed during germination. Therefore, we focus here on the secondary metabolite production during this developmental stage. Using high-performance liquid chromatography-mass spectrometry, we found that the sesquiterpenoid antibiotic albaflavenone, the polyketide germicidin A, and chalcone are produced during germination of the model streptomycete, S. coelicolor. Interestingly, the last two compounds revealed an inhibitory effect on the germination process. The secondary metabolites originating from the early stage of microbial growth may coordinate the development of the producer (quorum sensing) and/or play a role in competitive microflora repression (quorum quenching) in their nature environments.
Collapse
Affiliation(s)
- Matouš Čihák
- First Faculty of Medicine, Institute of Immunology and Microbiology, Charles University, Prague, Czechia
| | - Zdeněk Kameník
- Institute of Microbiology, The Czech Academy of Sciences, Prague, Czechia
| | - Klára Šmídová
- First Faculty of Medicine, Institute of Immunology and Microbiology, Charles University, Prague, Czechia.,Institute of Microbiology, The Czech Academy of Sciences, Prague, Czechia
| | - Natalie Bergman
- Chemistry Department, Faculty of Science, J. E. Purkinje University, Ústí nad Labem, Czechia
| | - Oldřich Benada
- Institute of Microbiology, The Czech Academy of Sciences, Prague, Czechia.,Chemistry Department, Faculty of Science, J. E. Purkinje University, Ústí nad Labem, Czechia
| | - Olga Kofroňová
- Institute of Microbiology, The Czech Academy of Sciences, Prague, Czechia
| | - Kateřina Petříčková
- First Faculty of Medicine, Institute of Immunology and Microbiology, Charles University, Prague, Czechia
| | - Jan Bobek
- First Faculty of Medicine, Institute of Immunology and Microbiology, Charles University, Prague, Czechia.,Institute of Microbiology, The Czech Academy of Sciences, Prague, Czechia.,Chemistry Department, Faculty of Science, J. E. Purkinje University, Ústí nad Labem, Czechia
| |
Collapse
|
48
|
Miles ZD, Diethelm S, Pepper HP, Huang DM, George JH, Moore BS. A unifying paradigm for naphthoquinone-based meroterpenoid (bio)synthesis. Nat Chem 2017; 9:1235-1242. [PMID: 29168495 PMCID: PMC5960991 DOI: 10.1038/nchem.2829] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 06/15/2017] [Indexed: 12/14/2022]
Abstract
Bacterial meroterpenoids constitute an important class of natural products with diverse biological properties and therapeutic potential. The biosynthetic logic for their production is unknown and defies explanation via classical biochemical paradigms. A large subgroup of naphthoquinone-based meroterpenoids exhibits a substitution pattern of the polyketide-derived aromatic core that seemingly contradicts the established reactivity pattern of polyketide phenol nucleophiles and terpene diphosphate electrophiles. We report the discovery of a hitherto unprecedented enzyme-promoted α-hydroxyketone rearrangement catalysed by vanadium-dependent haloperoxidases to account for these discrepancies in the merochlorin and napyradiomycin class of meroterpenoid antibiotics, and we demonstrate that the α-hydroxyketone rearrangement is potentially a conserved biosynthetic reaction in this molecular class. The biosynthetic α-hydroxyketone rearrangement was applied in a concise total synthesis of naphthomevalin, a prominent member of the napyradiomycin meroterpenes, and sheds further light on the mechanism of this unifying enzymatic transformation.
Collapse
Affiliation(s)
- Zachary D. Miles
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, USA
| | - Stefan Diethelm
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, USA
| | - Henry P. Pepper
- Department of Chemistry, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - David M. Huang
- Department of Chemistry, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Jonathan H. George
- Department of Chemistry, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Bradley S. Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, USA
| |
Collapse
|
49
|
Su X, Sun X, Cheng X, Wang Y, Abdullah M, Li M, Li D, Gao J, Cai Y, Lin Y. Comparative genomic analysis of the PKS genes in five species and expression analysis in upland cotton. PeerJ 2017; 5:e3974. [PMID: 29104824 PMCID: PMC5667535 DOI: 10.7717/peerj.3974] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 10/10/2017] [Indexed: 01/08/2023] Open
Abstract
Plant type III polyketide synthase (PKS) can catalyse the formation of a series of secondary metabolites with different structures and different biological functions; the enzyme plays an important role in plant growth, development and resistance to stress. At present, the PKS gene has been identified and studied in a variety of plants. Here, we identified 11 PKS genes from upland cotton (Gossypium hirsutum) and compared them with 41 PKS genes in Populus tremula, Vitis vinifera, Malus domestica and Arabidopsis thaliana. According to the phylogenetic tree, a total of 52 PKS genes can be divided into four subfamilies (I-IV). The analysis of gene structures and conserved motifs revealed that most of the PKS genes were composed of two exons and one intron and there are two characteristic conserved domains (Chal_sti_synt_N and Chal_sti_synt_C) of the PKS gene family. In our study of the five species, gene duplication was found in addition to Arabidopsis thaliana and we determined that purifying selection has been of great significance in maintaining the function of PKS gene family. From qRT-PCR analysis and a combination of the role of the accumulation of proanthocyanidins (PAs) in brown cotton fibers, we concluded that five PKS genes are candidate genes involved in brown cotton fiber pigment synthesis. These results are important for the further study of brown cotton PKS genes. It not only reveals the relationship between PKS gene family and pigment in brown cotton, but also creates conditions for improving the quality of brown cotton fiber.
Collapse
Affiliation(s)
- Xueqiang Su
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Xu Sun
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Xi Cheng
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Yanan Wang
- School of Life Science, Anhui Agricultural University, Hefei, China
| | | | - Manli Li
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Dahui Li
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Junshan Gao
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Yongping Cai
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Yi Lin
- School of Life Science, Anhui Agricultural University, Hefei, China
| |
Collapse
|
50
|
Meng L, Xiong Z, Chu J, Wang Y. Enhanced production of avermectin by deletion of type III polyketide synthases biosynthetic cluster rpp in Streptomyces avermitilis. Lett Appl Microbiol 2017; 63:384-390. [PMID: 27538855 DOI: 10.1111/lam.12635] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 08/02/2016] [Accepted: 08/16/2016] [Indexed: 01/19/2023]
Abstract
The rpp biosynthetic gene cluster (sav7130-7131) in Streptomyces avermitilis contains a type III polyketide synthases (PKSs) and a cytochrome P450 and was reportedly involved in producing a diffusible brown pigment. Since the same precursor malonyl-CoA was used as substrate for the type I PKSs and type III PKSs, there might be a competition for precursor between rpp gene cluster and avermectin biosynthetic cluster. In this work, rpp biosynthetic gene cluster deletion mutants were constructed to improve avermectin production. In an industrial strain AV-LP, rpp deletion improved avermectin production from 1024 to 1262 mg l-1 without any effect on the cell growth. In the same way, the production of an industrial overproducer increased from 3582 to 4450 mg l-1 . Transcriptional analysis suggested that the deletion of rpp gene cluster stimulated transcription of aveR, leading to increased transcription of biosynthetic gene aveA1 and a consequent increase in avermectin production. SIGNIFICANCE AND IMPACT OF THE STUDY Because of the wide use of avermectins, many efforts have been made to improve the productivity via conventional genetic engineering technique. However, due to the lack of the molecular and genetic basis underlying such a yield enhancement after iterative rounds of mutagenesis and selection, it is often difficult to improve the titre in overproducers. Here, we report knocking out rpp biosynthetic gene cluster improved the production of an industrial overproducer by 24%. This work enriched the strategy to improve the production of antibiotics in industrial strains and may help further understanding of the interaction between type III polyketide synthases and other types.
Collapse
Affiliation(s)
- L Meng
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.,Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Z Xiong
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - J Chu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Y Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China. .,Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
| |
Collapse
|