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Fungal Depsides-Naturally Inspiring Molecules: Biosynthesis, Structural Characterization, and Biological Activities. Metabolites 2021; 11:metabo11100683. [PMID: 34677398 PMCID: PMC8540757 DOI: 10.3390/metabo11100683] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/05/2021] [Accepted: 10/02/2021] [Indexed: 11/23/2022] Open
Abstract
Fungi represent a huge reservoir of structurally diverse bio-metabolites. Although there has been a marked increase in the number of isolated fungal metabolites over the past years, many hidden metabolites still need to be discovered. Depsides are a group of polyketides consisting of two or more ester-linked hydroxybenzoic acid moieties. They possess valuable bioactive properties, such as anticancer, antidiabetic, antibacterial, antiviral, anti-inflammatory, antifungal, antifouling, and antioxidant qualities, as well as various human enzyme-inhibitory activities. This review provides an overview of the reported data on fungal depsides, including their sources, biosynthesis, physical and spectral data, and bioactivities in the period from 1975 to 2020. Overall, 110 metabolites and more than 122 references are confirmed. This is the first review of these multi-faceted metabolites from fungi.
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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.
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Transcriptional heterologous expression of two type III PKS from the lichen Cladonia uncialis. Mycol Prog 2019. [DOI: 10.1007/s11557-019-01539-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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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.
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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.
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A comprehensive catalogue of polyketide synthase gene clusters in lichenizing fungi. J Ind Microbiol Biotechnol 2018; 45:1067-1081. [PMID: 30206732 DOI: 10.1007/s10295-018-2080-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 08/24/2018] [Indexed: 10/28/2022]
Abstract
Lichens are fungi that form symbiotic partnerships with algae. Although lichens produce diverse polyketides, difficulties in establishing and maintaining lichen cultures have prohibited detailed studies of their biosynthetic pathways. Creative, albeit non-definitive, methods have been developed to assign function to biosynthetic gene clusters in lieu of techniques such as gene knockout and heterologous expressions that are commonly applied to easily cultivatable organisms. We review a total of 81 completely sequenced polyketide synthase (PKS) genes from lichenizing fungi, comprising to our best efforts all complete and reported PKS genes in lichenizing fungi to date. This review provides an overview of the approaches used to locate and sequence PKS genes in lichen genomes, current approaches to assign function to lichen PKS gene clusters, and what polyketides are proposed to be biosynthesized by these PKS. We conclude with remarks on prospects for genomics-based natural products discovery in lichens. We hope that this review will serve as a guide to ongoing research efforts on polyketide biosynthesis in lichenizing fungi.
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Bertrand RL, Abdel-Hameed M, Sorensen JL. Lichen Biosynthetic Gene Clusters. Part I. Genome Sequencing Reveals a Rich Biosynthetic Potential. JOURNAL OF NATURAL PRODUCTS 2018; 81:723-731. [PMID: 29485276 DOI: 10.1021/acs.jnatprod.7b00769] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Lichens are symbionts of fungi and algae that produce diverse secondary metabolites with useful properties. Little is known of lichen natural product biosynthesis because of the challenges of working with lichenizing fungi. We describe the first attempt to comprehensively profile the genetic secondary metabolome of a lichenizing fungus. An Illumina platform combined with the Antibiotics and Secondary Metabolites Analysis Shell (FungiSMASH, version 4.0) was used to sequence and annotate assembled contigs of the fungal partner of Cladonia uncialis. Up to 48 putative gene clusters are described comprising type I and type III polyketide synthases (PKS), nonribosomal peptide synthetases (NRPS), hybrid PKS-NRPS, and terpene synthases. The number of gene clusters revealed by this work dwarfs the number of known secondary metabolites from C. uncialis, suggesting that lichenizing fungi have an unexplored biosynthetic potential.
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Affiliation(s)
- Robert L Bertrand
- Department of Chemistry , University of Manitoba , Winnipeg , Manitoba R3T 2N2 , Canada
| | - Mona Abdel-Hameed
- Department of Chemistry , University of Manitoba , Winnipeg , Manitoba R3T 2N2 , Canada
| | - John L Sorensen
- Department of Chemistry , University of Manitoba , Winnipeg , Manitoba R3T 2N2 , Canada
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Ramakrishnan D, Tiwari MK, Manoharan G, Sairam T, Thangamani R, Lee JK, Marimuthu J. Molecular characterization of two alkylresorcylic acid synthases from Sordariomycetes fungi. Enzyme Microb Technol 2018; 115:16-22. [PMID: 29859598 DOI: 10.1016/j.enzmictec.2018.04.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 04/09/2018] [Accepted: 04/10/2018] [Indexed: 10/17/2022]
Abstract
Two putative type III polyketide synthase genes (PKS) were identified from Sordariomycetes fungi. These two type III PKS genes from Sordaria macrospora (SmPKS) and Chaetomium thermophilum (CtPKS), shared 59.8% sequence identity. Both, full-length and truncated versions of type III PKSs were successfully cloned and overexpressed in a bacterial host, Escherichia Coli BL21 (DE3) using a N-terminus hexa-histidine tag. The full-length and the truncated construct of PKSs showed similar activity profiles, suggesting that additional amino acid residues at the C-terminal of both SmPKS and CtPKS may not be involved in catalytic functions. We demonstrate that these two recombinant polyketide synthases could efficiently synthesize tri- and tetraketide pyrones, resorcinols and resorcylic acids using various acyl-CoAs (C4-C20) as starter units. The truncated S. macrospora polyketide synthases (TrSmPKS) showed a maximum of 7.0 × 104 s-1 M-1 catalytic efficiency towards stearoyl-CoA.Whereas, truncated C. thermophilum polyketide synthases (TrCtPKS) preferred the long-chain acyl-CoA starter arachidoyl-CoA, to produce pentaketide and hexaketide resorcinols with a high catalytic efficiency of 6.2 × 104 s-1 M-1. Homology model and substrate docking analyses suggest a shorter distance between sulfur of catalytic Cys152 and thioester carbonyl group of arachidoyl-CoA as well as stronger imidazolium-thiolate ion pair distance in TrCtPKS between catalytic Cys152-His309 compared to TrSmPKS- arachidoyl CoA complex. Enhanced binding interactions of CtPKS residues forming intermolecular contacts at the active site could be attributed to its high specificity towards arachidoyl-CoA. This study reports the functional characterization of two fungal type III polyketide synthases, SmPKS and CtPKS with high catalytic efficiency from S. macrospora and C. thermophilum respectively. Furthermore, the results suggested that the both SmPKS and CtPKS could be attractive targets for protein engineering to discern the unique substrate specificity and catalytic efficiency.
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Affiliation(s)
- Dhivya Ramakrishnan
- PSG Centre for Molecular Medicine and Therapeutics, PSG Institute of Medical Sciences and Research, Coimbatore 641001, India
| | - Manish K Tiwari
- Department of Chemistry, University of Copenhagen,Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Gomathi Manoharan
- PSG Centre for Molecular Medicine and Therapeutics, PSG Institute of Medical Sciences and Research, Coimbatore 641001, India
| | - Thiagarajan Sairam
- PSG Centre for Molecular Medicine and Therapeutics, PSG Institute of Medical Sciences and Research, Coimbatore 641001, India
| | - Rajesh Thangamani
- Biotechnology Division, CSIR-National Environmental Engineering Research Institute, CMC, Chennai 600113, India
| | - 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 641001, India.
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Fortuna L, Baracchini E, Adami G, Tretiach M. Melanization Affects the Content of Selected Elements in Parmelioid Lichens. J Chem Ecol 2017; 43:1086-1096. [PMID: 29098563 DOI: 10.1007/s10886-017-0899-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 10/13/2017] [Accepted: 10/26/2017] [Indexed: 11/28/2022]
Abstract
Lichens belonging to Parmeliaceae are highly diversified, but most of them share an extremely conserved morpho-chemical trait: the lower cortex is heavily melanized. The adaptive value of this character is still uncertain. Melanins are ubiquitous compounds found in most organisms since they fulfil several biological functions including defense against UV radiation, oxidizing agents, microbial stress, and metal complexation. This work aims to establish whether melanization can affect the elemental content of lichen thalli. The relative abundance of macro- (Ca, K and S) and micro- (Fe, Mn and Zn) nutrients in melanized and non-melanized pseudotissues of nine species was first evaluated by a non-destructive micro-X-ray fluorescence elemental analysis on either the upper and lower cortex, and on the internal medulla, which was artificially exposed to the mechanical removal of the lower cortex. Afterwards, the total concentration of the same elements was measured in composite samples by inductively coupled plasma atomic emission spectroscopy after acidic digestion. In order to verify whether Fe and Zn are chemically bound to the melanized pseudotissues, a sequential elution experiment was performed on two species: the two-side heavily melanized Melanelixia glabratula and the one-side lightly melanized Punctelia subrudecta. The content of Fe and Zn was higher in the melanized species than in the non-melanized ones. Species deprived of their melanized lower cortex showed a sharp decrease in Fe but not in Zn, suggesting that the melanized lower cortex is involved in Fe complexation, whereas Zn is homogeneously distributed throughout the thallus.
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Affiliation(s)
- Lorenzo Fortuna
- Department of Life Sciences, University of Trieste, Via L. Giorgieri 10, I-34127, Trieste, Italy
| | - Elena Baracchini
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, I-34127, Trieste, Italy
| | - Gianpiero Adami
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, I-34127, Trieste, Italy
| | - Mauro Tretiach
- Department of Life Sciences, University of Trieste, Via L. Giorgieri 10, I-34127, Trieste, Italy.
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Mishra VK, Passari AK, Leo VV, Singh BP. Molecular Diversity and Detection of Endophytic Fungi Based on Their Antimicrobial Biosynthetic Genes. Fungal Biol 2017. [DOI: 10.1007/978-3-319-34106-4_1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Exploiting the Biosynthetic Potential of Type III Polyketide Synthases. Molecules 2016; 21:molecules21060806. [PMID: 27338328 PMCID: PMC6274091 DOI: 10.3390/molecules21060806] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 06/15/2016] [Accepted: 06/17/2016] [Indexed: 11/17/2022] Open
Abstract
Polyketides are structurally and functionally diverse secondary metabolites that are biosynthesized by polyketide synthases (PKSs) using acyl-CoA precursors. Recent studies in the engineering and structural characterization of PKSs have facilitated the use of target enzymes as biocatalysts to produce novel functionally optimized polyketides. These compounds may serve as potential drug leads. This review summarizes the insights gained from research on type III PKSs, from the discovery of chalcone synthase in plants to novel PKSs in bacteria and fungi. To date, at least 15 families of type III PKSs have been characterized, highlighting the utility of PKSs in the development of natural product libraries for therapeutic development.
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Meessen J, Sánchez FJ, Sadowsky A, de la Torre R, Ott S, de Vera JP. Extremotolerance and resistance of lichens: comparative studies on five species used in astrobiological research II. Secondary lichen compounds. ORIGINS LIFE EVOL B 2013; 43:501-26. [PMID: 24362711 DOI: 10.1007/s11084-013-9348-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 10/25/2013] [Indexed: 10/25/2022]
Abstract
Lichens, which are symbioses of a fungus and one or two photoautotrophs, frequently tolerate extreme environmental conditions. This makes them valuable model systems in astrobiological research to fathom the limits and limitations of eukaryotic symbioses. Various studies demonstrated the high resistance of selected extremotolerant lichens towards extreme, non-terrestrial abiotic factors including space exposure, hypervelocity impact simulations as well as space and Martian parameter simulations. This study focusses on the diverse set of secondary lichen compounds (SLCs) that act as photo- and UVR-protective substances. Five lichen species used in present-day astrobiological research were compared: Buellia frigida, Circinaria gyrosa, Rhizocarpon geographicum, Xanthoria elegans, and Pleopsidium chlorophanum. Detailed investigation of secondary substances including photosynthetic pigments was performed for whole lichen thalli but also for axenically cultivated mycobionts and photobionts by methods of UV/VIS-spectrophotometry and two types of high performance liquid chromatography (HPLC). Additionally, a set of chemical tests is presented to confirm the formation of melanic compounds in lichen and mycobiont samples. All investigated lichens reveal various sets of SLCs, except C. gyrosa where only melanin was putatively identified. Such studies will help to assess the contribution of SLCs on lichen extremotolerance, to understand the adaptation of lichens to prevalent abiotic stressors of the respective habitat, and to form a basis for interpreting recent and future astrobiological experiments. As most of the identified SLCs demonstrated a high capacity in absorbing UVR, they may also explain the high resistance of lichens towards non-terrestrial UVR.
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Affiliation(s)
- J Meessen
- Institut für Botanik, Heinrich-Heine-Universität (HHU), Universitätsstr.1, 40225, Düsseldorf, Germany,
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