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Shende VV, Bauman KD, Moore BS. The shikimate pathway: gateway to metabolic diversity. Nat Prod Rep 2024; 41:604-648. [PMID: 38170905 PMCID: PMC11043010 DOI: 10.1039/d3np00037k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Covering: 1997 to 2023The shikimate pathway is the metabolic process responsible for the biosynthesis of the aromatic amino acids phenylalanine, tyrosine, and tryptophan. Seven metabolic steps convert phosphoenolpyruvate (PEP) and erythrose 4-phosphate (E4P) into shikimate and ultimately chorismate, which serves as the branch point for dedicated aromatic amino acid biosynthesis. Bacteria, fungi, algae, and plants (yet not animals) biosynthesize chorismate and exploit its intermediates in their specialized metabolism. This review highlights the metabolic diversity derived from intermediates of the shikimate pathway along the seven steps from PEP and E4P to chorismate, as well as additional sections on compounds derived from prephenate, anthranilate and the synonymous aminoshikimate pathway. We discuss the genomic basis and biochemical support leading to shikimate-derived antibiotics, lipids, pigments, cofactors, and other metabolites across the tree of life.
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Affiliation(s)
- Vikram V Shende
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Katherine D Bauman
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Bradley S Moore
- Scripps Institution of Oceanography, 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
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2
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Ramage KS, Lock A, White JM, Ekins MG, Kiefel MJ, Avery VM, Davis RA. Semisynthesis and Cytotoxic Evaluation of an Ether Analogue Library Based on a Polyhalogenated Diphenyl Ether Scaffold Isolated from a Lamellodysidea Sponge. Mar Drugs 2024; 22:33. [PMID: 38248658 PMCID: PMC10817568 DOI: 10.3390/md22010033] [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: 12/04/2023] [Revised: 12/20/2023] [Accepted: 12/23/2023] [Indexed: 01/23/2024] Open
Abstract
The known oxygenated polyhalogenated diphenyl ether, 2-(2',4'-dibromophenoxy)-3,5-dibromophenol (1), with previously reported activity in multiple cytotoxicity assays was isolated from the sponge Lamellodysidea sp. and proved to be an amenable scaffold for semisynthetic library generation. The phenol group of 1 was targeted to generate 12 ether analogues in low-to-excellent yields, and the new library was fully characterized by NMR, UV, and MS analyses. The chemical structures for 2, 8, and 9 were additionally determined via single-crystal X-ray diffraction analysis. All natural and semisynthetic compounds were evaluated for their ability to inhibit the growth of DU145, LNCaP, MCF-7, and MDA-MB-231 cancer cell lines. Compound 3 was shown to have near-equivalent activity compared to scaffold 1 in two in vitro assays, and the activity of the compounds with an additional benzyl ring appeared to be reliant on the presence and position of additional halogens.
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Affiliation(s)
- Kelsey S. Ramage
- Griffith Institute for Drug Discovery, School of Environment and Science, Griffith University, Brisbane, QLD 4111, Australia; (K.S.R.); (M.G.E.)
| | - Aaron Lock
- Discovery Biology, School of Environment and Science, Griffith University, Brisbane, QLD 4111, Australia; (A.L.); (V.M.A.)
| | - Jonathan M. White
- School of Chemistry and Bio21 Institute, The University of Melbourne, Parkville, VIC 3010, Australia;
| | - Merrick G. Ekins
- Griffith Institute for Drug Discovery, School of Environment and Science, Griffith University, Brisbane, QLD 4111, Australia; (K.S.R.); (M.G.E.)
- Queensland Museum, South Brisbane, QLD 4101, Australia
| | - Milton J. Kiefel
- Institute for Glycomics, School of Environment and Science, Griffith University, Gold Coast, QLD 4222, Australia;
| | - Vicky M. Avery
- Discovery Biology, School of Environment and Science, Griffith University, Brisbane, QLD 4111, Australia; (A.L.); (V.M.A.)
| | - Rohan A. Davis
- Griffith Institute for Drug Discovery, School of Environment and Science, Griffith University, Brisbane, QLD 4111, Australia; (K.S.R.); (M.G.E.)
- NatureBank, Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD 4111, Australia
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3
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Entfellner E, Baumann KBL, Edwards C, Kurmayer R. High Structural Diversity of Aeruginosins in Bloom-Forming Cyanobacteria of the Genus Planktothrix as a Consequence of Multiple Recombination Events. Mar Drugs 2023; 21:638. [PMID: 38132959 PMCID: PMC10744761 DOI: 10.3390/md21120638] [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: 10/29/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023] Open
Abstract
Many compounds produced by cyanobacteria act as serine protease inhibitors, such as the tetrapeptides aeruginosins (Aer), which are found widely distributed. The structural diversity of Aer is intriguingly high. However, the genetic basis of this remains elusive. In this study, we explored the genetic basis of Aer synthesis among the filamentous cyanobacteria Planktothrix spp. In total, 124 strains, isolated from diverse freshwater waterbodies, have been compared regarding variability within Aer biosynthesis genes and the consequences for structural diversity. The high structural variability could be explained by various recombination processes affecting Aer synthesis, above all, the acquisition of accessory enzymes involved in post synthesis modification of the Aer peptide (e.g., halogenases, glycosyltransferases, sulfotransferases) as well as a large-range recombination of Aer biosynthesis genes, probably transferred from the bloom-forming cyanobacterium Microcystis. The Aer structural composition differed between evolutionary Planktothrix lineages, adapted to either shallow or deep waterbodies of the temperate climatic zone. Thus, for the first time among bloom-forming cyanobacteria, chemical diversification of a peptide family related to eco-evolutionary diversification has been described. It is concluded that various Aer peptides resulting from the recombination event act in chemical defense, possibly as a replacement for microcystins.
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Affiliation(s)
- Elisabeth Entfellner
- Research Department for Limnology, Universität Innsbruck, Mondseestrasse 9, 5310 Mondsee, Austria; (E.E.); (K.B.L.B.)
| | - Kathrin B. L. Baumann
- Research Department for Limnology, Universität Innsbruck, Mondseestrasse 9, 5310 Mondsee, Austria; (E.E.); (K.B.L.B.)
| | - Christine Edwards
- CyanoSol Research Group, Pharmacy & Life Sciences, Robert Gordon University, Aberdeen AB10 7GJ, UK;
| | - Rainer Kurmayer
- Research Department for Limnology, Universität Innsbruck, Mondseestrasse 9, 5310 Mondsee, Austria; (E.E.); (K.B.L.B.)
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4
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D'Agostino PM. Highlights of biosynthetic enzymes and natural products from symbiotic cyanobacteria. Nat Prod Rep 2023; 40:1701-1717. [PMID: 37233731 DOI: 10.1039/d3np00011g] [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: 05/27/2023]
Abstract
Covering: up to 2023Cyanobacteria have long been known for their intriguing repertoire of natural product scaffolds, which are often distinct from other phyla. Cyanobacteria are ecologically significant organisms that form a myriad of different symbioses including with sponges and ascidians in the marine environment or with plants and fungi, in the form of lichens, in terrestrial environments. Whilst there have been several high-profile discoveries of symbiotic cyanobacterial natural products, genomic data is scarce and discovery efforts have remained limited. However, the rise of (meta-)genomic sequencing has improved these efforts, emphasized by a steep increase in publications in recent years. This highlight focuses on selected examples of symbiotic cyanobacterial-derived natural products and their biosyntheses to link chemistry with corresponding biosynthetic logic. Further highlighted are remaining gaps in knowledge for the formation of characteristic structural motifs. It is anticipated that the continued rise of (meta-)genomic next-generation sequencing of symbiontic cyanobacterial systems will lead to many exciting discoveries in the future.
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Affiliation(s)
- Paul M D'Agostino
- Technical University of Dresden, Chair of Technical Biochemistry, Bergstraβe 66, 01069 Dresden, Germany.
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5
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Manochkumar J, Cherukuri AK, Kumar RS, Almansour AI, Ramamoorthy S, Efferth T. A critical review of machine-learning for "multi-omics" marine metabolite datasets. Comput Biol Med 2023; 165:107425. [PMID: 37696182 DOI: 10.1016/j.compbiomed.2023.107425] [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: 07/12/2023] [Accepted: 08/28/2023] [Indexed: 09/13/2023]
Abstract
During the last decade, genomic, transcriptomic, proteomic, metabolomic, and other omics datasets have been generated for a wide range of marine organisms, and even more are still on the way. Marine organisms possess unique and diverse biosynthetic pathways contributing to the synthesis of novel secondary metabolites with significant bioactivities. As marine organisms have a greater tendency to adapt to stressed environmental conditions, the chance to identify novel bioactive metabolites with potential biotechnological application is very high. This review presents a comprehensive overview of the available "-omics" and "multi-omics" approaches employed for characterizing marine metabolites along with novel data integration tools. The need for the development of machine-learning algorithms for "multi-omics" approaches is briefly discussed. In addition, the challenges involved in the analysis of "multi-omics" data and recommendations for conducting "multi-omics" study were discussed.
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Affiliation(s)
- Janani Manochkumar
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, 632014, India
| | - Aswani Kumar Cherukuri
- School of Information Technology and Engineering, Vellore Institute of Technology, Vellore, 632014, India
| | - Raju Suresh Kumar
- Department of Chemistry, College of Science, King Saud University, P. O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Abdulrahman I Almansour
- Department of Chemistry, College of Science, King Saud University, P. O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Siva Ramamoorthy
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, 632014, India.
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Mainz, Germany.
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6
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Liu J, Zhang M, Huang Z, Fang J, Wang Z, Zhou C, Qiu X. Diversity, Biosynthesis and Bioactivity of Aeruginosins, a Family of Cyanobacteria-Derived Nonribosomal Linear Tetrapeptides. Mar Drugs 2023; 21:md21040217. [PMID: 37103356 PMCID: PMC10143770 DOI: 10.3390/md21040217] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/14/2023] [Accepted: 03/24/2023] [Indexed: 03/31/2023] Open
Abstract
Aeruginosins, a family of nonribosomal linear tetrapeptides discovered from cyanobacteria and sponges, exhibit in vitro inhibitory activity on various types of serine proteases. This family is characterized by the existence of the 2-carboxy-6-hydroxy-octahydroindole (Choi) moiety occupied at the central position of the tetrapeptide. Aeruginosins have attracted much attention due to their special structures and unique bioactivities. Although many studies on aeruginosins have been published, there has not yet been a comprehensive review that summarizes the diverse research ranging from biogenesis, structural characterization and biosynthesis to bioactivity. In this review, we provide an overview of the source, chemical structure as well as spectrum of bioactivities of aeruginosins. Furthermore, possible opportunities for future research and development of aeruginosins were discussed.
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Affiliation(s)
- Jiameng Liu
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China
- Institute of Marine Biotechnology, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315800, China
| | - Mengli Zhang
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China
- Institute of Marine Biotechnology, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315800, China
| | - Zhenkuai Huang
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China
- Institute of Marine Biotechnology, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315800, China
| | - Jiaqi Fang
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China
- Institute of Marine Biotechnology, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315800, China
| | - Zhongyuan Wang
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China
- Institute of Marine Biotechnology, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315800, China
| | - Chengxu Zhou
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China
- Institute of Marine Biotechnology, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315800, China
| | - Xiaoting Qiu
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China
- Institute of Marine Biotechnology, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Ningbo University, Ningbo 315800, China
- Correspondence:
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7
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Impact of Marine Chemical Ecology Research on the Discovery and Development of New Pharmaceuticals. Mar Drugs 2023; 21:md21030174. [PMID: 36976223 PMCID: PMC10055925 DOI: 10.3390/md21030174] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/04/2023] [Accepted: 03/08/2023] [Indexed: 03/12/2023] Open
Abstract
Diverse ecologically important metabolites, such as allelochemicals, infochemicals and volatile organic chemicals, are involved in marine organismal interactions. Chemically mediated interactions between intra- and interspecific organisms can have a significant impact on community organization, population structure and ecosystem functioning. Advances in analytical techniques, microscopy and genomics are providing insights on the chemistry and functional roles of the metabolites involved in such interactions. This review highlights the targeted translational value of several marine chemical ecology-driven research studies and their impact on the sustainable discovery of novel therapeutic agents. These chemical ecology-based approaches include activated defense, allelochemicals arising from organismal interactions, spatio-temporal variations of allelochemicals and phylogeny-based approaches. In addition, innovative analytical techniques used in the mapping of surface metabolites as well as in metabolite translocation within marine holobionts are summarized. Chemical information related to the maintenance of the marine symbioses and biosyntheses of specialized compounds can be harnessed for biomedical applications, particularly in microbial fermentation and compound production. Furthermore, the impact of climate change on the chemical ecology of marine organisms—especially on the production, functionality and perception of allelochemicals—and its implications on drug discovery efforts will be presented.
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8
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Schneider YKH, Liaimer A, Isaksson J, Wilhelmsen OSB, Andersen JH, Hansen KØ, Hansen EH. Four new suomilides isolated from the cyanobacterium Nostoc sp. KVJ20 and proposal of their biosynthetic origin. Front Microbiol 2023; 14:1130018. [PMID: 37152725 PMCID: PMC10157211 DOI: 10.3389/fmicb.2023.1130018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/24/2023] [Indexed: 05/09/2023] Open
Abstract
The suomilide and the banyasides are highly modified and functionalized non-ribosomal peptides produced by cyanobacteria of the order Nostocales. These compound classes share several substructures, including a complex azabicyclononane core, which was previously assumed to be derived from the amino acid tyrosine. In our study we were able to isolate and determine the structures of four suomilides, named suomilide B - E (1-4). The compounds differ from the previously isolated suomilide A by the functionalization of the glycosyl group. Compounds 1-4 were assayed for anti-proliferative, anti-biofilm and anti-bacterial activities, but no significant activity was detected. The sequenced genome of the producer organism Nostoc sp. KVJ20 enabled us to propose a biosynthetic gene cluster for suomilides. Our findings indicated that the azabicyclononane core of the suomilides is derived from prephenate and is most likely incorporated by a proline specific non-ribosomal peptide synthetase-unit.
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Affiliation(s)
- Yannik K.-H. Schneider
- Marbio, Faculty of Biosciences, Fisheries and Economics, UiT—The Arctic University of Norway, Tromsø, Norway
- *Correspondence: Yannik K.-H. Schneider,
| | - Anton Liaimer
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT—The Arctic University of Norway, Tromsø, Norway
| | - Johan Isaksson
- Department of Chemistry, Faculty of Natural Sciences, UiT—The Arctic University of Norway, Tromsø, Norway
| | - Oda S. B. Wilhelmsen
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT—The Arctic University of Norway, Tromsø, Norway
| | - Jeanette H. Andersen
- Marbio, Faculty of Biosciences, Fisheries and Economics, UiT—The Arctic University of Norway, Tromsø, Norway
| | - Kine Ø. Hansen
- Marbio, Faculty of Biosciences, Fisheries and Economics, UiT—The Arctic University of Norway, Tromsø, Norway
| | - Espen H. Hansen
- Marbio, Faculty of Biosciences, Fisheries and Economics, UiT—The Arctic University of Norway, Tromsø, Norway
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9
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The Porifera microeukaryome: Addressing the neglected associations between sponges and protists. Microbiol Res 2022; 265:127210. [PMID: 36183422 DOI: 10.1016/j.micres.2022.127210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 09/15/2022] [Accepted: 09/16/2022] [Indexed: 11/22/2022]
Abstract
While bacterial and archaeal communities of sponges are intensively studied, given their importance to the animal's physiology as well as sources of several new bioactive molecules, the potential and roles of associated protists remain poorly known. Historically, culture-dependent approaches dominated the investigations of sponge-protist interactions. With the advances in omics techniques, these associations could be visualized at other equally important scales. Of the few existing studies, there is a strong tendency to focus on interactions with photosynthesizing taxa such as dinoflagellates and diatoms, with fewer works dissecting the interactions with other less common groups. In addition, there are bottlenecks and inherent biases in using primer pairs and bioinformatics approaches in the most commonly used metabarcoding studies. Thus, this review addresses the issues underlying this association, using the term "microeukaryome" to refer exclusively to protists associated with an animal host. We aim to highlight the diversity and community composition of protists associated with sponges and place them on the same level as other microorganisms already well studied in this context. Among other shortcomings, it could be observed that the biotechnological potential of the microeukaryome is still largely unexplored, possibly being a valuable source of new pharmacological compounds, enzymes and metabolic processes.
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10
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Amelia TSM, Suaberon FAC, Vad J, Fahmi ADM, Saludes JP, Bhubalan K. Recent Advances of Marine Sponge-Associated Microorganisms as a Source of Commercially Viable Natural Products. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:492-512. [PMID: 35567600 DOI: 10.1007/s10126-022-10130-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 04/25/2022] [Indexed: 06/15/2023]
Abstract
Many industrially significant compounds have been derived from natural products in the environment. Research efforts so far have contributed to the discovery of beneficial natural products that have improved the quality of life on Earth. As one of the sources of natural products, marine sponges have been progressively recognised as microbial hotspots with reports of the sponges harbouring diverse microbial assemblages, genetic material, and metabolites with multiple industrial applications. Therefore, this paper aims at reviewing the recent literature (primarily published between 2016 and 2022) on the types and functions of natural products synthesised by sponge-associated microorganisms, thereby helping to bridge the gap between research and industrial applications. The metabolites that have been derived from sponge-associated microorganisms, mostly bacteria, fungi, and algae, have shown application prospects especially in medicine, cosmeceutical, environmental protection, and manufacturing industries. Sponge bacteria-derived natural products with medical properties harboured anticancer, antibacterial, antifungal, and antiviral functions. Efforts in re-identifying the origin of known and future sponge-sourced natural products would further clarify the roles and significance of microbes within marine sponges.
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Affiliation(s)
- Tan Suet May Amelia
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia
| | - Ferr Angelus C Suaberon
- Center for Natural Drug Discovery & Development (CND3), University of San Agustin, 5000, Iloilo City, Philippines
| | - Johanne Vad
- Changing Oceans Research Group, School of GeoSciences, University of Edinburgh, Edinburgh, UK
| | - Afiq Durrani Mohd Fahmi
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia
- Eco-Innovation Research Interest Group, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia
| | - Jonel P Saludes
- Center for Natural Drug Discovery & Development (CND3), University of San Agustin, 5000, Iloilo City, Philippines
- Department of Chemistry, University of San Agustin, 5000, Iloilo City, Philippines
- Department of Science and Technology, Balik Scientist Program, Philippine Council for Health Research & Development (PCHRD), Bicutan, 1631, Taguig, Philippines
| | - Kesaven Bhubalan
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia.
- Eco-Innovation Research Interest Group, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia.
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia.
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11
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Expression of Cyanobacterial Biosynthetic Gene Clusters in Escherichia coli. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2489:315-332. [PMID: 35524058 DOI: 10.1007/978-1-0716-2273-5_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Cyanobacteria represent an attractive source of natural bioactive compounds, ranging from sunscreens to cancer treatments. While many biosynthetic gene clusters (BGCs) that encode cyanobacterial natural products are known, the slow growth and lack of genetic tools in the native producers hampers their modification, characterization, and large-scale production. By engineering heterologous hosts for the expression of cyanobacterial BGCs, sufficient material can be produced for research or industry. Although several hosts have been evaluated for the expression of cyanobacterial natural products, this work details the process of expressing BGCs in Escherichia coli via promoter exchange.
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12
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Heinilä LMP, Jokela J, Ahmed MN, Wahlsten M, Kumar S, Hrouzek P, Permi P, Koistinen H, Fewer DP, Sivonen K. Discovery of varlaxins, new aeruginosin-type inhibitors of human trypsins. Org Biomol Chem 2022; 20:2681-2692. [PMID: 35293909 DOI: 10.1039/d1ob02454j] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Low-molecular weight natural products display vast structural diversity and have played a key role in the development of novel therapeutics. Here we report the discovery of novel members of the aeruginosin family of natural products, which we named varlaxins. The chemical structures of varlaxins 1046A and 1022A were determined using a combination of mass spectrometry, analysis of one- and two-dimensional NMR spectra, and HPLC analysis of Marfey's derivatives. These analyses revealed that varlaxins 1046A and 1022A are composed of the following moieties: 2-O-methylglyceric acid 3-O-sulfate, isoleucine, 2-carboxy-6-hydroxyoctahydroindole (Choi), and a terminal arginine derivative. Varlaxins 1046A and 1022A differ in the cyclization of this arginine moiety. Interestingly, an unusual α-D-glucopyranose moiety derivatized with two 4-hydroxyphenylacetic acid residues was bound to Choi, a structure not previously reported for other members of the aeruginosin family. We sequenced the complete genome of Nostoc sp. UHCC 0870 and identified the putative 36 kb varlaxin biosynthetic gene cluster. Bioinformatics analysis confirmed that varlaxins belong to the aeruginosin family of natural products. Varlaxins 1046A and 1022A strongly inhibited the three human trypsin isoenzymes with IC50 of 0.62-3.6 nM and 97-230 nM, respectively, including a prometastatic trypsin-3, which is a therapeutically relevant target in several types of cancer. These results substantially broaden the genetic and chemical diversity of the aeruginosin family and provide evidence that the aeruginosin family is a source of strong inhibitors of human serine proteases.
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Affiliation(s)
- L M P Heinilä
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland.
| | - J Jokela
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland.
| | - M N Ahmed
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland. .,Department of Clinical Chemistry, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - M Wahlsten
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland.
| | - S Kumar
- Laboratory of Algal Biotechnology-Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czech Republic
| | - P Hrouzek
- Laboratory of Algal Biotechnology-Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czech Republic
| | - P Permi
- Department of Chemistry, University of Jyväskylä, Jyväskylä, Finland.,Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - H Koistinen
- Department of Clinical Chemistry, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - D P Fewer
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland.
| | - K Sivonen
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland.
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13
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Lailaja VP, Sumithra TG, Reshma KJ, Anusree VN, Amala PV, Kishor TG, Sanil NK. Characterization of novel L-asparaginases having clinically safe profiles from bacteria inhabiting the hemolymph of the crab, Scylla serrata (Forskål, 1775). Folia Microbiol (Praha) 2022; 67:491-505. [PMID: 35138564 DOI: 10.1007/s12223-022-00952-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 01/24/2022] [Indexed: 11/04/2022]
Abstract
L-asparaginase (ASNase) is the principal chemotherapeutic agent against different blood cancers. The risks associated with current clinical preparations demand screening for novel ASNases. Accordingly, the study was conducted to shortlist ASNases having clinically safer profiles from a novel niche, namely, microbes in the gut and hemolymph of apparently healthy Scylla serrata. A four-step strategic approach incorporating the essential requirements for clinically safer profiles was followed. The initial step through plate assay showed five (9.61%) potential ASNase producers. The relative prevalence of ASNase producers was higher in hemolymph (13.33%) than gut (4.5%). The positive isolates were identified as Priestia aryabhattai, Priestia megaterium, Bacillus altitudinis, Shewanella decolorationis, and Chryseomicrobium amylolyticum. Quantitative profiles revealed high ASNase production (114.29 to 287.36 U/mL) without any optimization, with an added advantage of the extracellular production. The second step for substrate specificity studies revealed the absence of L-glutaminase and urease activities in ASNases from C. amylolyticum and P. megaterium, the most desirable properties for safe clinical applications. This is the first report of glutaminase and urease-free ASNase from these two bacteria. The third step ensured type II nature of selected ASNases, the targeted form in clinical applications. The fourth step confirmed the activity and stability in human physiological conditions. Altogether, the results revealed two potential ASNases with clinically compatible profiles.
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Affiliation(s)
- V P Lailaja
- Marine Biotechnology Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Ernakulam North P.O, Post Box No. 1603, Kochi, 682 018, India
| | - T G Sumithra
- Marine Biotechnology Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Ernakulam North P.O, Post Box No. 1603, Kochi, 682 018, India.
| | - K J Reshma
- Marine Biotechnology Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Ernakulam North P.O, Post Box No. 1603, Kochi, 682 018, India
| | - V N Anusree
- Marine Biotechnology Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Ernakulam North P.O, Post Box No. 1603, Kochi, 682 018, India
| | - P V Amala
- Marine Biotechnology Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Ernakulam North P.O, Post Box No. 1603, Kochi, 682 018, India
| | - T G Kishor
- Fishery Resources Assessment Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Ernakulam North P.O, Post Box No. 1603, Kochi, 682 018, India
| | - N K Sanil
- Marine Biotechnology Division, ICAR-Central Marine Fisheries Research Institute (CMFRI), Ernakulam North P.O, Post Box No. 1603, Kochi, 682 018, India
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14
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Di Cesare Mannelli L, Palma Esposito F, Sangiovanni E, Pagano E, Mannucci C, Polini B, Ghelardini C, Dell’Agli M, Izzo AA, Calapai G, de Pascale D, Nieri P. Pharmacological Activities of Extracts and Compounds Isolated from Mediterranean Sponge Sources. Pharmaceuticals (Basel) 2021; 14:ph14121329. [PMID: 34959729 PMCID: PMC8715745 DOI: 10.3390/ph14121329] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 12/11/2022] Open
Abstract
Marine pharmacology is an exciting and growing discipline that blends blue biotechnology and natural compound pharmacology together. Several sea-derived compounds that are approved on the pharmaceutical market were discovered in sponges, marine organisms that are particularly rich in bioactive metabolites. This paper was specifically aimed at reviewing the pharmacological activities of extracts or purified compounds from marine sponges that were collected in the Mediterranean Sea, one of the most biodiverse marine habitats, filling the gap in the literature about the research of natural products from this geographical area. Findings regarding different Mediterranean sponge species were individuated, reporting consistent evidence of efficacy mainly against cancer, infections, inflammatory, and neurological disorders. The sustainable exploitation of Mediterranean sponges as pharmaceutical sources is strongly encouraged to discover new compounds.
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Affiliation(s)
- Lorenzo Di Cesare Mannelli
- Department of Neuroscience, Psychology, Drug Research and Child Health—Neurofarba—Section of Pharmacology and Toxicology, University of Florence, 50139 Florence, Italy;
- Correspondence:
| | - Fortunato Palma Esposito
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, 80121 Naples, Italy; (F.P.E.); (D.d.P.)
| | - Enrico Sangiovanni
- Department of Pharmacological and Biomolecular Sciences, University of Milan, 20133 Milan, Italy; (E.S.); (M.D.)
| | - Ester Pagano
- Department of Pharmacy, School of Medicine and Surgery, University of Naples Federico II, 80131 Naples, Italy; (E.P.); (A.A.I.)
| | - Carmen Mannucci
- Department of Biomedical and Dental Sciences and Morphological and Functional Imaging, University of Messina, 98125 Messina, Italy; (C.M.); (G.C.)
| | - Beatrice Polini
- Department of Pharmacy, University of Pisa, 56126 Pisa, Italy; (B.P.); (P.N.)
| | - Carla Ghelardini
- Department of Neuroscience, Psychology, Drug Research and Child Health—Neurofarba—Section of Pharmacology and Toxicology, University of Florence, 50139 Florence, Italy;
| | - Mario Dell’Agli
- Department of Pharmacological and Biomolecular Sciences, University of Milan, 20133 Milan, Italy; (E.S.); (M.D.)
| | - Angelo Antonio Izzo
- Department of Pharmacy, School of Medicine and Surgery, University of Naples Federico II, 80131 Naples, Italy; (E.P.); (A.A.I.)
| | - Gioacchino Calapai
- Department of Biomedical and Dental Sciences and Morphological and Functional Imaging, University of Messina, 98125 Messina, Italy; (C.M.); (G.C.)
| | - Donatella de Pascale
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, 80121 Naples, Italy; (F.P.E.); (D.d.P.)
| | - Paola Nieri
- Department of Pharmacy, University of Pisa, 56126 Pisa, Italy; (B.P.); (P.N.)
- Interdepartmental Center of Marine Pharmacology (MarinePHARMA), University of Pisa, 56126 Pisa, Italy
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15
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Ahmed MN, Wahlsten M, Jokela J, Nees M, Stenman UH, Alvarenga DO, Strandin T, Sivonen K, Poso A, Permi P, Metsä-Ketelä M, Koistinen H, Fewer DP. Potent Inhibitor of Human Trypsins from the Aeruginosin Family of Natural Products. ACS Chem Biol 2021; 16:2537-2546. [PMID: 34661384 PMCID: PMC8609519 DOI: 10.1021/acschembio.1c00611] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Serine proteases
regulate many physiological processes and play
a key role in a variety of cancers. Aeruginosins are a family of natural
products produced by cyanobacteria that exhibit pronounced structural
diversity and potent serine protease inhibition. Here, we sequenced
the complete genome of Nodularia sphaerocarpa UHCC 0038 and identified the 43.7 kb suomilide biosynthetic gene
cluster. Bioinformatic analysis demonstrated that suomilide belongs
to the aeruginosin family of natural products. We identified 103 complete
aeruginosin biosynthetic gene clusters from 12 cyanobacterial genera
and showed that they encode an unexpected chemical diversity. Surprisingly,
purified suomilide inhibited human trypsin-2 and -3, with IC50 values of 4.7 and 11.5 nM, respectively, while trypsin-1 was inhibited
with an IC50 of 104 nM. Molecular dynamics simulations
suggested that suomilide has a long residence time when bound to trypsins.
This was confirmed experimentally for trypsin-1 and -3 (residence
times of 1.5 and 57 min, respectively). Suomilide also inhibited the
invasion of aggressive and metastatic PC-3M prostate cancer cells
without affecting cell proliferation. The potent inhibition of trypsin-3,
together with a long residence time and the ability to inhibit prostate
cancer cell invasion, makes suomilide an attractive drug lead for
targeting cancers that overexpress trypsin-3. These results substantially
broaden the genetic and chemical diversity of the aeruginosin family
and suggest that aeruginosins may be a source of selective inhibitors
of human serine proteases.
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Affiliation(s)
- Muhammad N. Ahmed
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Viikinkaari 9, Biocenter 1, P.O. Box 56, Helsinki FIN-00014, Finland
- Department of Clinical Chemistry and Haematology, Faculty of Medicine, University of Helsinki and Helsinki University Hospital, Haartmaninkatu 8, P.O. Box 63, Helsinki FIN-00014, Finland
| | - Matti Wahlsten
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Viikinkaari 9, Biocenter 1, P.O. Box 56, Helsinki FIN-00014, Finland
| | - Jouni Jokela
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Viikinkaari 9, Biocenter 1, P.O. Box 56, Helsinki FIN-00014, Finland
| | - Matthias Nees
- Department of Biochemistry and Molecular Biology, Medical University in Lublin, ul. Chodzki 1, Lublin 20-093, Poland
- Institute of Biomedicine and Western Cancer Centre FICAN West, University of Turku, Turku 20101, Finland
| | - Ulf-Håkan Stenman
- Department of Clinical Chemistry and Haematology, Faculty of Medicine, University of Helsinki and Helsinki University Hospital, Haartmaninkatu 8, P.O. Box 63, Helsinki FIN-00014, Finland
| | - Danillo O. Alvarenga
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Viikinkaari 9, Biocenter 1, P.O. Box 56, Helsinki FIN-00014, Finland
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Tomas Strandin
- Department of Virology, Faculty of Medicine, University of Helsinki, Haartmaninkatu 3, P.O. Box 21, Helsinki FIN-00014, Finland
| | - Kaarina Sivonen
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Viikinkaari 9, Biocenter 1, P.O. Box 56, Helsinki FIN-00014, Finland
| | - Antti Poso
- School of Pharmacy, University of Eastern Finland, P.O. Box 1627, Kuopio FIN-70211, Finland
- Dept. of Internal Medicine VIII, University Hospital Tübingen, Otfried-Müller-Strasse 14, Tübingen DE-72076, Germany
| | - Perttu Permi
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, Jyväskylä FI-40014, Finland
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, P.O. Box
35, Jyväskylä FI-40014, Finland
| | - Mikko Metsä-Ketelä
- Department of Biochemistry, University of Turku, Turku FIN-20014, Finland
| | - Hannu Koistinen
- Department of Clinical Chemistry and Haematology, Faculty of Medicine, University of Helsinki and Helsinki University Hospital, Haartmaninkatu 8, P.O. Box 63, Helsinki FIN-00014, Finland
| | - David P. Fewer
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Viikinkaari 9, Biocenter 1, P.O. Box 56, Helsinki FIN-00014, Finland
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16
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Campana S, Busch K, Hentschel U, Muyzer G, de Goeij JM. DNA-stable isotope probing (DNA-SIP) identifies marine sponge-associated bacteria actively utilizing dissolved organic matter (DOM). Environ Microbiol 2021; 23:4489-4504. [PMID: 34159693 PMCID: PMC8453545 DOI: 10.1111/1462-2920.15642] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 06/11/2021] [Accepted: 06/11/2021] [Indexed: 12/30/2022]
Abstract
Sponges possess exceptionally diverse associated microbial communities and play a major role in (re)cycling of dissolved organic matter (DOM) in marine ecosystems. Linking sponge-associated community structure with DOM utilization is essential to understand host-microbe interactions in the uptake, processing, and exchange of resources. We coupled, for the first time, DNA-stable isotope probing (DNA-SIP) with 16S rRNA amplicon sequencing in a sponge holobiont to identify which symbiotic bacterial taxa are metabolically active in DOM uptake. Parallel incubation experiments with the sponge Plakortis angulospiculatus were amended with equimolar quantities of unlabelled (12 C) and labelled (13 C) DOM. Seven bacterial amplicon sequence variants (ASVs), belonging to the phyla PAUC34f, Proteobacteria, Poribacteria, Nitrospirae, and Chloroflexi, were identified as the first active consumers of DOM. Our results support the predictions that PAUC34f, Poribacteria, and Chloroflexi are capable of organic matter degradation through heterotrophic carbon metabolism, while Nitrospirae may have a potential mixotrophic metabolism. We present a new analytical application of DNA-SIP to detect substrate incorporation into a marine holobiont with a complex associated bacterial community and provide new experimental evidence that links the identity of diverse sponge-associated bacteria to the consumption of DOM.
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Affiliation(s)
- Sara Campana
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE Amsterdam, Netherlands
| | - Kathrin Busch
- Department of Marine Ecology, Research Unit Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - Ute Hentschel
- Department of Marine Ecology, Research Unit Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - Gerard Muyzer
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE Amsterdam, Netherlands
| | - Jasper M de Goeij
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE Amsterdam, Netherlands.,CARMABI Foundation, Piscaderabaai z/n, P.O. Box 2090, Willemstad, Curaçao
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17
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Leber CA, Reyes AJ, Biggs JS, Gerwick WH. Cyanobacteria-shrimp colonies in the Mariana Islands. AQUATIC ECOLOGY 2021; 55:453-465. [PMID: 34177357 PMCID: PMC8223766 DOI: 10.1007/s10452-021-09837-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 02/03/2021] [Indexed: 06/13/2023]
Abstract
Cyanobacteria have multifaceted ecological roles on coral reefs. Moorena bouillonii, a chemically rich filamentous cyanobacterium, has been characterized as a pathogenic organism with an unusual ability to overgrow gorgonian corals, but little has been done to study its general growth habits or its unique association with the snapping shrimp Alpheus frontalis. Quantitative benthic surveys, and field and photographic observations were utilized to develop a better understanding of the ecology of these species, while growth experiments and nutrient analysis were performed to examine how this cyanobacterium may be benefiting from its shrimp symbiont. Colonies of M. bouillonii and A. frontalis displayed considerable habitat specificity in terms of occupied substrate. Although found to vary in abundance and density across survey sites and transects, M. bouillonii was consistently found to be thriving with A. frontalis within interstitial spaces on the reef. Removal of A. frontalis from cyanobacterial colonies in a laboratory experiment altered M. bouillonii pigmentation, whereas cyanobacteria-shrimp colonies in the field exhibited elevated nutrient levels compared to the surrounding seawater.
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Affiliation(s)
- Christopher A. Leber
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093 USA
| | | | - Jason S. Biggs
- University of Guam Marine Laboratory, UOG Station, Mangilao, GU 96923 USA
| | - William H. Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, 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
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18
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Genome Reduction and Secondary Metabolism of the Marine Sponge-Associated Cyanobacterium Leptothoe. Mar Drugs 2021; 19:md19060298. [PMID: 34073758 PMCID: PMC8225149 DOI: 10.3390/md19060298] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 11/16/2022] Open
Abstract
Sponges form symbiotic relationships with diverse and abundant microbial communities. Cyanobacteria are among the most important members of the microbial communities that are associated with sponges. Here, we performed a genus-wide comparative genomic analysis of the newly described marine benthic cyanobacterial genus Leptothoe (Synechococcales). We obtained draft genomes from Le. kymatousa TAU-MAC 1615 and Le. spongobia TAU-MAC 1115, isolated from marine sponges. We identified five additional Leptothoe genomes, host-associated or free-living, using a phylogenomic approach, and the comparison of all genomes showed that the sponge-associated strains display features of a symbiotic lifestyle. Le. kymatousa and Le. spongobia have undergone genome reduction; they harbored considerably fewer genes encoding for (i) cofactors, vitamins, prosthetic groups, pigments, proteins, and amino acid biosynthesis; (ii) DNA repair; (iii) antioxidant enzymes; and (iv) biosynthesis of capsular and extracellular polysaccharides. They have also lost several genes related to chemotaxis and motility. Eukaryotic-like proteins, such as ankyrin repeats, playing important roles in sponge-symbiont interactions, were identified in sponge-associated Leptothoe genomes. The sponge-associated Leptothoe stains harbored biosynthetic gene clusters encoding novel natural products despite genome reduction. Comparisons of the biosynthetic capacities of Leptothoe with chemically rich cyanobacteria revealed that Leptothoe is another promising marine cyanobacterium for the biosynthesis of novel natural products.
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19
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Sagita R, Quax WJ, Haslinger K. Current State and Future Directions of Genetics and Genomics of Endophytic Fungi for Bioprospecting Efforts. Front Bioeng Biotechnol 2021; 9:649906. [PMID: 33791289 PMCID: PMC8005728 DOI: 10.3389/fbioe.2021.649906] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 02/16/2021] [Indexed: 12/16/2022] Open
Abstract
The bioprospecting of secondary metabolites from endophytic fungi received great attention in the 1990s and 2000s, when the controversy around taxol production from Taxus spp. endophytes was at its height. Since then, hundreds of reports have described the isolation and characterization of putative secondary metabolites from endophytic fungi. However, only very few studies also report the genetic basis for these phenotypic observations. With low sequencing cost and fast sample turnaround, genetics- and genomics-based approaches have risen to become comprehensive approaches to study natural products from a wide-range of organisms, especially to elucidate underlying biosynthetic pathways. However, in the field of fungal endophyte biology, elucidation of biosynthetic pathways is still a major challenge. As a relatively poorly investigated group of microorganisms, even in the light of recent efforts to sequence more fungal genomes, such as the 1000 Fungal Genomes Project at the Joint Genome Institute (JGI), the basis for bioprospecting of enzymes and pathways from endophytic fungi is still rather slim. In this review we want to discuss the current approaches and tools used to associate phenotype and genotype to elucidate biosynthetic pathways of secondary metabolites in endophytic fungi through the lens of bioprospecting. This review will point out the reported successes and shortcomings, and discuss future directions in sampling, and genetics and genomics of endophytic fungi. Identifying responsible biosynthetic genes for the numerous secondary metabolites isolated from endophytic fungi opens the opportunity to explore the genetic potential of producer strains to discover novel secondary metabolites and enhance secondary metabolite production by metabolic engineering resulting in novel and more affordable medicines and food additives.
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Affiliation(s)
| | | | - Kristina Haslinger
- Groningen Institute of Pharmacy, Chemical and Pharmaceutical Biology, University of Groningen, Groningen, Netherlands
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20
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Rathour R, Medhi K, Gupta J, Thakur IS. Integrated approach of whole-genome analysis, toxicological evaluation and life cycle assessment for pyrene biodegradation by a psychrophilic strain, Shewanella sp. ISTPL2. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 269:116176. [PMID: 33307397 DOI: 10.1016/j.envpol.2020.116176] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 11/18/2020] [Accepted: 11/27/2020] [Indexed: 06/12/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) such as pyrene are universal contaminants existing in the environment which have known cancer-causing and mutagenic characteristics. A psychrophilic bacterial strain Shewanella sp. ISTPL2 was isolated from the sediment sample collected from the Pangong lake, Jammu & Kashmir, India. In our previous study, the pyrene degradation potential of the ISTPL2 strain was studied in both mineral salt media as well as in soil artificially spiked with different concentrations of pyrene. Whole-genome sequencing of ISTPL2 strain in the current study highlighted the key genes of pyrene metabolism, including alcohol dehydrogenase and ring hydroxylating dioxygenase alpha-subunit. Pyrene cytotoxicity was evaluated on HepG2, a human hepato-carcinoma cell line. The cytotoxicity of the organic extract decreased with the increasing duration of bacterial treatment. To develop a more sustainable biodegradation approach, the potential impacts were evaluated for human health and ecosystem using life-cycle assessment (LCA) following the ReCiPe methodology for the considered PAH. The results implemented that global warming potential (GWP) had the highest impact, whereas both ecotoxicity and human toxicity had least from this study.
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Affiliation(s)
- Rashmi Rathour
- School of Environmental Sciences, Jawaharlal Nehru University, Delhi, 110067, India.
| | - Kristina Medhi
- School of Environmental Sciences, Jawaharlal Nehru University, Delhi, 110067, India; Central Pollution Control Board (CPCB), Regional Directorate (North), PICUP Bhawan, Lucknow, Uttar Pradesh, 226010, India.
| | - Juhi Gupta
- School of Environmental Sciences, Jawaharlal Nehru University, Delhi, 110067, India.
| | - Indu Shekhar Thakur
- School of Environmental Sciences, Jawaharlal Nehru University, Delhi, 110067, India.
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21
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Gupta J, Rathour R, Dupont CL, Kaul D, Thakur IS. Genomic insights into waste valorized extracellular polymeric substances (EPS) produced by Bacillus sp. ISTL8. ENVIRONMENTAL RESEARCH 2021; 192:110277. [PMID: 33069701 DOI: 10.1016/j.envres.2020.110277] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 09/07/2020] [Accepted: 09/12/2020] [Indexed: 06/11/2023]
Abstract
The present study discusses the genomic analysis of Bacillus sp. ISTL8 along with the production of EPS (Extracellular polymeric substances) using carbofuran, a toxic carbamate pesticide. Bacillus strain was isolated from landfill soil and evaluated for high growth rates and EPS production. One strain, renamed ISTL8 grew on a broad range of carbon sources, including toxic carbofuran, while producing copious EPS. Growth assays verified the strain to be thermophilic, low salt tolerant, and with a preference for neutral pH. SEM (Scanning Electron Microscopy) was used for morphological characterization of the EPS while the monomeric composition, bonding patterns and functional groups were deduced by GC-MS (Gas Chromatography-Mass Spectrometry), 1H and 13C NMR (Nuclear Magnetic Resonance) and FTIR (Fourier Transform Infrared Spectroscopy). The production of EPS using carbofuran (carbamate pesticide) as a carbon source was found to be 6.20 ± 0.29 g L-1 containing 61.17% w/w carbohydrates, 29.72% w/w proteins and 6.11% w/w lipids (of dry EPS). The potential cytotoxicity of EPS was evaluated with 3- (4,5-dimethyl thiazol-2-Yl) -2,5-diphenyl tetrazolium bromide (MTT) assay and found non-toxic (2.25%). WGS (Whole genome sequencing) was performed for the strain Bacillus sp. ISTL8 producing EPS; an array of genes putatively involved in the EPS production were identified in several different genomic locations, guiding potential genetic manipulation studies in the future. The results highlight the potency of a bacterial isolate Bacillus sp. ISTL8 to produce non-cytotoxic EPS using carbofuran that can be further harnessed for environmental and commercial applications. Additionally, WGS revealed an array of EPS specific genes which can be effectively engineered for much enhanced production.
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Affiliation(s)
- Juhi Gupta
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India; Environment and Sustainability Group, J. Craig Venter Institute, La Jolla, CA, USA
| | - Rashmi Rathour
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Christopher L Dupont
- Environment and Sustainability Group, J. Craig Venter Institute, La Jolla, CA, USA
| | - Drishti Kaul
- Environment and Sustainability Group, J. Craig Venter Institute, La Jolla, CA, USA
| | - Indu Shekhar Thakur
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India.
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22
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Mote S, Gupta V, De K, Nanajkar M, Damare SR, Ingole B. Bacterial diversity associated with a newly described bioeroding sponge, Cliona thomasi, from the coral reefs on the West Coast of India. Folia Microbiol (Praha) 2020; 66:203-211. [PMID: 33140282 DOI: 10.1007/s12223-020-00830-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 10/16/2020] [Indexed: 10/23/2022]
Abstract
The bacterial diversity associated with eroding sponges belonging to the Cliona viridis species complex is scarcely known. Cliona thomasi described from the West Coast of India is a new introduction to the viridis species complex. In this study, we determined the bacterial diversity associated with C. thomasi using next-generation sequencing. The results revealed the dominance of Proteobacteria followed by Cyanobacteria, Actinobacteria and Firmicutes. Among Proteobacteria, the Alphaproteobacteria were found to be the most dominant class. Furthermore, at the genus level, Rhodothalassium were highly abundant followed by Endozoicomonas in sponge samples. The beta-diversity and species richness measures showed remarkably lower diversity in Cliona thomasi than the ambient environment. The determined lower bacterial diversity in C. thomasi than the environmental samples, thus, categorized it as a low microbial abundance (LMA). Functional annotation of the C. thomasi-associated bacterial community indicates their possible role in photo-autotrophy, aerobic nitrification, coupling of sulphate reduction and sulphide oxidization. The present study unveils the bacterial diversity in bioeroding C. thomasi, which is a crucial step to determine the functions of the sponge holobiont in coral reef ecosystem.
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Affiliation(s)
- Sambhaji Mote
- CSIR-National Institute of Oceanography, Dona Paula, Goa, India.,Department of Marine Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - Vishal Gupta
- CSIR-National Institute of Oceanography, Dona Paula, Goa, India. .,School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Kalyan De
- CSIR-National Institute of Oceanography, Dona Paula, Goa, India.,School of Earth, Ocean, and Atmospheric Sciences, Goa University, Taleigao, Goa, India
| | - Mandar Nanajkar
- CSIR-National Institute of Oceanography, Dona Paula, Goa, India
| | - Samir R Damare
- CSIR-National Institute of Oceanography, Dona Paula, Goa, India
| | - Baban Ingole
- CSIR-National Institute of Oceanography, Dona Paula, Goa, India.
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Analysis of nonribosomal peptide synthetase genes in haemolymph microbes of marine crabs. Arch Microbiol 2020; 203:1251-1258. [PMID: 33128575 DOI: 10.1007/s00203-020-02101-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 08/10/2020] [Accepted: 10/19/2020] [Indexed: 10/23/2022]
Abstract
Nonribosomal peptide synthetases (NRPS) are multi-domain enzymes that have innumerably beneficial health applications. Realizing the significance of marine microorganisms in search for NRPS sequences, study was conducted for analysis of NRPS gene sequences of marine crab haemolymph bacteria for the first time. Strains belonging to five different species were found to have NRPS genes. The study generated NRPS sequences from four bacterial species, for which NRPS gene information was not available earlier. Two new putative adenylation domain signatures were identified from phylum Firmicutes. In silico analysis of amino acid sequences from four species showed less identity (42-50%) to the characterized NRPS compounds that integrate serine residue in active site, suggesting the novelty or uncharacterized nature. Altogether, the study warrants future research exploiting marine crab haemolymph bacteria, an unexplored niche of microbial genetic wealth to discover microbial novel NRPS genes and natural products using emerging tools and technologies.
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Podell S, Blanton JM, Oliver A, Schorn MA, Agarwal V, Biggs JS, Moore BS, Allen EE. A genomic view of trophic and metabolic diversity in clade-specific Lamellodysidea sponge microbiomes. MICROBIOME 2020; 8:97. [PMID: 32576248 PMCID: PMC7313196 DOI: 10.1186/s40168-020-00877-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 05/28/2020] [Indexed: 05/09/2023]
Abstract
BACKGROUND Marine sponges and their microbiomes contribute significantly to carbon and nutrient cycling in global reefs, processing and remineralizing dissolved and particulate organic matter. Lamellodysidea herbacea sponges obtain additional energy from abundant photosynthetic Hormoscilla cyanobacterial symbionts, which also produce polybrominated diphenyl ethers (PBDEs) chemically similar to anthropogenic pollutants of environmental concern. Potential contributions of non-Hormoscilla bacteria to Lamellodysidea microbiome metabolism and the synthesis and degradation of additional secondary metabolites are currently unknown. RESULTS This study has determined relative abundance, taxonomic novelty, metabolic capacities, and secondary metabolite potential in 21 previously uncharacterized, uncultured Lamellodysidea-associated microbial populations by reconstructing near-complete metagenome-assembled genomes (MAGs) to complement 16S rRNA gene amplicon studies. Microbial community compositions aligned with sponge host subgroup phylogeny in 16 samples from four host clades collected from multiple sites in Guam over a 3-year period, including representatives of Alphaproteobacteria, Gammaproteobacteria, Oligoflexia, and Bacteroidetes as well as Cyanobacteria (Hormoscilla). Unexpectedly, microbiomes from one host clade also included Cyanobacteria from the prolific secondary metabolite-producer genus Prochloron, a common tunicate symbiont. Two novel Alphaproteobacteria MAGs encoded pathways diagnostic for methylotrophic metabolism as well as type III secretion systems, and have been provisionally assigned to a new order, designated Candidatus Methylospongiales. MAGs from other taxonomic groups encoded light-driven energy production pathways using not only chlorophyll, but also bacteriochlorophyll and proteorhodopsin. Diverse heterotrophic capabilities favoring aerobic versus anaerobic conditions included pathways for degrading chitin, eukaryotic extracellular matrix polymers, phosphonates, dimethylsulfoniopropionate, trimethylamine, and benzoate. Genetic evidence identified an aerobic catabolic pathway for halogenated aromatics that may enable endogenous PBDEs to be used as a carbon and energy source. CONCLUSIONS The reconstruction of high-quality MAGs from all microbial taxa comprising greater than 0.1% of the sponge microbiome enabled species-specific assignment of unique metabolic features that could not have been predicted from taxonomic data alone. This information will promote more representative models of marine invertebrate microbiome contributions to host bioenergetics, the identification of potential new sponge parasites and pathogens based on conserved metabolic and physiological markers, and a better understanding of biosynthetic and degradative pathways for secondary metabolites and halogenated compounds in sponge-associated microbiota. Video Abstract.
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Affiliation(s)
- Sheila Podell
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Jessica M Blanton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Aaron Oliver
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Michelle A Schorn
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Vinayak Agarwal
- School of Chemistry and Biochemistry and School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Jason S Biggs
- University of Guam Marine Laboratory, UoG Station, Mangilao, GU, USA
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Eric E Allen
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA.
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.
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Brumley DA, Gunasekera SP, Chen QY, Paul VJ, Luesch H. Discovery, Total Synthesis, and SAR of Anaenamides A and B: Anticancer Cyanobacterial Depsipeptides with a Chlorinated Pharmacophore. Org Lett 2020; 22:4235-4239. [PMID: 32418432 DOI: 10.1021/acs.orglett.0c01281] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
New modified depsipeptides and geometric isomers, termed anaenamides A (1a) and B (1b), along with the presumptive biosynthetic intermediate, anaenoic acid (2), were discovered from a marine cyanobacterium from Guam. Structures were confirmed by total synthesis. The alkylsalicylic acid fragment and the C-terminal α-chlorinated α,β-unsaturated ester are novelties in cyanobacterial natural products. Cancer cell viability assays indicated that the C-terminal unit serves as the pharmacophore and that the double-bond geometry impacts the cytotoxicity.
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Affiliation(s)
| | - Sarath P Gunasekera
- Smithsonian Marine Station, 701 Seaway Drive, Ft. Pierce, Florida 34949, United States
| | | | - Valerie J Paul
- Smithsonian Marine Station, 701 Seaway Drive, Ft. Pierce, Florida 34949, United States
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Song R, Shi H, Zhu J, Wang H, Shen Y. A Single-Component Flavoenzyme Catalyzed Regioselective Halogenation of Pyrone in the Biosynthesis of Venemycins. ACS Chem Biol 2019; 14:2533-2537. [PMID: 31774264 DOI: 10.1021/acschembio.9b00554] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Flavin-dependent halogenases (FDHs) are known for installing halogens on natural products. To date, most reported FDHs are two-component FDHs, which require a flavin reductase as the reaction partner to function. Here, we report the identification of a new halogenated biaryl compound 2-chloro venemycin (1) through constitutive expression of the regulator gene vemR in the vem gene cluster in Streptomyces sp. S006 and media optimization. In addition, we provide biochemical evidence that, in the absence of the flavin reductase, purified FDH VemK catalyzes the regioselective halogenation of the pyrone moiety of venemycin (2). Mutagenesis studies showed that T315 and R317 residues are likely crucial for catalysis and NAD(P)H binding. VemK represents the first characterized single-component FDH from Streptomyces and the first FDH that halogenates a pyrone moiety.
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Affiliation(s)
- Rentai Song
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People’s Republic of China
| | - Haixia Shi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People’s Republic of China
| | - Jing Zhu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People’s Republic of China
| | - Haoxin Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People’s Republic of China
| | - Yuemao Shen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People’s Republic of China
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong 250012, People’s Republic of China
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