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Peters EE, Cahn JKB, Lotti A, Gavriilidou A, Steffens UAE, Loureiro C, Schorn MA, Cárdenas P, Vickneswaran N, Crews P, Sipkema D, Piel J. Distribution and diversity of 'Tectomicrobia', a deep-branching uncultivated bacterial lineage harboring rich producers of bioactive metabolites. ISME COMMUNICATIONS 2023; 3:50. [PMID: 37248312 PMCID: PMC10227082 DOI: 10.1038/s43705-023-00259-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/09/2023] [Accepted: 05/18/2023] [Indexed: 05/31/2023]
Abstract
Genomic and functional analyses of bacterial sponge symbionts belonging to the uncultivated candidate genus 'Entotheonella' has revealed them as the prolific producers of bioactive compounds previously identified from their invertebrate hosts. These studies also suggested 'Entotheonella' as the first members of a new candidate phylum, 'Tectomicrobia'. Here we analyzed the phylogenetic structure and environmental distribution of this as-yet sparsely populated phylum-like lineage. The data show that 'Entotheonella' and other 'Tectomicrobia' are not restricted to marine habitats but widely distributed among terrestrial locations. The inferred phylogenetic trees suggest several intra-phylum lineages with diverse lifestyles. Of these, the previously described 'Entotheonella' lineage can be more accurately divided into at least three different candidate genera with the terrestrial 'Candidatus Prasianella', the largely terrestrial 'Candidatus Allonella', the 'Candidatus Thalassonella' comprising sponge-associated members, and the more widely distributed 'Candidatus Entotheonella'. Genomic characterization of 'Thalassonella' members from a range of sponge hosts did not suggest a role as providers of natural products, despite high genomic similarity to 'Entotheonella' regarding primary metabolism and implied lifestyle. In contrast, the analysis revealed a correlation between the revised 'Entotheonella' 16S rRNA gene phylogeny and a specific association with sponges and their natural products. This feature might serve as a discovery method to accelerate the identification of new chemically rich 'Entotheonella' variants, and led to the identification of the first 'Entotheonella' symbiont in a non-tetractinellid sponge, Psammocinia sp., indicating a wide host distribution of 'Entotheonella'-based chemical symbiosis.
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Affiliation(s)
- Eike E Peters
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Jackson K B Cahn
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Alessandro Lotti
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Asimenia Gavriilidou
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE, Wageningen, The Netherlands
| | - Ursula A E Steffens
- Kekule Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - Catarina Loureiro
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE, Wageningen, The Netherlands
| | - Michelle A Schorn
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE, Wageningen, The Netherlands
| | - Paco Cárdenas
- Pharmacognosy, Department of Pharmaceutical Biosciences, BioMedical Center, Uppsala University, Husargatan 3, 75124, Uppsala, Sweden
| | - Nilani Vickneswaran
- Kekule Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - Phillip Crews
- Department of Chemistry and Biochemistry, University of California at Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE, Wageningen, The Netherlands
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland.
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Diversity of Bacterial Secondary Metabolite Biosynthetic Gene Clusters in Three Vietnamese Sponges. Mar Drugs 2022; 21:md21010029. [PMID: 36662202 PMCID: PMC9864124 DOI: 10.3390/md21010029] [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: 11/22/2022] [Revised: 12/23/2022] [Accepted: 12/27/2022] [Indexed: 12/31/2022] Open
Abstract
Recent reviews have reinforced sponge-associated bacteria as a valuable source of structurally diverse secondary metabolites with potent biological properties, which makes these microbial communities promising sources of new drug candidates. However, the overall diversity of secondary metabolite biosynthetic potential present in bacteria is difficult to access due to the fact that the majority of bacteria are not readily cultured in the laboratory. Thus, use of cultivation-independent approaches may allow accessing "silent" and "cryptic" secondary metabolite biosynthetic gene clusters present in bacteria that cannot yet be cultured. In the present study, we investigated the diversity of secondary metabolite biosynthetic gene clusters (BGCs) in metagenomes of bacterial communities associated with three sponge species: Clathria reinwardti, Rhabdastrella globostellata, and Spheciospongia sp. The results reveal that the three metagenomes contain a high number of predicted BGCs, ranging from 282 to 463 BGCs per metagenome. The types of BGCs were diverse and represented 12 different cluster types. Clusters predicted to encode fatty acid synthases and polyketide synthases (PKS) were the most dominant BGC types, followed by clusters encoding synthesis of terpenes and bacteriocins. Based on BGC sequence similarity analysis, 363 gene cluster families (GCFs) were identified. Interestingly, no GCFs were assigned to pathways responsible for the production of known compounds, implying that the clusters detected might be responsible for production of several novel compounds. The KS gene sequences from PKS clusters were used to predict the taxonomic origin of the clusters involved. The KS sequences were related to 12 bacterial phyla with Actinobacteria, Proteobacteria, and Firmicutes as the most predominant. At the genus level, the KSs were most related to those found in the genera Mycolicibacterium, Mycobacterium, Burkholderia, and Streptomyces. Phylogenetic analysis of KS sequences resulted in detection of two known 'sponge-specific' BGCs, i.e., SupA and SwfA, as well as a new 'sponge-specific' cluster related to fatty acid synthesis in the phylum Candidatus Poribacteria and composed only by KS sequences of the three sponge-associated bacterial communities assessed here.
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Comparative Metagenomic Analysis of Biosynthetic Diversity across Sponge Microbiomes Highlights Metabolic Novelty, Conservation, and Diversification. mSystems 2022; 7:e0035722. [PMID: 35862823 PMCID: PMC9426513 DOI: 10.1128/msystems.00357-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Marine sponges and their microbial symbiotic communities are rich sources of diverse natural products (NPs) that often display biological activity, yet little is known about the global distribution of NPs and the symbionts that produce them. Since the majority of sponge symbionts remain uncultured, it is a challenge to characterize their NP biosynthetic pathways, assess their prevalence within the holobiont, and measure the diversity of NP biosynthetic gene clusters (BGCs) across sponge taxa and environments. Here, we explore the microbial biosynthetic landscapes of three high-microbial-abundance (HMA) sponges from the Atlantic Ocean and the Mediterranean Sea. This data set reveals striking novelty, with <1% of the recovered gene cluster families (GCFs) showing similarity to any characterized BGC. When zooming in on the microbial communities of each sponge, we observed higher variability of specialized metabolic and taxonomic profiles between sponge species than within species. Nonetheless, we identified conservation of GCFs, with 20% of sponge GCFs being shared between at least two sponge species and a GCF core comprised of 6% of GCFs shared across all species. Within this functional core, we identified a set of widespread and diverse GCFs encoding nonribosomal peptide synthetases that are potentially involved in the production of diversified ether lipids, as well as GCFs putatively encoding the production of highly modified proteusins. The present work contributes to the small, yet growing body of data characterizing NP landscapes of marine sponge symbionts and to the cryptic biosynthetic potential contained in this environmental niche. IMPORTANCE Marine sponges and their microbial symbiotic communities are a rich source of diverse natural products (NPs). However, little is known about the sponge NP global distribution landscape and the symbionts that produce them. Here, we make use of recently developed tools to perform untargeted mining and comparative analysis of sponge microbiome metagenomes of three sponge species in the first study considering replicate metagenomes of multiple sponge species. We present an overview of the biosynthetic diversity across these sponge holobionts, which displays extreme biosynthetic novelty. We report not only the conservation of biosynthetic and taxonomic diversity but also a core of conserved specialized metabolic pathways. Finally, we highlight several novel GCFs with unknown ecological function, and observe particularly high biosynthetic potential in Acidobacteriota and Latescibacteria symbionts. This study paves the way toward a better understanding of the marine sponge holobionts' biosynthetic potential and the functional and ecological role of sponge microbiomes.
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Caso A, da Silva FB, Esposito G, Teta R, Sala GD, Cavalcanti LPAN, Valverde AL, Martins RCC, Costantino V. Exploring Chemical Diversity of Phorbas Sponges as a Source of Novel Lead Compounds in Drug Discovery. Mar Drugs 2021; 19:667. [PMID: 34940666 PMCID: PMC8708981 DOI: 10.3390/md19120667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 11/23/2021] [Accepted: 11/23/2021] [Indexed: 12/30/2022] Open
Abstract
Porifera, commonly referred to as marine sponges, are acknowledged as major producers of marine natural products (MNPs). Sponges of the genus Phorbas have attracted much attention over the years. They are widespread in all continents, and several structurally unique compounds have been identified from this species. Terpenes, mainly sesterterpenoids, are the major secondary metabolites isolated from Phorbas species, even though several alkaloids and steroids have also been reported. Many of these compounds have presented interesting biological activities. Particularly, Phorbas sponges have been demonstrated to be a source of cytotoxic metabolites. In addition, MNPs exhibiting cytostatic, antimicrobial, and anti-inflammatory activities have been isolated and structurally characterized. This review provides an overview of almost 130 secondary metabolites from Phorbas sponges and their biological activities, and it covers the literature since the first study published in 1993 until November 2021, including approximately 60 records. The synthetic routes to the most interesting compounds are briefly outlined.
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Affiliation(s)
- Alessia Caso
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano, 49, 80131 Naples, Italy; (A.C.); (G.E.); (R.T.)
| | - Fernanda Barbosa da Silva
- Instituto de Química de Produtos Naturais Walter Mors, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Rio de Janeiro 21941-599, Brazil; (F.B.d.S.); (L.P.A.N.C.); (R.C.C.M.)
| | - Germana Esposito
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano, 49, 80131 Naples, Italy; (A.C.); (G.E.); (R.T.)
| | - Roberta Teta
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano, 49, 80131 Naples, Italy; (A.C.); (G.E.); (R.T.)
| | - Gerardo Della Sala
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80125 Naples, Italy;
| | - Laura P. A. Nunes Cavalcanti
- Instituto de Química de Produtos Naturais Walter Mors, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Rio de Janeiro 21941-599, Brazil; (F.B.d.S.); (L.P.A.N.C.); (R.C.C.M.)
| | - Alessandra Leda Valverde
- Departamento de Química Orgânica, Instituto de Química, Universidade Federal Fluminense, Outeiro de São João Batista s/n, Niterói, Rio de Janeiro 24020-141, Brazil;
| | - Roberto Carlos C. Martins
- Instituto de Química de Produtos Naturais Walter Mors, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Rio de Janeiro 21941-599, Brazil; (F.B.d.S.); (L.P.A.N.C.); (R.C.C.M.)
| | - Valeria Costantino
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano, 49, 80131 Naples, Italy; (A.C.); (G.E.); (R.T.)
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Horchani M, Della Sala G, Caso A, D’Aria F, Esposito G, Laurenzana I, Giancola C, Costantino V, Jannet HB, Romdhane A. Molecular Docking and Biophysical Studies for Antiproliferative Assessment of Synthetic Pyrazolo-Pyrimidinones Tethered with Hydrazide-Hydrazones. Int J Mol Sci 2021; 22:2742. [PMID: 33800505 PMCID: PMC7962976 DOI: 10.3390/ijms22052742] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/01/2021] [Accepted: 03/03/2021] [Indexed: 12/22/2022] Open
Abstract
Chemotherapy represents the most applied approach to cancer treatment. Owing to the frequent onset of chemoresistance and tumor relapses, there is an urgent need to discover novel and more effective anticancer drugs. In the search for therapeutic alternatives to treat the cancer disease, a series of hybrid pyrazolo[3,4-d]pyrimidin-4(5H)-ones tethered with hydrazide-hydrazones, 5a-h, was synthesized from condensation reaction of pyrazolopyrimidinone-hydrazide 4 with a series of arylaldehydes in ethanol, in acid catalysis. In vitro assessment of antiproliferative effects against MCF-7 breast cancer cells, unveiled that 5a, 5e, 5g, and 5h were the most effective compounds of the series and exerted their cytotoxic activity through apoptosis induction and G0/G1 phase cell-cycle arrest. To explore their mechanism at a molecular level, 5a, 5e, 5g, and 5h were evaluated for their binding interactions with two well-known anticancer targets, namely the epidermal growth factor receptor (EGFR) and the G-quadruplex DNA structures. Molecular docking simulations highlighted high binding affinity of 5a, 5e, 5g, and 5h towards EGFR. Circular dichroism (CD) experiments suggested 5a as a stabilizer agent of the G-quadruplex from the Kirsten ras (KRAS) oncogene promoter. In the light of these findings, we propose the pyrazolo-pyrimidinone scaffold bearing a hydrazide-hydrazone moiety as a lead skeleton for designing novel anticancer compounds.
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Affiliation(s)
- Mabrouk Horchani
- Laboratory of Heterocyclic Chemistry, Natural Products and Reactivity, Medicinal Chemistry and Natural Products (LR11ES39), Faculty of Sciences of Monastir, University of Monastir, 5000 Monastir, Tunisia; (M.H.); (A.R.)
| | - Gerardo Della Sala
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80125 Naples, Italy;
- Laboratory of Pre-Clinical and Translational Research, IRCCS-CROB, Referral Cancer Center of Basilicata, 85028 Rionero in Vulture, Italy;
| | - Alessia Caso
- The Blue Chemistry Lab, Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (A.C.); (G.E.)
| | - Federica D’Aria
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (F.D.); (C.G.)
| | - Germana Esposito
- The Blue Chemistry Lab, Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (A.C.); (G.E.)
| | - Ilaria Laurenzana
- Laboratory of Pre-Clinical and Translational Research, IRCCS-CROB, Referral Cancer Center of Basilicata, 85028 Rionero in Vulture, Italy;
| | - Concetta Giancola
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (F.D.); (C.G.)
| | - Valeria Costantino
- The Blue Chemistry Lab, Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (A.C.); (G.E.)
| | - Hichem Ben Jannet
- Laboratory of Heterocyclic Chemistry, Natural Products and Reactivity, Medicinal Chemistry and Natural Products (LR11ES39), Faculty of Sciences of Monastir, University of Monastir, 5000 Monastir, Tunisia; (M.H.); (A.R.)
| | - Anis Romdhane
- Laboratory of Heterocyclic Chemistry, Natural Products and Reactivity, Medicinal Chemistry and Natural Products (LR11ES39), Faculty of Sciences of Monastir, University of Monastir, 5000 Monastir, Tunisia; (M.H.); (A.R.)
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Della Sala G, Mangoni A, Costantino V, Teta R. Identification of the Biosynthetic Gene Cluster of Thermoactinoamides and Discovery of New Congeners by Integrated Genome Mining and MS-Based Molecular Networking. Front Chem 2020; 8:397. [PMID: 32528927 PMCID: PMC7253712 DOI: 10.3389/fchem.2020.00397] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 04/15/2020] [Indexed: 11/21/2022] Open
Abstract
The putative non-ribosomal peptide synthetase (NRPS) gene cluster encoding the biosynthesis of the bioactive cyclohexapeptide thermoactinoamide A (1) was identified in Thermoactinomyces vulgaris DSM 43016. Based on an in silico prediction, the biosynthetic operon was shown to contain two trimodular NRPSs, designated as ThdA and ThdB, respectively. Chemical analysis of a bacterial crude extract showed the presence of thermoactinoamide A (1), thereby supporting this biosynthetic hypothesis. Notably, integrating genome mining with a LC-HRMS/MS molecular networking-based investigation of the microbial metabolome, we succeeded in the identification of 10 structural variants (2–11) of thermoactinoamide A (1), five of them being new compounds (thermoactinoamides G-K, 7–11). As only one thermoactinoamide operon was found in T. vulgaris, it can be assumed that all thermoactinoamide congeners are assembled by the same multimodular NRPS system. In light of these findings, we suggest that the thermoactinoamide synthetase is able to create chemical diversity, combining the relaxed substrate selectivity of some adenylation domains with the iterative and/or alternative use of specific modules. In the frame of our screening program to discover antitumor natural products, thermoactinoamide A (1) was shown to exert a moderate growth-inhibitory effect in BxPC-3 cancer cells in the low micromolar range, while being inactive in PANC-1 and 3AB-OS solid tumor models.
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Affiliation(s)
- Gerardo Della Sala
- Laboratory of Pre-clinical and Translational Research, IRCCS-CROB, Referral Cancer Center of Basilicata, Rionero in Vulture, Italy
| | - Alfonso Mangoni
- Dipartimento di Farmacia, Università degli Studi di Naples Federico II, Naples, Italy
| | - Valeria Costantino
- Dipartimento di Farmacia, Università degli Studi di Naples Federico II, Naples, Italy
| | - Roberta Teta
- Dipartimento di Farmacia, Università degli Studi di Naples Federico II, Naples, Italy
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Gutleben J, Koehorst JJ, McPherson K, Pomponi S, Wijffels RH, Smidt H, Sipkema D. Diversity of tryptophan halogenases in sponges of the genus Aplysina. FEMS Microbiol Ecol 2019; 95:fiz108. [PMID: 31276591 PMCID: PMC6644159 DOI: 10.1093/femsec/fiz108] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 07/04/2019] [Indexed: 12/21/2022] Open
Abstract
Marine sponges are a prolific source of novel enzymes with promising biotechnological potential. Especially halogenases, which are key enzymes in the biosynthesis of brominated and chlorinated secondary metabolites, possess interesting properties towards the production of pharmaceuticals that are often halogenated. In this study we used a polymerase chain reaction (PCR)-based screening to simultaneously examine and compare the richness and diversity of putative tryptophan halogenase protein sequences and bacterial community structures of six Aplysina species from the Mediterranean and Caribbean seas. At the phylum level, bacterial community composition was similar amongst all investigated species and predominated by Actinobacteria, Chloroflexi, Cyanobacteria, Gemmatimonadetes, and Proteobacteria. We detected four phylogenetically diverse clades of putative tryptophan halogenase protein sequences, which were only distantly related to previously reported halogenases. The Mediterranean species Aplysina aerophoba harbored unique halogenase sequences, of which the most predominant was related to a sponge-associated Psychrobacter-derived sequence. In contrast, the Caribbean species shared numerous novel halogenase sequence variants and exhibited a highly similar bacterial community composition at the operational taxonomic unit (OTU) level. Correlations of relative abundances of halogenases with those of bacterial taxa suggest that prominent sponge symbiotic bacteria, including Chloroflexi and Actinobacteria, are putative producers of the detected enzymes and may thus contribute to the chemical defense of their host.
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Affiliation(s)
- Johanna Gutleben
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Jasper J Koehorst
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Kyle McPherson
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Shirley Pomponi
- Bioprocess Engineering, AlgaePARC, Wageningen University & Research, 6700 AA, Wageningen, The Netherlands
- Florida Atlantic University – Harbor Branch, 5600 U.S. 1, Fort Pierce, FL 34946, the United States
| | - René H Wijffels
- Bioprocess Engineering, AlgaePARC, Wageningen University & Research, 6700 AA, Wageningen, The Netherlands
- Faculty of Biosciences and Aquaculture, Nord University, 8026 Bodø, Norway
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
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Belikov S, Belkova N, Butina T, Chernogor L, Martynova-Van Kley A, Nalian A, Rorex C, Khanaev I, Maikova O, Feranchuk S. Diversity and shifts of the bacterial community associated with Baikal sponge mass mortalities. PLoS One 2019; 14:e0213926. [PMID: 30921366 PMCID: PMC6438488 DOI: 10.1371/journal.pone.0213926] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 03/04/2019] [Indexed: 01/01/2023] Open
Abstract
The disease of freshwater sponges was first discovered in 2011, when pink samples were found in the Central Basin of Lake Baikal. Subsequently, the visible signs of the disease have changed, and now sponges appear with various symptoms of damage to the body, such as discoloration, tissue necrosis, the formation of brown patches and dirty-purple biofilms on some branches. These signs of the disease are accompanied by the mass death of sponges. We identified differences in microbiomes by sequencing 16S rRNA genes and found changes in the consortium of microorganisms of freshwater Baikal sponges. We found that the observed imbalance in the studied microbial communities of diseased sponges is caused by several different conditionally pathogenic microorganisms that increase their negative effect by acting together and in concert, which leads to the death of photosynthetic microalgae and sponges. Sponges are an important component of coastal communities, and the massive loss of sponges can obviously affect the structure of benthic communities and the purity of water.
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Affiliation(s)
- Sergei Belikov
- Laboratory of Analytical Bioorganic Chemistry, Limnological Institute of Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
- * E-mail:
| | - Natalia Belkova
- Laboratory of Analytical Bioorganic Chemistry, Limnological Institute of Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Tatiana Butina
- Laboratory of Analytical Bioorganic Chemistry, Limnological Institute of Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Lubov Chernogor
- Laboratory of Analytical Bioorganic Chemistry, Limnological Institute of Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | | | - Armen Nalian
- Department of Biology, Stephen F. Austin State University, Nacogdoches, Texas, United States of America
| | - Colin Rorex
- Department of Biology, Stephen F. Austin State University, Nacogdoches, Texas, United States of America
| | - Igor Khanaev
- Laboratory of Analytical Bioorganic Chemistry, Limnological Institute of Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Olga Maikova
- Laboratory of Analytical Bioorganic Chemistry, Limnological Institute of Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Sergey Feranchuk
- Laboratory of Analytical Bioorganic Chemistry, Limnological Institute of Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
- Department of Informatics, National Research Technical University, Irkutsk, Russia
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Wei Z, Liu X, Zhou Z, Xu J. De novo transcriptomic analysis of gonad of Strongylocentrotus nudus and gene discovery for biosynthesis of polyunsaturated fatty acids. Genes Genomics 2019; 41:583-597. [PMID: 30830682 DOI: 10.1007/s13258-019-00799-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 02/19/2019] [Indexed: 11/26/2022]
Abstract
BACKGROUND Strongylocentrotus nudus is an important cultured sea urchin species in north China, because its gonad is rich in unsaturated fatty acids, particularly long polyunsaturated fatty acids (LC-PUFAs). These PUFAs play pleiotropic and crucial roles in a wide range of biological process. OBJECTIVE However, the genes contributing to biosynthesis PUFAs have not been elucidated yet, and the molecular mechanism relative to the difference in PUFA composition between male and female gonad as been revealed but the corresponding has not been understood. METHODS In this paper, solexa sequencing based transcriptomic approach was used to identify and characterize the key genes relative to PUFA synthesis and further conducted different expressed genes between male and female gonad. RESULTS A total of 130,124 transcripts and 189330 unigenes were de novo assembled from 64.32 Gb data. Next, these unigenes were subjected to functional annotation by mapping to six public databases, and this process revealed a lot of genes involving in lipid metabolism. In addition, three types of fatty acids front-end desaturase and three species of very long fatty acids elongase were identified and the pathway for PUFA biosynthesis was hypothesized. Last, comparative analysis revealed the higher expression level of Δ5 desaturase, Δ6 desaturase, ELOVL-4, -6 and -7 in male gonad compared with female. CONCLUSION This results could plausible explain the differ in composition of PUFAs between male and female gonad of sea urchin.
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Affiliation(s)
- Zhenlin Wei
- Biological Sciences Department, Dezhou University, Dezhou, 253023, Shandong, China.
| | - Xiaolin Liu
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zunchun Zhou
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, 116023, Liaoning, China
| | - Junxiao Xu
- Biological Sciences Department, Dezhou University, Dezhou, 253023, Shandong, China
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BluePharmTrain: Biology and Biotechnology of Marine Sponges. GRAND CHALLENGES IN MARINE BIOTECHNOLOGY 2018. [DOI: 10.1007/978-3-319-69075-9_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Grand Challenges in Marine Biotechnology: Overview of Recent EU-Funded Projects. GRAND CHALLENGES IN MARINE BIOTECHNOLOGY 2018. [DOI: 10.1007/978-3-319-69075-9_11] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Discovery Strategies of Bioactive Compounds Synthesized by Nonribosomal Peptide Synthetases and Type-I Polyketide Synthases Derived from Marine Microbiomes. Mar Drugs 2016; 14:md14040080. [PMID: 27092515 PMCID: PMC4849084 DOI: 10.3390/md14040080] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 04/01/2016] [Accepted: 04/08/2016] [Indexed: 11/17/2022] Open
Abstract
Considering that 70% of our planet's surface is covered by oceans, it is likely that undiscovered biodiversity is still enormous. A large portion of marine biodiversity consists of microbiomes. They are very attractive targets of bioprospecting because they are able to produce a vast repertoire of secondary metabolites in order to adapt in diverse environments. In many cases secondary metabolites of pharmaceutical and biotechnological interest such as nonribosomal peptides (NRPs) and polyketides (PKs) are synthesized by multimodular enzymes named nonribosomal peptide synthetases (NRPSes) and type-I polyketide synthases (PKSes-I), respectively. Novel findings regarding the mechanisms underlying NRPS and PKS evolution demonstrate how microorganisms could leverage their metabolic potential. Moreover, these findings could facilitate synthetic biology approaches leading to novel bioactive compounds. Ongoing advances in bioinformatics and next-generation sequencing (NGS) technologies are driving the discovery of NRPs and PKs derived from marine microbiomes mainly through two strategies: genome-mining and metagenomics. Microbial genomes are now sequenced at an unprecedented rate and this vast quantity of biological information can be analyzed through genome mining in order to identify gene clusters encoding NRPSes and PKSes of interest. On the other hand, metagenomics is a fast-growing research field which directly studies microbial genomes and their products present in marine environments using culture-independent approaches. The aim of this review is to examine recent developments regarding discovery strategies of bioactive compounds synthesized by NRPS and type-I PKS derived from marine microbiomes and to highlight the vast diversity of NRPSes and PKSes present in marine environments by giving examples of recently discovered bioactive compounds.
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13
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Norris MD, Perkins MV. Structural diversity and chemical synthesis of peroxide and peroxide-derived polyketide metabolites from marine sponges. Nat Prod Rep 2016; 33:861-80. [DOI: 10.1039/c5np00142k] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The structural elucidation, chemical synthesis and therapeutic potential of peroxide and peroxide-derived sponge metabolites, with special focus on their intriguing structural similarities and differences from a biogenetic perspective, are reviewed.
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Affiliation(s)
- Matthew D. Norris
- School of Chemical and Physical Sciences
- Flinders University
- Adelaide
- Australia
| | - Michael V. Perkins
- School of Chemical and Physical Sciences
- Flinders University
- Adelaide
- Australia
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14
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Teta R, Sala GD, Glukhov E, Gerwick L, Gerwick WH, Mangoni A, Costantino V. Combined LC-MS/MS and Molecular Networking Approach Reveals New Cyanotoxins from the 2014 Cyanobacterial Bloom in Green Lake, Seattle. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:14301-10. [PMID: 26567695 PMCID: PMC4851459 DOI: 10.1021/acs.est.5b04415] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Cyanotoxins obtained from a freshwater cyanobacterial collection at Green Lake, Seattle during a cyanobacterial harmful algal bloom in the summer of 2014 were studied using a new approach based on molecular networking analysis of liquid chromatography tandem mass spectrometry (LC-MS/MS) data. This MS networking approach is particularly well-suited for the detection of new cyanotoxin variants and resulted in the discovery of three new cyclic peptides, namely microcystin-MhtyR (6), which comprised about half of the total microcystin content in the bloom, and ferintoic acids C (12) and D (13). Structure elucidation of 6 was aided by a new microscale methylation procedure. Metagenomic analysis of the bloom using the 16S-ITS rRNA region identified Microcystis aeruginosa as the predominant cyanobacterium in the sample. Fragments of the putative biosynthetic genes for the new cyanotoxins were also identified, and their sequences correlated to the structure of the isolated cyanotoxins.
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Affiliation(s)
- Roberta Teta
- The NeaNat Group (www.neanat.unina.it), Dipartimento di Farmacia, Universita degli Studi di Napoli Federico II, via D. Montesano 49, 80131 Napoli, Italy
| | - Gerardo Della Sala
- The NeaNat Group (www.neanat.unina.it), Dipartimento di Farmacia, Universita degli Studi di Napoli Federico II, via D. Montesano 49, 80131 Napoli, Italy
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, 9500 Gilman Drive, MC 0212, La Jolla, CA 92093-0212, USA
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, 9500 Gilman Drive, MC 0212, La Jolla, CA 92093-0212, USA
| | - William H. Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, 9500 Gilman Drive, MC 0212, La Jolla, CA 92093-0212, USA
| | - Alfonso Mangoni
- The NeaNat Group (www.neanat.unina.it), Dipartimento di Farmacia, Universita degli Studi di Napoli Federico II, via D. Montesano 49, 80131 Napoli, Italy
| | - Valeria Costantino
- The NeaNat Group (www.neanat.unina.it), Dipartimento di Farmacia, Universita degli Studi di Napoli Federico II, via D. Montesano 49, 80131 Napoli, Italy
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15
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Trindade M, van Zyl LJ, Navarro-Fernández J, Abd Elrazak A. Targeted metagenomics as a tool to tap into marine natural product diversity for the discovery and production of drug candidates. Front Microbiol 2015; 6:890. [PMID: 26379658 PMCID: PMC4552006 DOI: 10.3389/fmicb.2015.00890] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 08/17/2015] [Indexed: 11/13/2022] Open
Abstract
Microbial natural products exhibit immense structural diversity and complexity and have captured the attention of researchers for several decades. They have been explored for a wide spectrum of applications, most noteworthy being their prominent role in medicine, and their versatility expands to application as drugs for many diseases. Accessing unexplored environments harboring unique microorganisms is expected to yield novel bioactive metabolites with distinguishing functionalities, which can be supplied to the starved pharmaceutical market. For this purpose the oceans have turned out to be an attractive and productive field. Owing to the enormous biodiversity of marine microorganisms, as well as the growing evidence that many metabolites previously isolated from marine invertebrates and algae are actually produced by their associated bacteria, the interest in marine microorganisms has intensified. Since the majority of the microorganisms are uncultured, metagenomic tools are required to exploit the untapped biochemistry. However, after years of employing metagenomics for marine drug discovery, new drugs are vastly under-represented. While a plethora of natural product biosynthetic genes and clusters are reported, only a minor number of potential therapeutic compounds have resulted through functional metagenomic screening. This review explores specific obstacles that have led to the low success rate. In addition to the typical problems encountered with traditional functional metagenomic-based screens for novel biocatalysts, there are enormous limitations which are particular to drug-like metabolites. We also present how targeted and function-guided strategies, employing modern, and multi-disciplinary approaches have yielded some of the most exciting discoveries attributed to uncultured marine bacteria. These discoveries set the stage for progressing the production of drug candidates from uncultured bacteria for pre-clinical and clinical development.
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Affiliation(s)
- Marla Trindade
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, BellvilleSouth Africa
| | - Leonardo Joaquim van Zyl
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, BellvilleSouth Africa
| | - José Navarro-Fernández
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, BellvilleSouth Africa
- Centro Regional de Hemodonación, Servicio de Hematología y Oncología Médica, Universidad de Murcia, IMIB-Arrixaca, MurciaSpain
| | - Ahmed Abd Elrazak
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, BellvilleSouth Africa
- Botany Department, Faculty of Science, Mansoura University, MansouraEgypt
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16
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Esposito G, Teta R, Miceli R, Ceccarelli LS, Della Sala G, Camerlingo R, Irollo E, Mangoni A, Pirozzi G, Costantino V. Isolation and assessment of the in vitro anti-tumor activity of smenothiazole A and B, chlorinated thiazole-containing peptide/polyketides from the Caribbean sponge, Smenospongia aurea. Mar Drugs 2015; 13:444-59. [PMID: 25603342 PMCID: PMC4306946 DOI: 10.3390/md13010444] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 01/04/2015] [Indexed: 01/17/2023] Open
Abstract
The study of the secondary metabolites contained in the organic extract of Caribbean sponge Smenospongia aurea led to the isolation of smenothiazole A (3) and B (4), hybrid peptide/polyketide compounds. Assays performed using four solid tumor cell lines showed that smenothiazoles exert a potent cytotoxic activity at nanomolar levels, with selectivity over ovarian cancer cells and a pro-apoptotic mechanism.
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Affiliation(s)
- Germana Esposito
- The NeaNat Group, Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy.
| | - Roberta Teta
- The NeaNat Group, Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy.
| | - Roberta Miceli
- Department of Experimental Oncology, Istituto Nazionale Tumori Fondazione "G. Pascale", Via M. Semmola, 80131 Napoli, Italy.
| | - Luca S Ceccarelli
- Department of Experimental Oncology, Istituto Nazionale Tumori Fondazione "G. Pascale", Via M. Semmola, 80131 Napoli, Italy.
| | - Gerardo Della Sala
- The NeaNat Group, Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy.
| | - Rosa Camerlingo
- Department of Experimental Oncology, Istituto Nazionale Tumori Fondazione "G. Pascale", Via M. Semmola, 80131 Napoli, Italy.
| | - Elena Irollo
- Department of Experimental Oncology, Istituto Nazionale Tumori Fondazione "G. Pascale", Via M. Semmola, 80131 Napoli, Italy.
| | - Alfonso Mangoni
- The NeaNat Group, Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy.
| | - Giuseppe Pirozzi
- Department of Experimental Oncology, Istituto Nazionale Tumori Fondazione "G. Pascale", Via M. Semmola, 80131 Napoli, Italy.
| | - Valeria Costantino
- The NeaNat Group, Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy.
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17
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Flórez LV, Biedermann PHW, Engl T, Kaltenpoth M. Defensive symbioses of animals with prokaryotic and eukaryotic microorganisms. Nat Prod Rep 2015; 32:904-36. [DOI: 10.1039/c5np00010f] [Citation(s) in RCA: 233] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Many organisms team up with symbiotic microbes for defense against predators, parasites, parasitoids, or pathogens. Here we review the known defensive symbioses in animals and the microbial secondary metabolites responsible for providing protection to the host.
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Affiliation(s)
- Laura V. Flórez
- Max Planck Institute for Chemical Ecology
- Insect Symbiosis Research Group
- 07745 Jena
- Germany
| | - Peter H. W. Biedermann
- Max Planck Institute for Chemical Ecology
- Insect Symbiosis Research Group
- 07745 Jena
- Germany
| | - Tobias Engl
- Max Planck Institute for Chemical Ecology
- Insect Symbiosis Research Group
- 07745 Jena
- Germany
| | - Martin Kaltenpoth
- Max Planck Institute for Chemical Ecology
- Insect Symbiosis Research Group
- 07745 Jena
- Germany
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Polyketide synthases in the microbiome of the marine sponge Plakortis halichondrioides: a metagenomic update. Mar Drugs 2014; 12:5425-40. [PMID: 25405856 PMCID: PMC4245539 DOI: 10.3390/md12115425] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 11/04/2014] [Accepted: 11/06/2014] [Indexed: 01/01/2023] Open
Abstract
Sponge-associated microorganisms are able to assemble the complex machinery for the production of secondary metabolites such as polyketides, the most important class of marine natural products from a drug discovery perspective. A comprehensive overview of polyketide biosynthetic genes of the sponge Plakortis halichondrioides and its symbionts was obtained in the present study by massively parallel 454 pyrosequencing of complex and heterogeneous PCR (Polymerase Chain Reaction) products amplified from the metagenomic DNA of a specimen of P. halichondrioides collected in the Caribbean Sea. This was accompanied by a survey of the bacterial diversity within the sponge. In line with previous studies, sequences belonging to supA and swfA, two widespread sponge-specific groups of polyketide synthase (PKS) genes were dominant. While they have been previously reported as belonging to Poribacteria (a novel bacterial phylum found exclusively in sponges), re-examination of current genomic sequencing data showed supA and swfA not to be present in the poribacterial genome. Several non-supA, non-swfA type-I PKS fragments were also identified. A significant portion of these fragments resembled type-I PKSs from protists, suggesting that bacteria may not be the only source of polyketides from P. halichondrioides, and that protistan PKSs should receive further investigation as a source of novel polyketides.
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19
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Fuerst JA. Diversity and biotechnological potential of microorganisms associated with marine sponges. Appl Microbiol Biotechnol 2014; 98:7331-47. [DOI: 10.1007/s00253-014-5861-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 05/21/2014] [Accepted: 05/21/2014] [Indexed: 12/13/2022]
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