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Gao Y, Zhong Z, Zhang D, Zhang J, Li YX. Exploring the roles of ribosomal peptides in prokaryote-phage interactions through deep learning-enabled metagenome mining. MICROBIOME 2024; 12:94. [PMID: 38790030 PMCID: PMC11118758 DOI: 10.1186/s40168-024-01807-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 04/04/2024] [Indexed: 05/26/2024]
Abstract
BACKGROUND Microbial secondary metabolites play a crucial role in the intricate interactions within the natural environment. Among these metabolites, ribosomally synthesized and post-translationally modified peptides (RiPPs) are becoming a promising source of therapeutic agents due to their structural diversity and functional versatility. However, their biosynthetic capacity and ecological functions remain largely underexplored. RESULTS Here, we aim to explore the biosynthetic profile of RiPPs and their potential roles in the interactions between microbes and viruses in the ocean, which encompasses a vast diversity of unique biomes that are rich in interactions and remains chemically underexplored. We first developed TrRiPP to identify RiPPs from ocean metagenomes, a deep learning method that detects RiPP precursors in a hallmark gene-independent manner to overcome the limitations of classic methods in processing highly fragmented metagenomic data. Applying this method to metagenomes from the global ocean microbiome, we uncover a diverse array of previously uncharacterized putative RiPP families with great novelty and diversity. Through correlation analysis based on metatranscriptomic data, we observed a high prevalence of antiphage defense-related and phage-related protein families that were co-expressed with RiPP families. Based on this putative association between RiPPs and phage infection, we constructed an Ocean Virus Database (OVD) and established a RiPP-involving host-phage interaction network through host prediction and co-expression analysis, revealing complex connectivities linking RiPP-encoding prokaryotes, RiPP families, viral protein families, and phages. These findings highlight the potential of RiPP families involved in prokaryote-phage interactions and coevolution, providing insights into their ecological functions in the ocean microbiome. CONCLUSIONS This study provides a systematic investigation of the biosynthetic potential of RiPPs from the ocean microbiome at a global scale, shedding light on the essential insights into the ecological functions of RiPPs in prokaryote-phage interactions through the integration of deep learning approaches, metatranscriptomic data, and host-phage connectivity. This study serves as a valuable example of exploring the ecological functions of bacterial secondary metabolites, particularly their associations with unexplored microbial interactions. Video Abstract.
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Affiliation(s)
- Ying Gao
- CYM305, Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region, 999077, China
| | - Zheng Zhong
- CYM305, Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region, 999077, China
| | - Dengwei Zhang
- CYM305, Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region, 999077, China
| | - Jian Zhang
- CYM305, Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region, 999077, China
| | - Yong-Xin Li
- CYM305, Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region, 999077, China.
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Virgens GS, Oliveira J, Cardoso MIO, Teodoro JA, Amaral DT. BioProtIS: Streamlining protein-ligand interaction pipeline for analysis in genomic and transcriptomic exploration. J Mol Graph Model 2024; 128:108721. [PMID: 38308972 DOI: 10.1016/j.jmgm.2024.108721] [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: 11/07/2023] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/05/2024]
Abstract
The identification of protein-ligand interactions plays a pivotal role in elucidating biological processes and discovering potential bioproducts. Harnessing the capabilities of computational methods in drug discovery, we introduce an innovative Inverted Virtual Screening (IVS) pipeline. This pipeline Integrated molecular dynamics and docking analyses to ensure that protein structures are not only energetically favorable but also representative of stable conformations. The primary objective of this pipeline is to automate and streamline the analysis of protein-ligand interactions at both genomic and transcriptomic scales. In the contemporary post-genomic era, high-throughput computational screening for bioproducts, biological systems, and therapeutic drugs has become a cornerstone practice. This approach offers the promise of cost-effectiveness, time efficiency, and optimization of laboratory work. Nevertheless, a notable deficiency persists in the availability of efficient pipelines capable of automating the virtual screening process, seamlessly integrating input and output, and leveraging the full potential of open-source tools. To bridge this critical gap, we have developed a versatile pipeline known as BioProtIS. This tool seamlessly integrates a suite of state-of-the-art tools, including Modeller, AlphaFold, Gromacs, FPOCKET, and AutoDock Vina, thus facilitating the streamlined docking of ligands with an expansive repertoire of proteins sourced from genomes and transcriptomes, and substrates. To assess the pipeline's performance, we employed the transcriptomes of Cereus jamacaru (a cactus species) and Aspisoma lineatum (firefly), along with the genome of Homo sapiens. This integration not only improves the accuracy of ligand-protein interactions by minimizing replicability deviations but also optimizes the discovery process by enabling the simultaneous evaluation of multiple substrates. Furthermore, our pipeline accommodates distinct testing scenarios, such as blind docking or site-specific targeting, which are invaluable in applications ranging from drug repositioning to the exploration of new allosteric binding sites and toxicity assessments. BioProtIS has been designed with modularity at its core. This inherent flexibility empowers users to make custom modifications directly within the source code, tailoring the pipeline to their specific research needs. Moreover, it lays the foundation for seamless integration of diverse docking algorithms in future iterations, promising ongoing advancements in the field of computational biology. This pipeline is available for free distribution and can be download at: https://github.com/BBMDO/BioProtIS.
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Affiliation(s)
- Graziela Sória Virgens
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, São Paulo, Brazil
| | - Júlia Oliveira
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, São Paulo, Brazil
| | | | - João Alfredo Teodoro
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, São Paulo, Brazil
| | - Danilo T Amaral
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, São Paulo, Brazil.
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Sirimangkalakitti N, Lin J, Harada K, Setiawan A, Arisawa M, Arai M. Chemical Constituents and Anticancer Activities of Marine-Derived Fungus Trichoderma lixii. Molecules 2024; 29:2048. [PMID: 38731537 PMCID: PMC11085134 DOI: 10.3390/molecules29092048] [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: 03/02/2024] [Revised: 04/17/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024] Open
Abstract
The fungal genus Trichoderma is a rich source of structurally diverse secondary metabolites with remarkable pharmaceutical properties. The chemical constituents and anticancer activities of the marine-derived fungus Trichoderma lixii have never been investigated. In this study, a bioactivity-guided investigation led to the isolation of eleven compounds, including trichodermamide A (1), trichodermamide B (2), aspergillazine A (3), DC1149B (4), ergosterol peroxide (5), cerebrosides D/C (6/7), 5-hydroxy-2,3-dimethyl-7-methoxychromone (8), nafuredin A (9), and harzianumols E/F (10/11). Their structures were identified by using various spectroscopic techniques and compared to those in the literature. Notably, compounds 2 and 5-11 were reported for the first time from this species. Evaluation of the anticancer activities of all isolated compounds was carried out. Compounds 2, 4, and 9 were the most active antiproliferative compounds against three cancer cell lines (human myeloma KMS-11, colorectal HT-29, and pancreas PANC-1). Intriguingly, compound 4 exhibited anti-austerity activity with an IC50 of 22.43 μM against PANC-1 cancer cells under glucose starvation conditions, while compound 2 did not.
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Affiliation(s)
- Natchanun Sirimangkalakitti
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita 565-0871, Osaka, Japan; (N.S.); (J.L.); (K.H.)
| | - Jianyu Lin
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita 565-0871, Osaka, Japan; (N.S.); (J.L.); (K.H.)
| | - Kazuo Harada
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita 565-0871, Osaka, Japan; (N.S.); (J.L.); (K.H.)
| | - Andi Setiawan
- Department of Chemistry, Faculty of Science, Lampung University, Jl. Prof. Dr. Sumantri Brodjonegoro No. 1, Bandar Lampung 35145, Lampung, Indonesia;
| | - Mitsuhiro Arisawa
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita 565-0871, Osaka, Japan; (N.S.); (J.L.); (K.H.)
| | - Masayoshi Arai
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita 565-0871, Osaka, Japan; (N.S.); (J.L.); (K.H.)
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Vieira H, Lestre GM, Solstad RG, Cabral AE, Botelho A, Helbig C, Coppola D, de Pascale D, Robbens J, Raes K, Lian K, Tsirtsidou K, Leal MC, Scheers N, Calado R, Corticeiro S, Rasche S, Altintzoglou T, Zou Y, Lillebø AI. Current and Expected Trends for the Marine Chitin/Chitosan and Collagen Value Chains. Mar Drugs 2023; 21:605. [PMID: 38132926 PMCID: PMC10744996 DOI: 10.3390/md21120605] [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: 10/25/2023] [Revised: 11/11/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023] Open
Abstract
Chitin/chitosan and collagen are two of the most important bioactive compounds, with applications in the pharmaceutical, veterinary, nutraceutical, cosmetic, biomaterials, and other industries. When extracted from non-edible parts of fish and shellfish, by-catches, and invasive species, their use contributes to a more sustainable and circular economy. The present article reviews the scientific knowledge and publication trends along the marine chitin/chitosan and collagen value chains and assesses how researchers, industry players, and end-users can bridge the gap between scientific understanding and industrial applications. Overall, research on chitin/chitosan remains focused on the compound itself rather than its market applications. Still, chitin/chitosan use is expected to increase in food and biomedical applications, while that of collagen is expected to increase in biomedical, cosmetic, pharmaceutical, and nutritional applications. Sustainable practices, such as the reuse of waste materials, contribute to strengthen both value chains; the identified weaknesses include the lack of studies considering market trends, social sustainability, and profitability, as well as insufficient examination of intellectual property rights. Government regulations, market demand, consumer preferences, technological advancements, environmental challenges, and legal frameworks play significant roles in shaping both value chains. Addressing these factors is crucial for seizing opportunities, fostering sustainability, complying with regulations, and maintaining competitiveness in these constantly evolving value chains.
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Affiliation(s)
- Helena Vieira
- CESAM—Centre for Environmental and Marine Studies, Department of Environment and Planning, Campus Universitário de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal; (H.V.); (G.M.L.); (S.C.)
| | - Gonçalo Moura Lestre
- CESAM—Centre for Environmental and Marine Studies, Department of Environment and Planning, Campus Universitário de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal; (H.V.); (G.M.L.); (S.C.)
| | - Runar Gjerp Solstad
- Nofima Norwegian Institute of Food Fisheries and Aquaculture Research, Muninbakken 9-13, 9019 Tromsø, Norway; (R.G.S.); (K.L.); (T.A.)
| | - Ana Elisa Cabral
- ECOMARE, CESAM—Centre for Environmental and Marine Studies, Department of Biology, Santiago University Campus, University of Aveiro, 3810-193 Aveiro, Portugal; (A.E.C.); (M.C.L.); (R.C.)
| | - Anabela Botelho
- GOVCOPP—Research Unit on Governance, Competitiveness and Public Policies, DEGEIT, Campus Universitário de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - Carlos Helbig
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstrasse 6, 52074 Aachen, Germany; (C.H.); (S.R.)
| | - Daniela Coppola
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio Ferdinando Acton 55, 80133 Napoli, Italy; (D.C.); (D.d.P.)
| | - Donatella de Pascale
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio Ferdinando Acton 55, 80133 Napoli, Italy; (D.C.); (D.d.P.)
| | - Johan Robbens
- Flanders Research Institute for Agriculture, Fisheries and Food, ILVO, Aquatic Environment and Quality, Jacobsenstraat 1, 8400 Ostend, Belgium; (J.R.); (K.T.)
| | - Katleen Raes
- Research Unit VEG-i-TEC, Department of Food Technology, Safety and Health, Ghent University Campus Kortrijk, Graaf Karel de Goedelaan 5, 8500 Kortrijk, Belgium; (K.R.); (Y.Z.)
| | - Kjersti Lian
- Nofima Norwegian Institute of Food Fisheries and Aquaculture Research, Muninbakken 9-13, 9019 Tromsø, Norway; (R.G.S.); (K.L.); (T.A.)
| | - Kyriaki Tsirtsidou
- Flanders Research Institute for Agriculture, Fisheries and Food, ILVO, Aquatic Environment and Quality, Jacobsenstraat 1, 8400 Ostend, Belgium; (J.R.); (K.T.)
- Research Unit VEG-i-TEC, Department of Food Technology, Safety and Health, Ghent University Campus Kortrijk, Graaf Karel de Goedelaan 5, 8500 Kortrijk, Belgium; (K.R.); (Y.Z.)
| | - Miguel C. Leal
- ECOMARE, CESAM—Centre for Environmental and Marine Studies, Department of Biology, Santiago University Campus, University of Aveiro, 3810-193 Aveiro, Portugal; (A.E.C.); (M.C.L.); (R.C.)
| | - Nathalie Scheers
- Department of Life Sciences, Chalmers University of Technology, 412 96 Göteborg, Sweden;
| | - Ricardo Calado
- ECOMARE, CESAM—Centre for Environmental and Marine Studies, Department of Biology, Santiago University Campus, University of Aveiro, 3810-193 Aveiro, Portugal; (A.E.C.); (M.C.L.); (R.C.)
| | - Sofia Corticeiro
- CESAM—Centre for Environmental and Marine Studies, Department of Environment and Planning, Campus Universitário de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal; (H.V.); (G.M.L.); (S.C.)
| | - Stefan Rasche
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstrasse 6, 52074 Aachen, Germany; (C.H.); (S.R.)
| | - Themistoklis Altintzoglou
- Nofima Norwegian Institute of Food Fisheries and Aquaculture Research, Muninbakken 9-13, 9019 Tromsø, Norway; (R.G.S.); (K.L.); (T.A.)
| | - Yang Zou
- Research Unit VEG-i-TEC, Department of Food Technology, Safety and Health, Ghent University Campus Kortrijk, Graaf Karel de Goedelaan 5, 8500 Kortrijk, Belgium; (K.R.); (Y.Z.)
| | - Ana I. Lillebø
- ECOMARE, CESAM—Centre for Environmental and Marine Studies, Department of Biology, Santiago University Campus, University of Aveiro, 3810-193 Aveiro, Portugal; (A.E.C.); (M.C.L.); (R.C.)
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Hérnández-Elizárraga VH, Vega-Tamayo JE, Olguín-López N, Ibarra-Alvarado C, Rojas-Molina A. Transcriptomic and proteomic analyses reveal the first occurrence of diverse toxin groups in Millepora alcicornis. J Proteomics 2023; 288:104984. [PMID: 37536522 DOI: 10.1016/j.jprot.2023.104984] [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: 03/07/2023] [Revised: 06/22/2023] [Accepted: 07/25/2023] [Indexed: 08/05/2023]
Abstract
Millepora alcicornis is a reef-forming cnidarian widely distributed in the Mexican Caribbean. Millepora species or "fire corals" inflict a painful stinging reaction in humans when touched. Even though hundreds of organic and polypeptide toxins have been characterized from sea anemones and jellyfish, there are few reports regarding the diversity of toxins synthesized by fire corals. Here, based on transcriptomic analysis of M. alcicornis, several predicted proteins that show amino acid sequence similarity to toxins were identified, including neurotoxins, metalloproteases, hemostasis-impairing toxins, serin proteases, cysteine-rich venom proteins, phospholipases, complement system-impairing toxins, phosphodiesterases, pore-forming toxins, and L-aminoacid oxidases. The soluble nematocyst proteome of this organism was shown to induce hemolytic, proteolytic, and phospholipase A2 effects by gel zymography. Protein bands or spots on 1D- and 2D-PAGE gels corresponding to zones of hemolytic and enzymatic activities were excised, subjected to in-gel digestion with trypsin, and analyzed by mass spectrometry. These proteins exhibited sequence homology to PLA2s, metalloproteinases, pore-forming toxins, and neurotoxins, such as actitoxins and CrTX-A. The complex array of venom-related transcripts that were identified in M. alcicornis, some of which are first reported in "fire corals", provide novel insight into the structural richness of Cnidarian toxins and their distribution among species. SIGNIFICANCE: Marine organisms are a promising source of bioactive compounds with valuable contributions in diverse fields such as human health, pharmaceuticals, and industrial application. Currently, not much attention has been paid to the study of fire corals, which possess a variety of molecules that exhibit diverse toxic effects and therefore have great pharmaceutical and biotechnological potential. The isolation and identification of novel marine-derived toxins by classical approaches are time-consuming and have low yields. Thus, next-generation strategies, like base-'omics technologies, are essential for the high-throughput characterization of venom compounds such as those synthesized by fire corals. This study moves the field forward because it provides new insights regarding the first occurrence of diverse toxin groups in Millepora alcicornis. The findings presented here will contribute to the current understanding of the mechanisms of action of Millepora toxins. This research also reveals important information related to the potential role of toxins in the defense and capture of prey mechanisms and for designing appropriate treatments for fire coral envenomation. Moreover, due to the lack of information on the taxonomic identification of Millepora, the insights presented here can advise the taxonomic classification of the species of this genus.
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Affiliation(s)
- Víctor Hugo Hérnández-Elizárraga
- Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, C.P. 76010 Querétaro, Qro, Mexico; University of Minnesota Genomics Center, 2231 6th Street SE, Minneapolis, MN 55455, USA
| | | | - Norma Olguín-López
- Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, C.P. 76010 Querétaro, Qro, Mexico; División Química y Energías Renovables, Universidad Tecnológica de San Juan del Río. Av La Palma No 125 Vista Hermosa, 76800 San Juan del Río, Qro, Mexico.
| | - César Ibarra-Alvarado
- Laboratorio de Investigación Química y Farmacológica de Productos Naturales, Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, C.P. 76010 Querétaro, Qro, Mexico
| | - Alejandra Rojas-Molina
- Laboratorio de Investigación Química y Farmacológica de Productos Naturales, Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, C.P. 76010 Querétaro, Qro, Mexico.
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Segaran TC, Azra MN, Lananan F, Wang Y. Microbe, climate change and marine environment: Linking trends and research hotspots. MARINE ENVIRONMENTAL RESEARCH 2023:106015. [PMID: 37291004 DOI: 10.1016/j.marenvres.2023.106015] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/26/2023] [Accepted: 04/30/2023] [Indexed: 06/10/2023]
Abstract
Microbes, or microorganisms, have been the foundation of the biosphere for over 3 billion years and have played an essential role in shaping our planet. The available knowledge on the topic of microbes associated with climate change has the potential to reshape upcoming research trends globally. As climate change impacts the ocean or marine ecosystem, the responses of these "unseen life" will heavily influence the achievement of a sustainable evolutionary environment. The present study aims to identify microbial-related research under changing climate within the marine environment through the mapping of visualized graphs of the available literature. We used scientometric methods to retrieve documents from the Web of Science platform in the Core Collection (WOSCC) database, analyzing a total of 2767 documents based on scientometric indicators. Our findings show that this research area is growing exponentially, with the most influential keywords being "microbial diversity," "bacteria," and "ocean acidification," and the most cited being "microorganism" and "diversity." The identification of influential clusters in the field of marine science provides insight into the hot spots and frontiers of research in this area. Prominent clusters include "coral microbiome," "hypoxic zone," "novel Thermoplasmatota clade," "marine dinoflagellate bloom," and "human health." Analyzing emerging trends and transformative changes in this field can inform the creation of special issues or research topics in selected journals, thus increasing visibility and engagement among the scientific community.
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Affiliation(s)
- Thirukanthan Chandra Segaran
- Climate Change Adaptation Laboratory, Institute of Marine Biotechnology (IMB), Universiti Malaysia Terengganu (UMT), 21030, Kuala Nerus, Terengganu, Malaysia.
| | - Mohamad Nor Azra
- Climate Change Adaptation Laboratory, Institute of Marine Biotechnology (IMB), Universiti Malaysia Terengganu (UMT), 21030, Kuala Nerus, Terengganu, Malaysia; Research Center for Marine and Land Bioindustry, Earth Sciences and Maritime Organization, National Research and Innovation Agency (BRIN), Pemenang, West Nusa Tenggara, 83352, Indonesia.
| | - Fathurrahman Lananan
- East Coast Environmental Research Institute, Universiti Sultan Zainal Abidin, Gong Badak Campus, 21300, Kuala Nerus, Terengganu, Malaysia.
| | - Youji Wang
- International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, China.
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Liu P, Ewald J, Pang Z, Legrand E, Jeon YS, Sangiovanni J, Hacariz O, Zhou G, Head JA, Basu N, Xia J. ExpressAnalyst: A unified platform for RNA-sequencing analysis in non-model species. Nat Commun 2023; 14:2995. [PMID: 37225696 DOI: 10.1038/s41467-023-38785-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 05/16/2023] [Indexed: 05/26/2023] Open
Abstract
The increasing application of RNA sequencing to study non-model species demands easy-to-use and efficient bioinformatics tools to help researchers quickly uncover biological and functional insights. We developed ExpressAnalyst ( www.expressanalyst.ca ), a web-based platform for processing, analyzing, and interpreting RNA-sequencing data from any eukaryotic species. ExpressAnalyst contains a series of modules that cover from processing and annotation of FASTQ files to statistical and functional analysis of count tables or gene lists. All modules are integrated with EcoOmicsDB, an ortholog database that enables comprehensive analysis for species without a reference transcriptome. By coupling ultra-fast read mapping algorithms with high-resolution ortholog databases through a user-friendly web interface, ExpressAnalyst allows researchers to obtain global expression profiles and gene-level insights from raw RNA-sequencing reads within 24 h. Here, we present ExpressAnalyst and demonstrate its utility with a case study of RNA-sequencing data from multiple non-model salamander species, including two that do not have a reference transcriptome.
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Affiliation(s)
- Peng Liu
- Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue, Canada
| | - Jessica Ewald
- Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue, Canada
| | - Zhiqiang Pang
- Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue, Canada
| | - Elena Legrand
- Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue, Canada
| | - Yeon Seon Jeon
- Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue, Canada
| | - Jonathan Sangiovanni
- Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue, Canada
| | - Orcun Hacariz
- Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue, Canada
| | - Guangyan Zhou
- Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue, Canada
| | - Jessica A Head
- Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue, Canada
| | - Niladri Basu
- Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue, Canada
| | - Jianguo Xia
- Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue, Canada.
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Rosic N, Climstein M, Boyle GM, Thanh Nguyen D, Feng Y. Exploring Mycosporine-like Amino Acid UV-Absorbing Natural Products for a New Generation of Environmentally Friendly Sunscreens. Mar Drugs 2023; 21:md21040253. [PMID: 37103392 PMCID: PMC10142268 DOI: 10.3390/md21040253] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/13/2023] [Accepted: 04/17/2023] [Indexed: 04/28/2023] Open
Abstract
Human skin needs additional protection from damaging ultraviolet radiation (UVR: 280-400 nm). Harmful UVR exposure leads to DNA damage and the development of skin cancer. Available sunscreens offer chemical protection from detrimental sun radiation to a certain extent. However, many synthetic sunscreens do not provide sufficient UVR protection due to the lack of photostability of their UV-absorbing active ingredients and/or the lack of ability to prevent the formation of free radicals, inevitably leading to skin damage. In addition, synthetic sunscreens may negatively affect human skin, causing irritation, accelerating skin aging and even resulting in allergic reactions. Beyond the potential negative effect on human health, some synthetic sunscreens have been shown to have a harmful impact on the environment. Consequently, identifying photostable, biodegradable, non-toxic, and renewable natural UV filters is imperative to address human health needs and provide a sustainable environmental solution. In nature, marine, freshwater, and terrestrial organisms are protected from harmful UVR through several important photoprotective mechanisms, including the synthesis of UV-absorbing compounds such as mycosporine-like amino acids (MAAs). Beyond MAAs, several other promising, natural UV-absorbing products could be considered for the future development of natural sunscreens. This review investigates the damaging impact of UVR on human health and the necessity of using sunscreens for UV protection, specifically UV-absorbing natural products that are more environmentally friendly than synthetic UV filters. Critical challenges and limitations related to using MAAs in sunscreen formulations are also evaluated. Furthermore, we explain how the genetic diversity of MAA biosynthetic pathways may be linked to their bioactivities and assess MAAs' potential for applications in human health.
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Affiliation(s)
- Nedeljka Rosic
- Faculty of Health, Southern Cross University, Gold Coast, QLD 4225, Australia
- Marine Ecology Research Centre, Southern Cross University, Lismore, NSW 2480, Australia
| | - Mike Climstein
- Physical Activity, Sport and Exercise Research (PASER) Theme, Faculty of Health, Southern Cross University, Gold Coast, QLD 4225, Australia
- Physical Activity, Lifestyle, Ageing and Wellbeing, Faculty Research Group, Faculty of Health Sciences, The University of Sydney, Sydney, NSW 2000, Australia
| | - Glen M Boyle
- Cancer Research Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD 4000, Australia
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, Brisbane, QLD 4072, Australia
| | - Duy Thanh Nguyen
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
| | - Yunjiang Feng
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
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9
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Ghattavi S, Homaei A. Marine enzymes: Classification and application in various industries. Int J Biol Macromol 2023; 230:123136. [PMID: 36621739 DOI: 10.1016/j.ijbiomac.2023.123136] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 12/23/2022] [Accepted: 01/01/2023] [Indexed: 01/06/2023]
Abstract
Oceans are regarded as a plentiful and sustainable source of biological compounds. Enzymes are a group of marine biomaterials that have recently drawn more attention because they are produced in harsh environmental conditions such as high salinity, extensive pH, a wide temperature range, and high pressure. Hence, marine-derived enzymes are capable of exhibiting remarkable properties due to their unique composition. In this review, we overviewed and discussed characteristics of marine enzymes as well as the sources of marine enzymes, ranging from primitive organisms to vertebrates, and presented the importance, advantages, and challenges of using marine enzymes with a summary of their applications in a variety of industries. Current biotechnological advancements need the study of novel marine enzymes that could be applied in a variety of ways. Resources of marine enzyme can benefit greatly for biotechnological applications duo to their biocompatible, ecofriendly and high effectiveness. It is beneficial to use the unique characteristics offered by marine enzymes to either develop new processes and products or improve existing ones. As a result, marine-derived enzymes have promising potential and are an excellent candidate for a variety of biotechnology applications and a future rise in the use of marine enzymes is to be anticipated.
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Affiliation(s)
- Saba Ghattavi
- Fisheries Department, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas, Iran
| | - Ahmad Homaei
- Department of Marine Biology, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas, Iran.
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10
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LeClair MM, Maw ZA, Grunwald AL, Kelly JR, Haltli BA, Kerr RG, Cartmell C. Discovery of Levesquamide B through Global Natural Product Social Molecular Networking. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27227794. [PMID: 36431895 PMCID: PMC9695545 DOI: 10.3390/molecules27227794] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/07/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022]
Abstract
Levesquamide A is an isothiazolinone-containing anti-tubercular natural product isolated from Streptomyces sp. RKND-216. Through the use of Global Natural Product Social Molecular Networking (GNPS), additional members of the levesquamide family were identified (B-G). Levesquamide B is a glycosylated analogue, isolated and structurally elucidated via spectroscopical techniques along with the putative structures of levesquamide C and D. For masses relating to the additional three levesquamides (E-G), their complete structures remain ambiguous.
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Affiliation(s)
- Mary M. LeClair
- Department of Chemistry, University of Prince Edward Island, 550 University Avenue, Charlottetown, PE C1A 4P3, Canada
| | - Zacharie A. Maw
- Department of Biomedical Sciences, Atlantic Veterinary College, 550 University Avenue, Charlottetown, PE C1A 4P3, Canada
| | - Alyssa L. Grunwald
- Nautilus Biosciences Croda, 550 University Avenue, Charlottetown, PE C1A 4P3, Canada
| | - Joshua R. Kelly
- Nautilus Biosciences Croda, 550 University Avenue, Charlottetown, PE C1A 4P3, Canada
| | - Bradley A. Haltli
- Department of Biomedical Sciences, Atlantic Veterinary College, 550 University Avenue, Charlottetown, PE C1A 4P3, Canada
- Nautilus Biosciences Croda, 550 University Avenue, Charlottetown, PE C1A 4P3, Canada
| | - Russell G. Kerr
- Department of Chemistry, University of Prince Edward Island, 550 University Avenue, Charlottetown, PE C1A 4P3, Canada
- Department of Biomedical Sciences, Atlantic Veterinary College, 550 University Avenue, Charlottetown, PE C1A 4P3, Canada
- Nautilus Biosciences Croda, 550 University Avenue, Charlottetown, PE C1A 4P3, Canada
| | - Christopher Cartmell
- Department of Chemistry, University of Prince Edward Island, 550 University Avenue, Charlottetown, PE C1A 4P3, Canada
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA 02115, USA
- Correspondence: or
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11
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Chen BS, Zhang D, de Souza FZR, Liu L. Recent Advances in the Synthesis of Marine-Derived Alkaloids via Enzymatic Reactions. Mar Drugs 2022; 20:md20060368. [PMID: 35736171 PMCID: PMC9229328 DOI: 10.3390/md20060368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/21/2022] [Accepted: 05/24/2022] [Indexed: 02/04/2023] Open
Abstract
Alkaloids are a large and structurally diverse group of marine-derived natural products. Most marine-derived alkaloids are biologically active and show promising applications in modern (agro)chemical, pharmaceutical, and fine chemical industries. Different approaches have been established to access these marine-derived alkaloids. Among these employed methods, biotechnological approaches, namely, (chemo)enzymatic synthesis, have significant potential for playing a central role in alkaloid production on an industrial scale. In this review, we discuss research progress on marine-derived alkaloid synthesis via enzymatic reactions and note the advantages and disadvantages of their applications for industrial production, as well as green chemistry for marine natural product research.
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Affiliation(s)
- Bi-Shuang Chen
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China; (B.-S.C.); (D.Z.); (L.L.)
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China
| | - Di Zhang
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China; (B.-S.C.); (D.Z.); (L.L.)
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China
| | - Fayene Zeferino Ribeiro de Souza
- Centro Universitário Planalto do Distrito Federal, Universidade Virtual do Estado de São Paulo (UNIPLAN), Campus Bauru 17014-350, Brazil
- Correspondence: ; Tel.: +55-014-32452580
| | - Lan Liu
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China; (B.-S.C.); (D.Z.); (L.L.)
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China
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12
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Xu Y, Du X, Yu X, Jiang Q, Zheng K, Xu J, Wang P. Recent Advances in the Heterologous Expression of Biosynthetic Gene Clusters for Marine Natural Products. Mar Drugs 2022; 20:341. [PMID: 35736144 PMCID: PMC9225448 DOI: 10.3390/md20060341] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/11/2022] [Accepted: 05/20/2022] [Indexed: 12/29/2022] Open
Abstract
Marine natural products (MNPs) are an important source of biologically active metabolites, particularly for therapeutic agent development after terrestrial plants and nonmarine microorganisms. Sequencing technologies have revealed that the number of biosynthetic gene clusters (BGCs) in marine microorganisms and the marine environment is much higher than expected. Unfortunately, the majority of them are silent or only weakly expressed under traditional laboratory culture conditions. Furthermore, the large proportion of marine microorganisms are either uncultivable or cannot be genetically manipulated. Efficient heterologous expression systems can activate cryptic BGCs and increase target compound yield, allowing researchers to explore more unknown MNPs. When developing heterologous expression of MNPs, it is critical to consider heterologous host selection as well as genetic manipulations for BGCs. In this review, we summarize current progress on the heterologous expression of MNPs as a reference for future research.
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Affiliation(s)
- Yushan Xu
- Ocean College, Zhejiang University, Zhoushan 316021, China; (Y.X.); (X.D.); (X.Y.); (Q.J.); (K.Z.); (J.X.)
| | - Xinhua Du
- Ocean College, Zhejiang University, Zhoushan 316021, China; (Y.X.); (X.D.); (X.Y.); (Q.J.); (K.Z.); (J.X.)
| | - Xionghui Yu
- Ocean College, Zhejiang University, Zhoushan 316021, China; (Y.X.); (X.D.); (X.Y.); (Q.J.); (K.Z.); (J.X.)
| | - Qian Jiang
- Ocean College, Zhejiang University, Zhoushan 316021, China; (Y.X.); (X.D.); (X.Y.); (Q.J.); (K.Z.); (J.X.)
| | - Kaiwen Zheng
- Ocean College, Zhejiang University, Zhoushan 316021, China; (Y.X.); (X.D.); (X.Y.); (Q.J.); (K.Z.); (J.X.)
| | - Jinzhong Xu
- Ocean College, Zhejiang University, Zhoushan 316021, China; (Y.X.); (X.D.); (X.Y.); (Q.J.); (K.Z.); (J.X.)
| | - Pinmei Wang
- Ocean College, Zhejiang University, Zhoushan 316021, China; (Y.X.); (X.D.); (X.Y.); (Q.J.); (K.Z.); (J.X.)
- State Key Laboratory of Motor Vehicle Biofuel Technology, Zhejiang University, Zhoushan 316021, China
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13
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Mungan MD, Harbig TA, Perez NH, Edenhart S, Stegmann E, Nieselt K, Ziemert N. Secondary Metabolite Transcriptomic Pipeline (SeMa-Trap), an expression-based exploration tool for increased secondary metabolite production in bacteria. Nucleic Acids Res 2022; 50:W682-W689. [PMID: 35580059 PMCID: PMC9252823 DOI: 10.1093/nar/gkac371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/20/2022] [Accepted: 04/29/2022] [Indexed: 11/14/2022] Open
Abstract
For decades, natural products have been used as a primary resource in drug discovery pipelines to find new antibiotics, which are mainly produced as secondary metabolites by bacteria. The biosynthesis of these compounds is encoded in co-localized genes termed biosynthetic gene clusters (BGCs). However, BGCs are often not expressed under laboratory conditions. Several genetic manipulation strategies have been developed in order to activate or overexpress silent BGCs. Significant increases in production levels of secondary metabolites were indeed achieved by modifying the expression of genes encoding regulators and transporters, as well as genes involved in resistance or precursor biosynthesis. However, the abundance of genes encoding such functions within bacterial genomes requires prioritization of the most promising ones for genetic manipulation strategies. Here, we introduce the ‘Secondary Metabolite Transcriptomic Pipeline’ (SeMa-Trap), a user-friendly web-server, available at https://sema-trap.ziemertlab.com. SeMa-Trap facilitates RNA-Seq based transcriptome analyses, finds co-expression patterns between certain genes and BGCs of interest, and helps optimize the design of comparative transcriptomic analyses. Finally, SeMa-Trap provides interactive result pages for each BGC, allowing the easy exploration and comparison of expression patterns. In summary, SeMa-Trap allows a straightforward prioritization of genes that could be targeted via genetic engineering approaches to (over)express BGCs of interest.
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Affiliation(s)
- Mehmet Direnç Mungan
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.,Interfaculty Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, 72076 Tübingen, Germany.,German Center for Infection Research (DZIF), Partnersite Tübingen, 72076 Tübingen, Germany
| | - Theresa Anisja Harbig
- Interfaculty Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, 72076 Tübingen, Germany
| | - Naybel Hernandez Perez
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Simone Edenhart
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Evi Stegmann
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.,German Center for Infection Research (DZIF), Partnersite Tübingen, 72076 Tübingen, Germany
| | - Kay Nieselt
- Interfaculty Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, 72076 Tübingen, Germany
| | - Nadine Ziemert
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany.,Interfaculty Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, 72076 Tübingen, Germany.,German Center for Infection Research (DZIF), Partnersite Tübingen, 72076 Tübingen, Germany
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14
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Hosseini H, Al-Jabri HM, Moheimani NR, Siddiqui SA, Saadaoui I. Marine microbial bioprospecting: Exploitation of marine biodiversity towards biotechnological applications-a review. J Basic Microbiol 2022; 62:1030-1043. [PMID: 35467037 DOI: 10.1002/jobm.202100504] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 03/14/2022] [Accepted: 04/07/2022] [Indexed: 11/09/2022]
Abstract
The increase in the human population causes an increase in the demand for nutritional supplies and energy resources. Thus, the novel, natural, and renewable resources became of great interest. Here comes the optimistic role of bioprospecting as a promising tool to isolate novel and interesting molecules and microorganisms from the marine environment as alternatives to the existing resources. Bioprospecting of marine metabolites and microorganisms with high biotechnological potentials has gained wide interest due to the variability and richness of the marine environment. Indeed, the existence of extreme conditions that increases the adaptability of marine organisms, especially planktons, allow the presence of interesting biological species that are able to produce novel compounds with multiple health benefits and high economical value. This review aims to provide a comprehensive overview of marine microbial bioprospecting as a growing field of interest. It emphasizes functional bioprospecting that facilitates the discovery of interesting metabolites. Marine bioprospecting was also discussed from a legal aspect for the first time, focusing on the shortcomings of international law. We also summarized the challenges facing bioprospecting in the marine environment including economic feasibility issues.
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Affiliation(s)
- Hoda Hosseini
- Algal Technologies Program, Centre for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Hareb M Al-Jabri
- Algal Technologies Program, Centre for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar.,Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Navid R Moheimani
- Algae R&D Centre, Harry Buttler Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Simil A Siddiqui
- Algal Technologies Program, Centre for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Imen Saadaoui
- Algal Technologies Program, Centre for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar.,Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
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15
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Understanding Interaction Patterns within Deep-Sea Microbial Communities and Their Potential Applications. Mar Drugs 2022; 20:md20020108. [PMID: 35200637 PMCID: PMC8874374 DOI: 10.3390/md20020108] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 01/17/2022] [Accepted: 01/21/2022] [Indexed: 11/17/2022] Open
Abstract
Environmental microbes living in communities engage in complex interspecies interactions that are challenging to decipher. Nevertheless, the interactions provide the basis for shaping community structure and functioning, which is crucial for ecosystem service. In addition, microbial interactions facilitate specific adaptation and ecological evolution processes particularly essential for microbial communities dwelling in resource-limiting habitats, such as the deep oceans. Recent technological and knowledge advancements provide an opportunity for the study of interactions within complex microbial communities, such as those inhabiting deep-sea waters and sediments. The microbial interaction studies provide insights into developing new strategies for biotechnical applications. For example, cooperative microbial interactions drive the degradation of complex organic matter such as chitins and celluloses. Such microbiologically-driven biogeochemical processes stimulate creative designs in many applied sciences. Understanding the interaction processes and mechanisms provides the basis for the development of synthetic communities and consequently the achievement of specific community functions. Microbial community engineering has many application potentials, including the production of novel antibiotics, biofuels, and other valuable chemicals and biomaterials. It can also be developed into biotechniques for waste processing and environmental contaminant bioremediation. This review summarizes our current understanding of the microbial interaction mechanisms and emerging techniques for inferring interactions in deep-sea microbial communities, aiding in future biotechnological and therapeutic applications.
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16
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Rego A, Fernandez-Guerra A, Duarte P, Assmy P, Leão PN, Magalhães C. Secondary metabolite biosynthetic diversity in Arctic Ocean metagenomes. Microb Genom 2021; 7. [PMID: 34904945 PMCID: PMC8767328 DOI: 10.1099/mgen.0.000731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Polyketide synthases (PKSs) and non-ribosomal peptide synthetases (NRPSs) are mega enzymes responsible for the biosynthesis of a large fraction of natural products (NPs). Molecular markers for biosynthetic genes, such as the ketosynthase (KS) domain of PKSs, have been used to assess the diversity and distribution of biosynthetic genes in complex microbial communities. More recently, metagenomic studies have complemented and enhanced this approach by allowing the recovery of complete biosynthetic gene clusters (BGCs) from environmental DNA. In this study, the distribution and diversity of biosynthetic genes and clusters from Arctic Ocean samples (NICE-2015 expedition), was assessed using PCR-based strategies coupled with high-throughput sequencing and metagenomic analysis. In total, 149 KS domain OTU sequences were recovered, 36 % of which could not be assigned to any known BGC. In addition, 74 bacterial metagenome-assembled genomes were recovered, from which 179 BGCs were extracted. A network analysis identified potential new NP families, including non-ribosomal peptides and polyketides. Complete or near-complete BGCs were recovered, which will enable future heterologous expression efforts to uncover the respective NPs. Our study represents the first report of biosynthetic diversity assessed for Arctic Ocean metagenomes and highlights the potential of Arctic Ocean planktonic microbiomes for the discovery of novel secondary metabolites. The strategy employed in this study will enable future bioprospection, by identifying promising samples for bacterial isolation efforts, while providing also full-length BGCs for heterologous expression.
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Affiliation(s)
- Adriana Rego
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
| | - Antonio Fernandez-Guerra
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Pedro Duarte
- Norwegian Polar Institute, Fram Centre, N-9296 Tromsø, Norway
| | - Philipp Assmy
- Norwegian Polar Institute, Fram Centre, N-9296 Tromsø, Norway
| | - Pedro N. Leão
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal
- *Correspondence: Pedro N. Leão,
| | - Catarina Magalhães
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal
- Faculty of Sciences, University of Porto, 4150-179 Porto, Portugal
- *Correspondence: Catarina Magalhães,
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17
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Rosic NN. Recent advances in the discovery of novel marine natural products and mycosporine-like amino acid UV-absorbing compounds. Appl Microbiol Biotechnol 2021; 105:7053-7067. [PMID: 34480237 PMCID: PMC8416575 DOI: 10.1007/s00253-021-11467-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 06/28/2021] [Accepted: 06/29/2021] [Indexed: 11/27/2022]
Abstract
Abstract Bioactive compounds from marine environments represent a rich source of bioproducts for potential use in medicine and biotechnology. To discover and identify novel marine natural products (MNPs), evaluating diverse biological activities is critical. Increased sensitivity and specificity of omics technologies, especially next-generation high-throughput sequencing combined with liquid chromatography-mass spectrometry and nuclear magnetic resonance, are speeding up the discovery of novel bioactive compounds. Mycosporine-like amino acids (MAAs) isolated from many marine microorganisms are among highly promising MNPs characterized by ultraviolet radiation (UV) absorbing capacities and are recognized as a potential source of ecologically friendly sunscreens. MAAs absorb damaging UV radiation with maximum absorption in the range of 310–360 nm, including both UVA and UVB ranges. MAAs are also characterized by other biological activities such as anti-oxidant, anti-cancer, and anti-inflammatory activities. The application of modern omics approaches promoted some recent developments in our understanding of MAAs’ functional significance and diversity. This review will summarize the various modern tools that could be applied during the identification and characterization of MNPs, including MAAs, to further their innovative applications. Key points • New omics technologies are speeding up the discovery of novel bio-products • The vast diversity of bioactive capacities of marine natural products described • Marine microorganisms as a source of environmentally friendly sunscreens
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Affiliation(s)
- Nedeljka N Rosic
- Faculty of Health, Southern Cross University, Southern Cross Drive, Gold Coast, QLD, 4225, Australia. .,Marine Ecology Research Centre, Southern Cross University, Military Rd, East Lismore, Lismore, NSW, 2480, Australia.
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18
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Varrella S, Barone G, Tangherlini M, Rastelli E, Dell’Anno A, Corinaldesi C. Diversity, Ecological Role and Biotechnological Potential of Antarctic Marine Fungi. J Fungi (Basel) 2021; 7:391. [PMID: 34067750 PMCID: PMC8157204 DOI: 10.3390/jof7050391] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/07/2021] [Accepted: 05/13/2021] [Indexed: 11/28/2022] Open
Abstract
The Antarctic Ocean is one of the most remote and inaccessible environments on our planet and hosts potentially high biodiversity, being largely unexplored and undescribed. Fungi have key functions and unique physiological and morphological adaptations even in extreme conditions, from shallow habitats to deep-sea sediments. Here, we summarized information on diversity, the ecological role, and biotechnological potential of marine fungi in the coldest biome on Earth. This review also discloses the importance of boosting research on Antarctic fungi as hidden treasures of biodiversity and bioactive molecules to better understand their role in marine ecosystem functioning and their applications in different biotechnological fields.
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Affiliation(s)
- Stefano Varrella
- Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Giulio Barone
- Institute for Biological Resources and Marine Biotechnologies, National Research Council (IRBIM-CNR), Largo Fiera della Pesca, 60125 Ancona, Italy;
| | - Michael Tangherlini
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica “Anton Dohrn”, Fano Marine Centre, Viale Adriatico 1-N, 61032 Fano, Italy;
| | - Eugenio Rastelli
- Department of Marine Biotechnology, Stazione Zoologica “Anton Dohrn”, Fano Marine Centre, Viale Adriatico 1-N, 61032 Fano, Italy;
| | - Antonio Dell’Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy;
| | - Cinzia Corinaldesi
- Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
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19
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Culture-Dependent Microbiome of the Ciona intestinalis Tunic: Isolation, Bioactivity Profiling and Untargeted Metabolomics. Microorganisms 2020; 8:microorganisms8111732. [PMID: 33167375 PMCID: PMC7694362 DOI: 10.3390/microorganisms8111732] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/01/2020] [Accepted: 11/03/2020] [Indexed: 01/28/2023] Open
Abstract
Ascidians and their associated microbiota are prolific producers of bioactive marine natural products. Recent culture-independent studies have revealed that the tunic of the solitary ascidian Cionaintestinalis (sea vase) is colonized by a diverse bacterial community, however, the biotechnological potential of this community has remained largely unexplored. In this study, we aimed at isolating the culturable microbiota associated with the tunic of C.intestinalis collected from the North and Baltic Seas, to investigate their antimicrobial and anticancer activities, and to gain first insights into their metabolite repertoire. The tunic of the sea vase was found to harbor a rich microbial community, from which 89 bacterial and 22 fungal strains were isolated. The diversity of the tunic-associated microbiota differed from that of the ambient seawater samples, but also between sampling sites. Fungi were isolated for the first time from the tunic of Ciona. The proportion of bioactive extracts was high, since 45% of the microbial extracts inhibited the growth of human pathogenic bacteria, fungi or cancer cell lines. In a subsequent bioactivity- and metabolite profiling-based approach, seven microbial extracts were prioritized for in-depth chemical investigations. Untargeted metabolomics analyses of the selected extracts by a UPLC-MS/MS-based molecular networking approach revealed a vast chemical diversity with compounds assigned to 22 natural product families, plus many metabolites that remained unidentified. This initial study indicates that bacteria and fungi associated with the tunic of C.intestinalis represent an untapped source of putatively new marine natural products with pharmacological relevance.
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20
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Willems T, De Mol ML, De Bruycker A, De Maeseneire SL, Soetaert WK. Alkaloids from Marine Fungi: Promising Antimicrobials. Antibiotics (Basel) 2020; 9:antibiotics9060340. [PMID: 32570899 PMCID: PMC7345139 DOI: 10.3390/antibiotics9060340] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/12/2020] [Accepted: 06/15/2020] [Indexed: 01/20/2023] Open
Abstract
Resistance of pathogenic microorganisms against antimicrobials is a major threat to contemporary human society. It necessitates a perpetual influx of novel antimicrobial compounds. More specifically, Gram− pathogens emerged as the most exigent danger. In our continuing quest to search for novel antimicrobial molecules, alkaloids from marine fungi show great promise. However, current reports of such newly discovered alkaloids are often limited to cytotoxicity studies and, moreover, neglect to discuss the enigma of their biosynthesis. Yet, the latter is often a prerequisite to make them available through sufficiently efficient processes. This review aims to summarize novel alkaloids with promising antimicrobial properties discovered in the past five years and produced by marine fungi. Several discovery strategies are summarized, and knowledge gaps in biochemical production routes are identified. Finally, links between the structure of the newly discovered molecules and their activity are proposed. Since 2015, a total of 35 new antimicrobial alkaloids from marine fungi were identified, of which 22 showed an antibacterial activity against Gram− microorganisms. Eight of them can be classified as narrow-spectrum Gram− antibiotics. Despite this promising ratio of novel alkaloids active against Gram− microorganisms, the number of newly discovered antimicrobial alkaloids is low, due to the narrow spectrum of discovery protocols that are used and the fact that antimicrobial properties of newly discovered alkaloids are barely characterized. Alternatives are proposed in this review. In conclusion, this review summarizes novel findings on antimicrobial alkaloids from marine fungi, shows their potential as promising therapeutic candidates, and hints on how to further improve this potential.
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21
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Nguyen CT, Dhakal D, Pham VTT, Nguyen HT, Sohng JK. Recent Advances in Strategies for Activation and Discovery/Characterization of Cryptic Biosynthetic Gene Clusters in Streptomyces. Microorganisms 2020; 8:E616. [PMID: 32344564 PMCID: PMC7232178 DOI: 10.3390/microorganisms8040616] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/20/2020] [Accepted: 04/22/2020] [Indexed: 12/12/2022] Open
Abstract
Streptomyces spp. are prolific sources of valuable natural products (NPs) that are of great interest in pharmaceutical industries such as antibiotics, anticancer chemotherapeutics, immunosuppressants, etc. Approximately two-thirds of all known antibiotics are produced by actinomycetes, most predominantly by Streptomyces. Nevertheless, in recent years, the chances of the discovery of novel and bioactive compounds from Streptomyces have significantly declined. The major hindrance for obtaining such bioactive compounds from Streptomyces is that most of the compounds are not produced in significant titers, or the biosynthetic gene clusters (BGCs) are cryptic. The rapid development of genome sequencing has provided access to a tremendous number of NP-BGCs embedded in the microbial genomes. In addition, the studies of metabolomics provide a portfolio of entire metabolites produced from the strain of interest. Therefore, through the integrated approaches of different-omics techniques, the connection between gene expression and metabolism can be established. Hence, in this review we summarized recent advancements in strategies for activating cryptic BGCs in Streptomyces by utilizing diverse state-of-the-art techniques.
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Affiliation(s)
- Chung Thanh Nguyen
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam 31460, Korea; (C.T.N.); (D.D.); (V.T.T.P.); (H.T.N.)
| | - Dipesh Dhakal
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam 31460, Korea; (C.T.N.); (D.D.); (V.T.T.P.); (H.T.N.)
| | - Van Thuy Thi Pham
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam 31460, Korea; (C.T.N.); (D.D.); (V.T.T.P.); (H.T.N.)
| | - Hue Thi Nguyen
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam 31460, Korea; (C.T.N.); (D.D.); (V.T.T.P.); (H.T.N.)
| | - Jae-Kyung Sohng
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam 31460, Korea; (C.T.N.); (D.D.); (V.T.T.P.); (H.T.N.)
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam 31460, Korea
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