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Liang J, She J, Fu J, Wang J, Ye Y, Yang B, Liu Y, Zhou X, Tao H. Advances in Natural Products from the Marine-Sponge-Associated Microorganisms with Antimicrobial Activity in the Last Decade. Mar Drugs 2023; 21:md21040236. [PMID: 37103375 PMCID: PMC10143917 DOI: 10.3390/md21040236] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/03/2023] [Accepted: 04/10/2023] [Indexed: 04/28/2023] Open
Abstract
Microorganisms are the dominating source of food and nutrition for sponges and play an important role in sponge structure, chemical defense, excretion and evolution. In recent years, plentiful secondary metabolites with novel structures and specific activities have been identified from sponge-associated microorganisms. Additionally, as the phenomenon of the drug resistance of pathogenic bacteria is becoming more and more common, it is urgent to discover new antimicrobial agents. In this paper, we reviewed 270 secondary metabolites with potential antimicrobial activity against a variety of pathogenic strains reported in the literature from 2012 to 2022. Among them, 68.5% were derived from fungi, 23.3% originated from actinomycetes, 3.7% were obtained from other bacteria and 4.4% were discovered using the co-culture method. The structures of these compounds include terpenoids (13%), polyketides (51.9%), alkaloids (17.4%), peptides (11.5%), glucosides (3.3%), etc. Significantly, there are 124 new compounds and 146 known compounds, 55 of which have antifungal activity in addition to antipathogenic bacteria. This review will provide a theoretical basis for the further development of antimicrobial drugs.
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Affiliation(s)
- Jiaqi Liang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianglian She
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Fu
- Guangdong Provincial Key Laboratory of Chinese Medicine Pharmaceutics, School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
| | - Jiamin Wang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuxiu Ye
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Bin Yang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Yonghong Liu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Xuefeng Zhou
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huaming Tao
- Guangdong Provincial Key Laboratory of Chinese Medicine Pharmaceutics, School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
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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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Chen J, Xu L, Zhou Y, Han B. Natural Products from Actinomycetes Associated with Marine Organisms. Mar Drugs 2021; 19:md19110629. [PMID: 34822500 PMCID: PMC8621598 DOI: 10.3390/md19110629] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/05/2021] [Accepted: 11/06/2021] [Indexed: 12/15/2022] Open
Abstract
The actinomycetes have proven to be a rich source of bioactive secondary metabolites and play a critical role in the development of pharmaceutical researches. With interactions of host organisms and having special ecological status, the actinomycetes associated with marine animals, marine plants, macroalgae, cyanobacteria, and lichens have more potential to produce active metabolites acting as chemical defenses to protect the host from predators as well as microbial infection. This review focuses on 536 secondary metabolites (SMs) from actinomycetes associated with these marine organisms covering the literature to mid-2021, which will highlight the taxonomic diversity of actinomycetes and the structural classes, biological activities of SMs. Among all the actinomycetes listed, members of Streptomyces (68%), Micromonospora (6%), and Nocardiopsis (3%) are dominant producers of secondary metabolites. Additionally, alkaloids (37%), polyketides (33%), and peptides (15%) comprise the largest proportion of natural products with mostly antimicrobial activity and cytotoxicity. Furthermore, the data analysis and clinical information of SMs have been summarized in this article, suggesting that some of these actinomycetes with multiple host organisms deserve more attention to their special ecological status and genetic factors.
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Cheng MM, Tang XL, Sun YT, Song DY, Cheng YJ, Liu H, Li PL, Li GQ. Biological and Chemical Diversity of Marine Sponge-Derived Microorganisms over the Last Two Decades from 1998 to 2017. Molecules 2020; 25:E853. [PMID: 32075151 PMCID: PMC7070270 DOI: 10.3390/molecules25040853] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/10/2020] [Accepted: 02/10/2020] [Indexed: 11/16/2022] Open
Abstract
Marine sponges are well known as rich sources of biologically natural products. Growing evidence indicates that sponges harbor a wealth of microorganisms in their bodies, which are likely to be the true producers of bioactive secondary metabolites. In order to promote the study of natural product chemistry and explore the relationship between microorganisms and their sponge hosts, in this review, we give a comprehensive overview of the structures, sources, and activities of the 774 new marine natural products from sponge-derived microorganisms described over the last two decades from 1998 to 2017.
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Affiliation(s)
- Mei-Mei Cheng
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Yushan Road 5, Qingdao 266003, China; (M.-M.C.); (Y.-T.S.); (D.-Y.S.); (Y.-J.C.); (H.L.)
- Laboratory of Marine Drugs and Biological Products, National Laboratory for Marine Science and Technology, Qingdao 266235, China
| | - Xu-Li Tang
- College of Chemistry and Chemical Engineering, Ocean University of China, Songling Road 238, Qingdao 266100, China;
| | - Yan-Ting Sun
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Yushan Road 5, Qingdao 266003, China; (M.-M.C.); (Y.-T.S.); (D.-Y.S.); (Y.-J.C.); (H.L.)
- Laboratory of Marine Drugs and Biological Products, National Laboratory for Marine Science and Technology, Qingdao 266235, China
| | - Dong-Yang Song
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Yushan Road 5, Qingdao 266003, China; (M.-M.C.); (Y.-T.S.); (D.-Y.S.); (Y.-J.C.); (H.L.)
- Laboratory of Marine Drugs and Biological Products, National Laboratory for Marine Science and Technology, Qingdao 266235, China
| | - Yu-Jing Cheng
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Yushan Road 5, Qingdao 266003, China; (M.-M.C.); (Y.-T.S.); (D.-Y.S.); (Y.-J.C.); (H.L.)
- Laboratory of Marine Drugs and Biological Products, National Laboratory for Marine Science and Technology, Qingdao 266235, China
| | - Hui Liu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Yushan Road 5, Qingdao 266003, China; (M.-M.C.); (Y.-T.S.); (D.-Y.S.); (Y.-J.C.); (H.L.)
- Laboratory of Marine Drugs and Biological Products, National Laboratory for Marine Science and Technology, Qingdao 266235, China
| | - Ping-Lin Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Yushan Road 5, Qingdao 266003, China; (M.-M.C.); (Y.-T.S.); (D.-Y.S.); (Y.-J.C.); (H.L.)
- Laboratory of Marine Drugs and Biological Products, National Laboratory for Marine Science and Technology, Qingdao 266235, China
| | - Guo-Qiang Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Yushan Road 5, Qingdao 266003, China; (M.-M.C.); (Y.-T.S.); (D.-Y.S.); (Y.-J.C.); (H.L.)
- Laboratory of Marine Drugs and Biological Products, National Laboratory for Marine Science and Technology, Qingdao 266235, China
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Chevrette MG, Gutiérrez-García K, Selem-Mojica N, Aguilar-Martínez C, Yañez-Olvera A, Ramos-Aboites HE, Hoskisson PA, Barona-Gómez F. Evolutionary dynamics of natural product biosynthesis in bacteria. Nat Prod Rep 2019; 37:566-599. [PMID: 31822877 DOI: 10.1039/c9np00048h] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Covering: 2008 up to 2019The forces of biochemical adaptive evolution operate at the level of genes, manifesting in complex phenotypes and the global biodiversity of proteins and metabolites. While evolutionary histories have been deciphered for some other complex traits, the origins of natural product biosynthesis largely remain a mystery. This fundamental knowledge gap is surprising given the many decades of research probing the genetic, chemical, and biophysical mechanisms of bacterial natural product biosynthesis. Recently, evolutionary thinking has begun to permeate this otherwise mechanistically dominated field. Natural products are now sometimes referred to as 'specialized' rather than 'secondary' metabolites, reinforcing the importance of their biological and ecological functions. Here, we review known evolutionary mechanisms underlying the overwhelming chemical diversity of bacterial secondary metabolism, focusing on enzyme promiscuity and the evolution of enzymatic domains that enable metabolic traits. We discuss the mechanisms that drive the assembly of natural product biosynthetic gene clusters and propose formal definitions for 'specialized' and 'secondary' metabolism. We further explore how biosynthetic gene clusters evolve to synthesize related molecular species, and in turn how the biological and ecological roles that emerge from metabolic diversity are acted on by selection. Finally, we reconcile chemical, functional, and genetic data into an evolutionary model, the dynamic chemical matrix evolutionary hypothesis, in which the relationships between chemical distance, biomolecular activity, and relative fitness shape adaptive landscapes.
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Affiliation(s)
- Marc G Chevrette
- Wisconsin Institute for Discovery, Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA.
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Yang Z, He J, Wei X, Ju J, Ma J. Exploration and genome mining of natural products from marine Streptomyces. Appl Microbiol Biotechnol 2019; 104:67-76. [PMID: 31773207 DOI: 10.1007/s00253-019-10227-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/22/2019] [Accepted: 10/27/2019] [Indexed: 12/22/2022]
Abstract
Marine Streptomyces sp. are an important source of bioactive compounds owing to their unique habitats and metabolic pathways. Whole-genome sequencing and bioinformatics analyses have shown that the potential of synthesizing secondary metabolites from marine-derived Streptomyces has been substantially underestimated. Genome mining is an integrated strategy used to discover natural products based on gene cluster sequences and biosynthetic pathways. Its emergence has greatly enhanced the discovery of natural compounds from marine Streptomyces, thereby yielding a large number of bioactive molecules with novel structures and potent activities. In this review, we briefly summarize the current applications of genome mining in marine Streptomyces, such as bioinformatics-based optimization of culture conditions, ribosome engineering, control of regulatory networks, heterologous expression of biosynthetic gene cluster, and combinatorial biosynthesis of natural compounds. Furthermore, we discuss the factors hindering the utilization of marine-derived natural products and conclude with the prospects for this technique.
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Affiliation(s)
- Zhijie Yang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianqiao He
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin Wei
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianhua Ju
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Junying Ma
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
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Maglangit F, Tong MH, Jaspars M, Kyeremeh K, Deng H. Legonoxamines A-B, two new hydroxamate siderophores from the soil bacterium, Streptomyces sp. MA37. Tetrahedron Lett 2019. [DOI: 10.1016/j.tetlet.2018.11.063] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Abstract
Covering: 2016. Previous review: Nat. Prod. Rep., 2017, 34, 235-294This review covers the literature published in 2016 for marine natural products (MNPs), with 757 citations (643 for the period January to December 2016) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1277 in 432 papers for 2016), together with the relevant biological activities, source organisms and country of origin. Reviews, biosynthetic studies, first syntheses, and syntheses that led to the revision of structures or stereochemistries, have been included.
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Affiliation(s)
- John W Blunt
- School of Physical and Chemical Sciences, University of Canterbury, Christchurch, New Zealand
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Sun YQ, Busche T, Rückert C, Paulus C, Rebets Y, Novakova R, Kalinowski J, Luzhetskyy A, Kormanec J, Sekurova ON, Zotchev SB. Development of a Biosensor Concept to Detect the Production of Cluster-Specific Secondary Metabolites. ACS Synth Biol 2017; 6:1026-1033. [PMID: 28221784 DOI: 10.1021/acssynbio.6b00353] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Genome mining of actinomycete bacteria aims at the discovery of novel bioactive secondary metabolites that can be developed into drugs. A new repressor-based biosensor to detect activated secondary metabolite biosynthesis gene clusters in Streptomyces was developed. Biosynthetic gene clusters for undecylprodigiosin and coelimycin in the genome of Streptomyces lividans TK24, which encoded TetR-like repressors and appeared to be almost "silent" based on the RNA-seq data, were chosen for the proof-of-principle studies. The bpsA reporter gene for indigoidine synthetase was placed under control of the promotor/operator regions presumed to be controlled by the cluster-associated TetR-like repressors. While the biosensor for undecylprodigiosin turned out to be nonfunctional, the coelimycin biosensor was shown to perform as expected, turning on biosynthesis of indigoidine in response to the concomitant production of coelimycin. The developed reporter system concept can be applied to those cryptic gene clusters that encode metabolite-sensing repressors to speed up discovery of novel bioactive compounds in Streptomyces.
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Affiliation(s)
- Yi-Qian Sun
- Department
of Biotechnology, Norwegian University of Science and Technology, 7491 Trondheim, Norway
- The
Department of Laboratory Medicine, Children’s and Women’s
Health (LBK), Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Tobias Busche
- Center
for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Christian Rückert
- Center
for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Constanze Paulus
- Helmholtz Institute for Pharmaceutical Research Saarland, Actinobacteria Metabolic Engineering Group, 66123 Saarbrücken, Germany
- Universität des Saarlandes, Pharmaceutical Biotechnology, 66123 Saarbrücken, Germany
| | - Yuriy Rebets
- Helmholtz Institute for Pharmaceutical Research Saarland, Actinobacteria Metabolic Engineering Group, 66123 Saarbrücken, Germany
| | - Renata Novakova
- Institute
of Molecular Biology, Slovak Academy of Sciences, 845 51 Bratislava, Slovak Republic
| | - Jörn Kalinowski
- Center
for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Andriy Luzhetskyy
- Helmholtz Institute for Pharmaceutical Research Saarland, Actinobacteria Metabolic Engineering Group, 66123 Saarbrücken, Germany
- Universität des Saarlandes, Pharmaceutical Biotechnology, 66123 Saarbrücken, Germany
| | - Jan Kormanec
- Institute
of Molecular Biology, Slovak Academy of Sciences, 845 51 Bratislava, Slovak Republic
| | - Olga N. Sekurova
- Department
of Pharmacognosy, University of Vienna, 1090 Vienna, Austria
| | - Sergey B. Zotchev
- Department
of Pharmacognosy, University of Vienna, 1090 Vienna, Austria
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