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Ngamcharungchit C, Chaimusik N, Panbangred W, Euanorasetr J, Intra B. Bioactive Metabolites from Terrestrial and Marine Actinomycetes. Molecules 2023; 28:5915. [PMID: 37570885 PMCID: PMC10421486 DOI: 10.3390/molecules28155915] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/27/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023] Open
Abstract
Actinomycetes inhabit both terrestrial and marine ecosystems and are highly proficient in producing a wide range of natural products with diverse biological functions, including antitumor, immunosuppressive, antimicrobial, and antiviral activities. In this review, we delve into the life cycle, ecology, taxonomy, and classification of actinomycetes, as well as their varied bioactive metabolites recently discovered between 2015 and 2023. Additionally, we explore promising strategies to unveil and investigate new bioactive metabolites, encompassing genome mining, activation of silent genes through signal molecules, and co-cultivation approaches. By presenting this comprehensive and up-to-date review, we hope to offer a potential solution to uncover novel bioactive compounds with essential activities.
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Affiliation(s)
- Chananan Ngamcharungchit
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
- Mahidol University and Osaka University Collaborative Research Center on Bioscience and Biotechnology, Bangkok 10400, Thailand
| | - Nutsuda Chaimusik
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
- Mahidol University and Osaka University Collaborative Research Center on Bioscience and Biotechnology, Bangkok 10400, Thailand
| | - Watanalai Panbangred
- Research, Innovation and Partnerships Office, King Mongkut’s University of Technology Thonburi, Bangkok 10140, Thailand
| | - Jirayut Euanorasetr
- Department of Microbiology, Faculty of Science, King Mongkut’s University of Technology Thonburi, Bangkok 10140, Thailand
- Laboratory of Biotechnological Research for Energy and Bioactive Compounds, Department of Microbiology, Faculty of Science, King Mongkut’s University of Technology Thonburi, Khet Thung Khru, Bangkok 10140, Thailand
| | - Bungonsiri Intra
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
- Mahidol University and Osaka University Collaborative Research Center on Bioscience and Biotechnology, Bangkok 10400, Thailand
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Mehdiratta K, Nain S, Sharma M, Singh S, Srivastava S, Dhamale BD, Mohanty D, Kamat SS, Natarajan VT, Sharma R, Gokhale RS. Respiratory Quinone Switches from Menaquinone to Polyketide Quinone during the Development Cycle in Streptomyces sp. Strain MNU77. Microbiol Spectr 2023; 11:e0259722. [PMID: 36507669 PMCID: PMC9927152 DOI: 10.1128/spectrum.02597-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 11/14/2022] [Indexed: 12/14/2022] Open
Abstract
Type III polyketide synthases (PKSs) found across Streptomyces species are primarily known for synthesis of a vast repertoire of clinically and industrially relevant secondary metabolites. However, our understanding of the functional relevance of these bioactive metabolites in Streptomyces physiology is still limited. Recently, a role of type III PKS harboring gene cluster in producing alternate electron carrier, polyketide quinone (PkQ) was established in a related member of the Actinobacteria, Mycobacteria, highlighting the critical role these secondary metabolites play in primary cellular metabolism of the producer organism. Here, we report the developmental stage-specific transcriptional regulation of homologous type III PKS containing gene cluster in freshwater Streptomyces sp. strain MNU77. Gene expression analysis revealed the type III PKS gene cluster to be stringently regulated, with significant upregulation observed during the dormant sporulation stage of Streptomyces sp. MNU77. In contrast, the expression levels of only known electron carrier, menaquinone biosynthetic genes were interestingly found to be downregulated. Our liquid chromatography-high-resolution mass spectrometry (LC-HRMS) analysis of a metabolite extract from the Streptomyces sp. MNU77 spores also showed 10 times more metabolic abundance of PkQs than menaquinones. Furthermore, through heterologous complementation studies, we demonstrate that Streptomyces sp. MNU77 type III PKS rescues a respiratory defect of the Mycobacterium smegmatis type III PKS deletion mutant. Together, our studies reveal that freshwater Streptomyces sp. MNU77 robustly produces novel PkQs during the sporulation stage, suggesting utilization of PkQs as alternate electron carriers across Actinobacteria during dormant hypoxic conditions. IMPORTANCE The complex developmental life cycle of Streptomyces sp. mandates efficient cellular respiratory reconfiguration for a smooth transition from aerated nutrient-rich vegetative hyphal growth to the hypoxic-dormant sporulation stage. Polyketide quinones (PkQs) have recently been identified as a class of alternate electron carriers from a related member of the Actinobacteria, Mycobacteria, that facilitates maintenance of membrane potential in oxygen-deficient niches. Our studies with the newly identified freshwater Streptomyces sp. strain MNU77 show conditional transcriptional upregulation and metabolic abundance of PkQs in the spore state of the Streptomyces life cycle. In parallel, the levels of menaquinones, the only known Streptomyces electron carrier, were downregulated, suggesting deployment of PkQs as universal electron carriers in low-oxygen, unfavorable conditions across the Actinobacteria family.
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Affiliation(s)
- Kritee Mehdiratta
- National Institute of Immunology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sonam Nain
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Meenakshi Sharma
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Shubham Singh
- Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra, India
| | | | | | | | - Siddhesh S. Kamat
- Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra, India
| | - Vivek T. Natarajan
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Rakesh Sharma
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Rajesh S. Gokhale
- National Institute of Immunology, New Delhi, India
- Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra, India
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Takahashi M, Shinohara S, Hamada M, Tamura T, Dohra H, Kodani S, Nakagawa Y, Kokubo S, Hayakawa M, Yamamura H. Streptomyces pacificus sp. nov., a novel spongiicolazolicin-producing actinomycete isolated from a coastal sediment. J Antibiot (Tokyo) 2023; 76:93-100. [PMID: 36564595 DOI: 10.1038/s41429-022-00589-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022]
Abstract
A polyphasic approach was used to determine the taxonomic position of a marine actinomycete, designated isolate CWH03T, which we previously reported to produce new linear azole-containing peptides spongiicolazolicins A and B. Strain CWH03T is mesophilic, neutrophilic, and halotolerant streptomycete that forms spiral spore chains on aerial mycelium. Comparative 16S rRNA gene sequencing showed that CWH03T was most closely related to Streptomyces tirandamycinicus HNM0039T (99.7%), Streptomyces spongiicola HNM0071T (99.4%), 'Streptomyces marianii' ICN19T (99.1%) and Streptomyces wuyuanensis CGMCC4.7042T (99.0%). The phylogenetic tree prepared using the 16S rRNA gene, as well as the phylogenomic tree using the genome BLAST distance phylogeny method and 81 core housekeeping genes, respectively, showed that the closest relative of strain CWH03T was S. spongiicola HNM0071T. The average nucleotide identity and digital DNA-DNA hybridization values between strains CWH03T and S. spongiicola HNM0071T were 91.46% and 44.2%, respectively, which were below the thresholds of 96% and 70% for prokaryotic conspecific assignation. The G+C content of the genomic DNA of strain CWH03T was 72.3%. Whole-cell hydrolysates of strain CWH03T contained LL-diaminopimelic acid. The predominant menaquinone was MK-9(H8) (88.3%), and the major fatty acids were iso-C16:0 (28.4%), anteiso-C15:0 (15.0%) and iso-C15:0 (12.9%). The major phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid. Based on data obtained from phenotypic, phylogenetic, genomic, and chemotaxonomic analyses, strain CWH03T represents a novel species of the genus Streptomyces, for which the proposed name is Streptomyces pacificus sp. nov. The type strain is CWH03T ( = NBRC 114659T = TBRC 15780T).
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Affiliation(s)
- Miku Takahashi
- Department of Biotechnology, Faculty of Life and Environmental Sciences, University of Yamanashi, Takeda-4-4-37, Kofu, 400-8510, Japan
| | - Shoya Shinohara
- Department of Biotechnology, Faculty of Life and Environmental Sciences, University of Yamanashi, Takeda-4-4-37, Kofu, 400-8510, Japan
| | - Moriyuki Hamada
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Tomohiko Tamura
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Hideo Dohra
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
- Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
- Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Shinya Kodani
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
- Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
- Academic Institute, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Youji Nakagawa
- Department of Biotechnology, Faculty of Life and Environmental Sciences, University of Yamanashi, Takeda-4-4-37, Kofu, 400-8510, Japan
| | - Susumu Kokubo
- Department of Biotechnology, Faculty of Life and Environmental Sciences, University of Yamanashi, Takeda-4-4-37, Kofu, 400-8510, Japan
| | - Masayuki Hayakawa
- Department of Biotechnology, Faculty of Life and Environmental Sciences, University of Yamanashi, Takeda-4-4-37, Kofu, 400-8510, Japan
- Yamanashi Prefectural University, Iida-5-11-1, Kofu, 400-0035, Japan
| | - Hideki Yamamura
- Department of Biotechnology, Faculty of Life and Environmental Sciences, University of Yamanashi, Takeda-4-4-37, Kofu, 400-8510, Japan.
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Cera G, Risdian C, Pira H, Wink J. Antimicrobial potential of culturable actinobacteria isolated from the Pacific oyster
Crassostrea gigas
(Bivalvia, Ostreidae). J Appl Microbiol 2022; 133:1099-1114. [DOI: 10.1111/jam.15635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 01/04/2022] [Accepted: 05/19/2022] [Indexed: 12/01/2022]
Affiliation(s)
- Guillermo Cera
- Microbial Strain Collection (MISG), Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig Germany
- Marine Biology Program, Faculty of Natural Sciences and Engineering, Universidad Jorge Tadeo Lozano Santa Marta Colombia
| | - Chandra Risdian
- Microbial Strain Collection (MISG), Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig Germany
- Research Unit for Clean Technology, National Research and Innovation Agency (BRIN), 40135 Bandung Indonesia
| | - Hani Pira
- Microbial Strain Collection (MISG), Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig Germany
| | - Joachim Wink
- Microbial Strain Collection (MISG), Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig Germany
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