1
|
Liu W, Zhai S, Zhang L, Chen Y, Liu Z, Ma W, Zhang T, Zhang W, Ma L, Zhang C, Zhang W. Expanding the Chemical Diversity of Grisechelins via Heterologous Expression. JOURNAL OF NATURAL PRODUCTS 2024; 87:371-380. [PMID: 38301035 DOI: 10.1021/acs.jnatprod.3c01132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
Thiazole scaffold-based small molecules exhibit a range of biological activities and play important roles in drug discovery. Based on bioinformatics analysis, a putative biosynthetic gene cluster (BGC) for thiazole-containing compounds was identified from Streptomyces sp. SCSIO 40020. Heterologous expression of this BGC led to the production of eight new thiazole-containing compounds, grisechelins E, F, and I-N (1, 2, 5-10), and two quinoline derivatives, grisechelins G and H (3 and 4). The structures of 1-10, including their absolute configurations, were elucidated by HRESIMS, NMR spectroscopic data, ECD calculations, and single-crystal X-ray diffraction analysis. Grisechelin F (2) is a unique derivative, distinguished by the presence of a salicylic acid moiety. The biosynthetic pathway for 2 was proposed based on bioinformatics analysis and in vivo gene knockout experiments. Grisechelin E (1) displayed moderate antimycobacterial activity against Mycobacterium tuberculosis H37Ra (MIC of 8 μg mL-1).
Collapse
Affiliation(s)
- Wei Liu
- 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, 164 West Xingang Road, Guangzhou 510301, People's Republic of China
- Department of Clinical Pharmacy, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, 96 Dongchuan Road, Guangzhou 510080, People's Republic of China
| | - Shilan Zhai
- 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, 164 West Xingang Road, Guangzhou 510301, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Liping Zhang
- 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, 164 West Xingang Road, Guangzhou 510301, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Yuchan Chen
- State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, 100 Central Xianlie Road, Guangzhou 510070, People's Republic of China
| | - Zhiyong Liu
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
- Tuberculosis Research Laboratory, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, People's Republic of China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, Guangzhou 510530, People's Republic of China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, People's Republic of China
- Guangzhou National Laboratory, Guangzhou 510005, People's Republic of China
| | - Wanli Ma
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
- Tuberculosis Research Laboratory, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, People's Republic of China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, Guangzhou 510530, People's Republic of China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, People's Republic of China
| | - Tianyu Zhang
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
- Tuberculosis Research Laboratory, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, People's Republic of China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, People's Republic of China
- Guangzhou National Laboratory, Guangzhou 510005, People's Republic of China
| | - Weimin Zhang
- State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, 100 Central Xianlie Road, Guangzhou 510070, People's Republic of China
| | - Liang Ma
- 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, 164 West Xingang Road, Guangzhou 510301, People's Republic of China
| | - Changsheng Zhang
- 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, 164 West Xingang Road, Guangzhou 510301, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Wenjun Zhang
- 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, 164 West Xingang Road, Guangzhou 510301, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| |
Collapse
|
2
|
Gribble GW. Naturally Occurring Organohalogen Compounds-A Comprehensive Review. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 2023; 121:1-546. [PMID: 37488466 DOI: 10.1007/978-3-031-26629-4_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
The present volume is the third in a trilogy that documents naturally occurring organohalogen compounds, bringing the total number-from fewer than 25 in 1968-to approximately 8000 compounds to date. Nearly all of these natural products contain chlorine or bromine, with a few containing iodine and, fewer still, fluorine. Produced by ubiquitous marine (algae, sponges, corals, bryozoa, nudibranchs, fungi, bacteria) and terrestrial organisms (plants, fungi, bacteria, insects, higher animals) and universal abiotic processes (volcanos, forest fires, geothermal events), organohalogens pervade the global ecosystem. Newly identified extraterrestrial sources are also documented. In addition to chemical structures, biological activity, biohalogenation, biodegradation, natural function, and future outlook are presented.
Collapse
Affiliation(s)
- Gordon W Gribble
- Department of Chemistry, Dartmouth College, Hanover, NH, 03755, USA.
| |
Collapse
|
3
|
Majer HM, Ehrlich RL, Ahmed A, Earl JP, Ehrlich GD, Beld J. Whole genome sequencing of Streptomyces actuosus ISP-5337, Streptomyces sioyaensis B-5408, and Actinospica acidiphila B-2296 reveals secondary metabolomes with antibiotic potential. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2021; 29:e00596. [PMID: 33643857 PMCID: PMC7893419 DOI: 10.1016/j.btre.2021.e00596] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 01/20/2021] [Accepted: 02/01/2021] [Indexed: 12/31/2022]
Abstract
Whole genome sequencing of Actinomycetes reveals metabolic potential. High quality genomes are necessary for mining of biosynthetic gene clusters. Characterization of thiopeptides by high resolution mass spectrometry. Thiopeptides are potent antibacterials against Staphylococcus aureus.
Streptomycetes are bacteria of biotechnological importance since they are avid producers of secondary metabolites, including antibiotics. Progress in genome mining has recently shown that Streptomyces species encode for many biosynthetic gene clusters which are mostly unexplored. Here, we selected three Actinomycetes species for whole genome sequencing that are known to produce potent thiopeptide antibiotics. Streptomyces actuosus biosynthesizes nosiheptide, Streptomyces sioyaensis produces siomycin, and Actinospica acidiphila is a member of the Actinomycete subfamily. Bioinformatic analyses demonstrated diverse secondary metabolomes with multiple antibiotic-encoding gene clusters. Detailed mass spectrometry analysis of metabolite extracts verified the active expression of nosiheptide and siomycin from S. actuosus and S. sioyaensis while fractionation of the bacterial extracts and subsequent challenge against Staphylococcus aureus demonstrated potent antibiotic activity of fractions containing these compounds. Whole genome sequencing of these species facilitates future bioengineering efforts for thiopeptides and characterization of relevant secondary metabolites.
Collapse
Affiliation(s)
- Haley M Majer
- Department of Microbiology and Immunology, Drexel University College of Medicine, 245 N 15 St, Philadelphia, PA 19102, USA
| | - Rachel L Ehrlich
- Department of Microbiology and Immunology, Drexel University College of Medicine, 245 N 15 St, Philadelphia, PA 19102, USA
| | - Azad Ahmed
- Department of Microbiology and Immunology, Drexel University College of Medicine, 245 N 15 St, Philadelphia, PA 19102, USA
| | - Joshua P Earl
- Department of Microbiology and Immunology, Drexel University College of Medicine, 245 N 15 St, Philadelphia, PA 19102, USA
| | - Garth D Ehrlich
- Department of Microbiology and Immunology, Drexel University College of Medicine, 245 N 15 St, Philadelphia, PA 19102, USA
| | - Joris Beld
- Department of Microbiology and Immunology, Drexel University College of Medicine, 245 N 15 St, Philadelphia, PA 19102, USA
| |
Collapse
|
4
|
Mini review: Genome mining approaches for the identification of secondary metabolite biosynthetic gene clusters in Streptomyces. Comput Struct Biotechnol J 2020; 18:1548-1556. [PMID: 32637051 PMCID: PMC7327026 DOI: 10.1016/j.csbj.2020.06.024] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 06/12/2020] [Accepted: 06/14/2020] [Indexed: 01/04/2023] Open
Abstract
Streptomyces are a large and valuable resource of bioactive and complex secondary metabolites, many of which have important clinical applications. With the advances in high throughput genome sequencing methods, various in silico genome mining strategies have been developed and applied to the mapping of the Streptomyces genome. These studies have revealed that Streptomyces possess an even more significant number of uncharacterized silent secondary metabolite biosynthetic gene clusters (smBGCs) than previously estimated. Linking smBGCs to their encoded products has played a critical role in the discovery of novel secondary metabolites, as well as, knowledge-based engineering of smBGCs to produce altered products. In this mini review, we discuss recent progress in Streptomyces genome sequencing and the application of genome mining approaches to identify and characterize smBGCs. Furthermore, we discuss several challenges that need to be overcome to accelerate the genome mining process and ultimately support the discovery of novel bioactive compounds.
Collapse
|
5
|
Almeida EL, Carrillo Rincón AF, Jackson SA, Dobson ADW. Comparative Genomics of Marine Sponge-Derived Streptomyces spp. Isolates SM17 and SM18 With Their Closest Terrestrial Relatives Provides Novel Insights Into Environmental Niche Adaptations and Secondary Metabolite Biosynthesis Potential. Front Microbiol 2019; 10:1713. [PMID: 31404169 PMCID: PMC6676996 DOI: 10.3389/fmicb.2019.01713] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 07/11/2019] [Indexed: 12/28/2022] Open
Abstract
The emergence of antibiotic resistant microorganisms has led to an increased need for the discovery and development of novel antimicrobial compounds. Frequent rediscovery of the same natural products (NPs) continues to decrease the likelihood of the discovery of new compounds from soil bacteria. Thus, efforts have shifted toward investigating microorganisms and their secondary metabolite biosynthesis potential, from diverse niche environments, such as those isolated from marine sponges. Here we investigated at the genomic level two Streptomyces spp. strains, namely SM17 and SM18, isolated from the marine sponge Haliclona simulans, with previously reported antimicrobial activity against clinically relevant pathogens; using single molecule real-time (SMRT) sequencing. We performed a series of comparative genomic analyses on SM17 and SM18 with their closest terrestrial relatives, namely S. albus J1074 and S. pratensis ATCC 33331 respectively; in an effort to provide further insights into potential environmental niche adaptations (ENAs) of marine sponge-associated Streptomyces, and on how these adaptations might be linked to their secondary metabolite biosynthesis potential. Prediction of secondary metabolite biosynthetic gene clusters (smBGCs) indicated that, even though the marine isolates are closely related to their terrestrial counterparts at a genomic level; they potentially produce different compounds. SM17 and SM18 displayed a better ability to grow in high salinity medium when compared to their terrestrial counterparts, and further analysis of their genomes indicated that they possess a pool of 29 potential ENA genes that are absent in S. albus J1074 and S. pratensis ATCC 33331. This ENA gene pool included functional categories of genes that are likely to be related to niche adaptations and which could be grouped based on potential biological functions such as osmotic stress, defense; transcriptional regulation; symbiotic interactions; antimicrobial compound production and resistance; ABC transporters; together with horizontal gene transfer and defense-related features.
Collapse
Affiliation(s)
| | | | - Stephen A. Jackson
- School of Microbiology, University College Cork, Cork, Ireland
- Environmental Research Institute, University College Cork, Cork, Ireland
| | - Alan D. W. Dobson
- School of Microbiology, University College Cork, Cork, Ireland
- Environmental Research Institute, University College Cork, Cork, Ireland
| |
Collapse
|
6
|
Zhang C, Yang Z, Qin X, Ma J, Sun C, Huang H, Li Q, Ju J. Genome Mining for Mycemycin: Discovery and Elucidation of Related Methylation and Chlorination Biosynthetic Chemistries. Org Lett 2018; 20:7633-7636. [PMID: 30474984 DOI: 10.1021/acs.orglett.8b03373] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A silent dibenzoxazepinone (DBP) biosynthetic gene cluster ( myc) was mutagenically activated in Streptomyces olivaceus SCSIO T05, enabling the discovery of mycemycin C (4) and three new analogues [mycemycins F-H (1-3)]. Gene disruption, complementation experiments, and enzymatic assays unveiled salicylic acid and 5-Cl-kynurenine as biosynthetic precursors and shed significant functional insights into MycO, MycB, MycR, and MycJ, enzymes responsible for fine-tuning of the DBP scaffold.
Collapse
Affiliation(s)
- Chunyan Zhang
- 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 , 164 West Xingang Road , Guangzhou 510301 , China.,University of Chinese Academy of Sciences , 19 Yuquan Road , Beijing , 100049 , China
| | - 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 , 164 West Xingang Road , Guangzhou 510301 , China.,University of Chinese Academy of Sciences , 19 Yuquan Road , Beijing , 100049 , China
| | - Xiangjing Qin
- 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 , 164 West Xingang Road , Guangzhou 510301 , 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 , 164 West Xingang Road , Guangzhou 510301 , China
| | - Changli Sun
- 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 , 164 West Xingang Road , Guangzhou 510301 , China
| | - Hongbo Huang
- 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 , 164 West Xingang Road , Guangzhou 510301 , China
| | - Qinglian Li
- 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 , 164 West Xingang Road , Guangzhou 510301 , 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 , 164 West Xingang Road , Guangzhou 510301 , China.,University of Chinese Academy of Sciences , 19 Yuquan Road , Beijing , 100049 , China
| |
Collapse
|