1
|
Lin J, Xiao Y, Liu H, Gao D, Duan Y, Zhu X. Combined transcriptomic and pangenomic analyses guide metabolic amelioration to enhance tiancimycins production. Appl Microbiol Biotechnol 2024; 108:18. [PMID: 38170317 DOI: 10.1007/s00253-023-12937-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 11/15/2023] [Accepted: 11/26/2023] [Indexed: 01/05/2024]
Abstract
Exploration of high-yield mechanism is important for further titer improvement of valuable antibiotics, but how to achieve this goal is challenging. Tiancimycins (TNMs) are anthraquinone-fused enediynes with promising drug development potentials, but their prospective applications are limited by low titers. This work aimed to explore the intrinsic high-yield mechanism in previously obtained TNMs high-producing strain Streptomyces sp. CB03234-S for the further titer amelioration of TNMs. First, the typical ribosomal RpsL(K43N) mutation in CB03234-S was validated to be merely responsible for the streptomycin resistance but not the titer improvement of TNMs. Subsequently, the combined transcriptomic, pan-genomic and KEGG analyses revealed that the significant changes in the carbon and amino acid metabolisms could reinforce the metabolic fluxes of key CoA precursors, and thus prompted the overproduction of TNMs in CB03234-S. Moreover, fatty acid metabolism was considered to exert adverse effects on the biosynthesis of TNMs by shunting and reducing the accumulation of CoA precursors. Therefore, different combinations of relevant genes were respectively overexpressed in CB03234-S to strengthen fatty acid degradation. The resulting mutants all showed the enhanced production of TNMs. Among them, the overexpression of fadD, a key gene responsible for the first step of fatty acid degradation, achieved the highest 21.7 ± 1.1 mg/L TNMs with a 63.2% titer improvement. Our studies suggested that comprehensive bioinformatic analyses are effective to explore metabolic changes and guide rational metabolic reconstitution for further titer improvement of target products. KEY POINTS: • Comprehensive bioinformatic analyses effectively reveal primary metabolic changes. • Primary metabolic changes cause precursor enrichment to enhance TNMs production. • Strengthening of fatty acid degradation further improves the titer of TNMs.
Collapse
Affiliation(s)
- Jing Lin
- Xiangya International Academy of Translational Medicine, Central South University, Yuelu District, Tongzipo Road, #172, Changsha, 410013, Hunan, China
| | - Yu Xiao
- Xiangya International Academy of Translational Medicine, Central South University, Yuelu District, Tongzipo Road, #172, Changsha, 410013, Hunan, China
| | - Huiming Liu
- Xiangya International Academy of Translational Medicine, Central South University, Yuelu District, Tongzipo Road, #172, Changsha, 410013, Hunan, China
| | - Die Gao
- Xiangya International Academy of Translational Medicine, Central South University, Yuelu District, Tongzipo Road, #172, Changsha, 410013, Hunan, China
| | - Yanwen Duan
- Xiangya International Academy of Translational Medicine, Central South University, Yuelu District, Tongzipo Road, #172, Changsha, 410013, Hunan, China.
- Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, 410013, Hunan, China.
- National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, 410013, Hunan, China.
| | - Xiangcheng Zhu
- Xiangya International Academy of Translational Medicine, Central South University, Yuelu District, Tongzipo Road, #172, Changsha, 410013, Hunan, China.
- Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, 410013, Hunan, China.
- National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, 410013, Hunan, China.
| |
Collapse
|
2
|
Zhao S, Wang J. Biodegradation of atrazine and nicosulfuron by Streptomyces nigra LM01: Performance, degradative pathway, and possible genes involved. J Hazard Mater 2024; 471:134336. [PMID: 38640665 DOI: 10.1016/j.jhazmat.2024.134336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 04/21/2024]
Abstract
Microbial herbicide degradation is an efficient bioremediation method. In this study, a strain of Streptomyces nigra, LM01, which efficiently degrades atrazine and nicosulfuron, was isolated from a corn field using a direct isolation method. The degradation effects of the identified strain on two herbicides were investigated and optimized using an artificial neural network. The maximum degradation rates of S. nigra LM01 were 58.09 % and 42.97 % for atrazine and nicosulfuron, respectively. The degradation rate of atrazine in the soil reached 67.94 % when the concentration was 108 CFU/g after 5 d and was less effective than that of nicosulfuron. Whole genome sequencing of strain LM01 helped elucidate the possible degradation pathways of atrazine and nicosulfuron. The protein sequences of strain LM01 were aligned with the sequences of the degraded proteins of the two herbicides by using the National Center for Biotechnology Information platform. The sequence (GE005358, GE001556, GE004212, GE005218, GE004846, GE002487) with the highest query cover was retained and docked with the small-molecule ligands of the herbicides. The results revealed a binding energy of - 6.23 kcal/mol between GE005358 and the atrazine ligand and - 6.66 kcal/mol between GE002487 and the nicosulfuron ligand.
Collapse
Affiliation(s)
- Shengchen Zhao
- College of Resource and Environmental Science, Jilin Agricultural University, Changchun 130118, Jilin, China
| | - Jihong Wang
- College of Resource and Environmental Science, Jilin Agricultural University, Changchun 130118, Jilin, China.
| |
Collapse
|
3
|
Ma B, Li A, Chen S, Guo H, Li N, Pan S, Chen K, Liu H, Kosolapov DB, Liu X, Zhi W, Chen Z, Mo Y, Sekar R, Huang T, Zhang H. Algicidal activity synchronized with nitrogen removal by actinomycetes: Algicidal mechanism, stress response of algal cells, denitrification performance, and indigenous bacterial community co-occurrence. J Hazard Mater 2024; 470:134117. [PMID: 38554519 DOI: 10.1016/j.jhazmat.2024.134117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/14/2024] [Accepted: 03/22/2024] [Indexed: 04/01/2024]
Abstract
The harmful algal blooms (HABs) can damage the ecological equilibrium of aquatic ecosystems and threaten human health. The bio-degradation of algal by algicidal bacteria is an environmentally friendly and economical approach to control HABs. This study applied an aerobic denitrification synchronization algicidal strain Streptomyces sp. LJH-12-1 (L1) to control HABs. The cell-free filtrate of the strain L1 showed a great algolytic effect on bloom-forming cyanobacterium, Microcystis aeruginosa (M. aeruginosa). The optimal algicidal property of strain L1 was indirect light-dependent algicidal with an algicidal rate of 85.0%. The functional metabolism, light-trapping, light-transfer efficiency, the content of pigments, and inhibition of photosynthesis of M. aeruginosa decreased after the addition of the supernatant of the strain L1 due to oxidative stress. Moreover, 96.05% nitrate removal rate synchronized with algicidal activity was achieved with the strain L1. The relative abundance of N cycling functional genes significantly increased during the strain L1 effect on M. aeruginosa. The algicidal efficiency of the strain L1 in the raw water was 76.70% with nitrate removal efficiency of 81.4%. Overall, this study provides a novel route to apply bacterial strain with the property of denitrification coupled with algicidal activity in treating micro-polluted water bodies.
Collapse
Affiliation(s)
- Ben Ma
- Collaborative Innovation Center of Water Pollution Control and Water Quality Security Assurance of Shaanxi Province, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountains, Xi'an University of Architecture and Technology, Xi'an 710055, China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Anyi Li
- Collaborative Innovation Center of Water Pollution Control and Water Quality Security Assurance of Shaanxi Province, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountains, Xi'an University of Architecture and Technology, Xi'an 710055, China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Shengnan Chen
- Collaborative Innovation Center of Water Pollution Control and Water Quality Security Assurance of Shaanxi Province, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountains, Xi'an University of Architecture and Technology, Xi'an 710055, China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Honghong Guo
- Collaborative Innovation Center of Water Pollution Control and Water Quality Security Assurance of Shaanxi Province, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountains, Xi'an University of Architecture and Technology, Xi'an 710055, China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China.
| | - Nan Li
- Collaborative Innovation Center of Water Pollution Control and Water Quality Security Assurance of Shaanxi Province, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountains, Xi'an University of Architecture and Technology, Xi'an 710055, China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Sixuan Pan
- Collaborative Innovation Center of Water Pollution Control and Water Quality Security Assurance of Shaanxi Province, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountains, Xi'an University of Architecture and Technology, Xi'an 710055, China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Kaige Chen
- Collaborative Innovation Center of Water Pollution Control and Water Quality Security Assurance of Shaanxi Province, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountains, Xi'an University of Architecture and Technology, Xi'an 710055, China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Hanyan Liu
- Collaborative Innovation Center of Water Pollution Control and Water Quality Security Assurance of Shaanxi Province, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountains, Xi'an University of Architecture and Technology, Xi'an 710055, China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Dmitry B Kosolapov
- Papanin Institute for Biology of Inland Waters of Russian Academy of Sciences (IBIW RAS) 109, Borok, Nekouz, Yaroslavl 152742, Russia
| | - Xiang Liu
- Collaborative Innovation Center of Water Pollution Control and Water Quality Security Assurance of Shaanxi Province, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountains, Xi'an University of Architecture and Technology, Xi'an 710055, China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Wei Zhi
- Department of Civil and Environmental Engineering, the Pennsylvania State University, USA
| | - Zhongbing Chen
- Department of Applied Ecology, Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, Praha-Suchdol, 16500, Czech Republic
| | - Yuanyuan Mo
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Raju Sekar
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China
| | - Tinglin Huang
- Collaborative Innovation Center of Water Pollution Control and Water Quality Security Assurance of Shaanxi Province, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountains, Xi'an University of Architecture and Technology, Xi'an 710055, China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Haihan Zhang
- Collaborative Innovation Center of Water Pollution Control and Water Quality Security Assurance of Shaanxi Province, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountains, Xi'an University of Architecture and Technology, Xi'an 710055, China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China.
| |
Collapse
|
4
|
Li W, Cheng Z, Zhao Z, Li H, Liu Y, Lu X, Zhao G, Du YL. Discovery of a Bacterial Hydrazine Transferase That Constructs the N-Aminolactam Pharmacophore in Albofungin Biosynthesis. J Am Chem Soc 2024; 146:13399-13405. [PMID: 38698691 DOI: 10.1021/jacs.4c02311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Structural motifs containing nitrogen-nitrogen (N-N) bonds are prevalent in a large number of clinical drugs and bioactive natural products. Hydrazine (N2H4) serves as a widely utilized building block for the preparation of these N-N-containing molecules in organic synthesis. Despite its common use in chemical processes, no enzyme has been identified to catalyze the incorporation of free hydrazine in natural product biosynthesis. Here, we report that a hydrazine transferase catalyzes the condensation of N2H4 and an aromatic polyketide pathway intermediate, leading to the formation of a rare N-aminolactam pharmacophore in the biosynthesis of broad-spectrum antibiotic albofungin. These results expand the current knowledge on the biosynthetic mechanism for natural products with N-N units and should facilitate future development of biocatalysts for the production of N-N-containing chemicals.
Collapse
Affiliation(s)
- Wei Li
- Department of Microbiology and Department of Pharmacy of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Ziyang Cheng
- Department of Microbiology and Department of Pharmacy of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Zhijie Zhao
- Department of Microbiology and Department of Pharmacy of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Hu Li
- Department of Microbiology and Department of Pharmacy of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yu Liu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xingyu Lu
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Instrumentation and Service Center for Molecular Sciences, Westlake University, Hangzhou 310024, China
| | - Guiyun Zhao
- Department of Microbiology and Department of Pharmacy of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yi-Ling Du
- Department of Microbiology and Department of Pharmacy of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| |
Collapse
|
5
|
Murayama K, Hosaka T, Shirouzu M, Sugimori D. Structure of a phosphodiesterase from Streptomyces sanglieri with a novel C-terminal domain. Biochem Biophys Res Commun 2024; 708:149784. [PMID: 38503170 DOI: 10.1016/j.bbrc.2024.149784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 03/12/2024] [Indexed: 03/21/2024]
Abstract
A glycerophosphoethanolamine ethanolaminephosphodiesterase (GPE-EP) from Streptomyces sanglieri hydrolyzes glycerophosphoethanolamine to phosphoethanolamine and glycerol. The structure of GPE-EP was determined by the molecular replacement method using a search model generated with AlphaFold2. This structure includes the entire length of the mature protein and it is composed of an N-terminal domain and a novel C-terminal domain connected to a flexible linker. The N-terminal domain is the catalytic domain containing calcium ions at the catalytic site. Coordination bonds were observed between five amino acid residues and glycerol. Although the function of the C-terminal domain is currently unknown, inter-domain interactions between the N- and C-terminal domains may contribute to its relatively high thermostability.
Collapse
Affiliation(s)
- Kazutaka Murayama
- Division of Biomedical Measurements and Diagnostics, Graduate School of Biomedical Engineering, Tohoku University, Sendai, 980-8575, Japan; Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, 230-0045, Japan.
| | - Toshiaki Hosaka
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, 230-0045, Japan
| | - Mikako Shirouzu
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, 230-0045, Japan
| | - Daisuke Sugimori
- Material Science Course, Faculty of Symbiotic Systems Science and Technology, Fukushima University, 1 Kanayagawa, Fukushima, 960-1296, Japan
| |
Collapse
|
6
|
Mahajan DM, Kumbhar PS, Jain R. Heterologous production of (-)-geosmin in Saccharomyces cerevisiae. J Biotechnol 2024; 386:1-9. [PMID: 38479473 DOI: 10.1016/j.jbiotec.2024.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 01/16/2024] [Accepted: 03/02/2024] [Indexed: 03/25/2024]
Abstract
(-)-Geosmin has high demand in perfumes and cosmetic products for its earthy congenial aroma. The current production of (-)-geosmin is either by distillation of sun-baked soil or by inefficient chemical synthesis because of the presence of multiple chiral centers. Fermentation processes are not viable as the titers of the Streptomyces sp. based processes are low. This work presents an alternative route by the heterologous synthesis of (-)-geosmin in Saccharomyces cerevisiae. The enzyme involved is the bifunctional geosmin synthase that catalyzes the conversion of farnesyl diphosphate to germacradienol and germacradienol to geosmin. This study evaluated the activity of many orthologs of geosmin synthase when expressed heterologously in S. cerevisiae. When the well-characterized CAB41566 from Streptomyces coelicolor origin was tested, germacradienol and germacrene D were detected but no geosmin. Bioinformatic analysis based on high/low identities to N-terminal and C-terminal domains of CAB41566 was carried out to identify different orthologs of geosmin synthase proteins from different bacterial and fungal origins. ADO68918 of Stigmatella aurantiaca origin showed the best activity among the tested orthologs, not only in terms of geosmin production but also an order of magnitude higher total abundance of the products of geosmin synthase as compared to CAB41566. This study successfully demonstrated the production of (-)-geosmin in S. cerevisiae and offers an alternative, sustainable and environment-friendly approach to producing (-)-geosmin.
Collapse
Affiliation(s)
- Dheeraj Madhukar Mahajan
- Praj-Matrix - R&D Centre (Division of Praj Industries Limited), 402/ 403/1098, Urawade, Pirangut, Mulshi, Pune 412115, India; Department of Technology, Savitribai Phule Pune University, Ganeshkhind, Pune 411007, India
| | - Pramod Shankar Kumbhar
- Praj-Matrix - R&D Centre (Division of Praj Industries Limited), 402/ 403/1098, Urawade, Pirangut, Mulshi, Pune 412115, India; Department of Technology, Savitribai Phule Pune University, Ganeshkhind, Pune 411007, India
| | - Rishi Jain
- Praj-Matrix - R&D Centre (Division of Praj Industries Limited), 402/ 403/1098, Urawade, Pirangut, Mulshi, Pune 412115, India; Department of Technology, Savitribai Phule Pune University, Ganeshkhind, Pune 411007, India.
| |
Collapse
|
7
|
Zhu Y, Lu T, Zhang H, Liu M, Pang X. SVEN_5003 is a Major Developmental Regulator in Streptomyces venezuelae. Curr Microbiol 2024; 81:166. [PMID: 38724665 DOI: 10.1007/s00284-024-03688-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 04/03/2024] [Indexed: 05/15/2024]
Abstract
Many regulatory genes that affect cellular development in Streptomyces, such as the canonical bld genes, have already been identified. However, in this study, we identified sven_5003 in Streptomyces venezuelae as a major new developmental regulatory gene, the deletion of which leads to a bald phenotype, typical of bld mutants, under multiple growth conditions. Our data indicated that disruption of sven_5003 also has a differential impact on the production of the two antibiotics jadomycin and chloramphenicol. Enhanced production of jadomycin but reduced production of chloramphenicol were detected in our sven_5003 mutant strain (S. venezuelae D5003). RNA-Seq analysis indicated that SVEN_5003 impacts expression of hundreds of genes, including genes involved in development, primary and secondary metabolism, and genes of unknown function, a finding confirmed by real-time PCR analysis. Transcriptional analysis indicated that sven_5003 is an auto-regulatory gene, repressing its own expression. Despite the evidence indicating that SVEN_5003 is a regulatory factor, a putative DNA-binding domain was not predicted from its primary amino acid sequence, implying an unknown regulatory mechanism by SVEN_5003. Our findings revealed that SVEN_5003 is a pleiotropic regulator with a critical role in morphological development in S. venezuelae.
Collapse
Affiliation(s)
- Yanping Zhu
- The State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Ting Lu
- The State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Hanlei Zhang
- The State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Meng Liu
- School of Municipal and Environmental Engineering, Shandong Jianzhu University, Jinan, 250101, China
| | - Xiuhua Pang
- The State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
| |
Collapse
|
8
|
Díaz-Cruz GA, Bignell DRD. Exploring the specialized metabolome of the plant pathogen Streptomyces sp. 11-1-2. Sci Rep 2024; 14:10414. [PMID: 38710735 DOI: 10.1038/s41598-024-60630-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 04/25/2024] [Indexed: 05/08/2024] Open
Abstract
Streptomyces bacteria are notable for producing chemically diverse specialized metabolites that exhibit various bioactivities and mediate interactions with different organisms. Streptomyces sp. 11-1-2 is a plant pathogen that produces nigericin and geldanamycin, both of which display toxic effects against various plants. Here, the 'One Strain Many Compounds' approach was used to characterize the metabolic potential of Streptomyces sp. 11-1-2. Organic extracts were prepared from 11-1-2 cultures grown on six different agar media, and the extracts were tested in antimicrobial and plant bioassays and were subjected to untargeted metabolomics and molecular networking. Most extracts displayed strong bioactivity against Gram-positive bacteria and yeast, and they exhibited phytotoxic activity against potato tuber tissue and radish seedlings. Several known specialized metabolites, including musacin D, galbonolide B, guanidylfungin A, meridamycins and elaiophylin, were predicted to be present in the extracts along with closely related compounds with unknown structure and bioactivity. Targeted detection confirmed the presence of elaiophylin in the extracts, and bioassays using pure elaiophylin revealed that it enhances the phytotoxic effects of geldanamycin and nigericin on potato tuber tissue. Overall, this study reveals novel insights into the specialized metabolites that may mediate interactions between Streptomyces sp. 11-1-2 and other bacteria and eukaryotic organisms.
Collapse
Affiliation(s)
- Gustavo A Díaz-Cruz
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
- Phytopathology Department, Plant Protection Research Center (CIPROC), Agronomy School, Universidad de Costa Rica, San Jose, Costa Rica
| | - Dawn R D Bignell
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada.
| |
Collapse
|
9
|
Zhuang Z, Kong W, Wen Z, Tong N, Lin J, Zhang F, Fan Z, Yi L, Huang Y, Duan Y, Yan X, Zhu X. Combinatorial metabolic engineering of Streptomyces sp. CB03234-S for the enhanced production of anthraquinone-fused enediyne tiancimycins. Microb Cell Fact 2024; 23:128. [PMID: 38704580 PMCID: PMC11069151 DOI: 10.1186/s12934-024-02399-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 04/23/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Anthraquinone-fused enediynes (AFEs) are excellent payloads for antibody-drug conjugates (ADCs). The yields of AFEs in the original bacterial hosts are extremely low. Multiple traditional methods had been adopted to enhance the production of the AFEs. Despite these efforts, the production titers of these compounds are still low, presenting a practical challenge for their development. Tiancimycins (TNMs) are a class of AFEs produced by Streptomyces sp. CB03234. One of their salient features is that they exhibit rapid and complete cell killing ability against various cancer cell lines. RESULTS In this study, a combinatorial metabolic engineering strategy guided by the CB03234-S genome and transcriptome was employed to improve the titers of TNMs. First, re-sequencing of CB03234-S (Ribosome engineered mutant strains) genome revealed the deletion of a 583-kb DNA fragment, accounting for about 7.5% of its genome. Second, by individual or combined inactivation of seven potential precursor competitive biosynthetic gene clusters (BGCs) in CB03234-S, a double-BGC inactivation mutant, S1009, was identified with an improved TNMs titer of 28.2 ± 0.8 mg/L. Third, overexpression of five essential biosynthetic genes, including two post-modification genes, and three self-resistance auxiliary genes, was also conducted, through which we discovered that mutants carrying the core genes, tnmE or tnmE10, exhibited enhanced TNMs production. The average TNMs yield reached 43.5 ± 2.4 mg/L in a 30-L fermenter, representing an approximately 360% increase over CB03234-S and the highest titer among all AFEs to date. Moreover, the resulting mutant produced TNM-W, a unique TNM derivative with a double bond instead of a common ethylene oxide moiety. Preliminary studies suggested that TNM-W was probably converted from TNM-A by both TnmE and TnmE10. CONCLUSIONS Based on the genome and transcriptome analyses, we adopted a combined metabolic engineering strategy for precursor enrichment and biosynthetic pathway reorganization to construct a high-yield strain of TNMs based on CB03234-S. Our study establishes a solid basis for the clinical development of AFE-based ADCs.
Collapse
Affiliation(s)
- Zhoukang Zhuang
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, 410013, China
| | - Wenping Kong
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, 410013, China
| | - Zhongqing Wen
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, 410013, China
| | - Nian Tong
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, 410013, China
| | - Jing Lin
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, 410013, China
| | - Fan Zhang
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, 410013, China
| | - Zhiying Fan
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, 410013, China
| | - Liwei Yi
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, 410013, China
- The Affiliated Nanhua Hospital, Department of Pharmacy, Institute of Clinical Pharmacy, Hengyang Medical School, University of South China, Hengyang, 421002, China
| | - Yong Huang
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, 410013, China
- Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, Changsha, 410011, China
| | - Yanwen Duan
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, 410013, China.
- Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, Changsha, 410011, China.
- National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, 410013, China.
| | - Xiaohui Yan
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, 410013, China.
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China.
| | - Xiangcheng Zhu
- Xiangya International Academy of Translational Medicine, Central South University, Changsha, 410013, China.
- Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, Changsha, 410011, China.
- National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, 410013, China.
| |
Collapse
|
10
|
Sang Z, Li X, Yan H, Wang W, Wen Y. Development of a group II intron-based genetic manipulation tool for Streptomyces. Microb Biotechnol 2024; 17:e14472. [PMID: 38683679 PMCID: PMC11057498 DOI: 10.1111/1751-7915.14472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/07/2024] [Accepted: 04/09/2024] [Indexed: 05/02/2024] Open
Abstract
The availability of an alternative and efficient genetic editing technology is critical for fundamental research and strain improvement engineering of Streptomyces species, which are prolific producers of complex secondary metabolites with significant pharmaceutical activities. The mobile group II introns are retrotransposons that employ activities of catalytic intron RNAs and intron-encoded reverse transcriptase to precisely insert into DNA target sites through a mechanism known as retrohoming. We here developed a group II intron-based gene editing tool to achieve precise chromosomal gene insertion in Streptomyces. Moreover, by repressing the potential competition of RecA-dependent homologous recombination, we enhanced site-specific insertion efficiency of this tool to 2.38%. Subsequently, we demonstrated the application of this tool by screening and characterizing the secondary metabolite biosynthetic gene cluster (BGC) responsible for synthesizing the red pigment in Streptomyces roseosporus. Accompanied with identifying and inactivating this BGC, we observed that the impair of this cluster promoted cell growth and daptomycin production. Additionally, we applied this tool to activate silent jadomycin BGC in Streptomyces venezuelae. Overall, this work demonstrates the potential of this method as an alternative tool for genetic engineering and cryptic natural product mining in Streptomyces species.
Collapse
Affiliation(s)
- Ziwei Sang
- State Key Laboratory of Animal Biotech Breeding and College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Xingwang Li
- State Key Laboratory of Animal Biotech Breeding and College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Hao Yan
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Weishan Wang
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Ying Wen
- State Key Laboratory of Animal Biotech Breeding and College of Biological SciencesChina Agricultural UniversityBeijingChina
| |
Collapse
|
11
|
Kudo K, Nishimura T, Izumikawa M, Kozone I, Hashimoto J, Fujie M, Suenaga H, Ikeda H, Satoh N, Shin-Ya K. Capability of a large bacterial artificial chromosome clone harboring multiple biosynthetic gene clusters for the production of diverse compounds. J Antibiot (Tokyo) 2024; 77:288-298. [PMID: 38438499 DOI: 10.1038/s41429-024-00711-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 02/02/2024] [Accepted: 02/12/2024] [Indexed: 03/06/2024]
Abstract
The biosynthetic gene clusters (BGCs) for the macrocyclic lactone-based polyketide compounds are extremely large-sized because the polyketide synthases that generate the polyketide chains of the basic backbone are of very high molecular weight. In developing a heterologous expression system for the large BGCs amenable to the production of such natural products, we selected concanamycin as an appropriate target. We obtained a bacterial artificial chromosome (BAC) clone with a 211-kb insert harboring the entire BGC responsible for the biosynthesis of concanamycin. Heterologous expression of this clone in a host strain, Streptomyces avermitilis SUKA32, permitted the production of concanamycin, as well as that of two additional aromatic polyketides. Structural elucidation identified these additional products as ent-gephyromycin and a novel compound that was designated JBIR-157. We describe herein sequencing and expression studies performed on these BGCs, demonstrating the utility of large BAC clones for the heterologous expression of cryptic or near-silent loci.
Collapse
Affiliation(s)
- Kei Kudo
- Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Takehiro Nishimura
- Technology Research Association for Next Generation Natural Products Chemistry, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
- Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo, 105-8512, Japan
| | - Miho Izumikawa
- Japan Biological Informatics Consortium (JBIC), 2-4-32 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Ikuko Kozone
- Japan Biological Informatics Consortium (JBIC), 2-4-32 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Junko Hashimoto
- Japan Biological Informatics Consortium (JBIC), 2-4-32 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Manabu Fujie
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Hikaru Suenaga
- Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Haruo Ikeda
- Kitasato Institute for Life Sciences, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
- Technology Research Association for Next Generation Natural Products Chemistry, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Nori Satoh
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Kazuo Shin-Ya
- Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan.
- Technology Research Association for Next Generation Natural Products Chemistry, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan.
| |
Collapse
|
12
|
Kimura SI, Watanabe Y, Shibasaki S, Shinzato N, Inahashi Y, Sunazuka T, Hokari R, Ishiyama A, Iwatsuki M. New antimalarial iromycin analogs produced by Streptomyces sp. RBL-0292. J Antibiot (Tokyo) 2024; 77:272-277. [PMID: 38438501 DOI: 10.1038/s41429-024-00707-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/17/2024] [Accepted: 01/22/2024] [Indexed: 03/06/2024]
Abstract
Two new antimalarial compounds, named prenylpyridones A (1) and B (2), were discovered from the actinomycete cultured material of Streptomyces sp. RBL-0292 isolated from the soil on Hamahiga Island in Okinawa prefecture. The structures of 1 and 2 were elucidated as new iromycin analogs having α-pyridone ring by MS and NMR analyses. Compounds 1 and 2 showed moderate in vitro antimalarial activity against chloroquine-sensitive and chloroquine-resistant Plasmodium falciparum strains, with IC50 values ranging from 80.7 to 106.7 µM.
Collapse
Affiliation(s)
- So-Ichiro Kimura
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Yoshihiro Watanabe
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
- Ōmura Satoshi Memorial Institute, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Shiori Shibasaki
- Ōmura Satoshi Memorial Institute, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Naoya Shinzato
- Tropical Biosphere Research Center, University of the Ryukyus, Senbaru 1, Nishihara-cho, Nakagami-gun, Okinawa, 903-0213, Japan
| | - Yuki Inahashi
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
- Ōmura Satoshi Memorial Institute, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Toshiaki Sunazuka
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
- Ōmura Satoshi Memorial Institute, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Rei Hokari
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
- Ōmura Satoshi Memorial Institute, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Aki Ishiyama
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan.
- Ōmura Satoshi Memorial Institute, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan.
| | - Masato Iwatsuki
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan.
- Ōmura Satoshi Memorial Institute, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan.
| |
Collapse
|
13
|
Zhou Z, Shi X, Bhople P, Jiang J, Chater CCC, Yang S, Perez-Moreno J, Yu F, Liu D. Enhancing C and N turnover, functional bacteria abundance, and the efficiency of biowaste conversion using Streptomyces-Bacillus inoculation. J Environ Manage 2024; 358:120895. [PMID: 38626487 DOI: 10.1016/j.jenvman.2024.120895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 03/01/2024] [Accepted: 04/10/2024] [Indexed: 04/18/2024]
Abstract
Microbial inoculation plays a significant role in promoting the efficiency of biowaste conversion. This study investigates the function of Streptomyces-Bacillus Inoculants (SBI) on carbon (C) and nitrogen (N) conversion, and microbial dynamics, during cow manure (10% and 20% addition) and corn straw co-composting. Compared to inoculant-free controls, inoculant application accelerated the compost's thermophilic stage (8 vs 15 days), and significantly increased compost total N contents (+47%) and N-reductase activities (nitrate reductase: +60%; nitrite reductase: +219%). Both bacterial and fungal community succession were significantly affected by DOC, urease, and NH4+-N, while the fungal community was also significantly affected by cellulase. The contribution rate of Cupriavidus to the physicochemical factors of compost was as high as 83.40%, but by contrast there were no significantly different contributions (∼60%) among the top 20 fungal genera. Application of SBI induced significant correlations between bacteria, compost C/N ratio, and catalase enzymes, indicative of compost maturation. We recommend SBI as a promising bio-composting additive to accelerate C and N turnover and high-quality biowaste maturation. SBI boosts organic cycling by transforming biowastes into bio-fertilizers efficiently. This highlights the potential for SBI application to improve plant growth and soil quality in multiple contexts.
Collapse
Affiliation(s)
- Ziyan Zhou
- The Germplasm Bank of Wild Species & Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Xiaofei Shi
- The Germplasm Bank of Wild Species & Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Parag Bhople
- Crops, Environment, And Land Use Department, Environment Research Centre, Teagasc, Johnstown Castle, Wexford, Y35TC98, Ireland
| | - Jishao Jiang
- School of Environment, Henan Normal University, Xinxiang, Henan, 453007, China
| | - Caspar C C Chater
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK; Plants, Photosynthesis, and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Shimei Yang
- The Germplasm Bank of Wild Species & Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Jesus Perez-Moreno
- Colegio de Postgraduados, Campus Montecillo, Edafologia, Texcoco, 56230, Mexico
| | - Fuqiang Yu
- The Germplasm Bank of Wild Species & Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
| | - Dong Liu
- The Germplasm Bank of Wild Species & Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
| |
Collapse
|
14
|
Yang M, Hao Y, Liu G, Wen Y. Enhancement of acyl-CoA precursor supply for increased avermectin B1a production by engineering meilingmycin polyketide synthase and key primary metabolic pathway genes. Microb Biotechnol 2024; 17:e14470. [PMID: 38683675 PMCID: PMC11057500 DOI: 10.1111/1751-7915.14470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/12/2024] [Accepted: 04/04/2024] [Indexed: 05/02/2024] Open
Abstract
Avermectins (AVEs), a family of macrocyclic polyketides produced by Streptomyces avermitilis, have eight components, among which B1a is noted for its strong insecticidal activity. Biosynthesis of AVE "a" components requires 2-methylbutyryl-CoA (MBCoA) as starter unit, and malonyl-CoA (MalCoA) and methylmalonyl-CoA (MMCoA) as extender units. We describe here a novel strategy for increasing B1a production by enhancing acyl-CoA precursor supply. First, we engineered meilingmycin (MEI) polyketide synthase (PKS) for increasing MBCoA precursor supply. The loading module (using acetyl-CoA as substrate), extension module 7 (using MMCoA as substrate) and TE domain of MEI PKS were assembled to produce 2-methylbutyrate, providing the starter unit for B1a production. Heterologous expression of the newly designed PKS (termed Mei-PKS) in S. avermitilis wild-type (WT) strain increased MBCoA level, leading to B1a titer 262.2 μg/mL - 4.36-fold higher than WT value (48.9 μg/mL). Next, we separately inhibited three key nodes in essential pathways using CRISPRi to increase MalCoA and MMCoA levels in WT. The resulting strains all showed increased B1a titer. Combined inhibition of these key nodes in Mei-PKS expression strain increased B1a titer to 341.9 μg/mL. Overexpression of fatty acid β-oxidation pathway genes in the strain further increased B1a titer to 452.8 μg/mL - 8.25-fold higher than WT value. Finally, we applied our precursor supply strategies to high-yield industrial strain A229. The strategies, in combination, led to B1a titer 8836.4 μg/mL - 37.8% higher than parental A229 value. These findings provide an effective combination strategy for increasing AVE B1a production in WT and industrial S. avermitilis strains, and our precursor supply strategies can be readily adapted for overproduction of other polyketides.
Collapse
Affiliation(s)
- Mengyao Yang
- State Key Laboratory of Animal Biotech Breeding and College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Yi Hao
- State Key Laboratory of Animal Biotech Breeding and College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Gang Liu
- State Key Laboratory of MycologyInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
| | - Ying Wen
- State Key Laboratory of Animal Biotech Breeding and College of Biological SciencesChina Agricultural UniversityBeijingChina
| |
Collapse
|
15
|
Li X, Zhu DY, Liu XR, Liu HJ, Tang SK, Cai L, Zhao LX. New Analogues of Amides and Quinolinones Produced by Streptomyces sp. YIM S01983. Chem Biodivers 2024; 21:e202400090. [PMID: 38486477 DOI: 10.1002/cbdv.202400090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 03/14/2024] [Indexed: 04/13/2024]
Abstract
Streptomide (1), a new amide analogue, streptomynone (2), a new quinolinone, and ten known compounds including three aliphatic acids (3-5), two amides (6-7), four cyclic dipeptides (8-11), and an adenosine (12) were isolated from the fermentation broth of Streptomyces sp. YIM S01983 isolated from a sediment sample collected in Bendong Village, Huadong Town, Chuxiong, China. Their structures were determined by analysis of the 1D/2D-NMR and HR-ESI-MS spectra. Compound 12 presented weak antimicrobial activities against Candida albicans and Aligenes faecalis (MIC=64 μg/mL). Compounds 7 and 12 showed weak cytotoxic activity against MHCC97H.
Collapse
Affiliation(s)
- Xia Li
- Key Laboratory of Functional Molecules Analysis and Biotransformation of Universities in Yunnan Province, Key Laboratory of Medicinal Chemistry for Natural Resource Ministry of Education, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, P. R. China
| | - Dou-Ying Zhu
- Key Laboratory of Functional Molecules Analysis and Biotransformation of Universities in Yunnan Province, Key Laboratory of Medicinal Chemistry for Natural Resource Ministry of Education, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, P. R. China
| | - Xi-Ru Liu
- Key Laboratory of Functional Molecules Analysis and Biotransformation of Universities in Yunnan Province, Key Laboratory of Medicinal Chemistry for Natural Resource Ministry of Education, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, P. R. China
| | - Hong-Jian Liu
- Key Laboratory of Functional Molecules Analysis and Biotransformation of Universities in Yunnan Province, Key Laboratory of Medicinal Chemistry for Natural Resource Ministry of Education, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, P. R. China
| | - Shu-Kun Tang
- Yunnan Institute of Microbiology, University, Kunming, 650091, P. R.China
| | - Le Cai
- Key Laboratory of Functional Molecules Analysis and Biotransformation of Universities in Yunnan Province, Key Laboratory of Medicinal Chemistry for Natural Resource Ministry of Education, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, P. R. China
| | - Li-Xing Zhao
- Key Laboratory of Functional Molecules Analysis and Biotransformation of Universities in Yunnan Province, Key Laboratory of Medicinal Chemistry for Natural Resource Ministry of Education, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, P. R. China
- Yunnan Institute of Microbiology, University, Kunming, 650091, P. R.China
| |
Collapse
|
16
|
Shigeno S, Kadowaki M, Nagai K, Hosoda K, Terahara T, Nishimura T, Hasegawa N, Tomoda H, Ohshiro T. New polycyclic tetramate macrolactams with antimycobacterial activity produced by marine-derived Streptomyces sp. KKMA-0239. J Antibiot (Tokyo) 2024; 77:265-271. [PMID: 38531967 DOI: 10.1038/s41429-024-00710-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/11/2024] [Accepted: 02/06/2024] [Indexed: 03/28/2024]
Abstract
During our screening for anti-mycobacterial agents against Mycobacterium avium complex (MAC), two new polycyclic tetramate macrolactams (PTMs), named hydroxycapsimycin (1) and brokamycin (2), were isolated along with the known PTM, ikarugamycin (3), from the culture broth of marine-derived Streptomyces sp. KKMA-0239. The relative structures of 1 and 2 were elucidated by spectroscopic data analyses, including 1D and 2D NMR. Furthermore, the absolute configuration of 1 was confirmed by a single-crystal X-ray diffraction analysis. Compounds 2 and 3 exhibited moderate antimycobacterial activities against MAC, including clinically isolated drug-resistant M. avium.
Collapse
Affiliation(s)
- Satoru Shigeno
- Department of Microbial Chemistry, Graduate School of Pharmaceutical Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
- Medicinal Research Laboratories, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Miyu Kadowaki
- Department of Microbial Chemistry, Graduate School of Pharmaceutical Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
- Medicinal Research Laboratories, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Kenichiro Nagai
- Medicinal Research Laboratories, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Kanji Hosoda
- Department of Microbial Chemistry, Graduate School of Pharmaceutical Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
- Medicinal Research Laboratories, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Takeshi Terahara
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo, 108-8477, Japan
| | - Tomoyasu Nishimura
- Keio University Health Center, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Naoki Hasegawa
- Department of Infectious Diseases, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Hiroshi Tomoda
- Department of Microbial Chemistry, Graduate School of Pharmaceutical Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan.
- Medicinal Research Laboratories, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan.
| | - Taichi Ohshiro
- Department of Microbial Chemistry, Graduate School of Pharmaceutical Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan.
- Medicinal Research Laboratories, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan.
| |
Collapse
|
17
|
Zhao J, Li Q, Zeeshan M, Zhang G, Wang C, Han X, Yang D. Integrative Genomics and Bioactivity-Guided Isolation of Novel Antimicrobial Compounds from Streptomyces sp. KN37 in Agricultural Applications. Molecules 2024; 29:2040. [PMID: 38731531 PMCID: PMC11085741 DOI: 10.3390/molecules29092040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/22/2024] [Accepted: 04/27/2024] [Indexed: 05/13/2024] Open
Abstract
Actinomycetes have long been recognized as an important source of antibacterial natural products. In recent years, actinomycetes in extreme environments have become one of the main research directions. Streptomyces sp. KN37 was isolated from the cold region of Kanas in Xinjiang. It demonstrated potent antimicrobial activity, but the primary active compounds remained unclear. Therefore, we aimed to combine genomics with traditional isolation methods to obtain bioactive compounds from the strain KN37. Whole-genome sequencing and KEGG enrichment analysis indicated that KN37 possesses the potential for synthesizing secondary metabolites, and 41 biosynthetic gene clusters were predicted, some of which showed high similarity to known gene clusters responsible for the biosynthesis of antimicrobial antibiotics. The traditional isolation methods and activity-guided fractionation were employed to isolate and purify seven compounds with strong bioactivity from the fermentation broth of the strain KN37. These compounds were identified as 4-(Diethylamino)salicylaldehyde (1), 4-Nitrosodiphenylamine (2), N-(2,4-Dimethylphenyl)formamide (3), 4-Nitrocatechol (4), Methylsuccinic acid (5), Phenyllactic acid (6) and 5,6-Dimethylbenzimidazole (7). Moreover, 4-(Diethylamino)salicylaldehyde exhibited the most potent inhibitory effect against Rhizoctonia solani, with an EC50 value of 14.487 mg/L, while 4-Nitrosodiphenylamine showed great antibacterial activity against Erwinia amylovora, with an EC50 value of 5.715 mg/L. This study successfully isolated several highly active antimicrobial compounds from the metabolites of the strain KN37, which could contribute as scaffolds for subsequent chemical synthesis. On the other hand, the newly predicted antibiotic-like substances have not yet been isolated, but they still hold significant research value. They are instructive in the study of active natural product biosynthetic pathways, activation of silent gene clusters, and engineering bacteria construction.
Collapse
Affiliation(s)
| | | | | | - Guoqiang Zhang
- The Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Utilization, College of Agriculture, Shihezi University, Shihezi 832003, China; (J.Z.); (Q.L.); (M.Z.); (X.H.); (D.Y.)
| | - Chunjuan Wang
- The Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Utilization, College of Agriculture, Shihezi University, Shihezi 832003, China; (J.Z.); (Q.L.); (M.Z.); (X.H.); (D.Y.)
| | | | | |
Collapse
|
18
|
Yang L, Yi L, Gong B, Chen L, Li M, Zhu X, Duan Y, Huang Y. Chalkophomycin Biosynthesis Revealing Unique Enzyme Architecture for a Hybrid Nonribosomal Peptide Synthetase and Polyketide Synthase. Molecules 2024; 29:1982. [PMID: 38731473 PMCID: PMC11085572 DOI: 10.3390/molecules29091982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/17/2024] [Accepted: 04/23/2024] [Indexed: 05/13/2024] Open
Abstract
Chalkophomycin is a novel chalkophore with antibiotic activities isolated from Streptomyces sp. CB00271, while its potential in studying cellular copper homeostasis makes it an important probe and drug lead. The constellation of N-hydroxylpyrrole, 2H-oxazoline, diazeniumdiolate, and methoxypyrrolinone functional groups into one compact molecular architecture capable of coordinating cupric ions draws interest to unprecedented enzymology responsible for chalkophomycin biosynthesis. To elucidate the biosynthetic machinery for chalkophomycin production, the chm biosynthetic gene cluster from S. sp. CB00271 was identified, and its involvement in chalkophomycin biosynthesis was confirmed by gene replacement. The chm cluster was localized to a ~31 kb DNA region, consisting of 19 open reading frames that encode five nonribosomal peptide synthetases (ChmHIJLO), one modular polyketide synthase (ChmP), six tailoring enzymes (ChmFGMNQR), two regulatory proteins (ChmAB), and four resistance proteins (ChmA'CDE). A model for chalkophomycin biosynthesis is proposed based on functional assignments from sequence analysis and structure modelling, and is further supported by analogy to over 100 chm-type gene clusters in public databases. Our studies thus set the stage to fully investigate chalkophomycin biosynthesis and to engineer chalkophomycin analogues through a synthetic biology approach.
Collapse
Affiliation(s)
- Long Yang
- Department of Immunology, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China;
- Hefei Comprehensive National Science Center, Institute of Health and Medicine, Hefei 230093, China;
| | - Liwei Yi
- Xiangya International Academy of Translational Medicine, Central South University, Changsha 410013, China; (L.Y.); (B.G.); (M.L.); (X.Z.); (Y.D.)
- Department of Pharmacy, The Affiliated Nanhua Hospital, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Bang Gong
- Xiangya International Academy of Translational Medicine, Central South University, Changsha 410013, China; (L.Y.); (B.G.); (M.L.); (X.Z.); (Y.D.)
- College of Pharmacy, Hunan Vocational College of Science and Technology, Changsha 410004, China
| | - Lili Chen
- Hefei Comprehensive National Science Center, Institute of Health and Medicine, Hefei 230093, China;
| | - Miao Li
- Xiangya International Academy of Translational Medicine, Central South University, Changsha 410013, China; (L.Y.); (B.G.); (M.L.); (X.Z.); (Y.D.)
| | - Xiangcheng Zhu
- Xiangya International Academy of Translational Medicine, Central South University, Changsha 410013, China; (L.Y.); (B.G.); (M.L.); (X.Z.); (Y.D.)
- Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, Changsha 410011, China
- National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha 410011, China
| | - Yanwen Duan
- Xiangya International Academy of Translational Medicine, Central South University, Changsha 410013, China; (L.Y.); (B.G.); (M.L.); (X.Z.); (Y.D.)
- Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, Changsha 410011, China
- National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha 410011, China
| | - Yong Huang
- Department of Immunology, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China;
- Hefei Comprehensive National Science Center, Institute of Health and Medicine, Hefei 230093, China;
- Xiangya International Academy of Translational Medicine, Central South University, Changsha 410013, China; (L.Y.); (B.G.); (M.L.); (X.Z.); (Y.D.)
| |
Collapse
|
19
|
Chen L, Liu K, Hong J, Cui Z, He W, Wang Y, Deng Z, Tao M. The Discovery of Weddellamycin, a Tricyclic Polyene Macrolactam Antibiotic from an Antarctic Deep-Sea-Derived Streptomyces sp. DSS69, by Heterologous Expression. Mar Drugs 2024; 22:189. [PMID: 38667806 PMCID: PMC11051340 DOI: 10.3390/md22040189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/11/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024] Open
Abstract
Polyene macrolactams are a special group of natural products with great diversity, unique structural features, and a wide range of biological activities. Herein, a cryptic gene cluster for the biosynthesis of putative macrolactams was disclosed from a sponge-associated bacterium, Streptomyces sp. DSS69, by genome mining. Cloning and heterologous expression of the whole biosynthetic gene cluster led to the discovery of weddellamycin, a polyene macrolactam bearing a 23/5/6 ring skeleton. A negative regulator, WdlO, and two positive regulators, WdlA and WdlB, involved in the regulation of weddellamycin production were unraveled. The fermentation titer of weddellamycin was significantly improved by overexpression of wdlA and wdlB and deletion of wdlO. Notably, weddellamycin showed remarkable antibacterial activity against various Gram-positive bacteria including MRSA, with MIC values of 0.10-0.83 μg/mL, and antifungal activity against Candida albicans, with an MIC value of 3.33 μg/mL. Weddellamycin also displayed cytotoxicity against several cancer cell lines, with IC50 values ranging from 2.07 to 11.50 µM.
Collapse
Affiliation(s)
- Lu Chen
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (L.C.); (K.L.); (J.H.); (Z.C.); (W.H.); (Y.W.); (Z.D.)
| | - Kai Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (L.C.); (K.L.); (J.H.); (Z.C.); (W.H.); (Y.W.); (Z.D.)
| | - Jiali Hong
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (L.C.); (K.L.); (J.H.); (Z.C.); (W.H.); (Y.W.); (Z.D.)
| | - Zhanzhao Cui
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (L.C.); (K.L.); (J.H.); (Z.C.); (W.H.); (Y.W.); (Z.D.)
| | - Weijun He
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (L.C.); (K.L.); (J.H.); (Z.C.); (W.H.); (Y.W.); (Z.D.)
| | - Yemin Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (L.C.); (K.L.); (J.H.); (Z.C.); (W.H.); (Y.W.); (Z.D.)
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (L.C.); (K.L.); (J.H.); (Z.C.); (W.H.); (Y.W.); (Z.D.)
- Haihe Laboratory of Synthetic Biology, Tianjin 300308, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Meifeng Tao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (L.C.); (K.L.); (J.H.); (Z.C.); (W.H.); (Y.W.); (Z.D.)
- Haihe Laboratory of Synthetic Biology, Tianjin 300308, China
| |
Collapse
|
20
|
Lee SQE, Ma GL, Candra H, Khandelwal S, Pang LM, Low ZJ, Cheang QW, Liang ZX. Streptomyces sungeiensis SD3 as a Microbial Chassis for the Heterologous Production of Secondary Metabolites. ACS Synth Biol 2024; 13:1259-1272. [PMID: 38513222 DOI: 10.1021/acssynbio.3c00750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
We present the newly isolated Streptomyces sungeiensis SD3 strain as a promising microbial chassis for heterologous production of secondary metabolites. S. sungeiensis SD3 exhibits several advantageous traits as a microbial chassis, including genetic tractability, rapid growth, susceptibility to antibiotics, and metabolic capability supporting secondary metabolism. Genomic and transcriptomic sequencing unveiled the primary metabolic capabilities and secondary biosynthetic pathways of S. sungeiensis SD3, including a previously unknown pathway responsible for the biosynthesis of streptazone B1. The unique placement of S. sungeiensis SD3 in the phylogenetic tree designates it as a type strain, setting it apart from other frequently employed Streptomyces chassis. This distinction makes it the preferred chassis for expressing biosynthetic gene clusters (BGCs) derived from strains within the same phylogenetic or neighboring phylogenetic clade. The successful expression of secondary biosynthetic pathways from a closely related yet slow-growing strain underscores the utility of S. sungeiensis SD3 as a heterologous expression chassis. Validation of CRISPR/Cas9-assisted genetic tools for chromosomal deletion and insertion paved the way for further strain improvement and BGC refactoring through rational genome editing. The addition of S. sungeiensis SD3 to the heterologous chassis toolkit will facilitate the discovery and production of secondary metabolites.
Collapse
Affiliation(s)
- Sean Qiu En Lee
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Guang-Lei Ma
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hartono Candra
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Srashti Khandelwal
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Li Mei Pang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Zhen Jie Low
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Qing Wei Cheang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| |
Collapse
|
21
|
Ding W, Li Y, Li X, Yin J, Shi S, Tian X, Zhang S, Yin H. Discovery of a Novel Chromone Enantiomer and the Precursors of Nonactic Acid from the Coral-Reef-Derived Streptomyces sp. SCSIO 66814. Mar Drugs 2024; 22:181. [PMID: 38667798 PMCID: PMC11051294 DOI: 10.3390/md22040181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/07/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
Three pairs of enantiomers (1-3)-the new 12R-aloesol (1a) and two new fatty acids (2 and 3)-and one new natural product (4) together three known compounds (5-7) were isolated from a coral-reef-derived Streptomyces sp. SCSIO 66814. Their structures were determined through extensive spectroscopic analysis, chiral analysis, and single-crystal X-ray diffraction data. Compounds 2 and 3 were presumed to be intermediates for further generating homononactic acid (5) and nonactic acid, and the latter two molecules were able to act as precursors to form macrotetrolides with remarkable biological activity. The isolation of related precursors, compounds 2-5, provided more evidence to support the proposal of a plausible biosynthetic pathway for nonactic acid and its homologs. Additionally, (+)-1 exhibited a weak activity against DPPH radicals.
Collapse
Affiliation(s)
- Wenping Ding
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (W.D.); (Y.L.); (X.L.); (J.Y.); (S.S.); (X.T.)
| | - Yanqun Li
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (W.D.); (Y.L.); (X.L.); (J.Y.); (S.S.); (X.T.)
| | - Xingyu Li
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (W.D.); (Y.L.); (X.L.); (J.Y.); (S.S.); (X.T.)
| | - Jiajia Yin
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (W.D.); (Y.L.); (X.L.); (J.Y.); (S.S.); (X.T.)
| | - Songbiao Shi
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (W.D.); (Y.L.); (X.L.); (J.Y.); (S.S.); (X.T.)
| | - Xinpeng Tian
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (W.D.); (Y.L.); (X.L.); (J.Y.); (S.S.); (X.T.)
| | - Si Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (W.D.); (Y.L.); (X.L.); (J.Y.); (S.S.); (X.T.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Hao Yin
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (W.D.); (Y.L.); (X.L.); (J.Y.); (S.S.); (X.T.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| |
Collapse
|
22
|
Zhang C, Xu Q, Fu J, Wu L, Li Y, Lu Y, Shi Y, Sun H, Li X, Wang L, Hong B. Engineering Streptomyces sp. CPCC 204095 for the targeted high-level production of isatropolone A by elucidating its pathway-specific regulatory mechanism. Microb Cell Fact 2024; 23:113. [PMID: 38622698 PMCID: PMC11020959 DOI: 10.1186/s12934-024-02387-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 04/05/2024] [Indexed: 04/17/2024] Open
Abstract
BACKGROUND Isatropolone A and C, produced by Streptomyces sp. CPCC 204095, belong to an unusual class of non-benzenoid aromatic compounds and contain a rare seven-membered ring structure. Isatropolone A exhibits potent activity against Leishmania donovani, comparable to the only oral drug miltefosine. However, its variably low productivity represents a limitation for this lead compound in the future development of new anti-leishmaniasis drugs to meet unmet clinical needs. RESULTS Here we first elucidated the regulatory cascade of biosynthesis of isatropolones, which consists of two SARP family regulators, IsaF and IsaJ. Through a series of in vivo and in vitro experiments, IsaF was identified as a pathway-specific activator that orchestrates the transcription of the gene cluster essential for isatropolone biosynthesis. Interestingly, IsaJ was found to only upregulate the expression of the cytochrome P450 monooxygenase IsaS, which is crucial for the yield and proportion of isatropolone A and C. Through targeted gene deletions of isaJ or isaS, we effectively impeded the conversion of isatropolone A to C. Concurrently, the facilitation of isaF overexpression governed by selected promoters, prompted the comprehensive activation of the production of isatropolone A. Furthermore, meticulous optimization of the fermentation parameters was conducted. These strategies culminated in the attainment of an unprecedented maximum yield-980.8 mg/L of isatropolone A-achieved in small-scale solid-state fermentation utilizing the genetically modified strains, thereby establishing the highest reported titer to date. CONCLUSION In Streptomyces sp. CPCC 204095, the production of isatropolone A and C is modulated by the SARP regulators IsaF and IsaJ. IsaF serves as a master pathway-specific regulator for the production of isatropolones. IsaJ, on the other hand, only dictates the transcription of IsaS, the enzyme responsible for the conversion of isatropolone A and C. By engineering the expression of these pivotal genes, we have devised a strategy for genetic modification aimed at the selective and high-yield biosynthesis of isatropolone A. This study not only unveils the unique regulatory mechanisms governing isatropolone biosynthesis for the first time, but also establishes an essential engineering framework for the targeted high-level production of isatropolone A.
Collapse
Affiliation(s)
- Cong Zhang
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, NHC Key Laboratory of Biotechnology for Microbial Drugs and State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Qianqian Xu
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, NHC Key Laboratory of Biotechnology for Microbial Drugs and State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Jie Fu
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, NHC Key Laboratory of Biotechnology for Microbial Drugs and State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Linzhuan Wu
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, NHC Key Laboratory of Biotechnology for Microbial Drugs and State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Yihong Li
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, NHC Key Laboratory of Biotechnology for Microbial Drugs and State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Yuan Lu
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, NHC Key Laboratory of Biotechnology for Microbial Drugs and State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Yuanyuan Shi
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, NHC Key Laboratory of Biotechnology for Microbial Drugs and State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Hongmin Sun
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, NHC Key Laboratory of Biotechnology for Microbial Drugs and State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Xingxing Li
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, NHC Key Laboratory of Biotechnology for Microbial Drugs and State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China.
| | - Lifei Wang
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, NHC Key Laboratory of Biotechnology for Microbial Drugs and State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China.
| | - Bin Hong
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, NHC Key Laboratory of Biotechnology for Microbial Drugs and State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China.
| |
Collapse
|
23
|
Tan LL, Heng E, Leong CY, Ng V, Yang LK, Seow DCS, Koduru L, Kanagasundaram Y, Ng SB, Peh G, Lim YH, Wong FT. Application of Cas12j for Streptomyces Editing. Biomolecules 2024; 14:486. [PMID: 38672502 PMCID: PMC11048056 DOI: 10.3390/biom14040486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/09/2024] [Accepted: 04/14/2024] [Indexed: 04/28/2024] Open
Abstract
In recent years, CRISPR-Cas toolboxes for Streptomyces editing have rapidly accelerated natural product discovery and engineering. However, Cas efficiencies are oftentimes strain-dependent, and the commonly used Streptococcus pyogenes Cas9 (SpCas9) is notorious for having high levels of off-target toxicity effects. Thus, a variety of Cas proteins is required for greater flexibility of genetic manipulation within a wider range of Streptomyces strains. This study explored the first use of Acidaminococcus sp. Cas12j, a hypercompact Cas12 subfamily, for genome editing in Streptomyces and its potential in activating silent biosynthetic gene clusters (BGCs) to enhance natural product synthesis. While the editing efficiencies of Cas12j were not as high as previously reported efficiencies of Cas12a and Cas9, Cas12j exhibited higher transformation efficiencies compared to SpCas9. Furthermore, Cas12j demonstrated significantly improved editing efficiencies compared to Cas12a in activating BGCs in Streptomyces sp. A34053, a strain wherein both SpCas9 and Cas12a faced limitations in accessing the genome. Overall, this study expanded the repertoire of Cas proteins for genome editing in actinomycetes and highlighted not only the potential of recently characterized Cas12j in Streptomyces but also the importance of having an extensive genetic toolbox for improving the editing success of these beneficial microbes.
Collapse
Affiliation(s)
- Lee Ling Tan
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos #07-06, Singapore 138673, Singapore; (L.L.T.); (E.H.)
| | - Elena Heng
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos #07-06, Singapore 138673, Singapore; (L.L.T.); (E.H.)
| | - Chung Yan Leong
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #02-01, Singapore 138669, Singapore; (C.Y.L.); (V.N.); (L.K.Y.); (D.C.S.S.); (Y.K.); (S.B.N.)
| | - Veronica Ng
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #02-01, Singapore 138669, Singapore; (C.Y.L.); (V.N.); (L.K.Y.); (D.C.S.S.); (Y.K.); (S.B.N.)
| | - Lay Kien Yang
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #02-01, Singapore 138669, Singapore; (C.Y.L.); (V.N.); (L.K.Y.); (D.C.S.S.); (Y.K.); (S.B.N.)
| | - Deborah Chwee San Seow
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #02-01, Singapore 138669, Singapore; (C.Y.L.); (V.N.); (L.K.Y.); (D.C.S.S.); (Y.K.); (S.B.N.)
| | - Lokanand Koduru
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos #07-06, Singapore 138673, Singapore; (L.L.T.); (E.H.)
| | - Yoganathan Kanagasundaram
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #02-01, Singapore 138669, Singapore; (C.Y.L.); (V.N.); (L.K.Y.); (D.C.S.S.); (Y.K.); (S.B.N.)
| | - Siew Bee Ng
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #02-01, Singapore 138669, Singapore; (C.Y.L.); (V.N.); (L.K.Y.); (D.C.S.S.); (Y.K.); (S.B.N.)
| | - Guangrong Peh
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, Neuros #07-01, Singapore 138665, Singapore; (G.P.); (Y.H.L.)
| | - Yee Hwee Lim
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, Neuros #07-01, Singapore 138665, Singapore; (G.P.); (Y.H.L.)
| | - Fong Tian Wong
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos #07-06, Singapore 138673, Singapore; (L.L.T.); (E.H.)
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, Neuros #07-01, Singapore 138665, Singapore; (G.P.); (Y.H.L.)
| |
Collapse
|
24
|
Shepherdson EMF, Elliot MA. Redefining development in Streptomyces venezuelae: integrating exploration into the classical sporulating life cycle. mBio 2024; 15:e0242423. [PMID: 38470267 PMCID: PMC11005364 DOI: 10.1128/mbio.02424-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 02/23/2024] [Indexed: 03/13/2024] Open
Abstract
Two growth modes have been described for the filamentous Streptomyces bacteria. Their classic developmental life cycle culminates in the formation of dormant spores, where movement to new environments is mediated through spore dispersal. In contrast, exploratory growth proceeds as a rapidly expanding vegetative mycelium that leads to extensive surface colonization and is associated with the release of volatile compounds that promote alkalinization (and reduced iron bioavailability) of its surrounding environment. Here, we report that exploratory growth in Streptomyces venezuelae can proceed in tandem with classic sporulating development in response to specific nutritional cues. Sporulating exploration is not accompanied by a rise in environmental pH but has the same iron acquisition requirements as conventional exploration. We found that mutants that were defective in their ability to sporulate were unaffected in exploration, but mutants undergoing precocious sporulation were compromised in their exploratory growth and this appeared to be mediated through premature activation of the developmental regulator WhiI. Cell envelope integrity was also found to be critical for exploration, as mutations in the cell envelope stress-responsive extracytoplasmic function sigma factor SigE led to a failure to explore robustly under all exploration-promoting conditions. Finally, in expanding the known exploration-promoting conditions, we discovered that the model species Streptomyces lividans exhibited exploration capabilities, supporting the proposal that exploration is conserved across diverse streptomycetes. IMPORTANCE Streptomyces bacteria have evolved diverse developmental and metabolic strategies to thrive in dynamic environmental niches. Here, we report the amalgamation of previously disparate developmental pathways, showing that colony expansion via exploration can proceed in tandem with colony sporulation. This developmental integration extends beyond phenotype to include shared genetic elements, with sporulation-specific repressors being required for successful exploration. Comparing this new exploration mode with previously identified strategies has revealed key differences (e.g., no need for environmental alkalinization), and simultaneously allowed us to define unifying requirements for Streptomyces exploration. The "reproductive exploration" phenomenon reported here represents a unique bet-hedging strategy, with the Streptomyces colony engaging in an aggressive colonization strategy while transporting a protected genetic repository.
Collapse
Affiliation(s)
- Evan M. F. Shepherdson
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Marie A. Elliot
- Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| |
Collapse
|
25
|
Thapa BB, Huo C, Budhathoki R, Chaudhary P, Joshi S, Poudel PB, Magar RT, Parajuli N, Kim KH, Sohng JK. Metabolic Comparison and Molecular Networking of Antimicrobials in Streptomyces Species. Int J Mol Sci 2024; 25:4193. [PMID: 38673777 PMCID: PMC11050201 DOI: 10.3390/ijms25084193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 04/03/2024] [Accepted: 04/07/2024] [Indexed: 04/28/2024] Open
Abstract
Streptomyces are well-known for producing bioactive secondary metabolites, with numerous antimicrobials essential to fight against infectious diseases. Globally, multidrug-resistant (MDR) microorganisms significantly challenge human and veterinary diseases. To tackle this issue, there is an urgent need for alternative antimicrobials. In the search for potent agents, we have isolated four Streptomyces species PC1, BT1, BT2, and BT3 from soils collected from various geographical regions of the Himalayan country Nepal, which were then identified based on morphology and 16S rRNA gene sequencing. The relationship of soil microbes with different Streptomyces species has been shown in phylogenetic trees. Antimicrobial potency of isolates was carried out against Staphylococcus aureus American Type Culture Collection (ATCC) 43300, Shigella sonnei ATCC 25931, Salmonella typhi ATCC 14028, Klebsiella pneumoniae ATCC 700603, and Escherichia coli ATCC 25922. Among them, Streptomyces species PC1 showed the highest zone of inhibition against tested pathogens. Furthermore, ethyl acetate extracts of shake flask fermentation of these Streptomyces strains were subjected to liquid chromatography-tandem mass spectrometric (LC-MS/MS) analysis for their metabolic comparison and Global Natural Products Social Molecular Networking (GNPS) web-based molecular networking. We found very similar metabolite composition in four strains, despite their geographical variation. In addition, we have identified thirty-seven metabolites using LC-MS/MS analysis, with the majority belonging to the diketopiperazine class. Among these, to the best of our knowledge, four metabolites, namely cyclo-(Ile-Ser), 2-n-hexyl-5-n-propylresorcinol, 3-[(6-methylpyrazin-2-yl) methyl]-1H-indole, and cyclo-(d-Leu-l-Trp), were detected for the first time in Streptomyces species. Besides these, other 23 metabolites including surfactin B, surfactin C, surfactin D, and valinomycin were identified with the help of GNPS-based molecular networking.
Collapse
Affiliation(s)
- Bijaya Bahadur Thapa
- Central Department of Chemistry, Tribhuvan University, Kirtipur 44618, Kathmandu, Nepal; (B.B.T.); (R.B.); (P.C.); (S.J.); (N.P.)
| | - Chen Huo
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea;
| | - Rabin Budhathoki
- Central Department of Chemistry, Tribhuvan University, Kirtipur 44618, Kathmandu, Nepal; (B.B.T.); (R.B.); (P.C.); (S.J.); (N.P.)
| | - Pratiksha Chaudhary
- Central Department of Chemistry, Tribhuvan University, Kirtipur 44618, Kathmandu, Nepal; (B.B.T.); (R.B.); (P.C.); (S.J.); (N.P.)
| | - Soniya Joshi
- Central Department of Chemistry, Tribhuvan University, Kirtipur 44618, Kathmandu, Nepal; (B.B.T.); (R.B.); (P.C.); (S.J.); (N.P.)
| | - Purna Bahadur Poudel
- Institute of Biomolecule Reconstruction (iBR), Department of Life Science and Biochemical Engineering, Sun Moon University, Asan 31460, Republic of Korea; (P.B.P.); (R.T.M.)
| | - Rubin Thapa Magar
- Institute of Biomolecule Reconstruction (iBR), Department of Life Science and Biochemical Engineering, Sun Moon University, Asan 31460, Republic of Korea; (P.B.P.); (R.T.M.)
| | - Niranjan Parajuli
- Central Department of Chemistry, Tribhuvan University, Kirtipur 44618, Kathmandu, Nepal; (B.B.T.); (R.B.); (P.C.); (S.J.); (N.P.)
- Institute of Biomolecule Reconstruction (iBR), Department of Life Science and Biochemical Engineering, Sun Moon University, Asan 31460, Republic of Korea; (P.B.P.); (R.T.M.)
| | - Ki Hyun Kim
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea;
| | - Jae Kyung Sohng
- Institute of Biomolecule Reconstruction (iBR), Department of Life Science and Biochemical Engineering, Sun Moon University, Asan 31460, Republic of Korea; (P.B.P.); (R.T.M.)
| |
Collapse
|
26
|
Tian J, Li Y, Zhang C, Su J, Lu W. Characterization of a pleiotropic regulator MtrA in Streptomyces avermitilis controlling avermectin production and morphological differentiation. Microb Cell Fact 2024; 23:103. [PMID: 38584273 PMCID: PMC11000389 DOI: 10.1186/s12934-024-02331-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 02/11/2024] [Indexed: 04/09/2024] Open
Abstract
BACKGROUND The macrolide antibiotic avermectin, a natural product derived from Streptomyces avermitilis, finds extensive applications in agriculture, animal husbandry and medicine. The mtrA (sav_5063) gene functions as a transcriptional regulator belonging to the OmpR family. As a pleiotropic regulator, mtrA not only influences the growth, development, and morphological differentiation of strains but also modulates genes associated with primary metabolism. However, the regulatory role of MtrA in avermectin biosynthesis remains to be elucidated. RESULTS In this study, we demonstrated that MtrA, a novel OmpR-family transcriptional regulator in S. avermitilis, exerts global regulator effects by negatively regulating avermectin biosynthesis and cell growth while positively controlling morphological differentiation. The deletion of the mtrA gene resulted in an increase in avermectin production, accompanied by a reduction in biomass and a delay in the formation of aerial hyphae and spores. The Electrophoretic Mobility Shift Assay (EMSA) revealed that MtrA exhibited binding affinity towards the upstream region of aveR, the intergenic region between aveA1 and aveA2 genes, as well as the upstream region of aveBVIII in vitro. These findings suggest that MtrA exerts a negative regulatory effect on avermectin biosynthesis by modulating the expression of avermectin biosynthesis cluster genes. Transcriptome sequencing and fluorescence quantitative PCR analysis showed that mtrA deletion increased the transcript levels of the cluster genes aveR, aveA1, aveA2, aveC, aveE, aveA4 and orf-1, which explains the observed increase in avermectin production in the knockout strain. Furthermore, our findings demonstrate that MtrA positively regulates the cell division and differentiation genes bldM and ssgC, while exerting a negative regulatory effect on bldD, thereby modulating the primary metabolic processes associated with cell division, differentiation and growth in S. avermitilis, consequently impacting avermectin biosynthesis. CONCLUSIONS In this study, we investigated the negative regulatory effect of the global regulator MtrA on avermectin biosynthesis and its effects on morphological differentiation and cell growth, and elucidated its transcriptional regulatory mechanism. Our findings indicate that MtrA plays crucial roles not only in the biosynthesis of avermectin but also in coordinating intricate physiological processes in S. avermitilis. These findings provide insights into the synthesis of avermectin and shed light on the primary and secondary metabolism of S. avermitilis mediated by OmpR-family regulators.
Collapse
Affiliation(s)
- Jinpin Tian
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China
| | - Yue Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China
| | - Chuanbo Zhang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China
- Frontiers Science Center for Synthetic Biology, Tianjin University, Tianjin, People's Republic of China
- Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education, Tianjin, People's Republic of China
| | - Jianyu Su
- Key Laboratory of the Ministry of Education for Conservation and Utilization of Special Biological Resources in the Western, Yinchuan, 750021, China.
- College of Life Science, Ningxia University, Yinchuan, 750021, Ningxia, China.
| | - Wenyu Lu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China.
- Frontiers Science Center for Synthetic Biology, Tianjin University, Tianjin, People's Republic of China.
- Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education, Tianjin, People's Republic of China.
| |
Collapse
|
27
|
Park HS, Kang SH, Choi SS, Kim ES. Isolation of Streptomyces inhibiting multiple-phytopathogenic fungi and characterization of lucensomycin biosynthetic gene cluster. Sci Rep 2024; 14:7757. [PMID: 38565875 PMCID: PMC10987574 DOI: 10.1038/s41598-024-57888-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/22/2024] [Indexed: 04/04/2024] Open
Abstract
Soil microorganisms with diverse bioactive compounds such as Streptomyces are appreciated as valuable resources for the discovery of eco-friendly fungicides. This study isolated a novel Streptomyces from soil samples collected in the organic green tea fields in South Korea. The isolation process involved antifungal activity screening around 2400 culture extracts, revealing a strain designated as S. collinus Inha504 with remarkable antifungal activity against diverse phytopathogenic fungi. S. collinus Inha504 not only inhibited seven phytopathogenic fungi including Fusarium oxysporum and Aspergillus niger in bioassays and but also showed a control effect against F. oxysporum infected red pepper, strawberry, and tomato in the in vivo pot test. Genome mining of S. collinus Inha504 revealed the presence of the biosynthetic gene cluster (BGC) in the chromosome encoding a polyene macrolide which is highly homologous to the lucensomycin (LCM), a compound known for effective in crop disease control. Through genetic confirmation and bioassays, the antifungal activity of S. collinus Inha504 was attributed to the presence of LCM BGC in the chromosome. These results could serve as an effective strategy to select novel Streptomyces strains with valuable biological activity through bioassay-based screening and identify biosynthetic gene clusters responsible for the metabolites using genome mining approach.
Collapse
Affiliation(s)
- Heung-Soon Park
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea
| | - Seung-Hoon Kang
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea
| | - Si-Sun Choi
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea
| | - Eung-Soo Kim
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea.
| |
Collapse
|
28
|
Liunardo JJ, Messerli S, Gregotsch A, Lang S, Schlosser K, Rückert‐Reed C, Busche T, Kalinowski J, Zischka M, Weller P, Nouioui I, Neumann‐Schaal M, Risdian C, Wink J, Mack M. Isolation, characterisation and description of the roseoflavin producer Streptomyces berlinensis sp. nov. Environ Microbiol Rep 2024; 16:e13266. [PMID: 38653477 PMCID: PMC11039241 DOI: 10.1111/1758-2229.13266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 04/06/2024] [Indexed: 04/25/2024]
Abstract
The Gram-positive bacteria Streptomyces davaonensis and Streptomyces cinnabarinus have been the only organisms known to produce roseoflavin, a riboflavin (vitamin B2) derived red antibiotic. Using a selective growth medium and a phenotypic screening, we were able to isolate a novel roseoflavin producer from a German soil sample. The isolation procedure was repeated twice, that is, the same strain could be isolated from the same location in Berlin 6 months and 12 months after its first isolation. Whole genome sequencing of the novel roseoflavin producer revealed an unusual chromosomal arrangement and the deposited genome sequence of the new isolate (G + C content of 71.47%) contains 897 genes per inverted terminal repeat, 6190 genes in the core and 107 genes located on an illegitimate terminal end. We identified the roseoflavin biosynthetic genes rosA, rosB and rosC and an unusually high number of riboflavin biosynthetic genes. Overexpression of rosA, rosB and rosC in Escherichia coli and enzyme assays confirmed their predicted functions in roseoflavin biosynthesis. A full taxonomic analysis revealed that the isolate represents a previously unknown Streptomyces species and we propose the name Streptomyces berlinensis sp. nov. for this roseoflavin producer.
Collapse
Affiliation(s)
- Jimmy Jonathan Liunardo
- Institute for Technical Microbiology, Department of BiotechnologyMannheim University of Applied SciencesMannheimGermany
| | - Sebastien Messerli
- Institute for Technical Microbiology, Department of BiotechnologyMannheim University of Applied SciencesMannheimGermany
| | - Ann‐Kathrin Gregotsch
- Institute for Technical Microbiology, Department of BiotechnologyMannheim University of Applied SciencesMannheimGermany
| | - Sonja Lang
- Institute for Technical Microbiology, Department of BiotechnologyMannheim University of Applied SciencesMannheimGermany
| | - Kerstin Schlosser
- Institute for Technical Microbiology, Department of BiotechnologyMannheim University of Applied SciencesMannheimGermany
| | - Christian Rückert‐Reed
- Medical School East Westphalia‐LippeBielefeld UniversityBielefeldGermany
- Technology Platform Genomics, Center for BiotechnologyBielefeld UniversityBielefeldGermany
| | - Tobias Busche
- Medical School East Westphalia‐LippeBielefeld UniversityBielefeldGermany
| | - Jörn Kalinowski
- Technology Platform Genomics, Center for BiotechnologyBielefeld UniversityBielefeldGermany
| | - Martin Zischka
- Institute for Instrumental Analytics and Bioanalytics, Department of BiotechnologyMannheim University of Applied SciencesMannheimGermany
| | - Philipp Weller
- Institute for Instrumental Analytics and Bioanalytics, Department of BiotechnologyMannheim University of Applied SciencesMannheimGermany
| | - Imen Nouioui
- Leibniz‐Institute DSMZ‐German Collection of Microorganisms and Cell CulturesBraunschweigGermany
| | - Meina Neumann‐Schaal
- Leibniz‐Institute DSMZ‐German Collection of Microorganisms and Cell CulturesBraunschweigGermany
| | - Chandra Risdian
- Department of Microbial Strain CollectionHelmholtz Centre for Infection ResearchBraunschweigGermany
- Research Center for Applied MicrobiologyNational Research and Innovation Agency (BRIN)BandungIndonesia
| | - Joachim Wink
- Department of Microbial Strain CollectionHelmholtz Centre for Infection ResearchBraunschweigGermany
- German Centre for Infection Research (DZIF)Partner Site Hannover‐BraunschweigBraunschweigGermany
| | - Matthias Mack
- Institute for Technical Microbiology, Department of BiotechnologyMannheim University of Applied SciencesMannheimGermany
| |
Collapse
|
29
|
Qiao M, Lv S, Qiao Y, Lin W, Gao Z, Tang X, Yang Z, Chen J. Exogenous Streptomyces spp. enhance the drought resistance of naked oat ( Avena nuda) seedlings by augmenting both the osmoregulation mechanisms and antioxidant capacities. Funct Plant Biol 2024; 51:FP23312. [PMID: 38588711 DOI: 10.1071/fp23312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 03/22/2024] [Indexed: 04/10/2024]
Abstract
Drought is a major obstacle to the development of naked oat industry. This work investigated mechanisms by which exogenous Streptomyces albidoflavus T4 and Streptomyces rochei D74 improved drought tolerance in naked oat (Avena nuda ) seedlings. Results showed that in the seed germination experiment, germination rate, radicle and hypocotyl length of naked oat seeds treated with the fermentation filtrate of T4 or D74 under PEG induced drought stress increased significantly. In the hydroponic experiment, the shoot and root dry weights of oat seedlings increased significantly when treated with the T4 or D74 fermentation filtrate under the 15% PEG induced drought stress (S15). Simultaneously, the T4 treatment also significantly increased the surface area, volume, the number of tips and the root activity of oat seedlings. Both T4 and D74 treatments elicited significant increases in proline and soluble sugar contents, as well as the catalase and peroxidase activities in oat seedlings. The results of comprehensive drought resistance capacity (CDRC) calculation of oat plants showed that the drought resistance of oat seedlings under the T4 treatment was better than that under the D74 treatment, and the effect was better under higher drought stress (S15). Findings of this study may provide a novel and effective approach for enhancing plant defenses against drought stress.
Collapse
Affiliation(s)
- Meixia Qiao
- College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi 030801, China
| | - Siyuan Lv
- College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi 030801, China
| | - Yuejing Qiao
- College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi 030801, China; and Ministerial and Provincial Co-Innovation Centre for Endemic Crops Production with High-quality and Efficiency in Loess Plateau, Taigu, Shanxi 030801, China
| | - Wen Lin
- College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi 030801, China; and Ministerial and Provincial Co-Innovation Centre for Endemic Crops Production with High-quality and Efficiency in Loess Plateau, Taigu, Shanxi 030801, China
| | - Zhiqiang Gao
- College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi 030801, China; and Ministerial and Provincial Co-Innovation Centre for Endemic Crops Production with High-quality and Efficiency in Loess Plateau, Taigu, Shanxi 030801, China
| | - Xiwang Tang
- Hebei Key Laboratory of Agroecological Safety, Hebei University of Environmental Engineering, Qinhuangdao, Hebei 066102, China
| | - Zhenping Yang
- College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi 030801, China; and Ministerial and Provincial Co-Innovation Centre for Endemic Crops Production with High-quality and Efficiency in Loess Plateau, Taigu, Shanxi 030801, China
| | - Jie Chen
- College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi 030801, China; and Ministerial and Provincial Co-Innovation Centre for Endemic Crops Production with High-quality and Efficiency in Loess Plateau, Taigu, Shanxi 030801, China
| |
Collapse
|
30
|
Ayoib A, Gopinath SCB, Zambry NS, Yahya ARM. Screening biosurfactant-producing actinomycetes: Identification of Streptomyces sp. RP1 as a potent species for bioremediation. J Basic Microbiol 2024; 64:e2300585. [PMID: 38346247 DOI: 10.1002/jobm.202300585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/25/2023] [Accepted: 01/21/2024] [Indexed: 03/03/2024]
Abstract
This study aimed to isolate biosurfactant-producing and hydrocarbon-degrading actinomycetes from different soils using glycerol-asparagine and starch-casein media with an antifungal agent. The glycerol-asparagine agar exhibited the highest number of actinomycetes, with a white, low-opacity medium supporting pigment production and high growth. Biosurfactant analyses, such as drop collapse, oil displacement, emulsification, tributyrin agar test, and surface tension measurement, were conducted. Out of 25 positive isolates, seven could utilize both olive oil and black oil for biosurfactant production, and only isolate RP1 could produce biosurfactant when grown in constrained conditions with black oil as the sole carbon source and inducer, demonstrating in situ bioremediation potential. Isolate RP1 from oil-spilled garden soil is Gram-staining-positive with a distinct earthy odor, melanin formation, and white filamentous colonies. It has a molecular size of ~621 bp and 100% sequence similarity to many Streptomyces spp. Morphological, biochemical, and 16 S rRNA analysis confirmed it as Streptomyces sp. RP1, showing positive results in all screenings, including high emulsification activity against kerosene (27.2%) and engine oil (95.8%), oil displacement efficiency against crude oil (7.45 cm), and a significant reduction in surface tension (56.7 dynes/cm). Streptomyces sp. RP1 can utilize citrate as a carbon source, tolerate sodium chloride, resist lysozyme, degrade petroleum hydrocarbons, and produce biosurfactant at 37°C in a 15 mL medium culture, indicating great potential for bioremediation and various downstream industrial applications with optimization.
Collapse
Affiliation(s)
- Adilah Ayoib
- Faculty of Chemical Engineering & Technology, Universiti Malaysia Perlis (UniMAP), Padang Besar, Perlis, Malaysia
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), Kangar, Perlis, Malaysia
- Carbon Sustainability Nexus (CaSNex), Special Interest Group (SIG), Universiti Malaysia Perlis (UniMAP), Arau, Perlis, Malaysia
| | - Subash C B Gopinath
- Faculty of Chemical Engineering & Technology, Universiti Malaysia Perlis (UniMAP), Padang Besar, Perlis, Malaysia
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), Kangar, Perlis, Malaysia
- Micro System Technology, Centre of Excellence (CoE), Universiti Malaysia Perlis (UniMAP), Arau, Perlis, Malaysia
| | - Nor Syafirah Zambry
- School of Biological Sciences, Universiti Sains Malaysia, USM, Pulau Pinang, Malaysia
| | | |
Collapse
|
31
|
Wang H, Sheng Y, Ou Y, Xu M, Tao M, Lin S, Deng Z, Bai L, Ding W, Kang Q. Streptomyces-based whole-cell biosensors for detecting diverse cell envelope-targeting antibiotics. Biosens Bioelectron 2024; 249:116004. [PMID: 38199083 DOI: 10.1016/j.bios.2024.116004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 12/25/2023] [Accepted: 01/04/2024] [Indexed: 01/12/2024]
Abstract
Cell envelope-targeting antibiotics are potent therapeutic agents against various bacterial infections. The emergence of multiple antibiotic-resistant strains underscores the significance of identifying potent antimicrobials specifically targeting the cell envelope. However, current drug screening approaches are tedious and lack sufficient specificity and sensitivity, warranting the development of more efficient methods. Genetic circuit-based whole-cell biosensors hold great promise for targeted drug discovery from natural products. Here, we performed comparative transcriptomic analysis of Streptomyces coelicolor M1146 exposed to diverse cell envelope-targeting antibiotics, aiming to identify regulatory elements involved in perceiving and responding to these compounds. Differential gene expression analysis revealed significant activation of VanS/R two-component system in response to the glycopeptide class of cell envelope-acting antibiotics. Therefore, we engineered a pair of VanS/R-based biosensors that exhibit functional complementarity and possess exceptional sensitivity and specificity for glycopeptides detection. Additionally, through promoter screening and characterization, we expanded the biosensor's detection range to include various cell envelope-acting antibiotics beyond glycopeptides. Our genetically engineered biosensor exhibits superior performance, including a dynamic range of up to 887-fold for detecting subtle antibiotic concentration changes in a rapid 2-h response time, enabling high-throughput screening of natural product libraries for antimicrobial agents targeting the bacterial cell envelope.
Collapse
Affiliation(s)
- Hengyu Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yong Sheng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yixin Ou
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China; Haihe Laboratory of Synthetic Biology, Tianjin, 300308, China
| | - Min Xu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, West 7th Avenue No. 32, 300308, Tianjin, China
| | - Meifeng Tao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China; Haihe Laboratory of Synthetic Biology, Tianjin, 300308, China
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China; Haihe Laboratory of Synthetic Biology, Tianjin, 300308, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China; Haihe Laboratory of Synthetic Biology, Tianjin, 300308, China
| | - Linquan Bai
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wei Ding
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Qianjin Kang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China; Haihe Laboratory of Synthetic Biology, Tianjin, 300308, China.
| |
Collapse
|
32
|
Matsuda K, Maruyama H, Imachi K, Ikeda H, Wakimoto T. Actinobacterial chalkophores: the biosynthesis of hazimycins. J Antibiot (Tokyo) 2024; 77:228-237. [PMID: 38378905 DOI: 10.1038/s41429-024-00706-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/22/2024]
Abstract
Copper is a transition metal element with significant effects on the morphological development and secondary metabolism of actinobacteria. In some microorganisms, copper-binding natural products are employed to modulate copper homeostasis, although their significance in actinobacteria remains largely unknown. Here, we identified the biosynthetic genes of the diisocyanide natural product hazimycin in Kitasatospora purpeofusca HV058, through gene knock-out and heterologous expression. Biochemical analyses revealed that hazimycin A specifically binds to copper, which diminishes its antimicrobial activity. The presence of a set of putative importer/exporter genes surrounding the biosynthetic genes suggested that hazimycin is a chalkophore that modulates the intracellular copper level. A bioinformatic survey of homologous gene cassettes, as well as the identification of two previously unknown hazimycin-producing Streptomyces strains, indicated that the isocyanide-based mechanism of copper homeostasis is prevalent in actinobacteria.
Collapse
Affiliation(s)
- Kenichi Matsuda
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan.
| | - Hiroto Maruyama
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan
| | - Kumiko Imachi
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan
| | - Haruo Ikeda
- Technology Research Association for Next generation natural products chemistry, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Toshiyuki Wakimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan.
| |
Collapse
|
33
|
Chagas FO, Garrido LM, Conti R, Borges RM, Bielinski VA, Padilla G, Pupo MT. Unusual Sesquiterpenes from Streptomyces olindensis DAUFPE 5622. J Nat Prod 2024; 87:491-500. [PMID: 38422010 DOI: 10.1021/acs.jnatprod.3c00752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
In nature, the vast majority of sesquiterpenes are produced by type I mechanisms, and glycosylated sesquiterpenes are rare in actinobacteria. Streptomyces olindensis DAUFPE 5622 produces the sesquiterpenes olindenones A-G, a new class of rearranged drimane sesquiterpenes. Olindenones B-D are oxygenated derivatives of olindenone A, while olindenones E-G are analogs glycosylated with dideoxysugars. 13C-isotope labeling studies demonstrated olindenone A biosynthesis occurs via the methylerythritol phosphate (MEP) pathway and suggested the rearrangement is only partially concerted. Based on the structures, one potential mechanism of olindenone A formation proceeds by cyclization of the linear terpenoid precursor, likely occurring via a terpene cyclase-mediated type II mechanism whereby the terminal alkene of the precursor is protonated, triggering carbocation-driven cyclization followed by rearrangement. Diphosphate hydrolysis may occur either before or after cyclization. Although a biosynthetic route is proposed, the terpene cyclase gene responsible for producing olindenones currently remains unidentified.
Collapse
Affiliation(s)
- Fernanda O Chagas
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP 05508-070, Brazil
- Instituto de Pesquisas de Produtos Naturais Walter Mors, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-617, Brazil
| | - Leandro M Garrido
- Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP 05508-070, Brazil
| | - Raphael Conti
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP 05508-070, Brazil
| | - Ricardo M Borges
- Instituto de Pesquisas de Produtos Naturais Walter Mors, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-617, Brazil
| | - Vincent A Bielinski
- Synthetic Biology and Bioenergy Group, J. Craig Venter Institute, La Jolla, California 92037, United States
- Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-617, Brazil
| | - Gabriel Padilla
- Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP 05508-070, Brazil
| | - Mônica T Pupo
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP 05508-070, Brazil
| |
Collapse
|
34
|
Xiao F, Xu M, Cheng Y, Li T, Hong K, Li W. Generation of streptocarbazoles with cytotoxicities by pathway engineering and insights into their biosynthesis. Appl Environ Microbiol 2024; 90:e0218723. [PMID: 38307543 PMCID: PMC10952482 DOI: 10.1128/aem.02187-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 01/06/2024] [Indexed: 02/04/2024] Open
Abstract
Streptocarbazoles are a class of indolocarbazole (ICZ) compounds produced by Streptomyces strains that feature unique cyclic N-glycosidic linkages between the 1,3-carbon atoms of the glycosyl moiety and the two indole nitrogen atoms. Although several streptocarbazole compounds display effective cytotoxic activity, their biosynthesis remains unclear. Herein, through the inactivation of the aminotransferase gene spcI in the staurosporine biosynthetic gene cluster spc followed by heterologous expression, two new streptocarbazole derivatives (1 and 3) and three known ICZs (2, 4, and 5) were generated. Their structures were determined by a combination of spectroscopic methods, circular dichroism measurements, and single-crystal X-ray diffraction. Compounds 1-4 displayed moderate cytotoxicity against HCT-116 cell line, and compounds 3 and 4 were effective against Huh 7 cell line. Double-gene knockout experiments allowed us to propose a biosynthetic pathway for streptocarbazole productions. Furthermore, by overexpression of the involving key enzymes, the production of streptocarbazoles 1 and 3 were improved by approximately 1.5-2.5 fold. IMPORTANCE Indolocarbazoles (ICZs) are a group of antitumor agents, with several analogs used in clinical trials. Therefore, the identification of novel ICZ compounds is important for drug discovery. Streptocarbazoles harbor unique N-glycosidic linkages (N13-C1' and N12-C3'), distinguishing them from the representative ICZ compound staurosporine; however, their biosynthesis remains unclear. In this study, two new streptocarbazoles (1 and 3) with cytotoxic activities were obtained by manipulating the staurosporine biosynthetic gene cluster spc followed by heterologous expression. The biosynthetic pathway of streptocarbazoles was proposed, and their productions were improved through the overexpression of the key enzymes involved. This study enriches the structural diversity of ICZ compounds and would facilitate the discovery of new streptocarbazoles via synthetic biological strategies.
Collapse
Affiliation(s)
- Fei Xiao
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Mingyuan Xu
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Yongmeng Cheng
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Tong Li
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Kui Hong
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education of China, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Wenli Li
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- College of Chemistry & Pharmacy, Northwest A&F University, Yangling, China
| |
Collapse
|
35
|
Maleckis M, Wibowo M, Gren T, Jarmusch SA, Sterndorff EB, Booth T, Henriksen NNSE, Whitford CM, Jiang X, Jørgensen TS, Ding L, Weber T. Biosynthesis of the Azoxy Compound Azodyrecin from Streptomyces mirabilis P8-A2. ACS Chem Biol 2024; 19:641-653. [PMID: 38340355 DOI: 10.1021/acschembio.3c00632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2024]
Abstract
Azoxy compounds are a distinctive group of bioactive secondary metabolites characterized by a unique RN═N+(O-)R moiety. The azoxy moiety is present in various classes of metabolites that exhibit various biological activities. The enzymatic mechanisms underlying azoxy bond formation remain enigmatic. Azodyrecins are cytotoxic azoxy metabolites produced by Streptomyces mirabilis P8-A2. Here, we cloned and confirmed the putative azd biosynthetic gene cluster through CATCH cloning followed by expression and production of azodyrecins in two heterologous hosts, S. albidoflavus J1074 and S. coelicolor M1146, respectively. We explored the function of 14 enzymes in azodyrecin biosynthesis through gene knockout using CRISPR-Cas9 base editing in the native producer, S. mirabilis P8-A2. The key intermediates were analyzed in the mutants through MS/MS fragmentation studies, revealing azoxy bond formation via the conversion of hydrazine to an azo compound followed by further oxygenation. Enzymes involved in modifications of the precursor could be postulated based on their predicted function and the intermediates identified in the knockout strains. Moreover, the distribution of the azoxy biosynthetic gene clusters across Streptomyces spp. genomes is explored, highlighting the presence of these clusters in over 20% of the Streptomyces spp. genomes and revealing that azoxymycin and valanimycin are scarce, while azodyrecin and KA57A-like clusters are widely distributed across the phylogenetic tree.
Collapse
Affiliation(s)
- Matiss Maleckis
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Mario Wibowo
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark, Søltofts Plads, Building 221, 2800 Kgs. Lyngby, Denmark
| | - Tetiana Gren
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Scott A Jarmusch
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark, Søltofts Plads, Building 221, 2800 Kgs. Lyngby, Denmark
| | - Eva B Sterndorff
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Thomas Booth
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Nathalie N S E Henriksen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark, Søltofts Plads, Building 221, 2800 Kgs. Lyngby, Denmark
| | - Christopher M Whitford
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Xinglin Jiang
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Tue S Jørgensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Ling Ding
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark, Søltofts Plads, Building 221, 2800 Kgs. Lyngby, Denmark
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Building 220, 2800 Kgs. Lyngby, Denmark
| |
Collapse
|
36
|
Bhat AM, Hussain A, Hassan QP, Bhat A. Culturable Streptomyces spp. from high-altitude, oligotrophic North Western Himalaya: a comprehensive study on the diversity, bioactivity and insights into the proteome of potential species. FEMS Microbiol Ecol 2024; 100:fiae026. [PMID: 38439700 PMCID: PMC10950047 DOI: 10.1093/femsec/fiae026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 11/27/2023] [Accepted: 03/02/2024] [Indexed: 03/06/2024] Open
Abstract
The increasing global concern of antimicrobial resistance and shortage of new antimicrobials necessitates exploring untapped terrestrial environments for new bioactive microbiome diversity. The low-temperature and oligotrophic North Western Himalaya (NWH) region has a vast diversity of Streptomyces with potential antimicrobial properties that remain largely unexplored. This study evaluates the diversity of culturable Streptomyces from high-altitude NWH and their potential as a source of new antimicrobials through genus-specific isolation and identification. The results demonstrate a distinct phylogenetic clustering of Streptomyces from different sampling regions of NWH, site-specific variation in culturable β-diversity and species commonness with varying intersite bioactivity among different sites. Further, the study optimized the media selection for large-scale culture cultivation in antibiotic production processes and demonstrated the antimicrobial efficacy of Streptomyces against a range of pathogens through in vitro bioassays using minimum inhibitory concentration determination and antibiofilm activity. Untargeted label-free proteomic profiling also revealed variable expression of stress-response proteins and antibiotic regulators as a competitive survival strategy for selective antagonistic Streptomyces. The findings highlight the potential of NWH in augmenting antimicrobial discovery and combating antimicrobial resistance through the isolation and study of novel bioactive Streptomyces.
Collapse
Affiliation(s)
- Aasif Majeed Bhat
- Plant Molecular Biology and Biotechnology Division, CSIR-Indian Institute of Integrative Medicine (IIIM), Sanatnagar, Srinagar, Jammu & Kashmir-190005, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh-201002, India
| | - Aehtesham Hussain
- NCMR-National Centre for Cell Science (NCCS), Pune-411007, Maharashtra, India
| | - Qazi Parvaiz Hassan
- Plant Molecular Biology and Biotechnology Division, CSIR-Indian Institute of Integrative Medicine (IIIM), Sanatnagar, Srinagar, Jammu & Kashmir-190005, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh-201002, India
| | - Adil Bhat
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| |
Collapse
|
37
|
Mao D, Yu P, Shinzato N, Zhang L, Zheng W, Lu S, Kakeya H. Precezomycin, a novel antibiotic biosynthetic precursor of cezomycin, from actinomycete Kitasatospora putterlickiae 10-13. J Antibiot (Tokyo) 2024; 77:189-192. [PMID: 38200162 DOI: 10.1038/s41429-023-00695-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/18/2023] [Accepted: 11/27/2023] [Indexed: 01/12/2024]
Abstract
A novel antibiotic biosynthetic precursor of cezomycin, named precezomycin (1), was isolated from culture broth of actinomycete Kitasatospora putterlickiae 10-13. The planar structure was determined by 1D/2D NMR and HR(ESI)MS data analyses, and the absolute configurations were established by TDDFT calculation of ECD spectra. Precezomycin (1) exhibited moderate antibacterial activity against gram-positive bacteria including Staphylococcus aureus and Bacillus subtilis. The discovery of 1 extends the natural product family of cezomycin and provides a new insight into understanding the biosynthetic process of these polyether ionophore metabolites.
Collapse
Affiliation(s)
- Di Mao
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, China
- Department of System Chemotherapy and Molecular Sciences, Division of Medicinal Frontier Sciences, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
| | - Pengwei Yu
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, China
| | - Naoya Shinzato
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, 903-0213, Japan
| | - Lei Zhang
- Department of System Chemotherapy and Molecular Sciences, Division of Medicinal Frontier Sciences, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
| | - Weiping Zheng
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, China
| | - Shan Lu
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, China.
| | - Hideaki Kakeya
- Department of System Chemotherapy and Molecular Sciences, Division of Medicinal Frontier Sciences, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan.
| |
Collapse
|
38
|
Wang Y, Yang X, Yu F, Deng Z, Lin S, Zheng J. Structural and functional characterization of AfsR, an SARP family transcriptional activator of antibiotic biosynthesis in Streptomyces. PLoS Biol 2024; 22:e3002528. [PMID: 38427710 PMCID: PMC10936776 DOI: 10.1371/journal.pbio.3002528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 03/13/2024] [Accepted: 01/29/2024] [Indexed: 03/03/2024] Open
Abstract
Streptomyces antibiotic regulatory proteins (SARPs) are widely distributed activators of antibiotic biosynthesis. Streptomyces coelicolor AfsR is an SARP regulator with an additional nucleotide-binding oligomerization domain (NOD) and a tetratricopeptide repeat (TPR) domain. Here, we present cryo-electron microscopy (cryo-EM) structures and in vitro assays to demonstrate how the SARP domain activates transcription and how it is modulated by NOD and TPR domains. The structures of transcription initiation complexes (TICs) show that the SARP domain forms a side-by-side dimer to simultaneously engage the afs box overlapping the -35 element and the σHrdB region 4 (R4), resembling a sigma adaptation mechanism. The SARP extensively interacts with the subunits of the RNA polymerase (RNAP) core enzyme including the β-flap tip helix (FTH), the β' zinc-binding domain (ZBD), and the highly flexible C-terminal domain of the α subunit (αCTD). Transcription assays of full-length AfsR and truncated proteins reveal the inhibitory effect of NOD and TPR on SARP transcription activation, which can be eliminated by ATP binding. In vitro phosphorylation hardly affects transcription activation of AfsR, but counteracts the disinhibition of ATP binding. Overall, our results present a detailed molecular view of how AfsR serves to activate transcription.
Collapse
Affiliation(s)
- Yiqun Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xu Yang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Feng Yu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jianting Zheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai, China
| |
Collapse
|
39
|
Taechowisan T, Chuen-Im T, Phutdhawong WS. Antioxidant and Antibacterial Properties of 1,3-Dihydroxy-,2', 2'-Dimethylpyrano-(5,6)-Xanthone from Streptomyces sp. SU84. Pak J Biol Sci 2024; 27:132-141. [PMID: 38686735 DOI: 10.3923/pjbs.2024.132.141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
<b>Background and Objective:</b> The SU84 was isolated from the rhizosphere of <i>Curcuma longa</i> and identified to be <i>Streptomyces</i> sp. via analysis of its 16S rDNA sequence, chemotaxonomy and morphology. This study aimed to isolate major compounds from the extract culture of strain SU84 and evaluate their antibacterial activity. <b>Materials and Methods:</b> The TLC and silica gel column chromatography were used to purify major compounds, elucidate 1,3-dihydroxy-,2',2'-dimethylpyrano-(5,6)-xanthone (compound <b>1</b>) and lupeol (compound <b>2</b>) using mass spectrometry and nuclear magnetic resonance. One new chemical, compound <b>1</b>, was first isolated from microbial sources. Antibacterial, antioxidant and cytotoxic properties of these compounds were carried out. <b>Results:</b> Various bioassays showed that compound <b>1</b> displayed antibacterial property against Gram-positive bacteria, with a minimum inhibitory concentration of 8-32 μg/mL and minimum bactericidal concentration of 32-128 μg/mL. In addition, the purified compounds were tested against normal cell lines using tetrazolium assay. The results did not show cytotoxic property against L929 and Vero cells, with IC<sub>50</sub> values of >512.00 μg/mL. Compounds <b>1</b> and <b>2</b> have also antioxidant properties, with IC<sub>50</sub> values of 16.67±7.48 and 38.86±8.45 μg/mL, respectively. <b>Conclusion:</b> The findings suggested that compounds of <i>Streptomyces</i> sp. SU84 displayed antibacterial and antioxidant properties without cytotoxic activity. Extensive studies of compound <b>1</b> may be useful for the advancement of improved methods for avoidance, control and management of bacterial infections and metabolic-related free radical contribution.
Collapse
|
40
|
Ye J, Yang P, Zhou J, Du G, Liu S. Efficient Production of a Thermostable Mutant of Transglutaminase by Streptomyces mobaraensis. J Agric Food Chem 2024; 72:4207-4216. [PMID: 38354706 DOI: 10.1021/acs.jafc.3c07621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
The transglutaminase (TGase) from Streptomyces mobaraensis is widely used to improve the texture of protein-based foods. However, wild-type TGase is not heat-resistant, which is unfavorable for its application. In this study, we successfully constructed a S. mobaraensis strain that can efficiently produce TGm2, a thermostable mutant of S. mobaraensis TGase. First, S. mobaraensis DSM40587 was subjected to atmospheric room temperature plasma mutagenesis, generating mutant smY2022 with a 12.2-fold increase in TGase activity. Then, based on the double-crossover recombination, we replaced the coding sequence of the TGase with that of TGm2 in smY2022, obtaining the strain smY2022-TGm2. The extracellular TGase activity of smY2022-TGm2 reached 61.7 U/mL, 147% higher than that of smY2022. Finally, the catalytic properties of TGm2 were characterized. The half-life time at 60 °C and specific activity of TGm2 reached 64 min and 71.15 U/mg, 35.6- and 2.9-fold higher than those of the wild-type TGase, respectively. As indicated by SDS-PAGE analysis, TGm2 exhibited demonstrably better protein cross-linking ability than the wild-type TGase at 70 °C, although both enzymes shared a similar ability at 40 °C. With improved enzyme production and thermal stability, smY2022-TGm2 could be a competitive strain for the industrial production of transglutaminase.
Collapse
Affiliation(s)
- Jiacai Ye
- Engineering Research Center of Ministry of Education on Food Synthetic Biorheology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Penghui Yang
- Engineering Research Center of Ministry of Education on Food Synthetic Biorheology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- Engineering Research Center of Ministry of Education on Food Synthetic Biorheology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Guocheng Du
- Engineering Research Center of Ministry of Education on Food Synthetic Biorheology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Song Liu
- Engineering Research Center of Ministry of Education on Food Synthetic Biorheology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| |
Collapse
|
41
|
El-Naggar NEA, El-Sawah AA, Elmansy MF, Elmessiry OT, El-Saidy ME, El-Sherbeny MK, Sarhan MT, Elhefnawy AA, Dalal SR. Process optimization for gold nanoparticles biosynthesis by Streptomyces albogriseolus using artificial neural network, characterization and antitumor activities. Sci Rep 2024; 14:4581. [PMID: 38403677 PMCID: PMC10894868 DOI: 10.1038/s41598-024-54698-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 02/15/2024] [Indexed: 02/27/2024] Open
Abstract
Gold nanoparticles (GNPs) are highly promising in cancer therapy, wound healing, drug delivery, biosensing, and biomedical imaging. Furthermore, GNPs have anti-inflammatory, anti-angiogenic, antioxidants, anti-proliferative and anti-diabetic effects. The present study presents an eco-friendly approach for GNPs biosynthesis using the cell-free supernatant of Streptomyces albogriseolus as a reducing and stabilizing agent. The biosynthesized GNPs have a maximum absorption peak at 540 nm. The TEM images showed that GNPs ranged in size from 5.42 to 13.34 nm and had a spherical shape. GNPs have a negatively charged surface with a Zeta potential of - 24.8 mV. FTIR analysis identified several functional groups including C-H, -OH, C-N, amines and amide groups. The crystalline structure of GNPs was verified by X-ray diffraction and the well-defined and distinct diffraction rings observed by the selected area electron diffraction analysis. To optimize the biosynthesis of GNPs using the cell-free supernatant of S. albogriseolus, 30 experimental runs were conducted using central composite design (CCD). The artificial neural network (ANN) was employed to analyze, validate, and predict GNPs biosynthesis compared to CCD. The maximum experimental yield of GNPs (778.74 μg/mL) was obtained with a cell-free supernatant concentration of 70%, a HAuCl4 concentration of 800 μg/mL, an initial pH of 7, and a 96-h incubation time. The theoretically predicted yields of GNPs by CCD and ANN were 809.89 and 777.32 μg/mL, respectively, which indicates that ANN has stronger prediction potential compared to the CCD. The anticancer activity of GNPs was compared to that of doxorubicin (Dox) in vitro against the HeP-G2 human cancer cell line. The IC50 values of Dox and GNPs-based treatments were 7.26 ± 0.4 and 22.13 ± 1.3 µg/mL, respectively. Interestingly, treatments combining Dox and GNPs together showed an IC50 value of 3.52 ± 0.1 µg/mL, indicating that they targeted cancer cells more efficiently.
Collapse
Affiliation(s)
- Noura El-Ahmady El-Naggar
- Department of Bioprocess Development, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications (SRTA-City), New Borg El- Arab City, Alexandria, 21934, Egypt.
| | - Asmaa A El-Sawah
- Botany Department, Faculty of Science, Mansoura University, Mansoura, 35516, Egypt
| | - Mohamed F Elmansy
- Biotechnology and its Application Program, Department of Botany, Faculty of Science, Mansoura University, Mansoura, 35516, Egypt
| | - Omar T Elmessiry
- Biotechnology and its Application Program, Department of Botany, Faculty of Science, Mansoura University, Mansoura, 35516, Egypt
| | - Mohanad E El-Saidy
- Biotechnology and its Application Program, Department of Botany, Faculty of Science, Mansoura University, Mansoura, 35516, Egypt
| | - Mostafa K El-Sherbeny
- Biotechnology and its Application Program, Department of Botany, Faculty of Science, Mansoura University, Mansoura, 35516, Egypt
| | - Mohamed T Sarhan
- Biotechnology and its Application Program, Department of Botany, Faculty of Science, Mansoura University, Mansoura, 35516, Egypt
| | - Aya Amin Elhefnawy
- Biotechnology and its Application Program, Department of Botany, Faculty of Science, Mansoura University, Mansoura, 35516, Egypt
| | - Shimaa R Dalal
- Botany Department, Faculty of Science, Mansoura University, Mansoura, 35516, Egypt
| |
Collapse
|
42
|
Sweeney D, Chase AB, Bogdanov A, Jensen PR. MAR4 Streptomyces: A Unique Resource for Natural Product Discovery. J Nat Prod 2024; 87:439-452. [PMID: 38353658 PMCID: PMC10897937 DOI: 10.1021/acs.jnatprod.3c01007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/22/2024] [Accepted: 01/22/2024] [Indexed: 02/24/2024]
Abstract
Marine-derived Streptomyces have long been recognized as a source of novel, pharmaceutically relevant natural products. Among these bacteria, the MAR4 clade within the genus Streptomyces has been identified as metabolically rich, yielding over 93 different compounds to date. MAR4 strains are particularly noteworthy for the production of halogenated hybrid isoprenoid natural products, a relatively rare class of bacterial metabolites that possess a wide range of biological activities. MAR4 genomes are enriched in vanadium haloperoxidase and prenyltransferase genes, thus accounting for the production of these compounds. Functional characterization of the enzymes encoded in MAR4 genomes has advanced our understanding of halogenated, hybrid isoprenoid biosynthesis. Despite the exceptional biosynthetic capabilities of MAR4 bacteria, the large body of research they have stimulated has yet to be compiled. Here we review 35 years of natural product research on MAR4 strains and update the molecular diversity of this unique group of bacteria.
Collapse
Affiliation(s)
- Douglas Sweeney
- Scripps
Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Alexander B. Chase
- Department
of Earth Sciences, Southern Methodist University, Dallas, Texas 75275, United States
| | - Alexander Bogdanov
- Scripps
Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Paul R. Jensen
- Scripps
Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| |
Collapse
|
43
|
García-Gutiérrez C, Pérez-Victoria I, Montero I, Fernández-De la Hoz J, Malmierca MG, Martín J, Salas JA, Olano C, Reyes F, Méndez C. Unearthing a Cryptic Biosynthetic Gene Cluster for the Piperazic Acid-Bearing Depsipeptide Diperamycin in the Ant-Dweller Streptomyces sp. CS113. Int J Mol Sci 2024; 25:2347. [PMID: 38397022 PMCID: PMC10888640 DOI: 10.3390/ijms25042347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Piperazic acid is a cyclic nonproteinogenic amino acid that contains a hydrazine N-N bond formed by a piperazate synthase (KtzT-like). This amino acid, found in bioactive natural products synthesized by non-ribosomal peptide synthetases (NRPSs), confers conformational constraint to peptides, an important feature for their biological activities. Genome mining of Streptomyces strains has been revealed as a strategy to identify biosynthetic gene clusters (BGCs) for potentially active compounds. Moreover, the isolation of new strains from underexplored habitats or associated with other organisms has allowed to uncover new BGCs for unknown compounds. The in-house "Carlos Sialer (CS)" strain collection consists of seventy-one Streptomyces strains isolated from the cuticle of leaf-cutting ants of the tribe Attini. Genomes from twelve of these strains have been sequenced and mined using bioinformatics tools, highlighting their potential to encode secondary metabolites. In this work, we have screened in silico those genomes, using KtzT as a hook to identify BGCs encoding piperazic acid-containing compounds. This resulted in uncovering the new BGC dpn in Streptomyces sp. CS113, which encodes the biosynthesis of the hybrid polyketide-depsipeptide diperamycin. Analysis of the diperamycin polyketide synthase (PKS) and NRPS reveals their functional similarity to those from the aurantimycin A biosynthetic pathway. Experimental proof linking the dpn BGC to its encoded compound was achieved by determining the growth conditions for the expression of the cluster and by inactivating the NRPS encoding gene dpnS2 and the piperazate synthase gene dpnZ. The identity of diperamycin was confirmed by High-Resolution Mass Spectrometry (HRMS) and Nuclear Magnetic Resonance (NMR) and by analysis of the domain composition of modules from the DpnP PKS and DpnS NRPS. The identification of the dpn BGC expands the number of BGCs that have been confirmed to encode the relatively scarcely represented BGCs for depsipeptides of the azinothricin family of compounds and will facilitate the generation of new-to-nature analogues by combinatorial biosynthesis.
Collapse
Affiliation(s)
- Coral García-Gutiérrez
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006 Oviedo, Spain; (C.G.-G.); (I.M.); (J.F.-D.l.H.); (M.G.M.); (J.A.S.); (C.O.)
- Instituto de Investigación Sanitaria de Asturias (ISPA), 33011 Oviedo, Spain
| | - Ignacio Pérez-Victoria
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, 18016 Granada, Spain; (I.P.-V.); (J.M.); (F.R.)
| | - Ignacio Montero
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006 Oviedo, Spain; (C.G.-G.); (I.M.); (J.F.-D.l.H.); (M.G.M.); (J.A.S.); (C.O.)
- Instituto de Investigación Sanitaria de Asturias (ISPA), 33011 Oviedo, Spain
| | - Jorge Fernández-De la Hoz
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006 Oviedo, Spain; (C.G.-G.); (I.M.); (J.F.-D.l.H.); (M.G.M.); (J.A.S.); (C.O.)
| | - Mónica G. Malmierca
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006 Oviedo, Spain; (C.G.-G.); (I.M.); (J.F.-D.l.H.); (M.G.M.); (J.A.S.); (C.O.)
| | - Jesús Martín
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, 18016 Granada, Spain; (I.P.-V.); (J.M.); (F.R.)
| | - José A. Salas
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006 Oviedo, Spain; (C.G.-G.); (I.M.); (J.F.-D.l.H.); (M.G.M.); (J.A.S.); (C.O.)
- Instituto de Investigación Sanitaria de Asturias (ISPA), 33011 Oviedo, Spain
| | - Carlos Olano
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006 Oviedo, Spain; (C.G.-G.); (I.M.); (J.F.-D.l.H.); (M.G.M.); (J.A.S.); (C.O.)
- Instituto de Investigación Sanitaria de Asturias (ISPA), 33011 Oviedo, Spain
| | - Fernando Reyes
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, 18016 Granada, Spain; (I.P.-V.); (J.M.); (F.R.)
| | - Carmen Méndez
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, 33006 Oviedo, Spain; (C.G.-G.); (I.M.); (J.F.-D.l.H.); (M.G.M.); (J.A.S.); (C.O.)
- Instituto de Investigación Sanitaria de Asturias (ISPA), 33011 Oviedo, Spain
| |
Collapse
|
44
|
Lu WJ, Zhang MS, Lu DL, Li ZW, Yang ZD, Wu L, Ni JT, Chen WD, Deng JJ, Luo XC. Sustainable valorizing high-protein feather waste utilization through solid-state fermentation by keratinase-enhanced Streptomyces sp. SCUT-3 using a novel promoter. Waste Manag 2024; 174:528-538. [PMID: 38134540 DOI: 10.1016/j.wasman.2023.12.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 11/24/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023]
Abstract
Feather waste, a rich source of proteins, has traditionally been processed through high-temperature puffing and acid-base hydrolysis, contributing to generation of greenhouse gases and H2S. To address this issue, we employed circular economy techniques to recover the nutritional value of feather waste. Streptomyces sp. SCUT-3, an efficient proteolytic and chitinolytic bacterium, was isolated for feather degradation previously. This study aimed to valorize feather waste for feed purposes by enhancing its feather transformation ability through promoter optimization. Seven promoters were identified through omics analysis and compared to a common Streptomyces promoter ermE*p. The strongest promoter, p24880, effectively enhanced the expression of three candidate keratinases (Sep39, Sep40, and Sep53). The expression efficiency of double-, triple-p24880 and sandwich p24880-sep39-p24880 promoters were further verified. The co-overexpression strain SCUT-3-p24880-sep39-p24880-sep40 exhibited a 16.21-fold increase in keratinase activity compared to the wild-type. Using this strain, a solid-state fermentation process was established that increased the feather/water ratio (w/w) to 1:1.5, shortened the fermentation time to 2.5 days, and increased soluble peptide and free amino acid yields to 0.41 g/g and 0.14 g/g, respectively. The resulting has high protein content (90.49 %), with high in vitro digestibility (94.20 %). This method has the potential to revolutionize the feather waste processing industry.
Collapse
Affiliation(s)
- Wen-Jun Lu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Panyu District, Guangzhou, Guangdong 510006, China
| | - Ming-Shu Zhang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Panyu District, Guangzhou, Guangdong 510006, China
| | - De-Lin Lu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Panyu District, Guangzhou, Guangdong 510006, China
| | - Zhi-Wei Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Panyu District, Guangzhou, Guangdong 510006, China
| | - Zhen-Dong Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Panyu District, Guangzhou, Guangdong 510006, China
| | - Lei Wu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Panyu District, Guangzhou, Guangdong 510006, China
| | - Jing-Tao Ni
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Panyu District, Guangzhou, Guangdong 510006, China
| | - Wei-Dong Chen
- Institute of Animal Sciences, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Jun-Jin Deng
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Panyu District, Guangzhou, Guangdong 510006, China; Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Laboratory of Crop Germplasm Resources Conservation and Utilization, Guangzhou 510640, China.
| | - Xiao-Chun Luo
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Panyu District, Guangzhou, Guangdong 510006, China.
| |
Collapse
|
45
|
Pulat S, Yang I, Lee J, Hwang S, Zhou R, Gamage CDB, Varlı M, Taş İ, Yang Y, Park SY, Hong A, Kim JH, Oh DC, Kim H, Nam SJ, Kang H. Anithiactin D, a Phenylthiazole Natural Product from Mudflat-Derived Streptomyces sp., Suppresses Motility of Cancer Cells. Mar Drugs 2024; 22:88. [PMID: 38393059 PMCID: PMC10889970 DOI: 10.3390/md22020088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/02/2024] [Accepted: 02/12/2024] [Indexed: 02/25/2024] Open
Abstract
Anithiactin D (1), a 2-phenylthiazole class of natural products, was isolated from marine mudflat-derived actinomycetes Streptomyces sp. 10A085. The chemical structure of 1 was elucidated based on the interpretation of NMR and MS data. The absolute configuration of 1 was determined by comparing the experimental and calculated electronic circular dichroism (ECD) spectral data. Anithiactin D (1) significantly decreased cancer cell migration and invasion activities at a concentration of 5 μM via downregulation of the epithelial-to-mesenchymal transition (EMT) markers in A549, AGS, and Caco-2 cell lines. Moreover, 1 inhibited the activity of Rho GTPases, including Rac1 and RhoA in the A549 cell line, suppressed RhoA in AGS and Caco-2 cell lines, and decreased the mRNA expression levels of some matrix metalloproteinases (MMPs) in AGS and Caco-2 cell lines. Thus 1, which is a new entity of the 2-phenylthiazole class of natural products with a unique aniline-indole fused moiety, is a potent inhibitor of the motility of cancer cells.
Collapse
Affiliation(s)
- Sultan Pulat
- College of Pharmacy, Sunchon National University, Sunchon 57922, Republic of Korea; (S.P.); (R.Z.); (C.D.B.G.); (M.V.); (İ.T.); (Y.Y.); (S.-Y.P.)
| | - Inho Yang
- Department of Convergence Study on the Ocean Science and Technology, Korea Maritime and Ocean University, Busan 49112, Republic of Korea;
| | - Jihye Lee
- Laboratories of Marine New Drugs, REDONE Seoul, Seoul 08594, Republic of Korea;
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea; (A.H.); (J.-H.K.)
| | - Sunghoon Hwang
- Natural Products Research Institute, College of Pharmacy, Seoul National University, NS-80, Seoul 08826, Republic of Korea; (S.H.); (D.-C.O.)
| | - Rui Zhou
- College of Pharmacy, Sunchon National University, Sunchon 57922, Republic of Korea; (S.P.); (R.Z.); (C.D.B.G.); (M.V.); (İ.T.); (Y.Y.); (S.-Y.P.)
| | - Chathurika D. B. Gamage
- College of Pharmacy, Sunchon National University, Sunchon 57922, Republic of Korea; (S.P.); (R.Z.); (C.D.B.G.); (M.V.); (İ.T.); (Y.Y.); (S.-Y.P.)
| | - Mücahit Varlı
- College of Pharmacy, Sunchon National University, Sunchon 57922, Republic of Korea; (S.P.); (R.Z.); (C.D.B.G.); (M.V.); (İ.T.); (Y.Y.); (S.-Y.P.)
| | - İsa Taş
- College of Pharmacy, Sunchon National University, Sunchon 57922, Republic of Korea; (S.P.); (R.Z.); (C.D.B.G.); (M.V.); (İ.T.); (Y.Y.); (S.-Y.P.)
| | - Yi Yang
- College of Pharmacy, Sunchon National University, Sunchon 57922, Republic of Korea; (S.P.); (R.Z.); (C.D.B.G.); (M.V.); (İ.T.); (Y.Y.); (S.-Y.P.)
| | - So-Yeon Park
- College of Pharmacy, Sunchon National University, Sunchon 57922, Republic of Korea; (S.P.); (R.Z.); (C.D.B.G.); (M.V.); (İ.T.); (Y.Y.); (S.-Y.P.)
| | - Ahreum Hong
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea; (A.H.); (J.-H.K.)
| | - Jeong-Hyeon Kim
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea; (A.H.); (J.-H.K.)
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, NS-80, Seoul 08826, Republic of Korea; (S.H.); (D.-C.O.)
| | - Hangun Kim
- College of Pharmacy, Sunchon National University, Sunchon 57922, Republic of Korea; (S.P.); (R.Z.); (C.D.B.G.); (M.V.); (İ.T.); (Y.Y.); (S.-Y.P.)
| | - Sang-Jip Nam
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea; (A.H.); (J.-H.K.)
| | - Heonjoong Kang
- Laboratory of Marine Drugs, School of Earth and Environmental Sciences, Seoul National University, NS-80, Seoul 08826, Republic of Korea
| |
Collapse
|
46
|
Wang M, Li H, Li J, Zhang W, Zhang J. Streptomyces Strains and Their Metabolites for Biocontrol of Phytopathogens in Agriculture. J Agric Food Chem 2024; 72:2077-2088. [PMID: 38230633 DOI: 10.1021/acs.jafc.3c08265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
Sustainable agriculture is increasingly linked to biological pesticides as alternatives to agro-chemicals. Streptomyces species suppress plant diseases through their unique traits and numerous metabolites. Although many Streptomyces strains have been developed into commercial products, their roles in the biocontrol of phytopathogens and mechanisms of functional metabolite synthesis remain poorly understood. In this review, biocontrol of plant diseases by Streptomyces is summarized on the basis of classification of fungal and bacterial diseases and secondary metabolites produced by Streptomyces that act on phytopathogenic microorganisms are discussed. The associated non-ribosomal peptide synthetases and polyketide synthetases responsible for biosynthesis of these secondary metabolites are also investigated, and advances in fermentation of Streptomyces are described. Finally, the need to develop precise and effective biocontrol methods for plant diseases is highlighted.
Collapse
Affiliation(s)
- Mingxuan Wang
- Institute of Food Science and Engineering, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, People's Republic of China
| | - Honglin Li
- Institute of Food Science and Engineering, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, People's Republic of China
| | - Jing Li
- Institute of Food Science and Engineering, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, People's Republic of China
| | - Wujin Zhang
- Institute of Food Science and Engineering, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, People's Republic of China
| | - Jianguo Zhang
- Institute of Food Science and Engineering, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, People's Republic of China
| |
Collapse
|
47
|
Kim JH, Chi WJ. Molecular and Biochemical Characterization of Xylanase Produced by Streptomyces viridodiastaticus MS9, a Newly Isolated Soil Bacterium. J Microbiol Biotechnol 2024; 34:176-184. [PMID: 38037397 PMCID: PMC10840471 DOI: 10.4014/jmb.2309.09029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/26/2023] [Accepted: 11/03/2023] [Indexed: 12/02/2023]
Abstract
A xylan-degrading bacterial strain, MS9, was recently isolated from soil samples collected in Namhae, Gyeongsangnam-do, Republic of Korea. This strain was identified as a variant of Streptomyces viridodiastaticus NBRC13106T based on 16S rRNA gene sequencing, DNA-DNA hybridization analysis, and other chemotaxonomic characteristics, and was named S. viridodiastaticus MS9 (=KCTC29014= DSM42055). In this study, we aimed to investigate the molecular and biochemical characteristics of a xylanase (XynCvir) identified from S. viridodiastaticus MS9. XynCvir (molecular weight ≍ 21 kDa) was purified from a modified Luria-Bertani medium, in which cell growth and xylanase production considerably increased after addition of xylan. Thin layer chromatography of xylan-hydrolysate showed that XynCvir is an endo-(1,4)-β-xylanase that degrades xylan into a series of xylooligosaccharides, ultimately converting it to xylobiose. The Km and Vmax values of XynCvir for beechwood xylan were 1.13 mg/ml and 270.3 U/mg, respectively. Only one protein (GHF93985.1, 242 amino acids) containing an amino acid sequence identical to the amino-terminal sequence of XynCvir was identified in the genome of S. viridodiastaticus. GHF93985.1 with the twin-arginine translocation signal peptide is cleaved between Ala-50 and Ala-51 to form the mature protein (21.1 kDa; 192 amino acids), which has the same amino-terminal sequence (ATTITTNQT) and molecular weight as XynCvir, indicating GHF93985.1 corresponds to XynCvir. Since none of the 100 open reading frames most homologous to GHF93985.1 listed in GenBank have been identified for their biochemical functions, our findings greatly contribute to the understanding of their biochemical characteristics.
Collapse
Affiliation(s)
- Jong-Hee Kim
- Department of Food and Nutrition, Seoil University, Seoul 02192, Republic of Korea
| | - Won-Jae Chi
- Species Diversity Research Division, National Institute of Biological Resources, Incheon 22689, Republic of Korea
| |
Collapse
|
48
|
Liu Z, Sun W, Hu Z, Wang W, Zhang H. Marine Streptomyces-Derived Novel Alkaloids Discovered in the Past Decade. Mar Drugs 2024; 22:51. [PMID: 38276653 PMCID: PMC10821133 DOI: 10.3390/md22010051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/21/2024] [Accepted: 01/21/2024] [Indexed: 01/27/2024] Open
Abstract
Natural alkaloids originating from actinomycetes and synthetic derivatives have always been among the important suppliers of small-molecule drugs. Among their biological sources, Streptomyces is the highest and most extensively researched genus. Marine-derived Streptomyces strains harbor unconventional metabolic pathways and have been demonstrated to be efficient producers of biologically active alkaloids; more than 60% of these compounds exhibit valuable activity such as antibacterial, antitumor, anti-inflammatory activities. This review comprehensively summarizes novel alkaloids produced by marine Streptomyces discovered in the past decade, focusing on their structural features, biological activity, and pharmacological mechanisms. Future perspectives on the discovery and development of novel alkaloids from marine Streptomyces are also provided.
Collapse
Affiliation(s)
| | | | | | | | - Huawei Zhang
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China; (Z.L.); (W.S.); (Z.H.); (W.W.)
| |
Collapse
|
49
|
El-Zawawy NA, Kenawy ER, Ahmed S, El-Sapagh S. Bioproduction and optimization of newly characterized melanin pigment from Streptomyces djakartensis NSS-3 with its anticancer, antimicrobial, and radioprotective properties. Microb Cell Fact 2024; 23:23. [PMID: 38229042 DOI: 10.1186/s12934-023-02276-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 12/15/2023] [Indexed: 01/18/2024] Open
Abstract
BACKGROUND Melanin is a natural pigment that is considered a promising biomaterial for numerous biotechnological applications across several industries. Melanin has biomedical applications as antimicrobial, anticancer, and antioxidant properties. Additionally, in the pharmaceutical and cosmetic industries, it is used in drug delivery and as a radioprotective agent. Also, melanin has environmental uses in the fields of bioremediation and the food industry. The biosynthesis of melanin pigment is an area of interest for researchers due to its multifunctionality, high compatibility, and biodegradability. Therefore, our present work is the first attempt to characterize and optimize the productivity of melanin pigment from Streptomyces djakartensis NSS-3 concerning its radioprotection and biological properties. RESULTS Forty isolates of soil actinobacteria were isolated from the Wadi Allaqui Biosphere Reserve, Egypt. Only one isolate, ACT3, produced a dark brown melanin pigment extracellularly. This isolate was identified according to phenotypic properties and molecular phylogenetic analysis as Streptomyces djakartensis NSS-3 with accession number OP912881. Plackett-Burman experimental design (PBD) and response surface methodology (RSM) using a Box-Behnken design (BBD) were performed for optimum medium and culturing conditions for maximum pigment production, resulting in a 4.19-fold improvement in melanin production (118.73 mg/10 mL). The extracted melanin pigment was purified and characterized as belonging to nitrogen-free pyomelanin based on ultraviolet-visible spectrophotometry (UV-VIS), Fourier transform infrared (FT-IR), Raman spectroscopy, scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy (EDX), and NMR studies. Purified melanin demonstrated potent scavenging activity with IC50 values of 18.03 µg/mL and revealed high potency as sunscreens (in vitro SPF = 18.5). Moreover, it showed a nontoxic effect on a normal cell line (WI38), while it had a concentration-dependent anticancer effect on HCT116, HEPG, and MCF7 cell lines with IC50 = 108.9, 43.83, and 81.99 µg/mL, respectively. Also, purified melanin had a detrimental effect on the tested MDR bacterial strains, of which PA-09 and SA-04 were clearly more susceptible to melanin compared with other strains with MICs of 6.25 and 25 µg/mL, respectively. CONCLUSION Our results demonstrated that the newly characterized pyomelanin from Streptomyces djakartensis NSS-3 has valuable biological properties due to its potential photoprotective, antioxidant, anticancer, antimicrobial, and lack of cytotoxic activities, which open up new prospects for using this natural melanin pigment in various biotechnological applications and avoiding chemical-based drugs.
Collapse
Affiliation(s)
- Nessma A El-Zawawy
- Department of Botany and Microbiology, Faculty of Science, Tanta University, Tanta, Egypt.
| | - El-Refaie Kenawy
- Chemistry Department, Polymer Research Unit, Faculty of Science, Tanta University, Tanta, Egypt
| | - Sara Ahmed
- Department of Botany and Microbiology, Faculty of Science, Tanta University, Tanta, Egypt
| | - Shimaa El-Sapagh
- Department of Botany and Microbiology, Faculty of Science, Tanta University, Tanta, Egypt
| |
Collapse
|
50
|
Rigolet A, Argüelles Arias A, Anckaert A, Quinton L, Rigali S, Tellatin D, Burguet P, Ongena M. Lipopeptides as rhizosphere public goods for microbial cooperation. Microbiol Spectr 2024; 12:e0310623. [PMID: 38047676 PMCID: PMC10783051 DOI: 10.1128/spectrum.03106-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 11/06/2023] [Indexed: 12/05/2023] Open
Abstract
IMPORTANCE Here, we provide new insights into the possible fate of cyclic lipopeptides as prominent specialized metabolites from beneficial bacilli and pseudomonads once released in the soil. Our data illustrate how the B. velezensis lipopeptidome may be enzymatically remodeled by Streptomyces as important members of the soil bacterial community. The enzymatic arsenal of S. venezuelae enables an unsuspected extensive degradation of these compounds, allowing the bacterium to feed on these exogenous products via a mechanism going beyond linearization, which was previously reported as a detoxification strategy. As soils are carbon-rich and nitrogen-poor environments, we propose a new role for cyclic lipopeptides in interspecies interactions, which is to fuel the nitrogen metabolism of a part of the rhizosphere microbial community. Streptomyces and other actinomycetes, producing numerous peptidases and displaying several traits of beneficial bacteria, should be at the front line to directly benefit from these metabolites as "public goods" for microbial cooperation.
Collapse
Affiliation(s)
- Augustin Rigolet
- Microbial Processes and Interactions laboratory, TERRA teaching and research centre, Gembloux Agro-Bio Tech,University of Liège, Gembloux, Belgium
| | - Anthony Argüelles Arias
- Microbial Processes and Interactions laboratory, TERRA teaching and research centre, Gembloux Agro-Bio Tech,University of Liège, Gembloux, Belgium
| | - Adrien Anckaert
- Microbial Processes and Interactions laboratory, TERRA teaching and research centre, Gembloux Agro-Bio Tech,University of Liège, Gembloux, Belgium
| | - Loïc Quinton
- Department of Chemistry, University of Liège, Liège, Belgium
| | - Sébastien Rigali
- InBioS—Centre for Protein Engineering,University of Liège, Liege, Belgium
- Hedera-22, Liege, Belgium
| | - Deborah Tellatin
- InBioS—Centre for Protein Engineering,University of Liège, Liege, Belgium
| | - Pierre Burguet
- Department of Chemistry, University of Liège, Liège, Belgium
| | - Marc Ongena
- Microbial Processes and Interactions laboratory, TERRA teaching and research centre, Gembloux Agro-Bio Tech,University of Liège, Gembloux, Belgium
| |
Collapse
|