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Adigoun RFR, Durand A, Tchokponhoué DA, Achigan-Dako EG, Aholoukpè HNS, Bokonon-Ganta AH, Benizri E. Drivers of the Sisrè berry plant [Synsepalum dulcificum (Schumach & Thonn.) Daniell] rhizosphere bacterial communities in Benin. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 938:173550. [PMID: 38810760 DOI: 10.1016/j.scitotenv.2024.173550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 05/31/2024]
Abstract
Each plant species has its own rhizobacteriome, whose activities determine both soil biological quality and plant growth. Little knowledge exists of the rhizosphere bacterial communities associated with opportunity crops with high economic potential such as Synsepalum dulcificum. Native to West Africa, this shrub is famous for its red berries representing the only natural source of miraculin, a glycoprotein, with sweetening properties, but also playing a role in the treatment of cancer and diabetes. This study aimed to characterize the structure and diversity of rhizobacterial communities associated with S. dulcificum and to identify the parameters determining this diversity. An initial sampling stage allowed the collection of rhizosphere soils from 29 S. dulcificum accessions, belonging to three distinct phenotypes, from 16 municipalities of Benin, located either on farms or in home gardens. The bacterial diversity of these rhizosphere soils was assessed by Illumina sequencing of the 16S rRNA gene after DNA extraction from these soils. Furthermore, an analysis of the physicochemical properties of these soils was carried out. All accessions combined, the most represented phylum appeared to be Actinobacteriota, with an average relative abundance of 43.5 %, followed by Proteobacteria (14.8 %), Firmicutes (14.3 %) and Chloroflexi (12.2 %), yet the relative abundance of dominant phyla varied significantly among accessions (p < 0.05). Plant phenotype, habitat, climate and soil physicochemical properties affected the bacterial communities, but our study pointed out that soil physicochemical parameters were the main driver of rhizobacterial communities' structure and diversity. Among them, the assimilable phosphorus, lead, potassium, arsenic and manganese contents, texture and cation exchange capacity of rhizosphere soils were the major determinants of the composition and diversity of rhizosphere bacterial communities. These results suggested the possibility of improving the growth conditions and productivity of S. dulcificum, by harnessing its associated bacteria of interest and better managing soil physicochemical properties.
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Affiliation(s)
- Rabiath F R Adigoun
- Université de Lorraine, INRAE, LSE, F-54000 Nancy, France; Genetics, Biotechnology and Seed Science Unit (GBioS), Laboratory of Plant Production, Physiology and Plant Breeding (PAGEV), Department of Plant Sciences, Faculty of Agronomic Sciences, University of Abomey-Calavi, Abomey-Calavi, Benin; Laboratoire d'Entomologie Agricole (LEAg), Department of Plant Sciences, Faculty of Agronomic Sciences, University of Abomey-Calavi, B.P. 526 Abomey-Calavi, Benin
| | - Alexis Durand
- Université de Lorraine, INRAE, LSE, F-54000 Nancy, France
| | - Dèdéou A Tchokponhoué
- Genetics, Biotechnology and Seed Science Unit (GBioS), Laboratory of Plant Production, Physiology and Plant Breeding (PAGEV), Department of Plant Sciences, Faculty of Agronomic Sciences, University of Abomey-Calavi, Abomey-Calavi, Benin
| | - Enoch G Achigan-Dako
- Genetics, Biotechnology and Seed Science Unit (GBioS), Laboratory of Plant Production, Physiology and Plant Breeding (PAGEV), Department of Plant Sciences, Faculty of Agronomic Sciences, University of Abomey-Calavi, Abomey-Calavi, Benin
| | - Hervé N S Aholoukpè
- Centre de Recherches Agricoles Plantes Pérennes (CRA-PP), Institut National des Recherches Agricoles du Bénin, BP 01 Pobè, Benin
| | - Aimé H Bokonon-Ganta
- Laboratoire d'Entomologie Agricole (LEAg), Department of Plant Sciences, Faculty of Agronomic Sciences, University of Abomey-Calavi, B.P. 526 Abomey-Calavi, Benin
| | - Emile Benizri
- Université de Lorraine, INRAE, LSE, F-54000 Nancy, France
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Qin YY, Gong Y, Kong SY, Wan ZY, Liu JQ, Xing K, Qin S. Aerial signaling by plant-associated Streptomyces setonii WY228 regulates plant growth and enhances salt stress tolerance. Microbiol Res 2024; 286:127823. [PMID: 38959523 DOI: 10.1016/j.micres.2024.127823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 06/25/2024] [Accepted: 06/26/2024] [Indexed: 07/05/2024]
Abstract
Plant-associated streptomycetes play important roles in plant growth and development. However, knowledge of volatile-mediated crosstalk between Streptomyces spp. and plants remains limited. In this study, we investigated the impact of volatiles from nine endophytic Streptomyces strains on the growth and development of plants. One versatile strain, Streptomyces setonii WY228, was found to significantly promote the growth of Arabidopsis thaliana and tomato seedlings, confer salt tolerance, and induce early flowering and increased fruit yield following volatile treatment. Analysis of plant growth-promoting traits revealed that S. setonii WY228 could produce indole-3-acetic acid, siderophores, ACC deaminase, fix nitrogen, and solubilize inorganic phosphate. These capabilities were further confirmed through genome sequencing and analysis. Volatilome analysis indicated that the volatile organic compounds emitted from ISP-2 medium predominantly comprised sesquiterpenes and 2-ethyl-5-methylpyrazine. Further investigations showed that 2-ethyl-5-methylpyrazine and sesquiterpenoid volatiles were the primary regulators promoting growth, as confirmed by experiments using the terpene synthesis inhibitor phosphomycin, pure compounds, and comparisons of volatile components. Transcriptome analysis, combined with mutant and inhibitor studies, demonstrated that WY228 volatiles promoted root growth by activating Arabidopsis auxin signaling and polar transport, and enhanced root hair development through ethylene signaling activation. Additionally, it was confirmed that volatiles can stimulate plant abscisic acid signaling and activate the MYB75 transcription factor, thereby promoting anthocyanin synthesis and enhancing plant salt stress tolerance. Our findings suggest that aerial signaling-mediated plant growth promotion and abiotic stress tolerance represent potentially overlooked mechanisms of Streptomyces-plant interactions. This study also provides an exciting strategy for the regulation of plant growth and the improvement of horticultural crop yields within sustainable agricultural practices.
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Affiliation(s)
- Yue-Ying Qin
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, PR China
| | - Yuan Gong
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, PR China
| | - Su-Yun Kong
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, PR China
| | - Zhi-Yuan Wan
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, PR China
| | - Jia-Qi Liu
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, PR China
| | - Ke Xing
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, PR China
| | - Sheng Qin
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, PR China.
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3
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Cuervo L, Méndez C, Salas JA, Olano C, Malmierca MG. Volatile communication in Actinobacteria: a language for secondary metabolism regulation. Microb Cell Fact 2024; 23:181. [PMID: 38890640 PMCID: PMC11186294 DOI: 10.1186/s12934-024-02456-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 06/08/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Volatile compounds are key elements in the interaction and communication between organisms at both interspecific and intraspecific levels. In complex bacterial communities, the emission of these fast-acting chemical messengers allows an exchange of information even at a certain distance that can cause different types of responses in the receiving organisms. The changes in secondary metabolism as a consequence of this interaction arouse great interest in the field of searching for bioactive compounds since they can be used as a tool to activate silenced metabolic pathways. Regarding the great metabolic potential that the Actinobacteria group presents in the production of compounds with attractive properties, we evaluated the reply the emitted volatile compounds can generate in other individuals of the same group. RESULTS We recently reported that volatile compounds released by different streptomycete species trigger the modulation of biosynthetic gene clusters in Streptomyces spp. which finally leads to the activation/repression of the production of secondary metabolites in the recipient strains. Here we present the application of this rationale in a broader bacterial community to evaluate volatiles as signaling effectors that drive the activation of biosynthesis of bioactive compounds in other members of the Actinobacteria group. Using cocultures of different actinobacteria (where only the volatile compounds reach the recipient strain) we were able to modify the bacterial secondary metabolism that drives overproduction (e.g., granaticins, actiphenol, chromomycins) and/or de novo production (e.g., collismycins, skyllamycins, cosmomycins) of compounds belonging to different chemical species that present important biological activities. CONCLUSIONS This work shows how the secondary metabolism of different Actinobacteria species can vary significantly when exposed in co-culture to the volatile compounds of other phylum-shared bacteria, these effects being variable depending on strains and culture media. This approach can be applied to the field of new drug discovery to increase the battery of bioactive compounds produced by bacteria that can potentially be used in treatments for humans and animals.
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Affiliation(s)
- Lorena Cuervo
- Department Functional Biology, University of Oviedo, 33006, Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A), University of Oviedo, 33006, Oviedo, Spain
- Health Research Institute of Asturias (ISPA), 33006, Oviedo, Spain
| | - Carmen Méndez
- Department Functional Biology, University of Oviedo, 33006, Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A), University of Oviedo, 33006, Oviedo, Spain
- Health Research Institute of Asturias (ISPA), 33006, Oviedo, Spain
| | - José A Salas
- Department Functional Biology, University of Oviedo, 33006, Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A), University of Oviedo, 33006, Oviedo, Spain
- Health Research Institute of Asturias (ISPA), 33006, Oviedo, Spain
| | - Carlos Olano
- Department Functional Biology, University of Oviedo, 33006, Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A), University of Oviedo, 33006, Oviedo, Spain
- Health Research Institute of Asturias (ISPA), 33006, Oviedo, Spain
| | - Mónica G Malmierca
- Department Functional Biology, University of Oviedo, 33006, Oviedo, Spain.
- University Institute of Oncology of Asturias (I.U.O.P.A), University of Oviedo, 33006, Oviedo, Spain.
- Health Research Institute of Asturias (ISPA), 33006, Oviedo, Spain.
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Ghezzi D, Salvi L, Costantini PE, Firrincieli A, Iorio M, Lopo E, Sosio M, Elbanna AH, Khalil ZG, Capon RJ, De Waele J, Vergara F, Sauro F, Cappelletti M. Ancient and remote quartzite caves as a novel source of culturable microbes with biotechnological potential. Microbiol Res 2024; 286:127793. [PMID: 38901277 DOI: 10.1016/j.micres.2024.127793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 05/23/2024] [Accepted: 05/29/2024] [Indexed: 06/22/2024]
Abstract
Quartzite caves located on table-top mountains (tepuis) in the Guyana Shield, are ancient, remote, and pristine subterranean environments where microbes have evolved peculiar metabolic strategies to thrive in silica-rich, slightly acidic and oligotrophic conditions. In this study, we explored the culturable fraction of the microbiota inhabiting the (ortho)quartzite cave systems in Venezuelan tepui (remote table-top mountains) and we investigated their metabolic and enzymatic activities in relation with silica solubilization and extracellular hydrolytic activities as well as the capacity to produce antimicrobial compounds. Eighty microbial strains were isolated with a range of different enzymatic capabilities. More than half of the isolated strains performed at least three enzymatic activities and four bacterial strains displayed antimicrobial activities. The antimicrobial producers Paraburkholderia bryophila CMB_CA002 and Sphingomonas sp. MEM_CA187, were further analyzed by conducting chemotaxonomy, phylogenomics, and phenomics. While the isolate MEM_CA187 represents a novel species of the genus Sphingomonas, for which the name Sphingomonas imawarii sp. nov. is proposed, P. bryophila CMB_CA002 is affiliated with a few strains of the same species that are antimicrobial producers. Chemical analyses demonstrated that CMB_CA002 produces ditropolonyl sulfide that has a broad range of activity and a possibly novel siderophore. Although the antimicrobial compounds produced by MEM_CA187 could not be identified through HPLC-MS analysis due to the absence of reference compounds, it represents the first soil-associated Sphingomonas strain with the capacity to produce antimicrobials. This work provides first insights into the metabolic potential present in quartzite cave systems pointing out that these environments are a novel and still understudied source of microbial strains with biotechnological potential.
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Affiliation(s)
- Daniele Ghezzi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Luca Salvi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Paolo E Costantini
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Andrea Firrincieli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy; Department for Innovation in Biological, Agro-Food and Forest systems, University of Tuscia, Viterbo 01100, Italy
| | | | - Ettore Lopo
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | | | - Ahmed H Elbanna
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; Department of Pharmacognosy, Cairo University, Cairo 11562, Egypt
| | - Zeinab G Khalil
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Robert J Capon
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jo De Waele
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna 40126, Italy; La Venta Geographic Explorations Association, Treviso 31100, Italy
| | - Freddy Vergara
- La Venta Geographic Explorations Association, Treviso 31100, Italy; Teraphosa Exploring Team, Puerto Ordaz, Venezuela
| | - Francesco Sauro
- La Venta Geographic Explorations Association, Treviso 31100, Italy
| | - Martina Cappelletti
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy; La Venta Geographic Explorations Association, Treviso 31100, Italy.
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5
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Ma X, Jin Z, Zhang Q, Dai L, Lu C. A polysubstituted cyclopentane and two glycerol esters from the engineered strain Streptomyces sp. S35-LAL1. Nat Prod Res 2024:1-6. [PMID: 38853409 DOI: 10.1080/14786419.2024.2364932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 06/03/2024] [Indexed: 06/11/2024]
Abstract
Activation of silencing gene clusters is an important way to discover structurally novel compounds. In this study, three undescribed compounds were obtained from an engineered strain of Streptomyces sp. S35-LAL1. They include a polysubstituted cyclopentane with an unprecedented 10-carbon skeleton (1) and two glycerol esters (2 and 3). The structures of compounds 1-3 were elucidated through analysis of their spectroscopic data including 1D, 2D NMR, optical rotation, and electronic circular dichroism (ECD).
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Affiliation(s)
- Xinyu Ma
- Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Zhuo Jin
- Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Qian Zhang
- Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Liping Dai
- Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Chunhua Lu
- Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
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Maimone NM, Apaza-Castillo GA, Quecine MC, de Lira SP. Accessing the specialized metabolome of actinobacteria from the bulk soil of Paullinia cupana Mart. on the Brazilian Amazon: a promising source of bioactive compounds against soybean phytopathogens. Braz J Microbiol 2024; 55:1863-1882. [PMID: 38421597 PMCID: PMC11153476 DOI: 10.1007/s42770-024-01286-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 02/10/2024] [Indexed: 03/02/2024] Open
Abstract
The Amazon rainforest, an incredibly biodiverse ecosystem, has been increasingly vulnerable to deforestation. Despite its undeniable importance and potential, the Amazonian microbiome has historically received limited study, particularly in relation to its unique arsenal of specialized metabolites. Therefore, in this study our aim was to assess the metabolic diversity and the antifungal activity of actinobacterial strains isolated from the bulk soil of Paullinia cupana, a native crop, in the Brazilian Amazon Rainforest. Extracts from 24 strains were subjected to UPLC-MS/MS analysis using an integrative approach that relied on the Chemical Structural and Compositional Similarity (CSCS) metric, GNPS molecular networking, and in silico dereplication tools. This procedure allowed the comprehensive understanding of the chemical space encompassed by these actinobacteria, which consists of features belonging to known bioactive metabolite classes and several unannotated molecular families. Among the evaluated strains, five isolates exhibited bioactivity against a panel of soybean fungal phytopathogens (Rhizoctonia solani, Macrophomina phaseolina, and Sclerotinia sclerotiorum). A focused inspection led to the annotation of pepstatins, oligomycins, hydroxamate siderophores and dorrigocins as metabolites produced by these bioactive strains, with potentially unknown compounds also comprising their metabolomes. This study introduces a pragmatic protocol grounded in established and readily available tools for the annotation of metabolites and the prioritization of strains to optimize further isolation of specialized metabolites. Conclusively, we demonstrate the relevance of the Amazonian actinobacteria as sources for bioactive metabolites useful for agriculture. We also emphasize the importance of preserving this biome and conducting more in-depth studies on its microbiota.
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Affiliation(s)
- Naydja Moralles Maimone
- College of Agriculture "Luiz de Queiroz", Department of Exact Sciences, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Gladys Angélica Apaza-Castillo
- College of Agriculture "Luiz de Queiroz", Department of Genetics, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Maria Carolina Quecine
- College of Agriculture "Luiz de Queiroz", Department of Genetics, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Simone Possedente de Lira
- College of Agriculture "Luiz de Queiroz", Department of Exact Sciences, University of São Paulo, Piracicaba, SP, 13418-900, Brazil.
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7
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Qi D, Liu Q, Zou L, Zhang M, Li K, Zhao Y, Chen Y, Feng J, Zhou D, Wei Y, Wang W, Zhang L, Xie J. Taxonomic identification and antagonistic activity of Streptomyces luomodiensis sp. nov. against phytopathogenic fungi. Front Microbiol 2024; 15:1402653. [PMID: 38860218 PMCID: PMC11163044 DOI: 10.3389/fmicb.2024.1402653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 05/09/2024] [Indexed: 06/12/2024] Open
Abstract
Banana wilt caused by Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) is a devastating fungal disease. Biocontrol strategies hold immense potential for inhibiting the spread of Foc TR4. Here, 30 actinobacteria were isolated from soils and screened for their antagonistic activity against Foc TR4. Strain SCA4-21T was selected due to its strongest antagonistic activity against Foc TR4. Strain SCA4-21T also exhibited strong antagonistic activity against the other eight phytopathogenic fungi. The strain was identified as the genus Streptomyces according to its physiological, biochemical, and phenotypic characteristics. The phylogenetic trees of 16S rRNA sequences demonstrated that strain SCA4-21T formed a subclade with S. iranensis HM 35T and/or S. rapamycinicus NRRL B-5491T with low bootstrap values. Considering that 16S rRNAs did not provide sufficient resolution for species-level identification, the whole genome of strain SCA4-21T was sequenced. Multilocus sequence analysis (MLSA) based on five housekeeping gene alleles (atpD, gyrB, recA, rpoB, and trpB) revealed that strain SCA4-21T clustered into S. hygroscopicus subsp. hygroscopicus NBRC 13472T with 100% of bootstrap value. The analysis of the genome-based phylogeny also approved the results. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) were 91.26 and 44.30%, respectively, with values below the respective species level threshold of 95 and 70%. Hence, strain SCA 4-21T represented a novel species within the genus Streptomyces, named Streptomyces luomodiensis sp. nov. The type strain is SCA4-21T (=GDMCC4.340T = JCM36555T). By the CAZymes analysis, 348 carbohydrate-active enzymes (CAZymes) were detected, including 15 chitinases and eight β-1,3-glucanases. The fermentation broth of strain SCA4-21T, exhibiting strong antagonistic activity against Foc TR4, demonstrated high activities of chitinase and β-1,3-glucanase, which might be involved in antifungal activity. Our results showed an innovative potential biocontrol agent for managing plant fungal diseases, specifically banana fusarium wilt.
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Affiliation(s)
- Dengfeng Qi
- National Key Laboratory of Biological Breeding of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Qiao Liu
- National Key Laboratory of Biological Breeding of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Liangping Zou
- National Key Laboratory of Biological Breeding of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Miaoyi Zhang
- National Key Laboratory of Biological Breeding of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Kai Li
- National Key Laboratory of Biological Breeding of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yankun Zhao
- National Key Laboratory of Biological Breeding of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yufeng Chen
- National Key Laboratory of Biological Breeding of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Junting Feng
- National Key Laboratory of Biological Breeding of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Dengbo Zhou
- National Key Laboratory of Biological Breeding of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yongzan Wei
- National Key Laboratory of Biological Breeding of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Wei Wang
- National Key Laboratory of Biological Breeding of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Lu Zhang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Jianghui Xie
- National Key Laboratory of Biological Breeding of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
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8
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Diab MK, Mead HM, Ahmad Khedr MM, Abu-Elsaoud AM, El-Shatoury SA. Actinomycetes are a natural resource for sustainable pest control and safeguarding agriculture. Arch Microbiol 2024; 206:268. [PMID: 38762847 DOI: 10.1007/s00203-024-03975-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 04/22/2024] [Indexed: 05/20/2024]
Abstract
Actinomycetes, a diverse group of bacteria with filamentous growth characteristics, have long captivated researchers and biochemists for their prolific production of secondary metabolites. Among the myriad roles played by actinomycete secondary metabolites, their historical significance in the field of biocontrol stands out prominently. The fascinating journey begins with the discovery of antibiotics, where renowned compounds like streptomycin, tetracycline, and erythromycin revolutionized medicine and agriculture. The history of biocontrol traces its roots back to the early twentieth century, when scientists recognized the potential of naturally occurring agents to combat pests and diseases. The emergence of synthetic pesticides in the mid-twentieth century temporarily overshadowed interest in biocontrol. However, with growing environmental concerns and the realization of the negative ecological impacts of chemical pesticides, the pendulum swung back towards exploring sustainable alternatives. Beyond their historical role as antibiotics, actinomycete-produced secondary metabolites encompass a rich repertoire with biopesticide potential. The classification of these compounds based on chemical structure and mode of action is highlighted, demonstrating their versatility against both plant pathogens and insect pests. Additionally, this review provides in-depth insights into how endophytic actinomycete strains play a pivotal role in biocontrol strategies. Case studies elucidate their effectiveness in inhibiting Spodoptera spp. and nematodes through the production of bioactive compounds. By unraveling the multifunctional roles of endophytic actinomycetes, this review contributes compelling narrative knowledge to the field of sustainable agriculture, emphasizing the potential of these microbial allies in crafting effective, environmentally friendly biocontrol strategies for combating agricultural pests.
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Affiliation(s)
- Mohamed Khaled Diab
- Agricultural Research Center, Pest Physiology Department, Plant Protection Research Institute, Giza, 12311, Egypt.
| | - Hala Mohamed Mead
- Agricultural Research Center, Pest Physiology Department, Plant Protection Research Institute, Giza, 12311, Egypt
| | - Mohamad M Ahmad Khedr
- Agricultural Research Center, Cotton Leafworm Department, Plant Protection Research Institute, Giza, 12311, Egypt
| | | | - Sahar Ahmed El-Shatoury
- Department of Botany and Microbiology, Faculty of Science, Suez Canal University, Ismailia, 41522, Egypt
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9
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Liu Z, Li K, Li J, Zhuang Z, Guo L, Bai L. Characterization and functional evidence for Orf2 of Streptomyces sp. 139 as a novel dipeptidase E. Appl Microbiol Biotechnol 2024; 108:326. [PMID: 38717487 PMCID: PMC11078827 DOI: 10.1007/s00253-024-13161-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 04/17/2024] [Accepted: 04/24/2024] [Indexed: 05/12/2024]
Abstract
Aspartyl dipeptidase (dipeptidase E) can hydrolyze Asp-X dipeptides (where X is any amino acid), and the enzyme plays a key role in the degradation of peptides as nutrient sources. Dipeptidase E remains uncharacterized in Streptomyces. Orf2 from Streptomyces sp. 139 is located in the exopolysaccharide biosynthesis gene cluster, which may be a novel dipeptidase E with "S134-H170-D198" catalytic triad by sequence and structure comparison. Herein, recombinant Orf2 was expressed in E. coli and characterized dipeptidase E activity using the Asp-ρNA substrate. The optimal pH and temperature for Orf2 are 7.5 and 40 ℃; Vmax and Km of Orf2 are 0.0787 mM·min-1 and 1.709 mM, respectively. Orf2 exhibits significant degradation activities to Asp-Gly-Gly, Asp-Leu, Asp-His, and isoAsp-Leu and minimal activities to Asp-Pro and Asp-Ala. Orf2 contains a Ser-His-Asp catalytic triad characterized by point mutation. In addition, the Asp147 residue of Orf2 is also proven to be critical for the enzyme's activity through molecular docking and point mutation. Transcriptome analysis reveals the upregulation of genes associated with ribosomes, amino acid biosynthesis, and aminoacyl-tRNA biosynthesis in the orf2 mutant strain. Compared with the orf2 mutant strain and WT, the yield of crude polysaccharide does not change significantly. However, crude polysaccharides from the orf2 mutant strain exhibit a wider range of molecular weight distribution. The results indicate that the Orf2 links nutrient stress to secondary metabolism as a novel dipeptidase E. KEY POINTS: • A novel dipeptidase E with a Ser-His-Asp catalytic triad was characterized from Streptomyces sp. 139. • Orf2 was involved in peptide metabolism both in vitro and in vivo. • Orf2 linked nutrient stress to mycelia formation and secondary metabolism in Streptomyces.
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Affiliation(s)
- Zhe Liu
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Kemeng Li
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Jialin Li
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Zhuochen Zhuang
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Lianhong Guo
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Liping Bai
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China.
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China.
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Jibola-Shittu MY, Heng Z, Keyhani NO, Dang Y, Chen R, Liu S, Lin Y, Lai P, Chen J, Yang C, Zhang W, Lv H, Wu Z, Huang S, Cao P, Tian L, Qiu Z, Zhang X, Guan X, Qiu J. Understanding and exploring the diversity of soil microorganisms in tea ( Camellia sinensis) gardens: toward sustainable tea production. Front Microbiol 2024; 15:1379879. [PMID: 38680916 PMCID: PMC11046421 DOI: 10.3389/fmicb.2024.1379879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 04/03/2024] [Indexed: 05/01/2024] Open
Abstract
Leaves of Camellia sinensis plants are used to produce tea, one of the most consumed beverages worldwide, containing a wide variety of bioactive compounds that help to promote human health. Tea cultivation is economically important, and its sustainable production can have significant consequences in providing agricultural opportunities and lowering extreme poverty. Soil parameters are well known to affect the quality of the resultant leaves and consequently, the understanding of the diversity and functions of soil microorganisms in tea gardens will provide insight to harnessing soil microbial communities to improve tea yield and quality. Current analyses indicate that tea garden soils possess a rich composition of diverse microorganisms (bacteria and fungi) of which the bacterial Proteobacteria, Actinobacteria, Acidobacteria, Firmicutes and Chloroflexi and fungal Ascomycota, Basidiomycota, Glomeromycota are the prominent groups. When optimized, these microbes' function in keeping garden soil ecosystems balanced by acting on nutrient cycling processes, biofertilizers, biocontrol of pests and pathogens, and bioremediation of persistent organic chemicals. Here, we summarize research on the activities of (tea garden) soil microorganisms as biofertilizers, biological control agents and as bioremediators to improve soil health and consequently, tea yield and quality, focusing mainly on bacterial and fungal members. Recent advances in molecular techniques that characterize the diverse microorganisms in tea gardens are examined. In terms of viruses there is a paucity of information regarding any beneficial functions of soil viruses in tea gardens, although in some instances insect pathogenic viruses have been used to control tea pests. The potential of soil microorganisms is reported here, as well as recent techniques used to study microbial diversity and their genetic manipulation, aimed at improving the yield and quality of tea plants for sustainable production.
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Affiliation(s)
- Motunrayo Y. Jibola-Shittu
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhiang Heng
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Nemat O. Keyhani
- Department of Biological Sciences, University of Illinois, Chicago, IL, United States
| | - Yuxiao Dang
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ruiya Chen
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sen Liu
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yongsheng Lin
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Pengyu Lai
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jinhui Chen
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chenjie Yang
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Weibin Zhang
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Huajun Lv
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ziyi Wu
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shuaishuai Huang
- School of Ecology and Environment, Tibet University, Lhasa, China
| | - Pengxi Cao
- School of Ecology and Environment, Tibet University, Lhasa, China
| | - Lin Tian
- Tibet Plateau Institute of Biology, Lhasa, China
| | - Zhenxing Qiu
- Fuzhou Technology and Business University, Fuzhou, Fujian, China
| | - Xiaoyan Zhang
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiayu Guan
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Junzhi Qiu
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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11
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Ribeiro I, Correia S, Blümel M, Albuquerque P, Gorb SN, Mendes MV, Tasdemir D, Mucha AP, Carvalho MF. Streptomyces profundus sp. nov., a novel marine actinobacterium isolated from deep-sea sediment of Madeira Archipelago, Portugal. Int J Syst Evol Microbiol 2024; 74. [PMID: 38639738 DOI: 10.1099/ijsem.0.006341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024] Open
Abstract
A novel strain, MA3_2.13T, was isolated from deep-sea sediment of Madeira Archipelago, Portugal, and characterized using a polyphasic approach. This strain produced dark brown soluble pigments, bronwish black substrate mycelia and an aerial mycelium with yellowish white spores, when grown on GYM 50SW agar. The main respiratory quinones were MK-10(H4), MK-10(H6) and MK-10(H8). Diphosphatidylglycerol, phosphatidylethanolamine, three unidentified phospholipids and two glycophospholipids were identified as the main phospholipids. The major cellular fatty acids were iso-C16 : 1, iso-C16 : 0, anteiso-C17 : 1 and anteiso-C17 : 0. Phylogenetic analyses based on 16S rRNA gene showed that strain MA3_2.13T is a member of the genus Streptomyces and was most closely related to Streptomyces triticirhizae NEAU-YY642T (NR_180032.1; 16S rRNA gene similarity 97.9 %), Streptomyces sedi YIM 65188T (NR_044582.1; 16S rRNA gene similarity 97.4 %), Streptomyces mimosae 3MP-10T (NR_170412.1; 16S rRNA gene similarity 97.3 %) and Streptomyces zhaozhouensis NEAU-LZS-5T (NR_133874.1; 16S rRNA gene similarity 97.0 %). Genome pairwise comparisons with closest related type strains retrieved values below the threshold for species delineation suggesting that strain MA3_2.13T represents a new branch within the genus Streptomyces. Based on these results, strain MA3_2.13T (=DSM 115980T=LMG 33094T) is proposed as the type strain of a novel species of the genus Streptomyces, for which the name Streptomyces profundus sp. nov. is proposed.
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Affiliation(s)
- Inês Ribeiro
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research,University of Porto, Terminal de Cruzeiros do Porto de Leixões, Porto, Portugal
- ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
| | - Sofia Correia
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research,University of Porto, Terminal de Cruzeiros do Porto de Leixões, Porto, Portugal
- ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
- FCUP - Faculty of Sciences of the University of Porto, Porto, Portugal
| | - Martina Blümel
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Pedro Albuquerque
- i3S - Institute for Research and Innovation in Health, University of Porto, Porto, Portugal
- IBMC - Institute for Molecular and Cell Biology, University of Porto, Porto, Portugal
| | - Stanislav N Gorb
- Functional Morphology and Biomechanics, Zoological Institute, Kiel University, Kiel, Germany
| | - Marta V Mendes
- ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
- i3S - Institute for Research and Innovation in Health, University of Porto, Porto, Portugal
- IBMC - Institute for Molecular and Cell Biology, University of Porto, Porto, Portugal
| | - Deniz Tasdemir
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Kiel University, Kiel, Germany
| | - Ana P Mucha
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research,University of Porto, Terminal de Cruzeiros do Porto de Leixões, Porto, Portugal
- FCUP - Faculty of Sciences of the University of Porto, Porto, Portugal
| | - Maria F Carvalho
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research,University of Porto, Terminal de Cruzeiros do Porto de Leixões, Porto, Portugal
- ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
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12
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Salehi-Najafabadi A, Tehrani Fateh S, Amoabediny G, Hamedi J. Insights into additional lactone-based signaling circuits in Streptomyces: existence of acyl-homoserine lactones and LuxI/LuxR homologs in six Streptomyces species. Front Microbiol 2024; 15:1342637. [PMID: 38389542 PMCID: PMC10883386 DOI: 10.3389/fmicb.2024.1342637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 01/18/2024] [Indexed: 02/24/2024] Open
Abstract
Acyl-homoserine lactones (AHLs), mediating pivotal physiological activities through quorum sensing (QS), have conventionally been considered limited to Gram-negative bacteria. However, few reports on the existence of AHLs in Gram-positive bacteria have questioned this conception. Streptomyces, as Gram-positive bacteria already utilizing a lactone-based QS molecule (i.e., gamma-butyrolactones), are yet to be explored for producing AHLs, considering their metabolic capacity and physiological distinction. In this regard, our study examined the potential production of AHLs within Streptomyces by deploying HPLC-MS/MS methods, which resulted in the discovery of multiple AHL productions by S. griseus, S. lavendulae FRI-5, S. clavuligerus, S. nodosus, S. lividans, and S. coelicolor A3(2). Each of these Streptomyces species possesses a combination of AHLs of different size ranges, possibly due to their distinct properties and regulatory roles. In light of additional lactone molecules, we further confirm that AHL- and GBL-synthases (i.e., LuxI and AfsA enzyme families, respectively) and their receptors (i.e., LuxR and ArpA) are evolutionarily distinct. To this end, we searched for the components of the AHL signaling circuit, i.e., AHL synthases and receptors, in the Streptomyces genus, and we have identified multiple potential LuxI and LuxR homologs in all 2,336 Streptomyces species included in this study. The 6 Streptomyces of interest in this study also had at least 4 LuxI homologs and 97 LuxR homologs. In conclusion, AHLs and associated gene regulatory systems could be more widespread within the prokaryotic realm than previously believed, potentially contributing to the control of secondary metabolites (e.g., antibiotics) and their complex life cycle, which leads to substantial industrial and clinical applications.
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Affiliation(s)
- Amir Salehi-Najafabadi
- Department of Microbial Biotechnology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
- Research Center for New Technologies in Life Science Engineering, University of Tehran, Tehran, Iran
| | - Sepand Tehrani Fateh
- Research Center for New Technologies in Life Science Engineering, University of Tehran, Tehran, Iran
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ghasem Amoabediny
- Research Center for New Technologies in Life Science Engineering, University of Tehran, Tehran, Iran
- Faculty of Chemical Engineering, College of Engineering, University of Tehran, Tehran, Iran
| | - Javad Hamedi
- Department of Microbial Biotechnology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
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13
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Mao J, Zhang M, Dai W, Fu C, Wang Z, Wang X, Yao Q, Kong L, Qin J. Metabolic perturbation of Streptomyces albulus by introducing NADP-dependent glyceraldehyde 3-phosphate dehydrogenase. Front Microbiol 2024; 15:1328321. [PMID: 38328422 PMCID: PMC10847347 DOI: 10.3389/fmicb.2024.1328321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 01/08/2024] [Indexed: 02/09/2024] Open
Abstract
The available resources of Streptomyces represent a valuable repository of bioactive natural products that warrant exploration. Streptomyces albulus is primarily utilized in the industrial synthesis of ε-poly-L-lysine (ε-PL). In this study, the NADP-dependent glyceraldehyde 3-phosphate dehydrogenase (GapN) from Streptococcus mutans was heterologously expressed in S. albulus CICC11022, leading to elevated intracellular NADPH levels and reduced NADH and ATP concentrations. The resulting perturbation of S. albulus metabolism was comprehensively analyzed using transcriptomic and metabolomic methodologies. A decrease in production of ε-PL was observed. The expression of gapN significantly impacted on 23 gene clusters responsible for the biosynthesis of secondary metabolites. A comprehensive analysis revealed a total of 21 metabolites exhibiting elevated levels both intracellularly and extracellularly in the gapN expressing strain compared to those in the control strain. These findings underscore the potential of S. albulus to generate diverse bioactive natural products, thus offering valuable insights for the utilization of known Streptomyces resources through genetic manipulation.
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Affiliation(s)
| | | | | | | | | | | | | | - Linghui Kong
- School of Pharmacy, Binzhou Medical University, Yantai, China
| | - Jiayang Qin
- School of Pharmacy, Binzhou Medical University, Yantai, China
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14
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Karimian S, Farahmandzad N, Mohammadipanah F. Manipulation and epigenetic control of silent biosynthetic pathways in actinobacteria. World J Microbiol Biotechnol 2024; 40:65. [PMID: 38191749 DOI: 10.1007/s11274-023-03861-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 11/29/2023] [Indexed: 01/10/2024]
Abstract
Most biosynthetic gene clusters (BGCs) of Actinobacteria are either silent or expressed less than the detectable level. The non-genetic approaches including biological interactions, chemical agents, and physical stresses that can be used to awaken silenced pathways are compared in this paper. These non-genetic induction strategies often need screening approaches, including one strain many compounds (OSMAC), reporter-guided mutant selection, and high throughput elicitor screening (HiTES) have been developed. Different types of genetic manipulations applied in the induction of cryptic BGCs of Actinobacteria can be categorized as genome-wide pleiotropic and targeted approaches like manipulation of global regulatory systems, modulation of regulatory genes, ribosome and engineering of RNA polymerase or phosphopantheteine transferases. Targeted approaches including genome editing by CRISPR, mutation in transcription factors and modification of BGCs promoters, inactivation of the highly expressed biosynthetic pathways, deleting the suppressors or awakening the activators, heterologous expression, or refactoring of gene clusters can be applied for activation of pathways which are predicted to synthesize new bioactive structures in genome mining studies of Acinobacteria. In this review, the challenges and advantages of employing these approaches in induction of Actinobacteria BGCs are discussed. Further, novel natural products needed as drug for pharmaceutical industry or as biofertilizers in agricultural industry can be discovered even from known species of Actinobactera by the innovative approaches of metabolite biosynthesis elicitation.
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Affiliation(s)
- Sanaz Karimian
- Department of Biotechnology, Faculty of Biological Science, Alzahra University, Tehran, Iran
| | - Navid Farahmandzad
- Department of Biosystems Engineering, Auburn university, Auburn, AL 36849, USA
- Pharmaceutical Biotechnology Lab, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, 14155-6455, Iran
| | - Fatemeh Mohammadipanah
- Pharmaceutical Biotechnology Lab, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, 14155-6455, Iran.
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15
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Baranova MN, Pilipenko EA, Gabibov AG, Terekhov SS, Smirnov IV. Animal Microbiomes as a Source of Novel Antibiotic-Producing Strains. Int J Mol Sci 2023; 25:537. [PMID: 38203702 PMCID: PMC10779147 DOI: 10.3390/ijms25010537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/25/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
Natural compounds continue to serve as the most fruitful source of new antimicrobials. Analysis of bacterial genomes have revealed that the biosynthetic potential of antibiotic producers by far exceeds the number of already discovered structures. However, due to the repeated discovery of known substances, it has become necessary to change both approaches to the search for antibiotics and the sources of producer strains. The pressure of natural selection and the diversity of interactions in symbiotic communities make animal microbiomes promising sources of novel substances. Here, microorganisms associated with various animals were examined in terms of their antimicrobial agents. The application of alternative cultivation techniques, ultrahigh-throughput screening, and genomic analysis facilitated the investigation of compounds produced by unique representatives of the animal microbiota. We believe that new strategies of antipathogen defense will be discovered by precisely studying cell-cell and host-microbe interactions in microbiomes in the wild.
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Affiliation(s)
- Margarita N. Baranova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (A.G.G.)
| | - Ekaterina A. Pilipenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (A.G.G.)
| | - Alexander G. Gabibov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (A.G.G.)
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Stanislav S. Terekhov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (A.G.G.)
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ivan V. Smirnov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia; (M.N.B.); (A.G.G.)
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
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Le Loarer A, Dufossé L, Bignon J, Frédérich M, Ledoux A, Fouillaud M, Gauvin-Bialecki A. OSMAC Method to Assess Impact of Culture Parameters on Metabolomic Diversity and Biological Activity of Marine-Derived Actinobacteria. Mar Drugs 2023; 22:23. [PMID: 38248648 PMCID: PMC10817652 DOI: 10.3390/md22010023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/23/2024] Open
Abstract
Actinobacteria are known for their production of bioactive specialized metabolites, but they are still under-exploited. This study uses the "One Strain Many Compounds" (OSMAC) method to explore the potential of three preselected marine-derived actinobacteria: Salinispora arenicola (SH-78) and two Micromonospora sp. strains (SH-82 and SH-57). Various parameters, including the duration of the culture and the nature of the growth medium, were modified to assess their impact on the production of specialized metabolites. This approach involved a characterization based on chemical analysis completed with the construction of molecular networks and biological testing to evaluate cytotoxic and antiplasmodial activities. The results indicated that the influence of culture parameters depended on the studied species and also varied in relation with the microbial metabolites targeted. However, common favorable parameters could be observed for all strains such as an increase in the duration of the culture or the use of the A1 medium. For Micromonospora sp. SH-82, the solid A1 medium culture over 21 days favored a greater chemical diversity. A rise in the antiplasmodial activity was observed with this culture duration, with a IC50 twice as low as for the 14-day culture. Micromonospora sp. SH-57 produced more diverse natural products in liquid culture, with approximately 54% of nodes from the molecular network specifically linked to the type of culture support. Enhanced biological activities were also observed with specific sets of parameters. Finally, for Salinispora arenicola SH-78, liquid culture allowed a greater diversity of metabolites, but intensity variations were specifically observed for some metabolites under other conditions. Notably, compounds related to staurosporine were more abundant in solid culture. Consequently, in the range of the chosen parameters, optimal conditions to enhance metabolic diversity and biological activities in these three marine-derived actinobacteria were identified, paving the way for future isolation works.
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Affiliation(s)
- Alexandre Le Loarer
- Laboratory of Chemistry and Biotechnology of Natural Products, Faculty of Sciences and Technology, University of La Réunion, 15 Avenue René Cassin, CS 92003, CEDEX 09, 97744 Saint-Denis, France; (A.L.L.); (L.D.); (M.F.)
| | - Laurent Dufossé
- Laboratory of Chemistry and Biotechnology of Natural Products, Faculty of Sciences and Technology, University of La Réunion, 15 Avenue René Cassin, CS 92003, CEDEX 09, 97744 Saint-Denis, France; (A.L.L.); (L.D.); (M.F.)
| | - Jérôme Bignon
- Institute of Chemistry of Natural Substances (ICSN), CNRS UPR 2301, Université Paris-Saclay, 1, av. de la Terrasse, 91198 Gif-sur-Yvette, France;
| | - Michel Frédérich
- Pharmacognosy Laboratory, Department of Pharmacy, Centre Interfacultaire de Recherche sur le Médicament (CIRM), University of Liège, Campus du Sart-Tilman, Quartier Hôpital, Avenue Hippocrate, 15, B36, 4000 Liege, Belgium; (M.F.); (A.L.)
| | - Allison Ledoux
- Pharmacognosy Laboratory, Department of Pharmacy, Centre Interfacultaire de Recherche sur le Médicament (CIRM), University of Liège, Campus du Sart-Tilman, Quartier Hôpital, Avenue Hippocrate, 15, B36, 4000 Liege, Belgium; (M.F.); (A.L.)
| | - Mireille Fouillaud
- Laboratory of Chemistry and Biotechnology of Natural Products, Faculty of Sciences and Technology, University of La Réunion, 15 Avenue René Cassin, CS 92003, CEDEX 09, 97744 Saint-Denis, France; (A.L.L.); (L.D.); (M.F.)
| | - Anne Gauvin-Bialecki
- Laboratory of Chemistry and Biotechnology of Natural Products, Faculty of Sciences and Technology, University of La Réunion, 15 Avenue René Cassin, CS 92003, CEDEX 09, 97744 Saint-Denis, France; (A.L.L.); (L.D.); (M.F.)
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17
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Lu J, Mao J, Qi X, Chen J, Xiong J. The assembly of gut microbiota implicates shrimp acute hepatopancreas necrosis disease progression. Appl Microbiol Biotechnol 2023; 107:7489-7500. [PMID: 37768346 DOI: 10.1007/s00253-023-12810-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/17/2023] [Accepted: 09/21/2023] [Indexed: 09/29/2023]
Abstract
Ample evidence shows dysbiosis in the gut microbiota when comparing healthy shrimp with those affected by severe acute hepatopancreatic necrosis disease (AHPND). However, the static comparison used in available studies leads to the uncertainties regarding how and to what extent the gut microbiota responds to the progressive severity of AHPND. In addition, shrimp AHPND is featured by rapid and massive mortality, thus the initiation of AHPND must be diagnosed for preemptive therapy. For these reasons, we explored the ecological assembly of gut microbiota over shrimp AHPND progression. Increasing AHPND severity was associated with linear increase in the copies of pirAB genes, relative abundance of gut Vibrio and potentially pathogenic, and reduction in the gut bacterial diversity, stability, and relative abundance of Bdellovibrio. Negative and significant association between gut Vibrio and Bdellovibrio were noted, indicating that compromised predation exerts a role in AHPND progression. Notably, the extents of departure to the healthy shrimp gut microbiota were positively coupled with the increasing severity of AHPND. After controlling the temporal variation in the gut microbiota as healthy shrimp age, we constructed a diagnosis model that accurately diagnosed the initial, progressed or moribund stages of AHPND, with an overall accuracy of 86.5%. Shrimp AHPND induced more stochastic gut microbiotas as a consequence of the attenuated ability of diseased shrimp to select their commensals, resulting in convergent bacterial communities between gut and rearing water over AHPND progression. Collectively, our findings provide important step toward the ecological assembly of gut microbiota implicating in AHPND etiology and in diagnosing AHPND stages. KEY POINTS: • The departure of shrimp gut microbiota positively linked with AHPND severity. • The diagnosis model accurately diagnosed the stages of AHPND. • Shrimp AHPND induced more stochastic gut microbiota.
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Affiliation(s)
- Jiaqi Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jiangning Mao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Xuejing Qi
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jinbo Xiong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, China.
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
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18
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Rathinam AJ, Santhaseelan H, Dahms HU, Dinakaran VT, Murugaiah SG. Bioprospecting of unexplored halophilic actinobacteria against human infectious pathogens. 3 Biotech 2023; 13:398. [PMID: 37974926 PMCID: PMC10645811 DOI: 10.1007/s13205-023-03812-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 10/08/2023] [Indexed: 11/19/2023] Open
Abstract
Human pathogenic diseases received much attention recently due to their uncontrolled spread of antimicrobial resistance (AMR) which causes several threads every year. Effective alternate antimicrobials are urgently required to combat those disease causing infectious microbes. Halophilic actinobacteria revealed huge potentials and unexplored cultivable/non-cultivable actinobacterial species producing enormous antimicrobials have been proved in several genomics approaches. Potential gene clusters, PKS and NRPKS from Nocardia, Salinospora, Rhodococcus, and Streptomyces have wide range coding genes of secondary metabolites. Biosynthetic pathways identification via various approaches like genome mining, In silico, OSMAC (one strain many compound) analysis provides better identification of knowing the active metabolites using several databases like AMP, APD and CRAMPR, etc. Genome constellations of actinobacteria particularly the prediction of BGCs (Biosynthetic Gene Clusters) to mine the bioactive molecules such as pigments, biosurfactants and few enzymes have been reported for antimicrobial activity. Saltpan, saltlake, lagoon and haloalkali environment exploring potential actinobacterial strains Micromonospora, Kocuria, Pseudonocardia, and Nocardiopsis revealed several acids and ester derivatives with antimicrobial potential. Marine sediments and marine macro organisms have been found as significant population holders of potential actinobacterial strains. Deadly infectious diseases (IDs) including tuberculosis, ventilator-associated pneumonia and Candidiasis, have been targeted by halo-actinobacterial metabolites with promising results. Methicillin resistant Staphylococus aureus and virus like Encephalitic alphaviruses were potentially targeted by halophilic actinobacterial metabolites by the compound Homoseongomycin from sponge associated antinobacterium. In this review, we discuss the potential antimicrobial properties of various biomolecules extracted from the unexplored halophilic actinobacterial strains specifically against human infectious pathogens along with prospective genomic constellations.
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Affiliation(s)
- Arthur James Rathinam
- Department of Marine Science, Bharathidasan University, Tiruchirappalli, 620 024 India
| | - Henciya Santhaseelan
- Department of Marine Science, Bharathidasan University, Tiruchirappalli, 620 024 India
| | - Hans-Uwe Dahms
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, 80708 Taiwan
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Wang R, Zhao J, Chen L, Ye J, Wu H, Zhang H. LcbR1, a newly identified GntR family regulator, represses lincomycin biosynthesis in Streptomyces lincolnensis. Appl Microbiol Biotechnol 2023; 107:7501-7514. [PMID: 37768348 DOI: 10.1007/s00253-023-12756-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/09/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023]
Abstract
The Actinomycetes Streptomyces lincolnensis is the producer of lincosamide-type antibiotic lincomycin, a widely utilized drug against Gram-positive bacteria and protozoans. In this work, through gene knockout, complementation, and overexpression experiments, we identified LcbR1 (SLINC_1595), a GntR family transcriptional regulator, as a repressor for lincomycin biosynthesis. Deletion of lcbR1 boosted lincomycin production by 3.8-fold, without obvious change in morphological development or cellular growth. The homologues of LcbR1 are widely distributed in Streptomyces. Heterologous expression of SCO1410 from Streptomyces coelicolor resulted in the reduction of lincomycin yield, implying that the function of LcbR1 is conserved across different species. Alignment among sequences upstream of lcbR1 and their homologues revealed a conserved 16-bp palindrome (-TTGAACGATCCTTCAA-), which was further proven to be the recognition motif of LcbR1 by electrophoretic mobility shift assays (EMSAs). Via this motif, LcbR1 suppressed the transcription of lcbR1 and SLINC_1596 sharing the same bi-directional promoter. SLINC_1596, one important target of LcbR1, exerted a positive effect on lincomycin production. As detected by quantitative real-time PCR (qRT-PCR) analyses, the expressions of all selected structural (lmbA, lmbC, lmbJ, lmbV, and lmbW), resistance (lmrA and lmrB) and regulatory genes (lmrC and lmbU) from lincomycin biosynthesis cluster were upregulated in deletion strain ΔlcbR1 at 48 h of fermentation, while the mRNA amounts of bldD, glnR, ramR, SLCG_Lrp, and SLCG_2919, previously characterized as the regulators on lincomycin production, were decreased in strain ΔlcbR1, although the regulatory effects of LcbR1 on the above differential expression genes seemed to be indirect. Besides, indicated by EMSAs, the expression of lcbR1 might be regulated by GlnR, SLCG_Lrp, and SLCG_2919, which shows the complexity of the regulatory network on lincomycin biosynthesis. KEY POINTS: • LcbR1 is a novel and conservative GntR family regulator regulating lincomycin production. • LcbR1 modulates the expressions of lcbR1 and SLINC_1596 through a palindromic motif. • GlnR, SLCG_Lrp, and SLCG_2919 can control the expression of lcbR1.
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Affiliation(s)
- Ruida Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
- Department of Applied Biology, School of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Jiaqi Zhao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
- Department of Applied Biology, School of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Lei Chen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
- Department of Applied Biology, School of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Jiang Ye
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
- Department of Applied Biology, School of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China.
| | - Haizhen Wu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
- Department of Applied Biology, School of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China.
| | - Huizhan Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
- Department of Applied Biology, School of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
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20
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Zhong J, Sui WW, Bai XY, Qiu ZL, Li XG, Zhu JZ. Characterization and biocontrol mechanism of Streptomyces olivoreticuli as a potential biocontrol agent against Rhizoctonia solani. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2023; 197:105681. [PMID: 38072538 DOI: 10.1016/j.pestbp.2023.105681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/27/2023] [Accepted: 10/28/2023] [Indexed: 12/18/2023]
Abstract
Rhizoctonia solani is a widespread and devastating plant pathogenic fungus that infects many important crops. This pathogen causes tobacco target spot, a disease that is widespread in many tobacco-growing countries and is destructive to tobacco. To identify antagonistic microorganisms with biocontrol potential against this disease, we isolated Streptomyces strains from forest inter-root soil and screened a promising biocontrol strain, ZZ-21. Based on in vitro antagonism assays, ZZ-21 showed a significant inhibitory effect on R. solani and various other phytopathogens. ZZ-21 was identified as Streptomyces olivoreticuli by its phenotypic, genetic, physiological and biochemical properties. Complete genome sequencing revealed that ZZ-21 harbored numerous antimicrobial biosynthesis gene clusters. ZZ-21 significantly reduced the lesion length in detached inoculated leaf assays and reduced the disease index under greenhouse and field conditions. Based on an in vitro antagonistic assay of ZZ-21 culture, the strain exhibited an antifungal activity against R. solani in a dose-dependent manner. The culture filtrate could impair membrane integrity, possibly through membrane lipid peroxidation. ZZ-21 could secrete multiple extracellular enzymes and siderophores. According to a series of antifungal assays, the extracellular metabolites of ZZ-21 contained antimicrobial bioactive compounds composed of proteins/peptides extracted using ammonium sulfate precipitation, which were stable under stress caused by high temperature and protease K. The EC50 value for ammonium sulfate precipitation was determined to be 21.11 μg/mL in this study. Moreover, the proteins/peptides also exhibited biocontrol ability and were observed to alter the plasma membrane integrity of R. solani which were evaluated by biocontrol efficacy assays on detached tobacco leaves and PI staining. Overall, strain ZZ-21 shows the potential to be developed into a biopesticide against tobacco target spot disease.
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Affiliation(s)
- Jie Zhong
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, Hunan Province 410128, PR China
| | - Wen Wen Sui
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, Hunan Province 410128, PR China
| | - Xin Yi Bai
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, Hunan Province 410128, PR China
| | - Ze Lan Qiu
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, Hunan Province 410128, PR China
| | - Xiao Gang Li
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, Hunan Province 410128, PR China.
| | - Jun Zi Zhu
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, Hunan Province 410128, PR China.
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21
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Manikkam R, Murthy S, Palaniappan S, Kaari M, Sahu AK, Said M, Ganesan V, Kannan S, Ramasamy B, Thirugnanasambandan S, Dastager SG, Hanna LE, Kumar V. Antibacterial and Anti-HIV Metabolites from Marine Streptomyces albus MAB56 Isolated from Andaman and Nicobar Islands, India. Appl Biochem Biotechnol 2023; 195:7738-7754. [PMID: 37086378 DOI: 10.1007/s12010-023-04493-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2023] [Indexed: 04/23/2023]
Abstract
Marine-derived actinobacteria have tremendous potential to produce novel metabolites with diverse biological activities. The Andaman coast of India has a lot of microbial diversity, but it is still a relatively unknown ecology for isolating novel actinobacteria with beneficial bioactive compounds. We have isolated 568 actinobacterial strains from mangrove rhizosphere sediments and sponge samples. Crude extracts from 75 distinct strains were produced by agar surface fermentation and extracted using ethyl acetate. In the disc diffusion method, 25 actinobacterial strains showed antimicrobial activity; notably, the strain MAB56 demonstrated promising broad-spectrum activity. Strain MAB56 was identified as Streptomyces albus by cultural, microscopic, and molecular methods. Conditions for bioactive metabolites from MAB56 were optimized and produced in a lab-scale fermenter. Three active metabolites (C1, C2, and C3) that showed promising broad-spectrum antimicrobial activity were isolated through HPLC-based purification. Based on the UV, FT-IR, NMR, and LC-MS analysis, the chemical nature of the active compounds was confirmed as 12-methyltetradecanoic acid (C1), palmitic acid (C2), and tridecanoic acid (C3) with molecular formulae C14H28O2, C16H32O2, and C13H26O2, respectively. Interestingly, palmitic acid (C2) also exhibited anti-HIV activity with an IC50 value of < 1 µg/ml. Our findings reveal that the actinobacteria from the Andaman marine ecosystems are promising for isolating anti-infective metabolites.
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Affiliation(s)
- Radhakrishnan Manikkam
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, 600119, Tamil Nadu, India.
| | - Sangeetha Murthy
- Department of Microbiology, Periyar University, Salem, 636011, Tamil Nadu, India
| | | | - Manigundan Kaari
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, 600119, Tamil Nadu, India
| | - Amit Kumar Sahu
- Microbial Resource Centre, National Chemical Laboratory, Pune, India
| | - Madhukar Said
- Microbial Resource Centre, National Chemical Laboratory, Pune, India
| | - Vijayalakshmi Ganesan
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, 600119, Tamil Nadu, India
| | - Sivakumar Kannan
- CAS in Marine Biology, Annamalai University, Parangipettai, Tamil Nadu, India
| | | | | | - Syed G Dastager
- Microbial Resource Centre, National Chemical Laboratory, Pune, India
| | - Luke Elizabeth Hanna
- National Institute for Research in Tuberculosis, Chennai, 600031, Tamil Nadu, India
| | - Vanaja Kumar
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, 600119, Tamil Nadu, India
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22
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Golder HM, Denman SE, McSweeney C, Celi P, Lean IJ. Effects of feed additives on rumen function and bacterial and archaeal communities during a starch and fructose challenge. J Dairy Sci 2023; 106:8787-8808. [PMID: 37678787 DOI: 10.3168/jds.2023-23486] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 07/18/2023] [Indexed: 09/09/2023]
Abstract
The objective of this study was to improve understandings of the rumen microbial ecosystem during ruminal acidosis and responses to feed additives to improve prudent use strategies for ruminal acidosis control. Rumen bacterial and archaeal community composition (BCC) and its associations with rumen fermentation measures were examined in Holstein heifers fed feed additives and challenged with starch and fructose. Heifers (n = 40) were randomly allocated to 5 treatment groups: (1) control (no additives); (2) virginiamycin (VM; 200 mg/d); (3) monensin (MT; 200 mg/d) + tylosin (110 mg/d); (4) monensin (MLY; 220 mg/d) + live yeast (5.0 × 1012 cfu/d); (5) sodium bicarbonate (BUF; 200 g/d) + magnesium oxide (30 g/d). Heifers were fed twice daily a 62% forage:38% concentrate total mixed ration at 1.25% of body weight (BW) dry matter (DM)/d for a 20-d adaptation period with their additive(s). Fructose (0.1% of BW/d) was added to the ration for the last 10 d of adaptation. On d 21 heifers were challenged once with a ration consisting of 1.0% of BW DM wheat and 0.2% of BW fructose plus their additive(s). A rumen sample was collected from each heifer via stomach tube weekly (d 0, 7, 14) and 5 times over a 3.6 h period at 5, 65, 115, 165, and 215 min after consumption of the challenge ration (d 21) and analyzed for pH, and ammonia, d- and l-lactate, volatile fatty acids (VFA), and histamine concentrations and total bacteria and archaea. The 16S rRNA gene spanning the V4 region was PCR amplified and sequenced. Alpha and β diversity and associations of relative abundances of taxa with rumen fermentation measures were evaluated. Rumen BCC shifted among treatment groups in the adaptation period and across the challenge sampling period, indicating the feed additives had different modes of action. The monensin-containing treatment groups, MT and MLY often had similar relative abundances of rumen bacterial phyla and families. The MLY treatment group was characterized in the challenge period by increased relative abundances of the lactate utilizing genera Anaerovibrio and Megasphaera. The MLY treatment group also had increased diversity of ruminal bacteria which may provide resilience to changes in substrates. The control and BUF treatment groups were most similar in BCC. A redundancy analysis showed the MLY treatment group differed from all other treatment groups and concentrations of histamine and valerate in the rumen were associated with the most variation in the microbiota, 5.3% and 4.8%, respectively. It was evident from the taxa common to all treatment groups that cattle have a core microbiota. Functional redundancy of rumen bacteria which was reflected in the greater sensitivity for the rumen BCC than rumen fermentation measures likely provide resilience to changes in substrate. This functional redundancy of microbes in cattle suggests that there is no single optimal ruminal microbial population and no universally superior feed additive(s). In summary, differences in modes of action suggest the potential for more targeted and improved prudent use of feed additives with no single feed additive(s) providing an optimal BCC in all heifers.
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Affiliation(s)
- H M Golder
- Scibus, Camden, New South Wales, 2570, Australia; Dairy Science Group, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Camden, New South Wales, Australia, 2567.
| | - S E Denman
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St. Lucia, QLD 4067, Australia
| | - C McSweeney
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St. Lucia, QLD 4067, Australia
| | - P Celi
- Melbourne School of Land and Environment, The University of Melbourne, Parkville, VIC 3052, Australia
| | - I J Lean
- Scibus, Camden, New South Wales, 2570, Australia; Dairy Science Group, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Camden, New South Wales, Australia, 2567
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23
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Tiong E, Koo YS, Bi J, Koduru L, Koh W, Lim YH, Wong FT. Expression and engineering of PET-degrading enzymes from Microbispora, Nonomuraea, and Micromonospora. Appl Environ Microbiol 2023; 89:e0063223. [PMID: 37943056 PMCID: PMC10686063 DOI: 10.1128/aem.00632-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 10/09/2023] [Indexed: 11/10/2023] Open
Abstract
IMPORTANCE Mismanagement of PET plastic waste significantly threatens human and environmental health. Together with the relentless increase in plastic production, plastic pollution is an issue of rising concern. In response to this challenge, scientists are investigating eco-friendly approaches, such as bioprocessing and microbial factories, to sustainably manage the growing quantity of plastic waste in our ecosystem. Industrial applicability of enzymes capable of degrading PET is limited by numerous factors, including their scarcity in nature. The objective of this study is to enhance our understanding of this group of enzymes by identifying and characterizing novel enzymes that can facilitate the breakdown of PET waste. This data will expand the enzymatic repertoire and provide valuable insights into the prerequisites for successful PET degradation.
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Grants
- C211917006 Agency for Science, Technology, and Research (A*STAR)
- C211917006 Agency for Science, Technology, and Research (A*STAR)
- C211917003 Agency for Science, Technology, and Research (A*STAR)
- A*STAR Graduate Academy Agency for Science, Technology, and Research (A*STAR)
- C233017006 Agency for Science, Technology, and Research (A*STAR)
- C233017004 Agency for Science, Technology, and Research (A*STAR)
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Affiliation(s)
- Elaine Tiong
- Molecular Engineering Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology, and Research (A*STAR), Proteos, Singapore
| | - Ying Sin Koo
- Chemical Biotechnology and Biocatalysis, Institute of Sustainability for Chemicals, Energy, and Environment (ISCE), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore
| | - Jiawu Bi
- Molecular Engineering Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology, and Research (A*STAR), Proteos, Singapore
| | - Lokanand Koduru
- Molecular Engineering Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology, and Research (A*STAR), Proteos, Singapore
| | - Winston Koh
- Chemical Biotechnology and Biocatalysis, Institute of Sustainability for Chemicals, Energy, and Environment (ISCE), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore
- Bioinformatics Institute (BII), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore
| | - Yee Hwee Lim
- Chemical Biotechnology and Biocatalysis, Institute of Sustainability for Chemicals, Energy, and Environment (ISCE), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore
- Synthetic Biology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Fong Tian Wong
- Molecular Engineering Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology, and Research (A*STAR), Proteos, Singapore
- Chemical Biotechnology and Biocatalysis, Institute of Sustainability for Chemicals, Energy, and Environment (ISCE), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore
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24
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Pang W, Zhang P, Zhang Y, Zhang X, Huang Y, Zhang T, Liu B. The Ectomycorrhizal Fungi and Soil Bacterial Communities of the Five Typical Tree Species in the Junzifeng National Nature Reserve, Southeast China. PLANTS (BASEL, SWITZERLAND) 2023; 12:3853. [PMID: 38005750 PMCID: PMC10675191 DOI: 10.3390/plants12223853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 10/28/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023]
Abstract
To explore the contribution of microorganisms to forest ecosystem function, we studied the ectomycorrhizal (ECM) fungal and soil bacterial community of the five typical tree species (Pinus massoniana, PM; Castanopsis carlesii, CC; Castanopsis eyrei, CE; Castanopsis fargesii, CF; and Keteleeria cyclolepis, KC) at the Junzifeng National Nature Reserve. The results indicated that the ECM fungal and soil bacterial diversity of CC and CF was similar, and the diversity rates of CC and CF were higher than those of PM, CE, and KC. Cenococcum geophilum and unclassified_Cortinariaceae II were the most prevalent occurring ECM fungi species in the five typical tree species, followed by unclassified_Cortinariaceae I and Lactarius atrofuscus. In bacteria, the dominant bacterial genera were Acidothermus, Bradyrhizobium, Acidibacter, Candidatus_Solibacter, Candidatus_Koribacter, Roseiarcus, and Bryobacter. EMF fungi and soil bacteria were correlated with edaphic factors, especially the soil pH, TP, and TK, caused by stand development. The results show that the community characteristics of ECM fungi and bacteria in the typical tree species of the Junzifeng National Nature Reserve reflect the critical role of soil microorganisms in stabilizing forest ecosystems.
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Affiliation(s)
- Wenbo Pang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (W.P.); (P.Z.); (Y.Z.)
| | - Panpan Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (W.P.); (P.Z.); (Y.Z.)
| | - Yuhu Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (W.P.); (P.Z.); (Y.Z.)
| | - Xiao Zhang
- Key Laboratory of Soil Ecosystem Health and Regulation of Fujian Provincial University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Yanbin Huang
- Administration Bureau of Fujian Junzifeng National Nature Reserve, Mingxi 365200, China;
| | - Taoxiang Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (W.P.); (P.Z.); (Y.Z.)
| | - Bao Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (W.P.); (P.Z.); (Y.Z.)
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25
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Martín-Aragón VR, Millán FR, Cuadrado C, Daranas AH, Medarde AF, López JMS. Induction of New Aromatic Polyketides from the Marine Actinobacterium Streptomyces griseorubiginosus through an OSMAC Approach. Mar Drugs 2023; 21:526. [PMID: 37888461 PMCID: PMC10608293 DOI: 10.3390/md21100526] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/29/2023] [Accepted: 09/30/2023] [Indexed: 10/28/2023] Open
Abstract
Using the OSMAC (One Strain Many Compounds) approach, the actinobacterium Streptomyces griseorubiginosus, derived from an unidentified cnidarian collected from a reef near Pointe de Bellevue in Réunion Island (France), was subjected to cultivation under diverse conditions. This endeavour yielded the isolation of a repertoire of 23 secondary metabolites (1-23), wherein five compounds were unprecedented as natural products (19-23). Specifically, compounds 19 and 20 showcased novel anthrone backbones, while compound 23 displayed a distinctive tetralone structure. Additionally, compounds 21 and 22 presented an unusual naphtho [2,3-c]furan-4(9H)-one chromophore. Interestingly, the detection of all these novel compounds (19-23) was exclusively achieved when the bacterium was cultured in FA-1 liquid medium supplemented with the epigenetic modifier γ-butyrolactone. The elucidation of the structural features of the newfound compounds was accomplished through a combination of HRESIMS, 1D and 2D NMR spectroscopy, as well as QM-NMR (Quantum Mechanical-Nuclear Magnetic Resonance) methods and by comparison with existing literature. Moreover, the determination of the relative configuration of compound 23 was facilitated by employing the mix-J-DP4 computational approach.
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Affiliation(s)
- Víctor Rodríguez Martín-Aragón
- Biomar Microbial Technologies, Parque Tecnológico de León, Parcela M-10.4, Armunia, 24009 León, Spain; (V.R.M.-A.); (F.R.M.); (A.F.M.)
| | - Francisco Romero Millán
- Biomar Microbial Technologies, Parque Tecnológico de León, Parcela M-10.4, Armunia, 24009 León, Spain; (V.R.M.-A.); (F.R.M.); (A.F.M.)
| | - Cristina Cuadrado
- Instituto de Productos Naturales y Agrobiología, Consejo Superior de Investigaciones Científicas (IPNA-CSIC), 38206 La Laguna, Tenerife, Spain;
| | - Antonio Hernández Daranas
- Instituto de Productos Naturales y Agrobiología, Consejo Superior de Investigaciones Científicas (IPNA-CSIC), 38206 La Laguna, Tenerife, Spain;
| | - Antonio Fernández Medarde
- Biomar Microbial Technologies, Parque Tecnológico de León, Parcela M-10.4, Armunia, 24009 León, Spain; (V.R.M.-A.); (F.R.M.); (A.F.M.)
| | - José M. Sánchez López
- Biomar Microbial Technologies, Parque Tecnológico de León, Parcela M-10.4, Armunia, 24009 León, Spain; (V.R.M.-A.); (F.R.M.); (A.F.M.)
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Liu SW, Zhai XX, Liu D, Liu YY, Sui LY, Luo KK, Yang Q, Li FN, Nikandrova AA, Imamutdinova AN, Lukianov DA, Osterman IA, Sergiev PV, Zhang BY, Zhang DJ, Xue CM, Sun CH. Bioprospecting of Actinobacterial Diversity and Antibacterial Secondary Metabolites from the Sediments of Four Saline Lakes on the Northern Tibetan Plateau. Microorganisms 2023; 11:2475. [PMID: 37894133 PMCID: PMC10609225 DOI: 10.3390/microorganisms11102475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/29/2023] Open
Abstract
The Tibetan Plateau, known as the "Roof of the World" and "The Third Pole", harbors numerous saline lakes primarily distributed in the Northern Tibetan Plateau. However, the challenging conditions of high altitude, low oxygen level, and harsh climate have limited investigations into the actinobacteria from these saline lakes. This study focuses on investigating the biodiversity and bioactive secondary metabolites of cultivable actinobacteria isolated from the sediments of four saline lakes on the Northern Tibetan Plateau. A total of 255 actinobacterial strains affiliated with 21 genera in 12 families of 7 orders were recovered by using the pure culture technique and 16S rRNA gene phylogenetic analysis. To facilitate a high-throughput bioactivity evaluation, 192 isolates underwent OSMAC cultivation in a miniaturized 24-well microbioreactor system (MATRIX cultivation). The antibacterial activity of crude extracts was then evaluated in a 96-well plate antibacterial assay. Forty-six strains demonstrated antagonistic effects against at least one tested pathogen, and their underlying antibacterial mechanisms were further investigated through a dual-fluorescent reporter assay (pDualrep2). Two Streptomyces strains (378 and 549) that produce compounds triggering DNA damage were prioritized for subsequent chemical investigations. Metabolomics profiling involving HPLC-UV/vis, UPLC-QTOF-MS/MS, and molecular networking identified three types of bioactive metabolites belonging to the aromatic polyketide family, i.e., cosmomycin, kidamycin, and hedamycin. In-depth analysis of the metabolomic data unveiled some potentially novel anthracycline compounds. A genome mining study based on the whole-genome sequences of strains 378 and 549 identified gene clusters potentially responsible for cosmomycin and kidamycin biosynthesis. This work highlights the effectiveness of combining metabolomic and genomic approaches to rapidly identify bioactive chemicals within microbial extracts. The saline lakes on the Northern Tibetan Plateau present prospective sources for discovering novel actinobacteria and biologically active compounds.
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Affiliation(s)
- Shao-Wei Liu
- Department of Microbial Chemistry, Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100050, China; (S.-W.L.)
| | - Xiao-Xu Zhai
- Department of Microbial Chemistry, Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100050, China; (S.-W.L.)
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
- College of Life Sciences, Jiamusi University, Jiamusi 154000, China
| | - Di Liu
- Department of Microbial Chemistry, Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100050, China; (S.-W.L.)
- College of Life Sciences, Jiamusi University, Jiamusi 154000, China
| | - Yu-Yu Liu
- Department of Microbial Chemistry, Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100050, China; (S.-W.L.)
| | - Li-Ying Sui
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Ke-Ke Luo
- Department of Microbial Chemistry, Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100050, China; (S.-W.L.)
| | - Qin Yang
- Department of Microbial Chemistry, Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100050, China; (S.-W.L.)
| | - Fei-Na Li
- Laboratory of Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children’s Health, Beijing 100045, China;
| | - Arina A. Nikandrova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Arina N. Imamutdinova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Dmitrii A. Lukianov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ilya A. Osterman
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Petr V. Sergiev
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ben-Yin Zhang
- College of Eco-Environmental Engineering, Qinghai University, Xining 810016, China; (B.-Y.Z.); (D.-J.Z.)
| | - De-Jun Zhang
- College of Eco-Environmental Engineering, Qinghai University, Xining 810016, China; (B.-Y.Z.); (D.-J.Z.)
| | - Chun-Mei Xue
- College of Life Sciences, Jiamusi University, Jiamusi 154000, China
| | - Cheng-Hang Sun
- Department of Microbial Chemistry, Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100050, China; (S.-W.L.)
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
- College of Eco-Environmental Engineering, Qinghai University, Xining 810016, China; (B.-Y.Z.); (D.-J.Z.)
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Wang R, Zhao J, Chen L, Ye J, Wu H, Zhang H. LcbR1, a newly identified GntR family regulator, represses lincomycin biosynthesis in Streptomyces lincolnensis. Appl Microbiol Biotechnol 2023. [DOI: doi.org/10.1007/s00253-023-12756-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/09/2023] [Accepted: 08/30/2023] [Indexed: 10/09/2023]
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Hu L, Guo C, Chen J, Jia R, Sun Y, Cao S, Xiang P, Wang Y. Venturicidin A Is a Potential Fungicide for Controlling Fusarium Head Blight by Affecting Deoxynivalenol Biosynthesis, Toxisome Formation, and Mitochondrial Structure. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:12440-12451. [PMID: 37566096 DOI: 10.1021/acs.jafc.3c02683] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
Fusarium graminearum, which causes Fusarium head blight (FHB) in cereals, is one of the most devastating fungal diseases by causing great yield losses and mycotoxin contamination. A major bioactive ingredient, venturicidin A (VentA), was isolated from Streptomyces pratensis S10 mycelial extract with an activity-guided approach. No report is available on antifungal activity of VentA against F. graminearum and effects on deoxynivalenol (DON) biosynthesis. Here, VentA showed a high antagonistic activity toward F. graminearum with an EC50 value of 3.69 μg/mL. As observed by scanning electron microscopy, after exposure to VentA, F. graminearum conidia and mycelia appeared abnormal. Different dyes staining revealed that VentA increased cell membrane permeability. In growth chamber and field trials, VentA effectively reduced disease severity of FHB. Moreover, VentA inhibited DON biosynthesis by reducing pyruvic acid, acetyl-CoA production, and accumulation of reactive oxygen species (ROS) and then inhibiting trichothecene (TRI) genes expression and toxisome formation. These results suggest that VentA is a potential fungicide for controlling FHB.
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Affiliation(s)
- Lifang Hu
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Cong Guo
- Shaanxi Key Laboratory of Natural Products and Chemical Biology, College of Chemistry and Pharmacy, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Jing Chen
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Ruimin Jia
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Yan Sun
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Shang Cao
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Ping Xiang
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
- State Key Laboratory of Crop Stress Biology for Arid Areas, NWAFU Purdue Joint Research Center, Yangling, Shaanxi 712100, People's Republic of China
| | - Yang Wang
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
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Charousová I, Hlebová M, Hleba L, Medo J, Wink J. Streptomyces iakyrus TA 36 as First-Reported Source of Quinone Antibiotic γ-Rubromycin. Molecules 2023; 28:5977. [PMID: 37630229 PMCID: PMC10458949 DOI: 10.3390/molecules28165977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
A wide range of bioactive compounds with potential medical applications are produced by members of the genus Streptomyces. A new actinomycete producer of the antibiotic γ-rubromycin, designated TA 36, was isolated from an alpine soil sample collected in Peru (Machu Picchu). Morphological, physiological and biochemical characteristics of the strain, together with data obtained via phylogenetic analysis and MALDI-TOF MS, were used for the correct identification of the isolate. The isolate TA 36 showed morphological characteristics that were consistent with its classification within the genus Streptomyces. Phylogenetic analysis based on 16S rRNA gene sequences showed that the TA 36 strain was most similar to S. iakyrus and S. violaceochromogenes with 99% similarity. Phylogenetic analysis together with the profile of whole cell proteins indicated that the strain tested could be identified as S. iakyrus TA 36. The crude extract Ext.5333.TA 36 showed various effects against the tested organisms with strong antimicrobial activity in the growth of Staphylococcus aureus (Newman) (MIC value of 0.00195 µg/µL). HPLC fractionation and LC/MS analysis of the crude extract led to the identification of the quinone antibiotic γ-rubromycin, a promising antitumour and antibacterial antibiotic. To the best of our knowledge, there is currently no report on the production of γ-rubromycin by S. iakyrus. Therefore, this study suggests S. iakyrus TA 36 as the first-reported source of this unique bioactive secondary metabolite.
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Affiliation(s)
- Ivana Charousová
- Clinical Microbiology Laboratory, Unilabs Slovensko, s.r.o., J. Bellu 66, SK-03495 Likavka, Slovakia;
- Institute of Biotechnology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture, Nitra, Tr. A. Hlinku 2, SK-94976 Nitra, Slovakia
| | - Miroslava Hlebová
- Department of Biology, Faculty of Natural Sciences, University of SS. Cyril and Methodius, Nám. J. Herdu 2, SK-91701 Trnava, Slovakia
| | - Lukas Hleba
- Institute of Biotechnology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture, Nitra, Tr. A. Hlinku 2, SK-94976 Nitra, Slovakia
| | - Juraj Medo
- Institute of Biotechnology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture, Nitra, Tr. A. Hlinku 2, SK-94976 Nitra, Slovakia
| | - Joachim Wink
- Microbial Strain Collection Group, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
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Ren Q, Zhang Y, Duan J, Li W, Dong X, Pei Y, Zhang R, Zhu Q. Distribution of corrosive microbial communities in rust layers of steel immersed in seawater. Can J Microbiol 2023; 69:309-320. [PMID: 37156011 DOI: 10.1139/cjm-2023-0015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
In this paper, high-throughput sequencing technology was adopted to visualize the microbial communities on the surfaces of two types of carbon steel immersed in Sea Area Ⅰ. The results showed that different microbial communities were formed on different carbon steel surfaces, in which the genus with the highest abundance on the surface of Q235 was Escherichia-Shigella, while anaerobic Desulfovibrio on the surface of 921a was the most abundant, and the dominant genus varied with the depth of the rust layer. In addition, the distribution of sulfate-reducing bacteria (SRB) on the surface of Q235 submerged in Sea Area Ⅱ was compared with the sulfate-reducing bacteria's distribution in Sea Area Ⅰ, using the environmental factors correlation analysis. The results showed that the concentrations of Ca2+, Na+, K+, Mg2+, and Al3+ were positively correlated with the distribution of SRB, while the concentrations of Cu2+, Zn2+, SO4 2-, Cl-, NO3 -, and organic carbon were negatively correlated with it. Furthermore, there was a highly significant correlation between each geochemical factor and Desulfotomaculum (p < 0.01).
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Affiliation(s)
- Qijing Ren
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- Open Studio for Marine Corrosion and Protection, National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Yimeng Zhang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Open Studio for Marine Corrosion and Protection, National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Jizhou Duan
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Open Studio for Marine Corrosion and Protection, National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Wangqiang Li
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- Open Studio for Marine Corrosion and Protection, National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Xucheng Dong
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- Open Studio for Marine Corrosion and Protection, National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Yingying Pei
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- Open Studio for Marine Corrosion and Protection, National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Ruiyong Zhang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Open Studio for Marine Corrosion and Protection, National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Qingjun Zhu
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Open Studio for Marine Corrosion and Protection, National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
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Xiong Z, Wang R, Xia T, Zhang S, Ma S, Guo Z. Natural Products and Biological Activity from Actinomycetes Associated with Marine Algae. Molecules 2023; 28:5138. [PMID: 37446800 DOI: 10.3390/molecules28135138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] Open
Abstract
Marine natural products have been recognized as the most promising source of bioactive substances for drug discovery research. This review illustrates the diversity of culturable actinobacteria associated with marine algae, their bioactivity and metabolites, and approaches to their isolation and determination of their biological properties. Furthermore, actinobacteria associated with marine algae are presented as a new subject for an extensive investigation to find novel and active natural products, which make them a potentially rich and innovative source for new drug development deserving more attention and exploration.
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Affiliation(s)
- Zijun Xiong
- Hainan Key Laboratory of Tropical Microbe Resources, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences & Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou 571101, China
| | - Rong Wang
- Hainan Provincial Key Laboratory of Tropical Maricultural Technologies, Hainan Academy of Ocean and Fisheries Sciences, Haikou 571126, China
| | - Tengfei Xia
- Institute of Tropical Horticulture Research, Hainan Academy of Agricultural Sciences, Haikou 571100, China
| | - Shiqing Zhang
- Hainan Key Laboratory of Tropical Microbe Resources, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences & Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou 571101, China
| | - Shuai Ma
- Hainan Key Laboratory of Tropical Microbe Resources, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences & Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou 571101, China
| | - Zhikai Guo
- Hainan Key Laboratory of Tropical Microbe Resources, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences & Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou 571101, China
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32
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Tang Q, Liu T, Teng K, Xiao Z, Cai H, Wang Y, Xiao Y, Chen W. Microbial interactions and metabolisms in response to bacterial wilt and black shank pathogens in the tobacco rhizosphere. FRONTIERS IN PLANT SCIENCE 2023; 14:1200136. [PMID: 37409299 PMCID: PMC10319149 DOI: 10.3389/fpls.2023.1200136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/31/2023] [Indexed: 07/07/2023]
Abstract
Background Tobacco bacterial wilt (TBW) and black shank (TBS) are responsible for substantial economic losses worldwide; however, microbial interactions and metabolisms in response to TBW and TBS pathogens in the tobacco rhizosphere remain unclear. Methods We explored and compared the response of rhizosphere microbial communities to these two plant diseases with the incidences in moderate and heavy degrees by sequencing of 16S rRNA gene amplicons and bioinformatics analysis. Results and discussions We found that the structure of rhizosphere soil bacterial communities was significantly (p < 0.05) changed from the incidences of TBW and TBS, which also led to decreased Shannon diversity and Pielou evenness. Compared with the healthy group (CK), the OTUs with significantly (p < 0.05) decreased relative abundances were mostly affiliated with Actinobacteria (e.g., Streptomyces and Arthrobacter) in the diseased groups, and the OTUs with significantly (p < 0.05) increased relative abundances were mainly identified as Proteobacteria and Acidobacteria. Also, molecular ecological network analysis showed that the nodes (<467) and links (<641) were decreased in the diseased groups compared with the control group (572; 1056), suggesting that both TBW and TBS weakened bacterial interactions. In addition, the predictive functional analysis indicated that the relative abundance of genes related to the biosynthesis of antibiotics (e.g., ansamycins and streptomycin) was significantly (p < 0.05) decreased due to incidences of TBW and TBS, and antimicrobial tests showed that some Actinobacteria strains (e.g., Streptomyces) and their secreted antibiotics (e.g., streptomycin) could effectively inhibit the growth of these two pathogens.
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Affiliation(s)
- Qianjun Tang
- College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Tianbo Liu
- College of Plant Protection, Hunan Agricultural University, Changsha, China
- Laboratory of Plant Protection, Hunan Tobacco Science Institute, Changsha, China
| | - Kai Teng
- Laboratory of Plant Protection, Hunan Tobacco Science Institute, Changsha, China
| | - Zhipeng Xiao
- Laboratory of Plant Protection, Hunan Tobacco Science Institute, Changsha, China
| | - Hailin Cai
- Laboratory of Plant Protection, Hunan Tobacco Science Institute, Changsha, China
| | - Yunsheng Wang
- College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Yunhua Xiao
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Wu Chen
- College of Plant Protection, Hunan Agricultural University, Changsha, China
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Tarasova EV, Luchnikova NA, Grishko VV, Ivshina IB. Actinomycetes as Producers of Biologically Active Terpenoids: Current Trends and Patents. Pharmaceuticals (Basel) 2023; 16:872. [PMID: 37375819 DOI: 10.3390/ph16060872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 06/04/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Terpenes and their derivatives (terpenoids and meroterpenoids, in particular) constitute the largest class of natural compounds, which have valuable biological activities and are promising therapeutic agents. The present review assesses the biosynthetic capabilities of actinomycetes to produce various terpene derivatives; reports the main methodological approaches to searching for new terpenes and their derivatives; identifies the most active terpene producers among actinomycetes; and describes the chemical diversity and biological properties of the obtained compounds. Among terpene derivatives isolated from actinomycetes, compounds with pronounced antifungal, antiviral, antitumor, anti-inflammatory, and other effects were determined. Actinomycete-produced terpenoids and meroterpenoids with high antimicrobial activity are of interest as a source of novel antibiotics effective against drug-resistant pathogenic bacteria. Most of the discovered terpene derivatives are produced by the genus Streptomyces; however, recent publications have reported terpene biosynthesis by members of the genera Actinomadura, Allokutzneria, Amycolatopsis, Kitasatosporia, Micromonospora, Nocardiopsis, Salinispora, Verrucosispora, etc. It should be noted that the use of genetically modified actinomycetes is an effective tool for studying and regulating terpenes, as well as increasing productivity of terpene biosynthesis in comparison with native producers. The review includes research articles on terpene biosynthesis by Actinomycetes between 2000 and 2022, and a patent analysis in this area shows current trends and actual research directions in this field.
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Affiliation(s)
- Ekaterina V Tarasova
- Perm Federal Research Center, Ural Branch of the Russian Academy of Sciences, 13A Lenina Str., 614990 Perm, Russia
| | - Natalia A Luchnikova
- Perm Federal Research Center, Ural Branch of the Russian Academy of Sciences, 13A Lenina Str., 614990 Perm, Russia
- Department of Microbiology and Immunology, Perm State University, 15 Bukirev Str., 614990 Perm, Russia
| | - Victoria V Grishko
- Perm Federal Research Center, Ural Branch of the Russian Academy of Sciences, 13A Lenina Str., 614990 Perm, Russia
| | - Irina B Ivshina
- Perm Federal Research Center, Ural Branch of the Russian Academy of Sciences, 13A Lenina Str., 614990 Perm, Russia
- Department of Microbiology and Immunology, Perm State University, 15 Bukirev Str., 614990 Perm, Russia
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Ye JJ, Zou RJ, Zhou DD, Deng XL, Wu NL, Chen DD, Xu J. Insights into the phylogenetic diversity, biological activities, and biosynthetic potential of mangrove rhizosphere Actinobacteria from Hainan Island. Front Microbiol 2023; 14:1157601. [PMID: 37323895 PMCID: PMC10264631 DOI: 10.3389/fmicb.2023.1157601] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 05/10/2023] [Indexed: 06/17/2023] Open
Abstract
Mangrove rhizosphere soils host diverse Actinobacteria tolerant to numerous stresses and are inevitably capable of exhibiting excellent biological activity by producing impressive numbers of bioactive natural products, including those with potential medicinal applications. In this study, we applied an integrated strategy of combining phylogenetic diversity, biological activities, and biosynthetic gene clusters (BGCs) screening approach to investigate the biotechnological importance of Actinobacteria isolated from mangrove rhizosphere soils from Hainan Island. The actinobacterial isolates were identifified using a combination of colony morphological characteristics and 16S rRNA gene sequence analysis. Based on the results of PCR-detected BGCs screening, type I and II polyketide synthase (PKS) and non-ribosomal synthetase (NRPS) genes were detected. Crude extracts of 87 representative isolates were subjected to antimicrobial evaluation by determining the minimum inhibitory concentration of each strain against six indicator microorganisms, anticancer activities were determined on human cancer cell lines HepG2, HeLa, and HCT-116 using an MTT colorimetric assay, and immunosuppressive activities against the proliferation of Con A-induced T murine splenic lymphocytes in vitro. A total of 287 actinobacterial isolates affiliated to 10 genera in eight families of six orders were isolated from five different mangrove rhizosphere soil samples, specififically, Streptomyces (68.29%) and Micromonospora (16.03%), of which 87 representative strains were selected for phylogenetic analysis. The crude extracts of 39 isolates (44.83%) showed antimicrobial activity against at least one of the six tested indicator pathogens, especially ethyl acetate extracts of A-30 (Streptomyces parvulus), which could inhibit the growth of six microbes with MIC values reaching 7.8 μg/mL against Staphylococcus aureus and its resistant strain, compared to the clinical antibiotic ciproflfloxacin. Furthermore, 79 crude extracts (90.80%) and 48 (55.17%) of the isolates displayed anticancer and immunosuppressive activities, respectively. Besides, four rare strains exhibited potent immunosuppressive activity against the proliferation of Con A-induced T murine splenic lymphocyte in vitro with an inhibition rate over 60% at 10 μg/mL. Type I and II polyketide synthase (PKS) and non-ribosomal synthetase (NRPS) genes were detected in 49.43, 66.67, and 88.51% of the 87 Actinobacteria, respectively. Signifificantly, these strains (26 isolates, 29.89%) harbored PKS I, PKS II, and NRPS genes in their genomes. Nevertheless, their bioactivity is independent of BGCs in this study. Our findings highlighted the antimicrobial, immunosuppressive, and anticancer potential of mangrove rhizosphere Actinobacteria from Hainan Island and the biosynthetic prospects of exploiting the corresponding bioactive natural product.
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Affiliation(s)
| | | | | | | | | | | | - Jing Xu
- Collaborative Innovation Center of Ecological Civilization, School of Chemical Engineering and Technology, Hainan University, Haikou, China
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Shi J, Feng Z, Xu J, Li F, Zhang Y, Wen A, Wang F, Song Q, Wang L, Cui H, Tong S, Chen P, Zhu Y, Zhao G, Wang S, Feng Y, Lin W. Structural insights into the transcription activation mechanism of the global regulator GlnR from actinobacteria. Proc Natl Acad Sci U S A 2023; 120:e2300282120. [PMID: 37216560 PMCID: PMC10235972 DOI: 10.1073/pnas.2300282120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 04/27/2023] [Indexed: 05/24/2023] Open
Abstract
In actinobacteria, an OmpR/PhoB subfamily protein called GlnR acts as an orphan response regulator and globally coordinates the expression of genes responsible for nitrogen, carbon, and phosphate metabolism in actinobacteria. Although many researchers have attempted to elucidate the mechanisms of GlnR-dependent transcription activation, progress is impeded by lacking of an overall structure of GlnR-dependent transcription activation complex (GlnR-TAC). Here, we report a co-crystal structure of the C-terminal DNA-binding domain of GlnR (GlnR_DBD) in complex with its regulatory cis-element DNA and a cryo-EM structure of GlnR-TAC which comprises Mycobacterium tuberculosis RNA polymerase, GlnR, and a promoter containing four well-characterized conserved GlnR binding sites. These structures illustrate how four GlnR protomers coordinate to engage promoter DNA in a head-to-tail manner, with four N-terminal receiver domains of GlnR (GlnR-RECs) bridging GlnR_DBDs and the RNAP core enzyme. Structural analysis also unravels that GlnR-TAC is stabilized by complex protein-protein interactions between GlnR and the conserved β flap, σAR4, αCTD, and αNTD domains of RNAP, which are further confirmed by our biochemical assays. Taken together, these results reveal a global transcription activation mechanism for the master regulator GlnR and other OmpR/PhoB subfamily proteins and present a unique mode of bacterial transcription regulation.
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Affiliation(s)
- Jing Shi
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, 210023Nanjing, China
- Department of Biophysics, Zhejiang University School of Medicine, 310058Hangzhou, China
- Department of Infectious Disease of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 310058Hangzhou, China
| | - Zhenzhen Feng
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, 210023Nanjing, China
| | - Juncao Xu
- Key Laboratory of Synthetic Biology, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 200032Shanghai, China
| | - Fangfang Li
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, 210023Nanjing, China
| | - Yuqiong Zhang
- MOE Key Laboratory of Laser Life Science and Institute of Laser Life Science, College of Biophotonics, South China Normal University, 510631Guangzhou, Guangdong, China
- Guangdong Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, 510631Guangzhou, Guangdong, China
- Songshan Lake Materials Laboratory, 523808Dongguan, Guangdong, China
| | - Aijia Wen
- Department of Biophysics, Zhejiang University School of Medicine, 310058Hangzhou, China
- Department of Infectious Disease of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 310058Hangzhou, China
| | - Fulin Wang
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, 210023Nanjing, China
| | - Qian Song
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, 210023Nanjing, China
| | - Lu Wang
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, 210023Nanjing, China
| | - Hong Cui
- Pasteurien College, Suzhou Medical College of Soochow University, Soochow University, 251000Soochow, China
| | - Shujuan Tong
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, 210023Nanjing, China
| | - Peiying Chen
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, 210023Nanjing, China
| | - Yejin Zhu
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, 210023Nanjing, China
| | - Guoping Zhao
- Key Laboratory of Synthetic Biology, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 200032Shanghai, China
| | - Shuang Wang
- Songshan Lake Materials Laboratory, 523808Dongguan, Guangdong, China
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, 100190Beijing, China
| | - Yu Feng
- Department of Biophysics, Zhejiang University School of Medicine, 310058Hangzhou, China
- Department of Infectious Disease of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 310058Hangzhou, China
| | - Wei Lin
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, 210023Nanjing, China
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai200237, China
- Nanjing Drum Tower Hospital Clinical College, Nanjing University of Chinese Medicine, 210023Nanjing, China
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Polyene Carboxylic Acids from a Streptomyces sp. Isolated from Tibet Soil. Molecules 2023; 28:molecules28062579. [PMID: 36985551 PMCID: PMC10054270 DOI: 10.3390/molecules28062579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/03/2023] [Accepted: 03/09/2023] [Indexed: 03/16/2023] Open
Abstract
Six new polyene carboxylic acids named serpentemycins E–J (1–6), together with three known analogs (7–9), were isolated from the fermentation medium of Streptomyces sp. TB060207, which was isolated from arid soil collected from Tibet, China. The structures of the new compounds were elucidated mainly on the basis of HR-ESI-MS and NMR spectroscopic analyses. The inhibitory activities of compounds 1–9 against NO production in LPS-activated RAW264.7 cells were evaluated. Compound 9 has an inhibition rate of 87.09% to 60.53% at concentrations ranging from 5.0 to 40.0 µM.
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Prioritization of Microorganisms Isolated from the Indian Ocean Sponge Scopalina hapalia Based on Metabolomic Diversity and Biological Activity for the Discovery of Natural Products. Microorganisms 2023; 11:microorganisms11030697. [PMID: 36985270 PMCID: PMC10057949 DOI: 10.3390/microorganisms11030697] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 03/11/2023] Open
Abstract
Despite considerable advances in medicine and technology, humanity still faces many deadly diseases such as cancer and malaria. In order to find appropriate treatments, the discovery of new bioactive substances is essential. Therefore, research is now turning to less frequently explored habitats with exceptional biodiversity such as the marine environment. Many studies have demonstrated the therapeutic potential of bioactive compounds from marine macro- and microorganisms. In this study, nine microbial strains isolated from an Indian Ocean sponge, Scopalina hapalia, were screened for their chemical potential. The isolates belong to different phyla, some of which are already known for their production of secondary metabolites, such as the actinobacteria. This article aims at describing the selection method used to identify the most promising microorganisms in the field of active metabolites production. The method is based on the combination of their biological and chemical screening, coupled with the use of bioinformatic tools. The dereplication of microbial extracts and the creation of a molecular network revealed the presence of known bioactive molecules such as staurosporin, erythromycin and chaetoglobosins. Molecular network exploration indicated the possible presence of novel compounds in clusters of interest. The biological activities targeted in the study were cytotoxicity against the HCT-116 and MDA-MB-231 cell lines and antiplasmodial activity against Plasmodium falciparum 3D7. Chaetomium globosum SH-123 and Salinispora arenicola SH-78 strains actually showed remarkable cytotoxic and antiplasmodial activities, while Micromonospora fluostatini SH-82 demonstrated promising antiplasmodial effects. The ranking of the microorganisms as a result of the different screening steps allowed the selection of a promising strain, Micromonospora fluostatini SH-82, as a premium candidate for the discovery of new drugs.
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Zhang H, Yang W, Ma B, Liu X, Huang T, Niu L, Zhao K, Yang Y, Li H. Aerobic denitrifying using actinobacterial consortium: Novel denitrifying microbe and its application. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 859:160236. [PMID: 36427714 DOI: 10.1016/j.scitotenv.2022.160236] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/01/2022] [Accepted: 11/13/2022] [Indexed: 06/16/2023]
Abstract
The aerobic denitrifying capacity of actinomycete strain has been investigated recently, while little is known about nitrogen and carbon substrate removal by mix-cultured aerobic denitrifying actinobacteria (Mix-CADA) community. Hence, three Mix-CADA consortiums, named Y23, X21, and Y27, were isolated from urban lakes to investigate their aerobic denitrification capacity, and their removal efficiency for nitrate and dissolved organic carbon were >97 % and 90 %, respectively. Illumina Miseq sequencing revealed that Streptomyces was the most dominant genus in the Mix-CADA consortium. Network analysis indicated that Streptomyces exfoliates, as the core species in the Mix-CADA consortium, majorly contributed to dissolved organic carbon and total nitrogen reduction. Moreover, the three Mix-CADA consortiums could remove 78 % of the total nitrogen and 61 % of the permanganate index from the micro-polluted l water. Meanwhile, humic-like was significantly utilized by three Mix-CADA consortiums, whereas Mix-CADA Y27 could also utilize aromatic protein and soluble microbial by-product-like in the micro-polluted raw water purification. In summary, this study will offer a novel perspective for the purification of micro-polluted raw water using the Mix-CADA consortium.
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Affiliation(s)
- Haihan Zhang
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, 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.
| | - Wanqiu Yang
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, 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
| | - Ben Ma
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, 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
| | - Xiang Liu
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, 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
| | - Tinglin Huang
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, 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
| | - Limin Niu
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, 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
| | - Kexin Zhao
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, 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
| | - Yansong Yang
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, 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
| | - Haiyun Li
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, 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
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Liu Z, Yashiroda Y, Sun P, Ma H, Wang Y, Li L, Yan F, Sun Y. Argenteolides A and B, Glycosylated Polyketide-Peptide Hybrid Macrolides from an Actinomycete Streptomyces argenteolus. Org Lett 2023; 25:571-575. [PMID: 36469481 DOI: 10.1021/acs.orglett.2c03290] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Two novel glycosylated polyketide-peptide hybrid macrolides, argenteolides A (1) and B (2), were isolated from an actinomycete Streptomyces argenteolus. Argenteolide A (1) contains a unique 5/5/5 tricyclic system in a 20-membered macrocycle. Their structures were elucidated by extensive spectroscopic analysis, and their stereochemical configurations were established through the application of chemical derivatization, J-based configuration analysis, DP4+ calculation, and electronic circular dichroism calculation. The analysis of the genome sequence revealed a plausible biosynthesis mechanism, and isotope-labeled feeding studies suggested their biogenetic origins. Argenteolides A and B exhibited moderate cytotoxicities against A549, p388, and Hela human carcinoma cell lines as well as antibacterial activities against Staphylococcus aureus and Escherichia coli ATCC25922.
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Affiliation(s)
- Zhiguo Liu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing100700, China
| | - Yoko Yashiroda
- RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama351-0198, Japan
| | - Peng Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing100700, China
| | - Hai Ma
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing100700, China
| | - Yanan Wang
- Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing100050, China
| | - Li Li
- Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing100050, China
| | - Fu Yan
- Helmholtz International Lab for Antiinfectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong266237, China
| | - Yi Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing100700, China
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Tian Y, Jiang Y, Wen Z, Guan L, Ouyang X, Ding W, Ma Z. Identification of Novel Sphydrofuran-Derived Derivatives with Lipid-Lowering Activity from the Active Crude Extracts of Nocardiopsis sp. ZHD001. Int J Mol Sci 2023; 24:ijms24032822. [PMID: 36769145 PMCID: PMC9917766 DOI: 10.3390/ijms24032822] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/19/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
Lipid-lowering is one of the most effective methods of prevention and treatment for cardiovascular diseases. However, most clinical lipid-lowering drugs have adverse effects and cannot achieve the desired efficacy in some complex hyperlipidemia patients, so it is of great significance to develop safe and effective novel lipid-lowering drugs. In the course of our project aimed at discovering the chemical novelty and bioactive natural products of marine-derived actinomycetes, we found that the organic crude extracts (OCEs) of Nocardiopsis sp. ZHD001 exhibited strong in vivo efficacies in reducing weight gain, lowering LDL-C, TC, and TG levels, and improving HDL-C levels in high-fat-diet-fed mice models. Chemical investigations of the active OCEs led to identifying two new sphydrofuran-derived compounds (1-2) and one known 2-methyl-4-(1-glycerol)-furan (3). Their structures were elucidated by the analysis of HRESIMS, 1D and 2D NMR spectroscopic data, and ECD calculations. Among these compounds, compound 1 represents a novel rearranged sphydrofuran-derived derivative. Bioactivity evaluations of these pure compounds showed that all the compounds exhibited significant lipid-lowering activity with lower cytotoxicity in vitro compared to simvastatin. Our results demonstrate that sphydrofuran-derived derivatives might be promising candidates for lipid-lowering drugs.
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Affiliation(s)
- Yuhong Tian
- School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China
| | - Yongjun Jiang
- School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China
- Correspondence: (Y.J.); (Z.M.)
| | - Zhengshun Wen
- School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China
| | - Liping Guan
- School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China
| | - Xiaokun Ouyang
- School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China
| | - Wanjing Ding
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, China
| | - Zhongjun Ma
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, China
- Correspondence: (Y.J.); (Z.M.)
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Takahashi M, Shinohara S, Hamada M, Tamura T, Dohra H, Kodani S, Nakagawa Y, Kokubo S, Hayakawa M, Yamamura H. Streptomyces pacificus sp. nov., a novel spongiicolazolicin-producing actinomycete isolated from a coastal sediment. J Antibiot (Tokyo) 2023; 76:93-100. [PMID: 36564595 DOI: 10.1038/s41429-022-00589-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022]
Abstract
A polyphasic approach was used to determine the taxonomic position of a marine actinomycete, designated isolate CWH03T, which we previously reported to produce new linear azole-containing peptides spongiicolazolicins A and B. Strain CWH03T is mesophilic, neutrophilic, and halotolerant streptomycete that forms spiral spore chains on aerial mycelium. Comparative 16S rRNA gene sequencing showed that CWH03T was most closely related to Streptomyces tirandamycinicus HNM0039T (99.7%), Streptomyces spongiicola HNM0071T (99.4%), 'Streptomyces marianii' ICN19T (99.1%) and Streptomyces wuyuanensis CGMCC4.7042T (99.0%). The phylogenetic tree prepared using the 16S rRNA gene, as well as the phylogenomic tree using the genome BLAST distance phylogeny method and 81 core housekeeping genes, respectively, showed that the closest relative of strain CWH03T was S. spongiicola HNM0071T. The average nucleotide identity and digital DNA-DNA hybridization values between strains CWH03T and S. spongiicola HNM0071T were 91.46% and 44.2%, respectively, which were below the thresholds of 96% and 70% for prokaryotic conspecific assignation. The G+C content of the genomic DNA of strain CWH03T was 72.3%. Whole-cell hydrolysates of strain CWH03T contained LL-diaminopimelic acid. The predominant menaquinone was MK-9(H8) (88.3%), and the major fatty acids were iso-C16:0 (28.4%), anteiso-C15:0 (15.0%) and iso-C15:0 (12.9%). The major phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid. Based on data obtained from phenotypic, phylogenetic, genomic, and chemotaxonomic analyses, strain CWH03T represents a novel species of the genus Streptomyces, for which the proposed name is Streptomyces pacificus sp. nov. The type strain is CWH03T ( = NBRC 114659T = TBRC 15780T).
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Affiliation(s)
- Miku Takahashi
- Department of Biotechnology, Faculty of Life and Environmental Sciences, University of Yamanashi, Takeda-4-4-37, Kofu, 400-8510, Japan
| | - Shoya Shinohara
- Department of Biotechnology, Faculty of Life and Environmental Sciences, University of Yamanashi, Takeda-4-4-37, Kofu, 400-8510, Japan
| | - Moriyuki Hamada
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Tomohiko Tamura
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Hideo Dohra
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
- Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
- Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Shinya Kodani
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
- Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
- Academic Institute, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Youji Nakagawa
- Department of Biotechnology, Faculty of Life and Environmental Sciences, University of Yamanashi, Takeda-4-4-37, Kofu, 400-8510, Japan
| | - Susumu Kokubo
- Department of Biotechnology, Faculty of Life and Environmental Sciences, University of Yamanashi, Takeda-4-4-37, Kofu, 400-8510, Japan
| | - Masayuki Hayakawa
- Department of Biotechnology, Faculty of Life and Environmental Sciences, University of Yamanashi, Takeda-4-4-37, Kofu, 400-8510, Japan
- Yamanashi Prefectural University, Iida-5-11-1, Kofu, 400-0035, Japan
| | - Hideki Yamamura
- Department of Biotechnology, Faculty of Life and Environmental Sciences, University of Yamanashi, Takeda-4-4-37, Kofu, 400-8510, Japan.
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Mazumdar R, Dutta PP, Saikia J, Borah JC, Thakur D. Streptomyces sp. Strain PBR11, a Forest-Derived Soil Actinomycetia with Antimicrobial Potential. Microbiol Spectr 2023; 11:e0348922. [PMID: 36719230 PMCID: PMC10101066 DOI: 10.1128/spectrum.03489-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 12/21/2022] [Indexed: 02/01/2023] Open
Abstract
The Actinomycetia isolate PBR11 was isolated from the forest rhizosphere soil of Pobitora Wildlife Sanctuary (PWS), Assam, India. The isolate was identified as Streptomyces sp. with 92.91% sequence similarity to their closest type strain, Streptomyces atrovirens NRRL B-16357 DQ026672. The strain demonstrated significant antimicrobial activity against 19 test pathogens, including multidrug-resistant (MDR) clinical isolates and dermatophytes. Phenol, 2,5-bis(1,1-dimethylethyl), is the major chemical compound detected by gas chromatography-mass spectrometry in the ethyl acetate extract of PBR11 (EtAc-PBR11). The presence of the PKS type II gene (type II polyketide synthases) and chitinase gene suggested that it has been involved in the production of antimicrobial compounds. Metabolic profiling of the EtAc-PBR11 was performed by thin-layer chromatography and flash chromatography resulted in the extraction of two bioactive fractions, namely, PBR11Fr-1 and PBR11Fr-2. Liquid chromatography-tandem mass spectrometry analysis of both the fractions demonstrated the presence of significant antimicrobial compounds, including ethambutol. This is the first report on the detection of antituberculosis drug in the bioactive fractions of Streptomyces sp. PBR11. EtAc-PBR11 and PBR11Fr-1 showed the lowest MIC values (>0.097 and >0.048 μg/mL, respectively) against Candida albicans MTCC 227, whereas they showed the highest MIC values (>0.390 and >0.195 μg/mL, respectively) against Escherichia coli ATCC BAA-2469. The effects of PBR11Fr-1 were investigated on the pathogens by using a scanning electron microscope. The results indicated major morphological alterations in the cytoplasmic membrane. PBR11Fr-1 exhibited low cytotoxicity on normal hepatocyte cell line (CC-1) and the percent cell viability started to decline as the concentration increased from 50 μg/mL (87.07% ± 3.22%) to 100 μg/mL (81.26% ± 2.99%). IMPORTANCE Novel antibiotic breakthroughs are urgently required to combat antimicrobial resistance. Actinomycetia are the principal producers of antibiotics. The present study demonstrated the broad-spectrum antimicrobial potential of an Actinomycetia strain Streptomyces sp. strain PBR11 isolated from the PWS of Assam, India, which represents diverse, poorly screened habitats for novel microorganisms. The strain displayed 92.4% sequence similarity with genes of the closest type strain, indicating that the strain may represent a novel taxon within the phylum Actinomycetota. The metabolomics studies of EtAc-PBR11 revealed structurally diverse antimicrobial agents, including the detection of the antituberculosis drug ethambutol, in the bioactive fraction of Streptomyces sp. PBR11 for the first time. The PBR11 strain also yielded positive results for the antibiotic synthesis gene and the chitinase gene, both of which are responsible for broad-spectrum antimicrobial activity. This suggests that the untouched forest ecosystems have a tremendous potential to harbor potent actinomycetia for future drug discovery.
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Affiliation(s)
- Rajkumari Mazumdar
- Life Sciences Division, Institute of Advanced Study in Science and Technology, Guwahati, India
- Department of Molecular Biology and Biotechnology, Cotton University, Guwahati, India
| | | | - Juri Saikia
- Life Sciences Division, Institute of Advanced Study in Science and Technology, Guwahati, India
- Department of Biotechnology, Gauhati University, Guwahati, India
| | - Jagat Chandra Borah
- Life Sciences Division, Institute of Advanced Study in Science and Technology, Guwahati, India
| | - Debajit Thakur
- Life Sciences Division, Institute of Advanced Study in Science and Technology, Guwahati, India
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Sánchez-Hidalgo M, García MJ, González I, Oves-Costales D, Genilloud O. Complete Genome Sequence Analysis of Kribbella sp. CA-293567 and Identification of the Kribbellichelins A & B and Sandramycin Biosynthetic Gene Clusters. Microorganisms 2023; 11:microorganisms11020265. [PMID: 36838228 PMCID: PMC9962454 DOI: 10.3390/microorganisms11020265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 01/20/2023] Open
Abstract
Minor genera actinomycetes are considered a promising source of new secondary metabolites. The strain Kribbella sp. CA-293567 produces sandramycin and kribbellichelins A & B In this work, we describe the complete genome sequencing of this strain and the in silico identification of biosynthetic gene clusters (BGCs), focusing on the pathways encoding sandramycin and kribbellichelins A-B. We also present a comparative analysis of the biosynthetic potential of 38 publicly available genomes from Kribbella strains.
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44
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Antiviral Activity of Benzoheterocyclic Compounds from Soil-Derived Streptomyces jiujiangensis NBERC-24992. Molecules 2023; 28:molecules28020878. [PMID: 36677936 PMCID: PMC9866866 DOI: 10.3390/molecules28020878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
Pseudorabies virus (PRV) is a pathogen that causes Aujeszky's disease (AD) in animals, leading to huge economic losses to swine farms. In order to discover anti-PRV compounds, we studied the extracts of the strain Streptomyces jiujiangensis NBERC-24992, which showed significant anti-PRV activity. Eight benzoheterocyclic secondary metabolites, including three new compounds (1-3, virantmycins D-G) and five known compounds (4-8, virantmycin, A-503451 D, A-503451 D acetylate, A-503451 A, and A-503451 B), were isolated from the broth of NBERC-24992. The structures of the new compounds were identified by using extensive spectroscopic data, including mass spectrometry (MS), nuclear magnetic resonance (NMR), and electronic circular dichroism (ECD). Compound 1 was found to be a novel heterocyclic compound with a tricyclic skeleton from natural product. All compounds were tested for antiviral activity, and 4 (virantmycin) showed an excellent effect against PRV and was better than ribavirin and acyclovir. Our study revealed that chlorine atom and tetrahydroquinoline skeleton were important active moiety for antiviral activity. Virantmycin could be a suitable leading compound for an antiviral drug against PRV.
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Cui P, Wu H, Jiang T, Tao J, Zhu Z, Liu P, Yu L, Zhang Y. Diversity and antibacterial potential of the Actinobacteria associated with Apis mellifera ligustica. Front Microbiol 2022; 13:1056176. [PMID: 36590398 PMCID: PMC9800615 DOI: 10.3389/fmicb.2022.1056176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022] Open
Abstract
Insect-associated Actinobacteria are a potentially rich source of novel natural products with antibacterial activity. Here, the community composition of Actinobacteria associated with Apis mellifera ligustica was investigated by integrated culture-dependent and independent methods. A total of 61 strains of Streptomyces genera were isolated from the honeycomb, larva, and different anatomical parts of the honeybee's body using the culture-dependent method. Amplicon sequencing analyses revealed that the actinobacterial communities were dominated by the family of Bifidobacteriaceae and Microbacteriaceae in the honeybee gut, and Nocardiaceae and Pseudonocardiaceae in the honeycomb, whereas only Streptomyces genera were isolated by the culture-dependent method. Culture-independent analyses showed more diverse actinobacterial communities than those of culture-dependent methods. The antibacterial bioassay showed that most crude extracts of representative isolates exhibited antibacterial activities. Among them, the crude extract of Streptomyces sp. FCF01 showed the best antibacterial activities against Staphylococcus aureus, Micrococcus tetragenus, and Pseudomonas syringae pv. actinidiae (Psa) with the disc diameter of inhibition zone diameter (IZD) of 23.00, 15.00, and 13.33 mm, respectively. Chemical analysis of Streptomyces sp. FCF01 led to the isolation of three secondary metabolites, including mayamycin (1), mayamycin B (2), and N-(2-Hydroxyphenyl) acetamide (3). Among them, compound 1 displayed strong antibacterial activity against S. aureus, M. tetragenus, and Psa with minimum inhibitory concentrations (MIC) values of 6.25, 12.5, and 6.25 μg/ml, respectively. In addition, two novel derivative compounds 1a and 1b were synthesized by acetylation of compound 1. Both compounds 1a and 1b displayed similar antibacterial activities with those of metabolite 1. These results indicated that Streptomyces species associated with honeybees had great potential in finding antibiotics.
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Affiliation(s)
- Pu Cui
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Haoyang Wu
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Taoshan Jiang
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Jian Tao
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Zhiwei Zhu
- School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Peng Liu
- School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Linsheng Yu
- School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Yinglao Zhang
- School of Life Sciences, Anhui Agricultural University, Hefei, China,*Correspondence: Yinglao Zhang,
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Gao ZY, Song YL, Li XT, Li TH, Lu CH, Shen YM. Effects of hydrolysable tannins from Terminalia citrina on type III secretion system (T3SS) and their intestinal metabolite urolithin B represses Salmonella T3SS through Hha–H-NS–HilD–HilC–RtsA–HilA regulatory pathway. Microb Pathog 2022; 173:105837. [DOI: 10.1016/j.micpath.2022.105837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 10/12/2022] [Accepted: 10/13/2022] [Indexed: 11/30/2022]
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Chen Y, Wei Y, Cai B, Zhou D, Qi D, Zhang M, Zhao Y, Li K, Wedge DE, Pan Z, Xie J, Wang W. Discovery of Niphimycin C from Streptomyces yongxingensis sp. nov. as a Promising Agrochemical Fungicide for Controlling Banana Fusarium Wilt by Destroying the Mitochondrial Structure and Function. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:12784-12795. [PMID: 36170206 DOI: 10.1021/acs.jafc.2c02810] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Banana Fusarium wilt caused by Fusarium oxysporum f. sp. cubense (Foc) is the most destructive soil-borne fungal disease. Tropical race 4 (Foc TR4), one of the strains of Foc, can infect many commercial cultivars, which represents a threat to global banana production. Currently, there are hardly any effective chemical fungicides to control the disease. To search for natural product-based fungicides for controlling banana Fusarium wilt, we identified a novel strain Streptomyces yongxingensis sp. nov. (JCM 34965) from a marine soft coral, from which a bioactive compound, niphimycin C, was isolated using an activity-guided method. Niphimycin C exhibited a strong antifungal activity against Foc TR4 with a value of 1.20 μg/mL for EC50 and obviously inhibited the mycelial growth and spore germination of Foc TR4. It caused the functional loss of mitochondria and the disorder of metabolism of Foc TR4 cells. Further study showed that niphimycin C reduced key enzyme activities of the tricarboxylic acid (TCA) cycle and the electron transport chain (ETC). It displayed broad-spectrum antifungal activities against the selected 12 phytopathogenic fungi. In pot experiments, niphimycin C reduced the disease indexes in banana plantlets and inhibited the infection of Foc TR4 in roots. Hence, niphimycin C could be a promising agrochemical fungicide for the management of fungal diseases.
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Affiliation(s)
- Yufeng Chen
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Yongzan Wei
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Bingyu Cai
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Dengbo Zhou
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Dengfeng Qi
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Miaoyi Zhang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Yankun Zhao
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Kai Li
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - David E Wedge
- United States Department of Agriculture-Agricultural Research Service, Natural Products Utilization Research Unit, University, Mississippi 38677, United States
| | - Zhiqiang Pan
- United States Department of Agriculture-Agricultural Research Service, Natural Products Utilization Research Unit, University, Mississippi 38677, United States
| | - Jianghui Xie
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Wei Wang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
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Evaluation of Mangrove Soil Streptomyces spp. Exhibiting Culture and Biochemical Variation for Determination of Antibacterial Activity. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2022. [DOI: 10.22207/jpam.16.4.06] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Among actinobacteria, the genus Streptomyces are found in abundance in specific soil environments. Streptomyces are cultivable using Streptomyces-specific media, including starch casein, yeast extract, or ISP 2 media. Streptomyces isolates can be identified based on their macroscopic culture morphology and microscopic observations, and can be taxonomically placed within the Streptomyces genus. In the present study, mangrove soil samples collected from the coast of Mangalore harboring a multitude of microorganisms were enriched with calcium carbonate and pre-heated to isolate Streptomyces organisms. Cultures were quantified in colony forming units and their diversity was evaluated based on phenotypic features, enzyme hydrolysis, biochemical testing, and antibiotic sensitivity tests. The cross streaking method was used to select Streptomyces isolates, which were then further subjected to intracellular buffer extraction and evaluated against test organisms to determine their antibacterial efficacy. This study highlights the occurrence of prominent Streptomyces species with effective antibacterial activity in a unique environmental habitat of mangrove soil on the Mangalore coast.
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Lei Z, Chen L, Hu Q, Yang Y, Tong F, Li K, Lin T, Nie Y, Rong H, Yu S, Song Q, Guo J. Ginsenoside Rb1 improves intestinal aging via regulating the expression of sirtuins in the intestinal epithelium and modulating the gut microbiota of mice. Front Pharmacol 2022; 13:991597. [PMID: 36238549 PMCID: PMC9552198 DOI: 10.3389/fphar.2022.991597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 09/07/2022] [Indexed: 11/29/2022] Open
Abstract
Intestinal aging seriously affects the absorption of nutrients of the aged people. Ginsenoside Rb1 (GRb1) which has multiple functions on treating gastrointestinal disorders is one of the important ingredients from Ginseng, the famous herb in tradition Chinese medicine. However, it is still unclear if GRb1 could improve intestinal aging. To investigate the function and mechanism of GRb1 on improving intestinal aging, GRb1 was administrated to 104-week-old C57BL/6 mice for 6 weeks. The jejunum, colon and feces were collected for morphology, histology, gene expression and gut microbiota tests using H&E staining, X-gal staining, qPCR, Western blot, immunofluorescence staining, and 16S rDNA sequencing technologies. The numbers of cells reduced and the accumulation of senescent cells increased in the intestinal crypts of old mice, and administration of GRb1 could reverse them. The protein levels of CLDN 2, 3, 7, and 15 were all decreased in the jejunum of old mice, and administration of GRb1 could significantly increase them. The expression levels of Tert, Lgr5, mKi67, and c-Myc were all significantly reduced in the small intestines of old mice, and GRb1 significantly increased them at transcriptional or posttranscriptional levels. The protein levels of SIRT1, SIRT3, and SIRT6 were all reduced in the jejunum of old mice, and GRb1 could increase the protein levels of them. The 16S rDNA sequencing results demonstrated the dysbiosis of the gut microbiota of old mice, and GRb1 changed the composition and functions of the gut microbiota in the old mice. In conclusion, GRb1 could improve the intestinal aging via regulating the expression of Sirtuins family and modulating the gut microbiota in the aged mice.
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Affiliation(s)
- Zili Lei
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, Guangdong Pharmaceutical University, Guangzhou, China
- *Correspondence: Zili Lei, , Jiao Guo,
| | - Lei Chen
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, Guangdong Pharmaceutical University, Guangzhou, China
| | - Qing Hu
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, Guangdong Pharmaceutical University, Guangzhou, China
| | - Yanhong Yang
- The First Affiliated Hospital (School of Clinical Medicine), Guangdong Pharmaceutical University, Guangzhou, China
| | - Fengxue Tong
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, Guangdong Pharmaceutical University, Guangzhou, China
| | - Keying Li
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, Guangdong Pharmaceutical University, Guangzhou, China
| | - Ting Lin
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, Guangdong Pharmaceutical University, Guangzhou, China
| | - Ya Nie
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, Guangdong Pharmaceutical University, Guangzhou, China
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Hedong Rong
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, Guangdong Pharmaceutical University, Guangzhou, China
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Siping Yu
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, Guangdong Pharmaceutical University, Guangzhou, China
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Qi Song
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, Guangdong Pharmaceutical University, Guangzhou, China
| | - Jiao Guo
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, Guangdong Pharmaceutical University, Guangzhou, China
- *Correspondence: Zili Lei, , Jiao Guo,
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Actinopolymorphols E and F, pyrazine alkaloids from a marine sediment-derived bacterium Streptomyces sp. J Antibiot (Tokyo) 2022; 75:619-625. [DOI: 10.1038/s41429-022-00562-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 11/09/2022]
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