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Nyambo K, Tapfuma KI, Adu-Amankwaah F, Julius L, Baatjies L, Niang IS, Smith L, Govender KK, Ngxande M, Watson DJ, Wiesner L, Mavumengwana V. Molecular docking, molecular dynamics simulations and binding free energy studies of interactions between Mycobacterium tuberculosis Pks13, PknG and bioactive constituents of extremophilic bacteria. Sci Rep 2024; 14:6794. [PMID: 38514663 PMCID: PMC10957976 DOI: 10.1038/s41598-024-57124-9] [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: 12/16/2023] [Accepted: 03/14/2024] [Indexed: 03/23/2024] Open
Abstract
Mycobacterial pathogens present a significant challenge to disease control efforts globally due to their inherent resistance to multiple antibiotics. The rise of drug-resistant strains of Mycobacterium tuberculosis has prompted an urgent need for innovative therapeutic solutions. One promising way to discover new tuberculosis drugs is by utilizing natural products from the vast biochemical space. Multidisciplinary methods can used to harness the bioactivity of these natural products. This study aimed to evaluate the antimycobacterial efficacy of functional crude extracts from bacteria isolated from gold mine tailings in South Africa. Bacterial strains were identified using 16S rRNA sequencing. The crude extracts obtained from the bacteria were tested against Mycobacterium tuberculosis H37Rv, Mycobacterium smegmatis mc2155, and Mycobacterium aurum A+. Untargeted HPLC-qTOF and molecular networking were used to identify the functional constituents present in extracts that exhibited inhibitory activity. A virtual screening workflow (VSW) was used to filter compounds that were strong binders to Mycobacterium tuberculosis Pks13 and PknG. The ligands returned from the VSW were subjected to optimization using density functional theory (DFT) at M06-2X/6-311++ (d,p) level of theory and basis set implemented in Gaussian16 Rev.C01. The optimized ligands were re-docked against Mycobacterium tuberculosis Pks13 and PknG. Molecular dynamics simulation and molecular mechanics generalized born surface area were used to evaluate the stability of the protein-ligand complexes formed by the identified hits. The hit that showed promising binding characteristics was virtually modified through multiple synthetic routes using reaction-driven enumeration. Three bacterial isolates showed significant activity against the two strains of Mycobacterium, while only two, Bacillus subtilis and Bacillus licheniformis, exhibited activity against both Mycobacterium tuberculosis H37Rv, Mycobacterium smegmatis mc2155, and Mycobacterium aurum A+. The tentatively identified compounds from the bacterial crude extracts belonged to various classes of natural compounds associated with antimicrobial activity. Two compounds, cyclo-(L-Pro-4-OH-L-Leu) and vazabitide A, showed strong binding against PknG and Pks13, with pre-MD MM-GBSA values of - 42.8 kcal/mol and - 47.6 kcal/mol, respectively. The DFT-optimized compounds exhibited the same docking scores as the ligands optimized using the OPSL-4 force field. After modifying vazabitide A, its affinity to the Pks13 binding site increased to - 85.8 kcal/mol, as revealed by the post-MD MM-GBSA analysis. This study highlights the potential of bacteria isolates from gold mine tailings as a source of new scaffolds for designing and optimizing anti-Mycobacterium agents. These agents synthesized in-silico can be further tested in-vitro to evaluate their efficacy.
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Affiliation(s)
- Kudakwashe Nyambo
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7505, Cape Town, South Africa
| | - Kudzanai Ian Tapfuma
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7505, Cape Town, South Africa
| | - Francis Adu-Amankwaah
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7505, Cape Town, South Africa
| | - Lauren Julius
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7505, Cape Town, South Africa
| | - Lucinda Baatjies
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7505, Cape Town, South Africa
| | - Idah Sithole Niang
- Department of Biotechnology and Biochemistry, University of Zimbabwe, B064, Mount Pleasant, Harare, Zimbabwe
| | - Liezel Smith
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7505, Cape Town, South Africa
| | - Krishna Kuben Govender
- Department of Chemical Sciences, University of Johannesburg, Doornfontein Campus, P.O. Box 17011, Johannesburg, 2028, South Africa
- National Institute for Theoretical and Computational Sciences (NITheCS), Cape Town, South Africa
| | - Mkhuseli Ngxande
- Computer Science Division, Department of Mathematical Sciences, Faculty of Science, University of Stellenbosch, Matieland, South Africa
| | - Daniel J Watson
- Division of Clinical Pharmacology, Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Lubbe Wiesner
- Division of Clinical Pharmacology, Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Vuyo Mavumengwana
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7505, Cape Town, South Africa.
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Fan SM, Li ZQ, Zhang SZ, Chen LY, Wei XY, Liang J, Zhao XQ, Su C. Multi-integrated approach for unraveling small open reading frames potentially associated with secondary metabolism in Streptomyces. mSystems 2023; 8:e0024523. [PMID: 37712700 PMCID: PMC10654065 DOI: 10.1128/msystems.00245-23] [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: 03/27/2023] [Accepted: 07/20/2023] [Indexed: 09/16/2023] Open
Abstract
IMPORTANCE Due to their small size and special chemical features, small open reading frame (smORF)-encoding peptides (SEPs) are often neglected. However, they may play critical roles in regulating gene expression, enzyme activity, and metabolite production. Studies on bacterial microproteins have mainly focused on pathogenic bacteria, which are importance to systematically investigate SEPs in streptomycetes and are rich sources of bioactive secondary metabolites. Our study is the first to perform a global identification of smORFs in streptomycetes. We established a peptidogenomic workflow for non-model microbial strains and identified multiple novel smORFs that are potentially linked to secondary metabolism in streptomycetes. Our multi-integrated approach in this study is meaningful to improve the quality and quantity of the detected smORFs. Ultimately, the workflow we established could be extended to other organisms and would benefit the genome mining of microproteins with critical functions for regulation and engineering useful microorganisms.
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Affiliation(s)
- Si-Min Fan
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Shaanxi, China
| | - Ze-Qi Li
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Shaanxi, China
| | - Shi-Zhe Zhang
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Shaanxi, China
| | - Liang-Yu Chen
- ProteinT (Tianjin) biotechnology Co. Ltd., Tianjin, China
| | - Xi-Ying Wei
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Shaanxi, China
| | - Jian Liang
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Shaanxi, China
- College of Biology and Geography, Yili Normal University, Yining, China
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai Jiao, China
| | - Chun Su
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Shaanxi, China
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Yin QJ, Ying TT, Zhou ZY, Hu GA, Yang CL, Hua Y, Wang H, Wei B. Species-specificity of the secondary biosynthetic potential in Bacillus. Front Microbiol 2023; 14:1271418. [PMID: 37937215 PMCID: PMC10626522 DOI: 10.3389/fmicb.2023.1271418] [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: 08/02/2023] [Accepted: 10/09/2023] [Indexed: 11/09/2023] Open
Abstract
Introduction Although Bacillus species have produced a wide variety of structurally diverse and biologically active natural products, the secondary biosynthetic potential of Bacillus species is widely underestimated due to the limited number of biosynthetic gene clusters (BGCs) in this genus. The significant variation in the diversity and novelty of BGCs across different species within the Bacillus genus presents a major obstacle to the efficient discovery of novel natural products from Bacillus. Methods In this study, the number of each class of BGCs in all 6,378 high-quality Bacillus genomes was predicted using antiSMASH, the species-specificity of BGC distribution in Bacillus was investigated by Principal component analysis. Then the structural diversity and novelty of the predicted secondary metabolites in Bacillus species with specific BGC distributions were analyzed using molecular networking. Results Our results revealed a certain degree of species-specificity in the distribution of BGCs in Bacillus, which was mainly contributed by siderophore, type III polyketide synthase (T3PKS), and transAT-PKS BGCs. B. wiedmannii, B. thuringiensis, and B. cereus are rich in RiPP-like and siderophore BGCs, but lack T3PKS BGCs, while B. amyloliquefaciens and B. velezensis are abundant in transAT-PKS BGCs. These Bacillus species collectively encode 77,541 BGCs, with NRPS and RiPPs being the two most dominant types, which are further categorized into 4,291 GCFs. Remarkably, approximately 54.5% of GCFs and 93.8% of the predicted metabolite scaffolds are found exclusively in a single Bacillus species. Notably, B. cereus, B. thuringiensis, and B. velezensis exhibit the highest potential for producing species-specific NRPS and PKS bioinformatic natural products. Taking two species-specific NRPS gene clusters as examples, the potential of Bacillus to synthesize novel species-specific natural products is illustrated. Conclusion This study highlights the species-specificity of the secondary biosynthetic potential in Bacillus and provides valuable insights for the targeted discovery of novel natural products from this genus.
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Affiliation(s)
- Qun-Jian Yin
- Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai, China
| | - Ti-Ti Ying
- College of Pharmaceutical Science and Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Key Laboratory of Marine Fishery Resources Exploitation and Utilization of Zhejiang Province, Zhejiang University of Technology, Hangzhou, China
| | - Zhen-Yi Zhou
- College of Pharmaceutical Science and Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Key Laboratory of Marine Fishery Resources Exploitation and Utilization of Zhejiang Province, Zhejiang University of Technology, Hangzhou, China
| | - Gang-Ao Hu
- College of Pharmaceutical Science and Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Key Laboratory of Marine Fishery Resources Exploitation and Utilization of Zhejiang Province, Zhejiang University of Technology, Hangzhou, China
| | - Cai-Ling Yang
- College of Pharmaceutical Science and Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Key Laboratory of Marine Fishery Resources Exploitation and Utilization of Zhejiang Province, Zhejiang University of Technology, Hangzhou, China
| | - Yi Hua
- College of Pharmaceutical Science and Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Key Laboratory of Marine Fishery Resources Exploitation and Utilization of Zhejiang Province, Zhejiang University of Technology, Hangzhou, China
| | - Hong Wang
- College of Pharmaceutical Science and Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Key Laboratory of Marine Fishery Resources Exploitation and Utilization of Zhejiang Province, Zhejiang University of Technology, Hangzhou, China
| | - Bin Wei
- College of Pharmaceutical Science and Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Key Laboratory of Marine Fishery Resources Exploitation and Utilization of Zhejiang Province, Zhejiang University of Technology, Hangzhou, China
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Bautista-Crescencio C, Casimiro-Ramos A, Fragoso-Vázquez MJ, Correa-Basurto J, Olano C, Hernández-Rodríguez C, Villa-Tanaca L. Streptomyces albidoflavus Q antifungal metabolites inhibit the ergosterol biosynthesis pathway and yeast growth in fluconazole-resistant Candida glabrata: phylogenomic and metabolomic analyses. Microbiol Spectr 2023; 11:e0127123. [PMID: 37754674 PMCID: PMC10581079 DOI: 10.1128/spectrum.01271-23] [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: 03/23/2023] [Accepted: 08/08/2023] [Indexed: 09/28/2023] Open
Abstract
There is an urgent need to develop new antifungals due to the increasing prevalence of multidrug-resistant fungal infections and the recent emergence of COVID-19-associated candidiasis. A good study model for evaluating new antifungal compounds is Candida glabrata, an opportunistic fungal pathogen with intrinsic resistance to azoles (the most common clinical drugs for treating fungal infections). The aim of the current contribution was to conduct in vitro tests of antifungal metabolites produced by the bacteria Streptomyces albidoflavus Q, identify their molecular structures, and utilize several techniques to provide evidence of their therapeutic target. S. albidoflavus was isolated from maize rhizospheric soil in Mexico and identified by phylogenomic analysis using a 92-gene core. Of the 66 metabolites identified in S. albidoflavus Q by a liquid chromatography-high resolution mass spectrometry (LC-HRMS) metabolomic analysis of the lyophilized supernatant, six were selected by the Way2drug server based on their in silico binding to the likely target, 3-hydroxy-3-methyl-glutaryl-CoA reductase (HMGR, the key enzyme in the ergosterol biosynthesis pathway). Molecular modeling studies show a relatively high binding affinity for the CgHMGR enzyme by two secondary metabolites: isogingerenone B (diaryl heptanoid) and notoginsenoside J (polycyclic triterpene). These secondary metabolites were able to inhibit ergosterol synthesis and affect yeast viability in vitro. They also caused alterations in the ultrastructure of the yeast cytoplasmic membrane, as evidenced by transmission electron microscopy. The putative target of isogingerenone B and notoginsenoside J is distinct from that of azole drugs (the most common clinical antifungals). The target for the latter is the lanosterol 14 alpha-demethylase enzyme (Erg11). IMPORTANCE Multidrug resistance has emerged among yeasts of the genus Candida, posing a severe threat to global health. The problem has been exacerbated by the pandemic associated with COVID-19, during which resistant strains of Candida auris and Candida glabrata have been isolated from patients infected with the SARS-CoV-2 virus. To confront this challenge, the World Health Organization has invoked scientists to search for new antifungals with alternative molecular targets. This study identified 66 metabolites produced by the bacteria Streptomyces albidoflavus Q, 6 of which had promising properties for potential antifungal activity. The metabolites were tested in vitro as inhibitors of ergosterol synthesis and C. glabrata growth, with positive results. They were also found to damage the cytoplasmic membrane of the fungus. The corresponding molecular structures and their probable therapeutic target were established. The target is apparently distinct from that of azole drugs.
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Affiliation(s)
- Celia Bautista-Crescencio
- Departamento de Microbiología, Laboratorio de Biología Molecular de Bacterias y Levaduras, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional. Prolongación de Carpio y Plan de Ayala, Casco de Santo Tomás, Ciudad de México, Ciudad de México, México
| | - Arturo Casimiro-Ramos
- Departamento de Microbiología, Laboratorio de Biología Molecular de Bacterias y Levaduras, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional. Prolongación de Carpio y Plan de Ayala, Casco de Santo Tomás, Ciudad de México, Ciudad de México, México
| | - M. Jonathan Fragoso-Vázquez
- Departamento de Química Orgánica, Escuela Nacional de Ciencias, Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala, Col. Casco de Santo Tomás, Ciudad de México, México
| | - José Correa-Basurto
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), SEPI-Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón, Casco de Santo Tomás, Ciudad de México, México
| | - Carlos Olano
- Departamento de Biología Funcional, Universidad de Oviedo, Oviedo, Spain
| | - César Hernández-Rodríguez
- Departamento de Microbiología, Laboratorio de Biología Molecular de Bacterias y Levaduras, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional. Prolongación de Carpio y Plan de Ayala, Casco de Santo Tomás, Ciudad de México, Ciudad de México, México
| | - Lourdes Villa-Tanaca
- Departamento de Microbiología, Laboratorio de Biología Molecular de Bacterias y Levaduras, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional. Prolongación de Carpio y Plan de Ayala, Casco de Santo Tomás, Ciudad de México, Ciudad de México, México
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Singh RP, Kumari K, Sharma PK, Ma Y. Characterization and in-depth genome analysis of a halotolerant probiotic bacterium Paenibacillus sp. S-12, a multifarious bacterium isolated from Rauvolfia serpentina. BMC Microbiol 2023; 23:192. [PMID: 37464310 PMCID: PMC10353221 DOI: 10.1186/s12866-023-02939-1] [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: 11/01/2022] [Accepted: 07/10/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND Members of Paenibacillus genus from diverse habitats have attracted great attention due to their multifarious properties. Considering that members of this genus are mostly free-living in soil, we characterized the genome of a halotolerant environmental isolate belonging to the genus Paenibacillus. The genome mining unravelled the presence of CAZymes, probiotic, and stress-protected genes that suggested strain S-12 for industrial and agricultural purposes. RESULTS Molecular identification by 16 S rRNA gene sequencing showed its closest match to other Paenibacillus species. The complete genome size of S-12 was 5.69 Mb, with a GC-content 46.5%. The genome analysis of S-12 unravelled the presence of an open reading frame (ORF) encoding the functions related to environmental stress tolerance, adhesion processes, multidrug efflux systems, and heavy metal resistance. Genome annotation identified the various genes for chemotaxis, flagellar motility, and biofilm production, illustrating its strong colonization ability. CONCLUSION The current findings provides the in-depth investigation of a probiotic Paenibacillus bacterium that possessed various genome features that enable the bacterium to survive under diverse conditions. The strain shows the strong ability for probiotic application purposes.
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Affiliation(s)
- Rajnish Prakash Singh
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India.
| | - Kiran Kumari
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, India
| | - Parva Kumar Sharma
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD-20742, USA
| | - Ying Ma
- College of Resources and Environment, Southwest University, Chongqing, China
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Wang M, Li CJ, Zhang Z, Li PP, Yang LL, Zhi XY. The evolution of morphological development is congruent with the species phylogeny in the genus Streptomyces. Front Microbiol 2023; 14:1102250. [PMID: 37065118 PMCID: PMC10090380 DOI: 10.3389/fmicb.2023.1102250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/14/2023] [Indexed: 03/31/2023] Open
Abstract
As the canonical model organism to dissect bacterial morphological development, Streptomyces species has attracted much attention from the microbiological society. However, the evolution of development-related genes in Streptomyces remains elusive. Here, we evaluated the distribution of development-related genes, thus indicating that the majority of these genes were ubiquitous in Streptomyces genomes. Furthermore, the phylogenetic topologies of related strict orthologous genes were compared to the species tree of Streptomyces from both concatenation and single-gene tree analyses. Meanwhile, the reconciled gene tree and normalization based on the number of parsimony-informative sites were also employed to reduce the impact of phylogenetic conflicts, which was induced by uncertainty in single-gene tree inference based merely on the sequence and the bias in the amount of phylogenetic information caused by variable numbers of parsimony-informative sites. We found that the development-related genes had higher congruence to the species tree than other strict orthologous genes. Considering that the development-related genes could also be tracked back to the common ancestor of Streptomyces, these results suggest that morphological development follows the same pattern as species divergence.
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Affiliation(s)
- Min Wang
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
- Zhaotong Health Vocational College, Zhaotong, China
| | - Cong-Jian Li
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
| | - Zhen Zhang
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
| | - Pan-Pan Li
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
| | - Ling-Ling Yang
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
| | - Xiao-Yang Zhi
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
- *Correspondence: Xiao-Yang Zhi,
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Leite VMB, Garrido LM, Tangerina MMP, Costa-Lotufo LV, Ferreira MJP, Padilla G. Genome mining of Streptomyces sp. BRB081 reveals the production of the antitumor pyrrolobenzodiazepine sibiromycin. 3 Biotech 2022; 12:249. [PMID: 36043042 PMCID: PMC9420162 DOI: 10.1007/s13205-022-03305-0] [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: 05/21/2022] [Accepted: 08/09/2022] [Indexed: 12/01/2022] Open
Abstract
Employing a genome mining approach, this work aimed to further explore the secondary metabolism associated genes of Streptomyces sp. BRB081, a marine isolate. The genomic DNA of BRB081 was sequenced and assembled in a synteny-based pipeline for biosynthetic gene clusters (BGCs) annotation. A total of 27 BGCs were annotated, including a sibiromycin complete cluster, a bioactive compound with potent antitumor activity. The production of sibiromycin, a pyrrolobenzodiazepine, was confirmed by the analysis of obtained BRB081 extract by HPLC-MS/MS, which showed the presence of the sibiromycin ions themselves, as well as its imine and methoxylated forms. To verify the presence of this cluster in other genomes available in public databases, a genome neighborhood network (GNN) was constructed with the non-ribosomal peptide synthetase (NRPS) gene from Streptomyces sp. BRB081. Although the literature does not report the occurrence of the sibiromycin BGC in any other microorganism than Streptosporangium sibiricum, we have located this BGC in 10 other genomes besides the BRB081 isolate, all of them belonging to the Actinomycetia class. These findings strengthen the importance of uninterrupted research for new producer strains of secondary metabolites with uncommon biological activities. These results reinforced the accuracy and robustness of genomics in the screening of natural products. Furthermore, the unprecedented nature of this discovery confirms the unknown metabolic potential of the Actinobacteria phylum and the importance of continuing screening studies in this taxon. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03305-0.
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Affiliation(s)
- Vida M. B. Leite
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, São Paulo 05508-000 Brazil
| | - Leandro M. Garrido
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, São Paulo 05508-000 Brazil
| | - Marcelo M. P. Tangerina
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo 05508-090 Brazil
| | - Leticia V. Costa-Lotufo
- Departamento de Farmacologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, São Paulo 05508-000 Brazil
| | - Marcelo J. P. Ferreira
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo 05508-090 Brazil
| | - Gabriel Padilla
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, São Paulo 05508-000 Brazil
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Ashraf N, Zafar S, Makitrynskyy R, Bechthold A, Spiteller D, Song L, Anwar MA, Luzhetskyy A, Khan AN, Akhtar K, Khaliq S. Revealing Genome-Based Biosynthetic Potential of Streptomyces sp. BR123 Isolated from Sunflower Rhizosphere with Broad Spectrum Antimicrobial Activity. Antibiotics (Basel) 2022; 11:antibiotics11081057. [PMID: 36009926 PMCID: PMC9405382 DOI: 10.3390/antibiotics11081057] [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: 07/02/2022] [Revised: 07/30/2022] [Accepted: 08/01/2022] [Indexed: 11/16/2022] Open
Abstract
Actinomycetes, most notably the genus Streptomyces, have great importance due to their role in the discovery of new natural products, especially for finding antimicrobial secondary metabolites that are useful in the medicinal science and biotechnology industries. In the current study, a genome-based evaluation of Streptomyces sp. isolate BR123 was analyzed to determine its biosynthetic potential, based on its in vitro antimicrobial activity against a broad range of microbial pathogens, including gram-positive and gram-negative bacteria and fungi. A draft genome sequence of 8.15 Mb of Streptomyces sp. isolate BR123 was attained, containing a GC content of 72.63% and 8103 protein coding genes. Many antimicrobial, antiparasitic, and anticancerous compounds were detected by the presence of multiple biosynthetic gene clusters, which was predicted by in silico analysis. A novel metabolite with a molecular mass of 1271.7773 in positive ion mode was detected through a high-performance liquid chromatography linked with mass spectrometry (HPLC-MS) analysis. In addition, another compound, meridamycin, was also identified through a HPLC-MS analysis. The current study reveals the biosynthetic potential of Streptomyces sp. isolate BR123, with respect to the synthesis of bioactive secondary metabolites through genomic and spectrometric analysis. Moreover, the comparative genome study compared the isolate BR123 with other Streptomyces strains, which may expand the knowledge concerning the mechanism involved in novel antimicrobial metabolite synthesis.
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Affiliation(s)
- Neelma Ashraf
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, PO Box 577, Faisalabad 38000, Pakistan
- Department of Chemical Ecology/Biological Chemistry, University of Konstanz, 78457 Konstanz, Germany
- Correspondence: (N.A.); (S.K.); Tel.: +92-41-9201316 (S.K.); Fax: +92-41-92014722 (S.K.)
| | - Sana Zafar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, PO Box 577, Faisalabad 38000, Pakistan
| | - Roman Makitrynskyy
- Department of Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, University of Freiburg, 79104 Freiburg im Breisgau, Germany
| | - Andreas Bechthold
- Department of Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, University of Freiburg, 79104 Freiburg im Breisgau, Germany
| | - Dieter Spiteller
- Department of Chemical Ecology/Biological Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - Lijiang Song
- Department of Chemistry, University of Warwick Coventry, Coventry CV4 7AL, UK
| | - Munir Ahmad Anwar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, PO Box 577, Faisalabad 38000, Pakistan
| | - Andriy Luzhetskyy
- Pharmaceutical Biotechnology Campus, Saarland University, Building C2.3, 66123 Saarbrucken, Germany
| | - Ali Nisar Khan
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, PO Box 577, Faisalabad 38000, Pakistan
| | - Kalsoom Akhtar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, PO Box 577, Faisalabad 38000, Pakistan
| | - Shazia Khaliq
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Jhang Road, PO Box 577, Faisalabad 38000, Pakistan
- Correspondence: (N.A.); (S.K.); Tel.: +92-41-9201316 (S.K.); Fax: +92-41-92014722 (S.K.)
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9
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Rivera-Chávez J, Ceapă CD, Figueroa M. Biological Dark Matter Exploration using Data Mining for the Discovery of Antimicrobial Natural Products. PLANTA MEDICA 2022; 88:702-720. [PMID: 35697058 DOI: 10.1055/a-1795-0562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The discovery of novel antimicrobials has significantly slowed down over the last three decades. At the same time, humans rely increasingly on antimicrobials because of the progressive antimicrobial resistance in medical practices, human communities, and the environment. Data mining is currently considered a promising option in the discovery of new antibiotics. Some of the advantages of data mining are the ability to predict chemical structures from sequence data, anticipation of the presence of novel metabolites, the understanding of gene evolution, and the corroboration of data from multiple omics technologies. This review analyzes the state-of-the-art for data mining in the fields of bacteria, fungi, and plant genomic data, as well as metabologenomics. It also summarizes some of the most recent research accomplishments in the field, all pinpointing to innovation through uncovering and implementing the next generation of antimicrobials.
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Affiliation(s)
- José Rivera-Chávez
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Corina-Diana Ceapă
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Mario Figueroa
- Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, México
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10
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Siro G, Pipite A, Christi K, Srinivasan S, Subramani R. Marine Actinomycetes Associated with Stony Corals: A Potential Hotspot for Specialized Metabolites. Microorganisms 2022; 10:microorganisms10071349. [PMID: 35889068 PMCID: PMC9319285 DOI: 10.3390/microorganisms10071349] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/29/2022] [Accepted: 07/02/2022] [Indexed: 02/05/2023] Open
Abstract
Microbial secondary metabolites are an important source of antibiotics currently available for combating drug-resistant pathogens. These important secondary metabolites are produced by various microorganisms, including Actinobacteria. Actinobacteria have a colossal genome with a wide array of genes that code for several bioactive metabolites and enzymes. Numerous studies have reported the isolation and screening of millions of strains of actinomycetes from various habitats for specialized metabolites worldwide. Looking at the extent of the importance of actinomycetes in various fields, corals are highlighted as a potential hotspot for untapped secondary metabolites and new bioactive metabolites. Unfortunately, knowledge about the diversity, distribution and biochemistry of marine actinomycetes compared to hard corals is limited. In this review, we aim to summarize the recent knowledge on the isolation, diversity, distribution and discovery of natural compounds from marine actinomycetes associated with hard corals. A total of 11 new species of actinomycetes, representing nine different families of actinomycetes, were recovered from hard corals during the period from 2007 to 2022. In addition, this study examined a total of 13 new compounds produced by five genera of actinomycetes reported from 2017 to 2022 with antibacterial, antifungal and cytotoxic activities. Coral-derived actinomycetes have different mechanisms of action against their competitors.
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Affiliation(s)
- Galana Siro
- School of Agriculture, Geography, Environment, Ocean and Natural Sciences (SAGEONS), The University of the South Pacific, Laucala Campus, Suva, Fiji; (G.S.); (K.C.); (R.S.)
| | - Atanas Pipite
- School of Agriculture, Geography, Environment, Ocean and Natural Sciences (SAGEONS), The University of the South Pacific, Laucala Campus, Suva, Fiji; (G.S.); (K.C.); (R.S.)
- Correspondence: (A.P.); or (S.S.)
| | - Ketan Christi
- School of Agriculture, Geography, Environment, Ocean and Natural Sciences (SAGEONS), The University of the South Pacific, Laucala Campus, Suva, Fiji; (G.S.); (K.C.); (R.S.)
| | - Sathiyaraj Srinivasan
- Department of Bio & Environmental Technology, Division of Environmental & Life Science, College of Natural Science, Seoul Women’s University, 623 Hwarangno, Nowon-gu, Seoul 01797, Korea
- Correspondence: (A.P.); or (S.S.)
| | - Ramesh Subramani
- School of Agriculture, Geography, Environment, Ocean and Natural Sciences (SAGEONS), The University of the South Pacific, Laucala Campus, Suva, Fiji; (G.S.); (K.C.); (R.S.)
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11
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Zhang X, Zheng L, Xamxidin M, Wang J, Wu Z, Wang T, Chen C, Wu M. Gramella crocea sp. nov., isolated from activated sludge of a seafood processing plant. Antonie van Leeuwenhoek 2022; 115:969-978. [PMID: 35670899 DOI: 10.1007/s10482-022-01749-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 05/12/2022] [Indexed: 11/28/2022]
Abstract
A novel aerobic Gram-negative strain, designated as YB25T, was isolated from an activated sludge sample collected from a seafood processing plant in Zhoushan, Zhejiang Province, China, and characterized by using a polyphasic taxonomic approach in this study. Strain YB25T was motile by gliding, and short-rod-shaped. The isolate grew at 4-37 °C (optimum 28 °C), pH 6.0-9.0 (optimum pH 7.0) and 0.0-10.0% NaCl (optimum 2.0%, w/v). Phylogenetic analysis based on 16S rRNA gene indicated that strain YB25T belonged to the genus Gramella, and showed the highest sequence similarity of 97.59% to Gramella lutea YJ019T. The DNA G + C content was 39.5%. In silico DNA-DNA hybridization (DDH) and average nucleotide identity (ANI) values between strain YB25T with most closely strains were below the threshold, which is considered to the phylogenetic definition of a novel species. Chemotaxonomic analysis indicated that the only respiratory quinone was menaquinone-6 and the major fatty acids were iso-C15:0, anteiso-C15:0, iso-C17:0 3-OH, and summed feature 9 (iso-C17:1ω9c and C16:0 10 methyl). The polar lipid profile was composed of phosphatidylethanolamine, an unidentified phospholipid, two unidentified amino lipids, three unidentified glycolipids, and four unidentified lipids. Compared with the reference strains, strain YB25T contained higher abundance of genes for carbohydrates metabolism,nitrogen metabolism, sulfur metabolism and respiration based on its genomic metabolic pathways and had been found a certain potential in the degradation of pectin. On the basis of the taxonomic evidence, strain YB25T represents a novel species of the genus Gramella, for which the name Gramella crocea sp. nov. is proposed. The type strain is YB25T (= KCTC 82680 T = MCCC 1K05761T).
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Affiliation(s)
- Xinyin Zhang
- Ocean College, Zhejiang University, Zhoushan, 316000, People's Republic of China
| | - Luhang Zheng
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Maripat Xamxidin
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Jiayan Wang
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Zhicheng Wu
- Ocean College, Zhejiang University, Zhoushan, 316000, People's Republic of China
| | - Tao Wang
- Department of Microbiology, University of Georgia, Athens, GA, USA
| | - Can Chen
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China.
| | - Min Wu
- Ocean College, Zhejiang University, Zhoushan, 316000, People's Republic of China. .,College of Life Sciences, Zhejiang University, Hangzhou, 310058, People's Republic of China.
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12
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Pontibrevibacter nitratireducens gen. nov., sp. nov., a member of the family Rhodobacteraceae isolated from seawater of the Indian Ocean and intertidal zone. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005341] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-stain-negative, facultatively anaerobic, non-motile, rod-shaped bacteria, strains h42T and ALG8, were isolated individually from the Indian Ocean and intertidal zone of Zhoushan, China. The results of 16S rRNA gene sequence analysis showed that the sequence similarity between strains h42T and ALG8 was 99.7 %, and the closest related strains were
Monaibacterium marinum
C7T (97.77 and 97.62 %) and
Pontivivens insulae
GYSW-23T (95.31 and 95.45 %). Phylogenetic analysis based on 16S rRNA gene sequences shows that these two novel strains belong to a distinct new lineage of the family
Rhodobacteraceae
in the order
Rhodobacterales
. The average nucleotide identity and in silico DNA–DNA hybridization values between the two novel strains and
M. marinum
C7T and
P. insulae
GYSW-23T were 72.73–78.15 % and 19.70–20.80 %, respectively. The DNA G+C content of strains h42T and ALG8 was 62.36 % and 62.17 mol %. The major fatty acids (>10 %) in strain h42T were C18 : 0, C19 : 0 cyclo ω8c and summed feature 8 (C18 : 1
ω6c and/or C18 : 1
ω7c), and in strain ALG8 were C19 : 0 cyclo ω8c and summed feature 8 (C18 : 1ω6c and/or C18 : 1
ω7c). The predominant isoprenoid ubiquinone of the two novel strains was Q-10; their major polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, two unidentified glycolipids, an unidentified aminoglycolipid, an unidentified phospholipid and an unidentified lipid. Based on the results of the morphological, physiological, chemotaxonomic and phylogenetic analysis of these two strains, a novel species of a new genus in the family
Rhodobacteraceae
is proposed, named as Pontibrevibacter nitratireducens gen. nov., sp. nov. The type strain and non-type strain of P. nitratireducens are h42T (=KCTC 72875T=CGMCC 1.17849T=MCCC 1K04735T) and ALG8 (=KCTC 82194=MCCC 1K04733).
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13
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Re-classification of Streptomyces venezuelae strains and mining secondary metabolite biosynthetic gene clusters. iScience 2021; 24:103410. [PMID: 34877485 PMCID: PMC8627960 DOI: 10.1016/j.isci.2021.103410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/05/2021] [Accepted: 11/04/2021] [Indexed: 11/20/2022] Open
Abstract
Streptomyces species have attracted considerable interest as a reservoir of medically important secondary metabolites, which are even diverse and different between strains. Here, we reassess ten Streptomyces venezuelae strains by presenting the highly resolved classification, using 16S rRNA sequencing, MALDI-TOF MS protein profiling, and whole-genome sequencing. The results revealed that seven of the ten strains were misclassified as S. venezuelae species. Secondary metabolite biosynthetic gene cluster (smBGC) mining and targeted LC-MS/MS based metabolite screening of S. venezuelae and misclassified strains identified in total 59 secondary metabolites production. In addition, a comparison of pyrrolamide-type antibiotic BGCs of four misclassified strains, followed by functional genomics, revealed that athv28 is critical in the synthesis of the anthelvencin precursor, 5-amino-3,4-dihydro-2H-pyrrole-2-carboxylate (ADPC). Our findings illustrate the importance of the accurate classification and better utilization of misclassified Streptomyces strains to discover smBGCs and their secondary metabolite products.
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14
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Caicedo-Montoya C, Manzo-Ruiz M, Ríos-Estepa R. Pan-Genome of the Genus Streptomyces and Prioritization of Biosynthetic Gene Clusters With Potential to Produce Antibiotic Compounds. Front Microbiol 2021; 12:677558. [PMID: 34659136 PMCID: PMC8510958 DOI: 10.3389/fmicb.2021.677558] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 08/30/2021] [Indexed: 01/07/2023] Open
Abstract
Species of the genus Streptomyces are known for their ability to produce multiple secondary metabolites; their genomes have been extensively explored to discover new bioactive compounds. The richness of genomic data currently available allows filtering for high quality genomes, which in turn permits reliable comparative genomics studies and an improved prediction of biosynthetic gene clusters (BGCs) through genome mining approaches. In this work, we used 121 genome sequences of the genus Streptomyces in a comparative genomics study with the aim of estimating the genomic diversity by protein domains content, sequence similarity of proteins and conservation of Intergenic Regions (IGRs). We also searched for BGCs but prioritizing those with potential antibiotic activity. Our analysis revealed that the pan-genome of the genus Streptomyces is clearly open, with a high quantity of unique gene families across the different species and that the IGRs are rarely conserved. We also described the phylogenetic relationships of the analyzed genomes using multiple markers, obtaining a trustworthy tree whose relationships were further validated by Average Nucleotide Identity (ANI) calculations. Finally, 33 biosynthetic gene clusters were detected to have potential antibiotic activity and a predicted mode of action, which might serve up as a guide to formulation of related experimental studies.
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Affiliation(s)
- Carlos Caicedo-Montoya
- Grupo de Bioprocesos, Departamento de Ingeniería Química, Universidad de Antioquia (UdeA), Medellín, Colombia
| | - Monserrat Manzo-Ruiz
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Rigoberto Ríos-Estepa
- Grupo de Bioprocesos, Departamento de Ingeniería Química, Universidad de Antioquia (UdeA), Medellín, Colombia
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15
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Wei B, Du AQ, Zhou ZY, Lai C, Yu WC, Yu JB, Yu YL, Chen JW, Zhang HW, Xu XW, Wang H. An atlas of bacterial secondary metabolite biosynthesis gene clusters. Environ Microbiol 2021; 23:6981-6992. [PMID: 34490968 DOI: 10.1111/1462-2920.15761] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 09/04/2021] [Indexed: 11/28/2022]
Abstract
Bacterial secondary metabolites are rich sources of novel drug leads. The diversity of secondary metabolite biosynthetic gene clusters (BGCs) in genome-sequenced bacteria, which will provide crucial information for the efficient discovery of novel natural products, has not been systematically investigated. Here, the distribution and genetic diversity of BGCs in 10 121 prokaryotic genomes (across 68 phyla) were obtained from their PRISM4 outputs using a custom python script. A total of 18 043 BGCs are detected from 5743 genomes with non-ribosomal peptide synthetases (25.4%) and polyketides (15.9%) as the dominant classes of BGCs. Bacterial strains harbouring the largest number of BGCs are revealed and BGC count in strains of some genera vary greatly, suggesting the necessity of individually evaluating the secondary metabolism potential. Additional analysis against 102 strains of discovered bacterial genera with abundant amounts of BGCs confirms that Kutzneria, Kibdelosporangium, Moorea, Saccharothrix, Cystobacter, Archangium, Actinosynnema, Kitasatospora, and Nocardia, may also be important sources of natural products and worthy of priority investigation. Comparative analysis of BGCs within these genera indicates the great diversity and novelty of the BGCs. This study presents an atlas of bacterial secondary metabolite BGCs that provides a lot of key information for the targeted discovery of novel natural products.
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Affiliation(s)
- Bin Wei
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, China.,Key Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, China.,Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Hangzhou, 310014, China
| | - Ao-Qi Du
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Zhen-Yi Zhou
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Cong Lai
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Wen-Chao Yu
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Jin-Biao Yu
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Yan-Lei Yu
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Jian-Wei Chen
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Hua-Wei Zhang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, China.,Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Hangzhou, 310014, China
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, China
| | - Hong Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, 310014, China.,Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Hangzhou, 310014, China
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16
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Jian SL, Xu L, Meng FX, Sun C, Xu XW. Euzebya pacifica sp. nov., a novel member of the class Nitriliruptoria. Int J Syst Evol Microbiol 2021; 71. [PMID: 34255620 DOI: 10.1099/ijsem.0.004864] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, aerobic, chemo-organotrophic, rod-shaped, non-spore-forming strain, which produced convex, circular, pink-pigmented colonies, designated as DY32-46T, was isolated from seawater collected from the Pacific Ocean. DY32-46T was found to grow at 20-40 °C (optimum, 30-35 °C), pH 6.0-8.0 (optimum, pH 6.5) and with 0-5 % (w/v) NaCl (optimum, 1-2 %). The results of chemotaxonomic analysis indicated that the respiratory quinone of DY32-46T was MK-9(H4), and major fatty acids (>10 %) were C17 : 1 ω8c, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0 and C15 : 1 ω6c. The polar lipids included diphosphatidylglycerol, phosphatidylglycerol, one unidentified aminophospholipid, three unidentified glycolipids, three unidentified phospholipids, one unidentified phosphoglycolipid and five unidentified lipids. The DNA G+C content of DY32-46T was 70.6 mol%. The results of phylogenetic analysis based on 16S rRNA gene sequences and genomic data indicated that DY32-46T should be assigned to the genus Euzebya. ANI and in silico DNA-DNA hybridization values between strain DY32-46T and type strains of Euzebya species were 73.1-87.2 % and 20.2-32.4 %, respectively. Different phenotypic properties, together with genetic distinctiveness, demonstrated that strain DY32-46T was clearly distinct from recognized species of the genus Euzebya. Therefore, DY32-46T represents a novel species within the genus Euzebya, for which the name Euzebya pacifica sp. nov is proposed. The type strain is DY32-46T (=MCCC 1K03476T=KCTC 49091T).
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Affiliation(s)
- Shu-Ling Jian
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
| | - Lin Xu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China.,College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Fan-Xu Meng
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
| | - Cong Sun
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China.,College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
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17
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Siupka P, Hansen FT, Schier A, Rocco S, Sørensen T, Piotrowska-Seget Z. Antifungal Activity and Biosynthetic Potential of New Streptomyces sp. MW-W600-10 Strain Isolated from Coal Mine Water. Int J Mol Sci 2021; 22:ijms22147441. [PMID: 34299061 PMCID: PMC8303363 DOI: 10.3390/ijms22147441] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/30/2021] [Accepted: 07/08/2021] [Indexed: 12/20/2022] Open
Abstract
Crop infections by fungi lead to severe losses in food production and pose risks for human health. The increasing resistance of pathogens to fungicides has led to the higher usage of these chemicals, which burdens the environment and highlights the need to find novel natural biocontrol agents. Members of the genus Streptomyces are known to produce a plethora of bioactive compounds. Recently, researchers have turned to extreme and previously unexplored niches in the search for new strains with antimicrobial activities. One such niche are underground coal mine environments. We isolated the new Streptomyces sp. MW-W600-10 strain from coal mine water samples collected at 665 m below ground level. We examined the antifungal activity of the strain against plant pathogens Fusarium culmorum DSM62188 and Nigrospora oryzae roseF7. Furthermore, we analyzed the strain’s biosynthetic potential with the antiSMASH tool. The strain showed inhibitory activity against both fungi strains. Genome mining revealed that it has 39 BGCs, among which 13 did not show similarity to those in databases. Additionally, we examined the activity of the Streptomyces sp. S-2 strain isolated from black soot against F. culmorum DSM62188. These results show that coal-related strains could be a source of novel bioactive compounds. Future studies will elucidate their full biotechnological potential.
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Affiliation(s)
- Piotr Siupka
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40032 Katowice, Poland; (A.S.); (S.R.); (Z.P.-S.)
- Correspondence:
| | - Frederik Teilfeldt Hansen
- Faculty of Engineering and Science, Department of Chemistry and Biosciences, University of Aalborg, 9220 Aalborg, Denmark; (F.T.H.); (T.S.)
| | - Aleksandra Schier
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40032 Katowice, Poland; (A.S.); (S.R.); (Z.P.-S.)
| | - Simone Rocco
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40032 Katowice, Poland; (A.S.); (S.R.); (Z.P.-S.)
| | - Trine Sørensen
- Faculty of Engineering and Science, Department of Chemistry and Biosciences, University of Aalborg, 9220 Aalborg, Denmark; (F.T.H.); (T.S.)
| | - Zofia Piotrowska-Seget
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40032 Katowice, Poland; (A.S.); (S.R.); (Z.P.-S.)
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18
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Wang YW, Ren WT, Xu YY, Zhang XQ. Muriiphilus fusiformis gen. nov., sp. nov., a novel non-marine bacterium belonging to the Roseobacter group, and reclassification of Maritimibacter lacisalsi (Zhong et al. 2015) as Muriicola lacisalsi gen. nov., comb. nov. Int J Syst Evol Microbiol 2021; 71. [PMID: 34181513 DOI: 10.1099/ijsem.0.004859] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An aerobic, Gram-stain-negative, non-sporulating, flagellated and spindle-like bacterium, designated HY14T, was isolated from a pickle-processing factory wastewater sample. The isolate chemoheterotrophically grew at 4-42 °C (optimum, 35 °C) and pH 5.5-9.0 (optimum, pH 6.0-6.5). Salt was required for growth (0.5-12 % NaCl, w/v). A deep brown and water-soluble uncharacterized pigment was produced when grown in certain media. The predominant fatty acids (>5 %) included C16 : 0, C18 : 1 ω7c, 11-methyl C18 : 1 ω7c and C19 : 0 cyclo ω8c. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, two unidentified aminolipids, two unidentified phospholipids, two unidentified glycolipids and five unknown lipids. The major isoprenoid quinone was ubiquinone-10. Pairwise alignment based on 16S rRNA gene sequences indicated that strain HY14T had the highest sequence similarity to genera Maritimibacter (95.61-96.05 %) and Boseongicola (95.82 %). Phylogenetic analysis based on core genome illustrated that strain HY14T formed a monophyletic lineage with members of the genus Maritimibacter in the clade of the Roseobacter group in the family Rhodobacteraeceae. The core-gene average amino acid identity used to define bacterial genera by a threshold of 60-80 % was calculated to be 68.56-76.5 % between HY14T and closely related taxa. Several genomic characteristics, such as carrying two RuBisCO-mediated pathways and different osmoprotectant transport pathways, exhibited the genotypic discrepancies of strain HY14T. Based on the polyphasic taxonomic characterization, strain HY14T is considered to represent a novel species of a novel genus belonging to the family Rhodobacteraeceae, for which the name Muriiphilus fusiformis gen. nov., sp. nov. is proposed. The type strain is HY14T (=CGMCC 1.15973T=KCTC 52499T). Maritimibacter lacisalsi (Zhong et al. 2015) is considered to diverge from Maritimibacter alkaliphilus at the genus level, and should be reassigned as a novel genus, for which the name Muriicola lacisalsi gen. nov., comb. nov. is proposed.
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Affiliation(s)
- Yu-Wen Wang
- College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, PR China
| | - Wen-Ting Ren
- College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, PR China
| | - Yuan-You Xu
- College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, PR China
| | - Xin-Qi Zhang
- College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, PR China
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19
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Dat TTH, Cuc NTK, Cuong PV, Smidt H, Sipkema D. Diversity and Antimicrobial Activity of Vietnamese Sponge-Associated Bacteria. Mar Drugs 2021; 19:md19070353. [PMID: 34206202 PMCID: PMC8307940 DOI: 10.3390/md19070353] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 06/16/2021] [Accepted: 06/18/2021] [Indexed: 12/13/2022] Open
Abstract
This study aimed to assess the diversity and antimicrobial activity of cultivable bacteria associated with Vietnamese sponges. In total, 460 bacterial isolates were obtained from 18 marine sponges. Of these, 58.3% belonged to Proteobacteria, 16.5% to Actinobacteria, 18.0% to Firmicutes, and 7.2% to Bacteroidetes. At the genus level, isolated strains belonged to 55 genera, of which several genera, such as Bacillus, Pseudovibrio, Ruegeria, Vibrio, and Streptomyces, were the most predominant. Culture media influenced the cultivable bacterial composition, whereas, from different sponge species, similar cultivable bacteria were recovered. Interestingly, there was little overlap of bacterial composition associated with sponges when the taxa isolated were compared to cultivation-independent data. Subsequent antimicrobial assays showed that 90 isolated strains exhibited antimicrobial activity against at least one of seven indicator microorganisms. From the culture broth of the isolated strain with the strongest activity (Bacillus sp. M1_CRV_171), four secondary metabolites were isolated and identified, including cyclo(L-Pro-L-Tyr) (1), macrolactin A (2), macrolactin H (3), and 15,17-epoxy-16-hydroxy macrolactin A (4). Of these, compounds 2-4 exhibited antimicrobial activity against a broad spectrum of reference microorganisms.
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Affiliation(s)
- Ton That Huu Dat
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, 321 Huynh Thuc Khang, Hue City, Thua Thien Hue 531600, Vietnam; (N.T.K.C.); (P.V.C.)
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands;
- Correspondence: (T.T.H.D.); (D.S.); Tel.: +84-94-949-2778 (T.T.H.D.); +31-317-483-113 (D.S.)
| | - Nguyen Thi Kim Cuc
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, 321 Huynh Thuc Khang, Hue City, Thua Thien Hue 531600, Vietnam; (N.T.K.C.); (P.V.C.)
| | - Pham Viet Cuong
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, 321 Huynh Thuc Khang, Hue City, Thua Thien Hue 531600, Vietnam; (N.T.K.C.); (P.V.C.)
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands;
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands;
- Correspondence: (T.T.H.D.); (D.S.); Tel.: +84-94-949-2778 (T.T.H.D.); +31-317-483-113 (D.S.)
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20
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Gao Y, Li G, Fang C, Shao Z, Wu YH, Xu XW. Tsuneonella suprasediminis sp. nov., isolated from the Pacific Ocean. Int J Syst Evol Microbiol 2021; 71. [PMID: 33528355 DOI: 10.1099/ijsem.0.004678] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, rod-shaped and aerobic bacterial strain, named Ery12T, was isolated from the overlying water of the Lau Basin in the Southwest Pacific Ocean. Strain Ery12T showed high 16S rRNA gene sequences similarity to Tsuneonella flava MS1-4T (99.9 %), T. mangrovi MCCC 1K03311T (98.1 %), Altererythrobacter ishigakiensis NBRC 107699T (97.3 %) and exhibited ≤97.0 % sequence similarity with other type strains of species with validly published names. Growth was observed in media with 0-10.0 % NaCl (optimum 0-1.0 %, w/v), pH 5.0-9.5 (optimum 6.0-7.0) and 10-42 °C (optimum 30-37 °C). The predominant respiratory quinone was ubiquinone 10 (Q-10). The major cellular fatty acid was summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The major polar lipids were sphingoglycolipid, phosphatidyglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, three unidentified glycolipids, one unidentified aminoglycolipid and one unidentified lipid. The DNA G+C content was 60.8 %. The ANI and in silico DDH values between strain Ery12T and the type strains of its closely related species were 71.0- 91.8 % and 19.5- 44.6 %, respectively. According to the phenotypic, chemotaxonomic, phylogenetic and genomic data, strain Ery12T represents a novel species of the genus Tsuneonella, for which the name Tsuneonella suprasediminis is proposed. The type strain is Ery12T (=CGMCC 1.16500 T=MCCC 1A04421T=KCTC 62388T). We further propose to reclassify Altererythrobacter rhizovicinus and Altererythrobacter spongiae as Pelagerythrobacter rhizovicinus comb. nov. and Altericroceibacterium spongiae comb. nov., respectively.
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Affiliation(s)
- Yan Gao
- China Ocean Mineral Resources Research and Development Association, Beijing, 100000, PR China.,Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
| | - Guangyu Li
- Marine Culture Collection of China, Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, PR China
| | - Chen Fang
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
| | - Zongze Shao
- Marine Culture Collection of China, Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, PR China
| | - Yue-Hong Wu
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200030, PR China.,Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China.,School of Oceanography, Shanghai Jiao Tong University, Shanghai 200030, PR China
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21
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Gavriilidou A, Mackenzie TA, Sánchez P, Tormo JR, Ingham C, Smidt H, Sipkema D. Bioactivity Screening and Gene-Trait Matching across Marine Sponge-Associated Bacteria. Mar Drugs 2021; 19:75. [PMID: 33573261 PMCID: PMC7912018 DOI: 10.3390/md19020075] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 12/23/2022] Open
Abstract
Marine sponges harbor diverse microbial communities that represent a significant source of natural products. In the present study, extracts of 21 sponge-associated bacteria were screened for their antimicrobial and anticancer activity, and their genomes were mined for secondary metabolite biosynthetic gene clusters (BGCs). Phylogenetic analysis assigned the strains to four major phyla in the sponge microbiome, namely Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. Bioassays identified one extract with anti-methicillin-resistant Staphylococcus aureus (MRSA) activity, and more than 70% of the total extracts had a moderate to high cytotoxicity. The most active extracts were derived from the Proteobacteria and Actinobacteria, prominent for producing bioactive substances. The strong bioactivity potential of the aforementioned strains was also evident in the abundance of BGCs, which encoded mainly beta-lactones, bacteriocins, non-ribosomal peptide synthetases (NRPS), terpenes, and siderophores. Gene-trait matching was performed for the most active strains, aiming at linking their biosynthetic potential with the experimental results. Genetic associations were established for the anti-MRSA and cytotoxic phenotypes based on the similarity of the detected BGCs with BGCs encoding natural products with known bioactivity. Overall, our study highlights the significance of combining in vitro and in silico approaches in the search of novel natural products of pharmaceutical interest.
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Affiliation(s)
- Asimenia Gavriilidou
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE Wageningen, The Netherlands; (H.S.); (D.S.)
| | - Thomas Andrew Mackenzie
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Granada, Spain; (T.A.M.); (P.S.); (J.R.T.)
| | - Pilar Sánchez
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Granada, Spain; (T.A.M.); (P.S.); (J.R.T.)
| | - José Ruben Tormo
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Granada, Spain; (T.A.M.); (P.S.); (J.R.T.)
| | | | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE Wageningen, The Netherlands; (H.S.); (D.S.)
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE Wageningen, The Netherlands; (H.S.); (D.S.)
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22
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Kloosterman AM, Cimermancic P, Elsayed SS, Du C, Hadjithomas M, Donia MS, Fischbach MA, van Wezel GP, Medema MH. Expansion of RiPP biosynthetic space through integration of pan-genomics and machine learning uncovers a novel class of lanthipeptides. PLoS Biol 2020; 18:e3001026. [PMID: 33351797 PMCID: PMC7794033 DOI: 10.1371/journal.pbio.3001026] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 01/08/2021] [Accepted: 12/07/2020] [Indexed: 12/22/2022] Open
Abstract
Microbial natural products constitute a wide variety of chemical compounds, many which can have antibiotic, antiviral, or anticancer properties that make them interesting for clinical purposes. Natural product classes include polyketides (PKs), nonribosomal peptides (NRPs), and ribosomally synthesized and post-translationally modified peptides (RiPPs). While variants of biosynthetic gene clusters (BGCs) for known classes of natural products are easy to identify in genome sequences, BGCs for new compound classes escape attention. In particular, evidence is accumulating that for RiPPs, subclasses known thus far may only represent the tip of an iceberg. Here, we present decRiPPter (Data-driven Exploratory Class-independent RiPP TrackER), a RiPP genome mining algorithm aimed at the discovery of novel RiPP classes. DecRiPPter combines a Support Vector Machine (SVM) that identifies candidate RiPP precursors with pan-genomic analyses to identify which of these are encoded within operon-like structures that are part of the accessory genome of a genus. Subsequently, it prioritizes such regions based on the presence of new enzymology and based on patterns of gene cluster and precursor peptide conservation across species. We then applied decRiPPter to mine 1,295 Streptomyces genomes, which led to the identification of 42 new candidate RiPP families that could not be found by existing programs. One of these was studied further and elucidated as a representative of a novel subfamily of lanthipeptides, which we designate class V. The 2D structure of the new RiPP, which we name pristinin A3 (1), was solved using nuclear magnetic resonance (NMR), tandem mass spectrometry (MS/MS) data, and chemical labeling. Two previously unidentified modifying enzymes are proposed to create the hallmark lanthionine bridges. Taken together, our work highlights how novel natural product families can be discovered by methods going beyond sequence similarity searches to integrate multiple pathway discovery criteria. This study shows that decRiPPter, an innovative algorithmic approach using pan-genomics and machine learning, can discover novel types of ribosomally synthesized peptide (RIPP) natural products, including a new class of lanthipeptides.
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Affiliation(s)
| | - Peter Cimermancic
- Verily Life Sciences, South San Francisco, CA, United States of America
| | | | - Chao Du
- Institute of Biology, Leiden University, the Netherlands
| | | | - Mohamed S. Donia
- Department of Molecular Biology, Princeton University, NJ, United States of America
| | | | - Gilles P. van Wezel
- Institute of Biology, Leiden University, the Netherlands
- Netherlands Institute for Ecology (NIOO-KNAW), Wageningen, the Netherlands
- * E-mail: (GPvW); (MHM)
| | - Marnix H. Medema
- Bioinformatics group, Wageningen University, the Netherlands
- * E-mail: (GPvW); (MHM)
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23
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Guo LL, Wu D, Sun C, Cheng H, Xu XW, Wu M, Wu YH. Muricauda maritima sp. nov., Muricauda aequoris sp. nov. and Muricauda oceanensis sp. nov., three marine bacteria isolated from seawater. Int J Syst Evol Microbiol 2020; 70:6240-6250. [DOI: 10.1099/ijsem.0.004522] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Three Gram-stain-negative, non-motile, rod-shaped strains, designated 72T, NH166T and 40DY170T, were isolated from seawater samples of the West Pacific Ocean, South China Sea and West Pacific Ocean, respectively. The 16S rRNA gene sequence similarity results revealed that strains 72Tand NH166T were most closely related to
Muricauda antarctica
Ar-22T,
Muricauda taeanensis
JCM 17757T,
Muricauda beolgyonensis
KCTC 23501T,
Muricauda lutimaris
KCTC 22173T and
Muricauda hadalis
MT-229T with 97.2–98.0% sequence similarity. 16S rRNA gene sequence analysis also indicated that strain 40DY170T was most closely related to
Muricauda ruestringensis
DSM 13258T,
Muricauda aquimarina
JCM 11811T,
Muricauda lutimaris
KCTC 22173T and
Muricauda oceani
501str8T with 97.6–98.1% sequence similarity. The 16S rRNA gene sequence similarity values among strains 72T, NH166T and 40DY170T were 96.5–99.2%. Phylogenetic analyses indicated that three new isolates represented three novel species by forming two distinctive lineages within the genus
Muricauda
. The DNA G+C contents of strain 72T, NH166T and 40DY170T were 43.4, 43.4 and 42.4 mol%, respectively. The average nucleotide identity and in silico DNA–DNA hybridization values between strains 72T, NH166T, 40DY170T and the reference strains were 76.5–93.5% and 19.2–53.5%, respectively. The sole respiratory quinone in all strains was menaquinone-6. Their major fatty acids were iso-C17:0 3-OH, iso-C15:0 and iso-C15 : 1 G. The major polar lipids of strains 72T and NH166T were phosphatidylethanolamine, one unidentified aminolipid and two unidentified lipids. The major polar lipids of strain 40DY170T were phosphatidylglycerol, one unidentified phospholipid, one unidentified aminolipid and two unidentified lipids. On the basis of their distinct taxonomic characteristics, the three isolates represent three novel species of the genus
Muricauda
, for which the names Muricauda maritima sp. nov. (type strain 72T=KCTC 62229T=MCCC 1K03350T), Muricauda aequoris sp. nov. (NH166T=KCTC 62228T=MCCC 1K03449T) and Muricauda oceanensis sp. nov. (40DY170T=KCTC 72200T=MCCC 1K03569T) are proposed.
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Affiliation(s)
- Li-Li Guo
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Dildar Wu
- College of Life and Geographic Sciences, Kashi University, Kashi 844000, PR China
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Cong Sun
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
| | - Hong Cheng
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
| | - Xue-Wei Xu
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200030, PR China
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
| | - Min Wu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Yue-Hong Wu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200030, PR China
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24
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Xu L, Sun C, Fang C, Oren A, Xu XW. Genomic-based taxonomic classification of the family Erythrobacteraceae. Int J Syst Evol Microbiol 2020; 70:4470-4495. [PMID: 32726199 PMCID: PMC7660246 DOI: 10.1099/ijsem.0.004293] [Citation(s) in RCA: 290] [Impact Index Per Article: 72.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 06/01/2020] [Indexed: 12/22/2022] Open
Abstract
The family Erythrobacteraceae, belonging to the order Sphingomonadales, class Alphaproteobacteria, is globally distributed in various environments. Currently, this family consist of seven genera: Altererythrobacter, Croceibacterium, Croceicoccus, Erythrobacter, Erythromicrobium, Porphyrobacter and Qipengyuania. As more species are identified, the taxonomic status of the family Erythrobacteraceae should be revised at the genomic level because of its polyphyletic nature evident from 16S rRNA gene sequence analysis. Phylogenomic reconstruction based on 288 single-copy orthologous clusters led to the identification of three separate clades. Pairwise comparisons of average nucleotide identity, average amino acid identity (AAI), percentage of conserved protein and evolutionary distance indicated that AAI and evolutionary distance had the highest correlation. Thresholds for genera boundaries were proposed as 70 % and 0.4 for AAI and evolutionary distance, respectively. Based on the phylo-genomic and genomic similarity analysis, the three clades were classified into 16 genera, including 11 novel ones, for which the names Alteraurantiacibacter, Altericroceibacterium, Alteriqipengyuania, Alteripontixanthobacter, Aurantiacibacter, Paraurantiacibacter, Parerythrobacter, Parapontixanthobacter, Pelagerythrobacter, Tsuneonella and Pontixanthobacter are proposed. We reclassified all species of Erythromicrobium and Porphyrobacter as species of Erythrobacter. This study is the first genomic-based study of the family Erythrobacteraceae, and will contribute to further insights into the evolution of this family.
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Affiliation(s)
- Lin Xu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Cong Sun
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Chen Fang
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
- College of Oceanography, Hohai University, Nanjing 210000, PR China
| | - Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 9190401, Israel
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200030, PR China
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25
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Ye Y, Anwar N, Mao X, Wu S, Yan C, Zhao Z, Zhang R, Nie Y, Zhang J, Wang J, Wu M. Discovery of Three 22-Membered Macrolides by Deciphering the Streamlined Genome of Mangrove-Derived Streptomyces sp. HM190. Front Microbiol 2020; 11:1464. [PMID: 32676068 PMCID: PMC7333363 DOI: 10.3389/fmicb.2020.01464] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/04/2020] [Indexed: 11/13/2022] Open
Abstract
Strain HM190, a moderate halophile, was isolated from rhizosphere soil of the mangrove Kandelia obovata in Fugong village, China. The 16S ribosomal RNA (rRNA) gene sequence and the results of phylogenetic analysis revealed that strain HM190 belonged to the genus Streptomyces and had the highest sequence similarity of 99.79% to Streptomyces heilongjiangensis NEAU-W2T. The complete genome of strain HM190 comprised 7,762,826 bp in a linear chromosome with 71.97% G + C content. According to antiSMASH analysis, a total of 30 biosynthetic gene clusters (BGCs) were predicted to be involved in secondary metabolism, 12 of which were responsible for the production of polyketide- and non-ribosomal peptide-derived secondary metabolites. Gene cluster 5 was responsible for macrolide biosynthesis in a strain-specific 126,331-bp genomic island belonging to the left-arm region. Combined genomics–metabolomics analysis led to the discovery of three 22-membered macrolides (compounds 1–3). Their structures were elucidated by using spectroscopic techniques including high-resolution electrospray ionization mass spectroscopy (HRESIMS) and nuclear magnetic resonance (NMR). The absolute configurations of compounds 1–3 were determined by the X-ray single crystal diffraction and NMR data analysis. All three compounds displayed moderate cytotoxic activities toward tumor cell lines HepG2, A549, and HCT116.
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Affiliation(s)
- Yanghui Ye
- Ocean College, Zhejiang University, Hangzhou, China
| | - Nusratgul Anwar
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xuming Mao
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Shihua Wu
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Cen Yan
- Ocean College, Zhejiang University, Hangzhou, China
| | - Zhe Zhao
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Ran Zhang
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yanfang Nie
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jianwei Zhang
- Cardiovascular Health Department, AstraZeneca Trading Co., Ltd., Wuxi, China
| | - Jidong Wang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Science, Huzhou University, Huzhou, China
| | - Min Wu
- Ocean College, Zhejiang University, Hangzhou, China
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26
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Noureen N, Cheema MT, Anwar S, Hasnain S, Sajid I. PCR-based Screening Approach: A Rapid Method to Detect the Biosynthetic Potential of Antimicrobials in Actinobacterial Strains. Pol J Microbiol 2020; 69:1-11. [PMID: 32396716 PMCID: PMC7324861 DOI: 10.33073/pjm-2020-016] [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: 11/29/2019] [Revised: 03/19/2020] [Accepted: 03/29/2020] [Indexed: 11/28/2022] Open
Abstract
This study aimed to investigate the PCR-based screening strategy for the prediction of the antimicrobial biosynthetic potential of the selected Streptomyces strains originated from an extreme environment (Cholistan Desert, Pakistan). The biosynthetic potential was determined by using both molecular and culture-dependent screening approaches. The four biosynthetic genes clusters, including the pks-1, nrps, cyp P450 hydroxylase (cyps), and glycopeptide oxy b genes, were investigated in the selected strains by PCR amplification, sequencing, and by subsequent bioinformatics approaches. Among the 40 selected Streptomyces strains, 33 strains possessed the nrps gene, 17 strains carried the pks-1 gene, four strains were found to have the cyps gene, and none of the strain carried oxy b gene. The Streptomyces strains including NR-1, NR-10, NR-14, and NR-15 were investigated for in vitro antifungal activity against Fusarium oxysporum, Rhizoctonia solani, and Aspergillus sp. The extracts were analyzed for chemical profiling (TLC and HPLC-UV), and a unique pattern of secondary metabolites was observed. The selected strains exhibited pronounced antifungal activity against the fungal test strains with the zone of inhibition up to 17, 18, and 19 mm, respectively. The study depicts that gene-based screening can be successfully applied to identify potentially bioactive strains by usin a single screening process. This PCR-based approach is rapid and can be used for sorting out and selecting the potential candidate among actinobacterial culture collections. Such a preselection or strain prioritization consequently decreases the time and efforts required for selecting the potential bioactive strain, which then can be subjected to the detailed chemical analysis.
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Affiliation(s)
- Naila Noureen
- Department of Microbiology and Molecular Genetics , University of the Punjab , Quid-i-Azam Campus , Lahore , Pakistan
| | - Mohsin Tassawar Cheema
- Department of Microbiology and Molecular Genetics , University of the Punjab , Quid-i-Azam Campus , Lahore , Pakistan
| | - Sumaira Anwar
- Department of Microbiology and Molecular Genetics , University of the Punjab , Quid-i-Azam Campus , Lahore , Pakistan
| | - Shahida Hasnain
- Department of Microbiology and Molecular Genetics , University of the Punjab , Quid-i-Azam Campus , Lahore , Pakistan
| | - Imran Sajid
- Department of Microbiology and Molecular Genetics , University of the Punjab , Quid-i-Azam Campus , Lahore , Pakistan
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