Species-specificity of the secondary biosynthetic potential in Bacillus
IntroductionAlthough 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 sig...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-10-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2023.1271418/full |
| _version_ | 1797653105917034496 |
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| author | Qun-Jian Yin Ti-Ti Ying Zhen-Yi Zhou Gang-Ao Hu Cai-Ling Yang Yi Hua Hong Wang Bin Wei |
| author_facet | Qun-Jian Yin Ti-Ti Ying Zhen-Yi Zhou Gang-Ao Hu Cai-Ling Yang Yi Hua Hong Wang Bin Wei |
| author_sort | Qun-Jian Yin |
| collection | DOAJ |
| description | IntroductionAlthough 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.MethodsIn 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.ResultsOur 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.ConclusionThis 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. |
| first_indexed | 2024-03-11T16:39:43Z |
| format | Article |
| id | doaj.art-e875c145ea304b849deaca496873fb3b |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-03-11T16:39:43Z |
| publishDate | 2023-10-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-e875c145ea304b849deaca496873fb3b2023-10-23T09:28:18ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2023-10-011410.3389/fmicb.2023.12714181271418Species-specificity of the secondary biosynthetic potential in BacillusQun-Jian Yin0Ti-Ti Ying1Zhen-Yi Zhou2Gang-Ao Hu3Cai-Ling Yang4Yi Hua5Hong Wang6Bin Wei7Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai, ChinaCollege 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, ChinaCollege 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, ChinaCollege 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, ChinaCollege 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, ChinaCollege 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, ChinaCollege 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, ChinaCollege 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, ChinaIntroductionAlthough 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.MethodsIn 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.ResultsOur 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.ConclusionThis 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.https://www.frontiersin.org/articles/10.3389/fmicb.2023.1271418/fullBacillusgenome miningspecies-specificitybiosynthetic potentialnatural products |
| spellingShingle | Qun-Jian Yin Ti-Ti Ying Zhen-Yi Zhou Gang-Ao Hu Cai-Ling Yang Yi Hua Hong Wang Bin Wei Species-specificity of the secondary biosynthetic potential in Bacillus Frontiers in Microbiology Bacillus genome mining species-specificity biosynthetic potential natural products |
| title | Species-specificity of the secondary biosynthetic potential in Bacillus |
| title_full | Species-specificity of the secondary biosynthetic potential in Bacillus |
| title_fullStr | Species-specificity of the secondary biosynthetic potential in Bacillus |
| title_full_unstemmed | Species-specificity of the secondary biosynthetic potential in Bacillus |
| title_short | Species-specificity of the secondary biosynthetic potential in Bacillus |
| title_sort | species specificity of the secondary biosynthetic potential in bacillus |
| topic | Bacillus genome mining species-specificity biosynthetic potential natural products |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2023.1271418/full |
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