In silico identification of silent primycin biosynthetic gene clusters within the family Pseudonocardiaceae
In the global effort to discover or design new effective antibiotics to fight infectious diseases, the increasingly available multi-omics data with novel bioinformatics tools open up new horizons for the exploration of the genetic potential of bacteria to synthesize bioactive secondary metabolites....
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Elsevier
2025-01-01
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S240584402417096X |
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| author | Márk Kovács-Valasek Csaba Fekete Andrea Kovács-Valasek |
| author_facet | Márk Kovács-Valasek Csaba Fekete Andrea Kovács-Valasek |
| author_sort | Márk Kovács-Valasek |
| collection | DOAJ |
| description | In the global effort to discover or design new effective antibiotics to fight infectious diseases, the increasingly available multi-omics data with novel bioinformatics tools open up new horizons for the exploration of the genetic potential of bacteria to synthesize bioactive secondary metabolites. Rare actinomycetes are a prolific source of structurally diverse secondary metabolites that exhibit remarkable clinical and industrial importance. Recently several excellent genome mining tools have been available for identifying biosynthetic gene clusters, however in cases of poor-quality sequences and inappropriate genome assembly, these tools are not always able to identify the corresponding gene clusters. In this context, based on the previously characterized primycin biosynthetic gene cluster (PBGC) of the Saccharomonospora azurea SZMC 14600 strain an extended genome mining analysis was performed to advance the industrial application of unexplored taxa outside the Saccharomonospora genus. Further improvement of S. azurea PBGC revealed 28 clustered genes including core sequences for type I polyketide synthase. Application of PBGC core elements and targeted genome mining workflows revealed three species from the family Pseudonocardiaceae that can be considered potential candidates for primycin production, despite the fact that the discovered biosynthetic gene clusters were silent under the currently applied laboratory-culture condition. The findings presented here demonstrate the potential of an in silico toolkit and draw attention to the importance of awakening the dormant biosynthetic potential. |
| format | Article |
| id | doaj-art-1ffba9332d614e449f081d2f6417e27d |
| institution | Kabale University |
| issn | 2405-8440 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Heliyon |
| spelling | doaj-art-1ffba9332d614e449f081d2f6417e27d2025-01-17T04:50:04ZengElsevierHeliyon2405-84402025-01-01111e41065In silico identification of silent primycin biosynthetic gene clusters within the family PseudonocardiaceaeMárk Kovács-Valasek0Csaba Fekete1Andrea Kovács-Valasek2PannonPharma Pharmaceutical Ltd., H-7720, Pécsvárad, Hungary; Institute of Biology, Faculty of Sciences, University of Pécs, H-7624, Pécs, HungaryInstitute of Biology, Faculty of Sciences, University of Pécs, H-7624, Pécs, HungaryInstitute of Biology, Faculty of Sciences, University of Pécs, H-7624, Pécs, Hungary; Corresponding author.In the global effort to discover or design new effective antibiotics to fight infectious diseases, the increasingly available multi-omics data with novel bioinformatics tools open up new horizons for the exploration of the genetic potential of bacteria to synthesize bioactive secondary metabolites. Rare actinomycetes are a prolific source of structurally diverse secondary metabolites that exhibit remarkable clinical and industrial importance. Recently several excellent genome mining tools have been available for identifying biosynthetic gene clusters, however in cases of poor-quality sequences and inappropriate genome assembly, these tools are not always able to identify the corresponding gene clusters. In this context, based on the previously characterized primycin biosynthetic gene cluster (PBGC) of the Saccharomonospora azurea SZMC 14600 strain an extended genome mining analysis was performed to advance the industrial application of unexplored taxa outside the Saccharomonospora genus. Further improvement of S. azurea PBGC revealed 28 clustered genes including core sequences for type I polyketide synthase. Application of PBGC core elements and targeted genome mining workflows revealed three species from the family Pseudonocardiaceae that can be considered potential candidates for primycin production, despite the fact that the discovered biosynthetic gene clusters were silent under the currently applied laboratory-culture condition. The findings presented here demonstrate the potential of an in silico toolkit and draw attention to the importance of awakening the dormant biosynthetic potential.http://www.sciencedirect.com/science/article/pii/S240584402417096XPrimycin biosynthetic gene cluster - PseudonocardiaceaeStructural genomics |
| spellingShingle | Márk Kovács-Valasek Csaba Fekete Andrea Kovács-Valasek In silico identification of silent primycin biosynthetic gene clusters within the family Pseudonocardiaceae Heliyon Primycin biosynthetic gene cluster - Pseudonocardiaceae Structural genomics |
| title | In silico identification of silent primycin biosynthetic gene clusters within the family Pseudonocardiaceae |
| title_full | In silico identification of silent primycin biosynthetic gene clusters within the family Pseudonocardiaceae |
| title_fullStr | In silico identification of silent primycin biosynthetic gene clusters within the family Pseudonocardiaceae |
| title_full_unstemmed | In silico identification of silent primycin biosynthetic gene clusters within the family Pseudonocardiaceae |
| title_short | In silico identification of silent primycin biosynthetic gene clusters within the family Pseudonocardiaceae |
| title_sort | in silico identification of silent primycin biosynthetic gene clusters within the family pseudonocardiaceae |
| topic | Primycin biosynthetic gene cluster - Pseudonocardiaceae Structural genomics |
| url | http://www.sciencedirect.com/science/article/pii/S240584402417096X |
| work_keys_str_mv | AT markkovacsvalasek insilicoidentificationofsilentprimycinbiosyntheticgeneclusterswithinthefamilypseudonocardiaceae AT csabafekete insilicoidentificationofsilentprimycinbiosyntheticgeneclusterswithinthefamilypseudonocardiaceae AT andreakovacsvalasek insilicoidentificationofsilentprimycinbiosyntheticgeneclusterswithinthefamilypseudonocardiaceae |