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Exploring the roles of ribosomal peptides in prokaryote-phage interactions through deep learning-enabled metagenome mining.
- Source :
- Microbiome; 5/24/2024, Vol. 12 Issue 1, p1-24, 24p
- Publication Year :
- 2024
-
Abstract
- Background: Microbial secondary metabolites play a crucial role in the intricate interactions within the natural environment. Among these metabolites, ribosomally synthesized and post-translationally modified peptides (RiPPs) are becoming a promising source of therapeutic agents due to their structural diversity and functional versatility. However, their biosynthetic capacity and ecological functions remain largely underexplored. Results: Here, we aim to explore the biosynthetic profile of RiPPs and their potential roles in the interactions between microbes and viruses in the ocean, which encompasses a vast diversity of unique biomes that are rich in interactions and remains chemically underexplored. We first developed TrRiPP to identify RiPPs from ocean metagenomes, a deep learning method that detects RiPP precursors in a hallmark gene-independent manner to overcome the limitations of classic methods in processing highly fragmented metagenomic data. Applying this method to metagenomes from the global ocean microbiome, we uncover a diverse array of previously uncharacterized putative RiPP families with great novelty and diversity. Through correlation analysis based on metatranscriptomic data, we observed a high prevalence of antiphage defense-related and phage-related protein families that were co-expressed with RiPP families. Based on this putative association between RiPPs and phage infection, we constructed an Ocean Virus Database (OVD) and established a RiPP-involving host-phage interaction network through host prediction and co-expression analysis, revealing complex connectivities linking RiPP-encoding prokaryotes, RiPP families, viral protein families, and phages. These findings highlight the potential of RiPP families involved in prokaryote-phage interactions and coevolution, providing insights into their ecological functions in the ocean microbiome. Conclusions: This study provides a systematic investigation of the biosynthetic potential of RiPPs from the ocean microbiome at a global scale, shedding light on the essential insights into the ecological functions of RiPPs in prokaryote-phage interactions through the integration of deep learning approaches, metatranscriptomic data, and host-phage connectivity. This study serves as a valuable example of exploring the ecological functions of bacterial secondary metabolites, particularly their associations with unexplored microbial interactions. CSrTVep6AzTb_yem78LPYE Video Abstract [ABSTRACT FROM AUTHOR]
- Subjects :
- BACTERIAL metabolites
MICROBIAL metabolites
METABOLITES
PEPTIDES
VIRAL proteins
Subjects
Details
- Language :
- English
- ISSN :
- 20492618
- Volume :
- 12
- Issue :
- 1
- Database :
- Complementary Index
- Journal :
- Microbiome
- Publication Type :
- Academic Journal
- Accession number :
- 177465920
- Full Text :
- https://doi.org/10.1186/s40168-024-01807-y