LucaPCycle: Illuminating microbial phosphorus cycling in deep-sea cold seep sediments using protein language models.

ABSTRACT: Phosphorus is essential for life and critically influences marine productivity. Despite geochemical evidence of active phosphorus cycling in deep-sea cold seeps, the microbial processes involved remain poorly understood. Traditional sequence-based searches often fail to detect proteins with remote homology. To address this, we developed a deep learning model, LucaPCycle, integrating raw sequences and contextual embeddings based on the protein language model ESM2-3B. LucaPCycle identified 5241 phosphorus-cycling protein families from global cold seep gene and genome catalogs, substantially enhancing our understanding of their diversity, ecology, and function. Among previously unannotated sequences, we discovered three alkaline phosphatase families that feature unique domain organizations an

SUBMITTER: Zhang C 

PROVIDER: S-EPMC12106651 | biostudies-literature | 2025 May

REPOSITORIES: biostudies-literature