Deep-sea ecosystems harbor extraordinary viral diversity, yet their potential as reservoirs of catalytic RNAs remains unexplored. Here, we systematically analyzed RNA viromes from 291 globally distributed deep-sea sediment samples, spanning seven distinct ecosystems across three oceans, and identified 1,305 distinct hammerhead ribozymes (485 type I, 561 type II, and 259 type III). Functional characterization revealed that ribozyme DP163 cleaved the HIV-1 pol mRNA, reducing viral copies and infection. Similarly, ribozyme DP162 suppressed HSV-1 infection by targeting the viral ICP4 gene, achieving ICP4 knockdown and enhancing antiviral immunity. Engineered variants of DP162 and DP163 demonstrated gene silencing efficiency comparable to siRNA. Our findings establish deep-sea RNA viruses as an untapped reservoir of natural ribozymes with dual functionality: intrinsic antiviral properties through immune activation and programmable gene silencing capacity, providing novel catalytic RNA scaffolds for therapeutic development and synthetic biology applications.
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