The exoribonuclease activity of TREX1 in RNA and DNA/RNA hybrid metabolism

Kuan-Wei Huang (黃冠偉)1,2, Chia-Yun Wu1,2, Shu-Ing Toh1,2, Tung-Chang Liu1,2, Chun-I Tu1,2, Yin-Hsin Lin2, An-Ju Cheng1, Jhih-Wei Chu (朱智瑋)1,2,3, Yu-Yuan Hsiao (蕭育源)1,2,3,*

1 Department of Biological Science and Technology, National Yang Ming Chiao Tung University.

2 Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University.

3 Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University.

TREX1 is a DNase belonging to the DEDDh exonuclease family and has been confirmed as RNase by in vitro study recently. Dysfunctional TREX1 leads to DNA/RNA hybrids accumulation in the cytoplasm and triggers the immune response, and TREX1-inactivated cells infected by RNA virus produced more IFN-β than normal cells. All evidence suggests that TREX1 involves processing cytoplasmic RNA or DNA/RNA hybrids, but the detailed mechanism remains unclear. Therefore, we aim to reveal how TREX1 works on RNA and DNA/RNA hybrids by biochemical and structural approaches. Our study indicates that TREX1 can work on ssRNA and DNA/RNA hybrids without sequence preference but cannot act on dsRNA. Our TREX1-NMP complex shares a similar overall structure as TREX1-dNMP complexes, only with an additional hydrogen bond between 2'-OH and TREX1, suggesting that TREX1 degrades RNA similar to degrading DNA. However, our activity shows TREX1 has higher activities on DNA than RNA, which may cause by the difference in the substrate-binding ability or product release rates. Our further structural and biochemical study identified that the main reason for the difference is the binding ability. In conclusion, TREX1 can degrade RNA and DNA/RNA hybrids without sequence preference but with structural selectivity. TREX1 has different activities in digesting DNA and RNA caused by the different binding affinity against DNA or RNA substrates. Our study provides a molecular basis for TREX1 metabolizing ssRNA and DNA/RNA hybrids.