Structural insights into RNase T in RNA maturation and DNA repair

Abstract

RNA maturation relies on various exonucleases to remove nucleotides successively from the 5′‐ or 3′‐end of nucleic acids. However, little is known regarding the molecular basis for substrate selection and cleavage preference of exonucleases. Here, we show how RNase T makes the final 3′‐end trimming to generate the mature ribosomal and transfer RNA with a precise 3′‐end by biochemical and structural approaches. Our crystal structural analyses on various RNase T‐DNA complexes show that RNase T dimer has an ideal architecture for binding a duplex with a short 3′ overhang to produce a digestion product of a duplex with 1 to 4 nucleotide overhangs depending on the sequence and structure of the substrates. Our results reveal the general principles for the final trimming step made by RNase T in the maturation of stable RNA. We also found that RNase T participates in trimming of structural intermediate DNA during DNA repair. The crystal structures of RNase T bound with a bubble and a Y‐structure DNA further demonstrate how RNase T binds and trims these structural DNA. These studies thus provide molecular insights into the nucleic acid 3′‐end trimming mechanism by RNase T during RNA maturation and DNA repair. These results can be extrapolated to the thousands of members of the RNase T superfamily of exonucleases, some of which are linked to human diseases.