How an RNA Ligase Discriminates RNA versus DNA Damage

Abstract

T4 RNA ligase 2 (Rnl2) exemplifies a family of RNA-joining enzymes that includes protozoan RNA-editing ligases. Rnl2 efficiently seals 3′-OH/5′-PO 4 RNA nicks in either a duplex RNA or an RNA:DNA hybrid but cannot seal DNA nicks. RNA specificity arises from a requirement for at least two ribonucleotides immediately flanking the 3′-OH of the nick; the rest of the nicked duplex can be replaced by DNA. The terminal 2′-OH at the nick is important for the attack of the 3′-OH on the 5′-adenylated strand to form a phosphodiester, but dispensable for nick recognition and adenylylation of the 5′-PO 4 strand. The penultimate 2′-OH is important for nick recognition. Stable binding of Rnl2 at a nick depends on contacts to both the N-terminal adenylyltransferase domain and its signature C-terminal domain. Nick sensing also requires adenylylation of Rnl2. These results provide insights to the evolution of nucleic acid repair systems.