NanoRNase from Aeropyrum pernix shows nuclease activity on ssDNA and ssRNA

Publication date: Available online 26 March 2018
Source:DNA Repair
Author(s): Yong-Jie Deng, Lei Feng, Huan Zhou, Xiang Xiao, Feng-Ping Wang, Xi-Peng Liu
In cells, degrading DNA and RNA by various nucleases is very important. These processes are strictly controlled and regulated to maintain DNA integrity and to mature or recycle various RNAs. NanoRNase (Nrn) is a 3′-exonuclease that specifically degrades nanoRNAs shorter than 5 nucleotides. Several Nrns have been identified and characterized in bacteria, mainly in Firmicutes. Archaea often grow in extreme environments and might be subjected to more damage to DNA/RNA, so DNA repair and recycling of damaged RNA are very important in archaea. There is no report on the identification and characterization of Nrn in archaea. Aeropyrum pernix encodes three potential Nrns: NrnA (Ape1437), NrnB (Ape0124), and an Nrn-like protein Ape2190. Biochemical characterization showed that only Ape0124 could degrade ssDNA and ssRNA from the 3′-end in the presence of Mn²⁺. Interestingly, unlike bacterial Nrns, Ape0124 preferred to ssDNA, including short nanoDNA, while degraded nanoRNA in lower efficiency. The 3′-DNA backbone was required for efficiently hydrolyzing the phosphodiester bonds. In addition, Ape0124 also degraded the 3′-overhang of double-stranded DNA. Interestingly, Ape0124 could hydrolyze pAp into AMP, which is a feature of bacterial NrnA, not NrnB. Our results indicate that Ape0124 is a novel Nrn with a combined substrate profile of bacterial NrnA and NrnB.



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