NanoRNase from Aeropyrum pernix shows nuclease activity on ssDNA and ssRNA

Yong-Jie Deng; Lei Feng; Huan Zhou; Xiang Xiao; Feng-Ping Wang; Xi-Peng Liu

doi:10.1016/j.dnarep.2018.03.005

NanoRNase from Aeropyrum pernix shows nuclease activity on ssDNA and ssRNA

DNA Repair (Amst). 2018 May:65:54-63. doi: 10.1016/j.dnarep.2018.03.005. Epub 2018 Mar 26.

Authors

Yong-Jie Deng¹, Lei Feng¹, Huan Zhou², Xiang Xiao³, Feng-Ping Wang³, Xi-Peng Liu⁴

Affiliations

¹ State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China.
² Shanghai Institute of Applied Physics, Chinese Academy of Sciences, No. 239 Zhangheng Road, Shanghai 201204, China.
³ State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China; State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China.
⁴ State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China; State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China. Electronic address: xpliu@sjtu.edu.cn.

PMID: 29609115
DOI: 10.1016/j.dnarep.2018.03.005

Abstract

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 prefers ssDNA, including short nanoDNA, and degrades nanoRNA with lower efficiency. The 3'-DNA backbone was found to be required for efficiently hydrolyzing the phosphodiester bonds. In addition, Ape0124 also degrads 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.

Keywords: Aeropyrum pernix; Archaea; NanoRNA; nanoRNase; pApase; ssDNA.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Aeropyrum / enzymology*
Archaeal Proteins / metabolism
DNA, Single-Stranded / metabolism*
Deoxyribonucleases / metabolism*
RNA / metabolism*
Ribonucleases / metabolism*
Substrate Specificity

Substances

Archaeal Proteins
DNA, Single-Stranded
RNA
Deoxyribonucleases
Ribonucleases