State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China.
Shanghai Institute of Applied Physics, Chinese Academy of Sciences, No. 239 Zhangheng Road, Shanghai 201204, China.
DNA Repair (Amst). 2018 May;65:54-63. doi: 10.1016/j.dnarep.2018.03.005. Epub 2018 Mar 26.
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 Mn. 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.
在细胞中，通过各种核酸酶降解 DNA 和 RNA 非常重要。这些过程受到严格的控制和调节，以维持 DNA 完整性并使各种 RNA 成熟或循环。NanoRNase (Nrn) 是一种 3'-核酸外切酶，可特异性降解短于 5 个核苷酸的 nanoRNA。已经在细菌中鉴定和表征了几种 Nrn，主要在厚壁菌门中。古菌通常在极端环境中生长，其 DNA/RNA 可能受到更多的损伤，因此 DNA 修复和受损 RNA 的回收在古菌中非常重要。尚未有关于古菌中 Nrn 的鉴定和表征的报道。嗜热菌 Aeropyrum pernix 编码三种潜在的 Nrn：NrnA (Ape1437)、NrnB (Ape0124) 和一种 Nrn 样蛋白 Ape2190。生化特性表明，只有 Ape0124 能够在 Mn 存在的情况下从 3'-末端降解 ssDNA 和 ssRNA。有趣的是，与细菌 Nrn 不同，Ape0124 更喜欢 ssDNA，包括短的 nanoDNA，并以较低的效率降解 nanoRNA。发现 3'-DNA 骨架对于有效地水解磷酸二酯键是必需的。此外，Ape0124 还可以降解双链 DNA 的 3'-突出端。有趣的是，Ape0124 可以将 pAp 水解为 AMP，这是细菌 NrnA 的特征，而不是 NrnB。我们的结果表明，Ape0124 是一种新型 Nrn，具有细菌 NrnA 和 NrnB 的组合底物特征。
