Two Archaeal RecJ Nucleases from Methanocaldococcus jannaschii Show Reverse Hydrolysis Polarity: Implication to Their Unique Function in Archaea

Gang-Shun Yi; Yang Song; Wei-Wei Wang; Jia-Nan Chen; Wei Deng; Weiguo Cao; Feng-Ping Wang; Xiang Xiao; Xi-Peng Liu

doi:10.3390/genes8090211

Two Archaeal RecJ Nucleases from Methanocaldococcus jannaschii Show Reverse Hydrolysis Polarity: Implication to Their Unique Function in Archaea

Genes (Basel). 2017 Aug 24;8(9):211. doi: 10.3390/genes8090211.

Authors

Gang-Shun Yi¹, Yang Song², Wei-Wei Wang³, Jia-Nan Chen⁴, Wei Deng⁵, Weiguo Cao⁶, Feng-Ping Wang^{7

8}, Xiang Xiao^{9

10}, Xi-Peng Liu^{11

12}

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. 13166228531@163.com.
² National Center for Protein Science, Chinese Academy of Sciences, Shanghai 201204, China. songyang@sibcb.ac.cn.
³ State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China. www1037554814@sjtu.edu.cn.
⁴ State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China. 14330101150369@sjtu.edu.cn.
⁵ National Center for Protein Science, Chinese Academy of Sciences, Shanghai 201204, China. dengwei@sibcb.ac.cn.
⁶ Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA. wgc@clemson.edu.
⁷ State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China. fengpingw@sjtu.edu.cn.
⁸ 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. fengpingw@sjtu.edu.cn.
⁹ State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China. xoxiang@sjtu.edu.cn.
¹⁰ 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. xoxiang@sjtu.edu.cn.
¹¹ State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China. xpliu@sjtu.edu.cn.
¹² 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. xpliu@sjtu.edu.cn.

Abstract

Bacterial nuclease RecJ, which exists in almost all bacterial species, specifically degrades single-stranded (ss) DNA in the 5' to 3' direction. Some archaeal phyla, except Crenarchaea, also encode RecJ homologs. Compared with bacterial RecJ, archaeal RecJ exhibits a largely different amino acid sequence and domain organization. Archaeal RecJs from Thermococcus kodakarensis and Pyrococcus furiosus show 5'→3' exonuclease activity on ssDNA. Interestingly, more than one RecJ exists in some Euryarchaeota classes, such as Methanomicrobia, Methanococci, Methanomicrobia, Methanobacteria, and Archaeoglobi. Here we report the biochemical characterization of two RecJs from Methanocaldococcus jannaschii, the long RecJ1 (MJ0977) and short RecJ2 (MJ0831) to understand their enzymatic properties. RecJ1 is a 5'→3' exonuclease with a preference to ssDNA; however, RecJ2 is a 3'→5' exonuclease with a preference to ssRNA. The 5' terminal phosphate promotes RecJ1 activity, but the 3' terminal phosphate inhibits RecJ2 nuclease. Go-Ichi-Ni-San (GINS) complex does not interact with two RecJs and does not promote their nuclease activities. Finally, we discuss the diversity, function, and molecular evolution of RecJ in archaeal taxonomy. Our analyses provide insight into the function and evolution of conserved archaeal RecJ/eukaryotic Cdc45 protein.

Keywords: Cdc45-MCM-GINS; GINS; archaeal RecJ; interaction; nuclease.