title: Sulfolobus acidocaldarius UDG Can Remove dU from the RNA Backbone: Insight into the Specific Recognition of Uracil Linked with Deoxyribose.
abstract: Sulfolobus acidocaldariusencodes family 4 and 5 uracil-DNA glycosylase (UDG). Two recombinantS. acidocaldariusUDGs (SacUDG) were prepared and biochemically characterized using oligonucleotides carrying a deaminated base. Both SacUDGs can remove deoxyuracil (dU) base from both double-stranded DNA and single-stranded DNA. Interestingly, they can remove U linked with deoxyribose from single-stranded RNA backbone, suggesting that the riboses on the backbone have less effect on the recognition of dU and hydrolysis of the C-N glycosidic bond. However, the removal of rU from DNA backbone is inefficient, suggesting strong steric hindrance comes from the 2' hydroxyl of ribose linked to uracil. Both SacUDGs cannot remove 2,2'-anhydro uridine, hypoxanthine, and 7-deazaxanthine from single-stranded DNA and single-stranded DNA. Compared with the family 2 MUG, other family UDGs have an extra N-terminal structure consisting of about 50 residues. Removal of the 46 N-terminal residues of family 5 SacUDG resulted in only a 40% decrease in activity, indicating that the [4Fe-4S] cluster and truncated secondary structure are not the key elements in hydrolyzing the glycosidic bond. Combining our biochemical and structural results with those of other groups, we discussed the UDGs' catalytic mechanism and the possible repair reactions of deaminated bases in prokaryotes.
authors.affiliation: State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China. 13166228531@163.com.
authors.forename: Gang-Shun
authors.initials: GS
authors.lastname: Yi
authors.affiliation: State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China. www1037554814@sjtu.edu.cn.
authors.forename: Wei-Wei
authors.initials: WW
authors.lastname: Wang
authors.affiliation: Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA. wgc@clemson.edu.
authors.forename: Wei-Guo
authors.initials: WG
authors.lastname: Cao
authors.affiliation: State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China. fengpingw@sjtu.edu.cn.|State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, Shanghai 200240, China. fengpingw@sjtu.edu.cn.
authors.forename: Feng-Ping
authors.initials: FP
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China. xpliu@sjtu.edu.cn.|State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, Shanghai 200240, China. xpliu@sjtu.edu.cn.
authors.forename: Xi-Peng
authors.initials: XP
authors.lastname: Liu
keywords: RNA backbone; S. acidocaldarius; [4Fe-4S] cluster; uracil-DNA glycosylase