Both OB Folds of Single-Stranded DNA-Binding Protein Are Essential for Its ssDNA Binding Activity in Deinococcus radiodurans

Xiaoting      Hua; Chao      Wang; Ye      Zhao; Hu      Wang; Lifen      Huang; Guangzhi      Xu; Mingfeng      Li; Yuan      Wang; Bing      Tian; Yuejin      Hua

Abstract

The single-stranded DNA-binding proteins are crucial in all kinds of DNA metabolic processes. Deinococcus SSB-like proteins are homodimers in nature and contain two OB folds per monomer, in contrast to other bacterial SSB proteins that are functionally active as homotetramers. We generated four truncated variants of DraSSB protein, based on its crystal structure (PDB code: 1SE8). Gel filtration showed that DraSSB, DSCT (lack C-tail) and DSCC (lack C-tail and C-terminal OB) were mostly homodimers, and DSN (lack N-terminal OB) and DSNC (lack N-terminal OB and connector) were mostly monomers. The gel filtration supported the hypothesis that the N-terminal domain played a predominant role in dimerisation. Biochemical characterization was used to determine the role of each OB fold in DNA binding, by EMSA and FRET. EMSA results suggested that binding of DraSSB to ssDNA substrate needed both N- and C-terminal OB-folds, and also their interaction to achieve optimum DNA binding. DSCT might possess two ssDNA binding modes compared with DraSSB. The C-terminal tail was not essential for binding of ssDNA substrates. The C-terminal OB-fold had the ability to bind to the bubble structure. Furthermore, the FRET results for DSCT verified the hypothesis that DSCT showed two different binding modes for ssDNA, similarly to EcoSSB.

Keywords: Deinococcus, Single-Strand Binding Protein, OB Fold, Subfunctionalization, DNA Repair

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