Research Article: Sequence-Dependent T:G Base Pair Opening in DNA Double Helix Bound by Cren7, a Chromatin Protein Conserved among Crenarchaea

Date Published: September 29, 2016

Publisher: Public Library of Science

Author(s): Lei Tian, Zhenfeng Zhang, Hanqian Wang, Mohan Zhao, Yuhui Dong, Yong Gong, Fenfei Leng.


T:G base pair arising from spontaneous deamination of 5mC or polymerase errors is a great challenge for DNA repair of hyperthermophilic archaea, especially Crenarchaea. Most strains in this phylum lack the protein homologues responsible for the recognition of the mismatch in the DNA repair pathways. To investigate whether Cren7, a highly conserved chromatin protein in Crenarchaea, serves a role in the repair of T:G mispairs, the crystal structures of Cren7-GTAATTGC and Cren7-GTGATCGC complexes were solved at 2.0 Å and 2.1 Å. In our structures, binding of Cren7 to the AT-rich DNA duplex (GTAATTGC) induces opening of T2:G15 but not T10:G7 base pair. By contrast, both T:G mispairs in the GC-rich DNA duplex (GTGATCGC) retain the classic wobble type. Structural analysis also showed DNA helical changes of GTAATTGC, especially in the steps around the open T:G base pair, as compared to GTGATCGC or the matched DNAs. Surface plasmon resonance assays revealed a 4-fold lower binding affinity of Cren7 for GTAATTGC than that for GTGATCGC, which was dominantly contributed by the decrease of association rate. These results suggested that binding of Cren7 to DNA leads to T:G mispair opening in a sequence dependent manner, and therefore propose the potential roles of Cren7 in DNA repair.

Partial Text

Thymine-guanine (T:G) and uracil-guanine (U:G) base pairs are generated in DNA either by the spontaneous hydrolytic deamination of 5-methyl cytosine (5mC) and cytosine (C) respectively [1] or by misincorporation during DNA replication[2]. Deamination of pyrimidines occurs approximately 200–300 events per cell per day, an about 50-fold higher rate than that for purines[3]. These mismatches cause C to T transition mutations in 50% of the progeny DNA if not repaired upon DNA replication[4]. There seems to be no problems in the case of the U:G mispair, since uracil, which is not a natural DNA base, is efficiently removed in a base-excision repair pathway initiated by uracil DNA-glycosylase (UDG)[5,6]. T:G mispair presents a greater challenge, however, as the thymine arising from deamination of 5mC is indistinguishable from other thymines in the genomic DNA.

The maintenance of genomic integrity is a crucial task for all living cells, as many environmental factors contribute to DNA damage. Of the environmental extremes accommodated by Crenarchaeota, high temperature has particular significance, as it cannot be excluded from the interior of microbial cells. High temperature directly leads to more rapid reactions such as hydrolytic deamination of nucleotide bases, which generate U:G or T:G base pairs. Despite the lack of the crucial protein homologues in MMR, NER or BER pathways, the rate of mutation in Sulfolobus, a model strain of Crenarchaea, is not higher than that for Escherichia coli [29], indicating that DNA damage is repaired efficiently.