DNA binding modes influence Rap1 activity in the regulation of telomere length and MRX functions at DNA ends

Abstract

The cellular response to DNA double-strand breaks (DSBs) is initiated by the Mre11–Rad50–Xrs2 (MRX) complex that has structural and catalytic functions. MRX association at DSBs is counteracted by Rif2, which is known to interact with Rap1 that binds telomeric DNA through two tandem Myb-like domains. Whether and how Rap1 acts at DSBs is unknown. Here we show that Rif2 inhibits MRX association to DSBs in a manner dependent on Rap1, which binds to DSBs and promotes Rif2 association to them. Rap1 in turn can negatively regulate MRX function at DNA ends also independently of Rif2. In fact, a characterization of Rap1 mutant variants shows that Rap1 binding to DNA through both Myb-like domains results in formation of Rap1-DNA complexes that control MRX functions at both DSBs and telomeres primarily through Rif2. By contrast, Rap1 binding to DNA through a single Myb-like domain results in formation of high stoichiometry complexes that act at DNA ends mostly in a Rif2-independent manner. Altogether these findings indicate that the DNA binding modes of Rap1 influence its functional properties, thus highlighting the structural plasticity of this protein.

The base flipping of A-DNA—a molecular dynamic simulation study

“…All MD simulations were performed using NAMD 2.14 multicore CUDA package, together with the Colvars module [23,24] , while trajectories were visualized and analyzed using VMD1.9.3 [25] , and the DNA conformational analyses were performed with Curves + [26] . CHARMM36 force eld was consistently used, because of its reliability for both B-DNA and A-DNA [27][28][29] .…”

Telomere maintenance in African trypanosomes

“…Telomere length is heavily regulated by telomere proteins (Kim et al, 1999;Smogorzewska et al, 2000;Li and de Lange, 2003;Hockemeyer et al, 2005;Mason and Skordalakes, 2010;Takai et al, 2016;Aramburu et al, 2020;Bonetti et al, 2020). In mammalian cells, the Shelterin and CST complexes are key proteins associated with the telomere and play essential roles in telomere maintenance (Figure 2) (Liu et al, 2004a;de Lange, 2005;Giraud-Panis et al, 2010a;Lim and Cech, 2021).…”

Dynamic Properties of the DNA Damage Response Mre11/Rad50 Complex

“…In fact, whereas Sae2 would be required to stabilize the cutting state, Rif2 binding seems to be incompatible with the transition into the cutting state [62,63]. The Rif2 partner at telomeres, Rap1, is also present at the DNA DSB and can influence MRX activity independently from Rif2 by a mechanism that is still uncharacterized [64]. Due to the different relative abundances of these two alternative partners at DSB DNA damage sites and at the telomeres, they would be good candidates to direct the distinct behavior of MRX complexes in these genomic loci.…”