Mesoscale conformational changes in the DNA-repair complex Rad50/Mre11/Nbs1 upon binding DNA

Abstract

The human Rad50/Mre11/Nbs1 complex (hR/M/N) functions as an essential guardian of genome integrity by directing the proper processing of DNA ends, including DNA breaks1. This biological function results from its ability to tether broken DNA molecules2,3. hR/M/N's dynamic molecular architecture consists of a globular DNA-binding domain from which two 50-nm-long coiled coils protrude. The coiled coils are flexible4 and their apices can self-associate5. The flexibility of the coiled coils allows their apices to adopt an orientation favourable for interaction. However, this also allows interaction between the tips of two coiled coils within the same complex, which competes with and frustrates the intercomplex interaction required for DNA tethering. Here we show that the dynamic architecture of hR/M/N is markedly affected by DNA binding. DNA binding by the hR/M/N globular domain leads to parallel orientation of the coiled coils; this prevents intracomplex interactions and favours intercomplex associations needed for DNA tethering. The hR/M/N complex thus is an example of a biological nanomachine in which binding to its ligand, in this case DNA, affects the functional conformation of a domain located 50 nm distant.

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Figure 1: Time-resolved high-resolution AFM images of the hR/M complex in buffer.
Figure 2: Effect of nucleotide cofactor binding on the orientation of hR/M coiled coils.
Figure 3: hR/M binding to DNA induces a parallel alignment of the coiled coils.
Figure 4: Mesoscale conformational change in hR/M/N upon DNA binding and its implications for DNA-end tethering.

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Acknowledgements

We thank T. Paull for the gift of the baculoviruses producing hRad50, hMre11 and hNbs1, and R. Seidel for useful discussions. F.M.-H. is supported by a postdoctoral fellowship from La Fundación Ramón Areces. M.d.J. is supported by an EUR fellowship from the Erasmus MC. This project is supported in part by a grant from NWO-FOM/ALW (Netherlands Organization for Scientific Research) to R.K., C.W. and C.D. Work in the laboratories of R.K. and C.W. is supported by grants from the European Commission, NWO and the Dutch Cancer Society. Work in the laboratory of C.D. and N.D. acknowledges support from FOM and NWO.

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Correspondence to Claire Wyman or Cees Dekker.

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Supplementary information

Supplementary Figure S1

The hR/M complexes move along the DNA while following the contour of the DNA molecule. (PDF 103 kb)

Supplementary Movies Legends

Text descriptions to accompany the below Supplementary Movies. (DOC 19 kb)

41586_2005_BFnature03927_MOESM3_ESM.avi

Atomic force microscopy movie of a free hR/M complex imaged in buffer. (AVI 4034 kb)

Supplementary Movie S1

Atomic force microscopy movie of a free hR/M complex imaged in buffer. (AVI 4034 kb)

41586_2005_BFnature03927_MOESM4_ESM.avi

Dynamic transition between the architecture of DNA-bound hR/M and DNA-free hR/M. (AVI 3842 kb)

Supplementary Movie S2

Dynamic transition between the architecture of DNA-bound hR/M and DNA-free hR/M. (AVI 3842 kb)

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Moreno-Herrero, F., de Jager, M., Dekker, N. et al. Mesoscale conformational changes in the DNA-repair complex Rad50/Mre11/Nbs1 upon binding DNA. Nature 437, 440–443 (2005). https://doi.org/10.1038/nature03927

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