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Molecular mimicry of SUMO promotes DNA repair

Nature Structural & Molecular Biology volume 16, pages 509–516 (2009)Cite this article

Abstract

Rad60 family members contain functionally enigmatic, integral SUMO-like domains (SLDs). We show here that despite their divergence from SUMO, each Rad60 SLD interacts with a subset of SUMO pathway enzymes: SLD2 specifically binds the SUMO E2 conjugating enzyme (Ubc9), whereas SLD1 binds the SUMO E1 (Fub2, also called Uba2) activating and E3 (Pli1, also called Siz1 and Siz2) specificity enzymes. The molecular basis of this selectivity is revealed by our 0.97-Å resolution crystal structure of Rad60 SLD2, which shows that apart from the conserved non-substrate SUMO:Ubc9 interface, the surface features of SLD2 are distinct from those of SUMO. Abrogation of the SLD2:Ubc9 FEG motif–dependent interaction results in hypersensitivity to genotoxic stress and an increase in spontaneous recombination associated with aberrant replication forks. Our results provide a mechanistic basis for the near-synonymous roles of Rad60 and SUMO in survival of genotoxic stress and suggest unprecedented DNA-damage-response functions for SLDs in regulating sumoylation.

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Figure 1: Rad60 SLDs interact with distinct components of the sumoylation machinery.
Figure 2: Rad60 SLD2 crystal structure.
Figure 3: Analysis of the Rad60 SLD2:Ubc9 interface.
Figure 4: The rad60E380R mutant is sensitive to genotoxic stress.
Figure 5: Genetic interactions between rad60E380R and mutants in the homologous recombination repair or sumoylation pathways.

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Acknowledgements

We thank B. Arcangioli (Institut Pasteur, Paris), P. Russell (TSRI, La Jolla, California, USA), S. Pebernard (TSRI) and G. Raffa (Università di Roma La Sapienza, Rome) for generously providing fission yeast strains and additional reagents and The Scripps Cell Cycle Group for support and encouragement. This study was funded in part by US National Institutes of Health grants GM068608 and GM081840 awarded to M.N.B. and CA104660 to J.A.T.

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  1. John Prudden and J Jefferson P Perry: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, USA

    John Prudden, J Jefferson P Perry, Andrew S Arvai, John A Tainer & Michael N Boddy

  2. School of Biotechnology, Amrita University, Kollam, Kerala, India

    J Jefferson P Perry

  3. Life Sciences Division, Department of Molecular Biology, Lawrence Berkeley National Laboratory, Berkeley, California, USA

    John A Tainer

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Contributions

J.P. conducted the yeast genetics studies, yeast in vivo analyses and in vitro pulldowns and aided protein purification and crystallization experiments. J.J.P.P. conducted protein purification, crystallization, data collection and structural refinement studies and assisted in manuscript preparation. A.S.A. successfully developed and used a high-throughput molecular replacement method for providing phasing data for Rad60 SLD2. J.A.T. and M.N.B. assisted in experimental design and manuscript preparation.

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Correspondence to John A Tainer or Michael N Boddy.

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Prudden, J., Perry, J., Arvai, A. et al. Molecular mimicry of SUMO promotes DNA repair. Nat Struct Mol Biol 16, 509–516 (2009). https://doi.org/10.1038/nsmb.1582

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