Answer to Question 2 from November, 2006

2. (10 points) Describe two cases in which protein ubiquitylation contributes to DNA repair. In each case, name the protein(s) that serve as ubiquitin-conjugating enzymes or ubiquitin ligases, and name the protein(s) that are ubiquitylated. In each case, briefly describe the importance of the ubiquitylation for successful repair.

I gave full credit for any two of the following possibilities:

1. Ubiquitylation of PCNA. Mono-ubiquitylation of PCNA by Rad6 and Rad18 promotes damage bypass by translesion synthesis.
2. Multi-ubiquitylation of PCNA by a complex consisting of Rad6, Rad18, Rad5, Ubc13 and MMS2 facilitates damage bypass by a recombinational mechanism.
3. The E3 ubiquitin ligase (E3UL) containing XPE (also known as DDB2) has three substrates that are important for the very early stages of global-genome NER (GG-NER). I gave full credit if you described any one of the three substrates:
   1. One substrate is histones. Ubiquitylation of histones is thought to facilitate chromatin remodeling at the damaged site, presumably to enhance the access of repair proteins to the damaged DNA.
   2. A second substrate is the XPC protein. The fact that XPC is a substrate of the XPE-containing E3UL may contribute to recruitment of XPC to the damaged site, since the XPE-containing E3UL binds to the damaged site before XPC. In addition, ubiquitylation of XPC enhances XPC's affinity for damaged DNA. Note that ubiquitylation of XPC does not cause XPC degradation.
   3. Finally, the third substrate of the XPE-containing E3UL is XPE itself. Ubiquitylation of XPE leads to its dissociation from the damaged site (along with the rest of the E3UL) and to its proteolytic degradation, thus clearing the way for XPC to bind to the damaged DNA.
4. The E3UL that contains CSA is able to ubiquitylate CSB, which promotes removal of CSB from the damaged template strand after repair is complete, thus permitting resumption of RNA synthesis.

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