DNA Repair: Clamping down on mismatches

Jul 12, 2016

Open access
Copyright information

Download
Cite
CommentOpen annotations (there are currently 0 annotations on this page).
Share

Guo-Min Li

University of Southern California Keck School of Medicine, United States

Errors made when DNA is replicated can lead to cancer and genetic disorders, so cells rely on a system called mismatch repair (MMR) to remove many of the errors from newly synthesized DNA (Hombauer et al., 2011; Kunkel and Erie, 2015; Simmons et al., 2008). These errors include mismatches that occur when the wrong DNA base is added into the new DNA strand (i.e. a base that does not match the one in the template strand). MMR must deal with these mistakes before the DNA is repackaged into nucleosomes, which would block the repair mechanisms. As such, a long-standing question in this field is how the MMR system discriminates the new strand (which contains the errors) from the template (which is error-free) both quickly and accurately.

Now, in eLife, Tatsuro Takahashi and colleagues at Osaka University and Kyushu University report a new twist in this story (Kawasoe et al., 2016). Newly synthesized strands of DNA have small gaps or nicks (Kunkel and Erie, 2015), and such signals can be used to direct MMR to a specific DNA strand in cell-free experiments (Holmes et al., 1990). However, Takahashi and colleagues – who include Yoshitaka Kawasoe as first author – found, via experiments with Xenopus cell extracts, that MMR can still correctly identify the new DNA strand even after any gaps or nicks had been filled in. This unexpectedly implied that there must be a second signal that allows MMR in eukaryotes to distinguish the new DNA strand from the template.

So, what is this second signal? PCNA is a ring-shaped complex that acts as a “sliding clamp” to coordinate DNA replication by traveling along the DNA template. Eukaryotes use PCNA and a mismatch recognition complex called MutSα to start MMR (Kadyrov et al., 2006; Kunkel and Erie, 2015; Umar et al., 1996), and these two complexes interact directly at the site of a mismatch (Clark et al., 1999; Flores-Rozas et al., 2000; Kleczkowska et al., 2001). Kawasoe et al. now reveal that the PCNA complex provides the secondary signal that allows the cell to “remember” which strand of DNA is which (Figure 1A,B).

Figure 1

Download asset Open asset

PCNA binds to DNA in an asymmetric way.

Base-base mismatches (dashed circle) result when a base is added into a newly synthesized DNA strand (red) that does not match the corresponding base in the template strand (blue). (A) Newly synthesized strands of DNA often have small gaps that are filled in and ligated later, and the ring-shaped complex PCNA forms non-identical complexes with 5’-gapped (top) or 3’-gapped (bottom) heteroduplex DNA. Note that one side of the complex (green) always faces towards the 5’ end of the new DNA strand, while the other (yellow) faces towards the 3’-end. (B) The asymmetry of the PCNA-DNA complexes is conserved after the DNA gaps are filled in and ligated; this could allow DNA mismatch repair to distinguish the error-containing new strand from the error-free template. (C) Kawasoe et al. show that PCNA spends little time on DNA containing a mismatch in the absence of the mismatch recognition complex MutSα (top). PCNA spends much longer on the DNA when MutSα is present (middle), but not quite so long if MutSα’s PCNA interacting protein (PIP) motif is removed (MutSα∆PIP; bottom). Times given in figure are the half-lives of the PCNA-DNA complexes (t_1/2).

The PCNA clamp loads onto DNA ends in an asymmetric way (Pluciennik et al., 2010). This means that one side of the ring complex always faces towards the 5’-end of the newly synthesized DNA, while the other faces towards its 3’-end. Kawasoe et al. propose that this inbuilt asymmetry is used to direct the enzymes that correct mismatches towards the new strand and not the template strand.

Kawasoe et al. also found that MutSα strongly encourages the PCNA clamp to remain loaded on the DNA. They showed that this effect was much weaker if MutSα lacked the domain that it uses to interact with PCNA (Figure 1C). These findings further suggest that the interaction between MutSα and PCNA might act in favor of MMR, rather than DNA replication. If, as Kawasoe et al. suggest, the asymmetric PCNA-DNA complex forms a biological “memory” of which DNA strand is which, then the interaction between MutSα and PCNA appears to make that memory more stable over time, similar to converting short-term memories to long-term ones.

However, several questions remain to be answered. For example, the PCNA asymmetry and its interaction with MutSα may create a long-term “memory” for strand-specific MMR, but why do cells delay the packing of DNA into nucleosomes? Also, do the various modifications that are made to PCNA (such as ubiquitination and phosphorylation; Ortega et al., 2015) alter its role in strand-discrimination in MMR? Finally, does MMR in bacteria also use β clamp (the bacterial counterpart of PCNA) in the same way (Simmons et al., 2008)? Additional studies are now needed to answer these important questions.

References

1. Clark AB
2. Cook ME
3. Tran HT
4. Gordenin DA
5. Resnick MA
6. Kunkel TA
(1999) Functional analysis of human MutSalpha and MutSbeta complexes in yeast
Nucleic Acids Research 27:736–742.

https://doi.org/10.1093/nar/27.3.736
- Google Scholar
(2000) Proliferating cell nuclear antigen and Msh2p-Msh6p interact to form an active mispair recognition complex
Nature Genetics 26:375–378.

https://doi.org/10.1038/81708
- Google Scholar
(1990) Strand-specific mismatch correction in nuclear extracts of human and Drosophila melanogaster cell lines
Proceedings of the National Academy of Sciences 87:5837–5841.

https://doi.org/10.1073/pnas.87.15.5837
- Google Scholar
(2011) Visualization of eukaryotic DNA mismatch repair reveals distinct recognition and repair intermediates
Cell 147:1040–1053.

https://doi.org/10.1016/j.cell.2011.10.025
- Google Scholar
(2006) Endonucleolytic function of MutLalpha in human mismatch repair
Cell 126:297–308.

https://doi.org/10.1016/j.cell.2006.05.039
- Google Scholar
(2016) MutSα maintains the mismatch repair capability by inhibiting PCNA unloading
eLife 5:e15155.

https://doi.org/10.7554/eLife.15155
- Google Scholar
(2001) hMSH3 and hMSH6 interact with PCNA and colocalize with it to replication foci
Genes & Development 15:724–736.

https://doi.org/10.1101/gad.191201
- Google Scholar
1. Kunkel TA
2. Erie DA
(2015) Eukaryotic Mismatch Repair in Relation to DNA Replication
Annual Review of Genetics 49:291–313.

https://doi.org/10.1146/annurev-genet-112414-054722
- Google Scholar
1. Ortega J
2. Li JY
3. Lee S
4. Tong D
5. Gu L
6. Li G-M
(2015) Phosphorylation of PCNA by EGFR inhibits mismatch repair and promotes misincorporation during DNA synthesis
Proceedings of the National Academy of Sciences of the United States of America 112:5667–5672.

https://doi.org/10.1073/pnas.1417711112
- Google Scholar
(2010) PCNA function in the activation and strand direction of MutLα endonuclease in mismatch repair
Proceedings of the National Academy of Sciences of the United States of America 107:16066–16071.

https://doi.org/10.1073/pnas.1010662107
- Google Scholar
(2008) Beta clamp directs localization of mismatch repair in Bacillus subtilis
Molecular Cell 29:291–301.

https://doi.org/10.1016/j.molcel.2007.10.036
- Google Scholar
1. Umar A
2. Buermeyer AB
3. Simon JA
4. Thomas DC
5. Clark AB
6. Liskay RM
7. Kunkel TA
(1996) Requirement for PCNA in DNA mismatch repair at a step preceding DNA resynthesis
Cell 87:65–73.

https://doi.org/10.1016/S0092-8674(00)81323-9
- Google Scholar

Article and author information

Author details

Guo-Min Li

Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, United States

For correspondence
guominli@usc.edu

Competing interests
The author declares that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-9842-4578

Publication history

Version of Record published: July 12, 2016

Copyright

This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.