DNA repair mismatched

Cells have many systems for DNA repair. Mismatch repair in E. coli is directed by transient nonmethylation of (5 )GATC sequences on the newly synthesized strand. 

Nucleotide-excision repair involves PCNA, DNA polymerase epsilon, and several accessory proteins, such as RF-C (replication factor C), RP-A (replication protein A), and Lig I (DNA ligase I). It could be that these proteins form an aggregate DNA repair machine. PCNA is a hollow circular protein that encircles DNA. PCNA binds and activates many proteins involved in DNA repair. Mismatch repair is less well characterized, but involves DNA polymerase delta. 

Mismatch Repair. Mispairs that break the normal base-pairing rules can arise spontaneously due to DNA biosynthetic errors, events associated with genetic recombination and the deamination of methylated cytosine (Modrich, 1987). With the latter, when cytosine deaminates to uracil, an endonuclease enzyme, /V-uracil-DNA glycosylase (Lindahl, 1979), excises the uracil residue before it can pair with adenine at the next replication. However, 5-methyl cytosine deaminates to form thymine and will not be excised by a glycosylase. As a result, thymine exits on one strand paired with guanine on the sister strand, that is, a mismatch. This will result in a spontaneous point mutation if left unrepaired. For this reason, methylated cytosines form spontaneous mutation hot-spots (Miller, 1985). The cell is able to repair mismatches by being able to distinguish between the DNA strand that exists before replication and a newly synthesized strand. 

Hereditary nonpolyposis colorectal cancer results from a deficiency in the ability to repair mismatched base pairs in DNA that are accidentally introduced during replication. 

A second group of inherited colon cancers are termed hereditary nonpolyposis colorectal cancer (HNPCC). HNPCC may account for 5% of all colon cancer cases and can be caused by mutations in any of five different genes. All of these genes encode proteins involved in DNA mismatch repair (Fig II-5-3). As with inherited breast cancer, fiiulty DNA repair leads to mutated cells capable of producing tumors. 

Fig. 1. Proteins in DNA repair pathways. DNA repair proteins are listed for each of the following pathways BER (Base Excision Repair), NER (Nucleotide Excision Repair), MMR (Mismatch Repair), HR (Homologous Recombination), and NHEJ (Nonhomologous End Joining). PARP1/2 and BRCA1/2 are relevant in BER and HR pathways, respectively.

DNA repair pathways can be divided into those that respond to SSB and those that respond to DSB. SSB repair pathways include base excision repair (BER), mismatch repair (MMR), and nucleotide excision repair (NER). DSB repair pathways include nonhomologous end joining (NHEJ) and homologous recombination (HR). The proteins involved in these DNA repair pathways are shown in Fig. 1. 

Nucleotide Chemistry The cells of many eukaryotic organisms have highly specialized systems that specifically repair G-T mismatches in DNA The mismatch is repaired to form a G=C (not A=T) base pair. This G-T mismatch repair mechanism occurs in addition to a more general system that repairs virtually all mismatches. Can you suggest why cells might require a specialized system to repair G-T mismatches ... 

Mismatch repair protein mutL Single-stranded DNA-binding protein ssb DNA repair uvrA Helicase dnaB RNA polymerase frpoB subunits rpoCJ... 

When base selection and proofreading are combined, DNA polymerase leaves behind one net error for every 106 to 108 bases added. Yet the measured accuracy of replication in E. coli is higher still. The additional accuracy is provided by a separate enzyme system that repairs the mismatched base pairs remaining after replication. We describe this mismatch repair, along with other DNA repair processes, in Section 25.2. 

DNA repair is possible largely because the DNA molecule consists of two complementary strands. DNA damage in one strand can be removed and accurately replaced by using the undamaged complementary strand as a template. We consider here the principal types of repair systems, beginning with those that repair the rare nucleotide mismatches that are left behind by replication. 

DNA Repair Mechanisms Vertebrate and plant cells often methylate cytosine in DNA to form 5-methylcytosine (see Fig. 8-5a). In these same cells, a specialized repair system recognizes G-T mismatches and repairs them to G=C base pairs. How might this repair system be advantageous to the cell (Explain in terms of the presence of 5-methylcytosine in the DNA.)... 

A final check of the fidelity of replication is made after a new strand has been formed. Mismatched base pairs are identified, and the incorrect nucleotides are cut out and replaced by correct ones.655 670 681 683 Some of the thymine dimers created by the action of light are also repaired photochemically by photolyases (see Chapter 23). Photoreactivation was the first DNA repair process recognized.684 However, most thymine... 

DNA Repair. A connection between p53 and DNA repair was observed in p53-deficient cells that exhibited less global DNA repair [197-199] (but see [200]), as well as a reduced capacity to reactivate cisplatin- and UV-damaged reporter plasmids [173][201 ][202]. Furthermore, pretreatment with low levels of UV activated a protective response in which the levels of repair activity were elevated, an effect not observed in p53-deficient cells [202] [203]. It is possible that the p53 protein is directly involved in removing DNA damage since the protein recognizes both irradiated DNA and mismatches [ 162]. There is also evidence that p53 can interact with several components of the excinuclease, including RPA and the TFIIH-associated factors XPB and XPD [204] [205]. So far, however, there is no evidence to demonstrate a direct role for p53 in the nucleotide excision repair pathway. 

Pol/3, like Pola and PolS is also located in the nucleus and is probably involved in DNA repair. Poly is localized in mitochondria, and although there is no direct evidence, it is thought to be responsible for the replication of that organelle s DNA. Pol5 has 3 — 5 proofreading exonuclease action that is highly selective for base mismatches. 

The importance of the repair of damaged DNA in keeping the cells alive and preventing cancer is also apparent from mutations in genes involved in nucleotide excision repair. The enzymes involved in nucleotide excision repair are other tools that cells have to repair mismatched DNA. Defects in DNA nucleotide excision repair can cause skin cancer (xeroderma pigmentosa) and colon cancer. 

DNA repair is the elimination of covalent DNA modifications and the correction of base mismatches. There are six basic repair categories direct repair, base excision repair, nucleotide excision repair, recombination, cross-link repair, and mismatch repair. 

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