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There are three major DNA repairing mechanisms: base excision, nucleotide excision and mismatch repair. Table 7-G-1. Proteins involved in the
DNA repairing of E. coli. Base excision DNA's bases may be modified by deamination or alkylation. The position of the modified (damaged) base is called the "abasic site" or "AP site". In E.coli, the DNA glycosylase can recognize the AP site and remove its base. Then, the AP endonuclease removes the AP site and neighboring nucleotides. The gap is filled by DNA polymerase I and DNA ligase.
Figure 7-G-1. DNA repair by base excision.
Nucleotide excision In E. coli, proteins UvrA, UvrB, and UvrC are involved in removing the damaged nucleotides (e.g., the dimer induced by UV light). The gap is then filled by DNA polymerase I and DNA ligase. In yeast, the proteins similar to Uvr's are named RADxx ("RAD" stands for "radiation"), such as RAD3, RAD10. etc.
Figure 7-G-2. DNA repair by nucleotide excision.
Mismatch repair To repair mismatched bases, the system has to know which base is the correct one. In E. coli, this is achieved by a special methylase called the "Dam methylase", which can methylate all adenines that occur within (5')GATC sequences. Immediately after DNA replication, the template strand has been methylated, but the newly synthesized strand is not methylated yet. Thus, the template strand and the new strand can be distinguished.
Figure 7-G-3. Mismatch repair. The repairing process begins with the protein MutS which binds to mismatched base pairs. Then, MutL is recruited to the complex and activates MutH which binds to GATC sequences. Activation of MutH cleaves the unmethylated strand at the GATC site. Subsequently, the segment from the cleavage site to the mismatch is removed by exonuclease (with assistance from helicase II and SSB proteins). If the cleavage occurs on the 3' side of the mismatch, this step is carried out by exonuclease I (which degrades a single strand only in the 3' to 5' direction). If the cleavage occurs on the 5' side of the mismatch, exonuclease VII or RecJ is used to degrade the single stranded DNA. The gap is filled by DNA polymerase III and DNA ligase. The distance between the GATC site and the mismatch could be as long as 1,000 base pairs. Therefore, mismatch repair is very expensive and inefficient. Mismatch repair in eukaryotes may be similar to that in E. coli. Homologs of MutS and MutL have been identified in yeast, mammals, and other eukaryotes. MSH1 to MSH5 are homologous to MutS; MLH1, PMS1 and PMS2 are homologous to MutL. Mutations of MSH2, PMS1 and PMS2 are related to colon cancer. In eukaryotes, the mechanism to distinguish the template strand from the new strand is still unclear.
Review Articles: Mechanisms in Eukaryotic Mismatch Repair - J. Biol. Chem., 2006. Cellular machineries for chromosomal DNA repair - Genes and Development, 2004. The discovery of a new family of mammalian enzymes for repair of oxidatively damaged DNA, and its physiological implications - Carcinogenesis, 2003. Sensing and repairing DNA double-strand breaks - Carcinogenesis, 2002. Base excision repair in a network of defence and tolerance - Carcinogenesis, 2001. DNA Damage Control by Novel DNA Polymerases: Translesion Replication and Mutagenesis - J. Biol. Chem., 2001. Roles for Mismatch Repair Factors in Regulating Genetic Recombination - Molecular and Cellular Biology, 2000. Interactions of DNA Helicases with Damaged DNA: Possible Biological Consequences - J. Bio. Chem., 2000. Molecular mechanism of nucleotide excision repair - Genes and Development, 1999 Recombinational Repair of DNA Damage in Escherichia coli and Bacteriophage l - Microbiology and Molecular Biology Reviews, 1999.
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