Excision repair systems in E. coli

Content
Chemistry of the Gene 2.  Synthesis, Modification and Repair of DNA
DNA replication: general features 
Semi-conservative DNA replication in E. coli
Semi-conservative replication of chromosomes in eukaryotes
Semi-discontinuous DNA replication
Unidirectional and bidirectional DNA replication
RNA primers in DNA replication
Regulation of DNA replication by anti-sense RNA primer
Prokaryotic DNA polymerases
Eukaryotic DNA polymerases
Replicons for DNA replication
DNA replication in prokaryotes 
Experimental approaches for the study of DNA replication
Initiation of DNA replication
Elongation of DNA chain
Replication fork movement
Termination of DNA replication
DNA replication in eukaryotes 
DNA replication and cell cycle
Replication origins and initiation of DNA replication (cis and trans-acting elements)
Comparison of initiation of DNA replication with transcription initiation
Different steps involved in eukaryotic DNA replication
Synthesis of telomeric DNA by telomerase
Models of DNA replication
Replication fork model
Rolling circle model of DNA replication
Mitochondrial DNA replication and D-loops
RNA directed DNA synthesis (reverse transcription)
DNA modification and DNA restriction
DNA repair
Excision repair systems in E. coli
An SOS repair system in E. coli
DNA repair and genetic diseases in humans
Excision repair systems in E. coli
Although excision repair systems vary in their specificity, the main pathway involves the following three steps : (i) in incision step, an endonuclease cleaves the DNA strand on both sides of the damage (7 nucleotides from 5' side and 3 nucleotides on the 3' side); (ii) in excision step, a 5'-3' exonuclease (DNA polymerase I) removes a stretch of the damaged strand (20 nucleotides); (iii) in synthesis step, the single stranded region of DNA is used as a template for synthesis of DNA by DNA polymerase I to replace the excised sequence.

Excision repair involves different lengths of DNA and is described as (i) very short patch repair (VSP), (ii) short patch repair and (iii) long patch repair. While VSP deals with single base mismatches, the other two deal with more extensive damages, which are repaired through uvr genes. (uvr A, B, C), coding for components of a repair endonuclease. Another enzyme uvr D is also needed for helicase activity. The mechanism involved in VSP is dealt in the following section under mismatch repair.

Mismatch repair system in E. coli
When there is mismatch in a base pair as in GC→GT, then theoretically it may repair to give rise to either wild type (GC) or to a mutant type (AT). Therefore, the repair system has to distinguish between old and new strands and repair only the new strand to restore the wild type. This is done by VSP system and requires four proteins, namely Mut L, Mut S, Mut U and Mut H coded in E. coli respectively by genes mut L, mutS, mut U and mut H. These mut genes are mutator loci, where a mutation leads to increased frequency of spontaneous mutations. It has been shown that a methylase (dam) coded by dam gene, brings about methylation in adenine of sequence GATC on both strands of DNA. Following replication, one strand remains methylated (only at A of GATC sequence) and other remains unmethylated till methylase acts on this new strand to bring about methylation. During this transition period, the unmethylated GATC allows recognition of mismatch by Mut L, and binding of Mut S to mismatch. Mut U helps in unwinding the single strands stabilised by SSB protein and Mut H cleaves the newly synthesized strand. Two models for repair have been suggested which are shown in Figure 26.34. In one model Mut H cleaves DNA at two GATC sequences flanking the mismatch, while in the other model the cleavage occurs on one side of mismatch at GATC sequence and on the other side at the mismatch itself.

Two models for the mechanism of mismatch repair. In both models proteins called MutL and MutS interact with mismatch site (G-T) and a protein called MutH cleaves the newly synthesized strand. The repair apparatus distinguishes the parental strand from the new one by means of methyl groups (black dots) within the parental GA-TC sequences. The strands surrounding the mismatch are separated with the help of protein MutU and stabilized by SSB. (For details of two models, see text).
Fig. 26.34. Two models for the mechanism of mismatch repair. In both models proteins called MutL and MutS interact with mismatch site (G-T) and a protein called MutH cleaves the newly synthesized strand. The repair apparatus distinguishes the parental strand from the new one by means of methyl groups (black dots) within the parental GA-TC sequences. The strands surrounding the mismatch are separated with the help of protein MutU and stabilized by SSB. (For details of two models, see text).