DAMAGE AND REPAIR.

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Both in prokaryotic and eukaryotic cells, there are repair enzyme systems to deal with DNA damage, which is caused rather frequently. The changes in DNA leading to damage are broadly divided into two general classes: (i) Single base changes may be caused by conversion of one base to another. These are corrected throught DNA replication leading to changes in DNA sequence. (ii) Structural distortions may results from a single strand nick, removal of a base or introduction of a covalent link between bases of same or different strands eg. formation of thymine dimer.

A cell may have several systems to deal with DNA damage. These systems include the following: (i) Direct repair involves reversal of the damage; for instance, photo reactivation of pyrimidine dimer involves reversal of covalent bonds giving the original structure. (ii) Excision repair involves recognition of damaged or altered base followed by excision of a sequence including damaged or altered base(s) followed by excision of a sequence including damaged bases. This is achieved by an endonuclease, or an exonuclease. A new stretch of DNA is then synthesized to replace the excised material. (iii)  Mismatch Repair involves correction of mismatches or pairing between bases which are not compulsory. Mismatches may arise either (a) during replication or (b) due to base conversion and are corrected by a process described as error correction during DNA replication.

Direct Repair

As mentioned above, direct repair involves reversal of DNA damage. Abnormal chemical bonds between bases or between a nucleotide and an abnormal substituent are broken down, thus restoring the original DNA structure. The enzymes currently known to catalyze this DNA repair include the following: (i) DNA photolyase repairs cyclobutane

Pyrimidine dimers, induced by Ultra-violet The enzyme splits the cyclobutane ring, only on activation by light. (ii) 6-4 photoproduct photolyase deals with the DNA damage involving the formation of ‘6-4 photoproduct’ due to UV. (iii) Spores photoproduct lyase repairs the lesion caused by UV in B. subtilis spores, where a spore photoproduct is produced instead of cyclobutane dimers on UV irradiation. (iv) O⁶- methyl guanine DNA methyl transferase (MGMT) is a common enzyme found in all species tested. The enzyme transfers the methyl group of O⁶- methylguanine to a cystine residue on the enzyme.

Excision Repair system in E.coli

Excision repair has been classified into the two types on the basis of the nature of excised products. Which can either be free bases as in base excision repair, or one or more nucleotides, as in nucleotide excision repair?

Base excision repair. BER is always initiated by a DNA glycosylase. A number of these glycosylases are known, depending upon the substrate used by each of them. These glycosylases hydrolyse N-glycosyl bonds linking bases to the sugar-phosphate backbone of the DNA, leaving sites that are abasic.Sites are then acted upon by an apurinic/aprrimidinic endonuclease and an AP lyase, so that sugar-phosphate group is removed by hydrolysis of 5’phosphodiester bond.

Nucleotide excision repair. NER is initiated by endonucleolytic excisions, either only on one side of the lesion or on each of the two sides of the lesion. In the endonuclease-exonuclease repair, an endonuclease first makes an incision at either the 5’ or the 3’ end of the lesion. The exonuclease then digests segment of the strand involving the lesion. The gap is later filled by DNA synthesis and ligation.

Relationship between NER and transcription

In prokaryotes, as well as in eukaryotes, it has been shown that the nucleotide excision repair of template strand of the transcriptionally active DNA is faster than that of its complementary strand.

Recombination repair (dimmer tolerance) involves DNA replication in E. Coli

Dimers, whenever formed in DNA, are reversed either by photo reactivation, due to Photolyase or removed by UvrABC catalyzed excision repair. However, some of the dimmers still remain and are tolerated by the replication machinery.

An SOS repair system in E.coli.

In E. coli, many treatments causing DNA damage or inhibition of DNA replication induce a complex series of phenotypic changes described as SOS response. The SOS response is initiated by interaction of RecA protein with LexA repressor.