Question

1. DNA repair mechanisms. A. What are the common themes for all the different repair mechanisms? B. What are the health consequences of inherited mutations in DNA repair pathway proteins? Can you name a couple mentioned in class? Are there others that you know of? 4. Homologous Recombination A. How are the repair of double strand breaks (DSBs) and production of DSBs for recombination connected? B. How does the general model of strand invasion, branch migration, and resolution of the Holliday junction work?

Answer 1

DNA damage can occur naturally from metabolic or hydrolysis processes. DNA damage is an abnormal chemical structure in DNA .

it can be due to following processes: oxidation, depurination, depyrimidation,single strand break, double strand break, methylation, deamination or alkylation.

for these damages there are several repair mechanisms

1. Base excision repair

it corrects DNA damage from oxidation, alkylation and deamination. Enzyme called DNA glycosylase generate apyrimidic/ apurinic site (AP site) where the sugar backbone stays connected to the DNA strand but nitrogenous bass is removed. AP endonuclease then cleaves phosphodiester bonds at AP site. This cleaved site is then repaired by exonuclease, DNA pol I and DNA ligase.

2. Nucleotide excision repair

it corrects damage from oxidative lesions such as thymine dimers,cyclopurine. The most studied nucleotide excision repair system is in E.coli where ABC exonuclease performs the repair. ABC exonuclease has three subunits- uvrA, uvrB, uvrC

uvrA and uvrB attaches to damaged site. uvrA recognises the damaged site and leaves where uvrC binds and forms uvrBC dimer. UvrBC cleaves 8th phosphodiester bond from 5 prime and 4-5th bond from 3 prime.

the gap is filled by DNA pol I and ligase.

3. DNA mismatch repair.

three types of repair system are present- long patch, short patch and very short patch.

long patch system involves 3 Mut proteins- MutH, mutS and mutL

mutH recognises the GATC site where methylation occurs in E.coli.

mutS recognises the mismatch in the proximity.

after the recognition of these two sites, mutH cleaves the DNA at the 5 prime of G in the GATC . MutL activates the helicase and exonuclease I and removes the strand . DNA pol III and DNA ligase fills the gap.

4. Direct reversal

6-O-methylguanine is reversed to guanine by O6methyguanine DNA methylation transferase.

Pyrimide dimers are reversed back to normal by DNA photolyase enzyme. This is called photo reactivation.

5. Homologous repair

this repair occurs during DNA replication where a break in one strand is corrected by recombination by homologous DNA. It is a lengthy topic for discussion as it involved various models such as Holliday model. Please ask about this topic in another question.

6. Non homologous repair

This is somewhat inaccurate as in this repair the strands are cleaved off to give a sticky end and then ligated together with some loss of DNA. It is done for ds breaks.

7.Translesion synthesis.

this is also called SOS response. The key regulators are lexA repressor and RecA protein.

DNA damage activates RecA protein. RecA protein cleaves lexA repressor and renders it inactive. Transcription of SOS gene starts and thus DNA pol V , a Y family DNA pol is transcribed which lacks proof reading activity and thus allows faulty synthesis of DNA. This is way this is an error prone pathway.

this is done during huge DNA damage and it is a survival mechanism.

cockayne syndrome is one such disease that is caused by defect in DNA repair mechanism. It is fatal neurodegenrative disorder. Stunted growth, eye disorders, premature age it are some common features.

another syndrome is Xeroderma pigmentosum (XP). This is caused by defect in DNA repair system of ABC exonuclease. This leads to sensitivity to sunlight and premature skin agening and skin cancers.

please, ask about homologous and non homologous DNA repair mechanism in different question.