Question

Compare and contrast the processes of base excision repair and methyl-directed mismatch repair in prokaryotes. In your answer discuss:

1. a) Under which circumstances this mechanism will need to be used in the cell.

2. b) The sequence of events that occur in the repair process.

3. c) The names and roles of the enzymes involved in each repair mechanism.

Answer 1

Base excision repair

circumstance in which BER occur- Damage to DNA caused by deamination, oxidation and alkylation are repaired by this

Sequence of events and enzymes

DNA glycosylases identify the damaged DNA site cleave the glycosidic bond between defective nitrogen base and sugar This create a AP site (ie a site without a nitogen base, apurinic or apyrimidinic site).

AP endonuclease (Endonuclease 4, exonuclease 3 etc are AP endonucleases in Ecoli) hydrolyze the phosphodiester bond to generate a nick (a 5' deoxyribo phosphate end and 3'OH end) . In some cases DNA glycosylase lyase can cleave both glycosidic and phosphodiester backbone).

DNA pol I add correct nucleotide to 3' OH end to the removed site. DNA ligase seal the nick.

Methyl-directed mismatch repair in prokaryotes

Mismatch repair system removes mostly mismatches in base pairing (C to A rather than T to A) and short deletions or insertions appered in DNA after replication. DNA polymerase prrof read for mismatches, yet there may be fee bases which escaped the proof reading. This daughter strand will be repaired by mismatch repair system (MMS).

The system functions by recognising the daughter strand that contain mismatches. This was facilitated by the presence of methylation only in parental strand GATC (enzyme methylate adenine in GATC of parental strand only, so daughtter strand can be identified soon after replication- hemi methylation). Dam methylase add methylation to daughter strand after some a few minutes. Thus it is not possible to distinguish the strands as parental and daughter.

Sequence of events and enzymes

The mismatch recognised by Mut S and Mut L protein. Mut H is recruited, which makes a cut at the daughter strand either at 5' or 3' to the lesion.

Helicase II enzyme unwind the double strand DNA from the cut site to the site of lesion, single stranded binding protein, SSB bind to the single strand to protect it. If incision is 5' to the mismatch Exo VII or Rec J endonucleases hydrolyse the nick strand in 5'-3' direction and if incision is 3' to the mismatch Exo I, Exo VII, Exo X endonucleases hydrolyse the nick strand in 3'-5' direction.. DNA pol III add nucleotides at the cleaved site. DNA ligase seal the nick. Finally deoxy adenosine methylase add a methyl group to GATC site.