Question S. Five DNA polymerases have been identified in E. coli. 4 of them are

Question

Question S. Five DNA polymerases have been identified in E. coli. 4 of them are very well characterized (DNA Pol I, IlI, IV and V). The replicative DNA polymerase (devoted to chromosome duplication) is DNA Polymerase III, which is the most highly processive of the DNA polymerase enzymes, as it associates with a DNA sliding clamp. DNA polymerase III is the DNA polymerase used for MMR in E. coli, while DNA Polymerase I, which does not associate with a DNA sliding clamp, is the DNA polymerase used for BER and NER in E. coli. Why does this make sense? A) Two of these E. coli DNA polymerases (IV and V) are TLS polymerases that do not contain a 35, exonuclease activity, what is the function of the 3, 5, exonuclease activity present in many DNA polymerases? How does the absence of such an activity in DNA polymerases IV and V make sense in the context of the cellular function of these enzymes? B)

Explanation / Answer

Mismatch repair (MMR) is corrected during the DNA synthesis to remove the mismatch base which is wrongly added to the replication site. Since DNA pol III associate with sliding clamp for longer processivity meaning it can synthesize longer stretch of DNA before falling off it is used to remove the mismatched base added to the replication site and then resume replication. Also it would be energetically unfavorable for the cell to replace this enzyme with other correction enzyme and and resume synthesis with DNA pol III again. BER and NER are the processes to remove damaged nucleotide from the DNA strand mostly which are not under replication processes. So no sliding clamp would be needed, hence DNA pol I which does not associate with sliding clamp does this job for nucleotide repair of damaged site. The 3’-5’ exonuclease activity is to proofread the DNA strand which is mostly used to correct mismatched nucleotide base during DNA synthesis at the replication fork. However, sometimes during DNA synthesis addition of wrong base creates a lesion in the DNA strand leading to stop of replication fork. DNA pol III is unable to repair this lesion with proofreading activity and so unable to resume replication. In this situation DNA pol IV and V are used which replace the DNA pol III and the lesion and carry out DNA replication past DNA lesion which then is taken over by DNA pol III again. The absence of   3’-5’ exonuclease activity benefit these enzymes by preventing them from engagement at the mismatch lesion and carryout DNA replication past to the lesion.

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