5) DNA repair mechanisms
DNA repair is a broad subject since there are many mechanisms of genome proofreading. Archaea has many similarities to eukarya in its DNA repair mechanisms. Often the archaea system has been used as a simpler model for eukarya. However, in recent years, it has become clear that archaea are actually a blend of features from all domains of life. I have found one good review on the subject of DNA repair in Archaea that would need to be dissected in detail before we pursue this issue farther Archaeal DNA replication and repair.
This is Table 2 from the paper above. It shows which DNA repair proteins have been discovered in different species of archaea.
After determining what is already known about DNA repair, we would need to determine which genes our species has, which genes our species ought to have, and if any genes with unknown functions could represent DNA repair genes.
I'm not sure if enough is known about Archaeal DNA repair for this to be our main goal this semester.