7) Two 'other' RNA genes
We have already been working on this project this semester and are making some headway. For more information, see the 'Missing Genes' page. I don't think this is really a semester long sort of question for the whole class, but it could be an interesting side project.
I did find a couple of interesting article on RNA genes. The first one is about small non-coding RNAs (sRNAs) that have been found in H. volcanii, an archaea we've noticed is very similar in sequence to our genome. sRNAs act as gene expression regulators. The second article notes that RNA modifications are very low in archaea possibly because the high salt concentration within the cell prevents mutation of nucleosides.