Identify Proteins In Cell Cycle

Question

[rabi313]

Hello everyone!

I am new here and this is the first question I am asking, so please tell me if I did anything wrong.

I am studying for my bioinformation technology exam right now and try to answer previous exam questions. Now I thought long about this question but it´s like there is a wall in my head and I have no clue how to solve this problem. I just copy the question in here:

"The Saccharomyces cerevisieae (bakers’yeast) cell cycle has been thoroughly investigated employing methods as diverse as mutational analysis to knock out genes one by on, protein-protein interaction studies as well as DNA micro array analysis. Describe how you would proceed to identify the proteins that are present in the protein complex that is trimming and sealing the ends of the Okazaki fragments in a related yeast species using the different conditions as outlined below. Hint: Okazaki fragments are short (1000 nt) pieces of DNA that make up the lagging strand during DNA synthesis.

a. The complete DNA sequence of the related yeast is not known.

b. The complete DNA sequence of the related yeast is known.

c. Do you expect to find all the proteins in the complex? If not, how could you improve your results?"

I am pretty sure that you could identify the proteins by comparing micro array expression of genes of S. cerevisiae and the other organism, but I don´t know what difference it makes if the sequence is known or unknown. If the genome is known, you could blast the genes S. cerevisiae uses for trimming the ends of the Okazaki fragments and see if it gives a hit with your organism, but I am sure there is a solution within the microarray data.

I would be really happy if anyone could answer that questions. Since I am having the exam on monday I don´t expect to get an answer until then, but I am interested in the solution anyway.

Thank you all, Robin

Answer 1

[Michael]

Sounds a bit like a trick question to me, and maybe I wouldn't pass that exam, better ask a lab biologist. My answer:

• In case of a.: sequence that genome (TM) and assemble it or align it to sequenced genome, procede with b.
• In case of b., use blastp
• c.: Most likely yes, given the proteins are highly conserved. Improve the results: perform the same experiments that were used to identify the proteins in S. cerevisiae (whatever those are)

In case your lab really couldn't afford re-sequencing, you could use PCR to amplify stretches of conserved gene sequence, and sanger sequence them.

Good luck!