Im doing a lab project about riboswitches. in short, thats a secondary structure formed on the 5'UTR of an mRNA, that structure can bind a ligand/metabolite, the binding alters the mRNA structure, and could prompt termination of trancrtiption, or inhibit translation of the mRNA. this is a way for the cell to regulate gene expression, for example - when B12 is present in medium, it can bind to a specific structure of mRNA's of proteins that are supposed to synthetize B12...
in my work- we simply checked for differences in expression of a CBI-A gene, which is involved in cobalamine synthesis, with and without adding B12.
the professor did some bioinformatical work and chose that CBI gene because he saw that a B12-binding structure is located upstream of CBI, and the hypothesis was that B12 acts as a down-regulator on CBI expression.
SO FAR SO GOOD, we did all the lab work, and our results showed that adding B12 to the medium led to lower expression of CBI, i was happy.
(hope youre still with me)
Now i want to finally finish writing the project and submit it, and i just found out some disturbing fact. i got to the supplement material of the article that we used as a reference, and i see that the B12-box is located UPSTREAM of the CBI-A gene, i mean - there isnt an overlapping region. instead- its located further next to an upstream gene, which we didnt analyze at all in the lab.
The thing is - i dont know now if the professor made a mistake and we worked 3 months on a wrong gene, or maybe (most probably) he knows better than me, and there's a good reason he chose that CBI-A gene.
IN SHORT - i guess my question here is (in case anyone here at all understands what im talking about) - IS there a way that the riboswitch activity could influence the CBI-A gene ? maybe the fact that its an operon of several genes together could help explaining this. (although it seems like lmo1190 is not a part of the operon).
IF ANYONE can help, i'd be so so so grateful!