How could I get some suggestion from the fact? - (Jul/08/2009 )

Recently I am studying one gene function in diabetes. I found this gene knock out mice has the very similar phenotype with another gene knock out mice. Both kinds of mice could induce the increasing of common protein level and have the same phenotype which strongly associated with the increased common protein level. How could get some suggestion from these fact? Whether the two genes-encoded protein work in the same pathway or binding together directly or indirectly or have the same function on the transcription factor of the common protein.

ucsd on Jul 8 2009, 12:44 AM said:

All of the possibilities you mentioned are possible. You have to do a lot of experiments, guided by the literature.

To further establish their genetic relationship:

1. Double Het experment: In two KOs with similar phenotype, a typical genetic experiment to do is to breed them together. Gene A KO and gene B KO both have same phenotype in homozgous genotype, but not in heterozygous mice. See if mice double het for A & B have a similar pehnotype too. That makes your argument stronger.

2. Rescue Expt: When you breed Gene A KO or Gene B KO with the mice KO for the common protein you mentioned, you should see resuce of the phenotype, as the common protein is increased in A and B KO mice.

Thanks very much for your suggestion.
I want to know whether I could get some stronger information from in vitro experiments
Also Do you think there still have the other possibilities except from what I mentioned.

ucsd on Jul 8 2009, 11:13 AM said:

I think you did it well.

Let us just list the theoretical possiblities here, that you have alredy mentioned. Without more info about your Genes A & B, and downstream target P, it is difficult to talk about the exact experiments you can do, because they vary based on mechanism of function of these genes (ie. TF, sig trans etc) and the pathways involved.

A -> B (A upstream)
B -> A (A downstream)
A ->X -> Y -> B (indirect upst)
B ->X -> Y -> A (indirect downst)
A ~ B ---| P (same pathway, similar, or overlapping, or parallel functions)
A:B (direct binding)
A:X:Y:B (indirect binding)

A could modify B in an important way (phosphorylation, acetylation, lipoylation) or vice-versa. This might be easy to rule out simply on the basis of A & B sequence and domain identification.

however. one protein is adaptor protein and one protein is nuclear receptor corepressor, I think they could not have the direct post translation modification.