please, need some help - (Apr/06/2009 )

I am fairly new to the protein field if anyone can help me answer this.

Say I have one gene transcript that encodes for two proteins in a cell line. The first 1/3 of the transcript encodes for the first protein ("small" protein) and the last 2/3 encodes for the second protein ("large" protein).

I tested this gene transcript in a cell line under normal and stress conditions. I also made separate transcripts where I could test just the first 1/3 of the transcript and the last 2/3, thereby isolating both proteins from each other, basically trying to see if there were any differences seen by individually encoding them.

My results were that when both proteins were encoded by the gene transcript, the cell was stress tolerant (viable, healthy). When just the small protein was encoded, the same was seen. But when just the large protein was encoded, the cell was stress sensitive (decrease in size, somewhat functional but not much). So there is a difference seen in the cell when the proteins are individually encoded.

Of course, I am thinking, well there is something else in the large protein that confers the cell stress sensitive. But as you remember from above, when both proteins were encoded, the cell was stress tolerant.

So I am wondering why the difference when the protein is isolated? I already checked it by in vitro and I know the two proteins are encoding separately.

Has anyone run across this kind of research in proteomics, where if the two proteins are encoded together, they show a specific response under one condition, but when one of the proteins is isolated, it shows the opposite response under the same condition?

If I could be directed towards some papers that would even be helpful!

I didn't get your problem.

both proteins are expressed - the cell is stress tolerant
only the small protein is expressed - the cell is stress tolerant
only the large protein is expressed - the cell is stress intolerant

That would mean that your large protein is responsible for stress tolerance. I think it's not unusual that proteins encoded from one mRNA have different impacts on the cell.

But I'm not sure if I got you right...

Hello mastermi,

Yes I think you got it, but in my case I have 2 mRNAs encoding for each of the two proteins, not just one. Would this make a difference?

The thing I am wondering about (or my "problem") is the large protein is stress intolerant when I isolate it by itself (cDNA form), not when it is encoded along with the entire transcript.

Still trying to understand how does this happen. Can you explain why you think this is not unusual?

Do you have papers or readings on this phenomenon? Thanks

I belieev this is subunit we are playing around here .

And for ur case.. i think te small subunit is the key player

Without small subunit the cell is confirmed intolerant?

the small subunit must have some important domain responsible for some catalytic activity.

while the big subunit probably have some less essential activity ( maybe regulation or something that's only required under special condition)

mastermi on Apr 8 2009, 06:23 PM said:

Sorry, I meant the small protein which is responsible for stress tolerance!



You have one primary transcript (an operon) which is processed into two mRNAs, right?

So hanming86 might be right that the small protein might be the active-site subunit of a protein complex. But I think that it doesn't have to be like that.
I just don't know any papers where that is described right now.

Do you have any function/domain prediction for the two proteins? That would help...