I further thought about this question, and I just didn't want to give in to the (for me) obvious answer concerning the acetylation. But thinking about it made me realise that the question hints to the acetylation activity on purpose....

In my opinion, the expressed but catalytically inhibited protein gets trapped in some way on promotors that are active. I could explain it somehow by protein dynamics and conformational change. As far as I know, enzymes are not static and therefore change conformation as soon as the environment changes or they bind to a substrate. Thus, the catalytically inactive protein is still able to bind promotors of actively transcribed genes which leads to a conformational change upon binding and creates a surface/region for its substrate to bind. After binding of its substrate, it would undergo another conformational change that would release the protein to be acetylated (e.g. histones, transcription factors or RNA polymerase II itself). However, the enzyme is not able to release the substrate since the reaction that would release the substrate is not taking place. We don’t know what precisely the enzyme is acetylating, but given the fact that acetylation is a regulatory process like phosphorylation, this would in turn lead to problems in actively transcribed regions and might also influence DNA replication.

But again, if this were true, why don't we see a phenotype in the knock-out? Is it maybe, as mentioned, not necessary for the organism and might just for example fine tune or further enhance transcription by further unwinding chromatin in actively transcribed regions? Also, other NATs or HATs may compensate for its loss?

Hoping for a response and thank you in advance.

Critical questions that need to be answered first:

1) how did you knock it out and are you sure it is in fact a complete knock-out?

2) what is the method of inhibition and how specific is your inhibitor?

3) what is your end-point phenotype analysis?

Without some specifics, a lot of answers can be correct, but not actually applicable to your situation.

Thank you for your reply Randolph!

I totally agree with you! However:

1) It is not stated how it was knocked out, and I assume that this is a complete knock-out given the fact that these are hypothetical results.

2) The only thing mentioned about the inhibitor is, and I quote: " An inhibitor of its catalytic activity caused impaired DNA replication and transcription." Also, specificity is questionable. Again, I assume that it is "hypothetically" specific to the enzyme.

3) It is also not stated how these cells are phenotyped in the end.

So, you see, that this question is merely hypothetical and therefore confusing because no concrete details are given. Because, as you already mentioned, a lot of my theories can be true. However, we can’t be sure about anything if we don't have more information than that.

I think that they want to test our creativity besides the basic knowledge to come up with an idea and there might not be one correct answer. However, I want to stress the point that I can't explain that there is no phenotype in the knock-out (assuming it is a complete knock-out and the analysis was performed correctly).

Protein analysis to confirm KO situation.

Expression analysis of inhibitor exposed and un-exposed cells.

Over-express truncated protein (removing active site) in KO confirmed cells.

Speculation without more information ends up being a laundry list of possibilities that are true, but again, may not be applicable to the conditions.

Knock-outs often show no differences when analyzing the wrong end-point.

Plus, inhibitors are notorious for off-target effects.

Thank you very much!

I'm still interested in additional opinions/theories. So, if there is anyone who is willing to contribute to this topic please don't hesitate to drop a comment. Thank you!