assuming a case where we see induction in protein expression levels of any gene X due to nutrient stress but the transcript levels getting saturated and plateaued after a minor induction with respect to control. is this phenomenon physiologically relevant and how robust the explanation could be?
Dear Sabyasachi,
If I took it well, are you referring to upregulation in protein levels, with little or null increase in gene expression. Is that right?
best,
Maybe you could block the transcription with Actinomycin D and then measure the transcript levels to see if your stimuli affect the longevity of the mRNA. Complimentary I would also try blocking translation with cyclohexamide and doing a western blot and measuring the protein concentration along the stimulation. This would give you good insight, on which level is your protein upregulated.
One possibility is that nutrient stress increases the stability of the protein. For example, there are many cases in which a protein is normally targeted for degradation by the ubiquitin system. When the cells are exposed to a hormone or an environmental factor, the protein is protected from degradation due to interactions with other proteins and/or relocalization. As for physiological relevance, changes in protein levels are generally considered more, not less relevant, than changes in transcript since the protein has a specific activity. Having a change in transcript that correlates with changes in protein may make it easier to convince reviewers of your conclusion, but as long as the protein data is clear, you should be good.
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