Suppose that after the comparative proteome analysis between two strains, I found one protein to be increased 5 fold in the mutant strain compared to wild type. Next I employ RT-qPCR to this gene of interest (RNA is isolated from the samples at exactly the same incubation time with that of used for the proteomic analysis) and the expression change is found to be, say, 3 fold this time. So even though the increase in the protein level corresponds to an increase in the expression (vica versa), there is no direct correlation between two analysis. For an eukaryotic organism there could be plenty of reasons such as post-transcriptional and post-translational modifications etc. In bacteria, the lag between the transcription and translation could be one of the reasons, as well as the very short half-life of mRNA. But what could be the other possible reasons for such a difference? Thanks!
Hey Samet,
A biological reason for this situation would be the reduction of the mechanisms of protein degradation, due to your conditions or not. When this happens, the accumulation of proteins does not necessarily follow a proportion with mRNA molecules. What was the method you used to achieve the proteome in your experiment?
Thank you for your answer Lucas, the method was mass spectrometry; both LC and MALDI-TOF actually resulted in a more fold increase in the level of protein compared to the fold increase of the expression. As the protease activity is also found to be increased in mutant strain, I believe there is no reduction in the protein degradation but the accumulation of the proteins can still be a good reason I guess.
Samet,
As I said, the accumulation of proteins seems to be a good hypothesis in this situation. But, remember the increased activity of proteases does not mean the degradation activity is not down. If any cofactor inside the protein degradation pathway is somehow impaired, the degradation will not happen as it should.
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