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Protein and mRNA Correlation

Different mRNAs are translated into protein with different efficiencies, hence mRNA levels are not always correlated with resulting proteins. Recent studies have determined the quantities of mRNAs (e.g., using RT-PCR or RNA-Seq) and proteins (usually using mass spectrometry). mRNA levels primarily determine protein amounts at steady state. Sometimes mRNA is not translated efficiently, which results in poor mRNA-protein correlations. In yeast, levels of mRNA expressions largely correlate with protein abundance, but the levels of latter can vary 20-fold or more. For instance, single copy of mRNA can be translated into 1000 protein molecules while another mRNA is translated into 100,000 protein molecules (Figure 1).



There are multiple reasons why mRNA and protein levels do not always correlate: translation efficiency is determined by multiple factors, including mRNA stability, mRNA folding, translational initiation rate or ribosomal occupancy. A second option for a general lack of correlation between mRNA and protein abundance may be that proteins have very different half-lives as the result of varied protein synthesis and degradation. Correlations have also been found between the mRNA expression levels of diverse protein subunits. Protein subunits in protein complexes are thought to be present in stoichiometric amounts, hence they should be expressed at similar levels. However, this is not always true. The amount of natural and created systematic noise in mRNA and protein expression experiments is thought to be a key stumbling block to identifying connections.The attempt to both explains and decrease this noise is ongoing. Meanwhile, to get around the noise, one may look at broad categories of proteins - for example, groups defined by function, structure, or localization - to cancel out part of the background noise. For example; comparison of different yeast signaling pathways reveals a surprising variety of different types of upstream signaling proteins that function to activate a MAPK cascade, yet how the upstream proteins actually activate the cascade remains unclear. Its also known that the yeast MAPK pathways regulate each other and interact with other signaling pathways to produce a coordinated pattern of gene expression, but the molecular mechanisms of this cross talk are poorly understood. Finally, to be fully able to understand the relationship between mRNA and protein abundances, the dynamic processes involved in protein synthesis and degradation have to be better understood.