Abstract
The ultimate goal of gene expression regulation is on the protein level. However, because the amounts of mRNAs and proteins are controlled by their synthesis and degradation rates, the cellular amount of a given protein can be attained by following different strategies. By studying omics data for six expression variables (mRNA and protein amounts, plus their synthesis and decay rates), we previously demonstrated the existence of common expression strategies (CESs) for functionally related genes in the yeast Saccharomyces cerevisiae. Here we extend that study to two other eukaryotes: the yeast Schizosaccharomyces pombe and cultured human HeLa cells. We also use genomic data from the model prokaryote Escherichia coli as an external reference. We show that six-variable profiles (6VPs) can be constructed for every gene and that these 6VPs are similar for genes with similar functions in all the studied organisms. The differences in 6VPs between organisms can be used to establish their phylogenetic relationships. The analysis of the correlations among the six variables supports the hypothesis that most gene expression control occurs in actively growing organisms at the transcription rate level, and that translation plays a minor role. We propose that living organisms use CESs for the genes acting on the same physiological pathways, especially for those belonging to stable macromolecular complexes, but CESs have been modeled by evolution to adapt to the specific life circumstances of each organism.
Highlights
The central dogma of molecular biology states that information flows from DNA to protein [1]
In a previous study conducted with the model yeast Saccharomyces cerevisiae, we addressed these questions by comparing omics data for the abundances of mRNAs and proteins, and their synthesis and degradation rates [3]
The right parameter to be used is concentration rather than amount, we can assume that the cell volume for each organism is constant for all their datasets obtained under the same culture conditions and, variations in the number of molecules and their concentrations are equivalent
Summary
The central dogma of molecular biology states that information flows from DNA to protein [1]. Given the central position of mRNA, and because both RA and PA are controlled by synthesis and degradation rates (Figure 1), the desired PA can be obtained through different strategies [3] that balance the contribution of productive and destructive steps, as well as the relative importance of transcriptional and translational regulation [4]. Several studies have suggested that changes in mRNA levels in dynamic scenarios strongly determine protein dynamics (discussed in [9]). This topic, is open to discussion [4,10,11,12]. It has been argued that under severe pleiotropic stress conditions, the contributions of protein-level regulation, translation rate (TLR) and protein stability (PS) are more important
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