Proteotype coevolution and quantitative diversity across 11 mammalian species

Area of Science:

• Comparative genomics and proteomics
• Evolutionary biology
• Mammalian systems biology

Background:

• Evolutionary profiling traditionally focused on nucleotide sequences.
• Understanding proteomic and phosphoproteomic evolution provides deeper insights into species divergence.
• Gene expression variability exists at both interindividual and interspecies levels.

Purpose of the Study:

• To quantify and compare proteomic and phosphoproteomic layers across 11 mammalian species.
• To investigate the coevolution of transcriptomes and proteomes.
• To analyze evolutionary patterns in gene expression variability, protein degradation, and phosphorylation.

Main Methods:

• Consistent proteomic and phosphoproteomic quantification in fibroblasts from 11 mammalian species.
• Transcriptome data used as a reference.
• Covariation analysis to assess relationships between expression levels and variability.

Main Results:

• Transcript and protein expression levels and variability across mammals strongly correlate with functional roles, especially for extracellular matrix proteins, indicating significant transcriptome-proteome coevolution.
• RNA metabolic processes exhibit greater interspecies variation compared to interindividual variation.
• The ubiquitin-proteasome system is highly conserved, while lysosome-mediated protein degradation shows significant variation across mammalian lineages.
• Phosphosite profiles reveal a distinct coevolution network independent of protein abundance.

Conclusions:

• Gene expression variability is a universal biological phenomenon across different scales.
• Extracellular matrix proteins demonstrate substantial evolutionary plasticity.
• Protein degradation pathways, particularly lysosomal degradation, have evolved diversely across mammals.
• Phosphorylation patterns suggest an independent evolutionary trajectory from protein abundance.