Upstream plasticity and downstream robustness in evolution of molecular networks

Area of Science:

• Evolutionary biology
• Systems biology
• Genomics

Background:

• Gene duplication is a primary mechanism for molecular network evolution.
• Species-wide data on protein interactions and gene regulation enable studying duplication's impact on network robustness and plasticity.

Purpose of the Study:

• To investigate the impact of gene duplication on the robustness and plasticity of molecular networks.
• To compare the divergence rates of transcriptional regulation and protein-protein interactions in duplicated genes.

Main Methods:

• Analysis of protein-protein interaction and transcriptional regulation data in Saccharomyces cerevisiae, Caenorhabditis elegans, Helicobacter pylori, and Drosophila melanogaster.
• Quantification of divergence rates in transcriptional factors and protein interaction partners.
• Functional assessment through gene knockout and RNAi experiments.

Main Results:

• Transcriptional regulation of duplicated genes diverges rapidly (3% loss of common transcription factors per 1% amino acid sequence divergence).
• Protein-protein interaction networks diverge slowly, with stability above 70% sequence similarity.
• Duplicated genes maintain functional roles and network positions even at low sequence similarity (around 20%).
• Upstream gene regulation evolves faster than downstream protein functions in yeast.

Conclusions:

• Gene duplication significantly impacts molecular network evolution, with regulatory changes playing a crucial role.
• Paralogous proteins retain network similarity compared to random pairs, indicating conserved network positioning.
• Future research should explore whether findings for paralogs apply to orthologs across species.