Upstream Plasticity and Downstream Robustness in Evolution of Molecular Networks

TL;DR

This paper investigates how gene duplication affects the robustness and flexibility of molecular networks in yeast, revealing rapid divergence in transcriptional regulation but stability in physical interactions and functional roles.

Contribution

It provides quantitative analysis of divergence rates in transcriptional regulation versus physical interactions of duplicated genes in yeast.

Findings

Upstream transcriptional regulation diverges rapidly after gene duplication.

Physical interaction partners of proteins change slowly, maintaining network stability.

Duplicated genes can often substitute for each other in knockout experiments.

Abstract

Evolving biomolecular networks have to combine the stability against perturbations with flexibility allowing their constituents to assume new roles in the cell. Gene duplication followed by functional divergence of associated proteins is a major force shaping molecular networks in living organisms. Recent availability of system-wide data for yeast S. Cerevisiae allow us to access the effects of gene duplication on robustness and plasticity of molecular networks. We demonstrate that the upstream transcriptional regulation of duplicated genes diverges fast, losing on average 4% of their common transcription factors for every 1% divergence of their amino acid sequences. In contrast, the set of physical interaction partners of their protein products changes much slower. The relative stability of downstream functions of duplicated genes, is further corroborated by their ability to substitute for each other in gene knockout experiments. We believe that the combination of the upstream plasticity and the downstream robustness is a general feature determining the evolvability of molecular networks.