Systems biology invites us to consider the dynamic interactions between the components of a living cell. Here, by evolving artificial organisms whose genomes encode protein networks, we show that a coupling emerges at the evolutionary time scale between the protein network and the structure of the genome. Gene order is more stable when the protein network is more densely connected, which most likely results from a long-term selection for mutational robustness. Understanding evolving organisms thus requires a systemic approach, taking into account the functional interactions between gene products, but also the global relationships between the genome and the proteome at the evolutionary time scale.

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