Tracing protein and proteome history with chronologies and networks: folding recapitulates evolution

Introduction While the origin and evolution of proteins remain mysterious, advances in evolutionary genomics and systems biology are facilitating the historical exploration of the structure, function and organization of proteins and proteomes. Molecular chronologies are series of time events describing the history of biological systems and subsystems and the rise of biological innovations. Together with time-varying networks, these chronologies provide a window into the past. Areas covered Here, we review molecular chronologies and networks built with modern methods of phylogeny reconstruction. We discuss how chronologies of structural domain families uncover the explosive emergence of metabolism, the late rise of translation, the co-evolution of ribosomal proteins and rRNA, and the late development of the ribosomal exit tunnel; events that coincided with a tendency to shorten folding time. Evolving networks described the early emergence of domains and a late 'big bang' of domain combinations. Expert opinion Two processes, folding and recruitment appear central to the evolutionary progression. The former increases protein persistence. The later fosters diversity. Chronologically, protein evolution mirrors folding by combining supersecondary structures into domains, developing translation machinery to facilitate folding speed and stability, and enhancing structural complexity by establishing long-distance interactions in novel structural and architectural designs.

Automated summary

The origin and evolution of proteins continues to be a mystery, but advancements in evolutionary genomics and systems biology are enabling the exploration of proteins and proteomes. Molecular chronologies and networks are providing insights into the history of biological systems and the rise of biological innovations. Two key processes, folding and recruitment, play central roles in evolutionary progression, with protein evolution mirroring folding and developing mechanisms to enhance stability, speed, and complexity.