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

TL;DR

This paper reviews how molecular chronologies and networks reveal the evolutionary history of proteins, highlighting the role of folding and recruitment in shaping structural and functional diversity over time.

Contribution

It introduces modern methods of phylogeny reconstruction to trace protein and proteome evolution through chronologies and networks, emphasizing folding and recruitment processes.

Findings

Folding times shortened during evolution, enhancing protein stability.

Metabolism emerged explosively, followed by late development of translation.

Protein evolution mirrors folding processes through structural complexity.

Abstract

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.