TY - JOUR
T1 - Tracing protein and proteome history with chronologies and networks
T2 - folding recapitulates evolution
AU - Caetano-Anollés, Gustavo
AU - Aziz, M. Fayez
AU - Mughal, Fizza
AU - Caetano-Anollés, Derek
N1 - Funding Information:
Supported by grants from the National Institute of Food and Agriculture of the United States Department of Agriculture (ILLU-802-909 and ILLU-483-625) and allocations from the National Center for Supercomputer Applications (NCSA).
Publisher Copyright:
© 2021 Informa UK Limited, trading as Taylor & Francis Group.
PY - 2021
Y1 - 2021
N2 - 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.
AB - 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.
KW - Cotranslational folding
KW - RNA structure
KW - domains
KW - evolution
KW - folding
KW - modularity
KW - multicellularity
KW - networks
KW - protein structure
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U2 - 10.1080/14789450.2021.1992277
DO - 10.1080/14789450.2021.1992277
M3 - Review article
C2 - 34628994
AN - SCOPUS:85119608673
VL - 18
SP - 863
EP - 880
JO - Expert Review of Proteomics
JF - Expert Review of Proteomics
SN - 1478-9450
IS - 10
ER -