Abstract
The spatial arrangements of secondary structures in proteins, irrespective of their connectivity, depict the overall shape and organization of protein domains. These features have been used in the CATH and SCOP classifications to hierarchically partition fold space and define the architectural make up of proteins. Here we use phylogenomic methods and a census of CATH structures in hundreds of genomes to study the origin and diversification of protein architectures (A) and their associated topologies (T) and superfamilies (H). Phylogenies that describe the evolution of domain structures and proteomes were reconstructed from the structural census and used to generate timelines of domain discovery. Phylogenies of CATH domains at T and H levels of structural abstraction and associated chronologies revealed patterns of reductive evolution, the early rise of Archaea, three epochs in the evolution of the protein world, and patterns of structural sharing between superkingdoms. Phylogenies of proteomes confirmed the early appearance of Archaea. While these findings are in agreement with previous phylogenomic studies based on the SCOP classification, phylogenies unveiled sharing patterns between Archaea and Eukarya that are recent and can explain the canonical bacterial rooting typically recovered from sequence analysis. Phylogenies of CATH domains at A level uncovered general patterns of architectural origin and diversification. The tree of A structures showed that ancient structural designs such as the 3-layer (αβα) sandwich (3.40) or the orthogonal bundle (1.10) are comparatively simpler in their makeup and are involved in basic cellular functions. In contrast, modern structural designs such as prisms, propellers, 2-solenoid, super-roll, clam, trefoil and box are not widely distributed and were probably adopted to perform specialized functions. Our timelines therefore uncover a universal tendency towards protein structural complexity that is remarkable.
Highlights
The polypeptide chains of proteins generally fold into highly ordered and well-packed three-dimensional (3D) atomic structures [1]
Major conclusions In this study we follow the history of protein fold structures and proteomes in the tripartite world of organisms
Structural phylogenies describing the evolution of CATH domains at A, T and homology superfamilies (Hs) levels of structural abstraction revealed patterns of reductive evolution and the three epochs in the evolution of the protein world that were previously proposed [7]
Summary
The polypeptide chains of proteins generally fold into highly ordered and well-packed three-dimensional (3D) atomic structures [1]. These protein folds represent spatial arrangements of more or less wound helices (generally a-helices) and extended chain segments (b-strands) that are separated by flexible loops and relatively rigid regions in the form of turns and coils. CATH [6] uses a combination of automated and manual techniques, which include computational algorithms, empirical and statistical evidence, literature review and expert analysis. Both classifications are hierarchical but dissect 3D structure differently, focusing more on either evolutionary or structural considerations [4]. SCOP unifies domain structures that are evolutionarily related at sequence level (.30% pairwise residue identities) and are unambiguously linked to specific molecular functions into fold families (FFs), FFs with common structures and functions with a common evolutionary
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