Origin and evolution of protein fold designs inferred from phylogenomic analysis of CATH domain structures in proteomes.

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...

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Autores principales:	Syed Abbas Bukhari, Gustavo Caetano-Anollés
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/9ce1720015e3481b82b564b942dc3958
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spelling	oai:doaj.org-article:9ce1720015e3481b82b564b942dc39582021-11-18T05:52:16ZOrigin and evolution of protein fold designs inferred from phylogenomic analysis of CATH domain structures in proteomes.1553-734X1553-735810.1371/journal.pcbi.1003009https://doaj.org/article/9ce1720015e3481b82b564b942dc39582013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23555236/pdf/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358The 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.Syed Abbas BukhariGustavo Caetano-AnollésPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 9, Iss 3, p e1003009 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Syed Abbas Bukhari Gustavo Caetano-Anollés Origin and evolution of protein fold designs inferred from phylogenomic analysis of CATH domain structures in proteomes.
description	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.
format	article
author	Syed Abbas Bukhari Gustavo Caetano-Anollés
author_facet	Syed Abbas Bukhari Gustavo Caetano-Anollés
author_sort	Syed Abbas Bukhari
title	Origin and evolution of protein fold designs inferred from phylogenomic analysis of CATH domain structures in proteomes.
title_short	Origin and evolution of protein fold designs inferred from phylogenomic analysis of CATH domain structures in proteomes.
title_full	Origin and evolution of protein fold designs inferred from phylogenomic analysis of CATH domain structures in proteomes.
title_fullStr	Origin and evolution of protein fold designs inferred from phylogenomic analysis of CATH domain structures in proteomes.
title_full_unstemmed	Origin and evolution of protein fold designs inferred from phylogenomic analysis of CATH domain structures in proteomes.
title_sort	origin and evolution of protein fold designs inferred from phylogenomic analysis of cath domain structures in proteomes.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/9ce1720015e3481b82b564b942dc3958
work_keys_str_mv	AT syedabbasbukhari originandevolutionofproteinfolddesignsinferredfromphylogenomicanalysisofcathdomainstructuresinproteomes AT gustavocaetanoanolles originandevolutionofproteinfolddesignsinferredfromphylogenomicanalysisofcathdomainstructuresinproteomes
_version_	1718424746285072384

Origin and evolution of protein fold designs inferred from phylogenomic analysis of CATH domain structures in proteomes.

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