Evolution of networks of protein domain organization

Abstract Domains are the structural, functional and evolutionary units of proteins. They combine to form multidomain proteins. The evolutionary history of this molecular combinatorics has been studied with phylogenomic methods. Here, we construct networks of domain organization and explore their evo...

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Autores principales:	M. Fayez Aziz, Gustavo Caetano-Anollés
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/5e3ea5d14cda4503a3a348ecdbd00710
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spelling	oai:doaj.org-article:5e3ea5d14cda4503a3a348ecdbd007102021-12-02T17:52:31ZEvolution of networks of protein domain organization10.1038/s41598-021-90498-82045-2322https://doaj.org/article/5e3ea5d14cda4503a3a348ecdbd007102021-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-90498-8https://doaj.org/toc/2045-2322Abstract Domains are the structural, functional and evolutionary units of proteins. They combine to form multidomain proteins. The evolutionary history of this molecular combinatorics has been studied with phylogenomic methods. Here, we construct networks of domain organization and explore their evolution. A time series of networks revealed two ancient waves of structural novelty arising from ancient ‘p-loop’ and ‘winged helix’ domains and a massive ‘big bang’ of domain organization. The evolutionary recruitment of domains was highly modular, hierarchical and ongoing. Domain rearrangements elicited non-random and scale-free network structure. Comparative analyses of preferential attachment, randomness and modularity showed yin-and-yang complementary transition and biphasic patterns along the structural chronology. Remarkably, the evolving networks highlighted a central evolutionary role of cofactor-supporting structures of non-ribosomal peptide synthesis pathways, likely crucial to the early development of the genetic code. Some highly modular domains featured dual response regulation in two-component signal transduction systems with DNA-binding activity linked to transcriptional regulation of responses to environmental change. Interestingly, hub domains across the evolving networks shared the historical role of DNA binding and editing, an ancient protein function in molecular evolution. Our investigation unfolds historical source-sink patterns of evolutionary recruitment that further our understanding of protein architectures and functions.M. Fayez AzizGustavo Caetano-AnollésNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-18 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q M. Fayez Aziz Gustavo Caetano-Anollés Evolution of networks of protein domain organization
description	Abstract Domains are the structural, functional and evolutionary units of proteins. They combine to form multidomain proteins. The evolutionary history of this molecular combinatorics has been studied with phylogenomic methods. Here, we construct networks of domain organization and explore their evolution. A time series of networks revealed two ancient waves of structural novelty arising from ancient ‘p-loop’ and ‘winged helix’ domains and a massive ‘big bang’ of domain organization. The evolutionary recruitment of domains was highly modular, hierarchical and ongoing. Domain rearrangements elicited non-random and scale-free network structure. Comparative analyses of preferential attachment, randomness and modularity showed yin-and-yang complementary transition and biphasic patterns along the structural chronology. Remarkably, the evolving networks highlighted a central evolutionary role of cofactor-supporting structures of non-ribosomal peptide synthesis pathways, likely crucial to the early development of the genetic code. Some highly modular domains featured dual response regulation in two-component signal transduction systems with DNA-binding activity linked to transcriptional regulation of responses to environmental change. Interestingly, hub domains across the evolving networks shared the historical role of DNA binding and editing, an ancient protein function in molecular evolution. Our investigation unfolds historical source-sink patterns of evolutionary recruitment that further our understanding of protein architectures and functions.
format	article
author	M. Fayez Aziz Gustavo Caetano-Anollés
author_facet	M. Fayez Aziz Gustavo Caetano-Anollés
author_sort	M. Fayez Aziz
title	Evolution of networks of protein domain organization
title_short	Evolution of networks of protein domain organization
title_full	Evolution of networks of protein domain organization
title_fullStr	Evolution of networks of protein domain organization
title_full_unstemmed	Evolution of networks of protein domain organization
title_sort	evolution of networks of protein domain organization
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/5e3ea5d14cda4503a3a348ecdbd00710
work_keys_str_mv	AT mfayezaziz evolutionofnetworksofproteindomainorganization AT gustavocaetanoanolles evolutionofnetworksofproteindomainorganization
_version_	1718379170304622592

Evolution of networks of protein domain organization

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