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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| Format: | Article |
| Language: | English |
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Nature Portfolio
2021-06-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-021-90498-8 |
| _version_ | 1818434990467186688 |
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| author | M. Fayez Aziz Gustavo Caetano-Anollés |
| author_facet | M. Fayez Aziz Gustavo Caetano-Anollés |
| author_sort | M. Fayez Aziz |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-14T16:45:46Z |
| format | Article |
| id | doaj.art-5e3ea5d14cda4503a3a348ecdbd00710 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-12-14T16:45:46Z |
| publishDate | 2021-06-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-5e3ea5d14cda4503a3a348ecdbd007102022-12-21T22:54:11ZengNature PortfolioScientific Reports2045-23222021-06-0111111810.1038/s41598-021-90498-8Evolution of networks of protein domain organizationM. Fayez Aziz0Gustavo Caetano-Anollés1Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of IllinoisEvolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of IllinoisAbstract 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.https://doi.org/10.1038/s41598-021-90498-8 |
| spellingShingle | M. Fayez Aziz Gustavo Caetano-Anollés Evolution of networks of protein domain organization Scientific Reports |
| title | 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_short | Evolution of networks of protein domain organization |
| title_sort | evolution of networks of protein domain organization |
| url | https://doi.org/10.1038/s41598-021-90498-8 |
| work_keys_str_mv | AT mfayezaziz evolutionofnetworksofproteindomainorganization AT gustavocaetanoanolles evolutionofnetworksofproteindomainorganization |