A proteome view of structural, functional, and taxonomic characteristics of major protein domain clusters

Abstract Proteome-scale bioinformatics research is increasingly conducted as the number of completely sequenced genomes increases, but analysis of protein domains (PDs) usually relies on similarity in their amino acid sequences and/or three-dimensional structures. Here, we present results from a bi-...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Chia-Tsen Sun, Austin W. T. Chiang, Ming-Jing Hwang
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/2b8ec53997fe4196aaff8ed8790d6336
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:2b8ec53997fe4196aaff8ed8790d6336
record_format	dspace
spelling	oai:doaj.org-article:2b8ec53997fe4196aaff8ed8790d63362021-12-02T11:40:44ZA proteome view of structural, functional, and taxonomic characteristics of major protein domain clusters10.1038/s41598-017-13297-02045-2322https://doaj.org/article/2b8ec53997fe4196aaff8ed8790d63362017-10-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-13297-0https://doaj.org/toc/2045-2322Abstract Proteome-scale bioinformatics research is increasingly conducted as the number of completely sequenced genomes increases, but analysis of protein domains (PDs) usually relies on similarity in their amino acid sequences and/or three-dimensional structures. Here, we present results from a bi-clustering analysis on presence/absence data for 6,580 unique PDs in 2,134 species with a sequenced genome, thus covering a complete set of proteins, for the three superkingdoms of life, Bacteria, Archaea, and Eukarya. Our analysis revealed eight distinctive PD clusters, which, following an analysis of enrichment of Gene Ontology functions and CATH classification of protein structures, were shown to exhibit structural and functional properties that are taxa-characteristic. For examples, the largest cluster is ubiquitous in all three superkingdoms, constituting a set of 1,472 persistent domains created early in evolution and retained in living organisms and characterized by basic cellular functions and ancient structural architectures, while an Archaea and Eukarya bi-superkingdom cluster suggests its PDs may have existed in the ancestor of the two superkingdoms, and others are single superkingdom- or taxa (e.g. Fungi)-specific. These results contribute to increase our appreciation of PD diversity and our knowledge of how PDs are used in species, yielding implications on species evolution.Chia-Tsen SunAustin W. T. ChiangMing-Jing HwangNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-9 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Chia-Tsen Sun Austin W. T. Chiang Ming-Jing Hwang A proteome view of structural, functional, and taxonomic characteristics of major protein domain clusters
description	Abstract Proteome-scale bioinformatics research is increasingly conducted as the number of completely sequenced genomes increases, but analysis of protein domains (PDs) usually relies on similarity in their amino acid sequences and/or three-dimensional structures. Here, we present results from a bi-clustering analysis on presence/absence data for 6,580 unique PDs in 2,134 species with a sequenced genome, thus covering a complete set of proteins, for the three superkingdoms of life, Bacteria, Archaea, and Eukarya. Our analysis revealed eight distinctive PD clusters, which, following an analysis of enrichment of Gene Ontology functions and CATH classification of protein structures, were shown to exhibit structural and functional properties that are taxa-characteristic. For examples, the largest cluster is ubiquitous in all three superkingdoms, constituting a set of 1,472 persistent domains created early in evolution and retained in living organisms and characterized by basic cellular functions and ancient structural architectures, while an Archaea and Eukarya bi-superkingdom cluster suggests its PDs may have existed in the ancestor of the two superkingdoms, and others are single superkingdom- or taxa (e.g. Fungi)-specific. These results contribute to increase our appreciation of PD diversity and our knowledge of how PDs are used in species, yielding implications on species evolution.
format	article
author	Chia-Tsen Sun Austin W. T. Chiang Ming-Jing Hwang
author_facet	Chia-Tsen Sun Austin W. T. Chiang Ming-Jing Hwang
author_sort	Chia-Tsen Sun
title	A proteome view of structural, functional, and taxonomic characteristics of major protein domain clusters
title_short	A proteome view of structural, functional, and taxonomic characteristics of major protein domain clusters
title_full	A proteome view of structural, functional, and taxonomic characteristics of major protein domain clusters
title_fullStr	A proteome view of structural, functional, and taxonomic characteristics of major protein domain clusters
title_full_unstemmed	A proteome view of structural, functional, and taxonomic characteristics of major protein domain clusters
title_sort	proteome view of structural, functional, and taxonomic characteristics of major protein domain clusters
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/2b8ec53997fe4196aaff8ed8790d6336
work_keys_str_mv	AT chiatsensun aproteomeviewofstructuralfunctionalandtaxonomiccharacteristicsofmajorproteindomainclusters AT austinwtchiang aproteomeviewofstructuralfunctionalandtaxonomiccharacteristicsofmajorproteindomainclusters AT mingjinghwang aproteomeviewofstructuralfunctionalandtaxonomiccharacteristicsofmajorproteindomainclusters AT chiatsensun proteomeviewofstructuralfunctionalandtaxonomiccharacteristicsofmajorproteindomainclusters AT austinwtchiang proteomeviewofstructuralfunctionalandtaxonomiccharacteristicsofmajorproteindomainclusters AT mingjinghwang proteomeviewofstructuralfunctionalandtaxonomiccharacteristicsofmajorproteindomainclusters
_version_	1718395571699449856

A proteome view of structural, functional, and taxonomic characteristics of major protein domain clusters

Ejemplares similares