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A proteome view of structural, functional, and taxonomic characteristics of major
protein domain clusters
#MMPMID29079755
Sun CT
; Chiang AWT
; Hwang MJ
Sci Rep
2017[Oct]; 7
(1
): 14210
PMID29079755
show ga
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.
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