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Tandem-repeat protein domains across the tree of life
- Source :
- PeerJ, Vol 3, p e732 (2015), PeerJ
- Publication Year :
- 2015
- Publisher :
- PeerJ Inc., 2015.
-
Abstract
- Tandem-repeat protein domains, composed of repeated units of conserved stretches of 20–40 amino acids, are required for a wide array of biological functions. Despite their diverse and fundamental functions, there has been no comprehensive assessment of their taxonomic distribution, incidence, and associations with organismal lifestyle and phylogeny. In this study, we assess for the first time the abundance of armadillo (ARM) and tetratricopeptide (TPR) repeat domains across all three domains in the tree of life and compare the results to our previous analysis on ankyrin (ANK) repeat domains in this journal. All eukaryotes and a majority of the bacterial and archaeal genomes analyzed have a minimum of one TPR and ARM repeat. In eukaryotes, the fraction of ARM-containing proteins is approximately double that of TPR and ANK-containing proteins, whereas bacteria and archaea are enriched in TPR-containing proteins relative to ARM- and ANK-containing proteins. We show in bacteria that phylogenetic history, rather than lifestyle or pathogenicity, is a predictor of TPR repeat domain abundance, while neither phylogenetic history nor lifestyle predicts ARM repeat domain abundance. Surprisingly, pathogenic bacteria were not enriched in TPR-containing proteins, which have been associated within virulence factors in certain species. Taken together, this comparative analysis provides a newly appreciated view of the prevalence and diversity of multiple types of tandem-repeat protein domains across the tree of life. A central finding of this analysis is that tandem repeat domain-containing proteins are prevalent not just in eukaryotes, but also in bacterial and archaeal species.
- Subjects :
- Protein domain
Protein domains
lcsh:Medicine
Biology
Tetratricopeptide repeat domains
Genome
Microbiology
General Biochemistry, Genetics and Molecular Biology
Ankyrin repeat domains
03 medical and health sciences
Tandem repeat
Phylogenetics
Ankyrin
Symbiosis
030304 developmental biology
Genetics
chemistry.chemical_classification
0303 health sciences
Phylogenetic tree
Bacteria
General Neuroscience
030302 biochemistry & molecular biology
lcsh:R
General Medicine
biology.organism_classification
Archaea
Evolutionary Studies
Tetratricopeptide
chemistry
General Agricultural and Biological Sciences
Armadillo repeat domain
Subjects
Details
- Language :
- English
- ISSN :
- 21678359
- Volume :
- 3
- Database :
- OpenAIRE
- Journal :
- PeerJ
- Accession number :
- edsair.doi.dedup.....4bafb42a988035d66ba701a62a292ccc