title: Context characterization of amino acid homorepeats using evolution, position, and order.
abstract: Amino acid repeats, or homorepeats, are low complexity protein motifs consisting of tandem repetitions of a single amino acid. Their presence and relative number vary in different proteomes, and some studies have tried to address this variation, proteome by proteome. In this work, we present a full characterization of amino acid homorepeats across evolution. We studied the presence and differential usage of each possible homorepeat in proteomes from various taxonomic groups, using clusters of very similar proteins to eliminate redundancy. The position of each amino acid repeat within proteins, and the order of co-occurring amino acid repeats were also addressed. As a result, we present evidence about the unevenly evolution of homorepeats, as well as the functional implications of their relative position in proteins. We discuss some of these cases in their taxonomic context. Collectively, our results show evolutionary and positional signals that suggest that homorepeats have biological function, likely creating unspecific protein interactions or modulating specific interactions in a context dependent manner. In conclusion, our work supports the functional importance of homorepeats and establishes a basis for the study of other low complexity repeats. Proteins 2017; 85:709-719. © 2016 Wiley Periodicals, Inc.
authors.affiliation: Faculty of Biology, Johannes Gutenberg University Mainz, Gresemundweg 2, Mainz, 55128, Germany.|Institute of Molecular Biology, Ackermannweg 4, Mainz, 55128, Germany.
authors.forename: Pablo
authors.identifier: 0000-0003-3663-2352
authors.initials: P
authors.lastname: Mier
authors.affiliation: Faculty of Biology, Johannes Gutenberg University Mainz, Gresemundweg 2, Mainz, 55128, Germany.|Institute of Molecular Biology, Ackermannweg 4, Mainz, 55128, Germany.
authors.forename: Gregorio
authors.initials: G
authors.lastname: Alanis-Lobato
authors.affiliation: Faculty of Biology, Johannes Gutenberg University Mainz, Gresemundweg 2, Mainz, 55128, Germany.|Institute of Molecular Biology, Ackermannweg 4, Mainz, 55128, Germany.
authors.forename: Miguel A
authors.initials: MA
authors.lastname: Andrade-Navarro
mesh_terms: D030562:Databases, Protein; D004023:Dictyostelium / Q000145:classification / Q000235:genetics*; D056890:Eukaryota / Q000145:classification / Q000235:genetics*; D019143:Evolution, Molecular; D006801:Humans / Q000235:genetics; D010802:Phylogeny; D011387:Prokaryotic Cells / Q000145:classification / Q000378:metabolism; D020543:Proteome; D040901:Proteomics / Q000379:methods; D020449:Repetitive Sequences, Amino Acid / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000145:classification / Q000235:genetics*; D020539:Sequence Analysis, Protein
chemical_list: D020543:Proteome
keywords: amino acid repeat; computational biology; data mining; evolutionary analysis; polyX