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Publication type: Article in scientific journal
Type of review: Peer review (publication)
Title: Deep conservation of human protein tandem repeats within the eukaryotes
Authors: Schaper, Elke
Gascuel, Olivier
Anisimova, Maria
DOI: 10.21256/zhaw-3885
Published in: Molecular Biology and Evolution
Volume(Issue): 31
Issue: 5
Page(s): 1132
Pages to: 1148
Issue Date: 2014
Publisher / Ed. Institution: Oxford University Press
ISSN: 0737-4038
Language: English
Subjects: Protein evolution; Tandem repeat; Conservation; Phylogenetic analysis
Subject (DDC): 572: Biochemistry
Abstract: Tandem repeats (TRs) are a major element of protein sequences in all domains of life. They are particularly abundant in mammals, where by conservative estimates one in three proteins contain a TR. High generation-scale duplication and deletion rates were reported for nucleic TR units. However, it is not known whether protein TR units can also be frequently lost or gained providing a source of variation for rapid adaptation of protein function, or alternatively, tend to have conserved TR unit configurations over long evolutionary times. To obtain a systematic picture for proteins TRs, we performed a proteome-wide analysis of the mode of evolution for human TRs. For this purpose, we propose a novel method for the detection of orthologous TRs based on circular profile hidden Markov models. For all detected TRs we reconstructed bi-species TR unit phylogenies across 61 eukaryotes ranging from human to yeast. Moreover, we performed additional analyses to correlate functional and structural annotations of human TRs with their mode of evolution. Surprisingly, we find that the vast majority of human TRs are ancient, with TR unit number and order preserved intact since distant speciation events. For example, ≥61% of all human TRs have been strongly conserved at least since the root of all mammals, approximately 300 Mya ago. Further, we find no human protein TR that shows evidence for strong recent duplications and deletions. The results are in contrast to high generation-scale mutability of nucleic TRs. Presumably, most protein TRs fold into stable and conserved structures that are indispensable for the function of the TR-containing protein. All of our data and results are available for download from
Fulltext version: Published version
License (according to publishing contract): CC BY 3.0: Attribution 3.0 Unported
Departement: Life Sciences and Facility Management
Organisational Unit: Institute of Computational Life Sciences (ICLS)
Appears in collections:Publikationen Life Sciences und Facility Management

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