Structure prediction and analysis of DNA transposon and LINE retrotransposon proteins

G. Abrusán, Yang Zhang, András Szilágyi

Research output: Article

6 Citations (Scopus)

Abstract

Despite the considerable amount of research on transposable elements, no large-scale structural analyses of the TE proteome have been performed so far. We predicted the structures of hundreds of proteins from a representative set of DNA and LINE transposable elements and used the obtained structural data to provide the first general structural characterization of TE proteins and to estimate the frequency of TE domestication and horizontal transfer events. We show that 1) ORF1 and Gag proteins of retrotransposons contain high amounts of structural disorder; thus, despite their very low conservation, the presence of disordered regions and probably their chaperone function is conserved. 2) The distribution of SCOP classes in DNA transposons and LINEs indicates that the proteins of DNA transposons are more ancient, containing folds that already existed when the first cellular organisms appeared. 3) DNA transposon proteins have lower contact order than randomly selected reference proteins, indicating rapid folding, most likely to avoid protein aggregation. 4) Structure-based searches for TE homologs indicate that the overall frequency of TE domestication events is low, whereas we found a relatively high number of cases where horizontal transfer, frequently involving parasites, is the most likely explanation for the observed homology.

Original languageEnglish
Pages (from-to)16127-16138
Number of pages12
JournalJournal of Biological Chemistry
Volume288
Issue number22
DOIs
Publication statusPublished - máj. 31 2013

Fingerprint

Retroelements
DNA Transposable Elements
Proteins
gag Gene Products
Proteome
Conservation
Parasites
Agglomeration
DNA
Research

ASJC Scopus subject areas

  • Biochemistry
  • Cell Biology
  • Molecular Biology

Cite this

Structure prediction and analysis of DNA transposon and LINE retrotransposon proteins. / Abrusán, G.; Zhang, Yang; Szilágyi, András.

In: Journal of Biological Chemistry, Vol. 288, No. 22, 31.05.2013, p. 16127-16138.

Research output: Article

Abrusán, G. ; Zhang, Yang ; Szilágyi, András. / Structure prediction and analysis of DNA transposon and LINE retrotransposon proteins. In: Journal of Biological Chemistry. 2013 ; Vol. 288, No. 22. pp. 16127-16138.
@article{d9a6242171b94f3193b391f815bf4e6a,
title = "Structure prediction and analysis of DNA transposon and LINE retrotransposon proteins",
abstract = "Despite the considerable amount of research on transposable elements, no large-scale structural analyses of the TE proteome have been performed so far. We predicted the structures of hundreds of proteins from a representative set of DNA and LINE transposable elements and used the obtained structural data to provide the first general structural characterization of TE proteins and to estimate the frequency of TE domestication and horizontal transfer events. We show that 1) ORF1 and Gag proteins of retrotransposons contain high amounts of structural disorder; thus, despite their very low conservation, the presence of disordered regions and probably their chaperone function is conserved. 2) The distribution of SCOP classes in DNA transposons and LINEs indicates that the proteins of DNA transposons are more ancient, containing folds that already existed when the first cellular organisms appeared. 3) DNA transposon proteins have lower contact order than randomly selected reference proteins, indicating rapid folding, most likely to avoid protein aggregation. 4) Structure-based searches for TE homologs indicate that the overall frequency of TE domestication events is low, whereas we found a relatively high number of cases where horizontal transfer, frequently involving parasites, is the most likely explanation for the observed homology.",
author = "G. Abrus{\'a}n and Yang Zhang and Andr{\'a}s Szil{\'a}gyi",
year = "2013",
month = "5",
day = "31",
doi = "10.1074/jbc.M113.451500",
language = "English",
volume = "288",
pages = "16127--16138",
journal = "Journal of Biological Chemistry",
issn = "0021-9258",
publisher = "American Society for Biochemistry and Molecular Biology Inc.",
number = "22",

}

TY - JOUR

T1 - Structure prediction and analysis of DNA transposon and LINE retrotransposon proteins

AU - Abrusán, G.

AU - Zhang, Yang

AU - Szilágyi, András

PY - 2013/5/31

Y1 - 2013/5/31

N2 - Despite the considerable amount of research on transposable elements, no large-scale structural analyses of the TE proteome have been performed so far. We predicted the structures of hundreds of proteins from a representative set of DNA and LINE transposable elements and used the obtained structural data to provide the first general structural characterization of TE proteins and to estimate the frequency of TE domestication and horizontal transfer events. We show that 1) ORF1 and Gag proteins of retrotransposons contain high amounts of structural disorder; thus, despite their very low conservation, the presence of disordered regions and probably their chaperone function is conserved. 2) The distribution of SCOP classes in DNA transposons and LINEs indicates that the proteins of DNA transposons are more ancient, containing folds that already existed when the first cellular organisms appeared. 3) DNA transposon proteins have lower contact order than randomly selected reference proteins, indicating rapid folding, most likely to avoid protein aggregation. 4) Structure-based searches for TE homologs indicate that the overall frequency of TE domestication events is low, whereas we found a relatively high number of cases where horizontal transfer, frequently involving parasites, is the most likely explanation for the observed homology.

AB - Despite the considerable amount of research on transposable elements, no large-scale structural analyses of the TE proteome have been performed so far. We predicted the structures of hundreds of proteins from a representative set of DNA and LINE transposable elements and used the obtained structural data to provide the first general structural characterization of TE proteins and to estimate the frequency of TE domestication and horizontal transfer events. We show that 1) ORF1 and Gag proteins of retrotransposons contain high amounts of structural disorder; thus, despite their very low conservation, the presence of disordered regions and probably their chaperone function is conserved. 2) The distribution of SCOP classes in DNA transposons and LINEs indicates that the proteins of DNA transposons are more ancient, containing folds that already existed when the first cellular organisms appeared. 3) DNA transposon proteins have lower contact order than randomly selected reference proteins, indicating rapid folding, most likely to avoid protein aggregation. 4) Structure-based searches for TE homologs indicate that the overall frequency of TE domestication events is low, whereas we found a relatively high number of cases where horizontal transfer, frequently involving parasites, is the most likely explanation for the observed homology.

UR - http://www.scopus.com/inward/record.url?scp=84878391284&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84878391284&partnerID=8YFLogxK

U2 - 10.1074/jbc.M113.451500

DO - 10.1074/jbc.M113.451500

M3 - Article

VL - 288

SP - 16127

EP - 16138

JO - Journal of Biological Chemistry

JF - Journal of Biological Chemistry

SN - 0021-9258

IS - 22

ER -