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Conserved structure and inferred evolutionary history of long terminal repeats (LTRs)

BACKGROUND: Long terminal repeats (LTRs, consisting of U3-R-U5 portions) are important elements of retroviruses and related retrotransposons. They are difficult to analyse due to their variability. The aim was to obtain a more comprehensive view of structure, diversity and phylogeny of LTRs than hit...

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Autores principales: Benachenhou, Farid, Sperber, Göran O, Bongcam-Rudloff, Erik, Andersson, Göran, Boeke, Jef D, Blomberg, Jonas
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3601003/
https://www.ncbi.nlm.nih.gov/pubmed/23369192
http://dx.doi.org/10.1186/1759-8753-4-5
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author Benachenhou, Farid
Sperber, Göran O
Bongcam-Rudloff, Erik
Andersson, Göran
Boeke, Jef D
Blomberg, Jonas
author_facet Benachenhou, Farid
Sperber, Göran O
Bongcam-Rudloff, Erik
Andersson, Göran
Boeke, Jef D
Blomberg, Jonas
author_sort Benachenhou, Farid
collection PubMed
description BACKGROUND: Long terminal repeats (LTRs, consisting of U3-R-U5 portions) are important elements of retroviruses and related retrotransposons. They are difficult to analyse due to their variability. The aim was to obtain a more comprehensive view of structure, diversity and phylogeny of LTRs than hitherto possible. RESULTS: Hidden Markov models (HMM) were created for 11 clades of LTRs belonging to Retroviridae (class III retroviruses), animal Metaviridae (Gypsy/Ty3) elements and plant Pseudoviridae (Copia/Ty1) elements, complementing our work with Orthoretrovirus HMMs. The great variation in LTR length of plant Metaviridae and the few divergent animal Pseudoviridae prevented building HMMs from both of these groups. Animal Metaviridae LTRs had the same conserved motifs as retroviral LTRs, confirming that the two groups are closely related. The conserved motifs were the short inverted repeats (SIRs), integrase recognition signals (5´TGTTRNR…YNYAACA 3´); the polyadenylation signal or AATAAA motif; a GT-rich stretch downstream of the polyadenylation signal; and a less conserved AT-rich stretch corresponding to the core promoter element, the TATA box. Plant Pseudoviridae LTRs differed slightly in having a conserved TATA-box, TATATA, but no conserved polyadenylation signal, plus a much shorter R region. The sensitivity of the HMMs for detection in genomic sequences was around 50% for most models, at a relatively high specificity, suitable for genome screening. The HMMs yielded consensus sequences, which were aligned by creating an HMM model (a ‘Superviterbi’ alignment). This yielded a phylogenetic tree that was compared with a Pol-based tree. Both LTR and Pol trees supported monophyly of retroviruses. In both, Pseudoviridae was ancestral to all other LTR retrotransposons. However, the LTR trees showed the chromovirus portion of Metaviridae clustering together with Pseudoviridae, dividing Metaviridae into two portions with distinct phylogeny. CONCLUSION: The HMMs clearly demonstrated a unitary conserved structure of LTRs, supporting that they arose once during evolution. We attempted to follow the evolution of LTRs by tracing their functional foundations, that is, acquisition of RNAse H, a combined promoter/ polyadenylation site, integrase, hairpin priming and the primer binding site (PBS). Available information did not support a simple evolutionary chain of events.
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spelling pubmed-36010032013-03-19 Conserved structure and inferred evolutionary history of long terminal repeats (LTRs) Benachenhou, Farid Sperber, Göran O Bongcam-Rudloff, Erik Andersson, Göran Boeke, Jef D Blomberg, Jonas Mob DNA Research BACKGROUND: Long terminal repeats (LTRs, consisting of U3-R-U5 portions) are important elements of retroviruses and related retrotransposons. They are difficult to analyse due to their variability. The aim was to obtain a more comprehensive view of structure, diversity and phylogeny of LTRs than hitherto possible. RESULTS: Hidden Markov models (HMM) were created for 11 clades of LTRs belonging to Retroviridae (class III retroviruses), animal Metaviridae (Gypsy/Ty3) elements and plant Pseudoviridae (Copia/Ty1) elements, complementing our work with Orthoretrovirus HMMs. The great variation in LTR length of plant Metaviridae and the few divergent animal Pseudoviridae prevented building HMMs from both of these groups. Animal Metaviridae LTRs had the same conserved motifs as retroviral LTRs, confirming that the two groups are closely related. The conserved motifs were the short inverted repeats (SIRs), integrase recognition signals (5´TGTTRNR…YNYAACA 3´); the polyadenylation signal or AATAAA motif; a GT-rich stretch downstream of the polyadenylation signal; and a less conserved AT-rich stretch corresponding to the core promoter element, the TATA box. Plant Pseudoviridae LTRs differed slightly in having a conserved TATA-box, TATATA, but no conserved polyadenylation signal, plus a much shorter R region. The sensitivity of the HMMs for detection in genomic sequences was around 50% for most models, at a relatively high specificity, suitable for genome screening. The HMMs yielded consensus sequences, which were aligned by creating an HMM model (a ‘Superviterbi’ alignment). This yielded a phylogenetic tree that was compared with a Pol-based tree. Both LTR and Pol trees supported monophyly of retroviruses. In both, Pseudoviridae was ancestral to all other LTR retrotransposons. However, the LTR trees showed the chromovirus portion of Metaviridae clustering together with Pseudoviridae, dividing Metaviridae into two portions with distinct phylogeny. CONCLUSION: The HMMs clearly demonstrated a unitary conserved structure of LTRs, supporting that they arose once during evolution. We attempted to follow the evolution of LTRs by tracing their functional foundations, that is, acquisition of RNAse H, a combined promoter/ polyadenylation site, integrase, hairpin priming and the primer binding site (PBS). Available information did not support a simple evolutionary chain of events. BioMed Central 2013-02-01 /pmc/articles/PMC3601003/ /pubmed/23369192 http://dx.doi.org/10.1186/1759-8753-4-5 Text en Copyright ©2013 Benachenhou et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research
Benachenhou, Farid
Sperber, Göran O
Bongcam-Rudloff, Erik
Andersson, Göran
Boeke, Jef D
Blomberg, Jonas
Conserved structure and inferred evolutionary history of long terminal repeats (LTRs)
title Conserved structure and inferred evolutionary history of long terminal repeats (LTRs)
title_full Conserved structure and inferred evolutionary history of long terminal repeats (LTRs)
title_fullStr Conserved structure and inferred evolutionary history of long terminal repeats (LTRs)
title_full_unstemmed Conserved structure and inferred evolutionary history of long terminal repeats (LTRs)
title_short Conserved structure and inferred evolutionary history of long terminal repeats (LTRs)
title_sort conserved structure and inferred evolutionary history of long terminal repeats (ltrs)
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3601003/
https://www.ncbi.nlm.nih.gov/pubmed/23369192
http://dx.doi.org/10.1186/1759-8753-4-5
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