Change search
ReferencesLink to record
Permanent link

Direct link
Conserved structure and inferred evolutionary history of long terminal repeats (LTRs)
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine, Clinical Virology.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Physiology.
Show others and affiliations
2013 (English)In: Mobile DNA, ISSN 1759-8753, Vol. 4, 5- p.Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
2013. Vol. 4, 5- p.
Keyword [en]
LTR, Long terminal repeat, Retrotransposon, Retrovirus, Phylogeny, Genome evolution
National Category
Medical and Health Sciences
URN: urn:nbn:se:uu:diva-200830DOI: 10.1186/1759-8753-4-5ISI: 000318308200001OAI: diva2:625089
Available from: 2013-06-04 Created: 2013-06-04 Last updated: 2013-06-04Bibliographically approved

Open Access in DiVA

fulltext(1256 kB)92 downloads
File information
File name FULLTEXT01.pdfFile size 1256 kBChecksum SHA-512
Type fulltextMimetype application/pdf

Other links

Publisher's full text

Search in DiVA

By author/editor
Sperber, Göran O.Blomberg, Jonas
By organisation
Clinical VirologyPhysiology
In the same journal
Mobile DNA
Medical and Health Sciences

Search outside of DiVA

GoogleGoogle Scholar
Total: 92 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

Altmetric score

Total: 168 hits
ReferencesLink to record
Permanent link

Direct link