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Mobile DNA

, 4:5

First Online: 01 February 2013Received: 17 July 2012Accepted: 14 December 2012


BackgroundLong 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.

ResultsHidden 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 5TGTTRNR…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.

ConclusionThe 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.

KeywordsLTR Long terminal repeat Retrotransposon Retrovirus Phylogeny Genome evolution AbbreviationsERVEndogenous retrovirus

gagGroup antigen gene, encoding structural proteins

GagGroup antigen protein

GPY-F domainA portion of the integrase C-terminal domain

HIVHuman immunodeficiency virus

HERVHuman endogenous retrovirus

HMLHuman MMTV-like sequence

HMMHidden Markov model

ICTVInternational Commission for Taxonomy of Viruses

INRInitiator of transcription

ININT: Integrase

IRInverted repeat

LTRLong terminal repeat

MMTVMouse mammary tumour virus

PASPolyadenylation site

PBSPrimer binding site

PolPolymerase protein

PROProtease domain

PPTPolypurine tract

RRepeat portion of LTR

RHRnase H

RTReverse transcriptase

SIRShort inverted repeat

TIRTerminal inverted repeat

TSDTarget site duplication

TSSTranscriptional start site

U3Unique 3 LTR portion

U5Unique 5 LTR portion

XRVExogenous retrovirus.

Electronic supplementary materialThe online version of this article doi:10.1186-1759-8753-4-5 contains supplementary material, which is available to authorized users.

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Autor: Farid Benachenhou - Göran O Sperber - Erik Bongcam-Rudloff - Göran Andersson - Jef D Boeke - Jonas Blomberg


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