Element:Retrosat-2

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Description

Retrosat-2 is a LTR retrotransposon described nested with Retrosat-1 (another LTR retrotransposon) in the genome Oryza sativa (Llaca et al 1998). Retrosat-2 belongs to the Chromoviridae branch, term suggested (Marín and Lloréns 2000) to describe the Ty3/Gypsy elements bearing chromodomain-integrases (Malik and Eickbush 1999). The chromovirus branch is probably the most ancient phylogenetic pattern of Ty3/Gypsy retroelements (Gorinsek, Gubensek and Kordis 2004; 2005; Kordis 2005).

At the genomic structure level Retrosat-2 is 12.7 Kb in size, including LTRs of 3.2 Kb. The internal region of this element displays a Primer Binding Site (PBS), a single Open Reading Frame (ORF) coding for a gag-pol precursor, and a Polypurine Tract (PPT) adjacent to the 3´LTR (Llaca et al 1998). This element presents a detectable chromodomain at the C-terminal end of the integrase domain. The PBS of fungi and vertebrate chromoviruses, differs significantly from that used by plant chromoviruses. While plant chromoviruses use a methionine starting tRNA (iMet), fungi and vertebrate chromoviruses use their own self-priming mechanism to start the reverse transcription (Levin 1995 ; Butler et al. 2001).

Structure

Retrosat-2.png


Figure not to scale. If present, long terminal repeats (LTRs) have been highlighted in blue. Amino acid motifs noted with lines indicate the conserved residues in each protein domain, abbreviations below mean:

MA=matrix PR=protease DU or DUT=dUTPase TM=transmembrane TAV or IBMP=transactivator/viroplasmin or inclusion body matrix protein
CA=capsid RT=reverse transcriptase INT=Integrase CHR=chromodomain
NC=nucleocapsid RH=RNaseH SU=surface MOV=movement protein
PPT=polypurine tract PBS=primer binding site ATF=aphid transmission factor VAP=virion associated protein

Related literature

Genbank accession: AF111709 (nuc. 25889- 38686)
Clade: Del
Cluster or genus: Plants
Branch or class: Chromoviruses
Family: Ty3/Gypsy
System: LTR retroelements
Host:
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Oryza sativa.gif
Oryza sativa
Image, Carlos Llorens,
Copyright, GyDB, Biotech Vana
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Welcome to the Gypsy Database (GyDB) an open editable database about the evolutionary relationship of viruses, mobile genetic elements (MGEs) and the genomic repeats where we invite all authors to contribute with their knowledge to improve and expand the topics.
Cite this project:

Llorens, C., Futami, R., Covelli, L., Dominguez-Escriba, L., Viu, J.M., Tamarit, D., Aguilar-Rodriguez, J. Vicente-Ripolles, M., Fuster, G., Bernet, G.P., Maumus, F., Munoz-Pomer, A., Sempere, J.M., LaTorre, A., Moya, A. (2011) The Gypsy Database (GyDB) of Mobile Genetic Elements: Release 2.0 Nucleic Acids Research (NARESE) 39 (suppl 1): D70-D74 doi: 10.1093/nar/gkq1061

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