Element:Endovir1-1

From The Gypsy Database

Description

Endovir1-1 is a LTR retroelement described in Arabidopsis thaliana (Peterson-Burch et al. 2000). Endovir1-1 belongs to the SIRE clade of Ty1/Copia plant LTR retrotransposons and potential retroviruses (Peterson-Burch et al. 2000; Fauquet et al. 2005;Peterson-Burch and Voytas, 2002), which is evolutionarily related to another clade called Oryco (Llorens et al. 2009). SIRE clade gives the name to a genus within the current ICTV classification of the Ty1/Copia into three genera – Pseudovirus, Hemivirus and Sirevirus (Boeke et al. 2005).

The full-lenght genome of Endovir1-1 is 9093 bp in size, including two 549-bp LTRs (Peterson-Burch et al. 2000). The internal region of this element contains a Primer Binding Site (PBS) complementary to a tRNAiMet, a coding region and a Polypurine tract (PPT) upstream its 3' LTR. The coding region displays two ORFs. The first ORF encodes for the typical gag and pol domains of Ty1/Copia LTR retrotransposons, while the second ORF, separated from the first one by 1031 nucleotides, contains the env-like domains that exhibit a 24% amino acid identity to SIRE-1 other sirevirus element (Peterson-Burch et al. 2000). In comparison to other Ty1/Copia elements, a taxonomically relevant feature specific of Sire-like elements is their extremely large gag c-terminus consistent with the NC domain, which may display two or three CCHC arrays (Llorens et al. 2009).

Structure

Endovir1-1.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:12584301
Clade:Sire
Cluster or genus:Sirevirus
Branch or class:Branch 2
Family:Ty1/Copia
System:LTR retroelements
Host:
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Arabidopsis thaliana.gif
Arabidopsis thaliana
Photo: www.knoch1.de
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