Element:REM1

From The Gypsy Database

Description

REM1 is a LTR retrotransposon characterized in the green algae Chlamydomonas reinhardtii (Perez Alegre et al. 2005). REM1 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 has been disclosed to be the most ancient phylogenetic pattern of Ty3/Gypsy retroelements (Gorinsek, Gubensek and Kordis 2004; 2005; Kordis 2005).

The genomic structure of REM1 is 5.8 Kb in size, including LTRs of 276-286 nt in size. The internal region displays a Primer Binding Site (PBS), and a Polypurine Tract (PPT) adjacent to the 3´LTR (Perez Alegre et al. 2005). The internal region also shows three Open Reading Frames (ORFs); two for the typical gag, and pol genes of LTR retrotransposons and another, in reverse frame, showing part of the integrase and the chromodomain typical of Ty3/Gypsy chromoviruses. This is, although the original description performed in (Perez Alegre et al. 2005) reported no RNAse H and Integrase domains in the typical pol frame, subsequent analyses revealed an small RNAse H domain after reverse transcriptase and that the third ORF in reverse frame is the rest of a putative rearrangement and partial loose of the original integrase of this element (Llorens et al. 2009).

Structure

Rem1.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:29423675
Clade:REM
Cluster or genus:Plants
Branch or class:Chromoviruses
Family:Ty3/Gypsy
System:LTR retroelements
Host:
Explore the Tree Life Project
Chlamydomonas reinhardtii.jpg
Chlamydomonas reinhardtii
Dartmouth Electron Microscope Facility, Dartmouth College
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