Element:CRM

From The Gypsy Database

Description

CRM is a LTR retrotransposon characterized in Zea Mays (Zhong et al 2002).CRM 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). In chromoviruses, CRM gives the name and belongs to CRM clade; a centromere-associated sub-lineage characterized for encoding integrases which are clearly divergent from that encoded by other lineages of chromoviruses (Gorinsek, Gubensek and Kordis 2004).

The genomic structure of CRM is 7.6 Kb in size, including LTRs of 931 nt. The internal region displays a Primer Binding site (PBS), a single Open Reading Frame (ORF) gag-pol, and a Polypurine Tract (PPT) adjacent to the 3´LTR (Zhong et al 2002). 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

Crm.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:AY129008
Clade:CRM
Cluster or genus:Plants
Branch or class:Chromoviruses
Family:Ty3/Gypsy
System:LTR retroelements
Host:
Explore the Tree Life Project
Zea mays.gif
Zea mays
Image, Carlos Llorens,
Copyright, GyDB, Biotech Vana
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