Element:TF1

From The Gypsy Database

Description

TF1 is an active LTR retrotransposon characterized, along with TF2, in Schizosaccharomyces pombe (Levin, Weaver and Boeke 1990; Weaber et al. 1993). TF1 and TF2 are related 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).

The genomic structure of TF1 is 4.9 Kb in size, including LTRs of 358 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 (Levin, Weaver and Boeke 1990; Weaber et al. 1993). Neither, TF1 nor TF2 codify for chromodomain-containing integrases. 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

Tf1.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:M38526
Clade:TF1-2
Cluster or genus:Fungi and vertebrates
Branch or class:Chromoviruses
Family:Ty3/Gypsy
System:LTR retroelements
Host:
Explore the Tree Life Project
Schizosaccharomyces pombe.gif
Schizosaccharomyces pombe
Image, courtesy of Rita Bernhardt, Lehrstuhl fur Biochemie, Universitat des Saarlandes
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