Element:Ty1B

From The Gypsy Database

Description

Ty1 is representative of one of the four sets of LTR retrotransposons (Ty1, Ty2, Ty3 and Ty4) described in the genome of yeast Saccharomyces cerevisiae (Boeke et al. 1988). Ty1 is the largest set and seems to exhibit the highest degree of variation (Boeke and Sandmeyer 1991). Ty1B element has been take as reference sequence to our studies. Ty1B belongs to Ty (Pseudovirus) clade one of the three original genera on which the in-progrees Pseudoviridae classification is constituted (Boeke et al 2005).

Ty1B genome is about of 5.9 Kb in size (5983 bp long) and includes a 334-bp 5’LTR and a 332-bp 3’LTR. The structure of this element contains a Primer Binding Site (PBS) complementary to a tRNAiMet, an internal region and two Polypurine Tracts (PPTs): one upstream to the 3’LTR (PPT1) and a second within the pol gene (PPT2)(Boeke and Sandmeyer 1991). The internal region is composed by two overlapping Open Reading Frames (ORFs) that contain respectively the gag protein (the first ORF) and the typical structure of the Ty1/Copia pol polyprotein domains: protease, integrase, reverse transcriptase and ribonuclease H (the second larger ORF) (Boeke and Sandmeyer 1991). The gag-associated RNA-binding motif (CCHC) has not been identified in this element (Peterson-Burch and Voytas 2002). The central PPT2 has been demonstrated to be not essential for the element transposition (Heyman et al. 2003; Friant et al. 1996).

Structure

Ty1B.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:535983 (nts 4201-9469)
Clade:Ty (Pseudovirus)
Cluster or genus:Pseudovirus
Branch or class:Branch 1
Family:Ty1/Copia
System:LTR retroelements
Host:
Explore the Tree Life Project
Saccharomyces cerevisiae.gif
Saccharomyces cerevisiae
Image, Joaquin Panadero,
Copyright, GyDB, Biotech Vana
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