Element:pCal

From The Gypsy Database

Description

pCal is a Ty1/Copia-like LTR retrotransposon characterized in the genome of the pathogenic yeast Candida albicans (Matthews et al. 1997). pCal element belongs to Ty (Pseudovirus) clade one of the three original genera on which the in-progrees Pseudoviridae classification is constituted (Boeke et al 2005).

The genome of pCal is 6426 bp in size, including two identical 280-bp LTRs that bound an internal coding region containing a Primer Binding Site (PBS), complementary to a tRNAArg, a long Open Reading Frame (ORF) interrupted by one stop codon, and a Polypurine Tract upstream to the 3’LTR (PPT1) (Matthews et al. 1997). Interestingly, a second sequence very similar to the 3’ PPT1 was found near the middle of pCal (bases 3455 to 3465), it probably serves as a site for plus-strand initiation during the reverse transcription process and to speed up this process (Matthews et al. 1997). The long ORF contains both gag and pol domain structures characteristic of Ty1/Copia retroelements: gag, protease, integrase, reverse transcriptase and ribonuclease H. The gag-associated RNA-binding motif (CCHC) has not been identified in this element (Matthews et al. 1997).

Structure

PCal.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:2636718
Clade:Ty (Pseudovirus)
Cluster or genus:Pseudovirus
Branch or class:Branch 1
Family:Ty1/Copia
System:LTR retroelements
Host:
Explore the Tree Life Project
Candida.jpg
Candida albicans
Courtesy of Dr. Dan Wiedbrauk, "Warde Medical Laboratory" (Ann Arbor, Michigan)
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