Element:DrFV-1

From The Gypsy Database

Description

Danio rerio Foamy Virus type 1 (DrFV-1) is a foamy retrovirus originally characterized in the genome of the Danio rerio zebrafish (Llorens et al. 2009). This element belongs to the genus Spumaretrovirus (for a review see Meiering and Linial 2001). The presence of this element in Danio rerio suggests that spumaretroviruses are more widely distributed than previously thought, as the remaining spumaretroviruses known so far are restricted to synapsids (mammals and their extincted relatives) (for more information about spumaretroviruses, see Katzourakis et al. 2009). Further analyses are anyway required to clarify whether spumaretroviruses also inhabit (or circulate in) the genomes of other fishes, amphibians and sauropsids, in order to calibrate the origin of spumaretroviruses.

The genomic structure of DrFV-1 is 12 Kb in size including LTRs of approximately 0.8 Kb. The internal region of this retrovirus displays a Primer Binding Site (PBS), Open Reading Frames (ORFs) for the typical gag and pol genes of retroviruses and LTR retrotransposons plus four additional ORFs that show no similarity to any sequence currently known (including env) (Llorens et al. 2009). It is thus unclear if DrFV-1 is a true retrovirus carrying a highly divergent env plus two accessory or additional genes or a LTR retrotransposon just carrying three additional genes. This suggests that DrFV-1 might be an intermediate sequence between Retroviridae retroviruses and other related LTR retrotransposons (Llorens et al. 2009)

Structure

DrFV-1.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:85857417
Clade:Undetermined
Cluster or genus:Spumaretrovirus
Branch or class:Class 3
Family:Retroviridae
System:LTR retroelements
Host:
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Danio rerio.jpg
Danio rerio
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