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Review
. 1999 Mar;73(3):1747-55.
doi: 10.1128/JVI.73.3.1747-1755.1999.

Foamy viruses are unconventional retroviruses

M L Linial  1
Affiliations
Review

Foamy viruses are unconventional retroviruses

M L Linial. J Virol. 1999 Mar.
No abstract available

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Figures

FIG. 1
FIG. 1
Unrooted tree of pol sequences from retroviral genomes. Alignment was done using the Clustal-X algorithm. The tree was derived from ungapped portions of the Pol protein alignment. Bootstrap analysis shows that HERV-L and MERV cluster with the foamy viruses 94 of 100 times. The viral designations not given in the text, are as follows: SFV-1 (rhesus macaques), SFV-3 (African green monkey), FFV (feline FV), SHRV (snakehead retrovirus), ALV (avian leukosis virus), MMTV (murine mammary tumor virus), HTLV1 and HTLV2 (human T-cell leukemia virus types 1 and 2), EIAV (equine infectious anemia virus), FIV (feline immunodeficiency virus), SIV (simian immunodeficiency virus type 1). The accession numbers used for endogenous element sequences are: MERV, EMBO no. Y12713, MERVLPOLY; HERV-L, GenBank no. AF070718 and AF070718 (reverse compliment of nucleotides 46480 to 44147, with frameshifts corrected).
FIG. 2
FIG. 2
Genome of HFV. Depicted is the molecular clone HFV-13 (Genbank accession no. U21247; 11,954 bp). This infectious clone has a deletion of 648 bp in the U3 region of each LTR relative to that of clone HFV-2 (Genbank accession no. Y07725; 13,242 bp). Otherwise, the two clones are essentially identical. The locations of the ORFs (boxes) indicate the reading frames of the deduced proteins. The thin lines indicate the mRNAs for which proteins have been identified. The shaded box depicts the HFV provirus and gives the locations of the LTR promoter and IP indicated by P and also shows the location of the major 5′ splice site (ss) used as the donor for all of the mRNAs originating from the LTR promoter. The shaded boxes at the bottom show the ΔHFV provirus lacking a functional Tas gene (see text). RNAs for Tas and Bet are encoded by both the LTR promoter and the IP, but only those originating from the IP are indicated. The ORFs are indicated in italics. The ATGs indicate translational start sites. GR, glycine-arginine-rich boxes; PR, protease domain; RT, RT domain; IN, integrase domain; SU, surface domain; TM, transmembrane domain. The tas gene (transactivator of spumavirus) was formerly called bel-1. bel-2 and bel-3 are ORFs for which a protein has not conclusively been demonstrated. The Bet protein is translated from a spliced RNA and contains residues from part of tas and from bel-2 (as also indicated by the diagonal arrow). The Env-Bet mRNA is a multiply spliced RNA encoding a protein of unknown function.
FIG. 3
FIG. 3
Details of the viral structural proteins. (Top) Gag protein. The locations of the three glycine-arginine-rich GR boxes (I, II, and III) are indicated by shaded boxes. The NAB and NLS are indicated below boxes I and II. The arrow indicates the cleavage site at which viral protease (PR) (encoded in Pol) cleaves about 3 kDa from the 78 kDa Gag precursor. The locations of the expected sites for the retroviral matrix (MA), capsid (CA), and nucleocapsid (NC) polypeptides are shown. These cleaved proteins, however, have not been found in mature, infectious virions. (Middle) Pol protein. The PR, RT, and integrase (IN) domains are shown. The PR cleavage site is indicated by the arrow labeled PR. (Bottom) Env protein. The surface (SU) and transmembrane (TM) domains are shown as well as the proteolytic cleavage site (arrow). MSD, membrane spanning domain in TM; ERS, endoplasmic reticulum sorting signal in the cytoplasmic tail.
FIG. 4
FIG. 4
Replication pathway of FV compared to that of the conventional retroviruses and hepadnaviruses. (A) Proposed replication pathway of FVs. Viral RNA is indicated by red lines, and DNA is indicated by blue bars. Gold indicates the viral Gag protein, and green circles are the glycoproteins. Grey circles indicate polysomes. ER denotes endoplasmic reticulum. Several intracellular particles are shown, which represent the large numbers of intracellular particles in infected tissue culture cells which have been detected by both electron microscopy and viral assays. It is not known whether such particles contain RNA or DNA or both. The uncertain steps in the life cycle are indicated by question marks. (B) Retroviral life cycle. Colors used are the same as in panel A. Immature particles are shown with gold centers; after protease cleavage, the mature extracellular particles are shown with white central cores. Details of the replication pathway can be found in reference . (C) Hepadnavirus life cycle. Abbreviations are as in panels A and B. Viral core proteins are indicated by purple, RNA by red, DNA by blue, and S glycoproteins by green. Details of the replication pathway can be found in reference .
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