Sequence analysis of the simian foamy virus type 1 genome

Kupiec, Jean-Jacques; Kay, Alan; Hayat, Maud; Ravier, Rodica; Périès, J.; Galibert, Francis

doi:10.1016/0378-1119(91)90410-d

Cited by 67 publications

(38 citation statements)

References 30 publications

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“…However, to obtain this result, two nontemplated nucleotides, which were complementary to the terminal U5 dinucleotide, were added to the U3 substrate (Pahl & Flu$ gel, 1993). In addition, their introduction would destroy the bet reading frame overlapping the ppt-U3 border in all FVs Kupiec et al, 1991 ;Renne et al, 1992 ;Baunach et al, 1993 ;Hahn et al, 1994 ;Renshaw & Casey, 1994 b ;Herchenro$ der et al, 1994 ;Helps & Harbour, 1997 ;Winkler et al, 1997). Therefore, we suggest that the report of Pahl & Flu$ gel (1993) showed that FV IN is able to cleave some kind of elongated U3 end, which may arise through the generation of untidy ends during reverse transcription.…”

Section: Discussionmentioning

confidence: 99%

“…It involves the recognition and trimming of BEEG Foamy virus integration Foamy virus integration (Rethwilm et al, 1990 ;Lo$ chelt et al, 1991 ; and published FV genome sequences from CFV/hu Maurer et al, 1988), CFV (Herchenro$ der et al, 1994), simian FV type 1 (SFV-1) (Kupiec et al, 1991), SFV-3 (Renne et al, 1992), bovine FV (BFV) (Renshaw & Casey, 1994 a, b) and feline FV (FFV) (Helps & Harbour, 1997 ;Winkler et al, 1997) were aligned. The sequences are arranged in such a way that the LTR borders can readily be compared with the proviral-cellular DNA junctions.…”

Section: Sequence Determination Of Proviral-cellular Dna Junctionsmentioning

confidence: 99%

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An active foamy virus integrase is required for virus replication.

Enssle

Moebes

Heinkelein

et al. 1999

Journal of General Virology

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Foamy viruses (FVs) make use of a replication strategy which is unique among retroviruses and shows analogies to hepadnaviruses. The presence of an integrase (IN) and obligate provirus integration distinguish retroviruses from hepadnaviruses. To clarify whether a functional IN is required for FV replication, a mutant in the highly conserved DD35E motif of the active centre was analysed. This mutant was found to be able to express Gag and Pol protein precursors and cleavage products and to generate and deliver cDNA. However, this mutant was replication-deficient. The junctions of individual foamy proviruses with cellular DNA were sequenced. The findings suggest that FV integration is asymmetrical, because the proviruses started with what is believed to be the U3 end of the free linear DNA to generate the conventional TG dinucleotide, while apparently two nucleotides from the U5 end were cleaved to create the complementary CA dinucleotide. Alignment of known FV genome sequences indicated that this mechanism of integration is not restricted to the two FV isolates from which integrates were studied, but appears to be a common feature of this retrovirus subfamily. In conclusion, with respect to the necessity of a functionally active IN for virus replication FVs behave like other retroviruses ; their mechanism of integration, however, is probably unique.

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Section: Discussionmentioning

confidence: 99%

Section: Sequence Determination Of Proviral-cellular Dna Junctionsmentioning

confidence: 99%

An active foamy virus integrase is required for virus replication.

Enssle

Moebes

Heinkelein

et al. 1999

Journal of General Virology

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“…FV have been isolated and cloned from a variety of primate (for references see below) and non-primate hosts (Holzschu et al, 1998;Tobaly-Tapiero et al, 2000;Winkler et al, 1997). Evolutionary studies would benefit from the characterization of the FV genomic diversity, but to date, only a few primate FVs from macaques (SFVmac) (Kupiec et al, 1991), African green monkey (SFVagm) (Renne et al, 1992), orang-utan (SFVora) (Verschoor et al, 2003), chimpanzees (SFVcpz) (Herchenröder et al, 1994(Herchenröder et al, , 1995, spider monkey (SFVspm) (Thümer et al, 2007), marmoset and squirrel monkey (Pacheco et al, 2010) have been cloned and completely sequenced. Although the gorilla simian FV (SFVgor) has been previously isolated and partially sequenced (Bieniasz et al, 1995;Calattini et al, 2004Calattini et al, , 2007Wolfe et al, 2004), the complete sequence of the SFVgor represents the last missing piece of the FV genomic puzzle within the great apes.…”

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confidence: 99%

Complete nucleotide sequence and evolutionary analysis of a Gorilla foamy virus

Schulze

Lemey

Schubert

et al. 2010

Journal of General Virology

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“…Same confusion was caused by previous results on the location of the protease reading frame in foamy viruses. While PR in simian foamy viruses (SFV 1 and 3) is located in the pol reading frame ( 18,19) it has been reported to be located in the gag reading frame for the related HFV (2,5). lf that were the case, one would expect pPR2 and pPR3 to give rise to shorter and Iongerfusion proteins, respectively, than shown in Fig.…”

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confidence: 99%

Identification of pol-Related Gene Products of Human Foamy Virus

et al. 1993

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Human foamy viruspol gene fragments were molecularly cloned into a procaryotic expression vector. The expression pattern of the cloned fragments and nucleotide sequence analysis of the 5' pol gene region revealed that in HFV the protease (PR) is located in the pol open reading frame. Purified recombinant proteins were used to generate antibodies in rats. ln immunoblot assay, using infected cells as antigen, a precursor protein with an apparent molecular mass (M,) Human foamy virus (HFV) belongs to the spumavirus subfamily of retroviruses ( 1). The HFV genome comprises the typical retroviral gag, pol, and env genes and accessory ORFs believed to encode for regulatory pro. teins (2). The viral genorne has been molecularly cloned and sequenced (3-5) but there is little informa· tion about the HFV gene products. Since the debate on natural human infections with HFV is controversal (6-8) and the significance of 1-lFV as a human pathogen is unresolved (9-11}, the characterization of viral proteins is a main issue in developing criteria tor the Serodiagnosis of HFV infections. Furthermore, knowledge of the viral proteins is essential for a better understanding of viral replication and structure.Previously, three viral glycoproteins with an apparent Mr of 170. 130, and 47K have been described, which probably represent env-related gene products ( 12). The study also revealed further viral proteins in the Mr range of 31-127K which were recognized by foamy virus·positive sera, but their functions remain obscure. Herewe report the use of antisera raised against bacterial-expressed pol gene fragments to identify the HFV pol gene products. Expression plasmids were constructed by inserting DNA fragments derived from restriction enzymatic digestion of the infectious molecular clone pHSRV ( 13) into the multiple cloning site of the bacterial expression vector pROS ( 14). The respective HFV genome organization and the DNA fragments cloned into pROS are 1 Present address: Medizinische Universitatsklinik IV, Krankenhausstrasse 12, 8520 Erlangen. Gerrnany.2 T o whom correspondence and reprint requests should be ad· dressed_ 0042-6822/93 $5.00 Copyright C 1993 by Academic Press. 1nc. All rights ol repl'oductlon in any form rescrved. 336shown in Fig. 1. The domains for the protease, reverse transcriptase, RNase H, and integrase were deduced by amino acid homology to other retroviruses.The 500-bp Mspi/Accl fragrnent comprising protease (PR) sequences was blunt-ended by Klenow polymerase and inserted into the Stul site of pROS. leading to pPR 1. Similarly, pPR2 and pPR3 were generated by inserting the 1520-bp Mspi!Ncol fragment and the 1 000-bp Accl fragment into the Stul site and the EcoRV site of pROS, respectively. pRTl was generated by cloning the 1 020-bp Acci!Ncol RT fragment into EcoRV cut vector, and the 770·bp Ncot/EcoRV fragment comprising RNaseH sequences was inserted into the Stul site of pROS, giving rise to pRN 1. Insertion of the 540-bp EcoRV/Accl and the 1 060-bp Styl integrase (IN} fragmentsintoSmal and EcoRV cut vecto...

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Sequence analysis of the simian foamy virus type 1 genome

Cited by 67 publications

References 30 publications

An active foamy virus integrase is required for virus replication.

An active foamy virus integrase is required for virus replication.

Complete nucleotide sequence and evolutionary analysis of a Gorilla foamy virus

Identification of pol-Related Gene Products of Human Foamy Virus

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