scholarly journals The Nucleotide Sequence and Spliced polmRNA Levels of the Nonprimate Spumavirus Bovine Foamy Virus

1998 ◽  
Vol 72 (3) ◽  
pp. 2177-2182 ◽  
Author(s):  
Donald L. Holzschu ◽  
Mari A. Delaney ◽  
Randall W. Renshaw ◽  
James W. Casey
Keyword(s):  
Nucleotide Sequence ◽  
Zinc Finger ◽  
Sequence Similarity ◽  
Foamy Virus ◽  
Open Reading Frames ◽  
Genomic Rna ◽  
Gag Protein ◽  
Protein Precursor ◽  
Bovine Foamy Virus ◽  
Virion Assembly

ABSTRACT We have determined the complete nucleotide sequence of a replication-competent clone of bovine foamy virus (BFV) and have quantitated the amount of splice pol mRNA processed early in infection. The 544-amino-acid Gag protein precursor has little sequence similarity with its primate foamy virus homologs, but the putative nucleocapsid (NC) protein, like the primate NCs, contains the three glycine-arginine-rich regions that are postulated to bind genomic RNA during virion assembly. The BFV gag and polopen reading frames overlap, with pro and polin the same translational frame. As with the human foamy virus (HFV) and feline foamy virus, we have detected a spliced pol mRNA by PCR. Quantitatively, this mRNA approximates the level of full-length genomic RNA early in infection. The integrase (IN) domain of reverse transcriptase does not contain the canonical HH-CC zinc finger motif present in all characterized retroviral INs, but it does contain a nearby histidine residue that could conceivably participate as a member of the zinc finger. The env gene encodes a protein that is over 40% identical in sequence to the HFV Env. By comparison, the Gag precursor of BFV is predicted to be only 28% identical to the HFV protein.

scholarly journals RNA and Protein Requirements for Incorporation of the Pol Protein into Foamy Virus Particles

2005 ◽  
Vol 79 (11) ◽  
pp. 7005-7013 ◽  
Author(s):  
Katrin Peters ◽  
Tatiana Wiktorowicz ◽  
Martin Heinkelein ◽  
Axel Rethwilm
Keyword(s):  
Foamy Virus ◽  
Genomic Rna ◽  
Rna Packaging ◽  
Gag Protein ◽  
Protein Precursor ◽  
Protein Requirements ◽  
Virus Particles ◽  
Foamy Viruses ◽  
Protein Incorporation ◽  
The Individual

ABSTRACT Foamy viruses (FVs) generate their Pol protein precursor molecule independently of the Gag protein from a spliced mRNA. This mode of expression raises the question of the mechanism of Pol protein incorporation into the viral particle (capsid). We previously showed that the packaging of (pre)genomic RNA is essential for Pol encapsidation (M. Heinkelein, C. Leurs, M. Rammling, K. Peters, H. Hanenberg, and A. Rethwilm, J. Virol. 76:10069-10073, 2002). Here, we demonstrate that distinct sequences in the RNA, which we termed Pol encapsidation sequences (PES), are required to incorporate Pol protein into the FV capsid. Two PES were found, which are contained in the previously identified cis-acting sequences necessary to transfer an FV vector. One PES is located in the U5 region of the 5′ long terminal repeat and one at the 3′ end of the pol gene region. Neither element has any significant effect on RNA packaging. However, deletion of either PES resulted in a significant reduction in Pol encapsidation. On the protein level, we show that only the Pol precursor, but not the individual reverse transcriptase (RT) and integrase (IN) subunits, is incorporated into FV particles. However, enzymatic activities of the protease (PR), RT, or IN are not required. Our results strengthen the view that in FVs, (pre)genomic RNA functions as a bridging molecule between Gag and Pol precursor proteins.

scholarly journals Generation of an improved foamy virus vector by dissection of cis-acting sequences

2009 ◽  
Vol 90 (2) ◽  
pp. 481-487 ◽  
Author(s):  
Tatiana Wiktorowicz ◽  
Katrin Peters ◽  
Nicole Armbruster ◽  
Andre F. Steinert ◽  
Axel Rethwilm
Keyword(s):  
Foamy Virus ◽  
Human Mesenchymal Stem Cells ◽  
Viral Capsid ◽  
Rna Packaging ◽  
Gag Protein ◽  
Protein Precursor ◽  
Cis Acting ◽  
Foamy Viruses ◽  
Protein Incorporation ◽  
Primary Human Cells

In contrast to other retroviruses, foamy viruses (FVs) generate their Pol protein precursor independently of the Gag protein from a spliced mRNA. The exact mechanism of Pol protein incorporation into the viral capsid is poorly understood. Previously, we showed that Pol encapsidation critically depends on the packaging of (pre-) genomic RNA and identified two distinct signals within the cis-acting sequences (CASI and CASII), Pol encapsidation sequences (PESI and PESII), which are required for Pol capsid incorporation. Here, we investigated whether the presence of PESI and PESII in an FV vector is sufficient for Pol encapsidation and whether the rather extended CASII element can be shortened without loss of functionality. Our results indicate that (i) the presence of PESI and II are not sufficient for Pol encapsidation, (ii) prototype FV vectors with a shortened CASII element retain Pol incorporation and full functionality, in particular upon transducing fibroblasts and primary human mesenchymal stem cells, (iii) the presence of the central poly purine tract significantly increased the transduction rates of FV vectors and (iv) Pol encapsidation and RNA packaging can be clearly separated. In essence, we designed a new FV vector that bears approximately 850 bp less of CAS than previously established vectors and is fully functional when analysed to transduce cell lines and primary human cells.

scholarly journals Complete Nucleotide Sequence of Plasmid Rts1: Implications for Evolution of Large Plasmid Genomes

2002 ◽  
Vol 184 (12) ◽  
pp. 3194-3202 ◽  
Author(s):  
Takahiro Murata ◽  
Makoto Ohnishi ◽  
Takeshi Ara ◽  
Jun Kaneko ◽  
Chang-Gyun Han ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Complete Nucleotide Sequence ◽  
Sequence Similarity ◽  
Open Reading Frames ◽  
Conjugative Plasmid ◽  
Proteus Vulgaris ◽  
Significant Sequence Similarity ◽  
Modular Evolution ◽  
Broad Array ◽  
Reading Frames

ABSTRACT Rts1, a large conjugative plasmid originally isolated from Proteus vulgaris, is a prototype for the IncT plasmids and exhibits pleiotropic thermosensitive phenotypes. Here we report the complete nucleotide sequence of Rts1. The genome is 217,182 bp in length and contains 300 potential open reading frames (ORFs). Among these, the products of 141 ORFs, including 9 previously identified genes, displayed significant sequence similarity to known proteins. The set of genes responsible for the conjugation function of Rts1 has been identified. A broad array of genes related to diverse processes of DNA metabolism were also identified. Of particular interest was the presence of tus-like genes that could be involved in replication termination. Inspection of the overall genome organization revealed that the Rts1 genome is composed of four large modules, providing an example of modular evolution of plasmid genomes.

scholarly journals Complete Nucleotide Sequence of the 27-Kilobase Virulence Related Locus (vrl) of Dichelobacter nodosus: Evidence for Extrachromosomal Origin

1999 ◽  
Vol 67 (3) ◽  
pp. 1277-1286 ◽  
Author(s):  
Stephen J. Billington ◽  
Andrea S. Huggins ◽  
Priscilla A. Johanesen ◽  
Paul K. Crellin ◽  
Jackie K. Cheung ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Complete Nucleotide Sequence ◽  
Expression Vector ◽  
Sequence Similarity ◽  
Open Reading Frames ◽  
Bacteriophage Resistance ◽  
Dichelobacter Nodosus ◽  
Resistance System ◽  
Reading Frames

ABSTRACT The vrl locus is preferentially associated with virulent isolates of the ovine footrot pathogen, Dichelobacter nodosus. The complete nucleotide sequence of this 27.1-kb region has now been determined. The data reveal that the locus has a G+C content much higher than the rest of the D. nodosuschromosome and contains 22 open reading frames (ORFs) encoding products including a putative adenine-specific methylase, two potential DEAH ATP-dependent helicases, and two products with sequence similarity to a bacteriophage resistance system. These ORFs are all in the same orientation, and most are either overlapping or separated by only a few nucleotides, suggesting that they comprise an operon and are translationally coupled. Expression vector studies have led to the identification of proteins that correspond to many of these ORFs. These data, in combination with evidence of insertion of vrl into the 3′ end of an ssrA gene, are consistent with the hypothesis that the vrl locus was derived from the insertion of a bacteriophage or plasmid into the D. nodosusgenome.

scholarly journals Characterization and Nucleotide Sequence of a Klebsiella oxytoca Cryptic Plasmid Encoding a CMY-Type β-Lactamase: Confirmation that the Plasmid-Mediated Cephamycinase Originated from the Citrobacter freundii AmpC β-Lactamase

1999 ◽  
Vol 43 (6) ◽  
pp. 1350-1357 ◽  
Author(s):  
Shang Wei Wu ◽  
Kathrine Dornbusch ◽  
Göran Kronvall ◽  
Mari Norgren
Keyword(s):  
Nucleotide Sequence ◽  
Sequence Similarity ◽  
Klebsiella Oxytoca ◽  
Open Reading Frames ◽  
Citrobacter Freundii ◽  
E Coli ◽  
Plasmid Preparation ◽  
High Level ◽  
Rna I

ABSTRACT Plasmid pTKH11, originally obtained by electroporation of aKlebsiella oxytoca plasmid preparation intoEscherichia coli XAC, expressed a high level of an AmpC-like β-lactamase. The enzyme, designated CMY-5, conferred resistance to extended-spectrum β-lactams in E. coli; nevertheless, the phenotype was cryptic in the K. oxytocadonor. Determination of the complete nucleotide sequence of pTKH11 revealed that the 8,193-bp plasmid encoded seven open reading frames, including that for the CMY-5 β-lactamase (bla CMY-5). Thebla CMY-5 product was similar to the plasmidic CMY-2 β-lactamase of K. pneumoniae and the chromosomal AmpC of Citrobacter freundii, with 99.7 and 97.0% identities, respectively; there was a substitution of phenylalanine in CMY-5 for isoleucine 105 in CMY-2. bla CMY-5 was followed by the Blc and SugE genes of C. freundii, and this cluster exhibited a genetic organization identical to that of the ampC region on the chromosome ofC. freundii; these results confirmed that C. freundii AmpC was the evolutionary origin of the plasmidic cephamycinases. In the K. oxytoca host, the copy number of pTKH11 was very low and the plasmid coexisted with plasmid pNBL63. Analysis of the replication regions of the two plasmids revealed 97% sequence similarity in the RNA I transcripts; this result implied that the two plasmids might be incompatible. Incompatibility of the two plasmids might explain the cryptic phenotype ofbla CMY-5 in K. oxytoca through an exclusion effect on pTKH11 by resident plasmid pNBL63.

scholarly journals Complete nucleotide sequence and genome organization of Grapevine fleck virus

2001 ◽  
Vol 82 (8) ◽  
pp. 2009-2015 ◽  
Author(s):  
Sead Sabanadzovic ◽  
Nina Abou Ghanem-Sabanadzovic ◽  
Pasquale Saldarelli ◽  
Giovanni P. Martelli
Keyword(s):  
Nucleotide Sequence ◽  
Coat Protein ◽  
Genome Organization ◽  
Complete Nucleotide Sequence ◽  
Open Reading Frames ◽  
Genomic Rna ◽  
Associated Proteins ◽  
Ca 50 ◽  
Positive Strand Rna ◽  
Terminal Poly

The complete nucleotide sequence of Grapevine fleck virus (GFkV) genomic RNA was determined. The genome is 7564 nt in size, excluding the 3′-terminal poly(A) tail, is characterized by an extremely high cytosine content (ca. 50%), and contains four putative open reading frames and untranslated regions of 291 and 35 nt at the 5′ and 3′ ends, respectively. ORF 1 potentially encodes a 215·4 kDa polypeptide (p215), which has the conserved motifs of replication-associated proteins of positive-strand RNA viruses. ORF 2 encodes a 24·3 kDa polypeptide (p24) identified as the coat protein. ORFs 3 and 4 are located at the extreme 3′ end of the viral genome and encode proline-rich proteins of 31·4 kDa (p31) and 15·9 kDa (p16), respectively, of unknown function. Phylogenetic analysis of the viral replicase and coat protein genes showed that GFkV is related to members of the Tymovirus and Marafivirus genera. Two subgenomic RNAs were present in the GFkV preparations as ascertained by molecular hybridization. The genome organization of GFkV resembles to some extent that of tymoviruses and marafiviruses. However, differences in the biological and epidemiological behaviour, cytopathology and molecular properties (i.e. size of genomic RNA and coat protein, and number of ORFs) support the notion that GFkV is a separate virus belonging in a new genus.

scholarly journals Development of a recombinant protein-based ELISA for detection of antibodies against bovine foamy virus

2017 ◽  
Vol 61 (3) ◽  
pp. 247-252 ◽  
Author(s):  
Magdalena Materniak-Kornas ◽  
Zbigniew Osiński ◽  
Marcin Rudzki ◽  
Jacek Kuźmak
Keyword(s):  
Dairy Cattle ◽  
Large Scale ◽  
Expression Vector ◽  
Operating Characteristic ◽  
Foamy Virus ◽  
Coding Region ◽  
Serum Samples ◽  
Gag Protein ◽  
Bovine Foamy Virus ◽  
High Level

Abstract Introduction: Infections with bovine foamy virus (BFV) were found in many countries but there is a lack of large-scale surveys on the prevalence of BFV among dairy cattle. The aim of this study was to develop and validate the recombinant Gag protein-based ELISA and to estimate the prevalence of antibodies against BFV. Material and Methods: Gag coding region from BFV was cloned into expression vector pT7Arg-STOP, which expressed a high level of recombinant Gag protein from E.coli. The ELISA was standardised, and the cut-off value and sensitivity and specificity of the test were calculated using a receiver operating characteristic and Bayesian estimation. Results: A total of 3,051 serum samples were tested by ELISA and 939 (30.8%) sera were recognised as positive. When Bayesian approach was used, the overall true BFV prevalence was 29.7% (95% CI: 25.9-33.4%). Conclusion: Expressed Gag protein of BFV has been used successfully as an antigen for ELISA. Eventually, this study provides basic information about the epidemiological status of infection with BFV in dairy cattle in Poland, which can be used for further studies on dissemination and transmission of BFV infection.

Nucleotide sequence and phylogenetic analysis of the medium (M) genomic RNA segments of three hantaviruses isolated in China

1998 ◽  
Vol 56 (1) ◽  
pp. 69-76 ◽  
Author(s):  
Xiaohong Shi ◽  
Mifang Liang ◽  
Changshou Hang ◽  
Gan Song ◽  
Conall McCaughey ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Nucleotide Sequence ◽  
Genomic Rna

scholarly journals Molecular Epidemiology and Whole-Genome Analysis of Bovine Foamy Virus in Japan

Viruses ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1017
Author(s):  
Hirohisa Mekata ◽  
Tomohiro Okagawa ◽  
Satoru Konnai ◽  
Takayuki Miyazawa
Keyword(s):  
Phylogenetic Analyses ◽  
Foamy Virus ◽  
Pcr Analysis ◽  
Whole Genome ◽  
Genome Sequences ◽  
Whole Genome Analysis ◽  
Virus Family ◽  
Bovine Foamy Virus ◽  
Novel Genotype

Bovine foamy virus (BFV) is a member of the foamy virus family in cattle. Information on the epidemiology, transmission routes, and whole-genome sequences of BFV is still limited. To understand the characteristics of BFV, this study included a molecular survey in Japan and the determination of the whole-genome sequences of 30 BFV isolates. A total of 30 (3.4%, 30/884) cattle were infected with BFV according to PCR analysis. Cattle less than 48 months old were scarcely infected with this virus, and older animals had a significantly higher rate of infection. To reveal the possibility of vertical transmission, we additionally surveyed 77 pairs of dams and 3-month-old calves in a farm already confirmed to have BFV. We confirmed that one of the calves born from a dam with BFV was infected. Phylogenetic analyses revealed that a novel genotype was spread in Japan. In conclusion, the prevalence of BFV in Japan is relatively low and three genotypes, including a novel genotype, are spread in Japan.

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