Mapping and characterization of antigenic epitopes and the nucleic acid-binding domains of the VP6 protein of bluetongue viruses

Oncolytic bluetongue viruses: promise, progress, and perspectives

Humans are sero-negative toward bluetongue viruses (BTVs) since BTVs do not infect normal human cells. Infection and selective degradation of several human cancer cell lines but not normal ones by five US BTV serotypes have been investigated. We determined the susceptibilities of many normal and human cancer cells to BTV infections and made comparative kinetic analyses of their cytopathic effects, survival rates, ultra-structural changes, cellular apoptosis and necrosis, cell cycle arrest, cytokine profiles, viral genome, mRNAs, and progeny titers. The wild-type US BTVs, without any genetic modifications, could preferentially infect and degrade several types of human cancer cells but not normal cells. Their selective and preferential BTV-degradation of human cancer cells is viral dose–dependent, leading to effective viral replication, and induced apoptosis. Xenograft tumors in mice were substantially reduced by a single intratumoral BTV injection in initial in vivo experiments. Thus, wild-type BTVs, without genetic modifications, have oncolytic potentials. They represent an attractive, next generation of oncolytic viral approach for potential human cancer therapy combined with current anti-cancer agents and irradiation.

Bioinformatic analysis suggests that the Orbivirus VP6 cistron encodes an overlapping gene

Background

The genus Orbivirus includes several species that infect livestock – including Bluetongue virus (BTV) and African horse sickness virus (AHSV). These viruses have linear dsRNA genomes divided into ten segments, all of which have previously been assumed to be monocistronic.

Results

Bioinformatic evidence is presented for a short overlapping coding sequence (CDS) in the Orbivirus genome segment 9, overlapping the VP6 cistron in the +1 reading frame. In BTV, a 77–79 codon AUG-initiated open reading frame (hereafter ORFX) is present in all 48 segment 9 sequences analysed. The pattern of base variations across the 48-sequence alignment indicates that ORFX is subject to functional constraints at the amino acid level (even when the constraints due to coding in the overlapping VP6 reading frame are taken into account; MLOGD software). In fact the translated ORFX shows greater amino acid conservation than the overlapping region of VP6. The ORFX AUG codon has a strong Kozak context in all 48 sequences. Each has only one or two upstream AUG codons, always in the VP6 reading frame, and (with a single exception) always with weak or medium Kozak context. Thus, in BTV, ORFX may be translated via leaky scanning. A long (83–169 codon) ORF is present in a corresponding location and reading frame in all other Orbivirus species analysed except Saint Croix River virus (SCRV; the most divergent). Again, the pattern of base variations across sequence alignments indicates multiple coding in the VP6 and ORFX reading frames.

Conclusion

At ~9.5 kDa, the putative ORFX product in BTV is too small to appear on most published protein gels. Nonetheless, a review of past literature reveals a number of possible detections. We hope that presentation of this bioinformatic analysis will stimulate an attempt to experimentally verify the expression and functional role of ORFX, and hence lead to a greater understanding of the molecular biology of these important pathogens.

Characterization of the nucleic acid binding activity of inner core protein VP6 of African horse sickness virus

Minor structural protein VP6 is the putative helicase of African horse sickness virus (AHSV), of the genus Orbivirus in the Reoviridae family. We investigated how the protein interacts with double-stranded (ds) RNA and other nucleic acids. Binding was assayed using an electrophoretic migration retardation assay and a nucleic acid overlay protein blot assay. VP6 bound double and single stranded RNA and DNA in a NaCl concentration sensitive reaction. Of six truncated VP6 peptides investigated, two partially overlapping peptides were found to bind dsRNA at pH 7.0, while other peptides with the same overlap did not. The distinction between the peptides appeared to be the pI which ranged from more than 8.0 to just above 6.0. Changing the pH of the binding buffer modified the binding activity. Regardless of assay conditions, only peptides with a specific region of amino acids in common, showed evidence of binding activity. No sequence homology was identified with other binding domains, however, the presence of charged amino acids are assumed to be important for binding activity. The results suggested dsRNA binding in the blot assay was strongly affected by the net charge on the peptide.

Localization of the single-stranded RNA-binding domains of bluetongue virus nonstructural protein NS2

The S2 gene of bluetongue virus, serotype 17, has been cloned, and the nonstructural protein NS2 has been expressed. Synthetic peptides matching regions within the amino acid sequence of NS2 were used to map three single-stranded RNA (ssRNA)-binding regions within the protein. A prokaryotic expression system was then used to generate a series of deletion mutants with the ssRNA-binding domains of NS2 removed, singly and in different combinations. These truncated proteins were expressed on a large scale and purified to near homogeneity. The affinity of each truncated protein towards ssRNA was then assayed by electrophoretic mobility shift assays. As a result, the three ssRNA-binding domains of BTV nonstructural protein NS2 have been conclusively localized, and removal of these three domains completely abrogates the ability of NS2 to bind to ssRNA.

Mechanism of action of the Rep protein from the Dictyostelium Ddp2 plasmid family

The two-hybrid system was used to show that the Rep proteins from three members of the Dictyostelium discoideum Ddp2 plasmid family, Ddp2, Ddp5, and Ddp6, form homomultimers but not heteromultimers when expressed in yeast cells. The results with deletion mutations suggest that multiple regions of the Rep proteins are involved in the multimerization. Electrophoretic mobility shift assays with heterologously expressed and purified Ddp2 Rep protein showed that it is a DNA binding protein. The nucleosomal organization of Ddp2 and Ddp6 in their inverted repeat and promoter regions was investigated. Analysis of mutants derived from the Ddp6 plasmid revealed that its Rep protein is required for nucleosome positioning (i.e., phasing) to occur in the promoter region. On the other hand, nucleosome positioning in the inverted repeat regions of both plasmids is not dependent on Rep protein but on either a feature of the DNA sequence or the binding of cellular factors, perhaps the Dictyostelium origin recognition complex. Rep protein is likely involved in transcription regulation and control of DNA replication, specifically amplification of plasmid at low copy numbers. The formation of homomultimers may be required for their regulatory activity.

Rice dwarf phytoreovirus segment S11 encodes a nucleic acid binding protein

The function of rice dwarf virus segment 11 and the corresponding segments of other phytoreoviruses is not yet determined. The amino acid sequence of Pns11, encoded by segment 11, contains a putative zinc finger and five flanking basic regions at the C-terminus. The full-length Pns11 protein and three truncated derivatives, which lack the N-terminus, the zinc-finger or the C-terminal five basic regions were expressed in Escherichia coli and their nucleic acid binding properties were studied. Pns11 interacts with single- and double-stranded forms of DNA and RNA in a sequence-nonspecific manner. The truncated derivative which contains both the zinc-finger and the C-terminal basic regions has the same binding properties as the full-length Pns11. However, removal of either of these domains prevents binding activity. The binding activity of Pns11 was drastically reduced when the blots were treated with a high concentration of EDTA. Moreover, Pns11 extracted from infected rice also binds to single-stranded RNA. These data suggest that RDV Pns11 binding activity is structure-dependent and it may play an important role in virus replication and/or genome assortment.

Bluetongue virus VP6 protein binds ATP and exhibits an RNA-dependent ATPase function and a helicase activity that catalyze the unwinding of double-stranded RNA substrates

RNA-dependent ATPase and helicase activities have been identified associated with the purified VP6 protein of bluetongue virus, a member of the Orbivirus genus of double-stranded RNA (dsRNA; Reoviridae family) viruses. In addition, the protein has an ATP binding activity. RNA unwinding of duplexes occurred with both 3' and 5' overhang templates, as well as with blunt-ended dsRNA, an activity not previously identified in other viral helicases. Although little sequence similarity to other helicases was detected, certain similarities to motifs commonly attributed to such proteins were identified.

Stable protein-RNA interaction involves the terminal domains of bluetongue virus mRNA, but not the terminally conserved sequences

The interaction of bluetongue virus (BTV) proteins with viral RNA was investigated in vitro by means of a biochemical approach. By subjecting cytoplasmic extracts from virus-infected baby hamster kidney cells and in vitro synthesized radiolabeled RNA to ultraviolet cross-linking assays, we demonstrated that, of all the BTV proteins, NS2 becomes most intimately associated with the labeled viral RNA. Competition binding studies indicated that NS2 has the greatest affinity for the 3' region of the viral transcripts. By analyzing the binding efficiency of NS2 to mutant RNA transcripts which lacked the fully conserved 5'- and/or 3'-terminal hexanucleotides, we have established that these sequences are not necessary for optimal binding. The specificity of the NS2-RNA interaction was investigated by competition experiments with unlabeled BTV-specific homologous and heterologous competitor RNAs as well as with viral double-stranded RNA (dsRNA). Although apparent differences in the ability of NS2 to bind to the different RNA transcripts were observed, it did not bind to the dsRNA.

Sequences within the VP6 molecule of bluetongue virus that determine cytoplasmic and nuclear targeting of the protein

Genome segment 9 of bluetongue virus serotype 10 encodes the minor protein VP6. The protein is abundant with basic residues particularly in two regions of the carboxy half of the molecule. A series of amino- and carboxy-terminal deletion mutants was expressed in mammalian cells by using a vaccinia virus T7 polymerase-driven transient expression system, and the intracellular fate of the products was monitored by both immunofluorescence staining and cell fractionation techniques. Data obtained indicated clearly that VP6 has nuclear transportation signals which may be correlated with positively charged domains of the molecule. In the intact molecule, though, these signals are masked and the protein is retained in the cytoplasm. The biochemical and immunofluorescence data obtained indicate that sequences in the region of residues 33 to 80 of the 328-amino acid protein are required for the retention of VP6 within the cell cytoplasm while amino acids 303 to 308 in the carboxy-terminal half of the molecule appear to possess nuclear localization capabilities.