Viral-encoded small RNAs in herpes virus saimiri induced tumors.

DNA sequences from the left terminus of herpes virus saimiri L-DNA are essential for the oncogenic and transforming potential of the virus, but these sequences are not required for replication. RNA derived from 0.0 to 6.7 map units (7.4 kbp) on the herpes virus saimiri genome was studied by Northern blot hybridization and by nuclease protection analyses. Although several poly(A)-containing RNAs were detected from this region in permissively-infected monolayer cells in vitro, these RNAs could not be detected in cells taken directly from viral-induced lymphomas nor in the lymphoblastoid tumor cell line 1670. Instead, these transformed T-cells expressed four small RNAs of approximately 73, 105, 110 and 135 nt derived from this region. These small RNAs were not detected at all during the course of lytic infection of monolayer cells. Thus, synthesis of these RNAs is stringently regulated in a cell-type specific manner. Genomic coding sequences for each of these small RNAs were mapped to 0.5-1.2 kbp DNA fragments stretched over 4.3 kbp of viral genetic information. These findings together with the biological properties of mutants with deletions in this region have led us to speculate that one or more of these small RNAs play an essential role in cell growth transformation by herpes virus saimiri.     

Nucleotide sequence relationships between vertebrate 5.8 S ribosomal RNAs.

Nucleotide sequences of the 5.8 S ribosomal RNAs from HeLa cells, Xenopus laevis and chick embryo fibroblasts were compared. Xenopus laevis 5.8 S RNA differs from that of HeLa cells in four internal positions and at the 3' end of the molecule. Chick 5.8 S RNA differs from that of HeLa cells in two positions. Six out of the seven interspecies differences are due to base substitutions. The other difference is due to the presence of an extra nucleotide, internally located, within the Xenopus 5.8 S sequence.     

Primary structure of the herpesvirus saimiri genome.

This report describes the complete nucleotide sequence of the genome of herpesvirus saimiri, the prototype of gammaherpesvirus subgroup 2 (rhadinoviruses). The unique low-G + C-content DNA region has 112,930 bp with an average base composition of 34.5% G + C and is flanked by about 35 noncoding high-G + C-content DNA repeats of 1,444 bp (70.8% G + C) in tandem orientation. We identified 76 major open reading frames and a set of seven U-RNA genes for a total of 83 potential genes. The genes are closely arranged, with only a few regions of sizable noncoding sequences. For 60 of the predicted proteins, homologous sequences are found in other herpesviruses. Genes conserved between herpesvirus saimiri and Epstein-Barr virus (gammaherpesvirus subgroup 1) show that their genomes are generally collinear, although conserved gene blocks are separated by unique genes that appear to determine the particular phenotype of these viruses. Several deduced protein sequences of herpesvirus saimiri without counterparts in most of the other sequenced herpesviruses exhibited significant homology with cellular proteins of known function. These include thymidylate synthase, dihydrofolate reductase, complement control proteins, the cell surface antigen CD59, cyclins, and G protein-coupled receptors. Searching for functional protein motifs revealed that the virus may encode a cytosine-specific methylase and a tyrosine-specific protein kinase. Several herpesvirus saimiri genes are potential candidates to cooperate with the gene for saimiri transformation-associated protein of subgroup A (STP-A) in T-lymphocyte growth stimulation.     

Expression of collagenlike sequences by a tumor virus, herpesvirus saimiri.

Sequencing demonstrates that the oncogenic regions of a group A strain and a group C strain of herpesvirus saimiri are nonhomologous. A bicistronic viral mRNA from this region is transcribed in tumor cells transformed by a highly oncogenic group C virus. The first open reading frame is homologous to collagen; no such sequences were found in group A or B strains. This is the first report that a virus encodes for sequences similar to those of a connective tissue protein.     

Organization of the thymidylate synthase gene of herpesvirus saimiri.

Herpesvirus saimiri codes, unlike most other herpesviruses, for a thymidylate synthase (TS). The TS gene of herpesvirus saimiri is unusual in structure and regulation of expression. It is transcribed into a nonspliced mRNA of 2,190 nucleotides. The single open reading frame of the viral TS gene, instructing a polypeptide of 33.5 kilodaltons, has extensive sequence homology with the corresponding TS coding sequences of human cells and of various procaryotes; the putative polypeptide derived from the nucleotide sequence of the herpesvirus saimiri TS gene is 70% identical with the human enzyme. The untranslated regions of the herpesvirus saimiri TS gene do not share homology with the other characterized eucaryotic or bacterial TS genes. The 5' untranslated sequence has 22 ATG triplets shortly followed by stop codons. The herpesvirus saimiri TS gene, which may be weakly transcribed during immediate early and early times of virus replication, is maximally expressed at the late phase. Various parameters suggest that the TS gene has been acquired in virus evolution by an ancestral herpesvirus from the cellular genome.     

Small RNA deep sequencing identifies microRNAs and other small noncoding RNAs from human herpesvirus 6B

Roseolovirus, or human herpesvirus 6 (HHV-6), is a ubiquitous human pathogen infecting over 95% of the population by the age of 2 years. As with other herpesviruses, reactivation of HHV-6 can present with severe complications in immunocompromised individuals. Recent studies have highlighted the importance of herpesvirus-derived microRNAs (miRNAs) in modulating both cellular and viral gene expression. An initial report which computed the likelihood of various viruses to encode miRNAs did not predict HHV-6 miRNAs. To experimentally screen for small HHV-6-encoded RNAs, we conducted large-scale sequencing of Sup-T-1 cells lytically infected with a laboratory strain of HHV-6B. This revealed an abundant, 60- to 65-nucleotide RNA of unknown function derived from the lytic origin of replication (OriLyt) that gave rise to smaller RNA species of 18 or 19 nucleotides. In addition, we identified four pre-miRNAs whose mature forms accumulated in Argonaute 2. In contrast to the case for other betaherpesviruses, HHV-6B miRNAs are expressed from direct repeat regions (DR(L) and DR(R)) located at either side of the genome. All miRNAs are conserved in the closely related HHV-6A variant, and one of them is a seed ortholog of the human miRNA miR-582-5p. Similar to alphaherpesvirus miRNAs, they are expressed in antisense orientation relative to immediate-early open reading frames (ORFs) and thus have the potential to regulate key viral genes.     

Identification and characterization of the herpesvirus saimiri oncoprotein STP-C488.

The protein encoded by herpesvirus saimiri transforming gene STP-C488 was identified and characterized. Antibodies were produced in rabbits by immunization with keyhole limpet hemocyanin-conjugated synthetic peptides specific for the predicted sequence of STP-C488. STP-C488-encoded protein was detected in recombinant Escherichia coli, transformed Rat-1 cells, transfected COS-1 cells, and in common marmoset T lymphocytes immortalized by herpesvirus saimiri strain 488. STP-C488 protein was sensitive to treatment by bacterial collagenase, consistent with the 18 uninterrupted collagenlike repeats predicted by the DNA sequence. The apparent molecular size of STP-C488 in sodium dodecyl sulfate (SDS)-polyacrylamide gels (20 to 22 kDa) was considerably larger than that predicted from the DNA sequence (9.9 kDa). Using indirect immunofluorescence tests and subcellular fractionation, STP-C488 was found to be membrane bound, primarily in perinuclear compartments. The 18 uninterrupted collagenlike repeats, sensitivity to collagenase, location in the cell, and anomalous migration through SDS-polyacrylamide gels suggest an unusual, membrane-associated, fibrous structure for this transforming herpesvirus oncoprotein.     

Nucleotide sequence analysis of pRS2 and pRS3, two small cryptic plasmids from Oenococcus oeni

Nucleotide sequence analysis of two cryptic plasmids, pRS2 (2544 bp) and pRS3 (3948 bp), from Oenococcus oeni revealed the presence in both of three major open reading frames with significant similarity to other small cryptic plasmids from O. oeni. The results suggest that those plasmids could be separated into two subfamilies, one represented by pLo13 and pRS3, the other represented by pOg32, pRS1, and pRS2.     

Analysis of herpesvirus saimiri structural proteins with monoclonal antibodies.

Herpesvirus saimiri is a lymphotrophic virus isolated from squirrel monkeys that causes highly malignant lymphomas in owl monkeys, marmosets, and rabbits, but not in its natural host. We have been interested in exploring immunological and biological aspects of this phenomenon and describe in this report the isolation of 27 monoclonal antibodies (MCAs) to herpesvirus saimiri which were grouped into 11 distinct sets based on the proteins they immunoprecipitated. In total, these 11 groups of MCAs identify the majority of the proteins present in the virion. Immunofluorescence was used to study how the viral antigens are compartmentalized in infected cells. One antibody produced intense nuclear staining and immunoprecipitated both the largest protein seen in gels (150,000 daltons) and one of the smallest (13,000 daltons). All of the other groups of MCAs principally stained the cytoplasm of infected cells. One of the unexpected results of this study was the observation that a majority of the MCAs precipitated more than one protein (15 of 27 antibodies, 7 of 11 groups). Whereas one group of MCAs, which normally precipitated four proteins, identified only single polypeptides after dithiothreitol pretreatment, the other sets of antibodies continued to recognize two or more viral antigens under reducing conditions. Immunoprecipitation of viral proteins with polyvalent sera obtained from virus-infected rabbits and monkeys was carried out to verify and extend previously published reports on the proteins of herpesvirus saimiri.     

Nucleotide sequence of a crustacean 18S ribosomal RNA gene and secondary structure of eukaryotic small subunit ribosomal RNAs

The primary structure of the gene for 18 S rRNA of the crustacean Artemia salina was determined. The sequence has been aligned with 13 other small ribosomal subunit RNA sequences of eukaryotic, archaebacterial, eubacterial, chloroplastic and plant mitochondrial origin. Secondary structure models for these RNAs were derived on the basis of previously proposed models and additional comparative evidence found in the alignment. Although there is a general similarity in the secondary structure models for eukaryotes and prokaryotes, the evidence seems to indicate a different topology in a central area of the structures.