(5) or integrated DNA (6). Expression of the viral genome is limited (7-10). However, at least three sites on the viral genome are characteristically transcribed. Three transcripts-from IR1 into U2, from U3 through IR3 into U4, and from U5-are each spliced into a cytoplasmic polyadenylylated RNA that is presumed to encode protein (11)(12)(13)(14)(15). The U3-IR3-U4 RNA is known to encode an Epstein-Barr nuclear antigen (EBNA) (EBNA1), and the U5 RNA encodes a membrane protein (12,14,(16)(17)(18)47).No protein has been assigned to the IR1-U2 RNA. This RNA is initiated by a promoter in any of the copies of IR1, transcribed through subsequent copies of IR1, terminated in U2, polyadenylylated, and spliced into a 3-kb cytoplasmic RNA (11,13). Hybridizations with the separated DNA strands of IR1 and U2 indicate that 5' exons of the RNA must be encoded by IR1 (13). These putative 5' exons have not been identified, however. Furthermore, the principal open reading frame in IR1, identified by DNA sequence analysis (19), does not hybridize to the 3-kb cytoplasmic RNA, suggesting a complex splicing program for the 5' exons. The principal 3' exons have been mapped to contiguous DNA fragments near the center of the U2 domain (13). The importance of this gene in growth transformation is suggested by the finding that a nontransforming EBV isolate, P3HR-1 (20), has undergone a deletion of the U2 region (21-24). Other reportedly transformation-competent isolates are, however, known to vary in their central U2 sequence (22).An EBNA-positive human serum that reacts poorly with the EBNA1 protein detected a second nuclear protein, designated EBNA2, in nuclei of each of five latently infected cell lines that were tested (16). EBNA2 was absent from noninfected continuous B-cell lines (16). The EBNA2 protein is 85 kDa, while EBNA1 varies in size from 68 to 85 kDa, depending on the length of the EBV IR3 repeat in each EBV isolate (14, 16). Antisera raised in rabbits against EBNA1-lacZ or EBV membrane-lacZ fusion proteins react with either EBNA1 or the membrane protein (16, 47) and not with EBNA2, indicating that EBNA2 is not encoded by the U3-IR3-U4 or U5 RNA.We now report the sequence of the U2 domain of the B95-8 and AG876 isolates of EBV. The B95-8 U2 DNA sequence reveals a 1545-base-pair (bp) open reading frame. The U2 domains of some isolates such as W91, Raji, Lamont, and Cherry are quite closely related to the B95-8 U2, while others such as AG876 and Jijoye are divergent from B95-8 U2 (22). These nucleotide sequence differences among EBV isolates correlate with differences in their EBNA2 proteins, indicating that the U2 open reading frame encodes EBNA2. MATERIALS AND METHODSCell Cultures and Viral DNAs. Viral DNA was purified from the supernatant virions of induced AG876 (26), or HVPapio (27) cultures or from cells of Jijoye (20) or HVPan (28) cultures by isopycnic centrifugation (21).Electrophoretic Blotting. Nuclei were prepared by resuspending washed cells in 2% sucrose/10 mM Tris-HCI, pH 7.5/10 mM NaCI/3 mM Mg(OA...
Human herpesvirus 6 variants A and B (HHV-6A and HHV-6B) are closely related viruses that can be readily distinguished by comparison of restriction endonuclease profiles and nucleotide sequences. The viruses are similar with respect to genomic and genetic organization, and their genomes cross-hybridize extensively, but they differ in biological and epidemiologic features. Differences include infectivity of T-cell lines, patterns of reactivity with monoclonal antibodies, and disease associations. Here we report the complete genome sequence of HHV-6B strain Z29 [HHV-6B(Z29)], describe its genetic content, and present an analysis of the relationships between HHV-6A and HHV-6B. As sequenced, the HHV-6B(Z29) genome is 162,114 bp long and is composed of a 144,528-bp unique segment (U) bracketed by 8,793-bp direct repeats (DR). The genomic sequence allows prediction of a total of 119 unique open reading frames (ORFs), 9 of which are present only in HHV-6B. Splicing is predicted in 11 genes, resulting in the 119 ORFs composing 97 unique genes. The overall nucleotide sequence identity between HHV-6A and HHV-6B is 90%. The most divergent regions are DR and the right end of U, spanning ORFs U86 to U100. These regions have 85 and 72% nucleotide sequence identity, respectively. The amino acid sequences of 13 of the 17 ORFs at the right end of U differ by more than 10%, with the notable exception of U94, the adeno-associated virus type 2 rep homolog, which differs by only 2.4%. This region also includes putative cis-acting sequences that are likely to be involved in transcriptional regulation of the major immediate-early locus. The catalog of variant-specific genetic differences resulting from our comparison of the genome sequences adds support to previous data indicating that HHV-6A and HHV-6B are distinct herpesvirus species.
A comparative analysis of three Epstein-Barr virus DNAs from American patients with infectious mononucleosis (B95-8, Cherry, and Lamont) and four Epstein-Barr virus DNAs from African patients with Burkitt lymphoma (AG876, W91, Raji, and P3HR-1) indicated that the usual format of Epstein-Barr virus DNA includes a variable number of direct repeats of a 0.35 X 10(6)-dalton sequence (TR) at both ends of the DNA, a 9 X 10(6)-dalton sequence of largely unique DNA (Us), a variable number of repeats of a 2 X 10(6)-dalton sequence (IR), and a 89 X 10(6)-dalton sequence of largely unique DNA (UL). Within UL there was homology between DNA at 26 X 10(6) to 28 X 10(6) daltons and DNA at 93 X 10(6) to 95 X 10(6) daltons. The relative sequence order (TR, US, IR, UL, TR) did not vary among "standard" Epstein-Barr virus DNA molecules of each isolate. B95-8 DNA had an unusual deletion extending from 91 X 10(6) to 100 X 10(6) daltons, and P3HR-1 DNA had an unusual deletion extending from 23.5 X 10(6) to 26 X 10(6) daltons. There was sufficient variability among the EcoRI and BamHI fragments of the DNAs to identify each isolate specifically. However, we discerned no distinguishing features for the two geographic or pathogenic origins of the seven isolates. Three intracellular DNAs (Raji, Lamont, and Cherry) and one virion DNA (P3HR-1) were heterogenous in molecular organization and had subpopulations of rearranged or defective molecules. Some regions, particularly 59 X 10(6) to 63 X 10(6) daltons and sequences around TR, frequently participated in rearrangements. Restriction endonuclease maps of the standard and rearranged DNAs of the seven isolates are presented.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.