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Donovan-Banfield I, Turnell AS, Hiscox JA, Leppard KN, Matthews DA. Deep splicing plasticity of the human adenovirus type 5 transcriptome drives virus evolution. Commun Biol 2020; 3:124. [PMID: 32170151 PMCID: PMC7070027 DOI: 10.1038/s42003-020-0849-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 02/12/2020] [Indexed: 02/06/2023] Open
Abstract
Viral genomes have high gene densities and complex transcription strategies rendering transcriptome analysis through short-read RNA-seq approaches problematic. Adenovirus transcription and splicing is especially complex. We used long-read direct RNA sequencing to study adenovirus transcription and splicing during infection. This revealed a previously unappreciated complexity of alternative splicing and potential for secondary initiating codon usage. Moreover, we find that most viral transcripts tend to shorten polyadenylation lengths as infection progresses. Development of an open reading frame centric bioinformatics analysis pipeline provided a deeper quantitative and qualitative understanding of adenovirus's genetic potential. Across the viral genome adenovirus makes multiple distinctly spliced transcripts that code for the same protein. Over 11,000 different splicing patterns were recorded across the viral genome, most occurring at low levels. This low-level use of alternative splicing patterns potentially enables the virus to maximise its coding potential over evolutionary timescales.
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Affiliation(s)
- I'ah Donovan-Banfield
- Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol, Bristol, BS8 1TD, UK
| | - Andrew S Turnell
- Institute of Cancer and Genomic Sciences College of Medical and Dental Sciences University of Birmingham Edgbaston, Birmingham, B15 2TT, UK
| | - Julian A Hiscox
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, ic2 Building, Liverpool, L3 5RF, UK
| | - Keith N Leppard
- Life Sciences University of Warwick Coventry, Coventry, CV4 7AL, UK
| | - David A Matthews
- Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol, Bristol, BS8 1TD, UK.
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2
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The tripartite leader sequence is required for ectopic expression of HAdV-B and HAdV-E E3 CR1 genes. Virology 2017; 505:139-147. [PMID: 28259047 DOI: 10.1016/j.virol.2017.02.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 02/23/2017] [Indexed: 01/09/2023]
Abstract
The unique repertoire of genes that characterizes the early region 3 (E3) of the different species of human adenovirus (HAdV) likely contributes to their distinct pathogenic traits. The function of many E3 CR1 proteins remains unknown possibly due to unidentified intrinsic properties that make them difficult to express ectopically. This study shows that the species HAdV-B- and HAdV-E-specific E3 CR1 genes can be expressed from vectors carrying the HAdV tripartite leader (TPL) sequence but not from traditional mammalian expression vectors. Insertion of the TPL sequence upstream of the HAdV-B and HAdV-E E3 CR1 open reading frames was sufficient to rescue protein expression from pCI-neo constructs in transfected 293T cells. The detection of higher levels of HAdV-B and HAdV-E E3 CR1 transcripts suggests that the TPL sequence may enhance gene expression at both the transcriptional and translational levels. Our findings will facilitate the characterization of additional AdV E3 proteins.
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3
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Gustin KE, Lutz P, Imperiale MJ. Interaction of the adenovirus L1 52/55-kilodalton protein with the IVa2 gene product during infection. J Virol 1996; 70:6463-7. [PMID: 8709283 PMCID: PMC190681 DOI: 10.1128/jvi.70.9.6463-6467.1996] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The adenovirus L1 52/55-kDa protein is expressed both in the early and late stages of infection, raising the possibility that it has multiple roles in the viral life cycle. To obtain possible insights into these roles, the yeast two-hybrid system was used to examine the interactions of the 52/55-kDa protein with viral and cellular factors. cDNA expression libraries from human 293 cells at both early and late stages of adenovirus type 5 infection were constructed and screened, with the 52/55-kDa protein being used as bait. Characterization of positive clones revealed that the adenovirus IVa2 gene product interacted specifically with the 52/55-kDa protein. In addition, the IVa2 protein was shown to interact with a bacterial glutathione S-transferase-52/55-kDa fusion protein in vitro, further supporting the finding with the yeast two-hybrid system. Finally, coimmunoprecipitation studies confirmed that the 52/55-kDa protein and IVa2 polypeptide interact specifically during the course of adenovirus infection. A potential role for the IVa2-52/55-kDa protein interaction in the regulation of transcription from the major late promoter and in viral assembly is discussed.
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Affiliation(s)
- K E Gustin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor 48109-0620, USA
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4
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Kring SC, Spindler KR. Sequence of mouse adenovirus type 1 DNA encoding the amino terminus of protein IVa2. Nucleic Acids Res 1990; 18:4003. [PMID: 2374728 PMCID: PMC331119 DOI: 10.1093/nar/18.13.4003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- S C Kring
- Department of Genetics, University of Georgia, Athens 30602
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5
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Hayes BW, Telling GC, Myat MM, Williams JF, Flint SJ. The adenovirus L4 100-kilodalton protein is necessary for efficient translation of viral late mRNA species. J Virol 1990; 64:2732-42. [PMID: 2335816 PMCID: PMC249453 DOI: 10.1128/jvi.64.6.2732-2742.1990] [Citation(s) in RCA: 92] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
When screening a number of adenovirus type 5 (Ad5) temperature-sensitive mutants for defects in viral gene expression, we observed that H5ts1-infected 293 cells accumulated reduced levels of newly synthesized viral late proteins. Pulse-labeling and pulse-chase experiments were used to establish that the late proteins synthesized in H5ts1-infected cells under nonpermissive conditions were as stable as those made in Ad5-infected cells. H5ts1-infected cells contained normal levels of viral late mRNAs. Because these observations implied that translation of viral mRNA species was defective in mutant virus-infected cells, the association of viral late mRNAs with polyribosomes was examined during the late phase of infection at a nonpermissive temperature. In Ad5-infected cells, the majority of the viral L2, L3, L4, pIX, and IVa2 late mRNA species were polyribosome bound. By contrast, these same mRNA species were recovered from H5ts1-infected cells in fractions nearer the top of polyribosome gradients, suggesting that initiation of translation was impaired. During the late phase of infection, neither the polyribosome association nor the translation of most viral early mRNA species was affected by the H5ts1 mutation. This lesion, mapped by marker rescue to the L4 100-kilodalton (kDa) nonstructural protein, has been identified as a single base pair substitution that replaces Ser-466 of the Ad5 100-kDa protein with Pro. A set of temperature-independent revertants of H5ts1 was isolated and characterized. Either true reversion of the H5ts1 mutation or second-site mutation of Pro-466 of the H5ts1 100-kDa protein to Thre, Leu, or His restored both temperature-independent growth and the efficient synthesis of viral late proteins. We therefore conclude that the Ad5 L4 100-kDa protein is necessary for efficient initiation of translation of viral late mRNA species during the late phase of infection.
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Affiliation(s)
- B W Hayes
- Department of Biology, Princeton University, Princeton, New Jersey 08544-1014
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6
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Ball AO, Beard CW, Redick SD, Spindler KR. Genome organization of mouse adenovirus type 1 early region 1: a novel transcription map. Virology 1989; 170:523-36. [PMID: 2543128 DOI: 10.1016/0042-6822(89)90444-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Mouse adenovirus type 1 (MAV-1) genomic DNA from 8.9 to 13.7 map units was sequenced and the early region 1 (E1) transcription map was determined by S1 nuclease, primer extension, and Northern analyses, and cDNA sequencing. The E1 transcription map of MAV-1 had marked dissimilarities from the conserved transcription maps of primate adenovirus E1s. One major E1A and two E1B mRNAs were identified in overlapping transcription units. The single E1A mRNA was composed of three exons; the last exon was coincident with the last exon of the E1B mRNAs. While human adenovirus type 2 (Ad2) utilizes alternate splice donors for the first E1A mRNA exon, MAV-1 does not. Thus, no protein is predicted that would correspond to the Ad2 243 amino acid protein, although MAV-1 can encode a protein similar to the Ad2 289 amino acid protein (A. O. Ball, M. E. Williams, and K. R. Spindler, 1988, J. Virol. 62, 3947-3957). Two spliced E1B mRNAs differed from each other in an intron near the 5' end of the smaller E1B mRNA. This smaller mRNA could encode only the 55K E1B protein, while the larger mRNA could encode both the 21K and 55K E1B proteins.
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Affiliation(s)
- A O Ball
- Department of Genetics, University of Georgia, Athens 30602
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7
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Viral Sequences. Viruses 1987. [DOI: 10.1016/b978-0-12-512516-1.50005-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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MESH Headings
- Adenovirus Infections, Human/genetics
- Adenoviruses, Human/genetics
- Cell Line
- Cells, Cultured
- DNA, Viral/biosynthesis
- Enhancer Elements, Genetic
- Gene Expression Regulation
- Genes, Viral
- Humans
- Promoter Regions, Genetic
- RNA Processing, Post-Transcriptional
- RNA, Messenger/biosynthesis
- RNA, Viral/biosynthesis
- Transcription, Genetic
- Viral Proteins/genetics
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Flügel RM, Bannert H, Suhai S, Darai G. The nucleotide sequence of the early region of the Tupaia adenovirus DNA corresponding to the oncogenic region E1b of human adenovirus 7. Gene X 1985; 34:73-80. [PMID: 3159623 DOI: 10.1016/0378-1119(85)90296-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The nucleotide sequence of the early region E1b of the tree shrew (Tupaia) adenovirus (TAV) DNA has been determined. The sequenced region includes the genes for polypeptides of Mr 15 000, 44 000 and 13 400, which are analogous to the small and large E1b proteins and protein IX, respectively, of the three human adenovirus serotypes 5, 7, and 12. The hexanucleotide consensus signal AATAAA occurs only at the 3' terminus of the gene for protein IX suggesting that the E1 region of TAV encompasses one transcription unit. The amino acid sequences of the TAV polypeptides have a higher degree of homology to those of Ad7 and Ad5 than to those of Ad12.
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10
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Niel C, D'Halluin JC. Restriction maps of human adenovirus types 2, 5, and 3 for BstEII, MluI, NdeI, NruI and SfiI endonucleases. Gene 1984; 31:305-8. [PMID: 6098535 DOI: 10.1016/0378-1119(84)90227-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The positions of cleavage sites for BstEII, MluI, NdeI, NruI and SfiI restriction endonucleases in the DNA from human adenovirus (Ad) serotypes 2, 5 and 3 were determined. In addition, the sites of cleavage for BglII in Ad3 DNA were located. All these enzymes possess a narrow specificity and generated a small number of discrete DNA fragments. Ad3 DNA was not cleaved by MluI and SfiI. It was the first observation of the absence of cleavage of an adenovirus DNA by a restriction endonuclease.
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11
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Aleström P, Akusjärvi G, Lager M, Yeh-kai L, Pettersson U. Genes encoding the core proteins of adenovirus type 2. J Biol Chem 1984. [DOI: 10.1016/s0021-9258(18)89841-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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12
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Binger MH, Flint SJ. Accumulation of early and intermediate mRNA species during subgroup C adenovirus productive infections. Virology 1984; 136:387-403. [PMID: 6205505 DOI: 10.1016/0042-6822(84)90175-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The cytoplasmic, poly(A)-containing RNA species complementary to all regions of the adenovirus type 2 (Ad2) genome expressed before the onset of viral DNA synthesis have been examined by "Northern" blotting. HeLa cells infected with low multiplicities of Ad2 were harvested at 2-hr intervals until late in the infectious cycle to establish the temporal patterns of expression of each viral gene. Under these conditions, such late mRNA products as those of the L3 and L5 families were not detected until 14 hr after infection. Although individual mRNA species complementary to several genes showed different patterns of expression, the order of appearance in the cytoplasm of substantial concentrations of adenoviral mRNA species was E1A, E3, and E4 (4 to 6 hr), E2A and E2B (8 hr), 3.7- and 4.1-kb L1 mRNA species (10-12 hr), IX and IVa2 mRNAs (12 hr), and those encoded in the major late transcriptional unit, such as members of the L3 and L5 families (14 hr). The mRNA species encoding polypeptides IX and IVa2 were not produced when viral DNA synthesis was blocked, whereas the larger L1 mRNA species was made under these conditions. Two E2B mRNA species, some 5.0 and 7 kb, were observed at low concentrations at 8 hr after infection and their concentration increased until 24 hr after infection, as did that of the E2A mRNA species: the products of the E2 transcription unit appeared to be expressed coordinately and at a constant ratio throughout infection. Few of the early mRNA species decreased in concentration after the onset of the late phase of infection. Examination of the viral mRNA produced when protein synthesis was inhibited by 10 microM anisomycin added 3 hr after infection suggested that processing of certain viral, early transcripts was altered in the presence of the drug.
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13
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Fujinaga K, Yoshida K, Yamashita T, Shimizu Y. Organization, integration, and transcription of transforming genes of oncogenic human adenovirus types 12 and 7. Curr Top Microbiol Immunol 1984; 110:53-72. [PMID: 6383724 DOI: 10.1007/978-3-642-46494-2_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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14
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Dekker BM, van Ormondt H. The nucleotide sequence of fragment HindIII-C of human adenovirus type 5 DNA (map positions 17.1-31.7). Gene 1984; 27:115-20. [PMID: 6325298 DOI: 10.1016/0378-1119(84)90244-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
This paper describes the sequence of nucleotides 6246-11570 between the two HindIII sites at map positions (m.p.) 17.1 and 31.7 of human adenovirus serotype 5 (Ad5) DNA. It is 99% homologous with the corresponding HindIII-B fragment of adenovirus type 2 (Ad2; Gingeras et al., 1982; Aleström et al., 1982) which has been shown to encode the second, "i", and third leaders of the major late RNAs, the virus-associated RNAs VAI and VAII (all rightward transcripts), and in the opposite sense the early-region E2b mRNAs for a DNA polymerase and for the terminal protein precursor (pTP). Except for the latter, it was possible to determine the coordinates of the corresponding Ad5 RNAs, either by sequence homology with Ad2, or by nuclease S1 analysis. The Ad5 DNA sequence contains the same open reading frames as that of Ad2. The longest of these lie in the r-strand and would specify proteins of Mr 120377 (DNA polymerase) and 74558 (pTP).
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16
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Abstract
S1 nuclease has been used as a probe for regions of DNA secondary structure in supercoiled recombinant plasmids containing adenovirus (Ad) DNA sequences. In the sequences examined two S1 sensitive sites were identified in the left-terminal 16.5% of Ad 12 DNA, one of which aligned approximately with an inverted repeat region in the DNA sequence. In addition an S1 sensitive site was dictated by a potential cruciform structure in the region of the Ad 2 major late promoter. In contrast to the expected cleavage site at the loop of the cruciform, cleavage occurred at the base of the stem in the region of the TATA box. All three S1 sensitive sites identified were more sensitive to S1 than the endogenous sites in the parent plasmids.
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D'Halluin JC, Milleville M, Boulanger PA. Restriction maps of human adenovirus types 2, 5 and 3 for BclI, ClaI, pvul and SphI endonucleases. Gene 1983; 21:165-9. [PMID: 6301946 DOI: 10.1016/0378-1119(83)90158-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The sites of cleavage by BclI, ClaI, PvuI and SphI in the DNA from adenovirus (Ad) serotypes 2, 5 and 3 have been located. Certain site coordinates were in accord with nucleotide sequences already published. A small difference in size between the PvuI-E fragments from Ad2 and Ad5 confirmed the existence of a deletion in the N-terminal moiety of Ad5 hexon gene, as previously implied by interserotypic recombinants (Boursnell and Mautner, Virology 112 (1981) 198-209) and more recently by amino acid sequencing (Von Bahr-Lindström et al., Virology 118 (1982) 352-362).
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Gingeras TR, Sciaky D, Gelinas RE, Bing-Dong J, Yen CE, Kelly MM, Bullock PA, Parsons BL, O'Neill KE, Roberts RJ. Nucleotide sequences from the adenovirus-2 genome. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(18)33473-2] [Citation(s) in RCA: 118] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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19
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Aleström P, Akusjärvi G, Pettersson M, Pettersson U. DNA sequence analysis of the region encoding the terminal protein and the hypothetical N-gene product of adenovirus type 2. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(18)33474-4] [Citation(s) in RCA: 61] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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20
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Abstract
The nucleotide sequences of cloned DNA segments encoding the IVa2 gene from Ad7 and a portion of Ad12 (group B and group A human adenoviruses, respectively) have been determined. When compared to Ad5, a group C adenovirus, these sequences have been found to be 80% homologous. Most changes are transitions or transversions. This high degree of nucleotide homology results in a high degree of amino acid conservation in the predicted polypeptides encoded from these genes; most nucleotide changes occur at the third position in the codon. The predicted polypeptide contains 448 amino acids and has a calculated Mr-value of 50700. The positions of the 5' end of the mRNA and of the donor and acceptor splice sites of Ad7 and Ad12 can be inferred by analogy to those of Ad5. A long open reading frame starting upstream from the IVa2 gene overlaps the N-terminal portion of the polypeptide but is encoded in a different reading frame. Within this overlapping region, the long open reading frame is more conserved in amino acid sequence than is the presumed IVa2 polypeptide, suggesting that evolutionary pressure was exerted on the longer protein, a product of viral early region 2B. The high degree of conservation of this E2B region within the overlapping segment suggests that its activities must be more important for adenovirus infection than are the functions encoded in the amino-terminus of the IVa2 gene.
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Westin G, Visser L, Zabielski J, van Mansfeld AD, Pettersson U, Rozijn TH. Sequence organization of a viral DNA insertion present in the adenovirus-type-5-transformed hamster line BHK268-C31. Gene 1982; 17:263-70. [PMID: 7106562 DOI: 10.1016/0378-1119(82)90142-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The hamster cell line BHK268-C31 contains two large viral inserts which both include sequences from the left-hand end of adenovirus type 5 (Ad5) DNA. One of these viral inserts has been cloned in the lambda vector Charon 4A. Electron microscopic analysis and restriction enzyme mapping shows that the recombinant carries a 4.4-kb-long colinear segment of viral DNA, which is located between map positions 1.5 and 14.2 in the Ad5 genome. The junctions between viral DNA and flanking sequences have been sequenced and found not to show any specific features. One of the junctions is located in the E1a coding region, 573 bp from the left-hand end of the Ad5 genome, whereas the other junction is situated in the coding region for polypeptide IVa2. The promoter region as well as the cap site for the mRNAs from region E1a are thus missing from this insert and its role in viral transformation is unclear.
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