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Stone D, Furthmann A, Sandig V, Lieber A. The complete nucleotide sequence, genome organization, and origin of human adenovirus type 11. Virology 2003; 309:152-65. [PMID: 12726735 DOI: 10.1016/s0042-6822(02)00085-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The complete DNA sequence and transcription map of human adenovirus type 11 are reported here. This is the first published sequence for a subgenera B human adenovirus and demonstrates a genome organization highly similar to those of other human adenoviruses. All of the genes from the early, intermediate, and late regions are present in the expected locations of the genome for a human adenovirus. The genome size is 34,794 bp in length and has a GC content of 48.9%. Sequence alignment with genomes of groups A (Ad12), C (Ad5), D (Ad17), E (Simian adenovirus 25), and F (Ad40) revealed homologies of 64, 54, 68, 75, and 52%, respectively. Detailed genomic analysis demonstrated that Ads 11 and 35 are highly conserved in all areas except the hexon hypervariable regions and fiber. Similarly, comparison of Ad11 with subgroup E SAV25 revealed poor homology between fibers but high homology in proteins encoded by all other areas of the genome. We propose an evolutionary model in which functional viruses can be reconstituted following fiber substitution from one serotype to another. According to this model either the Ad11 genome is a derivative of Ad35, from which the fiber was substituted with Ad7, or the Ad35 genome is the product of a fiber substitution from Ad21 into the Ad11 genome. This model also provides a possible explanation for the origin of group E Ads, which are evolutionarily derived from a group C fiber substitution into a group B genome.
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Affiliation(s)
- Daniel Stone
- Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA
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2
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Cauthen AN, Spindler KR. Sequence of the mouse adenovirus type-1 DNA encoding the 100-kDa, 33-kDa and DNA-binding proteins. Gene X 1996; 168:183-7. [PMID: 8654941 DOI: 10.1016/0378-1119(95)00715-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The genomic nucleotide sequence for the region of 66 to 77 map units (m.u.) of mouse adenovirus type 1 (MAV-1) was determined and predicted to encode proteins homologous to the human adenovirus (Ad) 100-kDa, 33kDa and DNA-binding proteins (DBP). The putative MAV-1 100-kDa protein has 65-70% amino-acid similarity to 100-kDa proteins from five different human Ad serotypes. The mRNA for the putative 33-kDa protein is internally spliced within the coding sequence, as are its human Ad counterparts [Oosterom-Dragon and Anderson, J. Virol 45 (1983) 251-263]. The N-terminal region of the putative MAV-1 33-kDa protein has 41-44% similarity to two human Ad 33-kDa N-termini, and the C-terminal regions are more conserved, with 60-65% similarity. The MAV-1 DBP is predicted to be encoded in this region and was compared to six different human Ad DBP N-and C-termini. The N-termini of the MAV-1 and Ad DBP were 33-48% similar and the C-termini were 56-60% similar. The MAV-1 DBP contains conserved regions (CR) 1,2 and 3, and it retains important residues for a putative zinc finger (Zf) motif identified in Ad DBP [Eagle and Klessig, Virology 187 (1992) 777-787]. Additional sequence features of these proteins have also been identified.
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Affiliation(s)
- A N Cauthen
- Department of Genetics, University of Georgia, Athens 30602-7223, USA
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3
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Brough DE, Cleghon V, Klessig DF. Construction, characterization, and utilization of cell lines which inducibly express the adenovirus DNA-binding protein. Virology 1992; 190:624-34. [PMID: 1387750 DOI: 10.1016/0042-6822(92)90900-a] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
To further our understanding of structure-function relationships within the multifunctional adenovirus DNA binding protein (DBP) a more diverse collection of mutants is necessary. DBP-expressing cell lines (gmDBP) were previously constructed that complemented DBP-negative mutants for viral growth. However, they did not allow severely defective viruses to form plaques. Since efficient mutant construction is reliant on plaque isolation of the desired mutant virus as a final step, additional gmDBP cell lines were constructed which allow all DBP-negative mutants to form plaques. Here we describe the construction and characterization of 12 new gmDBP cell lines. The utility of these lines was demonstrated by the efficient construction of a new defective mutant, H5in804, using a combination of DBP-expressing lines. The H5in804 mutation adds 22 amino acids at the carboxyl end of an otherwise wild type protein. Characterization of H5in804 revealed that it was altered in its ability to replicate viral DNA. The depression of DNA synthesis most probably results from a reduced ability of H5in804 DBP to bind ssDNA.
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Affiliation(s)
- D E Brough
- Waksman Institute, Rutgers, State University of New Jersey, Piscataway 08855
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4
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Neale GA, Kitchingman GR. Conserved region 3 of the adenovirus type 5 DNA-binding protein is important for interaction with single-stranded DNA. J Virol 1990; 64:630-8. [PMID: 2296078 PMCID: PMC249153 DOI: 10.1128/jvi.64.2.630-638.1990] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The adenovirus-encoded single-stranded DNA-binding protein (DBP) functions in viral DNA replication and several aspects of RNA metabolism. Previous studies (G. A. M. Neale and G. R. Kitchingman, J. Biol. Chem. 264:3153-3159, 1989) have defined three highly conserved regions in the carboxy-terminal domain of the protein (amino acids 178 to 186, 322 to 330, and 464 to 475) that may be involved in the binding of the protein to single-stranded DNA. We examined the role of conserved region 3 (464 to 475) by constructing nine classes of point mutants with from one to four amino acid changes. The point mutants were tested for their ability to assist adeno-associated virus DNA replication. All nine differed from wild-type DBP; seven were essentially nonfunctional, whereas two had 55 and 145%, respectively, of the wild-type DBP helper activity. Three of the mutants were found to be temperature sensitive, with significantly greater helper activity at 33 degrees C than at 37 degrees C. All nine mutants produced essentially wild-type levels of protein. One monoclonal antibody against the DBP, termed 2/4, did not immunoprecipitate the mutant DBPs as well as wild-type DBP, indicating either that the antibody recognized sequences around CR3 or that the conformation of the protein around the epitope recognized by 2/4 had changed. Two of the three temperature-sensitive DBP mutants bound to single-stranded DNA-cellulose with the same affinity as wild-type DBP at 4 degrees C; the remaining mutants all showed reduced affinity. These results demonstrated that many of the residues within conserved region 3 of the DBP are important for interaction of the protein with nucleic acid.
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Affiliation(s)
- G A Neale
- Department of Virology and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38101
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5
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Vos HL, Brough DE, Van der Lee FM, Hoeben RC, Verheijden GF, Dooijes D, Klessig DF, Sussenbach JS. Characterization of adenovirus type 5 insertion and deletion mutants encoding altered DNA binding proteins. Virology 1989; 172:634-42. [PMID: 2800341 DOI: 10.1016/0042-6822(89)90206-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We have introduced insertion and deletion mutations in the cloned DNA binding protein (DBP) gene of adenovirus type 5. The mutated DBP genes were subsequently introduced in the viral genome by a combination of in vitro and in vivo methods. The resulting mutant viruses were tested for their viability in human 293 cells and an initial characterization of these viruses was performed. Viable mutants with insertions in the carboxyl-terminal portion of the gene could not be obtained. In contrast, a number of viable mutants were constructed that contained insertions or deletions in the amino-terminal half of DBP. Several of these, which covered the region between amino acid (aa) residues 39 and 81, were phenotypically wild type, implying that this segment is completely dispensable for DBP function. However, mutations altering the region encompassed by aa 2-38 were, at least, partially defective suggesting that this region is important for full activity of the protein.
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Affiliation(s)
- H L Vos
- Laboratory for Physiological Chemistry, State University of Utrecht, the Netherlands
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6
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Cleghon V, Voelkerding K, Morin N, Delsert C, Klessig DF. Isolation and characterization of a viable adenovirus mutant defective in nuclear transport of the DNA-binding protein. J Virol 1989; 63:2289-99. [PMID: 2523000 PMCID: PMC250647 DOI: 10.1128/jvi.63.5.2289-2299.1989] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The isolation and characterization of an adenovirus mutant, Ad5dl802r1, containing two independent deletions in the 72-kilodalton (kDa) DNA-binding protein (DBP) gene is described. The two deletions remove amino acids 23 through 105 of DBP, resulting in the production of a 50-kDa product. Expression of this truncated DBP was delayed 12 to 24 h compared with that of the 72-kDa protein produced by wild-type adenovirus type 5. The DBP was located primarily in the cytoplasm of infected cells, whereas the wild-type product was predominantly nuclear. Therefore, DBP appears to contain a nuclear localization signal within the deleted region. Ad5dl802r1 DNA synthesis, viral late gene expression, and virus production were all delayed 12 to 24 h and were approximately 10-fold lower than with wild-type adenovirus type 5. These phenotypic properties can be accounted for by the delay in synthesis and the inefficient accumulation of the 50-kDa DBP within the nucleus of infected cells. The truncated DBP also lacks the majority of amino acids which are phosphorylated in the normal protein. The loss of these phosphorylation sites does not appear to seriously impair the ability of the protein to carry out its functions.
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Affiliation(s)
- V Cleghon
- Waksman Institute of Microbiology Rutgers, State University of New Jersey, Piscataway 08855-0759
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7
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Choli T, Wittmann-Liebold B, Reinhardt R. Microsequence analysis of DNA-binding proteins 7a, 7b, and 7e from the archaebacterium Sulfolobus acidocaldarius. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(18)68608-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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8
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Vos HL, van der Lee FM, Reemst AM, van Loon AE, Sussenbach JS. The genes encoding the DNA binding protein and the 23K protease of adenovirus types 40 and 41. Virology 1988; 163:1-10. [PMID: 3279700 DOI: 10.1016/0042-6822(88)90227-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The adenovirus (Ad) single-stranded DNA binding protein (DBP) is a multifunctional protein. It is thought to consist of two domains, the amino-terminal domain involved in host-range determination and the carboxyl-terminal domain functioning in DNA replication and DNA binding. We have determined the nucleotide sequences of the DBP genes of Ad40 and Ad41, two human adenoviral serotypes that differ significantly from other adenoviruses. Regions of structural and functional importance in the corresponding proteins could be identified by comparison of the amino acid sequences with those of other known DBPs. In addition, the nucleotide sequences of the DBP early promoters, of the 23K protease genes, and of parts of the hexon and 100K protein genes have been determined. It can be deduced from the nucleotide sequences, that the Ad40 and Ad41 DBPs are relatively small (473 and 474 amino acids (a.a.), respectively, versus 529 a.a. for the Ad5 DBP). This is caused by the presence of very small amino-terminal domains of 119 a.a. (Ad40) and 120 a.a. (Ad41), as compared to 173 a.a. for the corresponding Ad5 domain. Only a few amino acids in this domain have been conserved in all known DBPs. The carboxyl-terminal domains show a higher degree of sequence conservation. In this domain, four strongly conserved regions can be identified, one of which might form a metal-binding site. The 23K proteases of both Ad40 and Ad41 show a strong homology to the Ad2 and Ad5 proteins, with the exception of the carboxyl-terminal end of the proteins. The 23K protease gene of Ad41 has an open reading frame that extends beyond the polyadenylation signal, in contrast to the Ad40 gene that ends well in front of the signal.
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Affiliation(s)
- H L Vos
- Laboratory of Physiological Chemistry, State University of Utrecht, the Netherlands
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9
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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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10
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Quinn CO, Kitchingman GR. Functional analysis of the adenovirus type 5 DNA-binding protein: site-directed mutants which are defective for adeno-associated virus helper activity. J Virol 1986; 60:653-61. [PMID: 3021998 PMCID: PMC288938 DOI: 10.1128/jvi.60.2.653-661.1986] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
We generated four point mutations in the DNA-binding protein (DBP) gene of adenovirus type 5 by oligonucleotide-directed site-specific mutagenesis. The sites mutated were in the three conserved regions (CR; amino acids 178-186 [CR1], 322-330 [CR2], and 464-475 [CR3]) identified previously by comparative sequence analysis (G. R. Kitchingman, Virology 146:90-101, 1985). The mutations resulted in changes in amino acids 181 (Trp to Leu), 323 (Arg to Leu), 324 (Trp to Leu), and 469 (Phe to Ile). The mutated DBP genes were put under the control of the simian virus 40 early promoter and analyzed by transfection for their ability to help adeno-associated virus replicate its DNA in COS-1 monkey cells. Mutations in the aromatic amino acids 324 and 469 reduced the amount of AAV DNA replication approximately 10-fold, while the mutation in Arg 323 produced a reduction of approximately fourfold. The Trp-to-Leu mutation in amino acid 181 had no effect on AAV DNA replication. The decreased helper activity of the 323, 324, and 469 mutations was not caused by any effect of the mutation on the stability of the DBP. These results suggest that CR2 and CR3 are involved in AAV helper activity, specifically in AAV DNA replication. The relevance of these findings to the identification of residues important for the functions of DBP in adenovirus infection is discussed.
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11
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Argos P, Tucker AD, Philipson L. Primary structural relationships may reflect similar DNA replication strategies. Virology 1986; 149:208-16. [PMID: 3004026 DOI: 10.1016/0042-6822(86)90122-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The primary structures of several proteins of bacterial and viral origin involved in the initiation of DNA synthesis and its subsequent elongation were compared. It was found that the known sequences of DNA polymerases and the single-stranded DNA binding proteins from phage T7 and Escherichia coli aligned well. Furthermore, segmental homologies were found in the phage phi 29 and adenovirus polymerases as well as in their DNA binding proteins. These results suggest similar mechanisms of DNA synthesis for E. coli and T7 on the one hand and for phi 29 and adenovirus on the other.
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12
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Kitchingman GR. Sequence of the DNA-binding protein of a human subgroup E adenovirus (type 4): comparisons with subgroup A (type 12), subgroup B (type 7), and subgroup C (type 5). Virology 1985; 146:90-101. [PMID: 4041089 DOI: 10.1016/0042-6822(85)90055-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The nucleotide sequence of the gene for the single-stranded DNA-binding protein of adenovirus type 4 (Ad4) has been determined. The gene codes for a protein of 512 amino acids. Comparison of the amino acid sequence with those previously determined for Ad5, Ad12, and Ad7 allowed identification of regions that are conserved between the four serotypes. These include stretches of 9, 9, and 12 amino acids in the carboxy-terminal domain of the protein; these sequences are similar to those identified in the single-stranded DNA-binding proteins of procaryotes as being important for interaction of the protein with single-stranded DNA. A conserved region of four amino acids in the amino-terminal domain is identical in sequence to a region of the SV40 large T antigen that has recently been implicated in the nuclear localization of the protein. Other conserved amino acids that may be important for the three-dimensional structure of the protein have also been identified. The overall homology between the DBPs of the four serotypes is 17.2% in the amino-terminal domain, 47.8% in the carboxy-terminal domain. Two-way comparisons between the DBPs of the four serotypes indicates that the DBP of Ad4 is most closely related to that of Ad7.
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