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Adenovirus encodes a 72-kDa single-stranded DNA binding protein (DBP) that is necessary for viral DNA replication and is involved in controlling viral RNA metabolism. Studies of temperature-sensitive (ts) and site-directed mutants of the DBP have identified at least four regions of the protein involved in binding to single-stranded DNA and hence in DNA replication. Two of the ts mutants, Ad2ts111A and Ad2ND1+ts23, are deficient in DNA binding and in supporting in vitro DNA replication. Their effects on viral RNA metabolism are presented here. At early and late times of infection, accumulation of RNAs from the viral E3 region is increased up to sevenfold in Ad2ts111A- and Ad2ND1+ts23-infected cells relative to wild-type virus. This effect is temperature-independent and seems to involve nuclear RNA stability. Steady-state levels of the viral E1B and E4 RNAs increase following the onset of viral DNA replication in cells infected by the wild-type virus, but not in cells infected by ts111A or ts23. The increase in E1B and E4 RNAs at late times of infection is due to a stabilization of the mRNA. The steady-state levels of L3 and L5 RNAs are two- to fourfold higher in cells infected with ts23 and ts111A than with wild-type virus. None of these differences were observed following infection of cells with a temperature-independent revertant of ts111, indicating that the mutations in the DBP were responsible for the phenotypes. However, for the E3 effect, the change brought about by the mutations in the DBP does not seem to be the result of a change in the normal function of the protein, as an essentially DBP-negative virus (Ad5d/802) shows no differences in E3 RNA metabolism compared to wild-type virus at early times of infection. These results demonstrate that mutation of amino acids 280 and 282 of the DBP significantly perturbs the normal regulation of viral RNA metabolism. These effects clearly differ from the phenotypes observed with adenoviruses containing mutations in other early genes and from those ascribed to the ts125 mutation by others. These results are discussed in terms of the mechanisms by which early and late viral RNA metabolism are controlled and the possible effects of the DBP mutations on them.

Adenovirus requires the virus-encoded single-stranded DNA-binding protein (DBP) to replicate its DNA. We have previously shown (M. Tsuji, P. C. van der Vliet, and G. R. Kitchingman, J. Biol. Chem. 266:16178-16187, 1991) that the inability of three temperature-sensitive (ts) mutant DBPs (Ad2+ ND1ts23, Ad2ts111A, and Ad5ts125) to support DNA replication at the nonpermissive temperature was associated with impaired ability to bind to DNA. In this study, we examined these mutant proteins for structural alterations that might be linked to the functional changes. All three ts mutants, but not the wild-type protein, showed different proteolytic cleavage patterns before and after heating at 40 degrees C (the nonpermissive temperature), suggesting a possible conformational change during heating. The Ad2+ND1ts23 and Ad2ts111A DBPs have single amino acid changes located in a putative zinc finger subdomain (positions 282 and 280). In the presence of zinc ions, these ts mutants showed significantly increased resistance to inactivation at 40 degrees C. Surprisingly, however, the stabilizing effect of zinc was also observed with the Ad5ts125DBP, which contains a mutation located more than 100 amino acids from the zinc finger. Other related metal ions, such as cobalt, cadmium, and mercury, did not protect the ts DBPs from inactivation at 40 degrees C. These results indicate that functional changes of the ts DBPs in DNA replication and DNA binding are accompanied by structural alterations in the protein and that zinc and the metal-binding subdomain may play an important role in the structure and/or function of the DBP.

The adenovirus single-stranded DNA-binding protein (DBP) is an essential factor in viral DNA replication. Three temperature-sensitive (ts) adenoviruses (Ad2+ND1ts23, Ad2ts111A, and Ad5ts125) are known to have single amino acid substitutions in their DBPs that result in defective DNA replication at the nonpermissive temperature. To elucidate the mechanism(s) involved in the ts phenotype, we purified the three mutant DBPs and studied their DNA-binding properties and their ability to support DNA replication in an in vitro system. The results confirm that the three ts DBPs were incapable of supporting DNA replication at the nonpermissive temperature (40 degrees C). The defect was found at both the initiation and elongation steps of DNA replication. The 2-fold stimulation of pTP.dCMP formation by the DBP was lost by prior heating of the ts DBPs. The pronounced effect of the DBP on the early elongation process was severely diminished, but not abolished, by prior heating to 40 degrees C. The functional change at 40 degrees C was irreversible, as the ts DBPs preincubated at 40 degrees C were no longer active when assayed at 30 degrees C. Upon heating to 40 degrees C, all three ts DBPs lost their ability to bind to oligonucleotides, although they still retained some binding activity for large single-stranded DNAs such as M13 DNA. Thus, the inability of these three ts DBPs to support DNA replication is attributable to their altered DNA-binding properties.

The distribution of three adenovirus-encoded DNA replication proteins in the nucleus of human 293 cells was studied by immunogold electron microscopy. The infected nuclei contained four morphologically distinct inclusions. They were highly electron-dense granules (type I), compact fibrogranular masses of medium electron density (type II), filamentous masses of low electron density (type III) and large polygonal crystals (type IV). In immunogold labelling studies, antibodies to the adenovirus single-stranded DNA-binding protein (DBP) and antibodies to single-stranded DNA showed extensive binding to the type III inclusions. The antibodies to the adenovirus DNA polymerase (AdPol) and terminal protein (TP) predominantly labelled type II inclusions. Double immunogold labelling studies detected low levels of AdPol and TP in type III inclusions and DBP in type II inclusions. The selective distribution of DNA replication proteins suggests that the type II and III inclusions represent two functionally different entities that may be involved in two different aspects of adenovirus DNA replication, i.e. chain initiation and elongation.

DNA copies of segments of Sendai virus genes P, NP and M, obtained by reverse transcription of virus mRNA species extracted from infected cells, were cloned in plasmid pBR322. Genes were identified by hybrid-arrested translation of viral mRNAs in vitro. Hybrid selection of NP mRNA confirmed the identity of an NP gene clone. Partial sequencing of this insert showed that it represents the 5'-terminal region of the gene, containing transcription termination signals. Hybridization of DNA inserts to blots of electrophoretically separated, denatured mRNA species indicated that the P, NP and M messages had sizes of 2400, 2100 and 1500 nucleotides, respectively. Specific T1 ribonuclease-resistant oligonucleotides, previously identified in the NP and M genes, were selected by hybridization to the respective inserts. Although most of the inserts are smaller than 500 base pairs, representing no more than 16% of the P gene and 24% of the NP gene, one of the M gene inserts, comprising 700 base pairs, represents almost half of that gene. These cloned virus gene segments will assist further investigations of the molecular biology of this model paramyxovirus.

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.

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.