Conservation of DNA sequence in the predicted major late promoter regions of selected mastadenoviruses

Murine adenoviruses: tools for studying adenovirus pathogenesis in a natural host

Small laboratory animals are powerful models for investigating in vivo viral pathogenesis of a number of viruses. For adenoviruses (AdVs), however, species-specificity poses limitations to studying human adenoviruses (HAdVs) in mice and other small laboratory animals. Thus, this review covers work on naturally occurring mouse AdVs, primarily mouse adenovirus type 1 (MAdV-1), a member of the species Murine mastadenovirus A. Molecular genetics, virus life cycle, cell and tissue tropism, interactions with the host immune response, persistence, and host genetics of susceptibility are described. A brief discussion of MAdV-2 (member of species Murine mastadenovirus B) and MAdV-3 (member of species Murine mastadenovirus C) is included. We report the use of MAdVs in the development of vectors and vaccines.

Molecular anatomy of Tupaia (tree shrew) adenovirus genome; evolution of viral genes and viral phylogeny

Adenoviruses are globally spread and infect species in all five taxons of vertebrates. Outstanding attention is focused on adenoviruses because of their transformation potential, their possible usability as vectors in gene therapy and their applicability in studies dealing with, e.g. cell cycle control, DNA replication, transcription, splicing, virus-host interactions, apoptosis, and viral evolution. The accumulation of genetic data provides the basis for the increase of our knowledge about adenoviruses. The Tupaia adenovirus (TAV) infects members of the genus Tupaiidae that are frequently used as laboratory animals in behavior research dealing with questions about biological and molecular processes of stress in mammals, in neurobiological and physiological studies, and as model organisms for human hepatitis B and C virus infections. In the present study the TAV genome underwent an extensive analysis including determination of codon usage, CG depletion, gene content, gene arrangement, potential splice sites, and phylogeny. The TAV genome has a length of 33,501 bp with a G+C content of 49.96%. The genome termini show a strong CG depletion that could be due to methylation of these genome regions during the viral replication cycle. The analysis of the coding capacity of the complete TAV genome resulted in the identification of 109 open reading frames (ORFs), of which 38 were predicted to be real viral genes. TAV was classified within the genus Mastadenovirus characterized by typical gene content, arrangement, and homology values of 29 conserved ORFs. Phylogenetic trees show that TAV is part of a separate evolutionary lineage and no mastadenovirus species can be considered as the most related. In contrast to other mastadenoviruses a direct ancestor of TAV captured a DUT gene from its mammalian host, presumably controlling local dUTP levels during replication and enhance viral replication in non-dividing host tissues. Furthermore, TAV possesses a second DNA-binding protein gene, that is likely to play a role in the determination of the host range. In view of these data it is conceivable that TAV underwent evolutionary adaptations to its biological environment resulting in the formation of special genomic components that provided TAV with the ability to expand its host range during viral evolution.

The structure and function of the adenovirus major late promoter

The adenovirus major late promoter (MLP) has played a pre-eminent role in the analysis of transcription initiation in mammalian cells, and is an outstanding example of the ways in which the study of adenovirus has led to fundamental insights into general cellular processes. The aim of this chapter is to give a comprehensive review of the structure and function of this model mammalian promoter. After a brief description of late transcription in the adenovirus replication cycle, the experimental evidence for the current consensus on the genetic structure of the MLP, including a consideration of non-primate adenovirus MLPs, will be reviewed. Next, the functions of the MLP in the viral life cycle will be examined, and some of the problems that remain to be resolved will be addressed. The review ends with some ideas on how the knowledge of the structure and function of the MLP can be used in designing virus vectors for specific experimental purposes.

Molecular evolution of adenoviruses

New advances in the field of genetic characterization of adenoviruses originating from different animal species are summarized. Variations seen in the host range and specificity, pathogenicity, genomic arrangement or gene complement are much wider than expected based on previous studies of human adenoviruses. Several exceptional adenoviruses from the two traditional conventional genera are now removed, and proposed to form at least two new genera. The eventual host origin of the new genera, however, is not clarified. Novel results from the genomic and phylogenetic analyses of adenoviruses originating from lower vertebrate species (including reptiles, amphibians and fish) seem to imply that probably five major clusters of adenoviruses exist corresponding to the five major classes of Vertebrata. Adenoviruses, which are now suspected to have common origin with enterobacterium phages from the family Tectiviridae, are perhaps very ancient indeed, and may have undergone a co-evolution with vertebrate hosts.

Genetic organization and sequence analysis of pVIII, fiber and early region 4 of bovine adenovirus type 7

The DNA sequence of 8,810 nucleotides at the right end of bovine adenovirus type 7 (BAV7) genome was determined and compared with similar regions of other adenoviruses. This genomic region of BAV7 consists of sequences encoding partial 33K, pVIII, fiber, putative early region 4 (E4) proteins and other unassigned proteins. However, BAV7 E3 region is not present in the expected location between pVIII and fiber as BAV7 intergenic region between pVIII and fiber genes is only 183 nucleotides. The predicted pVIII and fiber demonstrates highest homology to corresponding proteins of ovine adenovirus 287 (OAV287), bovine adenovirus-4 (BAV4) and egg drop syndrome virus (EDSV). The E4 region encodes three ORFs, which shows significant homology only to corresponding proteins encoded by E4 region of OAV287 and BAV4. Sequence comparisons, phylogenetic analysis and overall genome organization in this region of BAV7 provide further evidence for the inclusion of BAV7 together with OAV287, BAV4, and EDSV in the proposed genus 'Atadenovirus'.

Characterization of the complete genome of the Tupaia (tree shrew) adenovirus

The members of the family Adenoviridae are widely spread among vertebrate host species and normally cause acute but innocuous infections. Special attention is focused on adenoviruses because of their ability to transform host cells, their possible application in vector technology, and their phylogeny. The primary structure of the genome of Tupaia adenovirus (TAV), which infects Tupaia spp. (tree shrew) was determined. Tree shrews are taxonomically assumed to be at the base of the phylogenetic tree of mammals and are frequently used as laboratory animals in neurological and behavior research. The TAV genome is 33,501 bp in length with a G+C content of 49.96% and has 166-bp inverted terminal repeats. Analysis of the complete nucleotide sequence resulted in the identification of 109 open reading frames (ORFs) with a coding capacity of at least 40 amino acid residues. Thirty-eight of them are predicted to encode viral proteins based on the presence of transcription and translation signals and sequence and positional conservation. Thirty viral ORFs were found to show significant similarities to known adenoviral genes, arranged into discrete early and late genome regions as they are known from mastadenoviruses. Analysis of the nucleotide content of the TAV genome revealed a significant CG dinucleotide depletion at the genome ends that suggests methylation of these genomic regions during the viral life cycle. Phylogenetic analysis of the viral gene products, including penton and hexon proteins, viral protease, terminal protein, protein VIII, DNA polymerase, protein IVa2, and 100,000-molecular-weight protein, revealed that the evolutionary lineage of TAV forms a separate branch within the phylogenetic tree of the Mastadenovirus genus.

Role of viruses in human evolution

The study of viral molecular genetics has produced a considerable body of research into the sequences and phylogenetic relationships of human and animal viruses. A review of this literature suggests that humans have been afflicted by viruses throughout their evolutionary history, although the number and types have changed. Some viruses show evidence of long-standing intimate relationship and cospeciation with hominids, while others are more recently acquired from other species, including African monkeys and apes while our line was evolving in that continent, and domesticated animals and rodents since the Neolithic. Viral selection for specific resistance polymorphisms is unlikely, but in conjunction with other parasites, viruses have probably contributed to selection pressure maintaining major histocompatibility complex (MHC) diversity and a strong immune response. They may also have played a role in the loss in our lineage of N-glycolylneuraminic acid (Neu5Gc), a cell-surface receptor for many infectious agents. Shared viruses could have affected hominid species diversity both by promoting divergence and by weeding out less resistant host populations, while viruses carried by humans and other animals migrating out of Africa may have contributed to declines in other populations. Endogenous retroviral insertions since the divergence between humans and chimpanzees were capable of directly affecting hominid evolution through changes in gene expression and development.

DNA sequencing and phylogenetic analysis of the protease gene of ovine adenovirus 3 suggest that adenoviruses of sheep belong to two different genera

Until now, the only published ovine adenovirus DNA sequence was the complete genome of ovine adenovirus isolate 287 (OAV287) which, compared to other mammalian adenoviruses, possesses strikingly unique genomic organisation and should properly be classified into a new adenovirus genus. The protease gene sequence of ovine adenovirus type 3 (OAdV-3) was determined and analysed. The results of phylogenetic analysis of the 205 residue long protein demonstrated that OAdV-3 belongs to the genus Mastadenovirus, and is surprisingly closely related to bovine adenovirus type 2. In spite of the common host origin, the evolutionary distance between OAdV-3 and OAV287 proved to be great suggesting that sheep, similarly to cattle and fowl, might be infected by distantly related adenoviruses belonging to different genera.

Novel human gene transfer vectors: evaluation of wild-type and recombinant animal adenoviruses in human-derived cells

Major disadvantages of human adenovirus (hAd) vectors in gene therapy include preexisting or induced immune responses, and possible coreplication of recombinant hAd in the presence of wild-type hAds. These disadvantages may be overcome by using nonhuman, animal adenoviruses (aAds). We evaluated four different aAds for their potential use as viral vectors. The canine adenovirus type 2 (CAV2) and bovine adenovirus type 3 (BAV3) appeared to be suitable systems, as they infect human cells. CAV2, but not BAV3, caused cytotoxicity, and only limited (CAV2) or no (BAV3) production of infectious virus particles was observed after infection of human cell lines. CAV2 showed higher expression of endogenous genes than did BAV3 in the tested human cells. No interference between hAd and CAV2 or BAV3, such as recombination of DNA or cross-activation of virus replication, was observed in up to five passages in double-infected human cells. Transfection of cloned genomic CAV2 or BAV3 DNA into appropriate permissive cell lines rescued infectious virus. Furthermore, we produced a recombinant E1-deleted BAV3, and showed that it could infect and express a reporter gene in various human cell types. The goal was to construct and evaluate recombinant (E1-deleted) animal adenoviruses (aAds) as new vector systems for human gene therapy. The rationale for developing aAds for human use is the potential higher safety and efficiency, as compared with human adenoviruses (hAds). Coreplication and recombination with preexisting hAds should not be possible owing to lack of homology, and preexisting immunity in the general population should be limited. Of the four aAds we evaluated, BAV3 appeared to be the best candidate. It infects human cells without showing growth or cytotoxic effects, viral gene expression was barely detectable, and no trans-activation of either virus was detected in coinfections with hAd5. Rescue of virus in permissive cells, from plasmids containing the CAV2 or BAV3 genome, confirmed our approach. Furthermore, an E1-deleted recombinant BAV3 was constructed and shown to transduce and express the lacZ reporter gene in human cells.

Novel expression of mouse adenovirus type 1 early region 3 gp11K at late times after infection

Mutations were introduced into mouse adenovirus type 1 (MAV-1) early region 3 (E3) initiator codons by homologous recombination between viral DNA and a plasmid containing a mutagenized E3 region. The resulting mutant virus, pmE312, contained ATG --> TTA mutations at codon positions 1 and 4 and was expected to be null for the expression of the E3 proteins. However, gp11K, an MAV-1 E3 glycoprotein of 14K molecular weight, was detected in mutant-infected cell lysates at levels about 10-12% of that of wild-type (wt) virus at late times in infection. The gp11K polypeptide produced by pmE312 at late times was immunoprecipitated with two E3-specific antisera prepared against different regions of the protein. Like gp11K produced by wt virus infections, it was sensitive to endoglycosidase H (endo H) and thus resident in the endoplasmic reticulum (ER). In pmE312-infected cells treated with cytosine arabinoside (araC), an inhibitor of DNA replication, the gp11K protein was not detected by immunoprecipitation. This indicates that gp11K expression in pmE312-infected cells at late times was dependent on DNA replication and that it was thus translated from a late transcript. In vitro translation of poly(A)+ RNA from mock-, wild-type-, and pmE312-infected cells showed that gp11K was translated from late mRNA as an approximately 28K fusion between a late protein and gp11K. Our data are consistent with a model in which gp11K is expressed at late times as a late protein-gp11K chimera in both wt- and mutant-infected cells. This chimera is then processed: removal of a large N-terminal sequence results in the observed 14K ER-localized gp11K.

Characterization of bovine adenovirus type 3 early region 2B

We have determined the nucleotide sequence of a 6999 base pair region of bovine adenovirus-3 covering map units 9.0 to 29.17, which contained the adenovirus homologs of IVa2 protein and the DNA replication proteins, precursor of terminal protein and DNA polymerase proteins. Analysis of the sequence for cis-acting elements suggests that transcripts of DNA polymerase and precursor of terminal protein are 3' co-terminal. In addition, this region also contains major late promoter sequence. The sequence to the left of IVa2 contains the ORF of pIX with a potential TATA box immediately upstream and two polyadenylation consensus signals immediately downstream of the ORF.

Functional analysis of the CAAT box in the major late promoter of the subgroup C human adenoviruses

Comparisons among sequences predicted to encode the major late promoter (MLP) of adenoviruses from a wide variety of host species show that an inverted CAAT box is among the most highly conserved transcription elements found in the putative MLPs. The high degree of conservation suggests that the CAAT box plays an important role in the function of the MLP in vivo, an idea supported by a previous mutational analysis of the core CCAAT sequence. To address the importance of the CAAT box, in terms both of quantitative levels of transcription and of specificity, a further set of mutations was created and examined in the context of the viral genome. One mutation, CAAT5, contains individual changes at five positions, four of which correspond to invariant residues in a CAAT box consensus derived either by computer analysis or empirically. The CAAT5 mutation had no discernible phenotype by itself but when coupled with the previously described USF0 mutation, which disrupts binding of the upstream stimulating factor (USF) but is otherwise phenotypically silent, gave rise to virus with a severe replication deficiency. Nuclear run-on assays showed that transcription initiation at the mutant MLP was significantly reduced compared with that of the wild type or the virus containing CAAT5 alone. Replication of the double mutant was lower than that of the previously described USF0::CCCAT virus, suggesting that the additional mutations in the CAAT box had further lowered the binding of transcription factor CP1 (also called CBF, NF-Y). Replacement of the CAAT box by an ATF binding site or an OCT1 binding site had no phenotypic effect in an otherwise wild-type background, but replacement in a USF0::CCCAT background led to only partial restoration of the wild-type phenotype. The failure to restore the functional redundancy normally exhibited by the CAAT box and the proximal upstream activating element is consistent with the idea that in the adenovirus MLP the CAAT box is preferred over others as the distal transcriptional element.

Nucleotide sequence, genome organization, and transcription map of bovine adenovirus type 3

The complete DNA sequence of bovine adenovirus type 3 is reported here. The size of the genome is 34,446 bp in length with a G+C content of 54%. All the genes of the early and late regions are present in the expected locations of the genome. However, the late-region genes are organized into seven families, instead of five as they are in human adenovirus type 2. The deduced amino acid sequences of open reading frames (ORFs) in the late regions and early region 2 (E2) and for IVa2 show higher degrees of homology, whereas the predicted amino acid sequences of ORFs in the E1, E3, and E4 regions and the pIX, fiber, and 33,000-molecular-weight nonstructural proteins show little or no homology with the corresponding proteins of other adenoviruses. In addition, the penton base protein lacks the integrin binding motif, RGD, but has an LDV motif instead of an MDV motif. Interestingly, as in other animal adenoviruses, the virus-associated RNA genes appear to be absent from their usual location. Sequence analysis of cDNA clones representing the early- and late-region genes identified splice acceptor and splice donor sites, polyadenylation signals and polyadenylation sites, and tripartite leader sequences.

Activation of the adenovirus major late promoter by transcription factors MAZ and Sp1

Multiple binding sites for the transcription factors MAZ and Sp1 within the adenovirus type 5 major late promoter have been identified by DNase I protection studies. In the proximal region of the promoter, both MAZ and Sp1 interact with GC-rich sequences flanking the TATA box. Two MAZ binding sites are centered at -18 and -36 relative to the transcriptional initiation site. Sp1 bound only to the -18 GC-rich sequence. Several sites of interaction were also evident in the distal region of the promoter. Both MAZ and Sp1 interacted with a sequence centered at -166, and MAZ bound weakly to an additional site centered at -130. Overexpression of MAZ or Sp1 activated expression from the major late promoter in transient expression assays. Mutational analysis of the GC-rich sequences in the major late promoter suggested that a primary target of MAZ activation is the GC-rich sequences flanking the TATA sequence, whereas Sp1 requires the distal GC-rich sequence elements to stimulate gene expression. This activation is enhanced by the adenovirus E1A protein, and evidence for interaction between E1A and both transcription factors was obtained by using an immunoprecipitation assay. Activation by MAZ and Sp1 also was observed in transfection studies using the complete adenovirus type 5 genome as the target. Increased levels of late mRNA from both the L1 and L5 regions were observed when MAZ or Sp1 expression plasmids were transfected with viral DNA. Unexpectedly, activation of the major late promoter by MAZ and Sp1 was detected irrespective of whether the viral DNA could replicate.

Completion of the DNA sequence of mouse adenovirus type 1: sequence of E2B, L1, and L2 (18-51 map units)

The DNA sequence of 9991 nt, corresponding to 18-51 map units of mouse adenovirus type 1 (MAV-1), was determined, completing the sequence of the Larsen strain of MAV-1. The length of the complete MAV-1 genome is 30,946 nucleotides, consistent with previous experimental estimates. The 18-51 map unit region encodes early region 2B proteins necessary for adenoviral replication as well as late region L1 and L2 structural and packaging proteins. Sequence comparison in this region with human adenoviruses indicates broad similarities, including colinear preservation of all recognized open reading frames (ORFs), with highest amino acid identity occurring in the DNA polymerase and polypeptide III (penton base subunit) ORFs. Virus-associated (VA) RNA is not encoded in the region where VA RNAs are found in the human adenoviruses, between E2B and L1, nor is it encoded anywhere in the entire MAV-1 genome. The MAV-1 polypeptide III lacks the arginine-glycine-aspartic acid (RGD) motif which is involved in an association with cell-surface integrins. Only one RGD sequence is found in an identified coding region in the entire MAV-1 genome. Similar to the porcine adenovirus, this RGD sequence is found in the C-terminus of the MAV-1 fiber protein.

Functional characterization of the major late promoter of mouse adenovirus type 1

During the late phase of adenovirus infection, the major late promoter (MLP) controls the regulated expression of the genes that encode most viral structural proteins. Recently, the region of the genome of mouse adenovirus type 1 (MAV-1), predicted to contain the MLP, was sequenced and compared to that of the human virus MLP. The general organization of the transcriptional elements of the putative MAV-1 MLP is similar to that of the human virus counterpart, with some interesting differences. We wished to investigate the function of the predicted MLP of MAV-1 and to determine the significance of the differences found in the MAV-1 MLP. To test the activity of the predicted MLP of MAV-1, both Northern blot and primer extension analyses were performed on intracellular RNA isolated from cells infected with MAV-1. The results show that late RNA can be detected 48 hr postinfection and increases up to 6 days p.i. Primer extension analysis revealed that the major start sites of transcription are 28 and 31 nt downstream of the first T residue of the predicted TATA box. To analyze the functional significance of the predicted transcriptional elements, a transient transfection system, using the firefly luciferase gene controlled by the MAV-1 MLP sequence, was established. The predicted MLP sequence was capable of directing luciferase gene expression, to a level some 60% of that of the human virus MLP. Mutations were created in the inverted CAAT box, the SP1 site, and the TATA box, either singly or in combination. Each single-element mutation causes a marked reduction in luciferase gene expression, with the SP1 mutation showing the greatest effect. Double mutations were even more deficient, suggesting a level of functional redundancy among the various transcriptional elements. Finally, the putative SP1-binding site was examined by gel mobility shift assay and shown to interact with purified SP1 protein specifically, supporting the functional significance of this transcriptional element. These findings contribute to a better understanding of gene expression in MAV-1 and to its development as an appropriate model for the study of the molecular basis of pathogenesis in a natural host animal.

Close phylogenetic relationship between egg drop syndrome virus, bovine adenovirus serotype 7, and ovine adenovirus strain 287

A cloned egg drop syndrome (EDS) virus genomic DNA fragment containing the protease gene has been identified and the complete nucleotide sequence of the protease and partial nucleotide sequence of the hexon genes has been determined. Phylogenetic analysis of the protease gene has revealed EDS virus to be genetically more closely related to bovine adenovirus type 7 (BAV-7) and ovine adenovirus isolate 287 (OAV287) than either of these two viruses are to other members of the genus Mastadenovirus or EDS virus is to an other member of the Aviadenovirus genus. The three viruses share further similarities in that they have a high percentage AT content in their genome and are characterized by having more compact genomes than other adenoviruses. The protease gene from all three viruses contained the active site residues (H55-D72-C122 triad) and C104 (providing a disulfide bond to cofactor pVIc). However, P137, found in all other members of the Mastadenovirus genus, and thought to be involved in trafficking, was missing from the protease of the EDS virus, BAV-7, and OAV287. These results suggest that EDS virus should be classified along with BAV-7 and OAV287 in a separate taxon.