Nucleotide sequence of ovine adenovirus tripartite leader sequence and homologues of the IVa2, DNA polymerase and terminal proteins

Completion of the genome analysis of snake adenovirus type 1, a representative of the reptilian lineage within the novel genus Atadenovirus

Genome sequencing and analysis of snake adenovirus type 1 (SnAdV-1), originating from corn snake, were completed. This is the first full genomic sequence of an adenovirus from reptilian hosts. The presence of characteristic genus-common genes and transcription units, showed that SnAdV-1 shares similar genome organisation with members of the recently established genus Atadenovirus. Three novel open reading frames of yet unknown functions were found. One of these seemed to be related to a putative gene, the so-called 105R that has recently been described from the genome of the tree shrew adenovirus. The other two putative genes were found to be unique for SnAdV-1. On phylogenetic trees, SnAdV-1 clustered within the atadenovirus clade. Thereby the hypothesis on the reptilian origin of atadenoviruses was further strengthened. Interestingly, however, one of the most striking features of atadenoviruses, namely the base content heavily biased towards A+T, is not characteristic for SnAdV-1 having a genome of balanced composition with a G+C value of 50.21%.

Ovine atadenovirus: a review of its biology, biosafety profile and application as a gene delivery vector

The ovine adenovirus isolate OAdV287 is the prototype of the newly recognized genus of atadenoviruses. Although not as well studied as human mastadenoviruses, a substantial amount of work has now been carried out with this virus and an understanding of its interesting and unique properties is beginning to emerge. In this article the biology and biosafety profile of the virus is reviewed. This knowledge underpins the exploitation of the virus as a gene delivery vector. Its potential as a vaccine vector and its application to the treatment of prostate cancer is summarized and discussed.

Identification of an ovine atadenovirus gene whose product activates the viral E2 promoter: possible involvement of E2F-1

Activation of the adenoviral E2 promoter is an early step in adenovirus gene expression. For members of the mast- and aviadenoviruses, this requires induction of the cellular transcription factor E2F by virally encoded gene products such as E1A, E4orf6/7 and orf22/GAM-1. The newly recognized genus atadenovirus, of which the ovine isolate OAdV is the prototype, lacks any sequence homology to those genes. To find a possible link between E2 promoter activation and OAdV gene expression, we utilized a screening method to search for genes within the OAdV genome that were capable of stimulating the viral E2 promoter. One such gene, E43, was identified within the proposed E4 region toward the right-hand end of the OAdV genome. The E43 gene product was also found to be capable of stimulating E2F-1-dependent gene expression. A closer inspection of the E2 promoter revealed the presence of a non-palindromic E2F binding site within the OAdV E2 promoter. Mutation of this site markedly reduced both E2F-1- and E43-dependent promoter activation. Moreover, a direct protein-protein interaction of the E43 gene product with E2F, but not with the retinoblastoma protein pRb, suggested a possible cooperation between these two proteins in activating the E2 promoter. The importance of the E43 gene product for virus replication is also underlined by the finding that an OAdV recombinant with a functionally inactivated E43 gene showed severely inhibited virus growth.

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.

Biology of ovine adenovirus infection of nonpermissive cells

Nonhuman adenoviruses, including those of the genus Atadenovirus, have the potential to serve as vectors for vaccine and gene therapy applications in humans, since they are resistant to preexisting immunity induced by human adenoviruses in the majority of the population. In this study, we elucidate the outcome of infection by ovine adenovirus type 7 isolate 287 (OAdV) of several nonovine cell types. We show here that OAdV infects a wide range of nonovine cells but is unable to complete its replication cycle in any of them. In nonovine, nonfibroblast cells, viral replication is blocked at an early stage before the onset of, or early in, DNA replication. Some fibroblasts, on the other hand, allow viral DNA replication but block virus production at a later stage during or after the translation of late viral proteins. Late viral proteins are expressed in cells where viral DNA replication takes place, albeit at a reduced level. Significantly, late proteins are not properly processed, and their cellular distribution differs from that observed in infected ovine cells. Thus, our results clearly show that OAdV infection of all nonovine cells tested is abortive even if significant viral DNA replication occurs. These findings have significant positive implications with respect to the safety of the vector system and its future use in humans.

Ovine adenovirus vectors mediate efficient gene transfer to skeletal muscle

Ovine adenovirus (OAV) vectors represent a promising tool for human gene therapy since these vectors overcome the problem of pre-existing immunity against human adenovirus vectors. In this report we investigated the in vivo characteristics of this novel vector system with respect to its potential for gene transfer into skeletal muscle. We found that moderate doses of an OAV-derived vector expressing the human alpha1-antitrypsin gene (OAVhaat) infected skeletal muscle in mice very efficiently resulting in high serum hAAT levels. The infection was restricted to skeletal muscle, but gene expression was transient and vector DNA was rapidly cleared. Vector clearance was also observed with a vector that lacked the transgene. The loss of vector DNA was accompanied by a cellular immune response in the infected muscle but was not connected with detectable expression of early or late genes of the viral backbone as analyzed by RT-PCR. A very low dose of OAVhaat (3x 10(7) infectious particles) was sufficient to produce reasonable amounts (>100 ng/ml) of serum hAAT, and this was accompanied by a weak immune response to the vector. Under these conditions, a second intramuscular injection of the same recombinant OAV vector was successful. Our study expands the known tissue tropism of OAV-derived vectors in vivo and points to the possible utility of the vector for muscle gene transfer and vaccination.

Ovine adenovirus vectors overcome preexisting humoral immunity against human adenoviruses in vivo

Recombinant human adenoviruses (hAd) have become widely used as tools to achieve efficient gene transfer. However, successful application of hAd-derived vectors in clinical trials is limited due to immunological and potential safety problems inherent in their human origin. In this study, we describe a recombinant ovine adenovirus (OAV) as an alternative vector for gene transfer in vivo. In contrast to an hAd vector, the OAV vector was not neutralized by human sera. An OAV vector which contained the cDNA of the human alpha1-antitrypsin (hAAT) gene linked to the Rous sarcoma virus promoter was generated and administered systemically to mice. The level and duration of hAAT gene expression was similar to that achieved with an hAd counterpart in both immunocompetent and immunodeficient mice. However, the tissue distribution of the OAV vector differed from that observed for hAd vectors in that the liver was not the dominant target. Significantly, we demonstrated efficient gene transfer with the OAV vector into mice immunized with hAd vectors and vice versa. We also confirm that the immune response to a transgene product can prevent its functional expression following sequential application of a vector. Our results suggest a possible solution to endemic humoral immunity against currently used hAd vectors and should therefore have an impact on the design of improved gene therapy protocols utilizing adenovirus vectors.

Nucleotide sequence and transcription map of porcine adenovirus type 3

The complete nucleotide sequence of porcine adenovirus type 3 was determined and a transcriptional map for the genome was constructed. The size of the genome is 34094 bp in length with an unusually high G + C content (63.7%), the highest thus far reported for any adenovirus. Overall organization of the genome is similar to that for previously sequenced adenoviral DNAs, but there also were distinct differences. The late regions genes are organized into six families, instead of five as they are in human adenovirus type 2. In contrast to bovine adenovirus type 3 and ovine adenovirus, which lack virion-associated RNA genes, the nucleotide sequence analysis of the viral genome indicates that it encodes one short VA RNA species. With the exception of the fiber and a 33-kDa nonstructural protein, the predicted amino acid sequences of the open reading frames in the late regions and the E2 region and IVa2 exhibited a high level of homology, whereas the deduced amino acid sequences of ORFs in E1, E3, and E4 regions, and the pIX showed a lesser homology with the corresponding proteins of other adenoviruses. The proteins V, VII, and IX are unusually long, and the protein VII lacks the consensus protease cleavage site. Genomic and cDNA sequence analysis has identified promoters, cap sites, intron-exon boundaries, polyadenylation signals, and polyadenylation sites in the viral genome.

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.

Identification of transcripts and promoter regions of ovine adenovirus OAV287

The ovine adenovirus isolated OAV287 represents a new group of adenoviruses that are distinct from the Mast- and Aviadenoviruses by several criteria, including genome arrangement. The OAV major late promoter and some late transcripts were previously mapped. To better define the probable coding sequences and to identify the approximate location of early promoters a partial transcription map of the genome was elucidated using a PCR-based approach. This was possible because the complete nucleotide sequence of the genome was known. The strategy permitted the identification of transcription start sites and RNA splice junctions and allowed the approximate location of promoters in the lefthand end, IVa2, E2, P32K, and E4 regions to be deduced. The data showed that lefthand end and E4 regions are controlled by three and two temporally distinct promoters, respectively. The E2 region is controlled by a single promoter, in contrast to Mastadenoviruses, where E2 expression is controlled by the E2A and E2B promoters. The p32kDa structural protein at the lefthand end and the IVa2 protein are also expressed from their own promoters. These data contribute to the first overview of transcription from a non-Mastadenovirus genome.

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.

Gene expression by atypical recombinant ovine adenovirus vectors during abortive infection of human and animal cells in vitro

An bovine adenovirus, which is phylogenetically distinct from the Mastadeno- and Aviadenoviruses, was used to construct recombinants in which reporter genes were expressed from the OAV major late, or human cytomegalovirus promoters. It was demonstrated by transgene expression that OAV could infect bovine nasal turbinate and rabbit kidney cells as well as a range of human cell types, including lung and foreskin fibroblasts as well as liver, prostate, breast, colon, and retinal lines. Some human lines, e.g., 293 and LNCaP were not detectably infected. Infection occurred even though OAV has a fiber protein with a unique cell binding domain and a penton protein that lacks the integrin-binding Arg-Gly-Asp motif which facilitates entry by human adenoviruses. Most cell lines showed little or no ill effect for several days after infection but a prominent cytopathic effect appeared in fibroblasts after 3-4 days. However, no viral DNA synthesis was detected and replication was abortive. Viral promoter activity during infection of nonpermissive cell types was assayed by RT-PCR. Early promoter activity was detectable in some, but not all cell types. In a liver and a colon carcinoma cell line, none of the promoters examined was significantly active, even when a higher multiplicity of infection was used. Major late promoter activity was not detectable in any cell type. The lack of DNA replication and MLP function suggests that a critical transition from early to late gene expression does not occur during abortive infection by OAV.

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.

Construction of ovine adenovirus recombinants by gene insertion or deletion of related terminal region sequences

An ovine adenovirus which may be the prototype for a new group of adenoviruses has been engineered as a gene transfer vector. One recombinant containing a 0.95-kb insertion expressed a sheep parasite antigen from the ovine adenovirus major late promoter and tripartite leader sequences. It was shown that insertions of at least 4.3 kb were tolerated at either one of two sites in the genome without the introduction of a compensating deletion. The unique structure of this viral genome was further emphasized by the discovery that four open reading frames at the right hand end show significant identity to each other but not to other sequences in the databases. Two other unrelated open reading frames were also present. RT-PCR analysis identified two transcripts in this region which were derived from a promoter which was located very close to, or within the ITR sequence. Splicing removed all but the first and last of the ORFs from these RNAs, suggesting that some sequences might be nonessential for replication in vitro. A approximately 2-kb deletion, which removed or truncated the internal reading frames was introduced into the region without affecting virus viability. The carrying capacity of OAV recombinants should therefore be at least 6.3 kb. The relative packaging capacity of OAV (114%) therefore exceeds that of Ad5 (105%), although a comparison of virus particle sizes by electron microscopy showed that OAV was smaller than Ad5. These studies improve the potential utility of OAV as a gene transfer vector.