Rescue of functional replication origins from embedded configurations in a plasmid carrying the adenovirus genome

☆DNA assembly technique simplifies the construction of infectious clone of fowl adenovirus

Plasmid bearing adenovirus genome is generally constructed with the method of homologous recombination in E. coli BJ5183 strain. Here, we utilized Gibson gene assembly technique to generate infectious clone of fowl adenovirus 4 (FAdV-4). Primers flanked with partial inverted terminal repeat (ITR) sequence of FAdV-4 were synthesized to amplify a plasmid backbone containing kanamycin-resistant gene and pBR322 origin (KAN-ORI). DNA assembly was carried out by combining the KAN-ORI fragment, virus genomic DNA and DNA assembly master mix. E. coli competent cells were transformed with the assembled product, and plasmids (pKFAV4) were extracted and confirmed to contain viral genome by restriction analysis and sequencing. Virus was successfully rescued from linear pKFAV4-transfected chicken LMH cells. This approach was further verified in cloning of human adenovirus 5 genome. Our results indicated that DNA assembly technique simplified the construction of infectious clone of adenovirus, suggesting its possible application in virus traditional or reverse genetics.

Viral Vector Production: Adenovirus

Adenoviral vectors have proven to be valuable resources in the development of novel therapies aimed at targeting pathological conditions of the central nervous system, including Alzheimer's disease and neoplastic brain lesions. Not only can some genetically engineered adenoviral vectors achieve remarkably efficient and specific gene delivery to target cells, but they also may act as anticancer agents by selectively replicating within cancer cells.Due to the great interest in using adenoviral vectors for various purposes, the need for a comprehensive protocol for viral vector production is especially apparent. Here, we describe the process of generating an adenoviral vector in its entirety, including the more complex process of adenoviral fiber modification to restrict viral tropism in order to achieve more efficient and specific gene delivery.

Cloning and rescue of the genome of Bombyx mori bidensovirus, and characterization of a recombinant virus

Background

Bombyx mori bidensovirus (BmBDV), which belongs to the Bidnaviridae family established by the International Committee on Taxonomy of Viruses in 2011, was the first bidensovirus identified in insects. The structure of BmBDV is similar to that of parvoviruses, while its replication is similar to that of adenoviruses. Although BmBDV has the potential to be used as a tool in biological pest control and as an expression vector, virus rescue has been a bottleneck in the application of this virus.

Methods

In this study, we constructed a full-length genomic clone of BmBDV and showed that its terminal structure was restored. A recombinant BmBDV that expressed the green fluorescence protein (GFP) gene was constructed. Then, BmN cells, which are an ovarian cell line, were co-transfected with the linearized genome using continuous culture and expanded cell culture methods.

Results

The results showed that the GFP gene was expressed successfully, and that cell lesions occurred in virus-infected cells. Furthermore, typical densonucleosis viruses were observed in reinfected silkworm larvae and larval midgut tissues infected by BmBDV, as evidenced by the emission of green fluorescence.

Conclusions

Overall, these results suggest that the virus could be rescued from the infected BmN cells after co-transfection with the linear full length virus genome.

Re-engineering adenovirus vector systems to enable high-throughput analyses of gene function

With the enhanced capacity of bioinformatics to interrogate extensive banks of sequence data, more efficient technologies are needed to test gene function predictions. Replication-deficient recombinant adenovirus (Ad) vectors are widely used in expression analysis since they provide for extremely efficient expression of transgenes in a wide range of cell types. To facilitate rapid, high-throughput generation of recombinant viruses, we have re-engineered an adenovirus vector (designated AdZ) to allow single-step, directional gene insertion using recombineering technology. Recombineering allows for direct insertion into the Ad vector of PCR products, synthesized sequences, or oligonucleotides encoding shRNAs without requirement for a transfer vector Vectors were optimized for high-throughput applications by making them "self-excising" through incorporating the I-SceI homing endonuclease into the vector removing the need to linearize vectors prior to transfection into packaging cells. AdZ vectors allow genes to be expressed in their native form or with strep, V5, or GFP tags. Insertion of tetracycline operators downstream of the human cytomegalovirus major immediate early (HCMV MIE) promoter permits silencing of transgenes in helper cells expressing the tet repressor thus making the vector compatible with the cloning of toxic gene products. The AdZ vector system is robust, straightforward, and suited to both sporadic and high-throughput applications.

Adenoviral vectors

Adenoviral vectors have been widely used as efficient gene delivery vehicles for gene therapy and vaccine development, as well as gene function studies. The recently developed AdEasy system is a simple and efficient method for rapid generation of recombinant adenoviruses. Unlike traditional adenoviral vectors, the viral backbone described here is supplied as a supercoiled plasmid rather than as a linear viral DNA, facilitating backbone amplification. The recombination step is performed in E. coli rather than in mammalian cells, taking advantage of the high efficiency of homologous recombination in bacteria. This unit includes the complete set of protocols needed to generate recombinant adenoviruses using the AdEasy system.

A protocol for rapid generation of recombinant adenoviruses using the AdEasy system

Recombinant adenoviruses provide a versatile system for gene expression studies and therapeutic applications. We have developed an approach that simplifies the generation and production of such viruses called the AdEasy system. A recombinant adenoviral plasmid is generated with a minimum of enzymatic manipulations, employing homologous recombination in bacteria rather than in eukaryotic cells. After transfection of such plasmids into a mammalian packaging cell line, viral production is conveniently followed with the aid of GFP encoded by a gene incorporated into the viral backbone. This system has expedited the process of generating and testing recombinant adenoviruses for a variety of purposes. In this protocol, we describe the practical aspects of using the AdEasy system for generating recombinant adenoviruses. The full protocol usually takes 4-5 weeks to complete.

Possible mechanism of adenovirus generation from a cloned viral genome tagged with nucleotides at its ends

The entire cloned human adenovirus type 5 (Ad5) genome is known to be able to generate infectious virus after transfection into 293 cells when the both ends of the genome are exposed by digestion with appropriate restriction enzymes. However, when one or both ends of the genome are tagged with nucleotides and are not intact, whether the tagged end of the viral genome was remained tagged or corrected to be intact during the generation of viral clones has been unclear and, if such oligonucleotide removal occurs, how does the virus remove these tagged sequences and thereby restore its proper structure? Here, we show in our semi-quantitative study that the generation efficiency of virus clones decreases depending on the length of nucleotide tags at the both ends and that both the oligonucleotide tags were precisely removed during virus generation with restoration of the proper terminal sequences. Interestingly the viral genome of which one end was tagged, while the other was attached about 12-kb sequences, did generate intact viral clones at a reduced but significant efficiency. From these results, we here propose a possible mechanism whereby the terminal-protein-deoxycytidine complex enters from the enzyme-cleaved end and reaches deoxyguanine at the initiating position of DNA synthesis in vivo. A replication origin at one end, embedded deeply in double-stranded DNA, can be activated by two cycles of one-directional full-length DNA synthesis initiated by the other exposed replication origin about 30 kilobases away. We also describe new cassette cosmids which can use not only Pac I but also Bst BI for construction of an adenovirus vector, without reducing construction efficiency.

Adenovirus vector library: an approach to the discovery of gene and protein function

A method was developed to generate a complex cDNA expression library within an adenovirus type 5 (Ad5)-based vector backbone, termed AdLibrary. Construction of the AdLibrary entailed the conversion of an Ad5 genome-containing cosmid to infectious virus particles. The Ad5 genome was modified by replacing the E1A and E1B genes with a Rous sarcoma virus-driven expression cassette. Conversion was accomplished by liberating the viral genome by restriction enzyme digestion and transfection in HEK 293 cells, which support the growth of E1A/E1B-deficient virus. A test AdLibrary demonstrated the possibility of converting and identifying a marker gene present at a frequency of 1/105 in the cosmid library. To demonstrate the utility of this technology, an AdLibrary was used to isolate a viral gene by its biological function. Virus growth was selected for with an AdLibrary on A549 cells, which do not complement for E1A/E1B function. The AdLibrary was generated with cDNAs derived from HeLa cells productively infected with Ad5. A cDNA corresponding to Ad5 E1A 13S was selected and isolated from the AdLibrary using this strategy. Since multiple genes are assayed simultaneously, this technology should expedite the discovery of genes affecting defined biological activities. This AdLibrary approach provides an opportunity to exploit the efficient gene delivery capabilities of adenovirus vectors for the rapid discovery of gene and protein function.

System for efficient helper-dependent minimal adenovirus construction and rescue

Helper-dependent minimal adenoviral vectors deleted for all viral coding sequences are promising vectors for gene therapy. They retain only the adenovirus cis elements for replication and packaging, can accommodate up to 36 kb of foreign DNA, and exhibit prolonged transgene expression and reduced tissue toxicity as compared with first-generation adenoviral vectors. We have developed a system consisting of a set of cosmid cloning vectors (pMV and pMVX) for simple routine construction and efficient rescue of minimal adenoviral vectors. In the cloning vectors the inverted terminal repeats (ITRs) are flanked by recognition sites for the super rare-cutting endonuclease I-SceI. This allows the release of linear minimal adenovirus genomes for rescue of minimal adenovirus regardless of the sequence of the insert DNA. pMV contains a multiple cloning site for the insertion of 26 to 36 kb of therapeutic DNA. pMVX contains a noncoding human X-chromosomal DNA fragment as a vector backbone, which provides endonuclease restriction sites that allow for complete or partial replacement of the vector backbone by 1 to 26 kb of therapeutic DNA sequences, while retaining a packageable final minimal adenovirus genome size between 27 and 37.5 kb. Both vectors exist in two forms, with or without an Escherichia coli lacZ reporter gene cassette. Several minimal adenoviral vectors with insert sizes ranging from 1.5 to 16 kb were constructed with these cloning vectors. Minimal adenoviruses were efficiently rescued and amplified to high titers, using a Cre/lox-based helper system. Vectors containing the X-chromosomal backbone were stable during amplification. This simple and efficient system facilitates the construction of minimal adenoviruses and should be useful for further improvement of these new vectors.

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.

Identification and sequence analysis of the E1 genomic region of a porcine adenovirus

The complete nucleotide sequence of the putative early transcriptional region 1 (E1) of the genome of NADC-1, a porcine adenovirus, was determined. The E1 region of NADC-1 was found to be 3658 bp and located between 0 and 11.2 map units. Twelve potential open reading frames (ORFs) and five polyadenylation signals were identified in the r strand. The nucleotide sequence and each predicted amino acid sequence were compared to sequences available on a number of databases by a BLAST search and comparison. A single region of nucleotide sequence similarity was identified with the sequence of human adenovirus 5. Only 2 of the 12 potential ORFs encode polypeptides that have homology to known adenovirus polypeptides. For these predicted proteins, similarities were found with a number of adenovirus proteins. The strongest homology was found to potential E1 products of bovine adenovirus 3.

The E1 sequence of bovine adenovirus type 3 and complementation of human adenovirus type 5 E1A function in bovine cells

The bovine adenovirus type 3 (BAV3) genome was sequenced from the left end to the HindIII site at 11%. This region comprises the entire E1 transcription unit including the open reading frames (ORF) for proteins homologous to the E1A, E1B proteins and protein IX of human adenovirus type 5 (Ad5). A portion of the BAV3 E1A protein showed significant homology with conserved region 3 (CR3), the principal transactivation region of Ad5 E1A. The BAV3 E1A protein also contains a consensus sequence known to be important for interaction with the cellular Rb protein but lacks most of the sequence corresponding to the second exon of Ad5 E1A. Promoter sequences for BAV3 E1B were not defined though the relevant region contains a 35-base pair repeat sequence. Two ORFs define the BAV3 E1B coding unit; one with regions homologous to sequences within the Ad5 E1B 19k protein, and an overlapping ORF with significant homology to the Ad5 E1B 55k protein. The encoded BAV3 E1B proteins of 157 and 420 amino acid residues (R) have predicted unmodified molecular weights of 17,393 and 46,734 respectively. Immediately following the E1B coding region there is a transcription unit containing an SP1 binding site and TATA box followed by an ORF which encodes a protein of 125R and predicted molecular weight of 13,706 with homology to protein IX of Ad5. Five concensus poly A addition sites are located in the 350 base pairs immediately following the protein IX coding region. The homology of sequences in the Ad5 E1A CR3 region and the corresponding BAV3 protein suggested that the BAV3 protein could transactivate certain Ad5 genes normally transactivated by the Ad5 E1A product. Evidence for this hypothesis was obtained in studies in which bovine cells in culture were coinfected with BAV3 and a human adenovirus type 5 (Ad5) recombinant viral vector lacking the E1A region and having a lacZ reporter gene within the E3 region dependent on E1A for its expression. Coinfection resulted in the induction of beta-galactosidase activity and the increased expression of other Ad5 early (E2A 72k) and late (hexon) proteins.

Genomic cloning and restriction site mapping of a porcine adenovirus isolate: demonstration of genomic stability in porcine adenovirus

Restriction endonuclease maps were constructed for the genome of a porcine adenovirus (PAV), NADC-1, which was isolated in 1972 from an adult swine. Genomic DNA libraries of NADC-1 Bam HI, Eco RI/Bam HI, and Sph I fragments were cloned into pUC-18. Using the cloned NADC-1 Bam HI and Eco RI/Bam HI fragments as probes, Southern blot hybridizations were performed to human adenovirus 2 (Ad-2) restriction fragments to determine the left-to-right orientation of the Bam HI and Eco RI/Bam HI fragments. Genomic NADC-1 DNA was cleaved with ten restriction endonucleases (RE). Using cloned NADC-1 genomic fragments as probes in Southern blot hybridizations, an RE site map was constructed. Nucleotide sequencing of four clones confirmed several RE sites. The size of the NADC-1 genome was determined to be approximately 32 kbp. The size of Hind III, Xba I, Sma I, Eco RI, Bam HI, Bgl II, Pst I, and Sph I RE fragments from NADC-1 was compared to those from the reference strain of PAV serotype 4 (F618), and to two recent isolates, NADC-2 and NADC-3. For all restriction enzymes examined, the sizes of the NADC-1 fragments were identical to PAV-4, NADC-2, and NADC-3 fragments, indicating that the NADC-1 isolate is very closely related, if not identical, to PAV-4 and two recent isolates. Southern blot hybridizations also indicated that NADC-1, NADC-2, NADC-3, and PAV-4 are very similar and revealed regions of sequence similarity between NADC-1 and human Ad-2 and human Ad-5.

Adenovirus vectors for gene expression

Adenoviruses possess a combination of features that make them highly suitable as vectors for expression of heterologous genes. Non-conditional and non-defective adeno-vectors have been constructed to obtain high level expression of a number of foreign genes and some of them have been shown in animal models to exhibit excellent promise as vaccine candidates.

Co-expression of hepatitis B virus antigens by a non-defective adenovirus vaccine vector

Adenovirus type 7 vaccine strain was engineered to express foreign antigens from both the E3 early promoter in the E3 region and the major late promoter inserted between the E4 region and the right inverted terminal repeat. This multiple expression vector was used to express hepatitis B core antigen (HBcAg), hepatitis B e antigen (HBeAg), and hepatitis B surface antigen (HBsAg). The gene inserted in the E3 region was derived from the core gene of the hepatitis B virus genome. When the precore region was present, an immunoreactive group of proteins with molecular weights ranging from 15,000 to 19,000 was secreted into the media. Velocity sedimentation centrifugation of media and lysates from cells infected with recombinants containing the core gene with the precore region resulted in peaks of HBeAg at the top of the gradient where authentic HBeAg should be found. In addition to the core gene in the E3 region, the surface antigen gene of hepatitis B virus was inserted behind the major late promoter in the E4 region resulting in an adeno-hepatitis recombinant virus capable of expressing both the core gene and the HBsAg cells. Cells infected with the adeno-hepatitis recombinants could also be stained with peroxidase-conjugates after reacting to antibody against HBcAg. Inoculation of dogs with the recombinant viruses which contained the core gene, with and without the precore sequence, resulted in a significant antibody response to HBcAg/HBeAg. The dogs also produced a significant antibody response to HBsAg as well as neutralizing antibody to adenovirus.

Replication of an adenovirus type 34 mutant DNA containing tandem reiterations of the inverted terminal repeat

A mutant of human adenovirus type 34 (Ad34) has been isolated which contains DNA molecules with tandem reiterations of from two to eight copies of a 131-bp sequence within the right-sided inverted terminal repetition. Terminal heterogeneity was not eliminated by repeated plaque purifications indicating that the population of DNA molecules with various numbers of reiterations could rapidly evolve from the DNA of a single virus particle. These enlarged DNA molecules were capable of replication both in vivo and in vitro. The nucleotide sequence of the mutant Ad34 inverted terminal repetitions contained most of the essential features of the Ad origin of DNA replication. These features include the ATAATATACC sequence which is present between the highly conserved bases 9-18 in all human adenoviruses, as well as the consensus sequences for the binding of nuclear factor I and nuclear factor III. However, the reiterated sequences lacked a dG appropriately placed on the template strand to serve as a potential site for internal initiation. It appears that the rapid amplification of two to eight copies of the reiterated terminal sequences does not arise from internal initiation during replication but probably from homologous recombination.

Adenovirus vaccine vectors expressing hepatitis B surface antigen: importance of regulatory elements in the adenovirus major late intron

Adenovirus types 4 and 7 are currently used as live oral vaccines for prevention of acute respiratory disease caused by these adenovirus serotypes. To investigate the concept of producing live recombinant vaccines using these serotypes, adenovirus types 4 (Ad4) and 7 (Ad7) were constructed that produce HBsAg upon infection of cell cultures. Ad4 recombinants were constructed that express HBsAg from a cassette inserted 135 bp from the right-hand terminus of the viral genome. The cassette contained the Ad4 major late promoter followed by leader 1 of the tripartite leader, the first intervening sequence between leaders 1 and 2, leaders 2 and 3, the HBsAg gene, and tandem polyadenylation signals from the Ad4 E3B and hexon genes. Using this same cassette, a series of Ad4 recombinants expressing HBsAg were constructed with deletions in the intervening sequence between leaders 1 and 2 to evaluate the contribution of the downstream control elements more precisely. Inclusion of regions located between +82 and +148 as well as +148 and +232 resulted in increases in expression levels of HBsAg in A549-infected cells by 22-fold and 44-fold, respectively, over the levels attained by an adenovirus recombinant retaining only sequences from +1 to +82, showing the importance of these elements in the activation of the major late promoter during the course of a natural Ad4 viral infection. Parallel increases were also observed in steady-state levels of cytoplasmic HBsAg-specific mRNA. When similar Ad7 recombinant viruses were constructed, these viruses also expressed 20-fold more HBsAg due to the presence of the intron. All Ad4 and Ad7 recombinants produced HBsAg particles containing gp27 and p24 which were secreted in the medium. When dogs were immunized intratracheally with one of these Ad7 recombinants, they seroconverted to both Ad7 and HBsAg to a high level.

Characterization of the simian adenovirus type 30 inverted terminal repeat

The presence of an inverted terminal repeat (ITR), which plays an important role in the initiation of DNA replication, is one of the characteristic properties of adenoviruses (Ads). We have established the nucleotide (nt) sequences for the ITR of simian adenovirus type 30 (SV30), a subgroup-III oncogenic virus. This repeat consists of 185 nt, representing the longest ITR found in an Ad so far. It contains multiple copies of internal repeats, as well as the consensus sequences of the putative binding sites for replication and transcription factors. The conserved features of the known ITRs are also found in SV30. Interestingly, the ITR of SV30 is more closely related to that of Ad5 (human), than to that of SA7 (simian).

The creation of adenovirus genomes with viable, stable, internal redundancies centered about the E2b region

During the course of constructing new adenoviral strains by overlap recombination, we have discovered that internally redundant viable genomes can be created by end-to-end joining of the input DNA molecules. The cellular functions responsible for the end-joining activity frequently ligated the overhanging single strands of the complementary ends to form a novel restriction site at the junction. In 2 of the 17 cases analyzed in detail by restriction digestion, and some sequence determinations, the cellular functions had repaired the ends, presumably prior to end-joining. Four of the isolates had suffered deletions at the junction ranging in size from 13 to 532 bp. The isolate with the largest deletion also had an insertion of 14 bp of unknown origin at the site of the deletion. All of the redundant isolates replicated as efficiently as isogenic unit length strains, and plaque dilution titrations obeyed one-hit kinetics, showing that the redundant genomes were nondefective. Nevertheless unit-length genomes were observed at a low level (some 5 to 10% of the total) in stocks of each isolate before and after plaque purification. They presumably arose by recombination between the redundant sequences either intra- or intermolecularly. Evidence from Southern blot analysis showed that molecules with three copies of the redundant sequences also arose and could be detected both in intracellular and in capsid viral DNA. These species would arise by unequal crossing-over between redundant genomes. The efficient replication of the redundant species demonstrates that the precise spatial relationships between splice donors and acceptors on either strand, in this region of the genome, do not have to be rigidly maintained. These data suggest that it may be possible to place other genetic information between the DNA polymerase and terminal protein precursor genes and have it expressed from the major late promoter in its normal location.

Characterization of an adenovirus type 5 mutant carrying embedded inverted terminal repeats

During construction of an adenovirus type 5 (Ad5) deletion mutant, dlE1,3, lacking E1 and E3 sequences, we isolated a variant, dlE1,3-1, which had a direct repeat of viral DNA terminal sequences attached to the left end of the genome. Analysis of this variant with restriction enzymes and by hybridization of Southern blots with specific probes indicated that the extra terminal segment contained the left 2.6% (920 bp) of Ad5 joined to 352 bp of pBR322 which in turn was linked to the left end (minus 21 bp) of dlE1,3. During replication of dlE1,3-1 the extra terminal segment was found to transfer to the right end of the genome resulting in a second variant, dlE1,3-2, with duplicated terminal sequences at both ends of the viral genome. DlE1,3-2 in turn was shown to revert back to dlE1,3-1 at high frequency. Although evidence was obtained indicating that the extra segment could be lost from the left end, spontaneous mutants which had lost direct repeats from both ends were never isolated. It was, however, possible to remove the extra terminal repeat of dlE1,3-1 by cleavage with a restriction enzyme and to isolate dlE1,3 containing wt termini. The rearrangements occurring during replication of dlE1,3-1 and dlE1,3-2 may be consequences of the mode of replication of Ad5 DNA and bear some resemblance to segment inversion in herpesviruses.