Promoter of the adenovirus polypeptide IX gene: similarity to E1B and inactivation by substitution of the simian virus 40 TATA element

Generation of a replication-deficient recombinant human adenovirus type 35 vector using bacteria-mediated homologous recombination

The use of adenovirus type 35 (Ad35) as a vector in vaccine and gene therapy studies is promising due to its broad cell tropism and low seroprevalence in humans. However, to date, a simple and effective system for producing recombinant Ad35 (rAd35) has not been well developed. This report describes a two-plasmid Ad35-Easy system to facilitate the production of recombinant Ad35 (rAd35). The system employed the pAd35-shuttle vector for foreign gene transfer and the pAd35-backbone vector to provide the Ad35 genomic backbone. A 293-Ad35E1B cell line was used to trans-complement rAd35 replication. rAd35 plasmids were obtained through homologous recombination following co-transformation of E. coli BJ5183 cells with recombinant pAd35-shuttle vectors harboring foreign genes. rAd35 viruses were obtained directly by transfecting 293-Ad35E1B cells with foreign gene-containing rAd35 plasmids and the pAd35-backbone vector. The production of E1 deficient rAd35 was evaluated by transfecting the 293-Ad35E1B cells with the rAd35 plasmid containing the enhanced green fluorescent protein (EGFP) gene. The virus grew effectively at a yield comparable to that of wild type Ad35 in HEp2 cells, indicating that the Ad35-Easy system is an efficient method for rapid production of rAd35 in sufficient quantities for vaccine development or gene therapy.

Quantitative analysis of the leaky expression of adenovirus genes in cells transduced with a replication-incompetent adenovirus vector

Theoretically, adenovirus (Ad) genes should not be expressed following transduction with a replication-incompetent Ad vector because the E1A gene, which is essential for the expression of other viral gene, is deleted in a replication-incompetent Ad vector. However, leaky expression of viral genes is known to occur following transduction with an E1-deleted Ad vector, leading to an induction of cellular immunity against Ad proteins. To date, no detailed analysis of the leaky expression profiles of Ad genes has been performed. In this study, we systematically examined the expression profiles of Ad genes in cells following transduction with a replication-incompetent Ad vector (Ad-L2) at multiplicities of infection (MOIs) of 10 and 100 using real-time RT-PCR. Significant expression was found for the E4 and pIX genes following transduction with Ad-L2 in cultured cells. The expression levels of the E4 and pIX genes were approximately 30- to 600-fold lower than those of the transgene (firefly luciferase), and 50- to 5000-fold lower than those of the E4 and pIX genes following transduction at the same MOI with the wild-type Ad. Unexpectedly, expression levels of the major capsid proteins were approximately the same as, or even slightly above, the background levels (Ad gene expression levels in mock-transduced cells). This study provides valuable information for the design of a safe and efficient replication-incompetent Ad vector.

Characterization of human adenovirus 35 and derivation of complex vectors

Background

Replication-deficient recombinant adenoviral vectors based on human serotype 35 (Ad35) are desirable due to the relatively low prevalence of neutralizing antibodies in the human population. The structure of the viral genome and life cycle of Ad35 differs from the better characterized Ad5 and these differences require differences in the strategies for the generation of vectors for gene delivery.

Results

Sequences essential for E1 and E4 function were identified and removed and the effects of the deletions on viral gene transcription were determined. In addition, the non-essential E3 region was deleted from rAd35 vectors and a sequence was found that did not have an effect on viability but reduced viral fitness. The packaging capacity of rAd35 was dependent on pIX and vectors were generated with stable genome sizes of up to 104% of the wild type genome size. These data were used to make an E1-, E3-, E4-deleted rAd35 vector. This rAd35 vector with multiple gene deletions has the advantages of multiple blocks to viral replication (i.e., E1 and E4 deletions) and a transgene packaging capacity of 7.6 Kb, comparable to rAd5 vectors.

Conclusions

The results reported here allow the generation of larger capacity rAd35 vectors and will guide the derivation of adenovirus vectors from other serotypes.

Adenovirus as a carrier for the development of influenza virus-free avian influenza vaccines

A long-sought goal during the battle against avian influenza is to develop a new generation of vaccines capable of mass immunizing humans as well as poultry (the major source of avian influenza for human infections) in a timely manner. Although administration of the currently licensed influenza vaccine is effective in eliciting protective immunity against seasonal influenza, this approach is associated with a number of insurmountable problems for preventing an avian influenza pandemic. Many of the hurdles may be eliminated by developing new avian influenza vaccines that do not require the propagation of an influenza virus during vaccine production. Replication-competent adenovirus-free adenovirus vectors hold promise as a carrier for influenza virus-free avian influenza vaccines owing to their safety profile and rapid manufacture using cultured suspension cells in a serum-free medium. Simple and efficient mass-immunization protocols, including nasal spray for people and automated in ovo vaccination for poultry, convey another advantage for this class of vaccines. In contrast to parenteral injection of adenovirus vector, the potency of adenovirus-vectored nasal vaccine is not appreciably interfered by pre-existing immunity to adenovirus.

Profiling the thermodynamic softness of adenoviral promoters

We showed previously that anharmonic DNA dynamical features correlate with transcriptional activity in selected viral promoters, and hypothesized that areas of DNA softness may represent loci of functional significance. The nine known promoters from human adenovirus type 5 were analyzed for inherent DNA softness using the Peyrard-Bishop-Dauxois model and a statistical mechanics approach, using a transfer integral operator. We found a loosely defined pattern of softness peaks distributed both upstream and downstream of the transcriptional start sites, and that early transcriptional regions tended to be softer than late promoter regions. When reported transcription factor binding sites were superimposed on our calculated softness profiles, we observed a close correspondence in many cases, which suggests that DNA duplex breathing dynamics may play a role in protein recognition of specific nucleotide sequences and protein-DNA binding. These results suggest that genetic information is stored not only in explicit codon sequences, but also may be encoded into local dynamic and structural features, and that it may be possible to access this obscured information using DNA dynamics calculations.

Novel replication-incompetent adenoviral B-group vectors: high vector stability and yield in PER.C6 cells

Adenoviral vectors based on adenovirus type 35 (rAd35) have the advantage of low natural vector immunity and induce strong, insert-specific T- and B-cell responses, making them prime-candidate vaccine carriers. However, severe vector-genome instability of E1-deleted rAd35 vectors was observed, hampering universal use. The instability of E1-deleted rAd35 vector proved to be caused by low pIX expression induced by removal of the pIX promoter, which was located in the E1B region of B-group viruses. Reinsertion of a minimal pIX promoter resulted in stable vectors able to harbour large DNA inserts (>5 kb). In addition, it is shown that replacement of the E4-Orf6 region of Ad35 by the E4-Orf6 region of Ad5 resulted in successful propagation of an E1-deleted rAd35 vector on existing E1-complementing cell lines, such as PER.C6 cells. The ability to produce these carriers on PER.C6 contributes significantly to the scale of manufacturing of rAd35-based vaccines. Next, a stable rAd35 vaccine was generated carrying Mycobacterium tuberculosis antigens Ag85A, Ag85B and TB10.4. The antigens were fused directly, resulting in expression of a single polyprotein. This vaccine induced dose-dependent CD4+ and CD8+ T-cell responses against multiple antigens in mice. It is concluded that the described improvements to the rAd35 vector contribute significantly to the further development of rAd35 carriers for mass-vaccination programmes for diseases such as tuberculosis, AIDS and malaria.

New helper cells and matched early region 1-deleted adenovirus vectors prevent generation of replication-competent adenoviruses

The presence of replication-competent adenoviruses (RCAs) in batches of replication-defective adenovirus (Ad) vectors is a major problem for the application of these vectors in gene therapy. RCAs are generated by recombination between sequences in the Ad vector and homologous Ad sequences in the helper cells, resulting in the acquisition by the vector of early region 1. To prevent the formation of RCAs, we have developed helper cell lines, which we named PER, and matched Ad vectors that do not have sequence overlap. PER cells contain the Ad serotype 5 (Ad5) E1A- and E1B-encoding sequences (Ad5 nucleotides 459-3510) under the control of the human phosphoglycerate kinase (PGK) promoter. We demonstrate that PER cells synthesize high levels of the Ad5 E1A and E1B proteins. The yields from PER cells of E1-deleted Ads are similar to those obtained from earlier helper cells, such as 911 and 293 cells. Propagation of matched Ad vectors, which lack Ad5 nucleotides 459-3510, in one of the PER clones, PER.C6, does not result in the generation of RCAs, in contrast to propagation in 293 cells. We conclude that the combination of PER.C6 cells and nonoverlapping E1-deleted adenoviral vectors eliminates the problem of RCA generation by homologous recombination, and allows cost-effective production of safe, clinical-grade batches of recombinant Ad vectors.

Pausing and termination by bacteriophage T7 RNA polymerase

Two types of sites are known to cause pausing and/or termination by bacteriophage T7 RNA polymerase (RNAP). Termination at class I sites (typified by the signal found in the late region of T7 DNA, TPhi) involves the formation of a stable stem-loop structure in the nascent RNA ahead of the point of termination, and results in termination near runs of U. Class II sites, typified by a signal first identified in the cloned human preproparathyroid hormone (PTH) gene, generate no evident structure in the RNA but contain a conserved sequence ahead of the point of termination, and also contain runs of U. Termination at class I and class II sites may involve non-equivalent mechanisms, as mutants of T7 RNA polymerase have been identified that fail to recognize class II sites yet continue to recognize class I sites. In this work, we have analyzed pausing and termination at several class II sites, and variants of them. We conclude that the 7 bp sequence ATCTGTT (5' to 3' in the non-template strand) causes transcribing T7 or T3 RNA polymerase to pause. Termination 6 to 8 bp past this sequence is favored by the presence of runs of U, perhaps because they destabilize an RNA:DNA hybrid. The effects of T7 lysozyme on pausing and termination are consistent with the idea that termination involves a reversion of the polymerase from the elongation to the initiation conformation, and that lysozyme inhibits the return to the elongation conformation. A kinetic model of pausing and termination is presented that provides a consistent interpretation of our results.

The mammalian transcriptional repressor RBP (CBF1) targets TFIID and TFIIA to prevent activated transcription

RBP is a cellular protein that functions as a transcriptional repressor in mammalian cells. RBP has elicited great interest lately because of its established roles in regulating gene expression, in Drosophila and mouse development, and as a component of the Notch signal transduction pathway. This report focuses on the mechanism by which RBP represses transcription and thereby regulates expression of a relatively simple, but natural, promoter. The results show that, irrespective of the close proximity between RBP and other transcription factors bound to the promoter, RBP does not occlude binding by these other transcription factors. Instead, RBP interacts with two transcriptional coactivators: dTAFII110, a subunit of TFIID, and TFIIA to repress transcription. The domain of dTAFII110 targeted by RBP is the same domain that interacts with TFIIA, but is disparate from the domain that interacts with Sp1. Repression can be thwarted when stable transcription preinitiation complexes are formed before RBP addition, suggesting that RBP interaction with TFIIA and TFIID perturbs optimal interactions between these coactivators. Consistent with this, interaction between RBP and TFIIA precludes interaction with dTAFII110. This is the first report of a repressor specifically targeting these two coactivators to subvert activated transcription.

The mammalian transcriptional repressor RBP (CBF1) regulates interleukin-6 gene expression

The cellular interleukin-6 (IL-6) gene contains a target site for the mammalian transcriptional repressor RBP. The target site is contained within the interleukin response element (ILRE), which mediates IL-6 activation by NF-kappa B. In this study, we show by using transient-expression assays that RBP represses activated transcription from the IL-6 gene. The presence and position of the RBP target site are crucial in mediating repression by RBP. While RBP binds within the ILRE, it does not target NF-kappa B alone; nonetheless, NF-kappa B binding to the ILRE is required for repression. Our results indicate that RBP represses coactivation by NF-kappa B and another cellular transcription factor, C/EBP-beta.

An efficient and flexible system for construction of adenovirus vectors with insertions or deletions in early regions 1 and 3

Human adenoviruses (Ads) are attracting considerable attention because of their potential utility for gene transfer and gene therapy, for development of live viral vectored vaccines, and for protein expression in mammalian cells. Engineering Ad vectors for these applications requires a variety of reagents in the form of Ads and bacterial plasmids containing viral DNA sequences and requires different strategies for construction of vectors for different purposes. To simplify Ad vector construction and develop a procedure with maximum flexibility, efficiency, and cloning capacity, we have developed a vector system based on use of Ad5 DNA sequences cloned in bacterial plasmids. Expanded deletions in early region 1 (3180 bp) and early region 3 (2690 or 3132 bp) can be combined in a single vector that should have a capacity for inserts of up to 8.3 kb, enough to accommodate the majority of cDNAs encoding proteins with regulatory elements. Genes can be inserted into either early region 1 or 3 or both and mutations or deletions can be readily introduced elsewhere in the viral genome. To illustrate the flexibility of the system, we have introduced a wild-type early region 3 into the vectors, and to illustrate the high capacity for inserts, we have isolated a vector with two genes totaling 7.8 kb.

The recombination signal sequence-binding protein RBP-2N functions as a transcriptional repressor

We have identified a cellular protein, RBP-2N, a presumed recombinase, as a repressor of transcription. Inhibition of transcription by RBP-2N was dependent on its DNA recognition site and was demonstrated in vitro and in vivo. This repression appears to be general, as transcription mediated by SP1 and Gal4/VP16 was inhibited by RBP-2N. The protein was purified to near homogeneity from human cells on the basis of its binding to a site present in the promoter of the adenovirus pIX gene. The DNA recognition sequence is 5'-TGGGAAAGAA, which is markedly different from the recombination signal sequence originally identified as the target site for this protein. The sequence of the purified protein is 97% identical with that published for the mouse RBP-2N protein. The reported homolog in Drosophila is Suppressor of Hairless. RBP-2N binding sites are present in a number of cellular and viral promoters, so RBP-2N may have a general role in transcriptional repression.

The recombination signal sequence-binding protein RBP-2N functions as a transcriptional repressor

We have identified a cellular protein, RBP-2N, a presumed recombinase, as a repressor of transcription. Inhibition of transcription by RBP-2N was dependent on its DNA recognition site and was demonstrated in vitro and in vivo. This repression appears to be general, as transcription mediated by SP1 and Gal4/VP16 was inhibited by RBP-2N. The protein was purified to near homogeneity from human cells on the basis of its binding to a site present in the promoter of the adenovirus pIX gene. The DNA recognition sequence is 5'-TGGGAAAGAA, which is markedly different from the recombination signal sequence originally identified as the target site for this protein. The sequence of the purified protein is 97% identical with that published for the mouse RBP-2N protein. The reported homolog in Drosophila is Suppressor of Hairless. RBP-2N binding sites are present in a number of cellular and viral promoters, so RBP-2N may have a general role in transcriptional repression.

Activation of the HLA-DRA gene in primary human T lymphocytes: novel usage of TATA and the X and Y promoter elements

Human T lymphocytes express human leukocyte antigen (HLA)-DR-alpha (DRA) upon mitogenic or antigenic stimulation. DR+ T cells are also found in a number of inflammatory and autoimmune diseases and have a proposed role in these diseases. The molecular mechanism of DR regulation in untransformed blood T lymphocytes was studied here by transient transfection of DRA-chloramphenicol acetyltransferase reporter gene constructs. Several novel features of this regulation were observed. During the early stages of T-cell activation by mitogens or antigens, strong promoter induction was exhibited with the proximal 43 bp of the DRA promoter which contains a TATTA motif. Addition of upstream X and Y DNA elements augmented the response. This contrasts with data from transformed cell lines in which the proximal 43 bp produced no detectable promoter function, and the inclusion of X and Y elements is essential for basal level expression. Mutation of the TATTA motif or substitution with a functional but different TATA element produced errant initiation and greatly reduced gene expression. Interestingly, T lymphocytes from a normal donor were DR+ prior to in vitro stimulation, and again, strong promoter activity was observed with 43 bp of proximal sequence. Unexpectedly, the presence of the X and Y elements correlated with a suppression of class II promoter function and surface antigen expression. This study of nontransformed lymphocytes reveals several novel features of DRA gene regulation and underscores the value and necessity of such studies.

Activation of the HLA-DRA gene in primary human T lymphocytes: novel usage of TATA and the X and Y promoter elements

Human T lymphocytes express human leukocyte antigen (HLA)-DR-alpha (DRA) upon mitogenic or antigenic stimulation. DR+ T cells are also found in a number of inflammatory and autoimmune diseases and have a proposed role in these diseases. The molecular mechanism of DR regulation in untransformed blood T lymphocytes was studied here by transient transfection of DRA-chloramphenicol acetyltransferase reporter gene constructs. Several novel features of this regulation were observed. During the early stages of T-cell activation by mitogens or antigens, strong promoter induction was exhibited with the proximal 43 bp of the DRA promoter which contains a TATTA motif. Addition of upstream X and Y DNA elements augmented the response. This contrasts with data from transformed cell lines in which the proximal 43 bp produced no detectable promoter function, and the inclusion of X and Y elements is essential for basal level expression. Mutation of the TATTA motif or substitution with a functional but different TATA element produced errant initiation and greatly reduced gene expression. Interestingly, T lymphocytes from a normal donor were DR+ prior to in vitro stimulation, and again, strong promoter activity was observed with 43 bp of proximal sequence. Unexpectedly, the presence of the X and Y elements correlated with a suppression of class II promoter function and surface antigen expression. This study of nontransformed lymphocytes reveals several novel features of DRA gene regulation and underscores the value and necessity of such studies.

Contribution of the TATA motif to Tat-mediated transcriptional activation of human immunodeficiency virus gene expression

Tat-mediated transcriptional activation of human immunodeficiency virus (HIV) gene expression requires the presence of the cis-acting Tat-responsive element, TAR, and a functional enhancer-promoter element. The ability of Tat to function with heterologous enhancer sequences led us to examine the role of the minimal basal promoter for trans activation. Substitution of HIV TATA sequences (nucleotides -20 to -35) with TATA elements derived from other promoters had little effect on the basal level of transcription or the ability to activate the HIV long terminal repeat upon stimulation through upstream activation sequences. In contrast, minimal alterations within the TATA motif had a profound effect on trans activation, as demonstrated by the 3- to 10-fold reduction in activation following expression of Tat. Our findings suggest that minor changes in the TATA motif affect the composition of the initiation-elongation complex and that the composition of this complex is critical for Tat-dependent activation of gene expression.