Comparative sequence analysis of the inverted terminal repetitions from different adenoviruses

An insertion and deletion mutant of adenovirus in Muscovy ducks

Duck adenovirus 3 (DuAdV-3; strain HB) was isolated and sequenced. The genome of the Muscovy-duck-origin virus contains a 54-bp insertion in pVIII, a 3-bp deletion in the overlap region of 100K, 22K, and 33K, a 42-bp deletion at the junction of ORF64 and ORF67, and a 715-bp deletion in right noncoding region of the genome. Notably, HB has a strikingly shorter right inverted terminal repeat (ITR) of 50 bp, whereas all other DuAdV-3 isolates have a 721-bp ITR. These findings demonstrate that HB is an insertion and deletion mutant of DuAdV-3.

An alternative to the adenovirus inverted terminal repeat sequence increases the viral genome replication rate and provides a selective advantage in vitro

During the development of human adenovirus 35-derived replication-incompetent (rAd35) vaccine vectors for prevention of infectious diseases, we detected mutations in the terminal 8 nt of the inverted terminal repeats (ITRs) of rAd35. The switch from the plasmid-encoded sequence 5'-CATCATCA-3' to the alternative sequence 5'-CTATCTAT-3' in the ITRs was found to be a general in vitro propagation phenomenon, as shown for several vectors carrying different transgenes or being derived from different adenovirus serotypes. In each tested case, the plasmid-encoded ITR sequence changed to exactly the same alternative ITR sequence, 5'-CTATCTAT-3'. The outgrowth of this alternative ITR version should result from a growth advantage conferred by the alternative ITR sequence. Indeed, replication kinetics studies of rAd35 harbouring either the original or alternative ITR sequence confirmed an increase in replication speed for rAd35 vectors with the alternative ITR sequence. These findings can be applied to generate recombinant adenoviral vectors harbouring the alternative ITR sequence, which will facilitate the generation of genetically homogeneous seed virus batches. Moreover, vector production may be accelerated by taking advantage of the observed improved replication kinetics associated with the alternative ITR sequence.

Comparative genomic analysis of two strains of human adenovirus type 3 isolated from children with acute respiratory infection in southern China

Human adenovirus type 3 (HAdV-3) is a causative agent of acute respiratory disease, which is prevalent throughout the world, especially in Asia. Here, the complete genome sequences of two field strains of HAdV-3 (strains GZ1 and GZ2) isolated from children with acute respiratory infection in southern China are reported (GenBank accession nos DQ099432 and DQ105654, respectively). The genomes were 35,273 bp (GZ1) and 35,269 bp (GZ2) and both had a G+C content of 51 mol%. They shared 99% nucleotide identity and the four early and five late regions that are characteristic of human adenoviruses. Thirty-nine protein- and two RNA-coding sequences were identified in the genome sequences of both strains. Protein pX had a predicted molecular mass of 8.3 kDa in strain GZ1; this was lower (7.6 kDa) in strain GZ2. Both strains contained 10 short inverted repeats, in addition to their inverted terminal repeats (111 bp). Comparative whole-genome analysis revealed 93 mismatches and four insertions/deletions between the two strains. Strain GZ1 infection produced a typical cytopathic effect, whereas strain GZ2 did not; non-synonymous substitutions in proteins of GZ2 may be responsible for this difference.

The nucleotide sequence and a first generation gene transfer vector of species B human adenovirus serotype 3

Human adenovirus (Ad) serotype 3 causes respiratory infections. It is considered highly virulent, accounting for about 13% of all Ad isolates. We report here the complete Ad3 DNA sequence of 35,343 base pairs (GenBank accession DQ086466). Ad3 shares 96.43% nucleotide identity with Ad7, another virulent subspecies B1 serotype, and 82.56 and 62.75% identity with the less virulent species B2 Ad11 and species C Ad5, respectively. The genomic organization of Ad3 is similar to the other human Ads comprising five early transcription units, E1A, E1B, E2, E3, and E4, two delayed early units IX and IVa2, and the major late unit, in total 39 putative and 7 hypothetical open reading frames. A recombinant E1-deleted Ad3 was generated on a bacterial artificial chromosome. This prototypic virus efficiently transduced CD46-positive rodent and human cells. Our results will help in clarifying the biology and pathology of adenoviruses and enhance therapeutic applications of viral vectors in clinical settings.

Promoter activity of left inverted terminal repeat and downstream sequences of porcine adenovirus type 3

Early region 1 (E1) of porcine adenovirus type 3 (PAdV-3) consists of E1A and E1B transcription units. The authentic promoter region of E1A contains a TATA box at nucleotide position (nt) 449 and a bifunctional regulatory element between nt 374 and 431, which enhances the transcription of E1A, but represses that of E1B. Here, we investigated the role of the left inverted terminal repeat (ITR) and its downstream sequences (between nt 151 and 312) in the transcription of early viral genes, and viral replication. Mutant PAdV-3s without the authentic E1A promoter region could be rescued by transfection of mutant genomic DNA into fetal porcine retina cells. Moreover, the mutant PAdV-3s produced E1A-specific mRNA and remained viable in swine testis (ST) cells suggesting that the left-terminal 151 bp including the ITR, can serve as a promoter for E1A expression. However, mutant PAdV-3s containing deletion including authentic E1A promoter region, displayed both reduced steady-state levels of early gene mRNAs (E1A, E1B, E2A, E3, and E4) and decreased rate of viral replication in ST cells. Interestingly, mutant PAdV-3s containing the left-terminal 312 bp displayed increased transcription of early genes including E1A. Our results suggest that the left ITR of PAdV-3 contain the promoter like elements and the sequences (between nt 151 and 312) downstream of left ITR can enhance its promoter activity.

Nucleotide sequence of human adenovirus type 12 DNA: comparative functional analysis

A fresh inoculum of human adenovirus type 12 (Ad12) was obtained from the American Type Culture Collection and passaged once on human embryonic kidney cells, and Ad12 DNA was prepared from the first-passage yield to avoid higher passages which might have generated host-virus DNA recombinants. The 18 PstI fragments of Ad12 DNA were cloned into the pBluescript KS vector, and the entire nucleotide sequence of both strands from all 18 fragments was determined by using successive oligodeoxyribonucleotide primers. Ad12 DNA extends over 34,125 nucleotide pairs, and its molecular weight is calculated to be about 22 x 10(6). The nucleotide sequence of Ad12 DNA was subjected to computer analyses that determined possible open reading of frames on the two strands, the leader sequences, the position of the virus-associated RNA coding region, possible TATA, and polyadenylation signals. The distribution of the Ad12 open reading frames was similar to that in the previously sequenced Ad2 DNA, but there were also distinct differences. Ad12 DNA has an inverted terminal redundancy of 161 nucleotides, compared with 102 nucleotides in Ad2 DNA. There were stretches of sequence identity between Ad2 and Ad12 DNAs at both termini; the overall sequence similarity between the two viral genomes ranged between 59% (polypeptide IX) and 77% (in the E2 region), with high homology also in the sequences for the adenovirus DNA polymerase.

The NFIII/OCT-1 binding site stimulates adenovirus DNA replication in vivo and is functionally redundant with adjacent sequences

The inverted terminal repeat (ITR) of adenovirus type 5 (Ad5) is 103 bp in length and contains the origin of DNA replication. Cellular transcription factors NFI/CTF and NFIII/OCT-1 bind to sites within the ITR and participate in the initiation of viral DNA replication in vitro. The ITR also contains multiple copies of two conserved sequence motifs that bind the cellular transcription factors SP1 and ATF. We have analyzed a series of viruses that carry deletions at the left terminus of Ad5. A virus carrying a deletion of the NFIII/OCT-1, SP1, and ATF sites within the ITR (mutant dl309-44/107) was wild type for virus growth. However, the deletion of these elements in addition to sequences immediately flanking the ITR (mutant dl309-44/195) resulted in a virus that grew poorly. The analysis of growth parameters of these and other mutants demonstrate that the NFIII/OCT-1 and adjacent SP1 sites augment the accumulation of viral DNA following infection. The function of these elements was most evident in coinfections with a wild-type virus, suggesting that these sites enhance the ability of a limiting trans-acting factor(s), that stimulates viral DNA replication, to interact with the ITR. The results of these analyses indicate functional redundancy between different transcription elements at the left terminus of the Ad5 genome and demonstrate that the NFIII/OCT-1 site and adjacent SP1 site, previously thought to be nonessential for adenovirus growth, play a role in viral DNA replication in vivo.

Sequence organization in regulatory regions of DNA of minute virus of mice

Analysis of the nucleotide sequence of minute virus of mice (MVM) DNA indicates that the DNA termini contain clusters of potential DNA regulatory elements and that there are repetitive DNA elements highly reiterated throughout the entire genome, which may also have a role in DNA function. The left end of MVM DNA, which contains the promoter for the nonstructural genes, has a cluster of DNA elements that includes homologies to the polyoma virus enhancer, three copies of an E1A-inducible transcription factor (ATF) binding site, and a potential Z-DNA element. The MVM right end, which contains the origin of DNA replication, has a cluster of DNA elements that includes several homologies to the polyoma virus replication origin and a potential Z-DNA element. In addition, oligonucleotide frequency analysis indicates the presence of highly recurring sequence elements throughout the entire MVM genome that may be involved in regulation. This computer-aided analysis suggests similarities and significant differences in regulatory sequence organization between MVM and polyoma virus, and identifies specific DNA elements for future genetic characterization.

The human ubiquitin gene family: structure of a gene and pseudogenes from the Ub B subfamily

An ubiquitin cDNA clone was isolated from a human liver cDNA library. This clone contained two complete, and a portion of a third, ubiquitin coding sequences joined head to tail with no spacer peptides. Screening a human genomic library with a probe derived from the coding region of this cDNA identified a large number of cross-hybridising clones. Differential screening of these genomic clones with the 3' non-coding region of the cDNA identified three different 3'-positive clones. Sequence analysis of these three clones revealed: a gene corresponding to the cDNA containing an intron in the 5' non-coding region and coding for three direct repeats of mature ubiquitin, and two related pseudogenes which appear to have arisen by reverse transcription and insertion into the genome. However, one pseudogene contains two repeats of the ubiquitin coding sequence, while the other contains only one. Hybridisation analysis of restricted human genomic DNA suggests the presence of one other closely related gene within the genome.

DNA sequences required for the in vitro replication of adenovirus DNA

Initiation of adenovirus (Ad) DNA replication occurs on viral DNA containing a 55-kilodalton (kDa) protein at the 5' terminus of each viral DNA strand and on plasmid DNAs containing the origin of Ad replication but lacking the 55-kDa terminal protein (TP). Initiation of replication proceeds via the synthesis of a covalent complex between an 80-kDa precursor to the TP (pTP) and the 5'-terminal deoxynucleotide, dCMP. Formation of the covalent pTP-dCMP initiation complex with Ad DNA as the template requires the viral-encoded pTP and DNA polymerase and, in the presence of the Ad DNA binding protein, is dependent upon a 47-kDa host protein, nuclear factor I. Initiation of replication with recombinant plasmid templates requires the aforementioned proteins and an additional host protein, factor pL. Deletion mutants of the Ad DNA replication origin contained within the 6.6-kilobase plasmid pLA1 were used to analyze the nucleotide sequences required for the formation and subsequent elongation of the pTP-dCMP initiation complex. The existence of two domains within the first 50 base pairs of the Ad genome, both of which are required for the efficient use of recombinant DNA molecules as templates in an in vitro DNA replication system, was demonstrated. The first domain, consisting of a 10-base-pair "core" sequence located at nucleotide positions 9-18, has been identified tentatively as a binding site for the pTP [ Rijinders , A. W. M., van Bergen, B. G. M., van der Vliet , P. C. & Sussenbach , J. S. (1983) Nucleic Acids Res. 11, 8777-8789]. The second domain, consisting of a 32-base-pair region spanning nucleotides 17-48, was shown to be essential for the binding of nuclear factor I.

Purification in a functional form of the terminal protein of Bacillus subtilis phage phi 29

Phage phi 29 terminal protein, p3, essentially pure, was isolated in a denatured form from viral particles, and anti-p3 antiserum was obtained. A radioimmunoassay to detect and quantitate protein p3 was developed. By using this assay, native protein p3 was highly purified from Escherichia coli cells harboring a gene 3-containing recombinant plasmid. After three purification steps, the protein was more than 96% pure; its amino acid composition was very similar to that deduced from the nucleotide sequence of gene 3. The purified protein was active in the formation of the covalent p3-dAMP initiation complex when supplemented with extracts of B. subtilis infected with a sus mutant of phi 29 in gene 3. No DNA polymerase or ATPase activities were present in the final preparation of protein p3.

Site-specific nicking within the adenovirus inverted terminal repetition

Site-specific nicking occurs on the l-strand, but not on the r-strand, of the adenovirus left inverted terminal repeat. Nicks are presumably introduced into double- or single-stranded DNA by a cellular endonuclease in an ATP-independent reaction. The consensus nick site has the sequence: (sequence in text).

Initiation of adenovirus DNA replication in vitro requires a specific DNA sequence

Initiation of adenovirus DNA replication in vitro occurs on a linearized plasmid DNA containing 3,327 base pairs of the adenovirus terminal sequence. Various deletions have been constructed in the plasmid DNA and their template activities examined. Deletions from an internal restriction enzyme cleavage site that retain only 20 base pairs or more of the adenovirus terminal sequence support initiation and limited chain elongation, whereas deletions that leave 14 base pairs or less of the terminal sequence do not. On the other hand, all deletions extending from the very terminus of the adenovirus DNA destroy the template activity. The terminal 20 base pairs of adenovirus DNA contain a sequence A-T-A-A-T-A-T-A-C-C, which is perfectly conserved in the DNAs from different serotypes of human adenovirus. Base changes within the conserved sequence greatly reduce the template activity. These results suggest that the terminal 20 base pairs constitute a functional origin for the initiation of adenovirus DNA replication in vitro.

Adenovirus isolates from urine of patients with acquired immunodeficiency syndrome

13 adenoviruses (Ad) from the urine of 10 patients with acquired immunodeficiency syndrome (AIDS) were characterised by haemagglutination inhibition and restriction endonuclease analysis of their DNA. The haemagglutinin (HA) for 6 of these isolates was found to be that of Ad34/35. 3 other isolates were found to have Ad7 HA and the remaining 4 viruses were found to have both phenotypes. In contrast, the restriction patterns were more homogeneous than anticipated from the serological analysis. 11 isolates had a SmaI-restriction pattern identical to Ad35, and 2 isolates, which lacked one of the 9 Ad35 SmaI-restriction sites, were identical to Ad34. Analyses with other restriction enzymes reinforced the conclusion that the genomes of all isolates resemble that of Ad35 (and Ad34) more than they resembled the previously isolated Ad7 subtypes. The discrepancy between the restriction endonuclease and the serological analyses is best explained by assuming that some of these new isolates are recombinants between a small part (less than 10%) of the Ad7 genome coding for HA and greater than 90% of the Ad35 genome. It is therefore important to characterise both the genotype and the HA for this potentially important group of pathogens in AIDS patients.

Conserved sequences at the origin of adenovirus DNA replication

The origin of adenovirus DNA replication lies within an inverted sequence repetition at either end of the linear, double-stranded viral DNA. Initiation of DNA replication is primed by a deoxynucleoside that is covalently linked to a protein, which remains bound to the newly synthesized DNA. We demonstrate that virion-derived DNA-protein complexes from five human adenovirus serological subgroups (A to E) can act as a template for both the initiation and the elongation of DNA replication in vitro, using nuclear extracts from adenovirus type 2 (Ad2)-infected HeLa cells. The heterologous template DNA-protein complexes were not as active as the homologous Ad2 DNA, most probably due to inefficient initiation by Ad2 replication factors. In an attempt to identify common features which may permit this replication, we have also sequenced the inverted terminal repeated DNA from human adenovirus serotypes Ad4 (group E), Ad9 and Ad10 (group D), and Ad31 (group A), and we have compared these to previously determined sequences from Ad2 and Ad5 (group C), Ad7 (group B), and Ad12 and Ad18 (group A) DNA. In all cases, the sequence around the origin of DNA replication can be divided into two structural domains: a proximal A . T-rich region which is partially conserved among these serotypes, and a distal G . C-rich region which is less well conserved. The G . C-rich region contains sequences similar to sequences present in papovavirus replication origins. The two domains may reflect a dual mechanism for initiation of DNA replication: adenovirus-specific protein priming of replication, and subsequent utilization of this primer by host replication factors for completion of DNA synthesis.

Initiation of phage phi 29 DNA replication in vitro: formation of a covalent complex between the terminal protein, p3, and 5'-dAMP

Incubation of extracts of phi 29-infected Bacillus subtilis with [alpha-32P]dATP produced a labeled protein having the electrophoretic mobility of p3, the 5'-terminal protein of phi 29 DNA. The reaction product was resistant to treatment with micrococcal nuclease, phosphatase, and RNases A and T1 and sensitive to proteinase K. Incubation of the 32P-labeled protein with piperidine under conditions in which the phi 29 DNA-protein p3 linkage is hydrolyzed released 5'-dAMP. The reaction with [alpha-32P]dATP was strongly inhibited by anti-p3 serum and required the preence of phi 29 DNA-protein p3 complex; no reaction took place with proteinase K-treated phi29 DNA. These results, together with those of acid hydrolysis and partial proteolysis, indicated that a covalent complex between protein p3 and 5'-dAMP is formed in vitro. The initiation complex (protein p3-dAMP) formed in the presence of 0.5 microM [alpha-32P]dATP can be elongated by addition of 40 microM dNTPs. Treatment with piperidine of the product elongated in the presence of 2',3'-dideoxycytidine 5'-triphosphate released the expected oligonucleotides, 9 and 12 bases long, taking into account the sequence at the left and right DNA ends, respectively.

Polar encapsidation of adenovirus DNA: cloning and DNA sequence of the left end of adenovirus type 3

The left-end adenovirus type 3 DNA sequence is very similar to those of other subgroup B adenoviruses, especially in the area between the HinfI site (320 base pairs) and the early-region Ia gene. This segment of the genome has been implicated as necessary for the left-end polarity of adenovirus DNA encapsidation. This segment and the sequences flanking it are compared with the corresponding sequences of adenovirus type 5 and adenovirus type 12, and the extent and pattern of intersubgroup homologies are discussed.

Formation of a covalent complex between the 80,000-dalton adenovirus terminal protein and 5'-dCMP in vitro

An in vitro adenovirus DNA replication system catalyzed the formation of a covalent complex between an 80,000-dalton protein and 5'-dCMP in the presence of [alpha-32P-dCTP, MgCl2, ATP, and adenovirus (Ad) DNA with a protein covalently bound to the 5' end of each strand (Ad DNA-prot). The requirement for Ad DNA-prot in this reaction was similar to that for in vitro DNA replication. When dATP, dTTP, and the 2',3'-dideoxynucleoside triphosphate (ddNTP) ddGTP were included in the reaction mixture, an elongated complex was detected, which consisted of an 80,000-dalton protein bound to a 26-base oligonucleotide. Formation of the elongated product, but not of the protein-dCMP complex, was inhibited by ddATP, ddCTP, or ddTTP. The requirements for formation of the protein-dCMP complex, the nature of the linkage between protein and dCMP, the size of the protein, and the existence of elongated forms indicated that the protein associated with the complex was identical to the 80,000-dalton Ad terminal protein found on replicating DNA molecules as described by Challberg et al. [Challberg, M. D., Desiderio, S. V. & Kelly, T. J., Jr. (1980) Proc. Natl. Acad. Sci. USA 77, 5105-5109].

Nucleotide sequence at the termini of the DNA of Bacillus subtilis phage phi 29

Phage phi 29 DNA cannot be phosphorylated with polynucleotide kinase and [gamma-32P]ATP because of the presence of a viral protein covalently linked to the 5' termini. The 5' ends can, however, be made susceptible to phosphorylation by treatment with alkali and alkaline phosphatase. Restriction fragments Hpa II C and Hpa II F, corresponding to the right and left ends of phi 29 DNA, respectively, were labeled at the 5' ends with polynucleotide kinase and [gamma-32P]ATP or at the 3' ends with terminal transferase and [alpha-32P]ATP or [alpha-32P]cordycepin 5'-triphosphate. After a secondary cleavage of the labeled fragments, the sequence of the first 150-180 nucleotides at the termini of phi 29 DNA was determined by the method of Maxam and Gilbert. The ends of phi 29 DNA are flush, and a six-nucleotides-long inverted terminal repetition was found. The functional implications of the sequences determined are discussed.