Nucleotide sequences from the adenovirus-2 genome

An Old Acquaintance: Could Adenoviruses Be Our Next Pandemic Threat?

Human adenoviruses (HAdV) are one of the most important pathogens detected in acute respiratory diseases in pediatrics and immunocompromised patients. In 1953, Wallace Rowe described it for the first time in oropharyngeal lymphatic tissue. To date, more than 110 types of HAdV have been described, with different cellular tropisms. They can cause respiratory and gastrointestinal symptoms, even urinary tract inflammation, although most infections are asymptomatic. However, there is a population at risk that can develop serious and even lethal conditions. These viruses have a double-stranded DNA genome, 25-48 kbp, 90 nm in diameter, without a mantle, are stable in the environment, and resistant to fat-soluble detergents. Currently the diagnosis is made with lateral flow immunochromatography or molecular biology through a polymerase chain reaction. This review aimed to highlight the HAdV variability and the pandemic potential that a HAdV3 and 7 recombinant could have considering the aggressive outbreaks produced in health facilities. Herein, we described the characteristics of HAdV, from the infection to treatment, vaccine development, and the evaluation of the social determinants of health associated with HAdV, suggesting the necessary measures for future sanitary control to prevent disasters such as the SARS-CoV-2 pandemic, with an emphasis on the use of recombinant AdV vaccines to control other potential pandemics.

Adenovirus Biology, Recombinant Adenovirus, and Adenovirus Usage in Gene Therapy

Gene therapy is currently in the public spotlight. Several gene therapy products, including oncolytic virus (OV), which predominantly replicates in and kills cancer cells, and COVID-19 vaccines have recently been commercialized. Recombinant adenoviruses, including replication-defective adenoviral vector and conditionally replicating adenovirus (CRA; oncolytic adenovirus), have been extensively studied and used in clinical trials for cancer and vaccines. Here, we review the biology of wild-type adenoviruses, the methodological principle for constructing recombinant adenoviruses, therapeutic applications of recombinant adenoviruses, and new technologies in pluripotent stem cell (PSC)-based regenerative medicine. Moreover, this article describes the technology platform for efficient construction of diverse "CRAs that can specifically target tumors with multiple factors" (m-CRAs). This technology allows for modification of four parts in the adenoviral E1 region and the subsequent insertion of a therapeutic gene and promoter to enhance cancer-specific viral replication (i.e., safety) as well as therapeutic effects. The screening study using the m-CRA technology successfully identified survivin-responsive m-CRA (Surv.m-CRA) as among the best m-CRAs, and clinical trials of Surv.m-CRA are underway for patients with cancer. This article also describes new recombinant adenovirus-based technologies for solving issues in PSC-based regenerative medicine.

Viral vector platforms within the gene therapy landscape

Throughout its 40-year history, the field of gene therapy has been marked by many transitions. It has seen great strides in combating human disease, has given hope to patients and families with limited treatment options, but has also been subject to many setbacks. Treatment of patients with this class of investigational drugs has resulted in severe adverse effects and, even in rare cases, death. At the heart of this dichotomous field are the viral-based vectors, the delivery vehicles that have allowed researchers and clinicians to develop powerful drug platforms, and have radically changed the face of medicine. Within the past 5 years, the gene therapy field has seen a wave of drugs based on viral vectors that have gained regulatory approval that come in a variety of designs and purposes. These modalities range from vector-based cancer therapies, to treating monogenic diseases with life-altering outcomes. At present, the three key vector strategies are based on adenoviruses, adeno-associated viruses, and lentiviruses. They have led the way in preclinical and clinical successes in the past two decades. However, despite these successes, many challenges still limit these approaches from attaining their full potential. To review the viral vector-based gene therapy landscape, we focus on these three highly regarded vector platforms and describe mechanisms of action and their roles in treating human disease.

Identification of the adenovirus type 2 C-168 protein

A hitherto predicted but undetected protein, C-168, in adenovirus type 2 (Ad2) has been identified using mass spectrometry (MS) based proteomics. The gene of this 17.7kDa protein is located on the forward strand in the major late transcription unit between base pairs 9294 and 9797. A tryptic peptide, derived from the C-terminal part of the protein, was identified with high amino acid sequence coverage. A candidate splice site for the corresponding mRNA is also presented. The protein sequence is unusual with repeats of serine, glycine and arginine. A bioinformatics prediction of protein function and localization is presented.

Adenovirus type 5 early region 1B 156R protein promotes cell transformation independently of repression of p53-stimulated transcription

Early region 1B (E1B) of adenovirus type 5 (Ad5) encodes at least five different polypeptides generated by alternative splicing of a common mRNA precursor. Two of these gene products, E1B-19K and E1B-55K, are individually capable of cooperating with the Ad5 E1A proteins to completely transform rodent cells in culture. Substantial evidence suggests that these two E1B proteins contribute to cell transformation by antagonizing growth arrest and apoptosis. Here, we performed genetic and biochemical analyses to assess the attributes of the remaining E1B proteins (E1B-156R, E1B-93R, and E1B-84R). Our results show that E1B-156R, which comprises the 79 amino-terminal and 77 carboxy-terminal amino acids of E1B-55K, also enhances focal transformation of primary rat cells in cooperation with E1A. Since E1B-156R seemed unable to relocalize p53 and inhibit its transactivating function, it must be assumed that it contributes to transformation independently of repression of p53-stimulated transcription. Furthermore, we discovered that E1B-156R contains a functional transcriptional repression domain and binds Ad5 E4orf6 and the cellular apoptosis regulator Daxx. While the ability to bind E4orf6 could indicate further biological functions of E1B-156R in viral infection, the interaction with Daxx might also be linked to its transforming potential. Taken together, these analyses introduce E1B-156R as a novel transformation-promoting E1B protein that acts without repressing p53 transactivation. Moreover, identification of the interaction partners E4orf6 and Daxx provides a first glance of E1B-156R's potential functions.

Virology in the 21st century: finding function with functional genomics

When functional genomics first appeared on the scene, the ability to perform global gene expression and protein profiling was hailed as a revolutionary new way to study biologic systems, likely to result in dramatic new discoveries. As time has passed, DNA microarrays and mass spectrometry have been used to generate huge amounts of data, and databases are overflowing with information. But how well is functional genomics living up to its promises, and has all this data resulted in an improved understanding of biologic processes? This article puts forward a perspective on what is required to ensure that data generated by microarrays and mass spectrometry provide real insights into how genes and proteins function and how this relates to the host response to infection.

Exogenously regulated stem cell-mediated gene therapy for bone regeneration

Regulated expression of transgene production and function is of great importance for gene therapy. Such regulation can potentially be used to monitor and control complex biological processes. We report here a regulated stem cell-based system for controlling bone regeneration, utilizing genetically engineered mesenchymal stem cells (MSCs) harboring a tetracycline-regulated expression vector encoding the osteogenic growth factor human BMP-2. We show that doxycycline (a tetracycline analogue) is able to control hBMP-2 expression and thus control MSC osteogenic differentiation both in vitro and in vivo. Following in vivo transplantation of genetically engineered MSCs, doxycycline administration controlled both bone formation and bone regeneration. Moreover, our findings showed increased angiogenesis accompanied by bone formation whenever genetically engineered MSCs were induced to express hBMP-2 in vivo. Thus, our results demonstrate that regulated gene expression in mesenchymal stem cells can be used as a means to control bone healing.

Analysis of proteins encoded in the bipartite genome of a new type of parvo-like virus isolated from silkworm - structural protein with DNA polymerase motif

Bombyx mori densonucleosis virus type 2 (BmDNV-2) is a small, spherical virus containing two complementary single-stranded linear DNA molecules (VD1, VD2). BmDNV-2 is a new type of virus with a unique, yet unspecified replication mechanism which is different from that of parvoviruses (Bando, H., Choi, H., Ito, Y., Nakagaki, M. , Kawase, S., 1992. Structural analysis on the single-stranded genomic DNAs of the virus newly isolated from silkworm: the DNA molecules share a common terminal sequence, Arch. Virol. 124, 187-193; Bando, H., Hayakawa, T., Asano, S., Sahara, K., Nakagaki, M. , Iizuka, T., 1995. Analysis of the genetic information of a DNA segment of a new virus from silkworm, Arch. Virol., 140, 1147-1155; Hayakawa, T., Asano, S., Sahara, K., Iizuka, T., Bando, H., 1997. Detection of replicative intermediate with closed terminus of Bombyx densonucleosis virus. Arch. Virol. 142, 1-7). Recent analyses on the genomic information of BmDNV-2 identified open reading frames which code for three tentative nonstructural proteins and four (VP1 to 4) of the six known structural proteins (Bando, H., Hayakawa, T., Asano, S., Sahara, K., Nakagaki, M., Iizuka, T., 1995. Analysis of the genetic information of a DNA segment of a new virus from silkworm, Arch. Virol., 140, 1147-1155; Nakagaki et al., in preparation). In this report we demonstrate that the two largest ORFs, VD1-ORF1 and VD2-ORF1, code for the two remaining structural proteins. In addition, computer-assisted analysis revealed that the structural protein encoded in VD1-ORF1 contains sequences conserved among various DNA polymerases, and showed an evolutionary relationship with the DNA polymerases involved in protein-primed replication.

A novel three-pronged approach to kill cancer cells selectively: concomitant viral, double suicide gene, and radiotherapy

Two obstacles limiting the efficacy of nearly all cancer gene therapy trials are low gene transduction efficiencies and the lack of tumor specificity. Recently, a replication-competent, E1B-attenuated adenovirus (ONYX-015) was developed that could overcome these limitations, because it was capable of efficiently and selectively destroying tumor cells lacking functional p53. In an attempt to improve both the efficacy and safety of this approach, we constructed a similar adenovirus (FGR) containing a cytosine deaminase (CD)/herpes simplex virus type-1 thymidine kinase (HSV-1 TK) fusion gene, thereby allowing for the utilization of double-suicide gene therapy, which has previously been demonstrated to produce significant antitumor effects and potentiate the therapeutic effects of radiation. The FGR virus exhibited the same tumor cell specificity and replication kinetics as the ONYX-015 virus in vitro. Importantly, both the CD/5-FC and HSV-1 TK/GCV suicide gene systems markedly enhanced the tumor cell-specific cytopathic effect of the virus, and, as expected, sensitized tumor cells to radiation. By contrast, neither the FGR virus nor either suicide gene system showed significant toxicity to normal human cells. Both suicide gene systems could be used to suppress viral replication effectively, thereby providing a means to control viral spread. The results support the thesis that the three-pronged approach of viral therapy, suicide gene therapy, and radiotherapy may represent a powerful and safe means of selectively destroying tumor cells in vivo.

Effects of mutations in the Exo III motif of the herpes simplex virus DNA polymerase gene on enzyme activities, viral replication, and replication fidelity

The herpes simplex virus DNA polymerase catalytic subunit, which has intrinsic polymerase and 3'-5' exonuclease activities, contains sequence motifs that are homologous to those important for 3'-5' exonuclease activity in other polymerases. The role of one such motif, Exo III, was examined in this study. Mutated polymerases containing either a single tyrosine-to-histidine change at residue 577 or this change plus an aspartic acid-to-alanine at residue 581 in the Exo III motif exhibited defective or undetectable exonuclease activity, respectively, yet retained substantial polymerase activity. Despite the defects in exonuclease activity, the mutant polymerases were able to support viral replication in transient complementation assays, albeit inefficiently. Viruses replicated via the action of these mutant polymerases exhibited substantially increased frequencies of mutants resistant to ganciclovir. Furthermore, when the Exo III mutations were incorporated into the viral genome, the resulting mutant viruses displayed only modestly defect in replication in Vero cells and exhibited substantially increased mutation frequencies. The results suggest that herpes simplex virus can replicate despite severely impaired exonuclease activity and that the 3'-5' exonuclease contributes substantially to the fidelity of viral DNA replication.

Adenovirus E1B 19-kDa death suppressor protein interacts with Bax but not with Bad

Adenovirus E1B 19-kDa protein (19K) is a member of the Bcl-2 family of suppressors of apoptosis. The suppressors function through heterodimerization with the death promoters, Bax and related proteins, thus establishing a set point within the cell that determines whether or not apoptosis is executed in response to a death signal. Sequence similarities between 19K and Bcl-2 are largely restricted to short Bcl-2 homology (BH) domains that mediate interaction with Bax. The BH1 sequence in 19K is degenerate but nevertheless contains a conserved glycine residue found in all family members that when mutated to alanine in Bcl-2 results in loss of Bcl-2 function and ability to dimerize with Bax (Yin, X.-M., Oltvai, Z. N., and Korsmeyer, S. J. (1994) Nature 369, 321-323). Here, we show that the analogous mutation in BH1 of 19K also abrogates the anti-apoptotic properties of 19K and its ability to interact with Bax, thus establishing the critical importance of this residue within BH1 and the likely similarity of Bcl-2 and 19K function. In distinct contrast to Bcl-2, however, 19K interaction was not detected with Bad, a Bcl-2/Bcl-XL dimerizing protein that can potentially regulate a Bax middle dotBcl-2/Bcl-XL survival set point and reinstate susceptibility to a death signal. Furthermore, the anti-apoptotic function of 19K was not overcome by enforced expression of Bad in transfected cells. This feature of 19K may provide adenovirus with a selective advantage in evading premature induction of apoptosis by the host cell.

Identification and characterization of a filament-associated protein encoded by Amsacta moorei entomopoxvirus

A novel protein which is expressed at high levels in insect cells infected with Amsacta moorei entomopoxvirus was identified by our laboratory. This viral gene product migrates as a 25/27-kDa doublet when subjected to electrophoresis on sodium dodecyl sulfate-polyacrylamide gels. It is expressed at late times of infection and is present in infected cells but is absent in purified extracellular virions and occlusion bodies. The gene encoding this polypeptide was mapped on the viral genome, and cDNA clones were generated and sequenced. The predicted protein was shown to be phosphorylated and contained an unusual 10-unit proline-glutamic acid repeat element. A polyclonal antiserum was produced against a recombinant form of the protein expressed in Escherichia coli, and a monoclonal antibody which reacted with the proline-glutamic acid motif was also identified. Immunofluorescence and immunoelectron microscopy techniques revealed that this protein is associated with large cytoplasmic fibrils which accumulate in the cytoplasm between 96 and 120 h postinfection. We subsequently called this viral polypeptide filament-associated late protein of entomopoxvirus. The fibrils containing this polypeptide are closely associated with occlusion bodies and may play a role in their morphogenesis and maturation.

A novel Streptomyces restriction endonuclease, Sse1825I, cleaving at 5'-GG/GWCCC-3'

We isolated and characterized from a Streptomyces species a new class-II restriction endonuclease, which recognizes the palindromic heptanucleotide sequence [sequence: see text] (where W = A or T) and cleaves double-stranded DNA after the second G in this sequence. This Sse1825I enzyme cleaves phage lambda DNA at one site, adenovirus type 2 DNA at eight sites, but does not cleave pBR322, SV40, ColE1, pUC18 and pUC19, and replicative forms of M13mp18 and M13mp19, and phiX174 DNAs.

Nucleotide sequence and transcriptional analysis of the DNA polymerase gene of Bombyx mori nuclear polyhedrosis virus

A gene encoding a putative DNA polymerase (pol) of Bombyx mori nuclear polyhedrosis virus (BmSNPV) was cloned and sequenced. The gene included an open reading frame (ORF) encoding a polypeptide of 988 amino acids with a predicted molecular mass of 114.65 kDa. The deduced amino acid sequence of the BmSNPV pol ORF showed an overall identity of 96 and 45% to those of the Autographa californica NPV (AcMNPV) pol ORF and the Lymantria dispar NPV pol ORF, respectively, and contained sequences conserved in a variety of eukaryotic and viral replicative DNA polymerases. The BmSNPV pol lacked a canonical TATAA element but contained a G+C-rich sequence in the transcriptional initiation region. Analyses by Northern blot hybridization, RNase protection assay, primer extension, and 3' and 5' RACE (rapid amplification of cDNA ends) showed that at least seven different transcripts of approximately 3.1 kb that shared a common 3' end were expressed from the BmSNPV pol. The expression of these transcripts from BmSNPV pol was regulated differentially during virus infection. Transcription of five of the seven species initiated in the close vicinity of and within the motif 5'-GCGTGCT-3'. One transcript placed its initiation site within the motif 5'-AGAGCGT-3' and the remaining one within the motif 5'-GGCGGTGG-3'. The motifs 5'-GCGTGCT-3' and 5'-AGAGCGT-3' have been identified in pol and other genes of AcMNPV as conserved sequences containing transcriptional initiation sites, whereas the motif 5'-GGCGGTGG-3', which is arranged as a direct repeat in BmSNPV pol but not in AcMNPV pol, has not been defined as the sequence responsible for transcriptional initiation sites. The BmSNPV pol transcripts were detectable at 2 hr postinfection (p.i.), peaked at 10 hr p.i., and declined to a low level by 18 hr p.i. The expression of BmSNPV pol was not inhibited but delayed dramatically by the protein synthesis inhibitor cycloheximide upon treatment of infected cells, whereas aphidicolin, an inhibitor of DNA polymerase, inhibited BmSNPV pol transcription. These results suggest a complicated and unique mechanism for the regulation of BmSNPV pol expression.

Genetic relationship between mouse adenovirus-2 (strain K87) and human adenovirus-2

The DNA of mouse adenovirus strain K87 (MAd-2) was cloned and mapped with restriction endonucleases BglII, ClaI, EcoRI, HindIII and SphI. Large differences were found between the MAd-2 and MAd-1 (strain FL) DNA molecules in terms of number and location of restriction sites. The MAd-2 genome also appeared as larger in size than the MAd-1 genome (34.72 kb vs. 30.14 kb). Our results confirm the existence of two distinct adenovirus species in the mouse. Hybridization experiments, on the other hand, indicate that both MAd-1 and MAd-2 are genetically related to human adenovirus type 2 (HAd-2). Overlapping regions of DNA homology are located in genes coding for HAd-2 structural components which could explain serological relationships observed between the human and the murine adenoviruses.

Genetic organization and structural features of maranhar, a senescence-inducing linear mitochondrial plasmid of Neurospora crassa

The nucleotide sequence of maranhar, a senescence-inducing linear mitochondrial plasmid of Neurospora crassa, was determined. The termini of the 7-kb plasmid are 349-bp inverted repeats (TIRs). Each DNA strand contains a long open reading frame (ORF) which begins within the TIR and extends toward the centre of the plasmid. ORF-1 codes for a single-subunit RNA polymerase that is not closely related to that encoded by another Neurospora plasmid, kalilo. The ORF-2 product may be a B-type DNA polymerase resembling those encoded by terminal protein-linked linear genetic elements, including linear mitochondrial plasmids and linear bacteriophages. A separate coding sequence for the terminal protein could not be identified; however, the DNA polymerase of maranhar has an amino-terminal extension with features that are also present in the terminal proteins of linear bacteriophages. The N-terminal extensions of the DNA polymerases of other linear mitochondrial plasmids contain similar features, suggesting that the terminal proteins of linear plasmids may be comprised, at least in part, of these cryptic domains. The terminal protein-DNA bond of maranhar is resistant to mild alkaline hydrolysis, indicating that it might involve a tyrosine or a lysine residue. Although maranhar and the senescence-inducing kalilo plasmid of N. intermedia are structurally similar, and integrate into mitochondrial DNA by a mechanism thus far unique to these two plasmids, they are not closely related to each other and they do not have any nucleotide sequence features, or ORFs, that distinguish them clearly from mitochondrial plasmids which are not associated with senescence and most of which are apparently non-integrative.

Deletion studies to reveal the basis for size discrepancy in proliferating cell nuclear antigen

Proliferating cell nuclear antigen (PCNA), an essential component for DNA replication in eukaryotes, is a highly conserved nonhistone nuclear protein of 261 amino acids. The molecular weight of mammalian PCNA, estimated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), differs notably from that predicted by the cDNA sequences, that is, 36,000 in comparison with 29,261 and 28,748 for human and rat PCNA, respectively. To investigate if this discrepancy is due to posttranslational modifications, we studied the PCNA protein synthesized by an in vitro transcription/translation system as well as the protein overproduced in bacteria. We found that both PCNA protein samples were indistinguishable from the authentic protein from the protein mobility in SDS-PAGE. The finding indicates that the size discrepancy is not due to the posttranslational modifications. Hence, the size discrepancy may be due to the protein sequence per se, namely a sequence-related anomaly in SDS-PAGE. Results from the analyses of a series of PCNA derivatives with various lengths of C- or N-terminal deletion indicate that the putative sequence is in the region of residues 128-150.

Transcription mapping of mouse adenovirus type 1 early region 4

Early region 4 (E4) of mouse adenovirus type 1 was analyzed by Northern blotting, cDNA sequencing, and S1 nuclease protection and primer extension assays. The transcription map of this region was dissimilar to the consensus human adenovirus E4 transcription map in which all transcripts have identical 5' and 3'-terminal sequences. Seven classes of mouse adenovirus type 1 mRNAs were identified; all shared the same 3' end. Three classes of unspliced mRNAs differed at their 5' start sites, two classes of spliced transcripts differed in the locations of their splice acceptors, and two classes of spliced messages differed in their splice donors and acceptors. From the structure of the various transcripts, translational products were predicted. In addition to a predicted polypeptide with similarity to the human adenovirus 2 E4 34K protein previously identified (A. O. Ball, C. W. Beard, P. Villegas, and K. R. Spindler, 1991, Virology 180, 257-265), two open reading frames with similarity to human adenovirus 2 E4 open reading frames 2 and 3 were found.

The 11,600-MW protein encoded by region E3 of adenovirus is expressed early but is greatly amplified at late stages of infection

We have reported that an 11,600-MW (11.6K) protein is coded by region E3 of adenovirus. We have now prepared two new antipeptide antisera that have allowed us to characterize this protein further. The 11.6K protein migrates as multiple diffuse bands having apparent Mws of about 14,000, 21,000, and 31,000 on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Immunoblotting as well as virus mutants with deletions in the 11.6K gene were used to show that the various gel bands represent forms of 11.6K. The 11.6K protein was synthesized in very low amounts during early stages of infection, from the scarce E3 mRNAs d and e which initiate from the E3 promoter. However, 11.6K was synthesized very abundantly at late stages of infection, approximately 400 times the rate at early stages, from new mRNAs termed d' and e'. Reverse transcriptase-polymerase chain reaction and RNA blot experiments indicated that mRNAs d' and e' had the same body (the coding portion) and the same middle exon (the y leader) as early E3 mRNAs d and e, but mRNAs d' and e' were spliced at their 5' termini to the major late tripartite leader which is found in all mRNAs in the major late transcription unit. mRNAs d' and e' and the 11.6K protein were the only E3 mRNAs and protein that were scarce early and were greatly amplified at late stages of infection. This suggests that specific cis- or trans-acting sequences may function to enhance the splicing of mRNAs d' and e' at late stages of infection and perhaps to suppress the splicing of mRNAs d and e at early stages of infection. We propose that the 11.6K gene be considered not only a member of region E3 but also a member of the major late transcription unit.

Expression of the adenovirus E1B 175R protein and its association with membranes of Escherichia coli

The E1B 175-amino-acid (175R) protein of adenovirus 2 is required for cellular transformation of primary cells and establishing cell morphology in lytically infected cells. To investigate the biochemical function of this protein, we constructed a bacterial expression vector (pKHB1-T) to produce the 175R protein in sufficient amounts for purification and biochemical analysis. On the basis of DNA sequencing, gel electrophoresis, and immunoblot analysis, the pKHB1-T-encoded 175R protein appears to be identical to that expressed transiently in mammalian or adenovirus-transformed cells. The bacterially produced viral protein was also found to be quite stable and without any modifications. Partial purification of the pKHB1-T-encoded protein revealed that the majority of its associates with the inner membrane of the bacterial cell. This, together with the possibility of the 175R protein containing an N-terminal amphipathic alpha-helix as a potential translocation signal, suggests that there may be a common mechanism of protein transport operating in both eucaryotic and procaryotic systems.

Phylogenetic relationships of linear, protein-primed replicating genomes

Relative phylogenetic distances were estimated for those linear plasmids for which sequencing data were available by comparing the amino-acid sequences of the putative DNA- and RNA-polymerases, and phylogenetic trees were calculated. The relationships obtained accord well with those indicated by other structural characteristics of these genetic elements. It is obvious that linear plasmids constitute a separate group of genetic traits when compared with those of the adenoviruses. However, an overall relationship to these viruses is evident. Among the linear plasmids at least two main groups can be recognized, namely the cytoplasmically and the mitochondrially localized elements.

Receptor sequence in the terminal protein of bacteriophage M2 that interacts with an RGD (Arg-Gly-Asp) sequence of the primer protein

At the initiation of protein-primed DNA replication of bacteriophages M2 and phi 29, the Arg-Gly-Asp (RGD) sequence of primer protein participates in the recognition of terminal protein (TP), where the initiation site for protein-primed DNA replication of template DNA is located. We compared the sequences of M2 and phi 29 TP with those of the members of the integrin superfamily and found the highly homologous sequences Lys-Lys-Ile-Pro-Pro-Asp-Asp (KKIPPDD) in M2 and phi 29 TP and Lys-Lys-Gly-Cys-Pro-Pro-Asp-Asp (KKGCPPDD) in the beta-subunit of fibronectin receptor protein. A synthetic 20mer peptide that contained the KKIPPDD sequence interfered with the inhibitory effect of the RGD peptide on both transfection and the protein-priming reaction in vitro. We propose that the sequence KKIPPDD of M2 TP is the receptor sequence for RGD.

The linear plasmid pMC3-2 from Morchella conica is structurally related to adenoviruses

pMC3-2, one of two linear plasmids localised in the mitochondria of the ascomycete Morchella conica, was completely sequenced. It is 6044 bp in size, contains terminal inverted repeats of 713 and 710 bp length and two open reading frames, ORF1 and ORF2, spanning 2706 bp and 918 bp, respectively. ORF1 probably encodes a viral B-type DNA-polymerase. Concerning ORF2, no homology to any other published protein- or DNA-sequence could be detected. According to the structure of DNA-polymerases, linear plasmids can be grouped into two classes reflecting their localisation either in the cytoplasm or within the mitochondria. In general, the structure of plasmid pMC3-2, as well as of other linear plasmids from filamentous fungi, indicates a close relationship of these genetic elements to adenoviruses.

The kalilo linear senescence-inducing plasmid of Neurospora is an invertron and encodes DNA and RNA polymerases

The nucleotide sequence of kalilo, a linear plasmid that induces senescence in Neurospora by integrating into the mitochondrial chromosome, reveals structural and genetic features germane to the unique properties of this element. Prominent features include: (1) very long perfect terminal inverted repeats of nucleotide sequences which are devoid of obvious genetic functions, but are unusually GC-rich near both ends of the linear DNA; (2) small imperfect palindromes that are situated at the termini of the plasmid and are cognate with the active sites for plasmid integration into mtDNA; (3) two large, non-overlapping open-reading frames, ORF-1 and ORF-2, which are located on opposite strands of the plasmid and potentially encode RNA and DNA polymerases, respectively, and (4) a set of imperfect palindromes that coincide with similar structures that have been detected at more or less identical locations in the nucleotide sequences of other linear mitochondrial plasmids. The nucleotide sequence does not reveal a distinct gene that codes for the protein that is attached to the ends of the plasmid. However, a 335-amino acid, cryptic, N-terminal domain of the putative DNA polymerase might function as the terminal protein. Although the plasmid has been co-purified with nuclei and mitochondria, its nucleotide composition and codon usage indicate that it is a mitochondrial genetic element.

Escherichia coli DNA polymerase II is homologous to alpha-like DNA polymerases

The Escherichia coli polB gene encodes DNA polymerase II and is regulated by the SOS system. We sequenced a 4081 nucleotide segment of the E. coli chromosome that contains the polB gene and its flanking regions. DNA polymerase II, as deduced from the DNA sequence, consists of 782 amino acids, has a molecular weight of 89,917, and is structurally homologous to alpha-like DNA polymerases, which include eukaryotic replicative DNA polymerases. Comparison of the sequences of the alpha-like DNA polymerases including E. coli DNA polymerase II showed that there were nine highly conserved regions, and we constructed an unrooted phylogenetic tree of the DNA polymerases based on the differences in these conserved regions. The DNA polymerases of herpes groups viruses and the DNA polymerases that use protein priming for the initiation of replication form two separate subfamilies that occupy opposite locations in the tree. Other DNA polymerases, including E. coli DNA polymerase II, human DNA polymerase alpha, and yeast DNA polymerase I, occupy the central regions between the two subfamilies and they are rather distantly related to each other. The transcription initiation site of polB was identified by analysis of in vivo transcripts, and the promoter was assigned upstream of the polB coding region. The recognition sequence of the LexA repressor (SOS box) was identified by a footprinting experiment. It overlaps the -35 sequence of the polB promoter.

Characterization of immunodominant epitopes of gag and pol gene-encoded proteins of human T-cell lymphotropic virus type I

A series of synthetic peptides derived from the corresponding regions of the gag, pol, and env proteins of human T-cell lymphotropic virus types I (HTLV-I) and II (HTLV-II) were used in an enzyme immunoassay to map the immunodominant epitopes of HTLV. Serum specimens from 79 of 87 (91%) HTLV-I-infected patients reacted with the synthetic peptide Gag-1a (amino acids [a.a.] 102 to 117) derived from the C terminus of the p19gag protein of HTLV-I. Minimal cross-reactivity (11%) was observed with serum specimens from HTLV-II-infected patients. Peptide Pol-3, encoded by the pol region of HTLV-I (a.a. 487 to 502), reacted with serum specimens from both HTLV-I- and HTLV-II-infected patients (94 and 86%, respectively). The antibody levels to Pol-3 were significantly higher (P less than 0.01) in patients with HTLV-I-associated myelopathy/tropical spastic paraparesis than in either adult T-cell leukemia patients or HTLV-I-positive asymptomatic carriers. None of the other peptides studied demonstrated significant binding to serum specimens obtained from HTLV-I- or HTLV-II-infected individuals. While Gag-1a did not react with serum specimens from normal controls, Pol-3 demonstrated some reaction with specimens from seronegative individuals (11.4%). The antibodies to Gag-1a and Pol-3 in serum specimens from HTLV-I-infected patients could be specifically inhibited by the corresponding synthetic peptides and by a crude HTLV-I antigen preparation, indicating that these peptides mimic native epitopes present in HTLV-I proteins that are recognized by serum antibodies from HTLV-I- and -II-infected individuals.

Genome organization of the linear plasmid, pSKL, isolated from Saccharomyces kluyveri

We have determined the complete nucleotide sequence of the linear DNA plasmid, pSKL, isolated from Saccharomyces kluyveri. Sequence analysis showed that pSKL has a high (A + T) content of 71.7%, and that there are 10 open reading frames (ORFs) larger than 250 nucleotides. All 10 ORFs were shown to be transcribed in S. kluyveri cells by S1 nuclease mapping analysis. The localization of ORFs, direction of transcription, and the predicted amino acid sequences of each ORF were quite similar to that of pGKL2, one of the killer plasmids found in Kluyveromyces lactis. The amino acid sequences of the largest two ORFs (ORF2 and ORF6) have homology with several DNA polymerases and RNA polymerases, respectively.

A complex family of class-II restriction endonucleases, DsaI-VI, in Dactylococcopsis salina

A series of class-II restriction endonucleases (ENases) was discovered in the halophilic, phototrophic, gas-vacuolated cyanobacterium Dactylococcopsis salina sp. nov. The six novel enzymes are characterized by the following recognition sequences and cut positions: 5'-C decreases CRYGG-3' (DsaI); 5'-GG decreases CC-3' (DsaII); 5'-R decreases GATCY-3' (DsaIII); 5'-G decreases GWCC-3' (DsaIV); 5'-decreases CCNGG-3' (DsaV); and 5'-GTMKAC-3' (DsaVI), where W = A or T, M = A or C, K = G or T, and N = A, G, C or T. In addition, traces of further possible activity were detected. DsaI has a novel sequence specificity and DsaV is an isoschizomer of ScrFI, but with a novel cut specificity. A purification procedure was established to separate all six ENases, resulting in their isolation free of contaminating nuclease activities. DsaI cleavage is influenced by N6-methyladenine residues [derived from the Escherichia coli-encoded DNA methyltransferase (MTase) M.Eco damI] within the overlapping sequence, 5'-CCRYMGGATC-3'; DsaV hydrolysis is inhibited by a C-5-methylcytosine residue in its recognition sequence (5'-CMCNGG-3'), generated in some DsaV sites by the E. coli-encoded MTase, M.Eco dcmI.

Linker mutation scanning of the genes encoding the adenovirus type 5 terminal protein precursor and DNA polymerase

The replication of adenovirus DNA requires, in addition to several host factors, three virus-encoded proteins: a DNA binding protein, the precursor of the terminal protein (pTP), and a DNA polymerase (Ad pol). Ad pol and pTP form a tight complex that is necessary for the initiation step in DNA replication. To perform mutation scanning of the adenovirus type 5 pTP and Ad pol a series of in-frame linker insertions of a 12-mer oligonucleotide d(CCCATCGATGGG) were introduced into cloned viral DNA fragments containing coding sequences of these proteins. The insertions are located at recognition sites for several blunt end-cutting restriction endonucleases. Forty different sites were mutagenized and the mutated genes were transferred to a plasmid that contains the left 42% of the adenovirus genome. They were rebuilt into the viral genome by means of in vivo recombination between plasmid DNA and digested adenovirus DNA-TP complex. The resulting viral genomes were tested for viability and rescued virus was analyzed for the presence of the inserted linker oligonucleotide. This procedure resulted in recovery of a number of viable virus mutants with insertions in the pTP or Ad pol genes, all of which are phenotypically silent. The other mutations did not allow virus production. The positions of these apparent lethal codon insertion mutations were useful to identify regions of functional importance in both proteins. It can be concluded that the precursor-specific region of pTP plays an important role in virus multiplication.

Identification and sequencing of the Choristoneura biennis entomopoxvirus DNA polymerase gene

A degenerate oligonucleotide probe corresponding to a highly conserved amino acid sequence in several DNA polymerases was used to locate the DNA polymerase gene in the Choristoneura biennis entomopoxvirus. Southern blot analysis of the entomopoxvirus genome using the degenerate oligonucleotide probe showed specific interaction between the probe and an eight kilobasepair EcoRI fragment from the entomopoxvirus genome. Sequencing this EcoRI fragment revealed an open reading frame 2892 nucleotides in length, capable of encoding a protein about 115 kilodaltons. Homology search of this open reading frame against other proteins indicated a high degree of homology in four distinct regions with DNA polymerases from other organisms. The highest degree of homology (24.9% at the amino acid level) was found between the vaccinia DNA polymerase gene and the entomopoxvirus open reading frame.

Early region 4 sequence and biological comparison of two isolates of mouse adenovirus type 1

The DNA sequence of 88-100 map units of mouse adenovirus type 1 (MAV-1) was determined. One translational open reading frame showed 48% sequence similarity to a human adenovirus type 2 early region 4 protein. Based on the protein similarity, genome location, and transcriptional polarity, we concluded that this region of MAV-1 corresponds to early region 4. A 241-bp sequence consisting of 10 imperfect direct repeats with sequence similarity to minisatellite DNA was found in this region. Two virus isolates with different passage histories were examined and were found to have a sequence polymorphism within this region. The two viruses were compared for growth in cell culture and mice and small quantitative differences were observed only in vivo.

Mutational analysis of single-stranded DNA templates active in the in vitro initiation assay for adenovirus DNA replication

Three distinct domains, A, the minimal origin, as well as B and C, the binding sites for the host nuclear factors, are required for efficient initiation of adenovirus (Ad) DNA replication at the termini. The initiation reaction was examined using partially purified nuclear extracts and various single-stranded oligomers as DNA templates. We observed that single-stranded oligomers containing Ad2 minimal origin (Ori) sequences (bp 1-18) from the I-strand of the Ad2 genome supported preterminal protein-dCMP complex formation in vitro. Using oligomers containing point mutations in the Ad2 minimal Ori sequence, six positions were identified as important to the function of the Ad2 minimal Ori sequence. Point mutations at position 7, 8, or 11 virtually abolished the ability of the oligomer to support the initiation reaction. Point mutations at position 4, 9, or 17 were found to decrease the ability of the oligomers to support the initiation reaction to 33, 67, and 58% of control, respectively. An oligomer complementary to the I-strand of the Ad2 minimal Ori was found to block initiation on minimal Ori template. A number of randomly selected nonspecific oligomers did not, in general, serve as templates for initiation with the exception of two oligomers, one of which was found to be about threefold more active than the control minimal Ori template. The biological significance of the in vitro initiation of Ad2 DNA replication on single-stranded DNA templates is discussed.

Physical mapping of two temperature-sensitive adenovirus mutants affected in the DNA polymerase and DNA binding protein

We have determined the exact nature of two thermosensitive (ts) adenovirus mutants, H5ts19 and H5ts149, which map to different genes in the E2 transcription unit. The H5ts19 mutation appears to stem from a single base-pair change of A-T to G-C at position 1840 (numbering as in ref. 1), corresponding to codon 154 of the gene coding for DBP. This results in a glutamine-to-arginine change in the amino-terminal domain of the protein. H5ts19 is defective in a late stage of infection, during virus assembly. This phenotype strongly differs from that described for the limited number of known DBP mutants, indicating that DBP is not only functional during DNA replication, but also plays a role in the late phase of the infection cycle. The defect of the (N group) mutant H5ts149 affects the initiation of viral DNA replication. Marker rescue experiments followed by nucleotide sequence analysis of H5ts149 DNA revealed a single point mutation in the gene coding for the Ad pol. A transition of C-G to A-T at position 7563 (numbering as in ref. 2) changes amino acid residue 411 of Ad pol, a leucine residue, to phenylalanine. This mutation is located in a region conserved among various DNA polymerases, which suggests an important role of this domain in DNA replication.

Inhibition of in vitro transcription by specific double-stranded oligodeoxyribonucleotides

A potential new therapeutic approach to control gene expression is the use of double-stranded (ds) oligodeoxyribonucleotides (oligos) to compete for the binding of nuclear factors to specific promoter and enhancer elements. As a model, we have tested the effect of oligo length, sequence and number of nuclear factor binding sites on in vitro transcription of adenovirus (Ad)E1b. Short ds oligos containing an SP1-binding sequence (sp1) inhibited transcription of E1b by more than 90%. Oligos containing multiple sp1 sequences were more effective inhibitors than would be expected for a comparable number of unlinked sp1 sites. A ds oligo with phosphorothioate (PS) linkages inhibited transcription at one-tenth the concentration needed for its normal homologue. An oligo with sp1 and a consensus TATA site was no more effective than one with sp1 alone. The stability of the PS-linked oligos will allow testing of this approach in vivo if they are adequately incorporated into whole cells.

Primary structure of bacteriophage M2 DNA polymerase: conserved segments within protein-priming DNA polymerases and DNA polymerase I of Escherichia coli

Bacteriophage M2 encodes its own DNA polymerase which catalyses the formation of a primer protein-5'dAMP initiation complex for DNA replication. To understand the relation of structure to function of this 'protein-priming DNA polymerase', we have determined the nucleotide sequence of the M2 DNA polymerase-encoding gene (gene G). The deduced 572-amino acid sequence of M2 DNA polymerase shows 82.3% overall homology to that of phi 29 DNA polymerase. A homology search with the mutation data matrix revealed that six segments (A-F, from the N terminus) of M2 and phi 29 DNA polymerases are homologous with the sequence of Escherichia coli DNA polymerase I (PolI). Segments D and F coincide with the conserved segments of many other DNA polymerases. Therefore, M2 and phi 29 DNA polymerases have structural features, at least in the conserved segments, similar to those of PolI and other DNA polymerases. Based on the homology with PolI and the location of the mutations for aphidicolin resistance and nucleoside analog resistance of M2, phi 29 and herpes simplex virus type-1 DNA polymerases, we propose that segments A-D of the M2 and phi 29 DNA polymerases constitute a structure which forms the cleft for holding template DNA and that segment D is a region for interacting with dNTP.

An inhibitory effect of RGD peptide on protein-priming reaction of bacteriophages phi 29 and M2

The amino acid sequence, arginine-glycine-aspartic acid (RGD), found in some cell adhesive proteins, is a recognition signal for the receptor protein. It is interesting that we have found the RGD sequence in terminal protein (TP) of bacteriophages phi 29 and M2 near an amino acid, the serine residue at 232, covalently linked to the terminal nucleotide of their DNAs. At the initiation of protein-primed DNA replication, TP is essential for the recognition of replication machinery containing DNA polymerase and primer protein (PP; PP becomes TP upon linking the first nucleotide, and hence the primary structure of TP is the same as that of PP). Synthetic peptide RGD specifically inhibited transfection of phi 29 and M2. The target of the RGD peptide is shown to be TP by marker rescue experiments, suggesting that a receptor for the RGD sequence exists in TP. Furthermore, the peptide inhibited the in vitro protein-priming reaction of DNA replication. We propose that the RGD sequence of PP and a putative receptor on TP is utilized for the molecular recognition initiating DNA replication.

Sequence characterization of the adenovirus 40 fiber gene

The fiber gene of human adenovirus type 40 has been characterized. The 6.1-kbp EcoRI fragment C of the Ad40 genome, from map units 74 through 92, was cloned and the right-most 2.8 kbp from 84 map units was sequenced. By analogy with Ad2, this region would be expected to contain the gene specifying the Ad40 fiber polypeptide. Sequencing revealed an open reading frame of 1641 bases on the r-strand, the first 53 bases of which had marked homology with the corresponding L5 (fiber) regions of Ad2 (77.2%), Ad5 (75.0%), and Ad3 (64.3%). In addition, base positions 1114 to 1146 of this open reading frame had 85% homology with base positions 1198 to 1230 of the Ad2 fiber gene. The predicted polypeptide sequence of 547 amino acids showed marked homology with the Ad2, Ad5, and Ad3 fiber polypeptides in two regions, in the first 55 amino acids from the N-terminus and from amino acids 372 through 382. Analysis of hydrophobic amino acid positions revealed a repeating pattern of approximately 15 residues between positions 42 and 374, with 21 repeats. The sequence of the Ad40 polypeptide thus fits the model of Green et al. [1983), EMBO J. 2, 1357-1365) for the structure of the adenovirus fiber, but is 35 amino acids shorter than the Ad2 fiber polypeptide, with one less 15-residue repeat in the shaft region. According to this model, the regions of highest homology between the Ad40 fiber polypeptide and those of Ad2, Ad5, and Ad3 correspond to the tail of the shaft and the base of the knob. The results of this analysis are in agreement with previously published EM data on the fiber length of subgroup F adenoviruses.

Genome organization of mouse adenovirus type 1 early region 1: a novel transcription map

Mouse adenovirus type 1 (MAV-1) genomic DNA from 8.9 to 13.7 map units was sequenced and the early region 1 (E1) transcription map was determined by S1 nuclease, primer extension, and Northern analyses, and cDNA sequencing. The E1 transcription map of MAV-1 had marked dissimilarities from the conserved transcription maps of primate adenovirus E1s. One major E1A and two E1B mRNAs were identified in overlapping transcription units. The single E1A mRNA was composed of three exons; the last exon was coincident with the last exon of the E1B mRNAs. While human adenovirus type 2 (Ad2) utilizes alternate splice donors for the first E1A mRNA exon, MAV-1 does not. Thus, no protein is predicted that would correspond to the Ad2 243 amino acid protein, although MAV-1 can encode a protein similar to the Ad2 289 amino acid protein (A. O. Ball, M. E. Williams, and K. R. Spindler, 1988, J. Virol. 62, 3947-3957). Two spliced E1B mRNAs differed from each other in an intron near the 5' end of the smaller E1B mRNA. This smaller mRNA could encode only the 55K E1B protein, while the larger mRNA could encode both the 21K and 55K E1B proteins.

Nuclear transport of adenovirus DNA polymerase is facilitated by interaction with preterminal protein

The mRNAs for the 80 kd adenovirus preterminal protein (pTP) and the 140 kd DNA polymerase (AdPol) contain several exons spliced to the main open reading frames (m-ORFs) located in the early transcription unit E2B. These proteins were transiently expressed in monkey kidney cells (CV1) utilizing the first ATG (pTP1 and AdPol1) or the ATG of a linker inserted at the beginning of the m-ORFs (pTP2 and AdPol2). Only pTP2 and AdPol2 were functionally active in an in vitro replication initiation assay. Both pTP1 and pTP2 were transported to the nucleus. The sequence RLPV(R)6VP, which is present in both pTPs, is identified as their nuclear localization signal. In contrast, AdPol1 was cytoplasmically localized, whereas AdPol2 was distributed in both compartments, suggesting that the nuclear localization signal for AdPol is within the first 139 amino acids. Interestingly, when AdPol1 and pTP1 or AdPol2 and pTP2 were coexpressed in the transfected cells, the nuclear distribution of AdPol1 or AdPol2 was significantly increased. We demonstrate that the nuclear transport of AdPol is facilitated, irrespective of the presence of its nuclear localization signal, by interaction with pTP.