1
|
Nuclear matrix associated RNAs in posterior silk glands show developmental dynamics in Bombyx mori in 5th instar larvae. BMC Res Notes 2022; 15:68. [PMID: 35183251 PMCID: PMC8858543 DOI: 10.1186/s13104-022-05951-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 02/03/2022] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVES The nuclear matrix maintains and regulates chromatin structure. RNA is an integral component of the nuclear matrix and is essential to its structural maintenance. Bombyx mori is a major economic contributor in the sericulture industry and produces fibroin-the most important silk protein in its posterior silk glands during 5th instar larval stage. The present study investigates the composition of nuclear matrix RNA prepared from the posterior silk glands of Bombyx mori during fifth instar larval stage where maximum silk production occurs. The datasets from which the analysis is carried out are part of data note titled "Nuclear matrix associated RNA datasets of posterior silk glands of Bombyx mori during 5th instar larval development". RESULTS The results showed significant enrichment of nuclear matrix RNA from day 1, to day 5 and day 7. Nuclear RNA showed increased abundance from day 1 to day 5 and day 7. Nuclear matrix RNA exhibited repetitive RNA sequences, of which UGUCC and GCUGGU were the most abundant. Genes involved in metabolic pathways showed significant enrichment correlating with silk production. These results emphasize the role of dynamic, repetitive DNA transcripts in chromatin architecture and further reveal the close association between the nuclear matrix and gene expression.
Collapse
|
2
|
Adenovirus Terminal Protein Contains a Bipartite Nuclear Localisation Signal Essential for Its Import into the Nucleus. Int J Mol Sci 2021; 22:ijms22073310. [PMID: 33804953 PMCID: PMC8036708 DOI: 10.3390/ijms22073310] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/16/2021] [Accepted: 03/16/2021] [Indexed: 01/22/2023] Open
Abstract
Adenoviruses contain dsDNA covalently linked to a terminal protein (TP) at the 5′end. TP plays a pivotal role in replication and long-lasting infectivity. TP has been reported to contain a nuclear localisation signal (NLS) that facilitates its import into the nucleus. We studied the potential NLS motifs within TP using molecular and cellular biology techniques to identify the motifs needed for optimum nuclear import. We used confocal imaging microscopy to monitor the localisation and nuclear association of GFP fusion proteins. We identified two nuclear localisation signals, PV(R)6VP and MRRRR, that are essential for fully efficient TP nuclear entry in transfected cells. To study TP–host interactions further, we expressed TP in Escherichia coli (E. coli). Nuclear uptake of purified protein was determined in digitonin-permeabilised cells. The data confirmed that nuclear uptake of TP requires active transport using energy and shuttling factors. This mechanism of nuclear transport was confirmed when expressed TP was microinjected into living cells. Finally, we uncovered the nature of TP binding to host nuclear shuttling proteins, revealing selective binding to Imp β, and a complex of Imp α/β but not Imp α alone. TP translocation to the nucleus could be inhibited using selective inhibitors of importins. Our results show that the bipartite NLS is required for fully efficient TP entry into the nucleus and suggest that this translocation can be carried out by binding to Imp β or Imp α/β. This work forms the biochemical foundation for future work determining the involvement of TP in nuclear delivery of adenovirus DNA.
Collapse
|
3
|
Hidalgo P, Gonzalez RA. Formation of adenovirus DNA replication compartments. FEBS Lett 2019; 593:3518-3530. [PMID: 31710378 DOI: 10.1002/1873-3468.13672] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/23/2019] [Accepted: 11/04/2019] [Indexed: 12/11/2022]
Abstract
Adenoviruses induce an extensive reorganization of the host cell nucleus during replication. Such a process results in the assembly of viral and cellular macromolecules into nuclear structures called adenovirus replication compartments (AdRCs), which function as platforms for viral DNA replication and gene expression. AdRCs co-opt host proteins and cellular pathways that restrict viral replication, suggesting that the mechanisms that control AdRC formation and function are essential for viral replication and lay at the basis of virus-host interactions. Here, we review the hallmarks of AdRCs and recent progress in our understanding of the formation, composition, and function of AdRCs. Furthermore, we discuss how AdRCs facilitate the interplay between viral and cellular machineries and hijack cellular functions to promote viral genome replication and expression.
Collapse
Affiliation(s)
- Paloma Hidalgo
- Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Ramón A Gonzalez
- Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| |
Collapse
|
4
|
In Vivo Labelling of Adenovirus DNA Identifies Chromatin Anchoring and Biphasic Genome Replication. J Virol 2018; 92:JVI.00795-18. [PMID: 29997215 PMCID: PMC6146703 DOI: 10.1128/jvi.00795-18] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 07/03/2018] [Indexed: 12/15/2022] Open
Abstract
Viruses must deliver their genomes to host cells to ensure replication and propagation. Characterizing the fate of viral genomes is crucial to understand the viral life cycle and the fate of virus-derived vector tools. Here, we integrated the ANCHOR3 system, an in vivo DNA-tagging technology, into the adenoviral genome for real-time genome detection. ANCHOR3 tagging permitted the in vivo visualization of incoming genomes at the onset of infection and of replicated genomes at late phases of infection. Using this system, we show viral genome attachment to condensed host chromosomes during mitosis, identifying this mechanism as a mode of cell-to-cell transfer. We characterize the spatiotemporal organization of adenovirus replication and identify two kinetically distinct phases of viral genome replication. The ANCHOR3 system is the first technique that allows the continuous visualization of adenoviral genomes during the entire virus life cycle, opening the way for further in-depth study. Adenoviruses are DNA viruses with a lytic infection cycle. Following the fate of incoming as well as recently replicated genomes during infections is a challenge. In this study, we used the ANCHOR3 technology based on a bacterial partitioning system to establish a versatile in vivo imaging system for adenoviral genomes. The system allows the visualization of both individual incoming and newly replicated genomes in real time in living cells. We demonstrate that incoming adenoviral genomes are attached to condensed cellular chromatin during mitosis, facilitating the equal distribution of viral genomes in daughter cells after cell division. We show that the formation of replication centers occurs in conjunction with in vivo genome replication and determine replication rates. Visualization of adenoviral DNA revealed that adenoviruses exhibit two kinetically distinct phases of genome replication. Low-level replication occurred during early replication, while high-level replication was associated with late replication phases. The transition between these phases occurred concomitantly with morphological changes of viral replication compartments and with the appearance of virus-induced postreplication (ViPR) bodies, identified by the nucleolar protein Mybbp1A. Taken together, our real-time genome imaging system revealed hitherto uncharacterized features of adenoviral genomes in vivo. The system is able to identify novel spatiotemporal aspects of the adenovirus life cycle and is potentially transferable to other viral systems with a double-stranded DNA phase. IMPORTANCE Viruses must deliver their genomes to host cells to ensure replication and propagation. Characterizing the fate of viral genomes is crucial to understand the viral life cycle and the fate of virus-derived vector tools. Here, we integrated the ANCHOR3 system, an in vivo DNA-tagging technology, into the adenoviral genome for real-time genome detection. ANCHOR3 tagging permitted the in vivo visualization of incoming genomes at the onset of infection and of replicated genomes at late phases of infection. Using this system, we show viral genome attachment to condensed host chromosomes during mitosis, identifying this mechanism as a mode of cell-to-cell transfer. We characterize the spatiotemporal organization of adenovirus replication and identify two kinetically distinct phases of viral genome replication. The ANCHOR3 system is the first technique that allows the continuous visualization of adenoviral genomes during the entire virus life cycle, opening the way for further in-depth study.
Collapse
|
5
|
Salas M, Holguera I, Redrejo-Rodríguez M, de Vega M. DNA-Binding Proteins Essential for Protein-Primed Bacteriophage Φ29 DNA Replication. Front Mol Biosci 2016; 3:37. [PMID: 27547754 PMCID: PMC4974454 DOI: 10.3389/fmolb.2016.00037] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 07/20/2016] [Indexed: 01/25/2023] Open
Abstract
Bacillus subtilis phage Φ29 has a linear, double-stranded DNA 19 kb long with an inverted terminal repeat of 6 nucleotides and a protein covalently linked to the 5′ ends of the DNA. This protein, called terminal protein (TP), is the primer for the initiation of replication, a reaction catalyzed by the viral DNA polymerase at the two DNA ends. The DNA polymerase further elongates the nascent DNA chain in a processive manner, coupling strand displacement with elongation. The viral protein p5 is a single-stranded DNA binding protein (SSB) that binds to the single strands generated by strand displacement during the elongation process. Viral protein p6 is a double-stranded DNA binding protein (DBP) that preferentially binds to the origins of replication at the Φ29 DNA ends and is required for the initiation of replication. Both SSB and DBP are essential for Φ29 DNA amplification. This review focuses on the role of these phage DNA-binding proteins in Φ29 DNA replication both in vitro and in vivo, as well as on the implication of several B. subtilis DNA-binding proteins in different processes of the viral cycle. We will revise the enzymatic activities of the Φ29 DNA polymerase: TP-deoxynucleotidylation, processive DNA polymerization coupled to strand displacement, 3′–5′ exonucleolysis and pyrophosphorolysis. The resolution of the Φ29 DNA polymerase structure has shed light on the translocation mechanism and the determinants responsible for processivity and strand displacement. These two properties have made Φ29 DNA polymerase one of the main enzymes used in the current DNA amplification technologies. The determination of the structure of Φ29 TP revealed the existence of three domains: the priming domain, where the primer residue Ser232, as well as Phe230, involved in the determination of the initiating nucleotide, are located, the intermediate domain, involved in DNA polymerase binding, and the N-terminal domain, responsible for DNA binding and localization of the TP at the bacterial nucleoid, where viral DNA replication takes place. The biochemical properties of the Φ29 DBP and SSB and their function in the initiation and elongation of Φ29 DNA replication, respectively, will be described.
Collapse
Affiliation(s)
- Margarita Salas
- Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas), Universidad Autónoma de Madrid Madrid, Spain
| | - Isabel Holguera
- Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas), Universidad Autónoma de Madrid Madrid, Spain
| | - Modesto Redrejo-Rodríguez
- Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas), Universidad Autónoma de Madrid Madrid, Spain
| | - Miguel de Vega
- Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas), Universidad Autónoma de Madrid Madrid, Spain
| |
Collapse
|
6
|
Wu N, Zhang H, Deng F, Li R, Zhang W, Chen X, Wen S, Wang N, Zhang J, Yin L, Liao Z, Zhang Z, Zhang Q, Yan Z, Liu W, Wu D, Ye J, Deng Y, Yang K, Luu HH, Haydon RC, He TC. Overexpression of Ad5 precursor terminal protein accelerates recombinant adenovirus packaging and amplification in HEK-293 packaging cells. Gene Ther 2014; 21:629-37. [PMID: 24784448 DOI: 10.1038/gt.2014.40] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 03/13/2014] [Accepted: 03/21/2014] [Indexed: 12/29/2022]
Abstract
Recombinant adenoviruses are one of the most common vehicles for efficient in vitro and in vivo gene deliveries. Here, we investigate whether exogenous precursor terminal protein (pTP) expression in 293 cells improves the efficiency of adenovirus packaging and amplification. We used a piggyBac transposon-based vector and engineered a stable 293 line that expresses high level of Ad5 pTP, designated as 293pTP. Using the AdBMP6-GLuc that expresses green fluorescent protein (GFP), BMP6 and Gaussia luciferase, we found that the infectivity of AdBMP6-GLuc viral samples packaged in 293pTP cells was titrated up to 19.3 times higher than that packaged in parental 293 cells. AdBMP6-GLuc viral samples packaged in 293pTP cells exhibited significantly higher transduction efficiency in 143B and immortalized mouse embryonic fibroblast (iMEF) cells, as assessed by fluorescence-activated cell sorting analysis of GFP-positive cells, the luciferase activity assay and BMP6-induced osteogenic marker alkaline phosphatase activities in iMEFs. When adenovirus amplification efficiency was analyzed, we found that 293pTP cells infected with AdBMP6-GLuc yielded up to 12.6 times higher titer than that in parental 293 cells, especially at lower multiplicities of infection. These results strongly suggest that exogenous pTP expression may accelerate the packaging and amplification of recombinant adenoviruses. Thus, the engineered 293pTP cells should be a superior packaging line for efficient adenovirus production.
Collapse
Affiliation(s)
- N Wu
- 1] Stem Cell Biology and Therapy Laboratory, Ministry of Education Key Laboratory for Pediatrics, and Chongqing Stem Cell Therapy and Engineering Center, The Children's Hospital of Chongqing Medical University, Chongqing, China [2] Department of Orthopaedic Surgery, Molecular Oncology Laboratory, University of Chicago Medical Center, Chicago, IL, USA [3] Ministry of Education Key Laboratory of Diagnostic Medicine and School of Clinical Diagnostic Medicine, and the Affiliated Hospitals of Chongqing Medical University, Chongqing, China
| | - H Zhang
- 1] Department of Orthopaedic Surgery, Molecular Oncology Laboratory, University of Chicago Medical Center, Chicago, IL, USA [2] Chongqing Key Laboratory for Oral Diseases and Biomedical Sciences, and the Affiliated Hospital of Stomatology, Chongqing Medical University, Chongqing, China
| | - F Deng
- 1] Department of Orthopaedic Surgery, Molecular Oncology Laboratory, University of Chicago Medical Center, Chicago, IL, USA [2] Departments of Cell Biology and Oncology of the Affiliated Southwest Hospital, the Third Military Medical University, Chongqing, China
| | - R Li
- 1] Department of Orthopaedic Surgery, Molecular Oncology Laboratory, University of Chicago Medical Center, Chicago, IL, USA [2] Ministry of Education Key Laboratory of Diagnostic Medicine and School of Clinical Diagnostic Medicine, and the Affiliated Hospitals of Chongqing Medical University, Chongqing, China
| | - W Zhang
- 1] Department of Orthopaedic Surgery, Molecular Oncology Laboratory, University of Chicago Medical Center, Chicago, IL, USA [2] Department of Laboratory Medicine, the Affiliated Hospital of Bingzhou Medical University, Yantai, China
| | - X Chen
- 1] Department of Orthopaedic Surgery, Molecular Oncology Laboratory, University of Chicago Medical Center, Chicago, IL, USA [2] Ministry of Education Key Laboratory of Diagnostic Medicine and School of Clinical Diagnostic Medicine, and the Affiliated Hospitals of Chongqing Medical University, Chongqing, China
| | - S Wen
- 1] Stem Cell Biology and Therapy Laboratory, Ministry of Education Key Laboratory for Pediatrics, and Chongqing Stem Cell Therapy and Engineering Center, The Children's Hospital of Chongqing Medical University, Chongqing, China [2] Department of Orthopaedic Surgery, Molecular Oncology Laboratory, University of Chicago Medical Center, Chicago, IL, USA
| | - N Wang
- 1] Department of Orthopaedic Surgery, Molecular Oncology Laboratory, University of Chicago Medical Center, Chicago, IL, USA [2] Departments of Cell Biology and Oncology of the Affiliated Southwest Hospital, the Third Military Medical University, Chongqing, China
| | - J Zhang
- 1] Department of Orthopaedic Surgery, Molecular Oncology Laboratory, University of Chicago Medical Center, Chicago, IL, USA [2] Ministry of Education Key Laboratory of Diagnostic Medicine and School of Clinical Diagnostic Medicine, and the Affiliated Hospitals of Chongqing Medical University, Chongqing, China
| | - L Yin
- 1] Department of Orthopaedic Surgery, Molecular Oncology Laboratory, University of Chicago Medical Center, Chicago, IL, USA [2] Ministry of Education Key Laboratory of Diagnostic Medicine and School of Clinical Diagnostic Medicine, and the Affiliated Hospitals of Chongqing Medical University, Chongqing, China
| | - Z Liao
- 1] Department of Orthopaedic Surgery, Molecular Oncology Laboratory, University of Chicago Medical Center, Chicago, IL, USA [2] Department of Orthopaedic Surgery, the Affiliated Xiang-Ya Hospital of Central South University, Changsha, China
| | - Z Zhang
- 1] Department of Orthopaedic Surgery, Molecular Oncology Laboratory, University of Chicago Medical Center, Chicago, IL, USA [2] Department of Surgery, the Affiliated Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Q Zhang
- 1] Stem Cell Biology and Therapy Laboratory, Ministry of Education Key Laboratory for Pediatrics, and Chongqing Stem Cell Therapy and Engineering Center, The Children's Hospital of Chongqing Medical University, Chongqing, China [2] Department of Orthopaedic Surgery, Molecular Oncology Laboratory, University of Chicago Medical Center, Chicago, IL, USA
| | - Z Yan
- 1] Department of Orthopaedic Surgery, Molecular Oncology Laboratory, University of Chicago Medical Center, Chicago, IL, USA [2] Ministry of Education Key Laboratory of Diagnostic Medicine and School of Clinical Diagnostic Medicine, and the Affiliated Hospitals of Chongqing Medical University, Chongqing, China
| | - W Liu
- 1] Stem Cell Biology and Therapy Laboratory, Ministry of Education Key Laboratory for Pediatrics, and Chongqing Stem Cell Therapy and Engineering Center, The Children's Hospital of Chongqing Medical University, Chongqing, China [2] Department of Orthopaedic Surgery, Molecular Oncology Laboratory, University of Chicago Medical Center, Chicago, IL, USA
| | - D Wu
- Department of Orthopaedic Surgery, Molecular Oncology Laboratory, University of Chicago Medical Center, Chicago, IL, USA
| | - J Ye
- 1] Department of Orthopaedic Surgery, Molecular Oncology Laboratory, University of Chicago Medical Center, Chicago, IL, USA [2] School of Bioengineering, Chongqing University, Chongqing, China
| | - Y Deng
- 1] Department of Orthopaedic Surgery, Molecular Oncology Laboratory, University of Chicago Medical Center, Chicago, IL, USA [2] Ministry of Education Key Laboratory of Diagnostic Medicine and School of Clinical Diagnostic Medicine, and the Affiliated Hospitals of Chongqing Medical University, Chongqing, China
| | - K Yang
- 1] Stem Cell Biology and Therapy Laboratory, Ministry of Education Key Laboratory for Pediatrics, and Chongqing Stem Cell Therapy and Engineering Center, The Children's Hospital of Chongqing Medical University, Chongqing, China [2] Department of Orthopaedic Surgery, Molecular Oncology Laboratory, University of Chicago Medical Center, Chicago, IL, USA
| | - H H Luu
- Department of Orthopaedic Surgery, Molecular Oncology Laboratory, University of Chicago Medical Center, Chicago, IL, USA
| | - R C Haydon
- Department of Orthopaedic Surgery, Molecular Oncology Laboratory, University of Chicago Medical Center, Chicago, IL, USA
| | - T-C He
- 1] Stem Cell Biology and Therapy Laboratory, Ministry of Education Key Laboratory for Pediatrics, and Chongqing Stem Cell Therapy and Engineering Center, The Children's Hospital of Chongqing Medical University, Chongqing, China [2] Department of Orthopaedic Surgery, Molecular Oncology Laboratory, University of Chicago Medical Center, Chicago, IL, USA [3] Ministry of Education Key Laboratory of Diagnostic Medicine and School of Clinical Diagnostic Medicine, and the Affiliated Hospitals of Chongqing Medical University, Chongqing, China
| |
Collapse
|
7
|
Zheng C, Baum BJ. Integration of the hybrid adenoretroviral vector AdLTR-luc involves both MoMLV elements flanking the transgene. Int J Med Sci 2014; 11:803-9. [PMID: 24936143 PMCID: PMC4057490 DOI: 10.7150/ijms.9084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 05/26/2014] [Indexed: 11/07/2022] Open
Abstract
Vector delivery is still a bottleneck for gene therapy. To overcome some disadvantages of adenoviral and retroviral vectors, we developed a hybrid vector. This hybrid vector, AdLTR-luc, was created by adding two elements from Moloney murine leukemia virus (MoMLV) flanking the luciferase cDNA into an E1/E3-deleted, replication deficient serotype 5 adenovirus vector (Zheng et al., Nature Biotechnol, 2000), and demonstrated that the MoMLV element upstream of the luciferase cDNA was broken during the integration event. The purpose of the current study was to determine if the MoMLV element downstream of the luciferase cDNA was also broken when integration occurred. We used the same A5 cell clones (#10 and 11) from the earlier the paper along with restriction endonuclease digestions, plus Southern hybridization, and PCR. Southern hybridization indicated that the luciferase cDNA was intact in the cloned cells. Results from Xho I and Sal I digestions showed that integration occurred in cloned cells. Southern hybridizations after Nco I digestion suggested that there was a break in both MoMLV elements, upstream and downstream of the luciferase cDNA. After DNA digestion with Not I, hybridization analyses indicated that the MoMLV upstream element was broken during integration. Digestion of genomic DNA with either Xba I/Kpn I, Bam HI/Sac I, or Bam HI/Nco I demonstrated that the MoMLV downstream element was also broken during integration. A PCR assay was unable to amplify the junctional region between the downstream MoMLV element and the adenoviral E2B gene, consistent with a break in that element. Although AdLTR-luc integration is atypical (Zheng et al., Nature Biotechnol, 2000), the present results suggest that both MoMLV elements have important roles in this event.
Collapse
Affiliation(s)
- Changyu Zheng
- Molecular Physiology and Therapeutics Branch, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892-1190, USA
| | - Bruce J Baum
- Molecular Physiology and Therapeutics Branch, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892-1190, USA
| |
Collapse
|
8
|
Holguera I, Redrejo-Rodríguez M, Salas M, Muñoz-Espín D. New insights in the ϕ29 terminal protein DNA-binding and host nucleoid localization functions. Mol Microbiol 2013; 91:232-41. [PMID: 24205926 DOI: 10.1111/mmi.12456] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/06/2013] [Indexed: 11/30/2022]
Abstract
Protein-primed DNA replication constitutes a strategy to initiate viral DNA synthesis in a variety of prokaryotic and eukaryotic organisms. Although the main function of viral terminal proteins (TPs) is to provide a free hydroxyl group to start initiation of DNA replication, there are compelling evidences that TPs can also play other biological roles. In the case of Bacillus subtilis bacteriophage ϕ29, the N-terminal domain of the TP organizes viral DNA replication at the bacterial nucleoid being essential for an efficient phage DNA replication, and it contains a nuclear localization signal (NLS) that is functional in eukaryotes. Here we provide information about the structural properties of the ϕ29 TP N-terminal domain, which possesses sequence-independent DNA-binding capacity, and dissect the amino acid residues important for its biological function. By mutating all the basic residues of the TP N-terminal domain we identify the amino acids responsible for its interaction with the B. subtilis genome, establishing a correlation between the capacity of DNA-binding and nucleoid localization of the protein. Significantly, these residues are important to recruit the DNA polymerase at the bacterial nucleoid and, subsequently, for an efficient phage DNA replication.
Collapse
Affiliation(s)
- Isabel Holguera
- Instituto de Biología Molecular 'Eladio Viñuela' (Consejo Superior de Investigaciones Científicas), Centro de Biología Molecular 'Severo Ochoa' (Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid), Universidad Autónoma, Cantoblanco, 28049, Madrid, Spain
| | | | | | | |
Collapse
|
9
|
Robert MA, Zeng Y, Raymond B, Desfossé L, Mairey E, Tremblay JP, Massie B, Gilbert R. Efficacy and site-specificity of adenoviral vector integration mediated by the phage φC31 integrase. Hum Gene Ther Methods 2013. [PMID: 23194172 DOI: 10.1089/hgtb.2012.122] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Adenoviral vectors deleted of all their viral genes (helper-dependent [HD]) are efficient gene-transfer vehicles. Because transgene expression is rapidly lost in actively dividing cells, we investigated the feasibility of using phage φC31 integrase (φC31-Int) to integrate an HD carrying an attB site and the puromycin resistance gene into human cells (HeLa) and murine myoblasts (C2C12) by co-infection with a second HD-expressing φC31-Int. Because the HD genome is linear, we also investigated whether its circularization, through expression of Cre using a third HD, affects integration. Efficacy and specificity were determined by scoring the number of puromycin-resistant colonies and by sequencing integration sites. Unexpectedly, circularization of HD was unnecessary and it even reduced the integration efficacy. The maximum integration efficacy achieved was 0.5% in HeLa cells and 0.1% in C2C12 myoblasts. Up to 76% of the integration events occurred at pseudo attP sites and previously characterized hotspots were found. A small (two- to three-fold) increase in the number of γ-H2AX positive foci, accompanied by no noticeable change in γ-H2AX expression, indicated the low genotoxicity of φC31-Int. In conclusion, integration of HD mediated by φC31-Int is an attractive alternative to engineer cells, because it permits site-specific integration of large DNA fragments with low genotoxicity.
Collapse
Affiliation(s)
- Marc-André Robert
- Biotechnology Research Institute, National Research Council Canada, Montréal, Canada, H4P 2R2
| | | | | | | | | | | | | | | |
Collapse
|
10
|
Choi EW, Seen DS, Song YB, Son HS, Jung NC, Huh WK, Hahn JS, Kim K, Jeong JY, Lee TG. AdHTS: a high-throughput system for generating recombinant adenoviruses. J Biotechnol 2012; 162:246-52. [PMID: 23063969 DOI: 10.1016/j.jbiotec.2012.10.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Revised: 09/18/2012] [Accepted: 10/02/2012] [Indexed: 10/27/2022]
Abstract
The need for efficient high-throughput gene delivery system for mammalian cells is rapidly increasing with the growing request for functional genomics studies and drug discoveries in various physiologically relevant systems. However, plasmid-based gene delivery has limitations in transfection efficiency and available cell types. Viral vectors have great advantages over plasmid-based vectors, but construction of recombinant viruses remains to be a big hurdle for high-throughput applications. Here we demonstrate a rapid and simple high-throughput system for constructing recombinant adenoviruses which have been used as efficient gene delivery tools in mammalian systems in vitro and in vivo. By combining Gateway-based site-specific recombination with Terminal protein-coupled adenovirus vector, the adenovirus high-throughput system (AdHTS) generates multiple recombinant adenoviruses in 96-well plates simultaneously without the need for additional cloning or recombination in bacteria or mammalian cells. The AdHTS allows rapid and robust cloning and expression of genes in mammalian cells by removing shuttle vector construction, bacterial transformation, or selection and by minimizing effort in plaque isolation. By shortening the time required to convert whole cDNA library into desired viral vector constructs, the AdHTS would greatly facilitate functional genomics and proteomics studies in various mammalian systems.
Collapse
Affiliation(s)
- Eun-Wook Choi
- R&D Center, BRN Science, Golden Helix, Seoul National University, Seoul 151-742, Republic of Korea
| | | | | | | | | | | | | | | | | | | |
Collapse
|
11
|
Reduced infectivity of adenovirus type 5 particles and degradation of entering viral genomes associated with incomplete processing of the preterminal protein. J Virol 2012; 86:13554-65. [PMID: 23035217 DOI: 10.1128/jvi.02337-12] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
To investigate further the contribution of the adenovirus type 5 (Ad5) E1B 55-kDa protein to genome replication, viral DNA accumulation was examined in primary human fibroblasts and epithelial cells infected with Ad5 or the E1B 55-kDa-null mutant Hr6. Unexpectedly, all cell types were observed to contain a significantly higher concentration of entering Hr6 than of Ad5 DNA, as did an infectious unit of Hr6. However, the great majority of the Hr6 genomes were degraded soon after entry. As this unusual phenotype cannot be ascribed to the Hr6 E1B frameshift mutation (J. S. Chahal and S. J. Flint, J. Virol. 86:3064-3072, 2012), the sequences of the Ad5 and Hr6 genomes were compared by using high-throughput sequencing. Seven previously unrecognized mutations were identified in the Hr6 genome, two of which result in substitutions in virion proteins, G315V in the preterminal protein (preTP) and A406V in fiber protein IV. Previous observations and the visualization by immunofluorescence of greater numbers of viral genomes entering the cytosol of Hr6-infected cells than of Ad5-infected cells indicated that the fiber mutation could not be responsible for the low-infectivity phenotype of Hr6. However, comparison of the forms of terminal protein present in purified virus particles indicated that the production of mature terminal protein from a processing intermediate is impaired in Hr6 particles. We therefore propose that complete processing of preTP within virus particles is necessary for the ability of viral genomes to become localized at appropriate sites and persist in infected cells.
Collapse
|
12
|
Ugai H, Dobbins GC, Wang M, Le LP, Matthews DA, Curiel DT. Adenoviral protein V promotes a process of viral assembly through nucleophosmin 1. Virology 2012; 432:283-95. [PMID: 22717133 DOI: 10.1016/j.virol.2012.05.028] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 05/08/2012] [Accepted: 05/24/2012] [Indexed: 12/19/2022]
Abstract
Adenoviral infection induces nucleoplasmic redistribution of a nucleolar nucleophosmin 1/NPM1/B23.1. NPM1 is preferentially localized in the nucleoli of normal cells, whereas it is also present at the nuclear matrix in cancer cells. However, the biological roles of NPM1 during infection are unknown. Here, by analyzing a pV-deletion mutant, Ad5-dV/TSB, we demonstrate that pV promotes the NPM1 translocation from the nucleoli to the nucleoplasm in normal cells, and the NPM1 translocation is correlated with adenoviral replication. Lack of pV causes a dramatic reduction of adenoviral replication in normal cells, but not cancer cells, and Ad5-dV/TSB was defective in viral assembly in normal cells. NPM1 knockdown inhibits adenoviral replication, suggesting an involvement of NPM1 in adenoviral biology. Further, we show that NPM1 interacts with empty adenovirus particles which are an intermediate during virion maturation by immunoelectron microscopy. Collectively, these data implicate that pV participates in a process of viral assembly through NPM1.
Collapse
Affiliation(s)
- Hideyo Ugai
- Division of Human Gene Therapy, Departments of Medicine, Obstetrics and Gynecology, Pathology, and Surgery, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | | | | | | | | | | |
Collapse
|
13
|
Zheng C, Cotrim AP, Nikolov N, Mineshiba F, Swaim W, Baum BJ. A novel hybrid adenoretroviral vector with more extensive E3 deletion extends transgene expression in submandibular glands. Hum Gene Ther Methods 2012; 23:169-81. [PMID: 22817829 PMCID: PMC4015066 DOI: 10.1089/hgtb.2011.175] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Accepted: 06/04/2012] [Indexed: 01/05/2023] Open
Abstract
Salivary glands are an attractive target for gene transfer. Salivary epithelial cells are considered to be highly differentiated and have low rates of cell division (~6 months), affording the opportunity to obtain relatively long-term transgene expression in the absence of genomic integration. Here, we report a novel modified hybrid adenoretroviral vector, which provides stable transgene expression in salivary epithelial cells in vivo for up to 6 months in the absence of genomic integration. This modified hybrid vector, Ad(ΔE1/3)LTR(2)EF1α-hEPO, encodes human erythropoietin (hEPO) and differs from a previously developed hybrid vector, AdLTR(2)EF1α-hEPO, by having more extensive E3 gene deletion. Following direct salivary gland gene transfer by retroductal cannulation, rats transduced with Ad(ΔE1/3)LTR(2)EF1α-hEPO had sustained, elevated serum hEPO levels and hematocrits for 6 months (length of experiment), as compared with ~2 months for animals administered the AdLTR(2)EF1α-hEPO vector. Immunohistochemistry demonstrated that this novel vector could transduce both acinar and ductal cells. Interestingly, the Ad(ΔE1/3)LTR(2)EF1α-hEPO vector evoked much weaker local (salivary gland) immune responses than seen after AdLTR(2)EF1α-hEPO vector delivery, which likely permits its significantly lengthened transgene expression in this tissue.
Collapse
Affiliation(s)
- Changyu Zheng
- Molecular Physiology and Therapeutics Branch, National Institute of Dental and Craniofacial Research, Bethesda, MD 20892, USA.
| | | | | | | | | | | |
Collapse
|
14
|
Viral terminal protein directs early organization of phage DNA replication at the bacterial nucleoid. Proc Natl Acad Sci U S A 2010; 107:16548-53. [PMID: 20823229 DOI: 10.1073/pnas.1010530107] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The mechanism leading to protein-primed DNA replication has been studied extensively in vitro. However, little is known about the in vivo organization of the proteins involved in this fundamental process. Here we show that the terminal proteins (TPs) of phages ϕ29 and PRD1, infecting the distantly related bacteria Bacillus subtilis and Escherichia coli, respectively, associate with the host bacterial nucleoid independently of other viral-encoded proteins. Analyses of phage ϕ29 revealed that the TP N-terminal domain (residues 1-73) possesses sequence-independent DNA-binding capacity and is responsible for its nucleoid association. Importantly, we show that in the absence of the TP N-terminal domain the efficiency of ϕ29 DNA replication is severely affected. Moreover, the TP recruits the phage DNA polymerase to the bacterial nucleoid, and both proteins later are redistributed to enlarged helix-like structures in an MreB cytoskeleton-dependent way. These data disclose a key function for the TP in vivo: organizing the early viral DNA replication machinery at the cell nucleoid.
Collapse
|
15
|
Sova P, Wang H, Bomsztyk K, Stamatoyannopoulos G, Lieber A. Role of chromatin structure in integration of helper-dependent adenoviral vectors containing the beta-globin locus control region. Hum Gene Ther 2008; 19:153-66. [PMID: 18177253 DOI: 10.1089/hum.2007.091] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We constructed helper-dependent, fiber-chimeric adenoviral vectors that efficiently transduce human hematopoietic stem cells. We found that vectors carrying a 23-kb fragment of the beta-globin locus control region (LCR) flanked by adeno-associated virus inverted terminal repeats (Ad.LCR) preferentially integrated into the chromosomal beta-globin LCR of human erythroid Mo7e cells. We hypothesized that this targeted integration involves beta-globin LCR-specific chromatin structures. Chromatin immunoprecipitation assays of the beta-globin LCR revealed active chromatin within, and immediately downstream of, DNase hypersensitivity region 2 (HS2) in erythroid Mo7e cells, but not in nonerythroid cells. Importantly, most of the Ad.LCR integrations in Mo7e cells were found within this area. We provide further data indicating tethering of incoming Ad.LCR genomes to the chromosomal LCR. We also provide data that suggest a role for active chromatin in AAV Rep78-mediated Ad.LCR integration. Our findings support a new strategy for achieving targeted integration through chromatin tethering of vector DNA.
Collapse
Affiliation(s)
- Pavel Sova
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | | | | | | | | |
Collapse
|
16
|
Extended transgene expression from a nonintegrating adenoviral vector containing retroviral elements. Mol Ther 2008; 16:1089-97. [PMID: 18388914 DOI: 10.1038/mt.2008.56] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
We studied the effects of specific retroviral elements in a first-generation serotype 5 adenoviral (Ad5) vector, AdLTR(2)EF1alpha-hEPO. This vector contains 858 base pair (bp) [251-bp envelope sequence plus 607-bp long-terminal repeat (LTR)] from Moloney murine leukemia virus (MoMLV), upstream of the human elongation factor-1alpha (EF1alpha) promoter and human erythropoietin (hEPO) cDNA, with the LTR sequence downstream of the polyadenylation signal. We compared expression of AdLTR(2)EF1alpha-hEPO with corresponding expressions of two conventional Ad5 vectors, AdEF1alpha-hEPO and AdCMV-hEPO, in vivo in submandibular glands in rats. Both the conventional vectors yielded low serum hEPO levels by day 7, and little change in hematocrits. In contrast, after receiving AdLTR(2)EF1alpha-hEPO, the rats showed elevated hEPO levels and hematocrits for 1-3 months. In vitro studies showed that the integration efficiencies of all the vectors were similar (approximately 10(-3)). Approximately 0.1% of the vector genomes were present 1 year after delivery in the case of each of the three vectors, primarily as intact linear double-strand DNA. The unique results seen with AdLTR(2)EF1alpha-hEPO are partly because of LTR enhancer activity. However, other cis-acting activity, which is not immunomodulatory but nevertheless influences promoter methylation, appears to be involved. A vector such as AdLTR(2)EF1alpha-hEPO may prove useful in clinical applications in which extended, but not "permanent," transgene expression is desirable.
Collapse
|
17
|
Spector DJ. Default assembly of early adenovirus chromatin. Virology 2007; 359:116-25. [PMID: 17034827 DOI: 10.1016/j.virol.2006.09.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2006] [Revised: 08/23/2006] [Accepted: 09/06/2006] [Indexed: 11/17/2022]
Abstract
In adenovirus particles, the viral nucleoprotein is organized into a highly compacted core structure. Upon delivery to the nucleus, the viral nucleoprotein is very likely to be remodeled to a form accessible to the transcription and replication machinery. Viral protein VII binds to intra-nuclear viral DNA, as do at least two cellular proteins, SET/TAF-Ibeta and pp32, components of a chromatin assembly complex that is implicated in template remodeling. We showed previously that viral DNA-protein complexes released from infecting particles were sensitive to shearing after cross-linking with formaldehyde, presumably after transport of the genome into the nucleus. We report here the application of equilibrium-density gradient centrifugation to the analysis of the fate of these complexes. Most of the incoming protein VII was recovered in a form that was not cross-linked to viral DNA. This release of protein VII, as well as the binding of SET/TAF-Ibeta and cellular transcription factors to the viral chromatin, did not require de novo viral gene expression. The distinct density profiles of viral DNA complexes containing protein VII, compared to those containing SET/TAF-Ibeta or transcription factors, were consistent with the notion that the assembly of early viral chromatin requires both the association of SET/TAF-1beta and the release of protein VII.
Collapse
Affiliation(s)
- David J Spector
- Department of Microbiology and Immunology, Pennsylvania State University College of Hershey, PA 17033, USA.
| |
Collapse
|
18
|
Hama S, Akita H, Iida S, Mizuguchi H, Harashima H. Quantitative and mechanism-based investigation of post-nuclear delivery events between adenovirus and lipoplex. Nucleic Acids Res 2007; 35:1533-43. [PMID: 17287293 PMCID: PMC1865055 DOI: 10.1093/nar/gkl1165] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Quantitative and mechanism-based information on differences in transfection efficiency between viral and non-viral vectors would be highly useful for improving the effectiveness of non-viral vectors. A previous quantitative comparison of intracellular trafficking between adenovirus and LipofectAMINE PLUS (LFN) revealed that the three orders of magnitude lower transfection efficiency of LFN was dominantly rate limited by the post-nuclear delivery process. In the present study, the contribution of transcription and translation processes to the overall differences in the transgene expression efficiency of nucleus-delivered DNA was independently evaluated by quantifying mRNA. As a result, transcription efficiency (Etranscript) of LFN, denoted as transgene expression divided by the amount of nuclear pDNA was about 16 times less than that for adenovirus. Furthermore, translation efficiency (Etranslate), denoted as transfection activity divided by mRNA expression was approximately 460 times less in LFN. Imaging of the decondensed form of DNA by in situ hybridization revealed that poor decondensation efficiency of LFN is involved in the inferior Etranscript. Moreover, the inferior translation efficiency (Etranslate) of LFN was mainly due to electrostatic interactions between LFN and mRNA. Collectively, an improvement in nuclear decondensation and the diminution of the interaction between vector and mRNA is essential for the development of new generations of non-viral vectors.
Collapse
Affiliation(s)
- Susumu Hama
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Hokkaido 060-0812, Japan, Laboratory of Gene Transfer and Regulation, National Institute of Biomedical Innovation, Osaka 567-0085, Japan and CREST, Japan Science and Technology Corporation (JST), Japan
| | - Hidetaka Akita
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Hokkaido 060-0812, Japan, Laboratory of Gene Transfer and Regulation, National Institute of Biomedical Innovation, Osaka 567-0085, Japan and CREST, Japan Science and Technology Corporation (JST), Japan
| | - Shinya Iida
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Hokkaido 060-0812, Japan, Laboratory of Gene Transfer and Regulation, National Institute of Biomedical Innovation, Osaka 567-0085, Japan and CREST, Japan Science and Technology Corporation (JST), Japan
| | - Hiroyuki Mizuguchi
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Hokkaido 060-0812, Japan, Laboratory of Gene Transfer and Regulation, National Institute of Biomedical Innovation, Osaka 567-0085, Japan and CREST, Japan Science and Technology Corporation (JST), Japan
| | - Hideyoshi Harashima
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Hokkaido 060-0812, Japan, Laboratory of Gene Transfer and Regulation, National Institute of Biomedical Innovation, Osaka 567-0085, Japan and CREST, Japan Science and Technology Corporation (JST), Japan
- *To whom correspondence should be addressed. +81 11 706 3919+81 11 706 4879
| |
Collapse
|
19
|
Nociari M, Ocheretina O, Schoggins JW, Falck-Pedersen E. Sensing infection by adenovirus: Toll-like receptor-independent viral DNA recognition signals activation of the interferon regulatory factor 3 master regulator. J Virol 2007; 81:4145-57. [PMID: 17251283 PMCID: PMC1866159 DOI: 10.1128/jvi.02685-06] [Citation(s) in RCA: 131] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Infection with adenovirus vectors (AdV) results in rapid activation of innate immunity, which serves the dual purpose of stimulating inflammatory antiviral host defenses and the adaptive immune system. Viral recognition by macrophages, dendritic cells, and other cell types requires an ability to sense the presence of a foreign molecular pattern by "pattern recognition receptors." The nature of the adenoviral sensor, the target ligand of the sensor, and the downstream antiviral signaling response triggered by virus infection have not been defined for this nonenveloped double-stranded DNA (dsDNA) virus. We have identified four critical links involved in AdV recognition by murine antigen-presenting cells (APC) and primary lung fibroblasts: (i) viral recognition occurs chiefly via a Toll-like receptor (TLR)-independent nucleic acid-sensing mechanism recognizing the viral dsDNA genome, (ii) the intact viral particle and capsid proteins are required for efficient intracellular delivery of the viral genome, (iii) delivery of the viral genome triggers interferon regulatory factor 3 (IRF3) phosphorylation, and (iv) IRF3 activation is the required dominant antiviral signaling pathway used by APC, whereas the "primary" involvement of NF-kappaB, mitogen-activated protein kinase, or Akt pathways is less prominent. In this study we provide the first direct evidence that infection by a dsDNA virus stimulates an IRF3-mediated interferon and proinflammatory response through a TLR-independent DNA-sensing mechanism.
Collapse
Affiliation(s)
- Marcelo Nociari
- Weill Medical College of Cornell University, Department of Microbiology and Immunology Box 62, 1300 York Ave. New York, NY 10021, USA
| | | | | | | |
Collapse
|
20
|
Carlisle RC, Briggs SS, Hale AB, Green NK, Fisher KD, Etrych T, Ulbrich K, Mautner V, Seymour LW. Use of synthetic vectors for neutralising antibody resistant delivery of replicating adenovirus DNA. Gene Ther 2006; 13:1579-86. [PMID: 16810196 DOI: 10.1038/sj.gt.3302814] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Use of synthetic vectors to deliver genomes of conditionally replicating lytic viruses combines the strengths of viral and non-viral approaches by enabling neutralising antibody resistant deployment of cancer virotherapy. Adenovirus is particularly suitable for this application since all proteins essential for replication can be expressed from the input DNA, although the presence of terminal protein (TP) covalently linked to the 5' termini of the input virus genomes both improves expression of transgenes encoded in the input DNA and also enhances replication. These roles of TP were distinguished in experiments where E1-deleted Ad(GFP)DNA bearing TP (Ad(GFP)DNA-TP), delivered with DOTAP, gave a two-fold greater frequency of transduction than Ad(GFP)DNA(without TP) in non-complementing A549 cells, while in 293 cells (which support replication of E1-deleted viruses) the presence of TP mediated a much greater differential transgene expression, commensurate with its ability to promote replication. Subsequent studies using AdDNA for virotherapy, therefore, included covalently linked TP. AdDNA-TP delivered to A549 cells using a synthetic polyplex vector was shown to be resistant to levels of neutralising antisera that completely ablated infection by wild-type adenovirus, enabling polyplex/Ad(wild type)DNA-TP to mediate a powerful cytopathic effect. Similarly in vivo, direct injection of a polyplex/Ad(wild type)DNA-TP into A549 tumours was neutralising antibody-resistant and enabled virus replication, whereas intact virus was neutralised by the antibody and failed to infect. The delivery of adenovirus genomes-TP using synthetic vectors should provide a strategy to bypass neutralising antibodies and facilitate clinical application of replicating adenovirus for cancer virotherapy.
Collapse
Affiliation(s)
- R C Carlisle
- Department of Clinical Pharmacology, Oxford University, Radcliffe Infirmary, Oxford, UK
| | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Bravo A, Serrano-Heras G, Salas M. Compartmentalization of prokaryotic DNA replication. FEMS Microbiol Rev 2005; 29:25-47. [PMID: 15652974 DOI: 10.1016/j.femsre.2004.06.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2004] [Revised: 06/15/2004] [Accepted: 06/17/2004] [Indexed: 11/22/2022] Open
Abstract
It becomes now apparent that prokaryotic DNA replication takes place at specific intracellular locations. Early studies indicated that chromosomal DNA replication, as well as plasmid and viral DNA replication, occurs in close association with the bacterial membrane. Moreover, over the last several years, it has been shown that some replication proteins and specific DNA sequences are localized to particular subcellular regions in bacteria, supporting the existence of replication compartments. Although the mechanisms underlying compartmentalization of prokaryotic DNA replication are largely unknown, the docking of replication factors to large organizing structures may be important for the assembly of active replication complexes. In this article, we review the current state of this subject in two bacterial species, Escherichia coli and Bacillus subtilis, focusing our attention in both chromosomal and extrachromosomal DNA replication. A comparison with eukaryotic systems is also presented.
Collapse
Affiliation(s)
- Alicia Bravo
- Instituto de Biología Molecular Eladio Viñuela (CSIC), Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma, Cantoblanco, 28049 Madrid, Spain.
| | | | | |
Collapse
|
22
|
Xing L, Tikoo SK. Promoter activity of left inverted terminal repeat and downstream sequences of porcine adenovirus type 3. Virus Res 2004; 109:51-8. [PMID: 15826912 DOI: 10.1016/j.virusres.2004.10.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2004] [Revised: 10/12/2004] [Accepted: 10/12/2004] [Indexed: 11/27/2022]
Abstract
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.
Collapse
Affiliation(s)
- Li Xing
- Vaccine and Infectious Disease Organization, University of Saskatchewan, 120 Veterinary Road, Saskatoon, Saskatchewan, Canada S7N 5E3
| | | |
Collapse
|
23
|
Mearini G, Nielsen PE, Fackelmayer FO. Localization and dynamics of small circular DNA in live mammalian nuclei. Nucleic Acids Res 2004; 32:2642-51. [PMID: 15141035 PMCID: PMC419472 DOI: 10.1093/nar/gkh587] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
While genomic DNA, packaged into chromatin, is known to be locally constrained but highly dynamic in the nuclei of living cells, little is known about the localization and dynamics of small circular DNA molecules that invade cells by virus infection, application of gene therapy vectors or experimental transfection. To address this point, we have created traceable model substrates by direct labeling of plasmid DNA with fluorescent peptide nucleic acids, and have investigated their fate after microinjection into living cells. Here, we report that foreign DNA rapidly undergoes interactions with intranuclear structural sites that strongly reduce its mobility and restrict the DNA to regions excluding nucleoli and nuclear bodies such as PML bodies. The labeled plasmids partially co-localize with SAF-A, a well characterized marker protein for the nuclear 'scaffold' or 'matrix', and are resistant towards extraction by detergent and, in part, elevated salt concentrations. We show that the localization and the low mobility of plasmids is independent of the plasmid sequence, and does not require the presence of either a scaffold attachment region (SAR) DNA element or a functional promoter.
Collapse
Affiliation(s)
- Giulia Mearini
- Department of Molecular Cell Biology, Heinrich-Pette-Institute, Martinistrasse 52, 20251 Hamburg, Germany
| | | | | |
Collapse
|
24
|
Russell IA, Royds JA, Braithwaite AW. Exploitation of Cell Cycle and Cell Death Controls by Adenoviruses: The Road to a Productive Infection. VIRUSES AND APOPTOSIS 2004; 36:207-43. [PMID: 15171614 DOI: 10.1007/978-3-540-74264-7_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- I Alasdair Russell
- Cell Transformation Group, Department of Pathology, Dunedin School of Medicine, University of Otago, Box 913, Dunedin, New Zealand
| | | | | |
Collapse
|
25
|
Serrano-Heras G, Salas M, Bravo A. In vivo assembly of phage phi 29 replication protein p1 into membrane-associated multimeric structures. J Biol Chem 2003; 278:40771-7. [PMID: 12904294 DOI: 10.1074/jbc.m306935200] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The mechanisms underlying compartmentalization of prokaryotic DNA replication are largely unknown. In the case of the Bacillus subtilis phage 29, the viral protein p1 enhances the rate of in vivo viral DNA replication. Previous work showed that p1 generates highly ordered structures in vitro. We now show that protein p1, like integral membrane proteins, has an amphiphilic nature. Furthermore, immunoelectron microscopy studies reveal that p1 has a peripheral subcellular location. By combining in vivo chemical cross-linking and cell fractionation techniques, we also demonstrate that p1 assembles in infected cells into multimeric structures that are associated with the bacterial membrane. These structures exist both during viral DNA replication and when 29 DNA synthesis is blocked due to the lack of viral replisome components. In addition, protein p1 encoded by plasmid generates membrane-associated multimers and supports DNA replication of a p1-lacking mutant phage, suggesting that the pre-assembled structures are functional. We propose that a phage structure assembled on the cell membrane provides a specific site for 29 DNA replication.
Collapse
Affiliation(s)
- Gemma Serrano-Heras
- Instituto de Biología Molecular Eladio Viñuela (CSIC), Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma, Cantoblanco, 28049 Madrid, Spain
| | | | | |
Collapse
|
26
|
Spector DJ, Johnson JS, Baird NL, Engel DA. Adenovirus type 5 DNA-protein complexes from formaldehyde cross-linked cells early after infection. Virology 2003; 312:204-12. [PMID: 12890633 DOI: 10.1016/s0042-6822(03)00194-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We report here the properties of viral DNA-protein complexes that purify with cellular chromatin following formaldehyde cross-linking of intact cells early after infection. The cross-linked viral DNA fractionated into shear-sensitive (S) and shear- resistant (R) components that were separable by sedimentation, which allowed independent characterization. The R component had the density and sedimentation properties expected for DNA-protein complexes and contained intact viral DNA. It accounted for about 50% of the viral DNA recovered at 1.5 h after infection but less than 20% by 4.5 h. The proportion of R component was independent of multiplicity of infection, even at less than one particle per cell. Viral hexon and protein VII, but not protein VI, were detected in the fractions containing the R component. These properties are consistent with those of partially uncoated virions associated with the nuclear envelope. A substantial proportion of the S component viral DNA had the same density as cellular chromatin. Protein VII was the most abundant viral protein present in gradient fractions that contained the S component. Complexes containing USF transcription factor cross-linked to the adenovirus major late promoter were detected by viral chromatin immunoprecipitation of the fractions containing S component. The S component probably contained uncoated nuclear viral DNA that assembles into early viral transcription complexes.
Collapse
Affiliation(s)
- David J Spector
- Department of Microbiology and Immunology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.
| | | | | | | |
Collapse
|
27
|
Interaction of EBV latent origin of replication with the nuclear matrix: identification of S/MAR sequences and protein components. FEBS Lett 2003; 547:119-24. [PMID: 12860398 DOI: 10.1016/s0014-5793(03)00690-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
During latency, Epstein Barr virus (EBV) genome, as an episome, is attached to the nuclear matrix (NM) via the latent origin of replication ori P. Within this element, we have found that a region, 580 bp long, encompassing the replicator DS element, shows the strongest affinity for the NM. In addition, by cross-linking with cis-diamminedichloroplatinum, we have identified two NM proteins with an apparent molecular weight of 85 and 60 kDa that, with high affinity and specificity, bind ori P. These proteins are not induced by EBV infection, but their interaction with ori P is lost upon induction of EBV lytic cycle. These data strongly suggest that the binding of ori P to specific components of the NM is required for EBV latent replication.
Collapse
|
28
|
Abstract
Replication of the adenovirus genome is catalysed by adenovirus DNA polymerase in which the adenovirus preterminal protein acts as a protein primer. DNA polymerase and preterminal protein form a heterodimer which, in the presence of the cellular transcription factors NFI/CTFI and NFIII/Oct-1, binds to the origin of DNA replication. DNA replication is initiated by DNA polymerase mediated transfer of dCMP onto preterminal protein. Further DNA synthesis is catalysed by DNA polymerase in a strand displacement mechanism which also requires adenovirus DNA binding protein. Here, we discuss the role of individual proteins in this process as revealed by biochemical analysis, mutagenesis and molecular modelling.
Collapse
Affiliation(s)
- H Liu
- Centre for Biomolecular Science, Biomolecular Science Building, The University of St. Andrews, North Haugh, St. Andrews, KY16 9ST, UK
| | | | | |
Collapse
|
29
|
Hösel M, Webb D, Schröer J, Doerfler W. The abortive infection of Syrian hamster cells with human adenovirus type 12. Curr Top Microbiol Immunol 2003; 272:415-40. [PMID: 12747558 DOI: 10.1007/978-3-662-05597-7_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Human adenovirus type 12 (Ad12) induces undifferentiated tumors in newborn Syrian hamsters, and this tumor model has been investigated in detail in our laboratory. One of the characteristics of the Ad12-hamster cell system is a strictly abortive infection cycle. In this chapter, we summarize previous and more recent results of studies on the interaction of Ad12 with the nonpermissive BHK21 hamster cell line. The block of Ad12 replication lies before viral DNA replication and late gene transcription which cannot be detected with the most sensitive techniques. Ad12 adsorption, cellular uptake and transport of the viral DNA to the nucleus are less efficient in the nonpermissive hamster cells than in permissive human cells. However, most of the early functions of the Ad12 genome are expressed in BHK21 cells, though at a low level. In the downstream region, the first exon, of the major late promoter (MLP) of Ad12 DNA, a mitigator element of 33 nucleotide pairs in length has been identified which contributes to the inactivity of the MLP in hamster cells and its markedly decreased activity in human cells. The E1 functions of Ad2 or Ad5 are capable of partly complementing the Ad12 deficiencies in hamster cells in that Ad12 viral DNA replication and late gene transcription can proceed, e.g. in a BHK hamster cell line, BHK297-C131,which carries in an integrated form and constitutively expresses the E1 region of Ad5 DNA. Nevertheless, the late Ad12 mRNAs, which are synthesized in this system with the authentic nucleotide sequence, fail to be translated to structural viral proteins. Hence, infectious virions are not produced in the partly complementing system. Probably there is also a translational block for late Ad12 mRNAs in hamster cells. We have recently shown that the overexpression of the Ad12 preterminal protein (pTP) gene or of the E1A gene facilitates the synthesis of full-length, authentic Ad12 DNA in BHK21 cells infected with Ad12. Apparently the pTP has a hitherto unknown function in eliciting full cycles of Ad12 DNA replication even in nonpermissive BHK21 cells when sufficient levels of Ad12 pTP are produced. We pursue the possibility that the completely abortive infection cycle of Ad12 in hamster cells ensures the survival of Ad12-induced hamster tumor cells which all carry, integrated in their genomes, multiple copies of Ad12 DNA. In this way, the viral genomes are immortalized and expanded in a huge number of tumor cells.
Collapse
Affiliation(s)
- M Hösel
- Institut für Genetik, Universität zu Köln, 50931 Köln, Germany.
| | | | | | | |
Collapse
|
30
|
Erturk E, Ostapchuk P, Wells SI, Yang J, Gregg K, Nepveu A, Dudley JP, Hearing P. Binding of CCAAT displacement protein CDP to adenovirus packaging sequences. J Virol 2003; 77:6255-64. [PMID: 12743282 PMCID: PMC154998 DOI: 10.1128/jvi.77.11.6255-6264.2003] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Adenovirus (Ad) type 5 DNA packaging is initiated in a polar fashion from the left end of the genome. The packaging process is dependent upon the cis-acting packaging domain located between nucleotides 194 and 380. Seven A/T-rich repeats have been identified within this domain that direct packaging. A1, A2, A5, and A6 are the most important repeats functionally and share a bipartite sequence motif. Several lines of evidence suggest that there is a limiting trans-acting factor(s) that plays a role in packaging. Two cellular activities that bind to minimal packaging domains in vitro have been previously identified. These binding activities are P complex, an uncharacterized protein(s), and chicken ovalbumin upstream promoter transcription factor (COUP-TF). In this work, we report that a third cellular protein, octamer-1 protein (Oct-1), binds to minimal packaging domains. In vitro binding analyses and in vivo packaging assays were used to examine the relevance of these DNA binding activities to Ad DNA packaging. The results of these experiments reveal that COUP-TF and Oct-1 binding does not play a functional role in Ad packaging, whereas P-complex binding directly correlates with packaging function. We demonstrate that P complex contains the cellular protein CCAAT displacement protein (CDP) and that full-length CDP is found in purified virus particles. In addition to cellular factors, previous evidence indicates that viral factors play a role in the initiation of viral DNA packaging. We propose that CDP, in conjunction with one or more viral proteins, binds to the packaging sequences of Ad to initiate the encapsidation process.
Collapse
Affiliation(s)
- Ece Erturk
- Department of Molecular Genetics and Microbiology, School of Medicine, Stony Brook University, New York 11794, USA
| | | | | | | | | | | | | | | |
Collapse
|
31
|
Abstract
The design of drugs for treatment of virus infections and the exploitation of viruses as drugs for treatment of diseases could be made more successful by understanding the molecular mechanisms of virus-specific events. The process of assembly, and more specifically packaging of the genome into a capsid, is an obligatory step leading to future infections. To enhance our understanding of the molecular mechanism of packaging, it is necessary to characterize the viral components necessary for the event. In the case of adenovirus, sequences between nucleotides 200 and 400 at the left end of the genome are essential for packaging. This region contains a series of redundant bipartite sequences, termed A repeats, that function in packaging. Synthetic packaging sequences made of multimers of a single A repeat substitute for the authentic adenovirus packaging domain. A repeats are binding sites for the CCAAT displacement protein and the viral protein IVa2. Several lines of evidence implicate these proteins in the packaging process. It was not known, however, whether other cis-acting elements play a role in the packaging process as well. We utilized an in vivo approach to address the role of the inverted terminal repeats and the covalently linked terminal proteins in packaging of the adenovirus genome. Our results show that these elements are not necessary for efficient packaging of the viral genome. A significant implication of these results applicable to gene therapy vector design is that the linkage of the adenovirus packaging domain to heterologous DNA sequences should suffice for targeting to the viral capsid.
Collapse
Affiliation(s)
- Philomena Ostapchuk
- Department of Molecular Genetics and Microbiology, School of Medicine, Stony Brook University, New York 11794-5222, USA
| | | |
Collapse
|
32
|
Stein GS, Lian JB, Stein JL, van Wijnen AJ, Montecino M, Pratap J, Choi J, Zaidi SK, Javed A, Gutierrez S, Harrington K, Shen J, Young D. Intranuclear organization of RUNX transcriptional regulatory machinery in biological control of skeletogenesis and cancer. Blood Cells Mol Dis 2003; 30:170-6. [PMID: 12732180 DOI: 10.1016/s1079-9796(03)00029-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
RUNX (AML/CBFA/PEBP2) transcription factors serve as paradigms for obligatory relationships between nuclear structure and physiological control of phenotypic gene expression. The RUNX proteins contribute to tissue restricted transcription by sequence-specific binding to promoter elements of target genes and serving as scaffolds for the assembly of coregulatory complexes that mediate biochemical and architectural control of activity. We will present an overview of approaches we are pursuing to address: (1) the involvement of RUNX proteins in governing competency for protein/DNA and protein/protein interactions at promoter regulatory sequences; (2) the recruitment of RUNX factors to subnuclear sites where the machinery for expression or repression of target genes is organized; and (3) the trafficking and integration of regulatory signals that control RUNX-mediated transcription.
Collapse
Affiliation(s)
- Gary S Stein
- Department of Cell Biology and Cancer Center, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Stein GS, Lian JB, Stein JL, Wijnen AJV, Montecino M, Javed A, Pratap J, Choi J, Zaidi SK, Gutierrez S, Harrington K, Shen J, Young D. Intranuclear trafficking of transcription factors: Requirements for vitamin D-mediated biological control of gene expression. J Cell Biochem 2003; 88:340-55. [PMID: 12520536 DOI: 10.1002/jcb.10364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The architecturally associated subnuclear organization of nucleic acids and cognate regulatory factors suggest functional interrelationships between nuclear structure and gene expression. Mechanisms that contribute to the spatial distribution of transcription factors within the three-dimensional context of nuclear architecture control the sorting of regulatory information as well as the assembly and activities of sites within the nucleus that support gene expression. Vitamin D control of gene expression serves as a paradigm for experimentally addressing mechanisms that govern the intranuclear targeting of regulatory factors to nuclear domains where transcription of developmental and tissue-specific genes occur. We will present an overview of molecular, cellular, genetic, and biochemical approaches that provide insight into the trafficking of regulatory factors that mediate vitamin D control of gene expression to transcriptionally active subnuclear sites. Examples will be presented that suggest modifications in the intranuclear targeting of transcription factors abrogate competency for vitamin D control of skeletal gene expression during development and fidelity of gene expression in tumor cells.
Collapse
Affiliation(s)
- Gary S Stein
- Department of Cell Biology, University of Massachusetts Medical School, 55 Lake Ave. North, Worcester, Massachusetts 01655, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Yamamoto M, Davydova J, Takayama K, Alemany R, Curiel DT. Transcription initiation activity of adenovirus left-end sequence in adenovirus vectors with e1 deleted. J Virol 2003; 77:1633-7. [PMID: 12502881 PMCID: PMC140768 DOI: 10.1128/jvi.77.2.1633-1637.2003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We analyzed the transcription initiation activity of the left-end sequence (first 342 bp) of the adenovirus genome in the context of an adenovirus vector with E1 deleted in in vitro and in vivo gene transfer models. While nucleotide sequences 1 to 190 and 1 to 342 showed strong activity in three out of three lung cancer cell lines, nucleotide sequence 1 to 103 showed limited activity in H358, cells which show characteristics of type 2 alveolar cells. In vivo, the transcription initiation activities of nucleotide sequence 1 to 103 in the liver and the lung were minimal, while nucleotide sequences 1 to 190 and 1 to 342 showed strong activity comparable to that of the cytomegalovirus promoter. Further understanding of the transcription initiation activity of the left-end sequence of the adenovirus genome should lead to optimization of adenovirus vectors.
Collapse
Affiliation(s)
- Masato Yamamoto
- Division of Human Gene Therapy, Department of Medicine, and the Gene Therapy Center, University of Alabama at Birmingham, 35294-2172, USA.
| | | | | | | | | |
Collapse
|
35
|
Abstract
Adenoviruses (Ads) are endemic in the human population and the well-studied group C Ads typically cause an acute infection in the respiratory epithelium. A growing body of evidence suggests that these viruses also establish a persistent infection. The Ad genome encodes several proteins that counteract the host anti-viral mechanisms, which function to limit viral infections. This review describes the adenovirus immuno-regulatory proteins and how they function to block apoptosis of infected cells. In addition to facilitating the successful completion of the viral replication cycle and spread of progeny virus, these functions may help maintain the virus in a persistent state.
Collapse
Affiliation(s)
- Adrienne L McNees
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | | |
Collapse
|
36
|
Affiliation(s)
- E Sadowy
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | | | | |
Collapse
|
37
|
Hösel M, Schröer J, Webb D, Jaroshevskaja E, Doerfler W. Cellular and early viral factors in the interaction of adenovirus type 12 with hamster cells: the abortive response. Virus Res 2001; 81:1-16. [PMID: 11682120 DOI: 10.1016/s0168-1702(01)00242-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The interaction of human adenovirus type 12 (Ad12) with Syrian hamster cells is remarkable in that there is a block of viral DNA replication and late gene transcription. We have screened several cellular factors known to play a role in adenovirus replication for their possible contributions to the interactions of Ad12 in the abortive BHK21 hamster cell system. (1) Western blot analyses of total protein extracts from Ad12- or Ad2-infected BHK21 cells do not reveal a significant difference in the accumulation of NFIII protein at different times after infection. Transcriptional levels of the NFIII gene in BHK21 cells are not altered upon the abortive infection with Ad12 or the productive infection with Ad2. The amount of NFIII protein is markedly reduced in nuclear extracts from BHK21 cells as compared with extracts from C131 hamster cells or human HeLa cells. A presumptive defect in NFIII transport to the nuclei rather than overall reduced NFIII gene transcription might explain the low abundance of NFIII in the nuclei of uninfected or Ad12-infected BHK21 cells. The productive infection of BHK21 or C131 cells with Ad2 leads to an increase in the NFIII concentration in the nuclei of infected cells, late after infection to a decrease; (2) NFI levels in the nuclei of mock-infected or Ad2- or Ad12-infected BHK21 cells are comparable with those in HeLa or in C131 cells. Thus, deficiencies in NFI may not play a role in the abortive system; (3) The absence of morphological alterations in PML protein domains from globular to track-like structures in the nuclei of Ad12-infected hamster cells correlates with the inability of Ad12 DNA to replicate in BHK21 cells. In BHK21 cells, the E4-ORF3 of Ad12 DNA is only weakly transcribed and only small amounts of the gene product are synthesized. In Ad12-infected C131 cells, which allow the replication of Ad12 DNA, the E4-ORF3 of Ad12 DNA is expressed, and track-like PML protein structures are observed. Transfection of the 12-E4-ORF3-EGFP construct leads to the expression of both the green fluorescent protein (GFP) and of the 12-E4-ORF3 gene product in 20-30% of the transfected BHK21 cells and elicits the morphological reorganization of the PML protein structures in the successfully transfected BHK21 cells. Similar results are obtained upon transfection of the 2-E4-ORF3 construct. Untransfected cells or cells transfected with the empty pIRES2-pEGFP vector carry the globular PML protein phenotype; (4) The expression of the 12-E4-ORF3-EGFP and/or of the NFIII-EGFP constructs upon transfection following Ad12-infection of BHK21 cells fails to promote Ad12 DNA replication. Hence, the formation of track-like PML protein structures in BHK21 cells by itself is not a sufficient precondition for Ad12 DNA replication in this abortive system. The data demonstrate that the expression of NFI, NFIII, and/or the conversion of the PML domains do not suffice to elicit Ad12 DNA replication in the abortive hamster cell system.
Collapse
Affiliation(s)
- M Hösel
- Institute for Genetics, University of Cologne, Weyertal 121, D-50931, Koeln, Germany
| | | | | | | | | |
Collapse
|
38
|
Hösel M, Webb D, Schröer J, Schmitz B, Doerfler W. Overexpression of the adenovirus type 12 (Ad12) pTP or E1A gene facilitates Ad12 DNA replication in nonpermissive BHK21 hamster cells. J Virol 2001; 75:10041-53. [PMID: 11581373 PMCID: PMC114579 DOI: 10.1128/jvi.75.21.10041-10053.2001] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In the adenovirus type 12 (Ad12) hamster cell system, abortive virus infection is one of the factors associated with the highly efficient oncogenesis in newborn Syrian hamsters. We have shown earlier that the replication and efficient late transcription of the Ad12 genome are blocked in Syrian hamster cells. Some of the early Ad12 functions are transcribed in these cells, although at a minimal rate. In the present study, we demonstrate that low expression levels of the E1A and precursor to terminal protein (pTP) genes of Ad12 seem to be responsible for the lack of Ad12 DNA replication in hamster cells. The Ad12 genes for the E1A functions or for pTP were tethered to the strong early promoter of the human cytomegalovirus and transfected into BHK21 cells. Subsequently, these cells were infected with Ad12 virions. In Ad12-infected BHK21 cells, which overexpressed pTP or E1A, full-length Ad12 DNA was de novo synthesized, as documented by metabolic labeling with [3H]thymidine and by zone velocity sedimentation in alkaline sucrose gradients followed by gel electrophoresis of the 3H-labeled DNA and Southern blot hybridization to 32P-labeled Ad12 DNA. Transfection of the cloned E1A region of Ad2 yielded similar results. The newly synthesized Ad12 DNA was covalently linked to pTP. The Ad12 DNA binding protein (DBP) and DNA polymerase (pol) genes were transcribed at levels similar to those in merely Ad12-infected cells. In pTP or E1A gene-transfected and Ad12-infected BHK21 cells, marginal levels of late Ad12 mRNA were detectable. Late Ad12 proteins were, however, not synthesized. Apparently, Ad12 DNA replication in hamster cells is rendered impossible due to insufficient threshold levels of the viral E1A and/or pTP.
Collapse
Affiliation(s)
- M Hösel
- Institut für Genetik, Universität zu Köln, D-50931 Cologne, Germany
| | | | | | | | | |
Collapse
|
39
|
Abstract
Because many viruses replicate in the nucleus of their host cells, they must have ways of transporting their genome and other components into and out of this compartment. For the incoming virus particle, nuclear entry is often one of the final steps in a complex transport and uncoating program. Typically, it involves recognition by importins (karyopherins), transport to the nucleus, and binding to nuclear pore complexes. Although all viruses take advantage of cellular signals and factors, viruses and viral capsids vary considerably in size, structure, and in how they interact with the nuclear import machinery. Influenza and adenoviruses undergo extensive disassembly prior to genome import; herpesviruses release their genome into the nucleus without immediate capsid disassembly. Polyoma viruses, parvoviruses, and lentivirus preintegration complexes are thought to enter in intact form, whereas the corresponding complexes of onco-retroviruses have to wait for mitosis because they cannot infect interphase nuclei.
Collapse
Affiliation(s)
- G R Whittaker
- Department of Microbiology and Immunology, Cornell University, Ithaca New York, USA.
| | | | | |
Collapse
|
40
|
Glotzer JB, Michou AI, Baker A, Saltik M, Cotten M. Microtubule-independent motility and nuclear targeting of adenoviruses with fluorescently labeled genomes. J Virol 2001; 75:2421-34. [PMID: 11160745 PMCID: PMC114825 DOI: 10.1128/jvi.75.5.2421-2434.2001] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
A novel adenovirus system for analyzing the adenovirus entry pathway has been developed that contains green fluorescent protein bound to the encapsidated viral DNA (AdLite viruses). AdLite viruses enter host cells and accumulate around the nuclei and near the microtubule organizing centers (MTOC). In live cells, individual AdLite particles were observed trafficking both toward and away from the nucleus. Depolymerization of microtubules during infection prevented AdLite accumulation around the MTOC; however, it did not abolish perinuclear localization of AdLite particles. Furthermore, depolymerization of microtubules did not affect AdLite motility and did not affect gene expression from wild-type adenovirus and adenovirus-derived vectors. These data revealed that adenovirus intracellular motility and nuclear targeting can be supported by a mechanism that does not rely on the microtubule network.
Collapse
Affiliation(s)
- J B Glotzer
- Institute for Molecular Pathology, 1030 Vienna, Austria
| | | | | | | | | |
Collapse
|
41
|
Lian JB, Stein JL, Stein GS, Montecino M, van Wijnen AJ, Javed A, Gutierrez S. Contributions of nuclear architecture and chromatin to vitamin D-dependent transcriptional control of the rat osteocalcin gene. Steroids 2001; 66:159-70. [PMID: 11179723 DOI: 10.1016/s0039-128x(00)00160-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The vitamin D response element in the bone tissue-specific osteocalcin gene has served as a prototype for understanding molecular mechanisms regulating physiologic responsiveness of vitamin D-dependent genes in bone cells. We briefly review factors which contribute to vitamin D transcriptional control. The organization of the vitamin D response element (VDRE), the multiple activities of the vitamin D receptor transactivation complex, and the necessity for protein-protein interactions between the VDR-RXR heterodimer activation complex and DNA binding proteins at other regulatory elements, including AP-1 sites and TATA boxes, provide for precise regulation of gene activity in concert with basal levels of transcription. We present evidence for molecular mechanisms regulating vitamin D-dependent mediated transcription of the osteocalcin gene that involve chromatin structure of the gene and nuclear architecture. Modifications in nucleosomal organization, DNase I hypersensitivity and localization of vitamin D receptor interacting proteins in subnuclear domains are regulatory components of vitamin D-dependent gene transcription. A model is proposed to account for the inability of vitamin D induction of the osteocalcin gene in the absence of ongoing basal transcription by competition of the YY1 nuclear matrix-associated transcription factor for TFIIB-VDR interactions. Activation of the VDR-RXR complex at the OC VDRE occurs through modifications in chromatin mediated in part by interaction of OC gene regulatory sequences with the nuclear matrix-associated Cbfa1 (Runx2) transcription factor which is required for osteogenesis.
Collapse
Affiliation(s)
- J B Lian
- Department of Cell Biology, University of Massachusetts Medical School, Worcester 01655-1016, USA.
| | | | | | | | | | | | | |
Collapse
|
42
|
Palková Z, Spanielová H, Gottifredi V, Hollanderová D, Forstová J, Amati P. The polyomavirus major capsid protein VP1 interacts with the nuclear matrix regulatory protein YY1. FEBS Lett 2000; 467:359-64. [PMID: 10675569 DOI: 10.1016/s0014-5793(00)01170-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Polyomavirus reaches the nucleus in a still encapsidated form, and the viral genome is readily found in association with the nuclear matrix. This association is thought to be essential for viral replication. In order to identify the protein(s) involved in the virus-nuclear matrix interaction, we focused on the possible roles exerted by the multifunctional cellular nuclear matrix protein Yin Yang 1 (YY1) and by the viral major capsid protein VP1. In the present work we report on the in vivo association between YY1 and VP1. Using the yeast two-hybrid system we demonstrate that the VP1 and YY1 proteins physically interact through the D-E region of VP1 and the activation domain of YY1.
Collapse
Affiliation(s)
- Z Palková
- Instituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Biotecnologie Cellulari ed Ematologia, Sezione di Genetica Molecolare, Università di Roma La Sapienza, Viale Regina Elena 324, 00161, Rome, Italy
| | | | | | | | | | | |
Collapse
|
43
|
Zheng C, Baum BJ, Iadarola MJ, O'Connell BC. Genomic integration and gene expression by a modified adenoviral vector. Nat Biotechnol 2000; 18:176-80. [PMID: 10657124 DOI: 10.1038/72628] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A replication-deficient recombinant adenovirus encoding luciferase was constructed using 5' and 3' long terminal repeat (LTR) sequences of the Moloney murine leukemia virus. Gene expression was observed in cultured cells in vitro and in submandibular gland, cortex, and caudate nucleus for as long as three months in vivo. The vector integrated randomly into the genome of both dividing and nondividing cells as determined by fluorescence in situ hybridization (FISH) (10-15% of cells in vitro and 5% in rat spleen in vivo), gene walking, Southern hybridization, and polymerase chain reaction (PCR), in the absence of transcomplementing reverse transcriptase or integrase activity. The new vector combines the high titer and versatility of adenoviral vectors with the long-term gene expression and integration of retroviral vectors.
Collapse
Affiliation(s)
- C Zheng
- Gene Therapy and Therapeutics Branch, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892-1190, USA
| | | | | | | |
Collapse
|
44
|
Affiliation(s)
- G S Stein
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA.
| | | | | | | | | |
Collapse
|
45
|
Schaack J, Ho WY, Tolman S, Ullyat E, Guo X, Frank N, Freimuth PI, Roovers DJ, Sussenbach JS. Construction and preliminary characterization of a library of "lethal" preterminal protein mutant adenoviruses. J Virol 1999; 73:9599-603. [PMID: 10516069 PMCID: PMC112995 DOI: 10.1128/jvi.73.11.9599-9603.1999] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Adenoviruses containing lethal in-frame insertion mutant alleles of the preterminal protein (pTP) gene were constructed with cell lines that express pTP. Thirty in-frame insertion mutant alleles, including 26 alleles previously characterized as lethal and 4 newly constructed mutant alleles, were introduced into the viral chromosome in place of the wild-type pTP gene. The viruses were tested for ability to form plaques at 37 degrees C in HeLa-pTP cells and at 32 degrees C and 39.5 degrees C in HeLa cells. Two of the newly constructed viruses exhibited temperature sensitivity for plaque formation, one virus did not form plaques in the absence of complementation, seven additional mutants exhibited a greater than 10-fold reduction in plaque formation in the absence of complementation, and another eight mutants exhibited stronger phenotypes than did previously characterized in-frame insertion mutants in the plaque assay. These mutant viruses offer promise for analysis of pTP functions.
Collapse
Affiliation(s)
- J Schaack
- Department of Microbiology, University of Colorado Health Sciences Center, Denver, Colorado, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Parks RJ, Bramson JL, Wan Y, Addison CL, Graham FL. Effects of stuffer DNA on transgene expression from helper-dependent adenovirus vectors. J Virol 1999; 73:8027-34. [PMID: 10482551 PMCID: PMC112818 DOI: 10.1128/jvi.73.10.8027-8034.1999] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
We have analyzed transgene (lacZ) expression from a first-generation adenovirus (Ad) vector in comparison to helper-dependent (hd) Ads deleted for various portions of the viral coding sequences and generated by using the Cre/loxP helper-dependent system (R. J. Parks et al., Proc. Natl. Acad. Sci. USA 93:13565-13570, 1996). An hd vector deleted for approximately 70% of the Ad genome (AdRP1001) provided levels and durations of transgene expression similar to those of a control first generation Ad vector containing an identical expression cassette. Deletion of all Ad sequences from the hdAd and replacement with a approximately 22-kb fragment of lambda DNA resulted in a decrease in the level and duration of lacZ expression which could not be reversed by the inclusion of a matrix attachment region. However, substitution of the lambda stuffer in the fully deleted hdAd with sequences from the human hypoxanthine-guanine phosphoribosyltransferase gene resulted in significantly improved transgene expression. In vitro assays for cytotoxic T lymphocytes (CTL) directed against putative peptides encoded by the vector backbone showed that, although CTL were generated against the vector containing the lambda DNA, no such CTL were generated against the vector containing the hypoxanthine-guanine phosphoribosyltransferase (HPRT) sequences. Surprisingly, the rate of loss of the HPRT- and lambda-containing vectors from mouse liver was similar, despite the differences in expression kinetics, indicating that the lambda stuffer-directed CTL were inefficient at eliminating the transduced cells. Thus, the nature of the DNA backbone of hdAds can have important effects on the functioning of the vector. Since most fully deleted vectors require "stuffer" DNA as part of the vector backbone to maintain optimum vector size, these observations must be taken into account in the design of hdAd vectors.
Collapse
Affiliation(s)
- R J Parks
- Departments of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | | | | | | | | |
Collapse
|
47
|
de Jong RN, van der Vliet PC. Mechanism of DNA replication in eukaryotic cells: cellular host factors stimulating adenovirus DNA replication. Gene 1999; 236:1-12. [PMID: 10433960 DOI: 10.1016/s0378-1119(99)00249-8] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Replication of adenovirus (Ad) DNA depends on interactions between three viral and three cellular proteins. Human transcription factors NFI and Oct-1 recruit the Ad DNA polymerase to the origin of DNA replication as a complex with the Ad protein primer pTP. High affinity and specificity DNA binding to recognition sites in this origin by the transcription factors stimulate and stabilize pre-initiation complex formation to compensate for the low binding specificity of the pTP/pol complex. In this review, we discuss the properties of NFI and Oct-1 and the mechanism by which they enhance initiation of DNA replication. We propose a model that describes the dynamics of initiation and elongation as well as the assembly and disassembly of the pre-initiation complex.
Collapse
Affiliation(s)
- R N de Jong
- Laboratory for Physiological Chemistry and Centre for Biomedical Genetics, Utrecht University, Utrecht, The Netherlands
| | | |
Collapse
|
48
|
Nguyen T, Nery J, Joseph S, Rocha C, Carney G, Spindler K, Villarreal L. Mouse adenovirus (MAV-1) expression in primary human endothelial cells and generation of a full-length infectious plasmid. Gene Ther 1999; 6:1291-7. [PMID: 10455438 DOI: 10.1038/sj.gt.3300949] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Using RT-PCR, we show that mouse adenovirus type I (MAV-1) is capable of infecting and expressing in various cell types, specifically human endothelial cells. The capability of MAV-1 to infect and express in human endothelial cells makes it a potentially useful alternative to the use of human adenoviruses type 2/5 (Ad2/5) in virus-based gene therapy, although presently MAV-1 can only be produced at lower titers than Ad2/5. In this report, we present methods for the purification of MAV-1 DNA and use of this DNA along with a modified bacteria-based homologous recombination protocol to generate a full-length plasmid clone of MAV-1 DNA. Using various transfection procedures, we show that this plasmid MAV-1 DNA can generate plaques of MAV-1 virus, albeit at low efficiencies (about 0. 2 p.f.u./microg DNA). Furthermore, the construction of an MAV-1 plasmid along with its capability to express in human cells justifies the full development of MAV-1 into a system of gene therapy.
Collapse
Affiliation(s)
- T Nguyen
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
| | | | | | | | | | | | | |
Collapse
|
49
|
Stein GS, van Wijnen AJ, Stein JL, Lian JB, Pockwinse SH, McNeil S. Implications for interrelationships between nuclear architecture and control of gene expression under microgravity conditions. FASEB J 1999; 13 Suppl:S157-66. [PMID: 10352158 DOI: 10.1096/fasebj.13.9001.s157] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Components of nuclear architecture are functionally interrelated with control of gene expression. There is growing appreciation that multiple levels of nuclear organization integrate the regulatory cues that support activation and suppression of genes as well as the processing of gene transcripts. The linear representation of genes and promoter elements provide the potential for responsiveness to physiological regulatory signals. Parameters of chromatin structure and nucleosome organization support synergism between activities at independent regulatory sequences and render promoter elements accessible or refractory to transcription factors. Association of genes, transcription factors, and the machinery for transcript processing with the nuclear matrix facilitates fidelity of gene expression within the three-dimensional context of nuclear architecture. Mechanisms must be defined that couple nuclear morphology with enzymatic parameters of gene expression. The recent characterization of factors that mediate chromatin remodeling and identification of intranuclear targeting signals that direct transcription factors to subnuclear domains where gene expression occurs link genetic and structural components of transcriptional control. Nuclear reorganization and aberrant intranuclear trafficking of transcription factors for developmental and tissue-specific control occurs in tumor cells and in neurological disorders. Compromises in nuclear structure-function interrelationships can occur as a consequence of microgravity-mediated perturbations in cellular architecture.
Collapse
Affiliation(s)
- G S Stein
- Department of Cell Biology and Cancer Center, University of Massachusetts Medical Center, Worcester, Massachusetts, USA.
| | | | | | | | | | | |
Collapse
|
50
|
|