1
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Saritas Erdogan S, Yilmaz AE, Kumbasar A. PIN1 is a novel interaction partner and a negative upstream regulator of the transcription factor NFIB. FEBS Lett 2024. [PMID: 39245791 DOI: 10.1002/1873-3468.15010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Accepted: 08/01/2024] [Indexed: 09/10/2024]
Abstract
NFIB is a transcription factor of the Nuclear Factor One (NFI) family that is essential for embryonic development. Post-translational control of NFIB or its upstream regulators have not been well characterized. Here, we show that PIN1 binds NFIB in a phosphorylation-dependent manner, via its WW domain. PIN1 interacts with the well-conserved N-terminal domains of all NFIs. Moreover, PIN1 attenuates the transcriptional activity of NFIB; this attenuation requires substrate binding by PIN1 but not its isomerase activity. Paradoxically, we found stabilization of NFIB by PIN1. We propose that PIN1 represses NFIB function not by regulating its abundance but by inducing a conformational change. These results identify NFIB as a novel PIN1 target and posit a role for PIN1 in post-translational regulation of NFIB and other NFIs.
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Affiliation(s)
| | - Ahmet Erdal Yilmaz
- Department of Molecular Biology and Genetics, Istanbul Technical University, Turkey
| | - Asli Kumbasar
- Department of Molecular Biology and Genetics, Istanbul Technical University, Turkey
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2
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Zhao S, Guan W, Ma K, Yan Y, Ou J, Zhang J, Yu Z, Wu J, Zhang Q. Development and Application of a Fast Method to Acquire the Accurate Whole-Genome Sequences of Human Adenoviruses. Front Microbiol 2021; 12:661382. [PMID: 34054762 PMCID: PMC8160523 DOI: 10.3389/fmicb.2021.661382] [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: 01/30/2021] [Accepted: 04/06/2021] [Indexed: 12/03/2022] Open
Abstract
The whole-genome sequencing (WGS) of human adenoviruses (HAdVs) plays an important role in identifying, typing, and mutation analysis of HAdVs. Nowadays, three generations of sequencing have been developed. The accuracy of first-generation sequencing is up to 99.99%, whereas this technology relies on PCR and is time consuming; the next-generation sequencing (NGS) is expensive and not cost effective for determining a few special samples; and the third-generation sequencing technology has a higher error rate. In this study, first, we developed an efficient HAdV genomic DNA extraction method. Using the complete genomic DNA instead of the PCR amplicons as the direct sequencing template and a set of walking primers, we developed the HAdV WGS method based on first-generation sequencing. The HAdV whole genomes were effectively sequenced by a set of one-way sequencing primers designed, which reduced the sequencing time and cost. More importantly, high sequence accuracy is guaranteed. Four HAdV strains (GZ01, GZ02, HK35, and HK91) were isolated from children with acute respiratory diseases (ARDs), and the complete genomes were sequenced using this method. The accurate sequences of the whole inverted terminal repeats (ITRs) at both ends of the HAdV genomes were also acquired. The genome sequence of human adenovirus type 14 (HAdV-B14) strain GZ01 acquired by this method is identical to the sequence released in GenBank, which indicates that this novel sequencing method has high accuracy. The comparative genomic analysis identified that strain GZ02 isolated in September 2010 had the identical genomic sequence with the HAdV-B14 strain GZ01 (October 2010). Therefore, strain GZ02 is the first HAdV-B14 isolate emergent in China (September 2010; GenBank acc no. MW692349). The WGS of HAdV-C2 strain HK91 and HAdV-E4 strain HK35 isolated from children with acute respiratory disease in Hong Kong were also determined by this sequencing method. In conclusion, this WGS method is fast, accurate, and universal for common human adenovirus species B, C, and E. The sequencing strategy may also be applied to the WGS of the other DNA viruses.
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Affiliation(s)
- Shan Zhao
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Wenyi Guan
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Kui Ma
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
| | - Yuqian Yan
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Junxian Ou
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Jing Zhang
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
| | - Zhiwu Yu
- Division of Laboratory Science, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
| | - Jianguo Wu
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
| | - Qiwei Zhang
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
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3
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Kang J, Ismail AM, Dehghan S, Rajaiya J, Allard MW, Lim HC, Dyer DW, Chodosh J, Seto D. Genomics-based re-examination of the taxonomy and phylogeny of human and simian Mastadenoviruses: an evolving whole genomes approach, revealing putative zoonosis, anthroponosis, and amphizoonosis. Cladistics 2020; 36:358-373. [PMID: 34618969 DOI: 10.1111/cla.12422] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2020] [Indexed: 02/06/2023] Open
Abstract
With the advent of high-resolution and cost-effective genomics and bioinformatics tools and methods contributing to a large database of both human (HAdV) and simian (SAdV) adenoviruses, a genomics-based re-evaluation of their taxonomy is warranted. Interest in these particular adenoviruses is growing in part due to the applications of both in gene transfer protocols, including gene therapy and vaccines, as well in oncolytic protocols. In particular, the re-evaluation of SAdVs as appropriate vectors in humans is important as zoonosis precludes the assumption that human immune system may be naïve to these vectors. Additionally, as important pathogens, adenoviruses are a model organism system for understanding viral pathogen emergence through zoonosis and anthroponosis, particularly among the primate species, along with recombination, host adaptation, and selection, as evidenced by one long-standing human respiratory pathogen HAdV-4 and a recent re-evaluation of another, HAdV-76. The latter reflects the insights on amphizoonosis, defined as infections in both directions among host species including "other than human", that are possible with the growing database of nonhuman adenovirus genomes. HAdV-76 is a recombinant that has been isolated from human, chimpanzee, and bonobo hosts. On-going and potential impacts of adenoviruses on public health and translational medicine drive this evaluation of 174 whole genome sequences from HAdVs and SAdVs archived in GenBank. The conclusion is that rather than separate HAdV and SAdV phylogenetic lineages, a single, intertwined tree is observed with all HAdVs and SAdVs forming mixed clades. Therefore, a single designation of "primate adenovirus" (PrAdV) superseding either HAdV and SAdV is proposed, or alternatively, keeping HAdV for human adenovirus but expanding the SAdV nomenclature officially to include host species identification as in ChAdV for chimpanzee adenovirus, GoAdV for gorilla adenovirus, BoAdV for bonobo adenovirus, and ad libitum.
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Affiliation(s)
- June Kang
- Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, VA, 20110, USA
| | - Ashrafali Mohamed Ismail
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, 02114, USA
| | - Shoaleh Dehghan
- Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, VA, 20110, USA.,Chemistry Department, American University, Washington, DC, 20016, USA
| | - Jaya Rajaiya
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, 02114, USA
| | - Marc W Allard
- Division of Microbiology (HFS-710), Center for Food Safety & Applied Nutrition, US Food & Drug Administration, College Park, MD, 20740, USA
| | - Haw Chuan Lim
- Department of Biology, George Mason University Manassas, VA, 20110, USA
| | - David W Dyer
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - James Chodosh
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, 02114, USA
| | - Donald Seto
- Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, VA, 20110, USA
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4
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Charman M, Herrmann C, Weitzman MD. Viral and cellular interactions during adenovirus DNA replication. FEBS Lett 2019; 593:3531-3550. [PMID: 31764999 DOI: 10.1002/1873-3468.13695] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/14/2019] [Accepted: 11/15/2019] [Indexed: 12/30/2022]
Abstract
Adenoviruses represent ubiquitous and clinically significant human pathogens, gene-delivery vectors, and oncolytic agents. The study of adenovirus-infected cells has long been used as an excellent model to investigate fundamental aspects of both DNA virus infection and cellular biology. While many key details supporting a well-established model of adenovirus replication have been elucidated over a period spanning several decades, more recent findings suggest that we have only started to appreciate the complex interplay between viral genome replication and cellular processes. Here, we present a concise overview of adenovirus DNA replication, including the biochemical process of replication, the spatial organization of replication within the host cell nucleus, and insights into the complex plethora of virus-host interactions that influence viral genome replication. Finally, we identify emerging areas of research relating to the replication of adenovirus genomes.
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Affiliation(s)
- Matthew Charman
- Division of Protective Immunity and Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Christin Herrmann
- Division of Protective Immunity and Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Cell and Molecular Biology Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Matthew D Weitzman
- Division of Protective Immunity and Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
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5
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Borkenhagen LK, Fieldhouse JK, Seto D, Gray GC. Are adenoviruses zoonotic? A systematic review of the evidence. Emerg Microbes Infect 2019; 8:1679-1687. [PMID: 31749409 PMCID: PMC6882429 DOI: 10.1080/22221751.2019.1690953] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Adenoviruses (AdVs) are major contributors to clinical illnesses. Novel human and animal AdVs continue to be identified and characterized. Comparative analyses using bioinformatic methods and Omics-based technologies allow insights into how these human pathogens have emerged and their potential for host cross-species transmission. Systematic review of literature published across ProQuest, Pubmed, and Web of Science databases for evidence of adenoviral zoonotic potential identified 589 citations. After removing duplicates, 327 citations were screened for relevance; of which, 74 articles received full-text reviews. Among these, 24 were included here, of which 16 demonstrated evidence of zoonotic transmission of AdVs. These documented instances of AdV crossing host species barriers between humans and non-human primate, bat, feline, swine, canine, ovine, and caprine. Eight studies sought to but did not find evidence of zoonosis. The findings demonstrate substantial evidence suggesting AdVs have previously and will continue crossing host species barriers. These have human health consequences both in terms of novel pathogen emergence and epidemic outbreaks, and of appropriate and safe use of non-human adenoviruses for therapeutics. As routine human clinical diagnostics may miss a novel cross-species adenovirus infection in humans, next generation sequencing or panspecies molecular diagnostics may be necessary to detect such incursions.
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Affiliation(s)
- Laura K Borkenhagen
- Division of Infectious Diseases, School of Medicine and Global Health Institute, Duke University, Durham, NC, USA
| | - Jane K Fieldhouse
- Division of Infectious Diseases, School of Medicine and Global Health Institute, Duke University, Durham, NC, USA
| | - Donald Seto
- Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Gregory C Gray
- Division of Infectious Diseases, School of Medicine and Global Health Institute, Duke University, Durham, NC, USA.,Global Health Research Center, Duke Kunshan University, Kunshan, People's Republic of China.,Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
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6
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Gonzalez G, Bair CR, Lamson DM, Watanabe H, Panto L, Carr MJ, Kajon AE. Genomic characterization of human adenovirus type 4 strains isolated worldwide since 1953 identifies two separable phylogroups evolving at different rates from their most recent common ancestor. Virology 2019; 538:11-23. [PMID: 31550608 DOI: 10.1016/j.virol.2019.08.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 08/28/2019] [Accepted: 08/29/2019] [Indexed: 11/29/2022]
Abstract
Species Human mastadenovirus E (HAdV-E) comprises several simian types and a single human type: HAdV-E4, a respiratory and ocular pathogen. RFLP analysis for the characterization of intratypic genetic variability has previously distinguished two HAdV-E4 clusters: prototype (p)-like and a-like. Our analysis of whole genome sequences confirmed two distinct lineages, which we refer to as phylogroups (PGs). PGs I and II comprise the p- and a-like genomes, respectively, and differ significantly in their G + C content (57.7% ± 0.013 vs 56.3% ± 0.015). Sequence differences distinguishing the two clades map to several regions of the genome including E3 and ITR. Bayesian analyses showed that the two phylogroups diverged approximately 602 years before the present. A relatively faster evolutionary rate was identified for PG II. Our data provide a rationale for the incorporation of phylogroup identity to HAdV-E4 strain designation to reflect the identified unique genetic characteristics that distinguish PGs I and II.
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Affiliation(s)
- Gabriel Gonzalez
- Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.
| | - Camden R Bair
- Infectious Disease Program, Lovelace Respiratory Research Institute, New Mexico, USA
| | - Daryl M Lamson
- Wadsworth Center, New York State Department of Health, New York, USA
| | - Hidemi Watanabe
- Graduate School of Information Science and Technology, Hokkaido University, Japan
| | - Laura Panto
- Graduate School of Information Science and Technology, Hokkaido University, Japan
| | - Michael J Carr
- Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Japan; National Virus Reference Laboratory, School of Medicine, University College Dublin, Ireland
| | - Adriana E Kajon
- Infectious Disease Program, Lovelace Respiratory Research Institute, New Mexico, USA.
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7
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A Zoonotic Adenoviral Human Pathogen Emerged through Genomic Recombination among Human and Nonhuman Simian Hosts. J Virol 2019; 93:JVI.00564-19. [PMID: 31243128 DOI: 10.1128/jvi.00564-19] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 06/18/2019] [Indexed: 12/14/2022] Open
Abstract
Genomics analysis of a historically intriguing and predicted emergent human adenovirus (HAdV) pathogen, which caused pneumonia and death, provides insight into a novel molecular evolution pathway involving "ping-pong" zoonosis and anthroponosis. The genome of this promiscuous pathogen is embedded with evidence of unprecedented multiple, multidirectional, stable, and reciprocal cross-species infections of hosts from three species (human, chimpanzee, and bonobo). This recombinant genome, typed as HAdV-B76, is identical to two recently reported simian AdV (SAdV) genomes isolated from chimpanzees and bonobos. Additionally, the presence of a critical adenoviral replication element found in HAdV genomes, in addition to genes that are highly similar to counterparts in other HAdVs, reinforces its potential as a human pathogen. Reservoirs in nonhuman hosts may explain periods of apparent absence and then reemergence of human adenoviral pathogens, as well as present pathways for the genesis of those thought to be newly emergent. The nature of the HAdV-D76 genome has implications for the use of SAdVs as gene delivery vectors in human gene therapy and vaccines, selected to avoid preexisting and potentially fatal host immune responses to HAdV.IMPORTANCE An emergent adenoviral human pathogen, HAdV-B76, associated with a fatality in 1965, shows a remarkable degree of genome identity with two recently isolated simian adenoviruses that contain cross-species genome recombination events from three hosts: human, chimpanzee, and bonobo. Zoonosis (nonhuman-to-human transmission) and anthroponosis (human to nonhuman transmission) may play significant roles in the emergence of human adenoviral pathogens.
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8
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A Survey of Recent Adenoviral Respiratory Pathogens in Hong Kong Reveals Emergent and Recombinant Human Adenovirus Type 4 (HAdV-E4) Circulating in Civilian Populations. Viruses 2019; 11:v11020129. [PMID: 30708990 PMCID: PMC6410123 DOI: 10.3390/v11020129] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 01/30/2019] [Indexed: 12/20/2022] Open
Abstract
Human adenovirus type 4 (HAdV-E4), which is intriguingly limited to military populations, causes acute respiratory disease with demonstrated morbidity and mortality implications. This respiratory pathogen contains genome identity with chimpanzee adenoviruses, indicating zoonotic origins. A signature of these “old” HAdV-E4 is the absence of a critical replication motif, NF-I, which is found in all HAdV respiratory pathogens and most HAdVs. However, our recent survey of flu-like disease in children in Hong Kong reveals that the emergent HAdV-E4 pathogens circulating in civilian populations contain NF-I, indicating recombination and reflecting host-adaptation that enables the “new” HAdV-E4 to replicate more efficiently in human cells and foretells more potential HAdV-E4 outbreaks in immune-naïve civilian populations. Special attention should be paid by clinicians to this emergent and recombinant HAdV-E4 circulating in civilian populations.
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9
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Ismail AM, Lee JS, Lee JY, Singh G, Dyer DW, Seto D, Chodosh J, Rajaiya J. Adenoviromics: Mining the Human Adenovirus Species D Genome. Front Microbiol 2018; 9:2178. [PMID: 30254627 PMCID: PMC6141750 DOI: 10.3389/fmicb.2018.02178] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 08/24/2018] [Indexed: 12/19/2022] Open
Abstract
Human adenovirus (HAdV) infections cause disease world-wide. Whole genome sequencing has now distinguished 90 distinct genotypes in 7 species (A-G). Over half of these 90 HAdVs fall within species D, with essentially all of the HAdV-D whole genome sequences generated in the last decade. Herein, we describe recent new findings made possible by mining of this expanded genome database, and propose future directions to elucidate new functional elements and new functions for previously known viral components.
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Affiliation(s)
- Ashrafali M Ismail
- Howe Laboratory, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, United States
| | - Ji Sun Lee
- Howe Laboratory, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, United States
| | - Jeong Yoon Lee
- Howe Laboratory, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, United States.,Molecular Virology Laboratory, Korea Zoonosis Research Institute, Jeonbuk National University, Jeonju, South Korea
| | - Gurdeep Singh
- Howe Laboratory, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, United States.,Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - David W Dyer
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Donald Seto
- Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, VI, United States
| | - James Chodosh
- Howe Laboratory, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, United States
| | - Jaya Rajaiya
- Howe Laboratory, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, United States
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10
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Comparative genomic analysis of two emergent human adenovirus type 14 respiratory pathogen isolates in China reveals similar yet divergent genomes. Emerg Microbes Infect 2017; 6:e92. [PMID: 29089589 PMCID: PMC5717082 DOI: 10.1038/emi.2017.78] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Revised: 08/08/2017] [Accepted: 08/21/2017] [Indexed: 02/04/2023]
Abstract
Human adenovirus type 14 (HAdV-B14p) was originally identified as an acute respiratory disease (ARD) pathogen in The Netherlands in 1955. For approximately fifty years, few sporadic infections were observed. In 2005, HAdV-B14p1, a genomic variant, re-emerged and was associated with several large ARD outbreaks across the U.S. and, subsequently, in Canada, the U.K., Ireland, and China. This strain was associated with an unusually higher fatality rate than previously reported for both this prototype and other HAdV types in general. In China, HAdV-B14 was first observed in 2010, when two unrelated HAdV-B14-associated ARD cases were reported in Southern China (GZ01) and Northern China (BJ430), followed by three subsequent outbreaks. While comparative genomic analysis, including indel analysis, shows that the three China isolates, with whole genome data available, are similar to the de Wit prototype, all are divergent from the U.S. strain (303600; 2007). Although the genomes of strains GZ01 and BJ430 are nearly identical, as per their genome type characterization and percent identities, they are subtly divergent in their genome mutation patterns. These genomes indicate possibly two lineages of HAdV-B14 and independent introductions into China from abroad, or subsequent divergence from one; CHN2012 likely represents a separate sub-lineage. Observations of these simultaneously reported emergent strains in China add to the understanding of the circulation, epidemiology, and evolution of these HAdV pathogens, as well as provide a foundation for developing effective vaccines and public health strategies, including nationwide surveillance in anticipation of larger outbreaks with potentially higher fatality rates associated with HAdV-B14p1.
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11
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Kuhn I, Bauzon M, Green N, Seymour L, Fisher K, Hermiston T. OvAd1, a Novel, Potent, and Selective Chimeric Oncolytic Virus Developed for Ovarian Cancer by 3D-Directed Evolution. Mol Ther Oncolytics 2017; 4:55-66. [PMID: 28345024 PMCID: PMC5363728 DOI: 10.1016/j.omto.2016.12.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 12/01/2016] [Indexed: 02/07/2023] Open
Abstract
Effective therapeutics for ovarian cancer continue to be urgently needed, particularly for chemotherapy-resistant cases. Here we present both a 3D-Matrigel culture-based expansion of our directed evolution method for generation of oncolytic virotherapies and two promising ovarian-cancer targeted oncolytic viruses, OvAd1 and OvAd2. OvAd1 was developed using Matrigel cell cultures, whereas OvAd2 was developed in parallel using traditional monolayer tissue culture methods. Both viruses are potent against a panel of platinum-resistant ovarian cancer cell lines and are attenuated on normal cells in vitro, resulting in therapeutic windows of ∼200-fold. We observed two benefits of the use of Matrigel-based cultures for directed evolution of these oncolytics: (1) use of Matrigel generated a bioselected pool that was more strongly attenuated on normal cells while retaining its potency against ovarian cancer cells, and (2) in an ovarian carcinomatosis model, the Matrigel-derived virus OvAd1 suppressed all tumor growth while the non-Matrigel-derived virus was 50% effective. Neither virus stimulated formation of peritoneal adhesions as seen for Ad5-based therapies. Consequently, these viruses are novel candidates for development as new effective treatments for aggressive ovarian cancer.
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Affiliation(s)
- Irene Kuhn
- Department of Biological Research, Bayer Pharmaceuticals, 455 Mission Bay Boulevard South, Suite 493, San Francisco, CA 94158, USA
| | - Maxine Bauzon
- Department of Biological Research, Bayer Pharmaceuticals, 455 Mission Bay Boulevard South, Suite 493, San Francisco, CA 94158, USA
| | - Nicola Green
- Department of Clinical Medicine, University of Oxford, Old Road Campus, OX3 7DQ, Oxford, UK
| | - Len Seymour
- Department of Oncology, University of Oxford, Old Road Campus, OX3 7DQ, Oxford, UK
| | - Kerry Fisher
- Department of Oncology, University of Oxford, Old Road Campus, OX3 7DQ, Oxford, UK
| | - Terry Hermiston
- Department of Biological Research, Bayer Pharmaceuticals, 455 Mission Bay Boulevard South, Suite 493, San Francisco, CA 94158, USA
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12
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Mahadevan P. An Analysis of Adenovirus Genomes Using Whole Genome Software Tools. Bioinformation 2016; 12:301-310. [PMID: 28293072 PMCID: PMC5320926 DOI: 10.6026/97320630012301] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 07/28/2016] [Accepted: 07/29/2016] [Indexed: 11/23/2022] Open
Abstract
The evolution of sequencing technology has lead to an enormous increase in the number of genomes that have been sequenced. This is especially true in the field of virus genomics. In order to extract meaningful biological information from these genomes, whole genome data mining software tools must be utilized. Hundreds of tools have been developed to analyze biological sequence data. However, only some of these tools are user-friendly to biologists. Several of these tools that have been successfully used to analyze adenovirus genomes are described here. These include Artemis, EMBOSS, pDRAW, zPicture, CoreGenes, GeneOrder, and PipMaker. These tools provide functionalities such as visualization, restriction enzyme analysis, alignment, and proteome comparisons that are extremely useful in the bioinformatics analysis of adenovirus genomes.
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Affiliation(s)
- Padmanabhan Mahadevan
- Department of Biology, University of Tampa, 401 W. Kennedy Blvd. Box 3F, Tampa, FL 33606
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13
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Dehghan S, Seto J, Jones MS, Dyer DW, Chodosh J, Seto D. Simian adenovirus type 35 has a recombinant genome comprising human and simian adenovirus sequences, which predicts its potential emergence as a human respiratory pathogen. Virology 2013; 447:265-73. [PMID: 24210123 DOI: 10.1016/j.virol.2013.09.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 09/05/2013] [Accepted: 09/12/2013] [Indexed: 11/19/2022]
Abstract
Emergent human and simian adenoviruses (HAdVs) may arise from genome recombination. Computational analysis of SAdV type 35 reveals a genome comprising a chassis with elements mostly from two simian adenoviruses, SAdV-B21 and -B27, and regions of high sequence similarity shared with HAdV-B21 and HAdV-B16. Although recombination direction cannot be determined, the presence of these regions suggests prior infections of humans by an ancestor of SAdV-B35, and/or vice versa. Absence of this virus in humans may reflect non-optimal conditions for zoonosis or incomplete typing, e.g., limited epitope-based. The presence of both a critical viral replication element found in HAdV genomes and genes that are highly similar to ones in HAdVs suggest the potential to establish in a human host. This allows a prediction that this virus may be a nascent human respiratory pathogen. The recombination potential of human and simian adenovirus genomes should be considered in the use of SAdVs as vectors for gene delivery in humans.
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Affiliation(s)
- Shoaleh Dehghan
- Chemistry Department, American University, Washington, D.C. 20016, USA; Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, VA 20110, USA
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14
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Mi Z, Butt AM, An X, Jiang T, Liu W, Qin C, Cao WC, Tong Y. Genomic analysis of HAdV-B14 isolate from the outbreak of febrile respiratory infection in China. Genomics 2013; 102:448-55. [PMID: 24055951 PMCID: PMC7126778 DOI: 10.1016/j.ygeno.2013.09.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 09/07/2013] [Accepted: 09/10/2013] [Indexed: 12/14/2022]
Abstract
Human adenovirus type 14 (HAdV-B14) was first reported in 1955 from the Netherlands and since then had been associated with outbreaks of febrile respiratory illness (FRI). In China, sporadic HAdV-B14 infections were first identified in 2010, in Guangzhou and Beijing. In 2012, an outbreak of FRI occurred in Beijing and the etiological agent was determined to be HAdV-B14. We present a complete HAdV-B14 genome sequence isolated from this recent FRI outbreak. Virus in 30 throat swab samples was detected using polymerase chain reaction assays, and confirmed by sequencing of the fiber, hexon and penton genes. Comparative genomics and phylogenetic analysis showed that the newly isolated HAdV-B14 (HAdV-B14 CHN) shared highest sequence homology with a 2006 isolate from the United States and clustered closely with other HAdV-B14 strains. It is expected that data from the present study will help in devising better protocols for virus surveillance, and in developing preventative measures. Isolation of HAdV-B14 was performed from the outbreak of febrile respiratory illness. Full genome sequence of HAdV-B14 CHN strain has been reported. Several nucleotide substitutions were reported in the HAdV-B14 CHN genome.
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Affiliation(s)
- Zhiqiang Mi
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, People's Republic of China
| | - Azeem Mehmood Butt
- Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore 53700, Pakistan
| | - Xiaoping An
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, People's Republic of China
| | - Tao Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, People's Republic of China
| | - Wei Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, People's Republic of China
| | - Chengfeng Qin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, People's Republic of China
| | - Wu-Chun Cao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, People's Republic of China.
| | - Yigang Tong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, People's Republic of China.
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15
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Dehghan S, Seto J, Liu EB, Walsh MP, Dyer DW, Chodosh J, Seto D. Computational analysis of four human adenovirus type 4 genomes reveals molecular evolution through two interspecies recombination events. Virology 2013; 443:197-207. [PMID: 23763770 DOI: 10.1016/j.virol.2013.05.014] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 05/03/2013] [Accepted: 05/09/2013] [Indexed: 11/17/2022]
Abstract
Computational analysis of human adenovirus type 4 (HAdV-E4), a pathogen that is the only HAdV member of species E, provides insights into its zoonotic origin and molecular adaptation. Its genome encodes a domain of the major capsid protein, hexon, from HAdV-B16 recombined into the genome chassis of a simian adenovirus. Genomes of two recent field strains provide a clue to its adaptation to the new host: recombination of a NF-I binding site motif, which is required for efficient viral replication, from another HAdV genome. This motif is absent in the chimpanzee adenoviruses and the HAdV-E4 prototype, but is conserved amongst other HAdVs. This is the first report of an interspecies recombination event for HAdVs, and the first documentation of a lateral partial gene transfer from a chimpanzee AdV. The potential for such recombination events are important when considering chimpanzee adenoviruses as candidate gene delivery vectors for human patients.
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Affiliation(s)
- Shoaleh Dehghan
- Chemistry Department, American University, Washington, D.C. 20016, USA; Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, VA 20110, USA
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16
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Molecular biology, epidemiology, and pathogenesis of progressive multifocal leukoencephalopathy, the JC virus-induced demyelinating disease of the human brain. Clin Microbiol Rev 2012; 25:471-506. [PMID: 22763635 DOI: 10.1128/cmr.05031-11] [Citation(s) in RCA: 289] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Progressive multifocal leukoencephalopathy (PML) is a debilitating and frequently fatal central nervous system (CNS) demyelinating disease caused by JC virus (JCV), for which there is currently no effective treatment. Lytic infection of oligodendrocytes in the brain leads to their eventual destruction and progressive demyelination, resulting in multiple foci of lesions in the white matter of the brain. Before the mid-1980s, PML was a relatively rare disease, reported to occur primarily in those with underlying neoplastic conditions affecting immune function and, more rarely, in allograft recipients receiving immunosuppressive drugs. However, with the onset of the AIDS pandemic, the incidence of PML has increased dramatically. Approximately 3 to 5% of HIV-infected individuals will develop PML, which is classified as an AIDS-defining illness. In addition, the recent advent of humanized monoclonal antibody therapy for the treatment of autoimmune inflammatory diseases such as multiple sclerosis (MS) and Crohn's disease has also led to an increased risk of PML as a side effect of immunotherapy. Thus, the study of JCV and the elucidation of the underlying causes of PML are important and active areas of research that may lead to new insights into immune function and host antiviral defense, as well as to potential new therapies.
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17
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Liang B, Tikhanovich I, Nasheuer HP, Folk WR. Stimulation of BK virus DNA replication by NFI family transcription factors. J Virol 2012; 86:3264-75. [PMID: 22205750 PMCID: PMC3302295 DOI: 10.1128/jvi.06369-11] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Accepted: 12/22/2011] [Indexed: 12/15/2022] Open
Abstract
BK polyomavirus (BKV) establishes persistent, low-level, and asymptomatic infections in most humans and causes polyomavirus-associated nephropathy (PVAN) and other pathologies in some individuals. The activation of BKV replication following kidney transplantation, leading to viruria, viremia, and, ultimately, PVAN, is associated with immune suppression as well as inflammation and stress from ischemia-reperfusion injury of the allograft, but the stimuli and molecular mechanisms leading to these pathologies are not well defined. The replication of BKV DNA in cell cultures is regulated by the viral noncoding control region (NCCR) comprising the core origin and flanking sequences, to which BKV T antigen (Tag), cellular proteins, and small regulatory RNAs bind. Six nuclear factor I (NFI) binding sites occur in sequences flanking the late side of the core origin (the enhancer) of the archetype virus, and their mutation, either individually or in toto, reduces BKV DNA replication when placed in competition with templates containing intact BKV NCCRs. NFI family members interacted with the helicase domain of BKV Tag in pulldown assays, suggesting that NFI helps recruit Tag to the viral core origin and may modulate its function. However, Tag may not be the sole target of the replication-modulatory activities of NFI: the NFIC/CTF1 isotype stimulates BKV template replication in vitro at low concentrations of DNA polymerase-α primase (Pol-primase), and the p58 subunit of Pol-primase associates with NFIC/CTF1, suggesting that NFI also recruits Pol-primase to the NCCR. These results suggest that NFI proteins (and the signaling pathways that target them) activate BKV replication and contribute to the consequent pathologies caused by acute infection.
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Affiliation(s)
- Bo Liang
- Department of Biochemistry and Genetics Area Program, University of Missouri—Columbia, Columbia, Missouri, USA
| | - Irina Tikhanovich
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland, Galway, Galway, Ireland
| | - Heinz Peter Nasheuer
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland, Galway, Galway, Ireland
| | - William R. Folk
- Department of Biochemistry and Genetics Area Program, University of Missouri—Columbia, Columbia, Missouri, USA
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18
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Walsh MP, Chintakuntlawar A, Robinson CM, Madisch I, Harrach B, Hudson NR, Schnurr D, Heim A, Chodosh J, Seto D, Jones MS. Evidence of molecular evolution driven by recombination events influencing tropism in a novel human adenovirus that causes epidemic keratoconjunctivitis. PLoS One 2009; 4:e5635. [PMID: 19492050 PMCID: PMC2685984 DOI: 10.1371/journal.pone.0005635] [Citation(s) in RCA: 176] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2009] [Accepted: 04/08/2009] [Indexed: 11/19/2022] Open
Abstract
In 2005, a human adenovirus strain (formerly known as HAdV-D22/H8 but renamed here HAdV-D53) was isolated from an outbreak of epidemic keratoconjunctititis (EKC), a disease that is usually caused by HAdV-D8, -D19, or -D37, not HAdV-D22. To date, a complete change of tropism compared to the prototype has never been observed, although apparent recombinant strains of other viruses from species Human adenovirus D (HAdV-D) have been described. The complete genome of HAdV-D53 was sequenced to elucidate recombination events that lead to the emergence of a viable and highly virulent virus with a modified tropism. Bioinformatic and phylogenetic analyses of this genome demonstrate that this adenovirus is a recombinant of HAdV-D8 (including the fiber gene encoding the primary cellular receptor binding site), HAdV-D22, (the epsilon determinant of the hexon gene), HAdV-D37 (including the penton base gene encoding the secondary cellular receptor binding site), and at least one unknown or unsequenced HAdV-D strain. Bootscanning analysis of the complete genomic sequence of this novel adenovirus, which we have re-named HAdV-D53, indicated at least five recombination events between the aforementioned adenoviruses. Intrahexon recombination sites perfectly framed the epsilon neutralization determinant that was almost identical to the HAdV-D22 prototype. Additional bootscan analysis of all HAdV-D hexon genes revealed recombinations in identical locations in several other adenoviruses. In addition, HAdV-D53 but not HAdV-D22 induced corneal inflammation in a mouse model. Serological analysis confirmed previous results and demonstrated that HAdV-D53 has a neutralization profile representative of the epsilon determinant of its hexon (HAdV-D22) and the fiber (HAdV-D8) proteins. Our recombinant hexon sequence is almost identical to the hexon sequences of the HAdV-D strain causing EKC outbreaks in Japan, suggesting that HAdV-D53 is pandemic as an emerging EKC agent. This documents the first genomic, bioinformatic, and biological descriptions of the molecular evolution events engendering an emerging pathogenic adenovirus.
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Affiliation(s)
- Michael P. Walsh
- Department of Bioinformatics and Computational Biology, George Mason University, Manassas, Virginia, United States of America
| | - Ashish Chintakuntlawar
- Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Christopher M. Robinson
- Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Ijad Madisch
- Insitut für Virologie, Medizinische Hochschule, Hannover, Germany
| | - Balázs Harrach
- Veterinary Medical Research Institute, Hungarian Academy of Sciences, Budapest, Hungary
| | - Nolan R. Hudson
- Clinical Investigation Facility, David Grant USAF Medical Center, Travis AFB, California, United States of America
| | - David Schnurr
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, California, United States of America
| | - Albert Heim
- Insitut für Virologie, Medizinische Hochschule, Hannover, Germany
| | - James Chodosh
- Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Donald Seto
- Department of Bioinformatics and Computational Biology, George Mason University, Manassas, Virginia, United States of America
| | - Morris S. Jones
- Clinical Investigation Facility, David Grant USAF Medical Center, Travis AFB, California, United States of America
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19
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Seto J, Walsh MP, Mahadevan P, Purkayastha A, Clark JM, Tibbetts C, Seto D. Genomic and bioinformatics analyses of HAdV-14p, reference strain of a re-emerging respiratory pathogen and analysis of B1/B2. Virus Res 2009; 143:94-105. [PMID: 19463726 DOI: 10.1016/j.virusres.2009.03.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2008] [Revised: 03/22/2009] [Accepted: 03/23/2009] [Indexed: 11/25/2022]
Abstract
Unlike other human adenovirus (HAdV) species, B is divided into subspecies B1 and B2. Originally this was partly based on restriction enzyme (RE) analysis. B1 members, except HAdV-50, are commonly associated with respiratory diseases while B2 members are rarely associated with reported respiratory diseases. Recently two members of B2 have been identified in outbreaks of acute respiratory disease (ARD). One, HAdV-14, has re-emerged after an apparent 52-year absence. Genomic analysis and bioinformatics data are reported for HAdV-14 prototype for use as a reference and to understand and counter its re-emergence. The data complement and extend the original criteria for subspecies designation, unique amongst the adenoviruses, and highlight differences between B1 and B2, representing the first comprehensive analysis of this division. These data also provide finer granularity into the pathoepidemiology of the HAdVs. Whole genome analysis uncovers heterogeneous identity structures of the hexon and fiber genes amongst the HAdV-14 and the B1/B2 subspecies, which may be important in prescient vaccine development. Analysis of cell surface proteins provides insight into HAdV-14 tropism, accounting for its role as a respiratory pathogen. This HAdV-14 prototype genome is also a reference for applications of B2 adenoviruses as vectors for vaccine development and gene therapy.
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Affiliation(s)
- Jason Seto
- Department of Bioinformatics and Computational Biology, George Mason University, 10900 University Blvd., MSN 5B3, Manassas, VA 20110, USA.
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20
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Lenaerts L, De Clercq E, Naesens L. Clinical features and treatment of adenovirus infections. Rev Med Virol 2008; 18:357-74. [PMID: 18655013 DOI: 10.1002/rmv.589] [Citation(s) in RCA: 172] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Adenoviruses (Ads) are common opportunistic pathogens that are rarely associated with severe clinical symptoms in healthy individuals. In contrast, in patients with compromised immunity, Ad infections often result in disseminated and potentially life-threatening disease. Among these are AIDS patients, individuals with hereditary immunodeficiencies and recipients of solid organ or haematopoietic stem cell transplants (HSCT) who receive immunosuppressive therapy. The latter account for the largest number of severe Ad infections. There is currently no formally approved antiviral therapy for the treatment of severe Ad keratoconjunctivitis and life-threatening Ad infections in immunocompromised patients. Here we update current knowledge on Ad biology, the clinical features observed in different patient groups and specific immune responses towards Ad infections. In addition, we review current and future treatment options, including: (i) the antiviral drugs cidofovir, ribavirin and new investigational compounds, as evaluated in the clinic or in relevant animal models, as well as (ii) novel immunotherapeutic strategies.
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Affiliation(s)
- Liesbeth Lenaerts
- Division of Virology and Chemotherapy, Rega Institute for Medical Research, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium
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21
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Rademaker HJ, Fallaux FJ, Van den Wollenberg DJM, De Jong RN, Van der Vliet PC, Hoeben RC. Relaxed template specificity in fowl adenovirus 1 DNA replication initiation. J Gen Virol 2006; 87:553-562. [PMID: 16476976 DOI: 10.1099/vir.0.81328-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The fowl adenovirus 1 (FAdV-1) isolates PHELPS and OTE are highly similar, but have striking differences in the repeat region of the inverted terminal repeat (ITR). Whilst the repeat region in OTE conforms to the conventional human adenovirus repeat region (5'-CATCATC), that of PHELPS contains guanidine residues at positions 1, 4 and 7 (5'-GATGATG). This implies that the FAdV-1 isolates PHELPS and OTE have either distinct template specificity at replication initiation or, alternatively, a relaxed specificity for replication initiation. In this study, the distinct sequence variation at the origin of DNA replication in the ITRs of the FAdV-1 PHELPS and OTE isolates was confirmed. Sequence analyses of the pTP and Pol genes of both PHELPS and OTE did not reveal differences that could explain the distinct template specificity. Replication assays demonstrated that linear DNA fragments flanked by either 5'-CATCATC or 5'-GATGATG termini replicated in cells upon infection with FAdV-1 OTE and FAdV-1 PHELPS. This was evident from the appearance of DpnI-resistant fragments in a minireplicon assay. From these data, it is concluded that FAdV-1 has relaxed, rather than changed, its template specificity at replication initiation.
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Affiliation(s)
- Hendrik J Rademaker
- Department of Molecular Cell Biology, Leiden University Medical Center, Wassenaarseweg 72, 2333 AL Leiden, The Netherlands
| | - Frits J Fallaux
- Department of Molecular Cell Biology, Leiden University Medical Center, Wassenaarseweg 72, 2333 AL Leiden, The Netherlands
| | - Diana J M Van den Wollenberg
- Department of Molecular Cell Biology, Leiden University Medical Center, Wassenaarseweg 72, 2333 AL Leiden, The Netherlands
| | - Rob N De Jong
- Department of Physiological Chemistry and Center for Biomedical Genetics, University Medical Center, Universiteitsweg 100, 3508 AB Utrecht, The Netherlands
| | - Peter C Van der Vliet
- Department of Physiological Chemistry and Center for Biomedical Genetics, University Medical Center, Universiteitsweg 100, 3508 AB Utrecht, The Netherlands
| | - Rob C Hoeben
- Department of Molecular Cell Biology, Leiden University Medical Center, Wassenaarseweg 72, 2333 AL Leiden, The Netherlands
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22
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Purkayastha A, Su J, McGraw J, Ditty SE, Hadfield TL, Seto J, Russell KL, Tibbetts C, Seto D. Genomic and bioinformatics analyses of HAdV-4vac and HAdV-7vac, two human adenovirus (HAdV) strains that constituted original prophylaxis against HAdV-related acute respiratory disease, a reemerging epidemic disease. J Clin Microbiol 2005; 43:3083-94. [PMID: 16000418 PMCID: PMC1169186 DOI: 10.1128/jcm.43.7.3083-3094.2005] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2004] [Revised: 03/21/2005] [Accepted: 04/06/2005] [Indexed: 11/20/2022] Open
Abstract
Vaccine strains of human adenovirus serotypes 4 and 7 (HAdV-4vac and HAdV-7vac) have been used successfully to prevent adenovirus-related acute respiratory disease outbreaks. The genomes of these two vaccine strains have been sequenced, annotated, and compared with their prototype equivalents with the goals of understanding their genomes for molecular diagnostics applications, vaccine redevelopment, and HAdV pathoepidemiology. These reference genomes are archived in GenBank as HAdV-4vac (35,994 bp; AY594254) and HAdV-7vac (35,240 bp; AY594256). Bioinformatics and comparative whole-genome analyses with their recently reported and archived prototype genomes reveal six mismatches and four insertions-deletions (indels) between the HAdV-4 prototype and vaccine strains, in contrast to the 611 mismatches and 130 indels between the HAdV-7 prototype and vaccine strains. Annotation reveals that the HAdV-4vac and HAdV-7vac genomes contain 51 and 50 coding units, respectively. Neither vaccine strain appears to be attenuated for virulence based on bioinformatics analyses. There is evidence of genome recombination, as the inverted terminal repeat of HAdV-4vac is initially identical to that of species C whereas the prototype is identical to species B1. These vaccine reference sequences yield unique genome signatures for molecular diagnostics. As a molecular forensics application, these references identify the circulating and problematic 1950s era field strains as the original HAdV-4 prototype and the Greider prototype, from which the vaccines are derived. Thus, they are useful for genomic comparisons to current epidemic and reemerging field strains, as well as leading to an understanding of pathoepidemiology among the human adenoviruses.
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Affiliation(s)
- Anjan Purkayastha
- Bioinformatics and Computational Biology Program, School of Computational Sciences, George Mason University, 10900 University Boulevard, MSN 5B3, Manassas, Virginia 20110, USA
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23
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Chen WK, Chang NCA, Chang YH, Chang KL, Wu SC, Yang TS, Wu SM, Chang AC. Characterization of the regulatory region of Adra2c, the gene encoding the murine alpha2C adrenoceptor subtype. J Biomed Sci 2005; 11:886-901. [PMID: 15591786 DOI: 10.1007/bf02254374] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2004] [Accepted: 06/29/2004] [Indexed: 01/17/2023] Open
Abstract
The 5' flanking sequence (3,227 base pairs, bp) of the mouse Adra2c subtype gene was determined and characterized. The transcription start site was mapped to nucleotide 'A' of two initiator motifs in tandem array, i.e. 1,159 and 1,153 bp upstream from the initiation codon of the open reading frame (ORF) of Adra2c, respectively. One structural feature salient to the 5' regulatory region of Adra2c is present in the sequence 1 kb immediately upstream from the receptor ORF, which is highly enriched in GC content (76%) and CpG island counts (i.e. CpG/GpC, 146:177), and thus rich in Sp1-binding motifs. At the 3' flanking region, the polyadenylation signal was mapped to 481 bp downstream from the termination codon. The transcript defined by sequence data thereby is consistent with a size of 3 kb (brain form) determined by Northern blot analysis. The transgene, Adra2c-NN- lacZ, which links the promoter region of Adra2c to the lacZ reporter gene, was constructed in order to evaluate the functional capacity of the promoter and the putative motifs residing within the defined regulatory region (1.9 kb upstream from the ORF) in directing the reporter gene expression in vitro in transiently transfected cells and in vivo in transgenic (Tg) mice. Permissive cell types to Adra2c-NN include those derived from neural and kidney lineages. Significant Adra2c-NN-driven reporter expression in Tg mice established suggests that alpha2C adrenoceptor expression is permissive under Adra2c-NN in central (cerebral cortex, hippocampus, subthalamus, hypothalamus, superior colliculus, cerebellum, and brain stem) and peripheral (pancreatic beta-islets) tissues.
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MESH Headings
- Amino Acid Motifs
- Animals
- Base Sequence
- Blotting, Northern
- Blotting, Southern
- Brain/metabolism
- Central Nervous System/metabolism
- Cloning, Molecular
- Codon
- Computational Biology
- CpG Islands
- Gene Library
- Gene Transfer Techniques
- Genes, Reporter
- Humans
- Islets of Langerhans/metabolism
- Lac Operon
- Mice
- Mice, Transgenic
- Models, Genetic
- Molecular Sequence Data
- Nucleic Acid Hybridization
- Open Reading Frames
- Polymerase Chain Reaction
- Promoter Regions, Genetic
- Receptors, Adrenergic, alpha-2/chemistry
- Receptors, Adrenergic, alpha-2/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Tissue Distribution
- Transcription Factors
- Transcription, Genetic
- Transfection
- Transgenes
- beta-Galactosidase/metabolism
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Affiliation(s)
- Wen-Kwei Chen
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, ROC
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24
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Mysiak ME, Wyman C, Holthuizen PE, van der Vliet PC. NFI and Oct-1 bend the Ad5 origin in the same direction leading to optimal DNA replication. Nucleic Acids Res 2004; 32:6218-25. [PMID: 15576348 PMCID: PMC535662 DOI: 10.1093/nar/gkh944] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Two cellular transcription factors, nuclear factor I (NFI) and octamer binding protein (Oct-1), bind simultaneously to their recognition sequences in the Ad5 origin of replication thereby enhancing initiation. Using scanning force microscopy we have previously shown that NFI induces a 60 degrees bend in the origin DNA. Here we demonstrate that Oct-1 induces a 42 degrees bend in the origin DNA. Simultaneous binding of NFI and Oct-1 induces an 82 degrees collective bend suggesting that both bends are oriented towards each other. In functional replication assays we further demonstrate that this extensive DNA bending leads to a synergistic enhancement of DNA replication. We propose that collective DNA bending induced by NFI and Oct-1 facilitates the optimal assembly of the preinitiation complex and plays an important role in the stimulatory mechanism of NFI and Oct-1 in replication.
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Affiliation(s)
- Monika E Mysiak
- Department of Physiological Chemistry, University Medical Centre Utrecht and Centre for Biomedical Genetics, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands
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25
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Lauer KP, Llorente I, Blair E, Seto J, Krasnov V, Purkayastha A, Ditty SE, Hadfield TL, Buck C, Tibbetts C, Seto D. Natural variation among human adenoviruses: genome sequence and annotation of human adenovirus serotype 1. J Gen Virol 2004; 85:2615-2625. [PMID: 15302955 DOI: 10.1099/vir.0.80118-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The 36,001 base pair DNA sequence of human adenovirus serotype 1 (HAdV-1) has been determined, using a 'leveraged primer sequencing strategy' to generate high quality sequences economically. This annotated genome (GenBank AF534906) confirms anticipated similarity to closely related species C (formerly subgroup), human adenoviruses HAdV-2 and -5, and near identity with earlier reports of sequences representing parts of the HAdV-1 genome. A first round of HAdV-1 sequence data acquisition used PCR amplification and sequencing primers from sequences common to the genomes of HAdV-2 and -5. The subsequent rounds of sequencing used primers derived from the newly generated data. Corroborative re-sequencing with primers selected from this HAdV-1 dataset generated sparsely tiled arrays of high quality sequencing ladders spanning both complementary strands of the HAdV-1 genome. These strategies allow for rapid and accurate low-pass sequencing of genomes. Such rapid genome determinations facilitate the development of specific probes for differentiation of family, serotype, subtype and strain (e.g. pathogen genome signatures). These will be used to monitor epidemic outbreaks of acute respiratory disease in a defined test bed by the Epidemic Outbreak Surveillance (EOS) project.
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Affiliation(s)
- Kim P Lauer
- Bioinformatics and Computational Biology, School of Computational Sciences, George Mason University, 10900 University Boulevard, MSN 5B3, Manassas, VA 20110, USA
| | - Isabel Llorente
- Bioinformatics and Computational Biology, School of Computational Sciences, George Mason University, 10900 University Boulevard, MSN 5B3, Manassas, VA 20110, USA
| | - Eric Blair
- Bioinformatics and Computational Biology, School of Computational Sciences, George Mason University, 10900 University Boulevard, MSN 5B3, Manassas, VA 20110, USA
| | - Jason Seto
- Bioinformatics and Computational Biology, School of Computational Sciences, George Mason University, 10900 University Boulevard, MSN 5B3, Manassas, VA 20110, USA
| | - Vladimir Krasnov
- Bioinformatics and Computational Biology, School of Computational Sciences, George Mason University, 10900 University Boulevard, MSN 5B3, Manassas, VA 20110, USA
| | - Anjan Purkayastha
- Epidemic Outbreak Surveillance (EOS) Consortium, 5201 Leesburg Pike, Suite 1401, Falls Church, VA 22041, USA
- HQ USAF Surgeon General Office, Directorate of Modernization (SGR), 5201 Leesburg Pike, Suite 1401, Falls Church, VA 22041, USA
- Bioinformatics and Computational Biology, School of Computational Sciences, George Mason University, 10900 University Boulevard, MSN 5B3, Manassas, VA 20110, USA
| | - Susan E Ditty
- Epidemic Outbreak Surveillance (EOS) Consortium, 5201 Leesburg Pike, Suite 1401, Falls Church, VA 22041, USA
- Division of Microbiology, Department of Infectious and Parasitic Diseases Pathology, Armed Forces Institute of Pathology, 5300 Georgia Avenue NW, Washington, DC 20306, USA
| | - Ted L Hadfield
- Epidemic Outbreak Surveillance (EOS) Consortium, 5201 Leesburg Pike, Suite 1401, Falls Church, VA 22041, USA
- Division of Microbiology, Department of Infectious and Parasitic Diseases Pathology, Armed Forces Institute of Pathology, 5300 Georgia Avenue NW, Washington, DC 20306, USA
| | - Charles Buck
- Department of Virology, American Type Culture Collection (ATCC), Manassas, VA 20108, USA
| | - Clark Tibbetts
- Epidemic Outbreak Surveillance (EOS) Consortium, 5201 Leesburg Pike, Suite 1401, Falls Church, VA 22041, USA
- HQ USAF Surgeon General Office, Directorate of Modernization (SGR), 5201 Leesburg Pike, Suite 1401, Falls Church, VA 22041, USA
| | - Donald Seto
- Epidemic Outbreak Surveillance (EOS) Consortium, 5201 Leesburg Pike, Suite 1401, Falls Church, VA 22041, USA
- HQ USAF Surgeon General Office, Directorate of Modernization (SGR), 5201 Leesburg Pike, Suite 1401, Falls Church, VA 22041, USA
- Bioinformatics and Computational Biology, School of Computational Sciences, George Mason University, 10900 University Boulevard, MSN 5B3, Manassas, VA 20110, USA
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26
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Mysiak ME, Bleijenberg MH, Wyman C, Holthuizen PE, van der Vliet PC. Bending of adenovirus origin DNA by nuclear factor I as shown by scanning force microscopy is required for optimal DNA replication. J Virol 2004; 78:1928-35. [PMID: 14747557 PMCID: PMC369512 DOI: 10.1128/jvi.78.4.1928-1935.2004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nuclear factor I (NFI) is a transcription factor that binds to the adenovirus type 5 (Ad5) origin of replication and recruits the adenovirus DNA polymerase, thereby stimulating initiation of DNA replication in vitro. Using scanning force microscopy, we demonstrate that NFI induces a 60 degrees bend upon binding to the origin. The A/T-rich region preceding the core recognition sequence of NFI influences the DNA bend angle, since substitution of A/T base pairs by G/C base pairs severely decreases bending. Mutations in the A/T-rich region do not affect binding of NFI to DNA. However, mutations that reduce the protein-induced bend lead to a loss of NFI-stimulated replication, indicating that DNA bending is functionally important. In contrast, basal initiation or DNA binding of the polymerase is not impaired by these origin mutations. We conclude that binding of NFI to the Ad5 origin causes structural changes in DNA that are essential for the stimulatory function of NFI in replication. We propose that NFI-induced origin bending facilitates the assembly of a functional initiation complex.
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Affiliation(s)
- Monika E Mysiak
- Department of Physiological Chemistry, University Medical Center Utrecht, and Centre for Biomedical Genetics, 3584 CG Utrecht, The Netherlands
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27
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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.
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Affiliation(s)
- H Liu
- Centre for Biomolecular Science, Biomolecular Science Building, The University of St. Andrews, North Haugh, St. Andrews, KY16 9ST, UK
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28
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van Breukelen B, Brenkman AB, Holthuizen PE, van der Vliet PC. Adenovirus type 5 DNA binding protein stimulates binding of DNA polymerase to the replication origin. J Virol 2003; 77:915-22. [PMID: 12502807 PMCID: PMC140850 DOI: 10.1128/jvi.77.2.915-922.2003] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The adenovirus (Ad) DNA-binding protein (DBP) is essential for the elongation phase of Ad DNA replication by unwinding the template in an ATP-independent fashion, employing its capacity to form multimers. DBP also enhances the rate of initiation, with the highest levels obtained at low concentrations of Ad DNA polymerase (Pol). Here, we show that stimulation of initiation depends on the template conformation. Maximal stimulation, up to 15-fold, is observed on double-stranded or viral TP-containing origins. The stimulation is reduced on partially single-stranded origins and DBP does not enhance initiation any more once the origin is completely unwound. This suggests a role for DBP in origin unwinding that is comparable to its unwinding capacity during elongation. However, mutant DBP proteins defective in unwinding and elongation can still enhance initiation on ds templates. DBP also stimulates the binding of nuclear factor I (NFI) to the origin and lowers the K(m) for coupling of the first nucleotide to the precursor terminal protein by Pol. Mobility shift experiments reveal that DBP stimulates the binding of Pol on double-stranded origin and nonorigin DNA but not on single-stranded DNA. This effect is specific for DBP and is also seen with other DNA Pols. Our results suggest that, rather than by origin unwinding, DBP enhances initiation by modulating the origin conformation such that DNA Pol can bind more efficiently.
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Affiliation(s)
- Bas van Breukelen
- Department of Physiological Chemistry and Centre for Biomedical Genetics, University Medical Center Utrecht, The Netherlands
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29
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de Jong R, Mysiak M, Meijer L, van der Linden M, van der Vliet P. Recruitment of the priming protein pTP and DNA binding occur by overlapping Oct-1 POU homeodomain surfaces. EMBO J 2002; 21:725-35. [PMID: 11847120 PMCID: PMC125863 DOI: 10.1093/emboj/21.4.725] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The human transcription factor Oct-1 can stimulate transcription from a variety of promoters by interacting with the coactivators OBF-1/OCA-B/BOB-1, SNAP190 and VP16. These proteins contact Oct-1 regions different from the DNA binding surface. Oct-1 also stimulates the DNA replication of adenovirus through its DNA binding site in the origin. The Oct-1 POU homeodomain (POUhd) binds the adenovirus precursor terminal protein pTP, which serves as the protein primer of DNA replication and recruits pTP to the origin. To map the interaction with pTP at the POUhd surface, we screened a library of randomly mutated POU domains and identified mutations that interfered with pTP interaction and DNA replication stimulation. These mutants clustered at a surface different from those recognized by OBF-1, SNAP190 and VP16. Unexpectedly, the pTP binding region largely overlapped with the DNA binding surface of POUhd. In agreement with this, pTP binding and DNA binding were mutually exclusive. We propose a model to reconcile pTP recruitment and DNA binding by Oct-1.
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Affiliation(s)
| | | | | | | | - P.C. van der Vliet
- Department of Physiological Chemistry, University Medical Center Utrecht and Centre for Biomedical Genetics, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands
Corresponding author e-mail:
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30
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Botting CH, Hay RT. Role of conserved residues in the activity of adenovirus preterminal protein. J Gen Virol 2001; 82:1917-1927. [PMID: 11457998 DOI: 10.1099/0022-1317-82-8-1917] [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: 11/18/2022] Open
Abstract
Preterminal protein (pTP) is a component of the preinitiation complex which forms at the adenovirus origin of DNA replication and acts as the protein primer during DNA synthesis. In order to determine the role of various regions of the molecule a series of 18 mutations was introduced into conserved motifs of pTP which were predicted to be surface exposed, and the mutants expressed in insect cells using a baculovirus expression system. Their ability to initiate DNA replication was assessed and the effect the mutations have on the individual interactions which contribute to the formation of the pre-initiation complex was determined. Classes of mutants could be identified which were unable to bind DNA or interact with the adenovirus DNA polymerase, but one class of mutants retained these activities and yet failed to initiate DNA replication. These mutants therefore identify regions of pTP required for different aspects of adenovirus DNA replication.
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Affiliation(s)
- Catherine H Botting
- Centre for Biomolecular Sciences, School of Biology, University of St Andrews, Biomolecular Sciences Building, North Haugh, St Andrews, Fife KY16 9ST, UK1
| | - Ronald T Hay
- Centre for Biomolecular Sciences, School of Biology, University of St Andrews, Biomolecular Sciences Building, North Haugh, St Andrews, Fife KY16 9ST, UK1
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31
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Dán A, Elo P, Harrach B, Zádori Z, Benko M. Four new inverted terminal repeat sequences from bovine adenoviruses reveal striking differences in the length and content of the ITRs. Virus Genes 2001; 22:175-9. [PMID: 11324754 DOI: 10.1023/a:1008125324346] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The inverted terminal repeat (ITR) of the genome of four bovine adenovirus (BAdV) types have been sequenced, analysed and compared to the ITRs of other adenoviruses. The length of ITRs of the examined BAdVs ranged between 59 and 368 base pairs, thus the presently known longest adenovirus ITR sequence is from BAdV-10. The conserved motifs and characteristic sequence elements of the ITRs providing different binding sites for replicative proteins of viral and cellular origin seemed to be distributed according to the proposed genus classification of BAdVs. The ITRs of BAdV-10 share similarity with the members of the genus Mastadenovirus, while the ITRs of the other three sequenced serotypes (BAdV-4, 5 and strain Rus) which are candidate members of the genus Atadenovirus are very short and contain NFI and Sp1 binding sites only. The analysis of the new ITRs implied that the nucleotide sequence of the so-called core origin is highly preserved within the mastadenovirus genus only.
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Affiliation(s)
- A Dán
- Veterinary Medical Research Institute, Hungarian Academy of Sciences, Budapest.
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32
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Andersen B, Rosenfeld MG. POU domain factors in the neuroendocrine system: lessons from developmental biology provide insights into human disease. Endocr Rev 2001; 22:2-35. [PMID: 11159814 DOI: 10.1210/edrv.22.1.0421] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
POU domain factors are transcriptional regulators characterized by a highly conserved DNA-binding domain referred to as the POU domain. The structure of the POU domain has been solved, facilitating the understanding of how these proteins bind to DNA and regulate transcription via complex protein-protein interactions. Several members of the POU domain family have been implicated in the control of development and function of the neuroendocrine system. Such roles have been most clearly established for Pit-1, which is required for formation of somatotropes, lactotropes, and thyrotropes in the anterior pituitary gland, and for Brn-2, which is critical for formation of magnocellular and parvocellular neurons in the paraventricular and supraoptic nuclei of the hypothalamus. While genetic evidence is lacking, molecular biology experiments have implicated several other POU factors in the regulation of gene expression in the hypothalamus and pituitary gland. Pit-1 mutations in humans cause combined pituitary hormone deficiency similar to that found in mice deleted for the Pit-1 gene, providing a striking example of how basic developmental biology studies have provided important insights into human disease.
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Affiliation(s)
- B Andersen
- Department of Medicine, University of California, San Diego, La Jolla, 92093-0648, USA.
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33
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Liu H, Naismith JH, Hay RT. Identification of conserved residues contributing to the activities of adenovirus DNA polymerase. J Virol 2000; 74:11681-9. [PMID: 11090167 PMCID: PMC112450 DOI: 10.1128/jvi.74.24.11681-11689.2000] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Adenovirus codes for a DNA polymerase that is a member of the DNA polymerase alpha family and uses a protein primer for initiation of DNA synthesis. It contains motifs characteristic of a proofreading 3'-5'-exonuclease domain located in the N-terminal region and several polymerase motifs located in the C-terminal region. To determine the role of adenovirus DNA polymerase in DNA replication, 22 site-directed mutations were introduced into the conserved DNA polymerase motifs in the C-terminal region of adenovirus DNA polymerase and the mutant forms were expressed in insect cells using a baculovirus expression system. Each mutant enzyme was tested for DNA binding activity, the ability to interact with pTP, DNA polymerase catalytic activity, and the ability to participate in the initiation of adenovirus DNA replication. The mutant phenotypes identify functional domains within the adenovirus DNA polymerase and allow discrimination between the roles of conserved residues in the various activities carried out by the protein. Using the functional data in this study and the previously published structure of the bacteriophage RB69 DNA polymerase (J. Wang et al., Cell 89:1087-1099, 1997), it is possible to envisage how the conserved domains in the adenovirus DNA polymerase function.
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Affiliation(s)
- H Liu
- Centre for Biomolecular Science, The University of St. Andrews, North Haugh, St. Andrews KY16 9ST, United Kingdom
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34
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Kennedy BK, Barbie DA, Classon M, Dyson N, Harlow E. Nuclear organization of DNA replication in primary mammalian cells. Genes Dev 2000; 14:2855-68. [PMID: 11090133 PMCID: PMC317063 DOI: 10.1101/gad.842600] [Citation(s) in RCA: 226] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Using methods that conserve nuclear architecture, we have reanalyzed the spatial organization of the initiation of mammalian DNA synthesis. Contrary to the commonly held view that replication begins at hundreds of dispersed nuclear sites, primary fibroblasts initiate synthesis in a limited number of foci that contain replication proteins, surround the nucleolus, and overlap with previously identified internal lamin A/C structures. These foci are established in early G(1)-phase and also contain members of the retinoblastoma protein family. Later, in S-phase, DNA replication sites distribute to regions located throughout the nucleus. As this progression occurs, association with the lamin structure and pRB family members is lost. A similar temporal progression is found in all the primary cells we have examined but not in most established cell lines, indicating that the immortalization process modifies spatial control of DNA replication. These findings indicate that in normal mammalian cells, the onset of DNA synthesis is coordinately regulated at a small number of previously unrecognized perinucleolar sites that are selected in early G(1)-phase.
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Affiliation(s)
- B K Kennedy
- Massachusetts General Hospital Cancer Center, Charlestown, Massachusetts 02129, USA.
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35
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Abstract
The Nuclear Factor I (NFI) family of site-specific DNA-binding proteins (also known as CTF or CAAT box transcription factor) functions both in viral DNA replication and in the regulation of gene expression. The classes of genes whose expression is modulated by NFI include those that are ubiquitously expressed, as well as those that are hormonally, nutritionally, and developmentally regulated. The NFI family is composed of four members in vertebrates (NFI-A, NFI-B, NFI-C and NFI-X), and the four NFI genes are expressed in unique, but overlapping, patterns during mouse embryogenesis and in the adult. Transcripts of each NFI gene are differentially spliced, yielding as many as nine distinct proteins from a single gene. Products of the four NFI genes differ in their abilities to either activate or repress transcription, likely through fundamentally different mechanisms. Here, we will review the properties of the NFI genes and proteins and their known functions in gene expression and development.
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Affiliation(s)
- R M Gronostajski
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic Foundation, Case Western Reserve University, OH 44195, USA.
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36
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Hartigan-O'Connor D, Amalfitano A, Chamberlain JS. Improved production of gutted adenovirus in cells expressing adenovirus preterminal protein and DNA polymerase. J Virol 1999; 73:7835-41. [PMID: 10438876 PMCID: PMC104313 DOI: 10.1128/jvi.73.9.7835-7841.1999] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Production of gutted, or helper-dependent, adenovirus vectors by current methods is inefficient. Typically, a plasmid form of the gutted genome is transfected with helper viral DNA into 293 cells; the resulting lysate is serially passaged to increase the titer of gutted virions. Inefficient production of gutted virus particles after cotransfection is likely due to suboptimal association of replication factors with the abnormal origins found in these plasmid substrates. To test this hypothesis, we explored whether gutted virus production would be facilitated by transfection into cells expressing various viral replication factors. We observed that C7 cells, coexpressing adenoviral DNA polymerase and preterminal protein, converted plasmid DNA into replicating virus approximately 50 times more efficiently than did 293 cells. This property of C7 cells can be used to greatly increase the efficiency of gutted virus production after cotransfection of gutted and helper viral DNA. These cells should also be useful for generation of recombinant adenovirus from any plasmid-based precursor.
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Affiliation(s)
- D Hartigan-O'Connor
- Program in Cellular and Molecular Biology, University of Michigan Medical School, Ann Arbor, Michigan 48109-0618, USA
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37
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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.
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Affiliation(s)
- R N de Jong
- Laboratory for Physiological Chemistry and Centre for Biomedical Genetics, Utrecht University, Utrecht, The Netherlands
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38
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Huang J, Levin DB. Identification and functional analysis of a putative non-hr origin of DNA replication from the Spodoptera littoralis type B multinucleocapsid nucleopolyhedrovirus. J Gen Virol 1999; 80 ( Pt 8):2263-2274. [PMID: 10466826 DOI: 10.1099/0022-1317-80-8-2263] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A putative non-hr origin of DNA replication was identified in the Spodoptera littoralis multinucleocapsid nucleopolyhedrovirus (SpliNPV) genome by transient replication assays. The putative SpliNPV ori was mapped to the PstI-J fragment between 75.1-77.9 map units in the SpliNPV genome. While the DNA sequence of the putative SpliNPV ori aligned with regions within the non-hr oris of Autographa californica, Orgyia pseudotsugata and Spodoptera exigua multinucleocapsid nucleopolyhedroviruses, it has limited DNA sequence identity with these elements. The sequence of the putative SpliNPV non-hr ori fragment contains a unique distribution of imperfect palindromes, multiple direct repeats and putative transcription factor-binding sites. Transient expression assays indicated that the putative SpliNPV ori fragment repressed SpliNPV lef-3 promoter-mediated luciferase reporter gene expression. However, the putative SpliNPV ori fragment itself was capable of directing luciferase expression in the absence of a recognizable baculovirus promoter element in an orientation-independent fashion, suggesting that DNA sequence motifs within its sequence can activate transcription. Gel mobility shift analyses confirmed that proteins within nuclear extracts from both uninfected and virus-infected cells bound with specificity to the putative SpliNPV ori fragment.
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Affiliation(s)
- Jianhe Huang
- Department of Biology, University of Victoria, PO Box 3020, Victoria, British Columbia, Canada V8W 3N51
| | - David B Levin
- Department of Biology, University of Victoria, PO Box 3020, Victoria, British Columbia, Canada V8W 3N51
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39
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Botting CH, Hay RT. Characterisation of the adenovirus preterminal protein and its interaction with the POU homeodomain of NFIII (Oct-1). Nucleic Acids Res 1999; 27:2799-805. [PMID: 10373599 PMCID: PMC148491 DOI: 10.1093/nar/27.13.2799] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Formation of the preinitiation complex for adenovirus DNA replication involves the incoming preterminal protein-adenovirus DNA polymerase heterodimer being positioned at the origin of replication by protein-DNA and protein-protein interactions. Preterminal protein directly binds to the cellular transcription factor nuclear factor III (Oct-1), via the POU homeodomain. Co-precipitation of POU with individual domains of preterminal protein expressed by in vitro translation indicated that POU contacts multiple sites on preterminal protein. Partial proteolysis of preterminal protein in the presence or absence of POU homeodomain demonstrated that many sites accessible to proteases in free preterminal protein were resistant to cleavage in the presence of POU homeodomain. The accessibility of sites in free preterminal protein to cleavage by trypsin was strongly dependent on the ionic strength, suggesting that preterminal protein may undergo a sodium chloride-induced conformational change. It is therefore likely that the POU homeodomain contacts a number of sites on preterminal protein to induce a conformational change which may influence the initiation of adenovirus DNA replication.
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Affiliation(s)
- C H Botting
- School of Biomedical Sciences, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
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40
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Ying B, Smith K, Spindler KR. Mouse adenovirus type 1 early region 1A is dispensable for growth in cultured fibroblasts. J Virol 1998; 72:6325-31. [PMID: 9658071 PMCID: PMC109774 DOI: 10.1128/jvi.72.8.6325-6331.1998] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/1998] [Accepted: 04/21/1998] [Indexed: 02/08/2023] Open
Abstract
Mouse adenovirus type 1 (MAV-1) mutants with deletions of conserved regions of early region 1A (E1A) or with point mutations that eliminate translation of E1A were used to determine the role of E1A in MAV-1 replication. MAV-1 E1A mutants expressing no E1A protein grew to titers comparable to wild-type MAV-1 titers on mouse fibroblasts (3T6 fibroblasts and fibroblasts derived from Rb+/+, Rb+/-, and Rb-/- transgenic embryos). To test the hypothesis that E1A could induce a quiescent cell to reenter the cell cycle, fibroblasts were serum starved to stop DNA replication and cellular replication and then infected with the E1A mutant and wild-type viruses. All grew to equivalent titers. Steady-state levels of MAV-1 early mRNAs (E1A, E1B, E2, E3, and E4) from 3T6 cells infected with wild-type or E1A mutant virus were examined by Northern analysis. Steady-state levels of mRNAs from the mutant-infected cells were comparable to or greater than the levels found in wild-type virus infections for most of the early regions and for two late genes. The E2 mRNA levels were slightly reduced in all mutant infections relative to wild-type infections. E1A mRNA was not detected from infections with the MAV-1 E1A null mutant, pmE109, or from infections with similar MAV-1 E1A null mutants, pmE112 and pmE113. The implications for the lack of a requirement of E1A in cell culture are discussed.
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Affiliation(s)
- B Ying
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
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41
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Webster A, Leith IR, Nicholson J, Hounsell J, Hay RT. Role of preterminal protein processing in adenovirus replication. J Virol 1997; 71:6381-9. [PMID: 9261355 PMCID: PMC191911 DOI: 10.1128/jvi.71.9.6381-6389.1997] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Preterminal protein (pTP), the protein primer for adenovirus DNA replication, is processed at two sites by the virus-encoded protease to yield mature terminal protein (TP). Here we demonstrate that processing to TP, via an intermediate (iTP), is conserved in all serotypes sequenced to date; and in determining the sites cleaved in Ad4 pTP, we extend the previously published substrate specificity of human adenovirus proteases to include a glutamine residue at P4. Furthermore, using monoclonal antibodies raised against pTP, we show that processing to iTP and TP are temporally separated in the infectious cycle, with processing to iTP taking place outside the virus particles. In vitro and in vivo studies of viral DNA replication reveal that iTP can act as a template for initiation and elongation and argue against a role for virus-encoded protease in switching off DNA replication. Virus DNA with TP attached to its 5' end (TP-DNA) has been studied extensively in in vitro DNA replication assays. Given that in vivo pTP-DNA, not TP-DNA, is the template for all but the first round of replication, the two templates were compared in vitro and shown to have different properties. Immunofluorescence studies suggest that a region spanning the TP cleavage site is involved in defining the subnuclear localization of pTP. Therefore, a likely role for the processing of pTP-DNA is to create a distinct template for early transcription (TP-DNA), while the terminal protein moiety, be it TP or pTP, serves to guide the template to the appropriate subcellular location through the course of infection.
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Affiliation(s)
- A Webster
- School of Biological and Medical Science, University of St. Andrews, Fife, Scotland
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42
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Veenstra GJ, van der Vliet PC, Destrée OH. POU domain transcription factors in embryonic development. Mol Biol Rep 1997; 24:139-55. [PMID: 9291088 DOI: 10.1023/a:1006855632268] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- G J Veenstra
- Hubrecht Laboratory, Netherlands Institute for Developmental Biology, Utrecht, The Netherlands
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43
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Abstract
DNA replication of papillomaviruses requires the viral E1 and E2 proteins. These proteins bind cooperatively to the viral origin of replication (ori), which contains binding sites for both proteins, forming an E1-E2-ori complex which is essential for initiation of DNA replication. To map the domains in E2 that are involved in the interaction with E1, we have used chimeric bovine papillomavirus (BPV)/human papillomavirus type 11 (HPV-11) E2 proteins. The results from this study show that both the DNA binding domain and the transactivation domain from BPV E2 independently can interact with BPV E1. However, the roles of these two interactions are different: the interaction between E1 and the activation domain of E2 is necessary and sufficient for cooperativity in binding and for DNA replication; the interaction between E1 and the DNA binding domain of E2 is required only when the binding sites for E1 and E2 are adjacent to each other, and the function of this interaction appears to be to facilitate the interaction between E1 and the transactivation domain of E2. These results indicate that the cooperative binding of E1 and E2 to the BPV ori takes place via a novel two-stage mechanism where one interaction serves as a trigger for the formation of the second, productive, interaction between the two proteins.
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Affiliation(s)
- M Berg
- Cold Spring Harbor Laboratory, New York 11724, USA
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44
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Dekker J, Kanellopoulos PN, Loonstra AK, van Oosterhout JA, Leonard K, Tucker PA, van der Vliet PC. Multimerization of the adenovirus DNA-binding protein is the driving force for ATP-independent DNA unwinding during strand displacement synthesis. EMBO J 1997; 16:1455-63. [PMID: 9135160 PMCID: PMC1169742 DOI: 10.1093/emboj/16.6.1455] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
In contrast to other replication systems, adenovirus DNA replication does not require a DNA helicase to unwind the double-stranded template. Elongation is dependent on the adenovirus DNA-binding protein (DBP) which has helix-destabilizing properties. DBP binds cooperatively to single-stranded DNA (ssDNA) in a non-sequence-specific manner. The crystal structure of DBP shows that the protein has a C-terminal extension that hooks on to an adjacent monomer which results in the formation of long protein chains. We show that deletion of this C-terminal arm results in a monomeric protein. The mutant binds with a greatly reduced affinity to ssDNA. The deletion mutant still stimulates initiation of DNA replication like the intact DBP. This shows that a high affinity of DBP for ssDNA is not required for initiation. On a single-stranded template, elongation is also observed in the absence of DBP. Addition of DBP or the deletion mutant has no effect on elongation, although both proteins stimulate initiation on this template. Strand displacement synthesis on a double-stranded template is only observed in the presence of DBP. The mutant, however, does not support elongation on a double-stranded template. The unwinding activity of the mutant is highly reduced compared with intact DBP. These data suggest that protein chain formation by DBP and high affinity binding to the displaced strand drive the ATP-independent unwinding of the template during adenovirus DNA replication.
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Affiliation(s)
- J Dekker
- Laboratory for Physiological Chemistry, Utrecht University, The Netherlands
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45
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van Leeuwen HC, Rensen M, van der Vliet PC. The Oct-1 POU homeodomain stabilizes the adenovirus preinitiation complex via a direct interaction with the priming protein and is displaced when the replication fork passes. J Biol Chem 1997; 272:3398-405. [PMID: 9013582 DOI: 10.1074/jbc.272.6.3398] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Initiation of adenovirus DNA replication is strongly enhanced by two cellular transcription factors, NFI and Oct-1, which bind to the auxiliary origin and tether the viral precursor terminal protein-DNA polymerase (pTP.pol) complex to the core origin. NFI acts through a direct contact with the DNA polymerase, but the mode of action of Oct 1 is unknown. Employing glutathione S-transferase-POU pull-down assays and protein affinity chromatography, we have established that the POU domain contacts pTP rather than pol. The POU homeodomain is responsible for this interaction. The protein-protein contacts lead to increased binding of pTP-pol to the core origin, which is caused by a reduced off-rate. The enhanced formation of a pTP.pol.POU complex on the origin correlates with stimulation of replication. Using an immobilized replication system, we have studied the kinetics of dissociation of the Oct-1 POU domain during replication. In contrast to NFI, which dissociates very early in initiation, Oct-1 dissociates only when the binding site is rendered single-stranded upon translocation of the replication fork. Our data indicate that NFI and Oct-1 enhance initiation synergistically by touching different targets in the preinitiation complex and dissociate independently after initiation.
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Affiliation(s)
- H C van Leeuwen
- Laboratory for Physiological Chemistry, Utrecht University, Stratenum, P. O. Box 80042, 3508 TA Utrecht, The Netherlands
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Christensen J, Cotmore SF, Tattersall P. A novel cellular site-specific DNA-binding protein cooperates with the viral NS1 polypeptide to initiate parvovirus DNA replication. J Virol 1997; 71:1405-16. [PMID: 8995666 PMCID: PMC191197 DOI: 10.1128/jvi.71.2.1405-1416.1997] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Replication of linear single-stranded parvovirus DNA proceeds by a rolling-hairpin mechanism which generates long, palindromic, duplex concatamers. Processing to monomer length requires initiation from origins of DNA replication located at the 3' and 5' ends of each embedded monomer, reactions which can be recapitulated in vitro for minute virus of mice (MVM). To determine which cellular proteins were essential for replication from these origins, S100 extracts from 293S cells were fractionated on phosphocellulose. When recombined, these fractions were able to support replication in vitro, dependent on the viral initiator protein NS1, using plasmid forms of the 5' origin or the minimal 3' origin as templates. Fraction P-cell 1 contains two factors, replication protein A (RPA) and proliferating-cell nuclear antigen (PCNA), known to be essential for simian virus 40 replication in vitro. When P-cell 1 was replaced with purified recombinant RPA and PCNA, NS1-mediated MVM replication initiated from the 5' origin but not from the 3' origin. The 3' origin is a 50-bp sequence containing three distinct recognition elements, an NS1 binding site, a site at which NS1 nicks the DNA to generate the priming 3' OH, and a region containing a consensus activated transcription factor (ATF) binding site. To identify the missing factor(s) for 3' origin replication, P-cell 1 was fractionated by further chromatography and active fractions were identified by their ability to complement RPA, PCNA, and P-cell 2 for NS1-mediated, origin-specific replication. Gel shift and UV cross-linking analysis of the replication-competent fractions revealed a novel 110-kDa sequence-specific DNA binding protein which recognized the consensus ATF binding site region of the origin and which we have termed parvovirus initiation factor, or PIF. Binding of PIF appears to activate the endonuclease function of NS1, allowing efficient and specific nicking of the 3' minimal origin under stringent conditions in vitro.
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Affiliation(s)
- J Christensen
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut 06510, USA
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47
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Abstract
In adenovirus-infected cells, the virus-encoded preterminal protein and DNA polymerase form a heterodimer that is directly involved in initiation of DNA replication. Monoclonal antibodies were raised against preterminal protein, and epitopes recognized by the antibodies were identified by using synthetic peptides. Partial proteolysis of preterminal protein reveals that it has a tripartite structure, with the three domains being separated by two protease-sensitive areas, located at sites processed by adenovirus protease. These areas of protease sensitivity are probably surface-exposed loops, as they are the sites, along with the C-terminal region of preterminal protein, recognized by the monoclonal antibodies. Preterminal protein is protected from proteolytic cleavage when bound to adenovirus DNA polymerase, suggesting either multiple contact points between the proteins or a DNA polymerase-induced conformational change in preterminal protein. Two of the preterminal protein-specific antibodies induced dissociation of the preterminal protein-adenovirus DNA polymerase heterodimer and inhibited initiation of adenovirus DNA replication in vitro. Antibodies binding close to the primary processing sites of adenovirus protease inhibited DNA binding, consistent with UV cross-linking results which reveal that an N-terminal, protease-resistant domain of preterminal protein contacts DNA. Monoclonal antibodies recognizing epitopes within the C-terminal 60 amino acids of preterminal protein stimulate DNA binding, an effect mediated through a decrease in the dissociation rate constant. These results suggest that preterminal protein contains a large, noncontiguous surface required for interaction with DNA polymerase, an N-terminal DNA binding domain, and a C-terminal regulatory domain.
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Affiliation(s)
- A Webster
- School of Biological and Medical Science, University of St. Andrews, Fife, Scotland
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Freire R, Serrano M, Salas M, Hermoso JM. Activation of replication origins in phi29-related phages requires the recognition of initiation proteins to specific nucleoprotein complexes. J Biol Chem 1996; 271:31000-7. [PMID: 8940089 DOI: 10.1074/jbc.271.48.31000] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Protein p6 of Bacillus subtilis phage phi29 activates the initiation of viral DNA replication by forming a multimeric nucleoprotein complex at the origins of replication, located at both ends of the linear genome. This activation requires a precise positioning of the protein p6 array with respect to the initiation site. To investigate this activation mechanism, we have purified the phi29 protein p6 counterparts from the related phages Nf and GA-1 and analyzed the formation of complexes with DNA. In the homologous protein p6-DNA complexes the phi29 and Nf protein arrays showed an identical positioning, different than that of the GA-1 protein array. In contrast, in the heterologous complexes the protein showed a different arrangement except in the case of the Nf protein-phi29 DNA complex. We have also purified the proteins involved in the initiation of replication (terminal protein and DNA polymerase) from phages Nf and GA-1 and measured the ability of the different p6 proteins to activate homologous and heterologous replication origins. The results obtained indicate that the activation requires not only the formation of a specific nucleoprotein complex but also its specific recognition by the proteins involved in the initiation of DNA replication.
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Affiliation(s)
- R Freire
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma, Cantoblanco, 28049 Madrid, Spain
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Schiedner G, Doerfler W. Insufficient levels of NFIII and its low affinity for the origin of adenovirus type 12 (Ad12) DNA replication contribute to the abortive infection of BHK21 hamster cells by Ad12. J Virol 1996; 70:8003-9. [PMID: 8892924 PMCID: PMC190873 DOI: 10.1128/jvi.70.11.8003-8009.1996] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Human adenovirus type 12 (Ad12) induces undifferentiated sarcomas in neonate Syrian hamsters and hence presents a suitable model for studies of the molecular mechanism of viral oncogenesis. Since we submit that an understanding of the early steps in the interaction between Ad12 and hamster cells might shed light on the initiation of malignant transformation, the abortive infection of BHK21 hamster cells with Ad12 has been investigated in detail. Ad12 replication in these cells is blocked in early stages, while Ad2 can replicate to moderate titers. Early Ad12 genes are expressed in BHK21 hamster cells, but there is a total block in Ad12 DNA replication and late gene transcription. The Ad5-transformed hamster cell line BHK297-C131, with the left terminus of Ad5 DNA chromosomally integrated and constitutively expressed, allows limited levels of Ad12 DNA replication and late transcription, probably through Ad5 E1 functions, but not the translation of late Ad12 gene products. We have now investigated the capacities of binding of nuclear proteins NFI and NFIII from permissive human KB cells, nonpermissive hamster BHK21 cells, and complementing BHK297-C131 cells to the origin of replication (ori) of Ad2 or Ad12 DNA. The electrophoretic mobility shift assay has been used to assess these binding reactions. The data support the notions that NFIII of BHK21 cells has a lower affinity for the ori of Ad12 DNA than for the ori of Ad2 DNA and that the levels of NFIII in BHK21 cells are markedly reduced compared with the levels in the permissive human KB cells or the complementing BHK297-C131 hamster cells. These deficiencies are contributing factors for the abortive infection of BHK21 hamster cells with Ad12. The lack of sufficient levels of NFIII in BHK21 cells is also consistent with the decreased replication capacity of Ad2 in hamster compared with human cell lines.
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Affiliation(s)
- G Schiedner
- Institut für Genetik, Universität zu Köln, Cologne, Germany
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50
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Abstract
Pyridoxal phosphate modification of adenovirus DNA polymerase results in loss of DNA polymerase activity, whereas the 3' --> 5' exonuclease activity is unaffected. Inhibition by pyridoxal phosphate is time-dependent, displays saturation kinetics, and is reversible in the presence of excess primary amine unless the pyridoxal phosphate-enzyme adduct is first reduced with NaBH4. Thus, inhibition is the consequence of Schiff base formation between the aldehyde moiety of pyridoxal phosphate and primary amino groups on the enzyme. In addition to inhibiting DNA polymerase activity, pyridoxal phosphate also inhibited the ability of the enzyme to initiate viral DNA replication, by transfer of dCMP onto the preterminal protein. Neither template-primer nor dNTP protect against pyridoxal phosphate inhibition, but the combination of template-primer and complementary substrate dNTP protected both initiation and DNA polymerase activities. Thus, it is likely that both the dCMP transfer activity required for initiation and DNA polymerase activity are carried out at the same site of the enzyme.
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Affiliation(s)
- A Monaghan
- School of Biological and Medical Sciences, Irvine Building, University of St. Andrews, Fife KY16 9AL, Scotland, United Kingdom
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