Viral Discovery and Sequence Recovery Using DNA Microarrays

Wang, David; Urisman, Anatoly; Liu, Yu‐Tsueng; Springer, Michael; Ksiazek, Thomas G.; Erdman, Dean D.; Mardis, Elaine R.; Hickenbotham, Matthew T.; Magrini, Vincent; Eldred, James M.; Latreille, Julie; Wilson, Richard K.; Ganem, Don; DeRisi, Joseph L.

doi:10.1371/journal.pbio.0000002

Cited by 415 publications

(439 citation statements)

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“…This pathway is induced by IFNα treatment and RNase L participates in mitochondrial mRNA degradation. Mitochondrial mRNA remained stable during IFNα treatment in cells where RNase L activity was decreased [137,138]. Because the array contains highly conserved sequences within viral nucleic acids, it can detect viruses not explicitly represented.…”

Section: ) Apoptosismentioning

confidence: 99%

“…Therefore, there is a possibility that the linkage of RNase L alterations to HPC might reflect enhanced susceptibility to a viral agent. To test this hypothesis, RNA derived from wild-type and RNase L variant (R462Q) prostate tumors was examined for evidence of viral sequences, by hybridization to a DNA microarray composed of the most conserved sequences of all known human, animal, plant and bacterial viruses [137,138]. Because the array contains highly conserved sequences within viral nucleic acids, it can detect viruses not explicitly represented.…”

Section: Iv) Implications In Pathology 1) Role Of Rnase L In the Biolmentioning

confidence: 99%

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Diverse functions of RNase L and implications in pathology

Bisbal

Silverman

2007

Biochimie

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The endoribonuclease L (RNase L) is the effector of the 2-5A system, a major enzymatic pathway involved in the molecular mechanism of interferons (IFN). RNase L is a very unusual nuclease with a complex mechanism of regulation. It is a latent enzyme, expressed in nearly every mammalian cell type. Its activation requires its binding to a small oligonucleotide, 2-5A. 2-5A is a series of unique 5′-triphosphorylated oligoadenylates with 2′-5′ phosphodiester bonds. By regulating viral and cellular RNA expression, RNase L plays an important role in the antiviral and antiproliferative activities of IFN and contributes to innate immunity and cell metabolism. The 2-5A/RNase L pathway is implicated in mediating apoptosis in response to viral infections and to several types of external stimuli. Several recent studies have suggested that RNase L could have a role in cancer biology and evidence of a tumor suppressor function of RNase L has emerged from studies on the genetics of hereditary prostate cancer. KeywordsInterferon; RNase L; RNA expression; apoptosis; prostate; virus; cancer I) IntroductionThe endoribonuclease L (RNase L) is the effector of the 2-5A system, a major enzymatic pathway regulated by interferons (IFN) [1] (Figure 1). The 2-5A system is one of the two antiviral pathways induced by IFN and activated by double stranded RNA (dsRNA), the other is mediated by the dsRNA dependent protein kinase (PKR) [2]. RNase L is a very unusual nuclease. It is a latent enzyme, expressed in nearly every mammalian cell type. Its activation requires its binding to a small oligonucleotide, 2-5A ( Figure 1). 2-5A itself is very unusual, consisting of a series of 5′-triphosphorylated oligoadenylates with 2′-5′ phosphodiester bonds in contrast to the 3′-5′ linkages found in RNA and DNA. The initial and essential observation was made by Ian Kerr's group in 1974 reporting an IFN-induced increase in the sensitivity of protein synthesis to inhibition by dsRNA [3]. Peter Lengyel's group observed increased nuclease activity in extracts of interferon treated cells incubated with dsRNA [4,5]. The identification by Ian Kerr's group of the activators of this nuclease, 2-5A [6] and of the enzyme responsible for their synthesis, the 2-5A-synthetase [7][8][9], led to the discovery of the 2-5A pathway. Clemens and Williams directly demonstrated a nuclease, now recognized as RNase Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. (Figure 2). The N-terminal domain could be considered as the regulatory domain of RNase L. It is composed of eight complete and one partial ankyrin motifs (R1-R9). Two wal...

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Section: ) Apoptosismentioning

confidence: 99%

Section: Iv) Implications In Pathology 1) Role Of Rnase L In the Biolmentioning

confidence: 99%

Diverse functions of RNase L and implications in pathology

Bisbal

Silverman

2007

Biochimie

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“…This led us to consider the possibility that the putative linkage of RNase L alterations to HPC might reflect enhanced susceptibility to a viral agent. To test our hypothesis, in collaboration with Don Ganem, Joseph DeRisi and Eric Klein we examined wild-type and RNase L variant (R462Q) prostate tumors for evidence of viral sequences, by hybridization to a DNA microarray composed of the most conserved sequences of all known human, animal, plant and bacterial viruses [101][102][103]. We reported in 2006 that 40% (8 of 20) of all tumors homozygous for the R462Q allele harbored the genome of a novel gammaretrovirus, called XMRV, which is closely related to xenotropic MuLVs [103].…”

Section: The Role Of Rnase L In Hereditary Prostate Cancer and Discovmentioning

confidence: 99%

A scientific journey through the 2-5A/RNase L system

Silverman

2007

Cytokine & Growth Factor Reviews

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The antiviral and antitumor actions of interferons are caused, in part, by a remarkable regulated RNA cleavage pathway known as the 2-5A/RNase L system. 2′-5′ linked oligoadenylates (2-5A) are produced from ATP by interferon-inducible synthetases. 2-5A activates pre-existing RNase L, resulting in the cleavage of RNAs within single-stranded regions. Activation of RNase L by 2-5A leads to an antiviral response, although precisely how this happens is a subject of ongoing investigations. Recently, RNase L was identified as the hereditary prostate cancer 1 gene. That finding has led to the discovery of a novel human retrovirus, XMRV. My scientific journey through the 2-5A system recounts some of the highlights of these efforts. Knowledge gained from studies on the 2-5A system could have an impact on development of therapies for important viral pathogens and cancer.Keywords 2-5A; RNase L; interferon; cancer; virus Background on the 2-5A/RNase L systemOver the past thirty-years, investigations into the mechanisms of interferon (IFN) action have elucidated how antiviral innate immunity operates within and between mammalian cells. The focus of my work over this period has been, and continues to be, probing the biology and biochemistry of the 2-5A/RNase L system, and studying its roles in health and disease. My scientific journey, from basic research to clinical studies, are summarized in this monograph. The 2-5A/RNase L system is one the principal pathways by which IFNs suppress viral infections. Exposure of cells to IFNs induces expression of genes that result in an "antiviral state". Type I IFNs bind to the IFN-α receptor 1 (IFNAR1) and IFNAR2 polypeptide chains on cell surfaces initiating JAK-STAT signaling to the IFN stimulated genes (ISGs) [1]. Included among over a hundred different ISGs are genes encoding 2-5A synthetases (OAS) [2,3]. The OAS genes are a family of ISGs that function in the 2-5A/RNase L system (Fig. 1). In humans there are three functional OAS genes (OAS1-3), resulting in 8 to 10 OAS isoforms due to alternative mRNA splicing [4]. In mice, in addition to OAS2 and OAS3 there are 7 separate OAS1 genes, including OAS1b, the flavivirus resistance gene (Flv r ] [5][6][7][8]. When stimulated by dsRNA, the functional OAS proteins produce a series of short 5′-phosphorylated, 2′,5′-linked oligoadenylates collectively referred to as 2-5A [p x 5′A(2′p5′A) n ; x = 1-3; n≥2] from ATP [9]. The first molecular clone for an OAS was obtained by Michel Revel's lab [10]. Biochemical characterization of OAS proteins by Ara Hovanessian's lab [11][12][13][14] and Ganes Sen's lab [15][16][17][18][19] and a crystal structure by Rune Hartmann and Vivien Yee (in collaboration with Ganes Sen and Just Justesen) [20] have led to functional and structural insight into the OAS family of Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, type...

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“…Panchip -The nucleic acids that were extracted from the C6/36 cell line were randomly amplified and hybridized to a pan-viral DNA microarray, as described by Wang et al (2003).…”

Section: Cells and Viruses -The Aedes Albopictus Cell Linementioning

confidence: 99%

Genetic and biological characterization of a densovirus isolate that affects dengue virus infection

Mosimann

Bordignon

Mazzarotto

et al. 2011

Mem. Inst. Oswaldo Cruz

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Brevidensoviruses have an encapsidated, single-stranded DNA genome that predominantly has a negative polarity. In recent years, they have received particular attention due to their potential role in the biological control of pathogenic arboviruses and to their unnoticed presence in cell cultures as contaminants. In addition, brevidensoviruses may also be useful as viral vectors. This study describes the first genetic and biological characterization of a mosquito densovirus that was isolated in Brazil; moreover, we examined the phylogenetic relationship between this isolate and the other brevidensoviruses. We further demonstrate that this densovirus has the potential to be used to biologically control dengue virus (DENV) infection with in vitro co-infection experiments. The present study provides evidence that this densovirus isolate is a fast-spreading virus that affects cell growth and DENV infection

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Viral Discovery and Sequence Recovery Using DNA Microarrays

Cited by 415 publications

References 10 publications

Diverse functions of RNase L and implications in pathology

Diverse functions of RNase L and implications in pathology

A scientific journey through the 2-5A/RNase L system

Genetic and biological characterization of a densovirus isolate that affects dengue virus infection

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