Viruses

26 pages, 16327 KiB

Open AccessReview

Histone Deacetylases in Herpesvirus Replication and Virus-Stimulated Host Defense

by Amanda J. Guise, Hanna G. Budayeva, Benjamin A. Diner and Ileana M. Cristea^*

Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA

Viruses 2013, 5(7), 1607-1632; https://doi.org/10.3390/v5071607 - 27 Jun 2013

Cited by 32 | Viewed by 11439

Emerging evidence highlights a critical role for protein acetylation during herpesvirus infection. As prominent modulators of protein acetylation, histone deacetylases (HDACs) are essential transcriptional and epigenetic regulators. Not surprisingly, viruses have evolved a wide array of mechanisms to subvert HDAC functions. Here, we [...] Read more.

Emerging evidence highlights a critical role for protein acetylation during herpesvirus infection. As prominent modulators of protein acetylation, histone deacetylases (HDACs) are essential transcriptional and epigenetic regulators. Not surprisingly, viruses have evolved a wide array of mechanisms to subvert HDAC functions. Here, we review the mechanisms underlying HDAC regulation during herpesvirus infection. We next discuss the roles of acetylation in host defense against herpesvirus infection. Finally, we provide a perspective on the contribution of current mass spectrometry-based “omic” technologies to infectious disease research, offering a systems biology view of infection. Full article

(This article belongs to the Special Issue Chromatin Control of Viral Infection)

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13 pages, 2196 KiB

Open AccessReview

Chromatin, Non-Coding RNAs, and the Expression of HIV

by Jessica N. Groen¹ and Kevin V. Morris^1,2,*

¹ School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, 2052, Australia

² Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA

Viruses 2013, 5(7), 1633-1645; https://doi.org/10.3390/v5071633 - 28 Jun 2013

Cited by 16 | Viewed by 8363

Abstract

HIV is a chronic viral infection affecting an estimated 34 million people worldwide. Current therapies employ the use of a cocktail of antiretroviral medications to reduce the spread and effects of HIV, however complete eradication from an individual currently remains unattainable. Viral latency [...] Read more.

HIV is a chronic viral infection affecting an estimated 34 million people worldwide. Current therapies employ the use of a cocktail of antiretroviral medications to reduce the spread and effects of HIV, however complete eradication from an individual currently remains unattainable. Viral latency and regulation of gene expression is a key consideration when developing effective treatments. While our understanding of these processes remains incomplete new developments suggest that non-coding RNA (ncRNA) mediated regulation may provide an avenue to controlling both viral expression and latency. Here we discuss the importance of known regulatory mechanisms and suggest directions for further study, in particular the use ncRNAs in controlling HIV expression. Full article

(This article belongs to the Special Issue Chromatin Control of Viral Infection)

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9 pages, 3387 KiB

Open AccessConcept Paper

Norovirus Contamination Levels in Ground Water Treatment Systems Used for Food-Catering Facilities in South Korea

by Bo-Ram Lee¹, Sung-Geun Lee², Jong-Hyun Park³, Kwang-Yup Kim⁴, Sang-Ryeol Ryu⁵

, Ok-Jae Rhee⁶, Jeong-Woong Park⁷, Jeong-Su Lee⁸ and Soon-Young Paik^1,*

¹ Department of Microbiology, College of Medicine, the Catholic University of Korea, Seoul 137-701, Korea

² Korea Zoonosis Research Institute, Chonbuk National University, Jeonju 561-756, Korea

³ Department of Food Science and Biotechnology, Kyungwon University, Seongnam 461-701, Korea

⁴ Department of Food Science and Technology, Chungbuk National University Korea, Chongju 361-763, Korea

⁵ Department of Food Science and Biotechnology, Seoul National University Korea, Seoul 151-742, Korea

⁶ DK EcoV Environmental Microbiology Lab, Biotechnology Business Incubating Center, Dankook University, Chungnam 330-714, Korea

⁷ Sanigen Co. Ltd., Juan-dong, Gwacheon-si, Gyeonggi-do 427-070, Korea

⁸ Food Microbiology Division, Food Safety Evaluation Department, National Institute of Food and Drug Safety Evaluation, Osong 363-700, Korea

Viruses 2013, 5(7), 1646-1654; https://doi.org/10.3390/v5071646 - 2 Jul 2013

Cited by 19 | Viewed by 7954

Abstract

This study aimed to inspect norovirus contamination of groundwater treatment systems used in food-catering facilities located in South Korea. A nationwide study was performed in 2010. Water samples were collected and, for the analysis of water quality, the temperature, pH, turbidity, and residual [...] Read more.

This study aimed to inspect norovirus contamination of groundwater treatment systems used in food-catering facilities located in South Korea. A nationwide study was performed in 2010. Water samples were collected and, for the analysis of water quality, the temperature, pH, turbidity, and residual chlorine content were assessed. To detect norovirus genotypes GI and GII, RT-PCR and semi-nested PCR were performed with specific NV-GI and NV-GII primer sets, respectively. The PCR products amplified from the detected strains were then subjected to sequence analyses. Of 1,090 samples collected in 2010, seven (0.64%) were found to be norovirus-positive. Specifically, one norovirus strain was identified to have the GI-6 genotype, and six GII strains had the GII, GII-3, GII-4, and GII-17 genotypes. The very low detection rate of norovirus most likely reflects the preventative measures used. However, this virus can spread rapidly from person to person in crowded, enclosed places such as the schools investigated in this study. To promote better public health and sanitary conditions, it is necessary to periodically monitor noroviruses that frequently cause epidemic food poisoning in South Korea. Full article

(This article belongs to the Section Animal Viruses)

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9 pages, 2557 KiB

Open AccessArticle

Differentiation and Distribution of Cordyline Viruses 1–4 in Hawaiian ti Plants (Cordyline fruticosa L.)

by Michael Melzer^1,*, Caleb Ayin¹, Jari Sugano², Janice Uchida¹, Michael Kawate¹, Wayne Borth¹ and John Hu¹

¹ Department of Plant and Environmental Protection Sciences, University of Hawaii, 3190 Maile Way, Honolulu, HI 96822, USA

² Department of Plant and Environmental Protection Sciences, University of Hawaii, 45-260 Waikalua Road, Kaneohe, HI 96744, USA

Viruses 2013, 5(7), 1655-1663; https://doi.org/10.3390/v5071655 - 5 Jul 2013

Cited by 7 | Viewed by 8118

Abstract

Common green ti plants (Cordyline fruticosa L.) in Hawaii can be infected by four recently characterized closteroviruses that are tentative members of the proposed genus Velarivirus. In this study, a reverse-transcription polymerase chain reaction (RT-PCR) assay developed to detect and distinguish [...] Read more.

Common green ti plants (Cordyline fruticosa L.) in Hawaii can be infected by four recently characterized closteroviruses that are tentative members of the proposed genus Velarivirus. In this study, a reverse-transcription polymerase chain reaction (RT-PCR) assay developed to detect and distinguish Cordyline virus 1 (CoV-1), CoV-2, CoV-3, and CoV-4 was used to determine: (i) the distribution of these viruses in Hawaii; and (ii) if they are involved in the etiology of ti ringspot disease. One hundred and thirty-seven common green ti plants with and without ti ringspot symptoms were sampled from 43 sites on five of the Hawaiian Islands and underwent the RT-PCR assay. Eleven ornamental ti varieties were also sampled and assayed. Based on this survey, it appears none of the CoVs are involved in the etiology of ti ringspot. The observation of a non-uniform geographic distribution of the CoVs in common green ti, combined with the presence of CoVs in seed-derived ornamental varieties, suggests active vector transmission. Eight herbarium specimens collected between 1903 and 2003 from plants on the island of Oahu also underwent the RT-PCR assay. Amplifiable RNA was isolated from accessions collected in 1985 or later, however only the 2003 accession was found to harbor CoVs. Full article

(This article belongs to the Special Issue Plant Viruses)

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18 pages, 35791 KiB

Open AccessArticle

Identification of Genes Critical for Resistance to Infection by West Nile Virus Using RNA-Seq Analysis

by Feng Qian¹, Lisa Chung^2,3, Wei Zheng², Vincent Bruno^4,†, Roger P. Alexander^4,5, Zhong Wang^4,‡, Xiaomei Wang¹, Sebastian Kurscheid⁶, Hongyu Zhao^2,3, Erol Fikrig^6,7, Mark Gerstein^4,5,8, Michael Snyder⁹ and Ruth R. Montgomery^1,*

¹ Section of Rheumatology, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA

² Keck Biotechnology Resource Laboratory, Yale University School of Medicine, New Haven, CT 06520, USA

³ Department of Biostatistics, Yale University School of Medicine, New Haven, CT 06520, USA

⁴ Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA

⁵ Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA

⁶ Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA

⁷ The Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA

⁸ Department of Computer Science, Yale University, New Haven, CT 06520, USA

⁹ Department of Genetics, Stanford University, Stanford, CA 94305, USA

^† Current address: Department of Microbiology and Immunology, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA.

^‡ Current address: DOE Joint Genome Institute, 2800 Mitchell Dr., MS100, Walnut Creek, CA 94598, USA.

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Viruses 2013, 5(7), 1664-1681; https://doi.org/10.3390/v5071664 - 8 Jul 2013

Cited by 22 | Viewed by 15399

Abstract

The West Nile virus (WNV) is an emerging infection of biodefense concern and there are no available treatments or vaccines. Here we used a high-throughput method based on a novel gene expression analysis, RNA-Seq, to give a global picture of differential gene expression [...] Read more.

The West Nile virus (WNV) is an emerging infection of biodefense concern and there are no available treatments or vaccines. Here we used a high-throughput method based on a novel gene expression analysis, RNA-Seq, to give a global picture of differential gene expression by primary human macrophages of 10 healthy donors infected in vitro with WNV. From a total of 28 million reads per sample, we identified 1,514 transcripts that were differentially expressed after infection. Both predicted and novel gene changes were detected, as were gene isoforms, and while many of the genes were expressed by all donors, some were unique. Knock-down of genes not previously known to be associated with WNV resistance identified their critical role in control of viral infection. Our study distinguishes both common gene pathways as well as novel cellular responses. Such analyses will be valuable for translational studies of susceptible and resistant individuals—and for targeting therapeutics—in multiple biological settings. Full article

(This article belongs to the Section Animal Viruses)

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Graphical abstract

2 pages, 124 KiB

Open AccessAddendum

Addendum: Bastos, J.C.S.; Kohn, L.K.; Fantinatti-Garboggini, F.; Padilla, M.A.; Flores, E.F.; da Silva, B.P.; de Menezes, C.B.A.; Arns, C.W. Antiviral Activity of Bacillus sp. Isolated from the Marine Sponge Petromica citrina against Bovine Viral Diarrhea Virus, a Surrogate Model of the Hepatitis C Virus. Viruses 2013, 5, 1219-1230.

by Juliana Cristina Santiago Bastos^1,*, Luciana Konecny Kohn¹, Fabiana Fantinatti-Garboggini¹, Marina Aiello Padilla¹, Eduardo Furtado Flores², Bárbara Pereira Da Silva¹, Cláudia Beatriz Afonso De Menezes¹ and Clarice Weis Arns¹

¹ Laboratório de Virologia, Departamento de Genética Evolução e Bioagentes, Instituto de Biologia/Universidade Estadual de Campinas-UNICAMP, Cx. Postal 6109, CEP 13083-970 , Campinas/SP/Brazil

² Centro de Ciências Rurais, Departamento de Medicina Veterinária Preventiva. Universidade Federal de Santa Maria (UFSM) CEP 97105-900 - Santa Maria/RS/Brazil

Viruses 2013, 5(7), 1682-1683; https://doi.org/10.3390/v5071682 - 11 Jul 2013

Viewed by 6213

Abstract

The authors wish to add the following Acknowledgments and completed Table 1 to their paper published in Viruses [1], doi:10.3390/v5051219, website: https://www.mdpi.com/1999-4915/5/5/1219. Full article

(This article belongs to the Section Viral Immunology, Vaccines, and Antivirals)

18 pages, 223 KiB

Open AccessReview

Cyclophilins as Modulators of Viral Replication

by Stephen D. Frausto, Emily Lee and Hengli Tang^*

Department of Biological Science, The Florida State University, Tallahassee, FL 32306, USA

Viruses 2013, 5(7), 1684-1701; https://doi.org/10.3390/v5071684 - 11 Jul 2013

Cited by 48 | Viewed by 8194

Abstract

Cyclophilins are peptidyl‐prolyl cis/trans isomerases important in the proper folding of certain proteins. Mounting evidence supports varied roles of cyclophilins, either positive or negative, in the life cycles of diverse viruses, but the nature and mechanisms of these roles are yet to be [...] Read more.

Cyclophilins are peptidyl‐prolyl cis/trans isomerases important in the proper folding of certain proteins. Mounting evidence supports varied roles of cyclophilins, either positive or negative, in the life cycles of diverse viruses, but the nature and mechanisms of these roles are yet to be defined. The potential for cyclophilins to serve as a drug target for antiviral therapy is evidenced by the success of non-immunosuppressive cyclophilin inhibitors (CPIs), including Alisporivir, in clinical trials targeting hepatitis C virus infection. In addition, as cyclophilins are implicated in the predisposition to, or severity of, various diseases, the ability to specifically and effectively modulate their function will prove increasingly useful for disease intervention. In this review, we will summarize the evidence of cyclophilins as key mediators of viral infection and prospective drug targets. Full article

(This article belongs to the Special Issue Cyclophilins and Viruses)

17 pages, 355 KiB

Open AccessReview

Feline Foamy Virus-Based Vectors: Advantages of an Authentic Animal Model

by Weibin Liu^†,‡, Janet Lei^†, Yang Liu, Dragana Slavkovic Lukic, Ann-Mareen Räthe, Qiuying Bao, Timo Kehl, Anne Bleiholder, Torsten Hechler^# and Martin Löchelt^*

¹ Department of Genome Modifications, Research Program Infection and Cancer, German Cancer Research Center, Im Neuenheimer Feld 242, 69120 Heidelberg, Germany

^† These authors contributed equally to this work.

^‡ Current address: Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA.

^# Current address: Department of Biochemistry, Heidelberg Pharma GmbH, Schriesheimer Str. 101, 68526 Ladenburg, Germany.

Viruses 2013, 5(7), 1702-1718; https://doi.org/10.3390/v5071702 - 12 Jul 2013

Cited by 14 | Viewed by 7906

Abstract

New-generation retroviral vectors have potential applications in vaccination and gene therapy. Foamy viruses are particularly interesting as vectors, because they are not associated to any disease. Vector research is mainly based on primate foamy viruses (PFV), but cats are an alternative animal model, [...] Read more.

New-generation retroviral vectors have potential applications in vaccination and gene therapy. Foamy viruses are particularly interesting as vectors, because they are not associated to any disease. Vector research is mainly based on primate foamy viruses (PFV), but cats are an alternative animal model, due to their smaller size and the existence of a cognate feline foamy virus (FFV). The potential of replication-competent (RC) FFV vectors for vaccination and replication-deficient (RD) FFV-based vectors for gene delivery purposes has been studied over the past years. In this review, the key achievements and functional evaluation of the existing vectors from in vitro cell culture systems to out-bred cats will be described. The data presented here demonstrate the broad application spectrum of FFV-based vectors, especially in pathogen-specific prophylactic and therapeutic vaccination using RD vectors in cats and in classical gene delivery. In the cat-based system, FFV-based vectors provide an advantageous platform to evaluate and optimize the applicability, efficacy and safety of foamy virus (FV) vectors, especially the understudied aspect of FV cell and organ tropism. Full article

(This article belongs to the Special Issue Recent Progress in Foamy Virus (FV) Research)

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21 pages, 687 KiB

Open AccessArticle

Development of a Magnetic Electrochemical Bar Code Array for Point Mutation Detection in the H5N1 Neuraminidase Gene

by Ludmila Krejcova¹, David Hynek^1,2, Pavel Kopel^1,2

, Miguel Angel Merlos Rodrigo^1,2, Vojtech Adam^1,2, Jaromir Hubalek^2,3

, Petr Babula^2,4, Libuse Trnkova^1,2,5 and Rene Kizek^1,2,*

¹ Department of Chemistry and Biochemistry, Faculty of Agronomy, Mendel University in Brno, Zemedelska 1, Brno CZ-613 00, Czech Republic

² Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, Brno CZ-616 00, Czech Republic

³ Department of Microelectronics, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technicka 10, Brno CZ-616 00, Czech Republic

⁴ Department of Natural Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences, Palackeho 1-3, Brno CZ-612 42, Czech Republic

⁵ Department of Chemistry, Faculty of Science, Masaryk University, Kotlarska 2, Brno CZ-611 37, Czech Republic

Viruses 2013, 5(7), 1719-1739; https://doi.org/10.3390/v5071719 - 15 Jul 2013

Cited by 19 | Viewed by 7428

Abstract

Since its first official detection in the Guangdong province of China in 1996, the highly pathogenic avian influenza virus of H5N1 subtype (HPAI H5N1) has reportedly been the cause of outbreaks in birds in more than 60 countries, 24 of which were European. [...] Read more.

Since its first official detection in the Guangdong province of China in 1996, the highly pathogenic avian influenza virus of H5N1 subtype (HPAI H5N1) has reportedly been the cause of outbreaks in birds in more than 60 countries, 24 of which were European. The main issue is still to develop effective antiviral drugs. In this case, single point mutation in the neuraminidase gene, which causes resistance to antiviral drug and is, therefore, subjected to many studies including ours, was observed. In this study, we developed magnetic electrochemical bar code array for detection of single point mutations (mismatches in up to four nucleotides) in H5N1 neuraminidase gene. Paramagnetic particles Dynabeads® with covalently bound oligo (dT)₂₅ were used as a tool for isolation of complementary H5N1 chains (H5N1 Zhejin, China and Aichi). For detection of H5N1 chains, oligonucleotide chains of lengths of 12 (+5 adenine) or 28 (+5 adenine) bp labeled with quantum dots (CdS, ZnS and/or PbS) were used. Individual probes hybridized to target molecules specifically with efficiency higher than 60%. The obtained signals identified mutations present in the sequence. Suggested experimental procedure allows obtaining further information from the redox signals of nucleic acids. Moreover, the used biosensor exhibits sequence specificity and low limits of detection of subnanogram quantities of target nucleic acids. Full article

(This article belongs to the Special Issue H5N1 Influenza Virus)

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18 pages, 10505 KiB

Open AccessReview

Role of Polycomb Proteins in Regulating HSV-1 Latency

by Zachary Watson, Adit Dhummakupt, Harald Messer, Dane Phelan and David Bloom^*

Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, Box 100266, Gainesville, FL 32610, USA

Viruses 2013, 5(7), 1740-1757; https://doi.org/10.3390/v5071740 - 15 Jul 2013

Cited by 13 | Viewed by 8819

Abstract

Herpes simplex virus (HSV) establishes a latent infection within sensory neurons of humans. Latency is characterized by the transcriptional repression of lytic genes by the condensation of lytic gene regions into heterochromatin. Recent data suggest that facultative heterochromatin predominates, and that cellular Polycomb [...] Read more.

Herpes simplex virus (HSV) establishes a latent infection within sensory neurons of humans. Latency is characterized by the transcriptional repression of lytic genes by the condensation of lytic gene regions into heterochromatin. Recent data suggest that facultative heterochromatin predominates, and that cellular Polycomb proteins are involved in the establishment and maintenance of transcriptional repression during latency. This review summarizes these data and discusses the implication of viral and cellular factors in regulating heterochromatin composition. Full article

(This article belongs to the Special Issue Chromatin Control of Viral Infection)

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29 pages, 2779 KiB

Open AccessReview

Chromatin Dynamics during Lytic Infection with Herpes Simplex Virus 1

by Kristen L. Conn^1,* and Luis M. Schang^1,2,*

¹ Department of Biochemistry, Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB T6G 2H7, Canada

² Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2E1, Canada

Viruses 2013, 5(7), 1758-1786; https://doi.org/10.3390/v5071758 - 16 Jul 2013

Cited by 27 | Viewed by 8910

Abstract

Latent HSV-1 genomes are chromatinized with silencing marks. Since 2004, however, there has been an apparent inconsistency in the studies of the chromatinization of the HSV-1 genomes in lytically infected cells. Nuclease protection and chromatin immunoprecipitation assays suggested that the genomes were not [...] Read more.

Latent HSV-1 genomes are chromatinized with silencing marks. Since 2004, however, there has been an apparent inconsistency in the studies of the chromatinization of the HSV-1 genomes in lytically infected cells. Nuclease protection and chromatin immunoprecipitation assays suggested that the genomes were not regularly chromatinized, having only low histone occupancy. However, the chromatin modifications associated with transcribed and non-transcribed HSV-1 genes were those associated with active or repressed transcription, respectively. Moreover, the three critical HSV-1 transcriptional activators all had the capability to induce chromatin remodelling, and interacted with critical chromatin modifying enzymes. Depletion or overexpression of some, but not all, chromatin modifying proteins affected HSV-1 transcription, but often in unexpected manners. Since 2010, it has become clear that both cellular and HSV-1 chromatins are highly dynamic in infected cells. These dynamics reconcile the weak interactions between HSV-1 genomes and chromatin proteins, detected by nuclease protection and chromatin immunoprecipitation, with the proposed regulation of HSV-1 gene expression by chromatin, supported by the marks in the chromatin in the viral genomes and the abilities of the HSV-1 transcription activators to modulate chromatin. It also explains the sometimes unexpected results of interventions to modulate chromatin remodelling activities in infected cells. Full article

(This article belongs to the Special Issue Chromatin Control of Viral Infection)

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15 pages, 341 KiB

Open AccessReview

Posttranslational Modifications of HIV-1 Integrase by Various Cellular Proteins during Viral Replication

by Yingfeng Zheng and Xiaojian Yao^*

Laboratory of Molecular Human Retrovirology, Department of Medical Microbiology, University of Manitoba, 508-730 William Avenue, Winnipeg, R3E 0W3, Canada

Viruses 2013, 5(7), 1787-1801; https://doi.org/10.3390/v5071787 - 16 Jul 2013

Cited by 26 | Viewed by 9626

Abstract

HIV-1 integrase (IN) is a key viral enzyme during HIV-1 replication that catalyzes the insertion of viral DNA into the host genome. Recent studies have provided important insights into the multiple posttranslational modifications (PTMs) of IN (e.g., ubiquitination, SUMOylation, acetylation and phosphorylation), which [...] Read more.

HIV-1 integrase (IN) is a key viral enzyme during HIV-1 replication that catalyzes the insertion of viral DNA into the host genome. Recent studies have provided important insights into the multiple posttranslational modifications (PTMs) of IN (e.g., ubiquitination, SUMOylation, acetylation and phosphorylation), which regulate its multifaceted functions. A number of host cellular proteins, including Lens Epithelium‑derived Growth factor (LEDGF/p75), p300 and Ku70 have been shown to interact with IN and be involved in the PTM process of IN, either facilitating or counteracting the IN PTMs. Although previous studies have revealed much about the important roles of IN PTMs, how IN functions are fine-tuned by these PTMs under the physiological setting still needs to be determined. Here, we review the advances in the understanding of the mechanisms and roles of multiple IN PTMs. Full article

(This article belongs to the Special Issue Viruses and the Ubiquitin/Proteasome System)

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13 pages, 962 KiB

Open AccessArticle

Deletions within the 3' Non-Translated Region of Alfalfa mosaic virus RNA4 Do Not Affect Replication but Significantly Reduce Long-Distance Movement of Chimeric Tobacco mosaic virus

by Gourgopal Roy, Oleg Fedorkin, Masaaki Fujiki, Marina Skarjinskaia, Elisabeth Knapp, Shailaja Rabindran and Vidadi Yusibov^*

Fraunhofer USA Center for Molecular Biotechnology, 9 Innovation Way, Newark, DE 19711, USA

Viruses 2013, 5(7), 1802-1814; https://doi.org/10.3390/v5071802 - 17 Jul 2013

Cited by 1 | Viewed by 7348

Abstract

Alfalfa mosaic virus (AlMV) RNAs 1 and 2 with deletions in their 3' non‑translated regions (NTRs) have been previously shown to be encapsidated into virions by coat protein (CP) expressed from RNA3, indicating that the 3' NTRs of RNAs 1 and 2 are [...] Read more.

Alfalfa mosaic virus (AlMV) RNAs 1 and 2 with deletions in their 3' non‑translated regions (NTRs) have been previously shown to be encapsidated into virions by coat protein (CP) expressed from RNA3, indicating that the 3' NTRs of RNAs 1 and 2 are not required for virion assembly. Here, we constructed various mutants by deleting sequences within the 3' NTR of AlMV subgenomic (sg) RNA4 (same as of RNA3) and examined the effect of these deletions on replication and translation of chimeric Tobacco mosaic virus (TMV) expressing AlMV sgRNA4 from the TMV CP sg promoter (Av/A4) in tobacco protoplasts and Nicotiana benthamiana plants. While the Av/A4 mutants were as competent as the wild-type Av/A4 in RNA replication in protoplasts, their encapsidation, long-distance movement and virus accumulation varied significantly in N. benthamiana. These data suggest that the 3' NTR of AlMV sgRNA4 contains potential elements necessary for virus encapsidation. Full article

(This article belongs to the Special Issue Plant Viruses)

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9 pages, 485 KiB

Open AccessCommunication

Complete Nucleotide Sequence of a South African Isolate of Grapevine Fanleaf Virus and Its Associated Satellite RNA

by Renate L. Lamprecht¹, Monique Spaltman¹, Dirk Stephan¹, Thierry Wetzel² and Johan T. Burger^1,*

¹ Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa

² RLP Agroscience, AlPlanta–Institute for Plant Research, Breitenweg 71, Neustadt an der 67435 Weinstrasse, Germany

Viruses 2013, 5(7), 1815-1823; https://doi.org/10.3390/v5071815 - 17 Jul 2013

Cited by 11 | Viewed by 7511

Abstract

The complete sequences of RNA1, RNA2 and satellite RNA have been determined for a South African isolate of Grapevine fanleaf virus (GFLV-SACH44). The two RNAs of GFLV-SACH44 are 7,341 nucleotides (nt) and 3,816 nt in length, respectively, and its satellite RNA (satRNA) is [...] Read more.

The complete sequences of RNA1, RNA2 and satellite RNA have been determined for a South African isolate of Grapevine fanleaf virus (GFLV-SACH44). The two RNAs of GFLV-SACH44 are 7,341 nucleotides (nt) and 3,816 nt in length, respectively, and its satellite RNA (satRNA) is 1,104 nt in length, all excluding the poly(A) tail. Multiple sequence alignment of these sequences showed that GFLV-SACH44 RNA1 and RNA2 were the closest to the South African isolate, GFLV-SAPCS3 (98.2% and 98.6% nt identity, respectively), followed by the French isolate, GFLV-F13 (87.3% and 90.1% nt identity, respectively). Interestingly, the GFLV-SACH44 satRNA is more similar to three Arabis mosaic virus satRNAs (85%–87.4% nt identity) than to the satRNA of GFLV-F13 (81.8% nt identity) and was most distantly related to the satRNA of GFLV-R2 (71.0% nt identity). Full-length infectious clones of GFLV-SACH44 satRNA were constructed. The infectivity of the clones was tested with three nepovirus isolates, GFLV-NW, Arabis mosaic virus (ArMV)-NW and GFLV-SAPCS3. The clones were mechanically inoculated in Chenopodium quinoa and were infectious when co-inoculated with the two GFLV helper viruses, but not when co-inoculated with ArMV-NW. Full article

(This article belongs to the Special Issue Plant Viruses)

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26 pages, 9901 KiB

Open AccessReview

Nuclear Imprisonment: Viral Strategies to Arrest Host mRNA Nuclear Export

by Sharon K. Kuss^*, Miguel A. Mata, Liang Zhang and Beatriz M. A. Fontoura

Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA

Viruses 2013, 5(7), 1824-1849; https://doi.org/10.3390/v5071824 - 18 Jul 2013

Cited by 56 | Viewed by 11604

Abstract

Viruses possess many strategies to impair host cellular responses to infection. Nuclear export of host messenger RNAs (mRNA) that encode antiviral factors is critical for antiviral protein production and control of viral infections. Several viruses have evolved sophisticated strategies to inhibit nuclear export [...] Read more.

Viruses possess many strategies to impair host cellular responses to infection. Nuclear export of host messenger RNAs (mRNA) that encode antiviral factors is critical for antiviral protein production and control of viral infections. Several viruses have evolved sophisticated strategies to inhibit nuclear export of host mRNAs, including targeting mRNA export factors and nucleoporins to compromise their roles in nucleo-cytoplasmic trafficking of cellular mRNA. Here, we present a review of research focused on suppression of host mRNA nuclear export by viruses, including influenza A virus and vesicular stomatitis virus, and the impact of this viral suppression on host antiviral responses. Full article

(This article belongs to the Special Issue Viral Nuclear Import)

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17 pages, 236 KiB

Open AccessReview

Structural and Functional Insights into Foamy Viral Integrase

by Md. Alamgir Hossain, Md. Khadem Ali and Cha-Gyun Shin^*

Department of Biotechnology, Chung-Ang University, Ansung 456-756, South Korea

Viruses 2013, 5(7), 1850-1866; https://doi.org/10.3390/v5071850 - 18 Jul 2013

Cited by 4 | Viewed by 7491

Abstract

Successful integration of retroviral DNA into the host chromosome is an essential step for viral replication. The process is mediated by virally encoded integrase (IN) and orchestrated by 3'-end processing and the strand transfer reaction. In vitro reaction conditions, such as substrate specificity, [...] Read more.

Successful integration of retroviral DNA into the host chromosome is an essential step for viral replication. The process is mediated by virally encoded integrase (IN) and orchestrated by 3'-end processing and the strand transfer reaction. In vitro reaction conditions, such as substrate specificity, cofactor usage, and cellular binding partners for such reactions by the three distinct domains of prototype foamy viral integrase (PFV-IN) have been described well in several reports. Recent studies on the three‑dimensional structure of the interacting complexes between PFV-IN and DNA, cofactors, binding partners, or inhibitors have explored the mechanistic details of such interactions and shown its utilization as an important target to develop anti-retroviral drugs. The presence of a potent, non-transferable nuclear localization signal in the PFV C-terminal domain extends its use as a model for investigating cellular trafficking of large molecular complexes through the nuclear pore complex and also to identify novel cellular targets for such trafficking. This review focuses on recent advancements in the structural analysis and in vitro functional aspects of PFV-IN. Full article

(This article belongs to the Special Issue Recent Progress in Foamy Virus (FV) Research)

18 pages, 387 KiB

Open AccessReview

Small Ruminant Lentiviruses (SRLVs) Break the Species Barrier to Acquire New Host Range

by Juliano Cezar Minardi da Cruz¹, Dinesh Kumar Singh², Ali Lamara³ and Yahia Chebloune^4,*

¹ Laboratory Animal Health, Embrapa Goat and Sheep Research Center, CP 145, CEP 62010-970, Sobral, Ceará, Brazil

² Department of Life Sciences, Winston-Salem State University, Winston Salem, NC 27110, USA

³ Veterinary Superior National School of Algiers, Route de Beaulieu-El Harrach-Alger 16200, Algeria

⁴ Laboratory Pathogenesis and Lentivirus Vaccination, PAVAL Lab, Université Joseph Fourier Grenoble-1, Bat. NanoBio2, 570 rue de la Chimie, BP 53, 38041-Grenoble Cedex 9, France

Viruses 2013, 5(7), 1867-1884; https://doi.org/10.3390/v5071867 - 23 Jul 2013

Cited by 73 | Viewed by 11621

Abstract

Zoonotic events of simian immunodeficiency virus (SIV) from non-human primates to humans have generated the acquired immunodeficiency syndrome (AIDS), one of the most devastating infectious disease of the last century with more than 30 million people dead and about 40.3 million people currently [...] Read more.

Zoonotic events of simian immunodeficiency virus (SIV) from non-human primates to humans have generated the acquired immunodeficiency syndrome (AIDS), one of the most devastating infectious disease of the last century with more than 30 million people dead and about 40.3 million people currently infected worldwide. Human immunodeficiency virus (HIV-1 and HIV-2), the two major viruses that cause AIDS in humans are retroviruses of the lentivirus genus. The genus includes arthritis-encephalitis virus (CAEV) and Maedi-Visna virus (MVV), and a heterogeneous group of viruses known as small ruminant lentiviruses (SRLVs), affecting goat and sheep. Lentivirus genome integrates into the host DNA, causing persistent infection associated with a remarkable diversity during viral replication. Direct evidence of mixed infections with these two closely related SRLVs was found in both sheep and goats. The evidence of a genetic continuum with caprine and ovine field isolates demonstrates the absence of an efficient species barrier preventing cross-species transmission. In dual-infected animals, persistent infections with both CAEV and MVV have been described, and viral chimeras have been detected. This not only complicates animal trade between countries but favors the risk that highly pathogenic variants may emerge as has already been observed in the past in Iceland and, more recently, in outbreaks with virulent strains in Spain. SRLVs affecting wildlife have already been identified, demonstrating the existence of emergent viruses adapted to new hosts. Viruses adapted to wildlife ruminants may acquire novel biopathological properties which may endanger not only the new host species but also domestic ruminants and humans. SRLVs infecting sheep and goats follow a genomic evolution similar to that observed in HIV or in other lentiviruses. Lentivirus genetic diversity and host factors leading to the establishment of naturally occurring virulent versus avirulent infections, in addition to the emergence of new strains, challenge every aspect of SRLV control measures for providing efficient tools to prevent the transmission of diseases between wild ungulates and livestock. Full article

(This article belongs to the Special Issue Small Ruminant Lentiviruses)

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Viruses, Volume 5, Issue 7 (July 2013) – 18 articles , Pages 1607-1900

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