Modulation of Expression of PVYNTN RNA-Dependent RNA Polymerase (NIb) and Heat Shock Cognate Host Protein HSC70 in Susceptible and Hypersensitive Potato Cultivars

Potato virus Y (PVY) belongs to the genus Potyvirus and is considered to be one of the most harmful and important plant pathogens. Its RNA-dependent RNA polymerase (RdRp) is known as nuclear inclusion protein b (NIb). The recent findings show that the genome of PVY replicates in the cytoplasm of the plant cell by binding the virus replication complex to the membranous structures of different organelles. In some potyviruses, NIb has been found to be localized in the nucleus and associated with the endoplasmic reticulum membranes. Moreover, NIb has been shown to interact with other host proteins that are particularly involved in promoting the virus infection cycle, such as the heat shock proteins (HSPs). HSP70 is the most conserved among the five major HSP families that are known to affect the plant–pathogen interactions. Some plant viruses can induce the production of HSP70 during the development of infection. To understand the molecular mechanisms underlying the interactive response to PVYNTN (necrotic tuber necrosis strain of PVY), the present study focused on StHSC70-8 and PVYNTN-NIb gene expression via localization of HSC70 and NIb proteins during compatible (susceptible) and incompatible (hypersensitive) potato–PVYNTN interactions. Our results demonstrate that NIb and HSC70 are involved in the response to PVYNTN infections and probably cooperate at some stages of the virus infection cycle. Enhanced deposition of HSC70 proteins during the infection cycle was associated with the dynamic induction of PVYNTN-NIb gene expression and NIb localization during susceptible infections. In hypersensitive response (HR), a significant increase in HSC70 expression was observed up to 3 days post-inoculation (dpi) in the nucleus and chloroplasts. Thereafter, between 3 and 21 dpi, the deposition of NIb decreased, which can be attributed to a reduction in the levels of both virus accumulation and PVYNTN-NIb gene expression. Therefore, we postulate that increase in the expression of both StHSC70-8 and PVYNTN-NIb induces the PVY infection during susceptible infections. In contrast, during HRs, HSC70 cooperates with PVYNTN only at the early stages of interaction and mediates the defense response signaling pathway at the later stages of infection.

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Phosphoproteomics to Characterize Host Response During H3N2 Canine Influenza Virus Infection of Dog Lung

Frontiers in Veterinary Science ◽

10.3389/fvets.2020.585071 ◽

2020 ◽

Vol 7 ◽

Author(s):

Yongbo Liu ◽

Cheng Fu ◽

Shaotang Ye ◽

Yingxin Liang ◽

Zhonghe Qi ◽

...

Keyword(s):

Virus Infection ◽

Influenza Virus Infection ◽

Enrichment Analysis ◽

Influenza Viruses ◽

Host Protein ◽

Differentially Expressed ◽

H3n2 Virus ◽

Post Inoculation ◽

Canine Influenza Virus ◽

Canine Influenza

Avian-origin H3N2 canine influenza viruses (CIVs) cause severe contagious respiratory disease in dogs, and quickly adapt to new environments. To further understand the mechanism of virus infection and host-virus interactions, we characterized the complete phosphoproteome of dogs infected with H3N2 CIV. Nine-week-old Beagle dogs were inoculated intranasally with 106 EID50 of A/canine/Guangdong/04/2014 (H3N2) virus. Lung sections were harvested at 5 days post-inoculation (dpi) and processed for global and quantitative analysis of differentially expressed phosphoproteins. A total of 1,235 differentially expressed phosphorylated proteins were identified in the dog lung after H3N2 CIV infection, and 3,016 modification sites were identified among all differentially expressed proteins. We then performed an enrichment analysis of functional annotations using Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene ontology (GO) database analyses to predict the functions of the identified differential phosphoproteins. Our data indicate that H3N2 CIV infection causes dramatic changes in the host protein phosphorylation of dog lungs. To our knowledge, this is the first study to assess the effect of H3N2 CIV infection on the phosphoproteome of beagles. These data provide novel insights into H3N2-CIV-triggered regulatory phosphorylation circuits and signaling networks and may improve our understanding of the mechanisms underlying CIV pathogenesis in dogs.

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The Dicer-like, Argonaute and RNA-dependent RNA polymerase gene families in Populus trichocarpa: gene structure, gene expression, phylogenetic analysis and evolution

Journal of Genetics ◽

10.1007/s12041-015-0508-y ◽

2015 ◽

Vol 94 (2) ◽

pp. 317-321 ◽

Cited By ~ 9

Author(s):

KANG ZHAO ◽

HUALIN ZHAO ◽

ZHU CHEN ◽

LIN FENG ◽

JIE REN ◽

...

Keyword(s):

Gene Expression ◽

Phylogenetic Analysis ◽

Rna Polymerase ◽

Gene Structure ◽

Populus Trichocarpa ◽

Gene Families ◽

Polymerase Gene ◽

Rna Dependent Rna Polymerase ◽

Rna Polymerase Gene

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Phosphorylation of RNA polymerase II C-terminal domain (CTD): a new control for heat shock gene expression?

Cell Stress and Chaperones ◽

10.1379/1466-1268(1998)003<0147:porpic>2.3.co;2 ◽

1998 ◽

Vol 3 (3) ◽

pp. 147 ◽

Cited By ~ 5

Author(s):

Marie-Françoise Dubois ◽

Olivier Bensaude

Keyword(s):

Gene Expression ◽

Heat Shock ◽

Rna Polymerase ◽

Rna Polymerase Ii ◽

Heat Shock Gene ◽

Terminal Domain ◽

Shock Gene ◽

Heat Shock Gene Expression

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Effects of the noncoding subgenomic RNA of red clover necrotic mosaic virus in virus infection

Journal of Virology ◽

10.1128/jvi.01815-21 ◽

2021 ◽

Author(s):

Pulkit Kanodia ◽

W. Allen Miller

Keyword(s):

Gene Expression ◽

Virus Infection ◽

Mosaic Virus ◽

Nicotiana Benthamiana ◽

Red Clover ◽

Plant Viruses ◽

Viral Rna ◽

Productive Infection ◽

Deficient Mutant ◽

Host Interactions

In recent years, a new class of viral noncoding subgenomic (ncsg)RNA has been identified. This RNA is generated as a stable degradation product via an exoribonuclease-resistant (xr) RNA structure, which blocks the progression of 5’→3’ exoribonuclease on viral RNAs in infected cells. Here, we assess the effects of the ncsgRNA of red clover necrotic mosaic virus (RCNMV), called SR1f, in infected plants. We demonstrate: (i) absence of SR1f reduces symptoms and decreases viral RNA accumulation in Nicotiana benthamiana and Arabidopsis thaliana plants; (ii) SR1f has an essential function other than suppression of RNA silencing; and (iii) the cytoplasmic exoribonuclease involved in mRNA turnover, XRN4, is not required for SR1f production or virus infection. A comparative transcriptomic analysis in N. benthamiana infected with wildtype RCNMV or an SR1f-deficient mutant RCNMV revealed that wt RCNMV infection, which produces SR1f and much higher levels of virus, has a greater and more significant impact on cellular gene expression than the SR1f-deficient mutant. Upregulated pathways include plant hormone signaling, plant-pathogen interaction, MAPK signaling, and several metabolic pathways, while photosynthesis-related genes were downregulated. We compare this to host genes known to participate in infection by other tombusvirids. Viral reads revealed a 10 to 100-fold ratio of positive to negative strand, and the abundance of reads of both strands mapping to the 3’ region of RCNMV RNA1 support the premature mechanism of synthesis for the coding sgRNA. These results provide a framework for future studies of the interactions and functions of noncoding RNAs of plant viruses. IMPORTANCE Knowledge of how RNA viruses manipulate host and viral gene expression is crucial to our understanding of infection and disease. Unlike viral protein-host interactions, little is known about the control of gene expression by viral RNA. Here we begin to address this question by investigating the noncoding subgenomic (ncsg)RNA of red clover necrotic mosaic virus (RCNMV), called SR1f. Similar exoribonuclease-resistant RNAs of flaviviruses are well-studied, but the roles of plant viral ncsgRNAs, and how they arise, are poorly understood. Surprisingly, we find the likely exonuclease candidate, XRN4, is not required to generate SR1f, and we assess the effects of SR1f on virus accumulation and symptom development. Finally, we compare the effects of infection by wildtype RCNMV vs an SR1f-deficient mutant on host gene expression in Nicotiana benthamiana , which reveals that ncsgRNAs such as SR1f are key players in virus-host interactions to facilitate productive infection.

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In vivo interactions of RNA polymerase II with genes of Drosophila melanogaster

Molecular and Cellular Biology ◽

10.1128/mcb.5.8.2009-2018.1985 ◽

1985 ◽

Vol 5 (8) ◽

pp. 2009-2018

Author(s):

D S Gilmour ◽

J T Lis

Keyword(s):

Gene Expression ◽

Drosophila Melanogaster ◽

Heat Shock ◽

Rna Polymerase ◽

Rna Polymerase Ii ◽

Protein Characterization ◽

Heat Shock Gene ◽

Transcriptional Level ◽

Intact Cells

We describe a method for examining the in vivo distribution of a protein on specific eucaryotic DNA sequences. In this method, proteins are cross-linked to DNA in intact cells, and the protein-DNA adducts are isolated by immunoprecipitation with antiserum against the protein. Characterization of the DNA cross-linked to the precipitated protein identifies the sequences with which the protein is associated in vivo. Here, we applied these methods to detect RNA polymerase II-DNA interactions in heat-shocked and untreated Drosophila melanogaster Schneider line 2 cells. The level of RNA polymerase II associated with several heat shock genes increased dramatically in response to heat shock, whereas the level associated with the copia genes decreased, indicating that both induction of heat shock gene expression and repression of the copia gene expression by heat shock occur at the transcriptional level. Low levels of RNA polymerase II were present on DNA outside of the transcription units, and for at least two genes, hsp83 and hsp26, RNA polymerase II initiated binding near the transcription start site. Moreover, for hsp70, the density of RNA polymerase II on sequences downstream of the polyadenylate addition site was much lower than that observed on the gene internal sequences. Examination of the amount of specific restriction fragments cross-linked to RNA polymerase II provides a means of detecting RNA polymerase II on individual members of multigene families. This analysis shows that RNA polymerase II is associated with only one of the two cytoplasmic actin genes.

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