Spatial Analysis of Arabidopsis thaliana Gene Expression in Response to Turnip mosaic virus Infection

Virus-infected leaf tissues comprise a heterogeneous mixture of cells at different stages of infection. The spatial and temporal relationships between sites of virus accumulation and the accompanying host responses, such as altered host gene expression, are not well defined. To address this issue, we utilized Turnip mosaic virus (TuMV) tagged with the green fluorescent protein to guide the dissection of infection foci into four distinct zones. The abundance of Arabidopsis thaliana mRNA transcripts in each of the four zones then was assayed using the Arabidopsis ATH1 GeneChip oligonucleotide microarray (Affymetrix). mRNA transcripts with significantly altered expression profiles were determined across gradients of virus accumulation spanning groups of cells in and around foci at different stages of infection. The extent to which TuMV-responsive genes were up- or downregulated primarily correlated with the amount of virus accumulation regardless of gene function. The spatial analysis also allowed new suites of coordinately regulated genes to be identified that are associated with chloroplast functions (decreased), sulfate assimilation (decreased), cell wall extensibility (decreased), and protein synthesis and turnover (induced). The functions of these downregulated genes are consistent with viral symptoms, such as chlorosis and stunted growth, providing new insight into mechanisms of pathogenesis.

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Tobacco mosaic virus Induced Alterations in the Gene Expression Profile of Arabidopsis thaliana

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi.2003.16.8.681 ◽

2003 ◽

Vol 16 (8) ◽

pp. 681-688 ◽

Cited By ~ 87

Author(s):

Sheetal Golem ◽

James N. Culver

Keyword(s):

Gene Expression ◽

Arabidopsis Thaliana ◽

Tobacco Mosaic Virus ◽

Mosaic Virus ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Infection Process ◽

Cellular Processes ◽

Genes Expression ◽

Identify Gene Expression

In this study, mRNA profiles generated from cDNA microarrays were used to identify gene expression changes in Arabidopsis thaliana ecotype Shahdara infected with Tobacco mosaic virus (TMV). Shahdara is a susceptible TMV host, permitting rapid accumulations of virus in both inoculated and systemic tissues, accompanied by defined disease symptoms that include stunting, necrosis, and leaf curling. Gene expression profiles were monitored in whole tissues of inoculated leaves at four days postinoculation (dpi) and in systemically infected leaves at 14 dpi. Microarrays contained cDNAs representing between 8,000 and 10,000 Arabidopsis genes. Expression analysis identified 68 genes that displayed significant and consistent changes in expression levels, either up or down, in either TMV inoculated or systemically infected tissues, or both. Identified TMV-responsive genes encode a diverse array of functional proteins that include transcription factors, antioxidants, metabolic enzymes, and transporters. Thus, the TMV infection process has a significant impact on a wide array of cellular processes that likely reflect the biochemical and physiological changes involved in the development of this disease syndrome.

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Multiple ER-to-nucleus stress signaling pathways become active during Plantago asiatica mosaic virus and Turnip mosaic virus infection in Arabidopsis thaliana

10.1101/786137 ◽

2019 ◽

Cited By ~ 2

Author(s):

Mathieu Gayral ◽

Omar Arias Gaguancela ◽

Evelyn Vasquez ◽

Venura Herath ◽

Mingxiong Pang ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Protein Folding ◽

Signaling Pathways ◽

Mosaic Virus ◽

Turnip Mosaic Virus ◽

Virus Accumulation ◽

Unfolded Protein ◽

Plantago Asiatica ◽

Protein Response

SummaryEndoplasmic reticulum (ER) stress due to biotic or abiotic stress activates the unfolded protein response (UPR) to restore ER homeostasis. The UPR relies on multiple ER-to-nucleus signaling factors which mainly induce the expression of cytoprotective ER-chaperones. The inositol requiring enzyme (IRE1) along with its splicing target, bZIP60, restrict potyvirus, and potexvirus accumulation. Until now, the involvement of the alternative UPR pathways and the role of UPR to limit virus accumulation have remained elusive. Here, we used the Plantago asiatica mosaic virus (PlAMV) and the Turnip mosaic virus (TuMV) to demonstrate that the potexvirus triple gene block 3 (TGB3) protein and the potyvirus 6K2 protein activate the bZIP17, bZIP28, bZIP60, BAG7, NAC089 and NAC103 signaling in Arabidopsis thaliana. Using the corresponding knock-out mutant lines, we demonstrated that these factors differentially restrict local and systemic virus accumulation. We show that bZIP17, bZIP60, BAG7, and NAC089 are factors in PlAMV infection, whereas bZIP28 and bZIP60 are factors in TuMV infection. TGB3 and 6K2 transient expression in leave reveal that these alternative pathways induce BiPs expression. Finally, using dithiothreitol (DTT) and tauroursodeoxycholic acid (TUDCA) treatment, we demonstrated that the protein folding capacity significantly influences PlAMV accumulation. Together, these results indicate that multiple ER-to-nucleus signaling pathways are activated during virus infection and restrict virus accumulation through increasing protein folding capacity.Significance statementThe IRE1/bZIP60 pathway of unfolded protein response (UPR) is activated by potyviruses and potexviruses, limiting their infection, but the role of alternative UPR pathways is unknown. This study reveals the activation of multiple ER-to-nucleus signaling pathways by the Plantago asiatica mosaic virus and the Turnip mosaic virus. We identify additional signaling pathways serve to restrict virus accumulation through increased protein folding capacity.

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The Oral Intake of Organic Germanium, Ge-132, Elevates α-Tocopherol Levels in the Plas-ma and Modulates Hepatic Gene Expression Profiles to Promote Immune Activation in Mice

International Journal for Vitamin and Nutrition Research ◽

10.1024/0300-9831/a000205 ◽

2014 ◽

Vol 84 (3-4) ◽

pp. 0183-0195 ◽

Cited By ~ 12

Author(s):

Takashi Nakamura ◽

Tomoya Takeda ◽

Yoshihiko Tokuji

Keyword(s):

Gene Expression ◽

Immune Activation ◽

Expression Profiles ◽

Water Soluble ◽

Alpha Tocopherol ◽

Hepatic Gene Expression ◽

Tocopherol Concentration ◽

Altered Expression ◽

Atp Production ◽

Transfer Protein

The common water-soluble organic germanium compound poly-trans-[(2-carboxyethyl) germasesquioxane] (Ge-132) exhibits activities related to immune responses and antioxidant induction. In this study, we evaluated the antioxidative effect of dietary Ge-132 in the plasma of mice. Male ICR mice (seven mice per group) received an AIN-76 diet with 0.05 % Ge-132; three groups received the Ge-132-containing diet for 0, 1 or 4 days. The plasma alpha-tocopherol (α-tocopherol) concentration increased from 6.85 to 9.60 μg/ml after 4 days of Ge-132 intake (p < 0.05). We evaluated the changes in hepatic gene expression related to antioxidative activity as well as in the entire expression profile after one day of Ge-132 intake, using DNA microarray technology. We identified 1,220 genes with altered expression levels greater than 1.5-fold (increased or decreased) as a result of Ge-132 intake, and α-tocopherol transfer protein (Ttpa) gene expression was increased 1.62-fold. Immune activation was identified as the category with the most changes (containing 60 Gene Ontology (GO) term biological processes (BPs), 41 genes) via functional clustering analysis of altered gene expression. Ge-132 affected genes in clusters related to ATP production (22 GO term BPs, 21 genes), lipid metabolism (4 GO term BPs, 38 genes) and apoptosis (5 GO term BPs). Many GO term BPs containing these categories were significantly affected by the Ge-132 intake. Oral Ge-132 intake may therefore have increased plasma α-tocopherol levels by up-regulating α-tocopherol transfer protein (Ttpa) gene expression.

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Comparison of two Turnip mosaic virus P1 proteins in their ability to co-localize with the Arabidopsis thaliana G3BP-2 protein

Virus Genes ◽

10.1007/s11262-021-01829-w ◽

2021 ◽

Vol 57 (2) ◽

pp. 233-237

Author(s):

Hendrik Reuper ◽

Björn Krenz

Keyword(s):

Arabidopsis Thaliana ◽

Mosaic Virus ◽

Specific Interaction ◽

Viral Proteins ◽

Turnip Mosaic Virus ◽

Stress Conditions ◽

C Terminus ◽

Positive Sense ◽

Key Factor ◽

Large Host

AbstractTurnip mosaic virus (TuMV), belonging to the genus Potyvirus (family Potyviridae), has a large host range and consists of a single-stranded positive sense RNA genome encoding 12 proteins, including the P1 protease. This protein which is separated from the polyprotein by cis cleavage at its respective C-terminus, has been attributed with different functions during potyviral infection of plants. P1 of Turnip mosaic virus (P1-TuMV) harbors an FGSF-motif and FGSL-motif at its N-terminus. This motif is predicted to be a binding site for the host Ras GTPase-activating protein-binding protein (G3BP), which is a key factor for stress granule (SG) formation in mammalian systems and often targeted by viruses to inhibit SG formation. We therefore hypothesized that P1-TuMV might interact with G3BP to control and regulate plant SGs to optimize cellular conditions for the production of viral proteins. Here, we analyzed the co-localization of the Arabidopsis thaliana G3BP-2 with the P1 of two TuMV isolates, namely UK 1 and DEU 2. Surprisingly, P1-TuMV-DEU 2 co-localized with AtG3BP-2 under abiotic stress conditions, whereas P1-TuMV-UK 1 did not. AtG3BP-2::RFP showed strong SGs formation after stress, while P1-UK 1::eGFP maintained a chloroplastic signal under stress conditions, the signal of P1-DEU 2::eGFP co-localized with that of AtG3BP-2::RFP. This indicates a specific interaction between P1-DEU 2 and the AtG3BP family which is not solely based on the canonical interaction motifs.

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Dose-response relationships in gene expression profiles in a harbor seal B lymphoma cell line exposed to 17α-ethinyl estradiol

Journal of Xenobiotics ◽

10.4081/xeno.2017.6702 ◽

2017 ◽

Vol 7 (1) ◽

Author(s):

Christine Kleinert ◽

Matthieu Blanchet ◽

François Gagné ◽

Michel Fournier

Keyword(s):

Gene Expression ◽

Cell Line ◽

Ethinyl Estradiol ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Harbor Seal ◽

Lymphoma Cell ◽

Lymphoma Cell Line ◽

Altered Expression ◽

B Lymphoma

The determination of changes in gene expression profiles with xenobiotic dose will allow identifying biomarkers and modes of toxicant action. The harbor seal (Phoca vitulina) 11B7501 B lymphoma cell line was exposed to 1, 10, 100, 1000, 10,000, or 25,000 μg/L 17α-ethinyl estradiol (EE2, the active compound of the contraceptive pill) for 24 h. Following exposure, RNA was extracted and transformed into cDNA. Transcript expression in exposed vs. control lymphocytes was analyzed via RT-qPCR to identify genes with altered expression. Our analysis indicates that gene expression for all but the reference gene varied with dose, suggesting that different doses induce distinct physiological responses. These findings demonstrate that RT-qPCR could be used to identify immunotoxicity and relative dose in harbor seal leukocytes.

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Effects of Collagen–Glycosaminoglycan Mesh on Gene Expression as Determined by Using Principal Component Analysis-Based Unsupervised Feature Extraction

Polymers ◽

10.3390/polym13234117 ◽

2021 ◽

Vol 13 (23) ◽

pp. 4117

Author(s):

Y-h. Taguchi ◽

Turki Turki

Keyword(s):

Gene Expression ◽

Principal Component Analysis ◽

Feature Extraction ◽

Cell Lines ◽

Time Course ◽

Expression Profiles ◽

Principal Component ◽

Component Analysis ◽

Altered Expression ◽

Unsupervised Feature Extraction

The development of the medical applications for substances or materials that contact cells is important. Hence, it is necessary to elucidate how substances that surround cells affect gene expression during incubation. In the current study, we compared the gene expression profiles of cell lines that were in contact with collagen–glycosaminoglycan mesh and control cells. Principal component analysis-based unsupervised feature extraction was applied to identify genes with altered expression during incubation in the treated cell lines but not in the controls. The identified genes were enriched in various biological terms. Our method also outperformed a conventional methodology, namely, gene selection based on linear regression with time course.

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Formation of Staphylococcus aureus Biofilm in the Presence of Sublethal Concentrations of Disinfectants Studied via a Transcriptomic Analysis Using Transcriptome Sequencing (RNA-seq)

Applied and Environmental Microbiology ◽

10.1128/aem.01643-17 ◽

2017 ◽

Vol 83 (24) ◽

Cited By ~ 12

Author(s):

M. Slany ◽

J. Oppelt ◽

L. Cincarova

Keyword(s):

Gene Expression ◽

Staphylococcus Aureus ◽

Biofilm Formation ◽

Transcriptome Sequencing ◽

Expression Profiles ◽

Bacterial Species ◽

Rna Seq ◽

Altered Expression ◽

Content Type ◽

Sublethal Concentrations

ABSTRACT Staphylococcus aureus is a common biofilm-forming pathogen. Low doses of disinfectants have previously been reported to promote biofilm formation and to increase virulence. The aim of this study was to use transcriptome sequencing (RNA-seq) analysis to investigate global transcriptional changes in S. aureus in response to sublethal concentrations of the commonly used food industry disinfectants ethanol (EtOH) and chloramine T (ChT) and their combination (EtOH_ChT) in order to better understand the effects of these agents on biofilm formation. Treatment with EtOH and EtOH_ChT resulted in more significantly altered expression profiles than treatment with ChT. Our results revealed that EtOH and EtOH_ChT treatments enhanced the expression of genes responsible for regulation of gene expression (sigB), cell surface factors (clfAB), adhesins (sdrDE), and capsular polysaccharides (cap8EFGL), resulting in more intact biofilm. In addition, in this study we were able to identify the pathways involved in the adaptation of S. aureus to the stress of ChT treatment. Further, EtOH suppressed the effect of ChT on gene expression when these agents were used together at sublethal concentrations. These data show that in the presence of sublethal concentrations of tested disinfectants, S. aureus cells trigger protective mechanisms and try to cope with them. IMPORTANCE So far, the effect of disinfectants is not satisfactorily explained. The presented data will allow a better understanding of the mode of disinfectant action with regard to biofilm formation and the ability of bacteria to survive the treatment. Such an understanding could contribute to the effort to eliminate possible sources of bacteria, making disinfectant application as efficient as possible. Biofilm formation plays significant role in the spread and pathogenesis of bacterial species.

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Effects of the collagen–glycosaminoglycan mesh on gene expression as determined by using principal component analysis-based unsupervised feature extraction

10.1101/2021.09.20.461131 ◽

2021 ◽

Author(s):

Y-h. Taguchi ◽

Turki Turki

Keyword(s):

Gene Expression ◽

Principal Component Analysis ◽

Feature Extraction ◽

Cell Lines ◽

Time Course ◽

Expression Profiles ◽

Principal Component ◽

Component Analysis ◽

Altered Expression ◽

Unsupervised Feature Extraction

AbstractDevelopment of the medical applications for substances or materials that contact the cells is important. Hence, it is necessary to elucidate how substance that surround cells affect the gene expression during incubation. Here, we compared the gene expression profiles of cell lines that were in contact with the collagen–glycosaminoglycan mesh and control cells. Principal component analysis-based unsupervised feature extraction was applied to identify genes with altered expression during incubation in the treated cell lines but not in the controls. The identified genes were enriched in various biological terms. Our method also outperformed a conventional methodology, namely, gene selection based on linear regression with time course.

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Tissue-specific transcriptome profiling of the Arabidopsis thaliana inflorescence stem reveals local cellular signatures

10.1101/2020.02.10.941492 ◽

2020 ◽

Author(s):

Dongbo Shi ◽

Virginie Jouannet ◽

Javier Agustí ◽

Verena Kaul ◽

Victor Levitsky ◽

...

Keyword(s):

Gene Expression ◽

Arabidopsis Thaliana ◽

Spatial Resolution ◽

High Spatial Resolution ◽

Expression Profiles ◽

Differentially Expressed ◽

Tissue Specific ◽

Inflorescence Stem ◽

Genome Wide ◽

A Genome

AbstractGenome-wide gene expression maps with a high spatial resolution have substantially accelerated molecular plant science. However, the number of characterized tissues and growth stages is still small because of the limited accessibility of most tissues for protoplast isolation. Here, we provide gene expression profiles of the mature inflorescence stem of Arabidopsis thaliana covering a comprehensive set of distinct tissues. By combining fluorescence-activated nucleus sorting and laser-capture microdissection with next generation RNA sequencing, we characterize transcriptomes of xylem vessels, fibers, the proximal and the distal cambium, phloem, phloem cap, pith, starch sheath, and epidermis cells. Our analyses classify more than 15,000 genes as being differentially expressed among different stem tissues and reveal known and novel tissue-specific cellular signatures. By determining transcription factor binding regions enriched in promoter regions of differentially expressed genes, we furthermore provide candidates for tissue-specific transcriptional regulators. Our datasets predict expression profiles of an exceptional amount of genes and allow generating hypotheses toward the spatial organization of physiological processes. Moreover, we demonstrate that information on gene expression in a broad range of mature plant tissues can be established with high spatial resolution by nuclear mRNA profiling.One sentence summaryA genome-wide high-resolution gene expression map of the Arabidopsis inflorescence stem is established.

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