scholarly journals Combined analysis of the time-resolved transcriptome and proteome of the pathogenicity-activated plant pathogen Xanthomonas oryzae pv. oryzae

2020 ◽  
Author(s):  
Seunghwan Kim ◽  
Wooyoung Eric Jang ◽  
Min-Sik Kim ◽  
Jeong-Gu Kim ◽  
Lin-Woo Kang
Keyword(s):  
Gene Expression ◽  
Plant Pathogen ◽  
Translational Regulation ◽  
Expression Patterns ◽  
Regulation Of Gene Expression ◽  
Early Response ◽  
Xanthomonas Oryzae ◽  
Initial Contact ◽  
Time Resolved ◽  
Inorganic Ion

AbstractXanthomonas oryzae pv. oryzae (Xoo) is a plant pathogen responsible for causing bacterial blight in rice. It is responsible for blight outbreaks in most rice-producing countries and can reduce the rice yield by 50% due to the lack of an effective pesticide. The immediate alterations in Xoo upon initial contact with rice at the infection site are essential for pathogenesis. Here, we studied time-resolved gene expression in pathogenicity-activated Xoo cells at the trans criptome and proteome levels. The early response genes of Xoo include genes related to cell motility, inorganic ion transport, and effectors, which aid the Xoo cells to invade damaged rice leaf tissues, obtain scarce cofactors, and evade rice immune responses, respectively. Alteration of gene expression is initiated as early as few minutes after the initial interaction and changes with time. Although there was a correlation between the overall expression patterns of mRNAs and proteins for many genes, some genes also exhibited differences with respect to the expression timing and level of mRNAs and proteins, suggesting an important role of translational regulation in the early stages of pathogenesis. Gene expression analysis using time-resolved transcriptome and proteome data provided valuable information regarding Xoo pathogenesis during the initial stages of Xoo-rice interaction and revealed translational regulation of gene expression in bacteria.

scholarly journals Combined Analysis of the Time-Resolved Transcriptome and Proteome of Plant Pathogen Xanthomonas oryzae pv. oryzae

2021 ◽  
Vol 12 ◽  
Author(s):  
Seunghwan Kim ◽  
Wooyoung Eric Jang ◽  
Jihwan Park ◽  
Min-Sik Kim ◽  
Jeong-Gu Kim ◽  
...  
Keyword(s):  
Gene Expression ◽  
Plant Pathogen ◽  
Translational Regulation ◽  
Early Response ◽  
Xanthomonas Oryzae ◽  
Initial Contact ◽  
Time Resolved ◽  
Inorganic Ion ◽  
Genome Wide

Xanthomonas oryzae pv. oryzae (Xoo) is a plant pathogen responsible for causing bacterial blight in rice. The immediate alterations in Xoo upon initial contact with rice are essential for pathogenesis. We studied time-resolved genome-wide gene expression in pathogenicity-activated Xoo cells at the transcriptome and proteome levels. The early response genes of Xoo include genes related to cell motility, inorganic ion transport, and effectors. The alteration of gene expression is initiated as early as few minutes after the initial interaction and changes with time. The time-resolved comparison of the transcriptome and proteome shows the differences between transcriptional and translational expression peaks in many genes, although the overall expression pattern of mRNAs and proteins is conserved. The discrepancy suggests an important role of translational regulation in Xoo at the early stages of pathogenesis. The gene expression analysis using time-resolved transcriptome and proteome provides unprecedented valuable information regarding Xoo pathogenesis.

scholarly journals Time-resolved pathogenic gene expression analysis of the plant pathogen Xanthomonas oryzae pv. oryzae

BMC Genomics ◽  
2016 ◽  
Vol 17 (1) ◽  
Author(s):  
Seunghwan Kim ◽  
Yong-Joon Cho ◽  
Eun-Sung Song ◽  
Sang Hee Lee ◽  
Jeong-Gu Kim ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Analysis ◽  
Plant Pathogen ◽  
Gene Expression Analysis ◽  
Xanthomonas Oryzae ◽  
Time Resolved ◽  
Pathogenic Gene

scholarly journals Transcriptional and translational regulation of pathogenesis in Alzheimer’s disease model mice

2021 ◽  
Author(s):  
Guillermo Eastman ◽  
Elizabeth R. Sharlow ◽  
John S. Lazo ◽  
George S. Bloom ◽  
José R. Sotelo-Silveira
Keyword(s):  
Gene Expression ◽  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Transcriptional Regulation ◽  
Translational Regulation ◽  
Expression Patterns ◽  
Regulation Of Gene Expression ◽  
Ribosome Profiling ◽  
Translational Efficiency ◽  
Rna Seq

ABSTRACTBackgroundDefining the cellular mechanisms that drive Alzheimer’s disease (AD) pathogenesis and progression will be aided by studies defining how gene expression patterns change during pre-symptomatic AD and the ensuing periods of steadily declining cognition. Previous studies have emphasized changes in transcriptional regulation, but not translational regulation, leaving the ultimate results of gene expression alterations relatively unexplored in the context of AD.ObjectiveTo identify genes whose expression might be regulated at the transcriptional, and especially at the translational levels in AD, we analyzed gene expression in cerebral cortex of two AD model mouse strains, CVN (APPSwDI;NOS2-/-) and Tg2576 (APPSw), and their companion wild type (WT) strains at 6 months of age by tandem RNA-Seq and Ribo-Seq (ribosome profiling).MethodsIdentical starting pools of bulk RNA were used for RNA-Seq and Ribo-Seq. Differential gene expression analysis was performed at the transcriptional and translational levels separately, and also at the translational efficiency level. Regulated genes were functionally evaluated by gene ontology tools.ResultsCompared to WT mice, AD model mice had similar levels of transcriptional regulation, but displayed differences in translational regulation. A specific microglial signature associated with early stages of Aβ accumulation was up-regulated at both transcriptome and translatome levels in CVN mice. Although the two mice strains did not share many regulated genes, they showed common regulated pathways related to APP metabolism associated with neurotoxicity and neuroprotection.ConclusionThis work represents the first genome-wide study of brain translational regulation in animal models of AD, and provides evidence of a tight and early translational regulation of gene expression controlling the balance between neuroprotective and neurodegenerative processes in brain.

scholarly journals Translational regulation of gene expression by Lin28 and Roquin

2015 ◽  
Vol 71 (a1) ◽  
pp. s29-s30
Author(s):  
Udo Heinemann ◽  
Yasuhiro Murakawa ◽  
Markus Landthaler ◽  
Florian Mayr ◽  
Anja Schütz
Keyword(s):  
Gene Expression ◽  
Translational Regulation ◽  
Regulation Of Gene Expression

scholarly journals Time-resolved transcriptional profiling of Trichinella-infected murine myocytes helps to elucidate host–pathogen interactions in the muscle stage

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Xiaoxiang Hu ◽  
Xiaolei Liu ◽  
Chen Li ◽  
Yulu Zhang ◽  
Chengyao Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Biology ◽  
Trichinella Spiralis ◽  
Expression Patterns ◽  
Muscle Cells ◽  
Host Cells ◽  
Initial Reaction ◽  
Global Changes ◽  
Mammalian Skeletal Muscle ◽  
Time Resolved

Abstract Background Parasites of the genus Trichinella are the pathogenic agents of trichinellosis, which is a widespread and severe foodborne parasitic disease. Trichinella spiralis resides primarily in mammalian skeletal muscle cells. After invading the cells of the host organism, T. spiralis must elude or invalidate the host’s innate and adaptive immune responses to survive. It is necessary to characterize the pathogenesis of trichinellosis to help to prevent the occurrence and further progression of this disease. The aims of this study were to elucidate the mechanisms of nurse cell formation, pathogenesis and immune evasion of T. spiralis, to provide valuable information for further research investigating the basic cell biology of Trichinella-infected muscle cells and the interaction between T. spiralis and its host. Methods We performed transcriptome profiling by RNA sequencing to identify global changes at 1, 3, 7, 10 and 15 days post-infection (dpi) in gene expression in the diaphragm after the parasite entered and persisted within the murine myocytes; the mice were infected by intravenous injection of newborn larvae. Gene expression analysis was based on the alignment results. Differentially expressed genes (DEGs) were identified based on their expression levels in various samples, and functional annotation and enrichment analysis were performed. Results The most extensive and dynamic gene expression responses in host diaphragms were observed during early infection (1 dpi). The number of DEGs and genes annotated in the Kyoto Encyclopedia of Genes and Genomes and Gene Ontology databases decreased significantly in the infected mice compared to the uninfected mice at 3 and 7 dpi, suddenly increased sharply at 10 dpi, and then decreased to a lower level at 15 dpi, similar to that observed at 3 and 7 dpi. The massive initial reaction of the murine muscle cells to Trichinella infection steadied in the later stages of infection, with little additional changes detected for the remaining duration of the studied process. Although there were hundreds of DEGs at each time point, only 11 genes were consistently up- or downregulated at all 5 time points. Conclusions The gene expression patterns identified in this study can be employed to characterize the coordinated response of T. spiralis-infected myocytes in a time-resolved manner. This comprehensive dataset presents a distinct and sensitive picture of the interaction between host and parasite during intracellular infection, which can help to elucidate how pathogens evade host defenses and coordinate the biological functions of host cells to survive in the mammalian environment.

scholarly journals Coordination of RNA Processing Regulation by Signal Transduction Pathways

Biomolecules ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 1475
Author(s):  
Veronica Ruta ◽  
Vittoria Pagliarini ◽  
Claudio Sette
Keyword(s):  
Gene Expression ◽  
Signal Transduction ◽  
Rna Processing ◽  
Translational Regulation ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Regulation Of Gene Expression ◽  
Signal Transduction Pathways ◽  
Challenges And Opportunities ◽  
Common Signal

Signal transduction pathways transmit the information received from external and internal cues and generate a response that allows the cell to adapt to changes in the surrounding environment. Signaling pathways trigger rapid responses by changing the activity or localization of existing molecules, as well as long-term responses that require the activation of gene expression programs. All steps involved in the regulation of gene expression, from transcription to processing and utilization of new transcripts, are modulated by multiple signal transduction pathways. This review provides a broad overview of the post-translational regulation of factors involved in RNA processing events by signal transduction pathways, with particular focus on the regulation of pre-mRNA splicing, cleavage and polyadenylation. The effects of several post-translational modifications (i.e., sumoylation, ubiquitination, methylation, acetylation and phosphorylation) on the expression, subcellular localization, stability and affinity for RNA and protein partners of many RNA-binding proteins are highlighted. Moreover, examples of how some of the most common signal transduction pathways can modulate biological processes through changes in RNA processing regulation are illustrated. Lastly, we discuss challenges and opportunities of therapeutic approaches that correct RNA processing defects and target signaling molecules.

scholarly journals Cell-type Specific Expression Quantitative Trait Loci Associated with Alzheimer Disease in Blood and Brain Tissue

2020 ◽  
Author(s):  
Devanshi Patel ◽  
Xiaoling Zhang ◽  
John J. Farrell ◽  
Jaeyoon Chung ◽  
Thor D. Stein ◽  
...  
Keyword(s):  
Gene Expression ◽  
Quantitative Trait ◽  
Expression Patterns ◽  
Regulation Of Gene Expression ◽  
Cell Types ◽  
Eqtl Analysis ◽  
Cell Type ◽  
Specific Expression ◽  
Cell Type Specific Expression ◽  
Cell Type Specific

ABSTRACTBecause regulation of gene expression is heritable and context-dependent, we investigated AD-related gene expression patterns in cell-types in blood and brain. Cis-expression quantitative trait locus (eQTL) mapping was performed genome-wide in blood from 5,257 Framingham Heart Study (FHS) participants and in brain donated by 475 Religious Orders Study/Memory & Aging Project (ROSMAP) participants. The association of gene expression with genotypes for all cis SNPs within 1Mb of genes was evaluated using linear regression models for unrelated subjects and linear mixed models for related subjects. Cell type-specific eQTL (ct-eQTL) models included an interaction term for expression of “proxy” genes that discriminate particular cell type. Ct-eQTL analysis identified 11,649 and 2,533 additional significant gene-SNP eQTL pairs in brain and blood, respectively, that were not detected in generic eQTL analysis. Of note, 386 unique target eGenes of significant eQTLs shared between blood and brain were enriched in apoptosis and Wnt signaling pathways. Five of these shared genes are established AD loci. The potential importance and relevance to AD of significant results in myeloid cell-types is supported by the observation that a large portion of GWS ct-eQTLs map within 1Mb of established AD loci and 58% (23/40) of the most significant eGenes in these eQTLs have previously been implicated in AD. This study identified cell-type specific expression patterns for established and potentially novel AD genes, found additional evidence for the role of myeloid cells in AD risk, and discovered potential novel blood and brain AD biomarkers that highlight the importance of cell-type specific analysis.

scholarly journals Gene Involved in Transcriptional Activation of the hrp Regulatory Gene hrpG in Xanthomonas oryzae pv. oryzae

2006 ◽  
Vol 188 (11) ◽  
pp. 4158-4162 ◽  
Author(s):  
Seiji Tsuge ◽  
Takeshi Nakayama ◽  
Shinsaku Terashima ◽  
Hirokazu Ochiai ◽  
Ayako Furutani ◽  
...  
Keyword(s):  
Gene Expression ◽  
Plant Pathogen ◽  
Transcriptional Activation ◽  
Regulatory Gene ◽  
Xanthomonas Oryzae ◽  
In Planta

ABSTRACT A novel regulatory gene, trh, which is involved in hrp gene expression, is identified in the plant pathogen Xanthomonas oryzae pv. oryzae. In the trh mutant, expression of HrpG, which is a key regulator for hrp gene expression, is reduced both under the in vitro hrp-inducing condition and in planta.

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