scholarly journals RNA Interference: A Natural Immune System of Plants to Counteract Biotic Stressors

Cells ◽  
2019 ◽  
Vol 8 (1) ◽  
pp. 38 ◽  
Author(s):  
Tayeb Muhammad ◽  
Fei Zhang ◽  
Yan Zhang ◽  
Yan Liang
Keyword(s):  
Gene Expression ◽  
Immune System ◽  
Rna Interference ◽  
Transposable Elements ◽  
Plant Pathogen ◽  
Rna Silencing ◽  
Defense Mechanisms ◽  
Biological Process ◽  
Inhibit Gene Expression ◽  
Plant Pathogen Interactions

During plant-pathogen interactions, plants have to defend the living transposable elements from pathogens. In response to such elements, plants activate a variety of defense mechanisms to counteract the aggressiveness of biotic stressors. RNA interference (RNAi) is a key biological process in plants to inhibit gene expression both transcriptionally and post-transcriptionally, using three different groups of proteins to resist the virulence of pathogens. However, pathogens trigger an anti-silencing mechanism through the expression of suppressors to block host RNAi. The disruption of the silencing mechanism is a virulence strategy of pathogens to promote infection in the invaded hosts. In this review, we summarize the RNA silencing pathway, anti-silencing suppressors, and counter-defenses of plants to viral, fungal, and bacterial pathogens.

Mammalian genome evolution as a result of epigenetic regulation of transposable elements

2014 ◽  
Vol 5 (3) ◽  
pp. 183-194 ◽  
Author(s):  
Reuben M. Buckley ◽  
David L. Adelson
Keyword(s):  
Gene Expression ◽  
Transposable Elements ◽  
Epigenetic Regulation ◽  
Dna Sequences ◽  
Defense Mechanisms ◽  
Regulatory Networks ◽  
Regulation Of Gene Expression ◽  
Epigenetic Marks ◽  
Rna Molecules ◽  
Mammalian Genomes

AbstractTransposable elements (TEs) make up a large proportion of mammalian genomes and are a strong evolutionary force capable of rewiring regulatory networks and causing genome rearrangements. Additionally, there are many eukaryotic epigenetic defense mechanisms able to transcriptionally silence TEs. Furthermore, small RNA molecules that target TE DNA sequences often mediate these epigenetic defense mechanisms. As a result, epigenetic marks associated with TE silencing can be reestablished after epigenetic reprogramming – an event during the mammalian life cycle that results in widespread loss of parental epigenetic marks. Furthermore, targeted epigenetic marks associated with TE silencing may have an impact on nearby gene expression. Therefore, TEs may have driven species evolution via their ability to heritably alter the epigenetic regulation of gene expression in mammals.

Gene expression investigations on plant-pathogen interactions between Xanthomonas campestris pv. vesicatoria and pepper ( Capsicum annuum L.) using the cDNA-AFLP technology

2009 ◽  
Vol 57 (2) ◽  
pp. 127-136
Author(s):  
E. Szabó ◽  
G. Bárdos ◽  
I. Nagy
Keyword(s):  
Gene Expression ◽  
Capsicum Annuum ◽  
Plant Pathogen ◽  
Xanthomonas Campestris ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Bacterial Pathogen ◽  
Sequence Comparisons ◽  
Time Courses ◽  
Plant Pathogen Interactions

In order to target factors involved in plant-pathogen interactions, gene expression differences were investigated on pepper ( Capsicum annuum L.) plants after artificial infection with the bacterial pathogen Xanthomonas campestris pv. vesicatoria . Amplified Fragment Length Polymorphism investigations on reverse transcribed DNA fragments (cDNA-AFLP) were used to compare the expression profiles of parental lines and of resistant and susceptible individuals from pepper populations segregating for the gds gene, which confers a general defence system in pepper. In total, 73 transcript-derived fragments (TDFs) displaying differential expression patterns could be identified (presence-absence and/or different time courses in resistant and susceptible genotypes). Of these, 67 fragments were cloned and sequenced. In the case of several TDFs, sequence comparisons revealed close homologies to genes known to be responsible for abiotic stress or biotic elicitors, presenting potentially interesting targets for more detailed studies on gene expression and signal transduction.

scholarly journals A circadian oscillator in the fungus Botrytis cinerea regulates virulence when infecting Arabidopsis thaliana

2015 ◽  
Vol 112 (28) ◽  
pp. 8744-8749 ◽  
Author(s):  
Montserrat A. Hevia ◽  
Paulo Canessa ◽  
Hanna Müller-Esparza ◽  
Luis F. Larrondo
Keyword(s):  
Arabidopsis Thaliana ◽  
Botrytis Cinerea ◽  
Plant Pathogen ◽  
Defense Mechanisms ◽  
Pathogenic Fungi ◽  
Circadian System ◽  
Main Role ◽  
Fungal Virulence ◽  
Virulence Potential ◽  
Plant Pathogen Interactions

The circadian clock of the plant model Arabidopsis thaliana modulates defense mechanisms impacting plant–pathogen interactions. Nevertheless, the effect of clock regulation on pathogenic traits has not been explored in detail. Moreover, molecular description of clocks in pathogenic fungi—or fungi in general other than the model ascomycete Neurospora crassa—has been neglected, leaving this type of question largely unaddressed. We sought to characterize, therefore, the circadian system of the plant pathogen Botrytis cinerea to assess if such oscillatory machinery can modulate its virulence potential. Herein, we show the existence of a functional clock in B. cinerea, which shares similar components and circuitry with the Neurospora circadian system, although we found that its core negative clock element FREQUENCY (BcFRQ1) serves additional roles, suggesting extracircadian functions for this protein. We observe that the lesions produced by this necrotrophic fungus on Arabidopsis leaves are smaller when the interaction between these two organisms occurs at dawn. Remarkably, this effect does not depend solely on the plant clock, but instead largely relies on the pathogen circadian system. Genetic disruption of the B. cinerea oscillator by mutation, overexpression of BcFRQ1, or by suppression of its rhythmicity by constant light, abrogates circadian regulation of fungal virulence. By conducting experiments with out-of-phase light:dark cycles, we confirm that indeed, it is the fungal clock that plays the main role in defining the outcome of the Arabidopsis–Botrytis interaction, providing to our knowledge the first evidence of a microbial clock modulating pathogenic traits at specific times of the day.

scholarly journals Transposable elements contribute to genome dynamics and gene expression variation in the fungal plant pathogen Verticillium dahliae

2021 ◽  
Author(s):  
David E Torres ◽  
Bart PHJ Thomma ◽  
Michael F Seidl
Keyword(s):  
Gene Expression ◽  
Transposable Elements ◽  
Verticillium Dahliae ◽  
Plant Pathogen ◽  
Plant Pathogens ◽  
Gene Expression Variation ◽  
Expression Variation ◽  
Regulatory Variation ◽  
Fungal Plant Pathogen ◽  
Genomic Regions

AbstractTransposable elements (TEs) are a major source of genetic and regulatory variation in their host genome and are consequently thought to play important roles in evolution. Many fungal and oomycete plant pathogens have evolved dynamic and TE-rich genomic regions containing genes that are implicated in host colonization. TEs embedded in these regions have typically been thought to accelerate the evolution of these genomic compartments, but little is known about their dynamics in strains that harbor them. Here, we used whole-genome sequencing data of 42 strains of the fungal plant pathogen Verticillium dahliae to systematically identify polymorphic TEs that may be implicated in genomic as well as in gene expression variation. We identified 2,523 TE polymorphisms and characterize a subset of 8% of the TEs as dynamic elements that are evolutionary younger, less methylated, and more highly expressed when compared with the remaining 92% of the TE complement. As expected, the dynamic TEs are enriched in the dynamic genomic regions. Besides, we observed an association of dynamic TEs with pathogenicity-related genes that localize nearby and that display high expression levels. Collectively, our analyses demonstrate that TE dynamics in V. dahliae contributes to genomic variation, correlates with expression of pathogenicity-related genes, and potentially impacts the evolution of dynamic genomic regions.Significance statementTransposable elements (TEs) are ubiquitous components of genomes and are major sources of genetic and regulatory variation. Many plant pathogens have evolved TE-rich genomic regions containing genes with roles in host colonization, and TEs are thought to contribute to accelerated evolution of these dynamic regions. We analyzed the fungal plant pathogen Verticillium dahliae to identify TE variation between strains and to demonstrate that polymorphic TEs have specific characteristic that separates them from the majority of TEs. Polymorphic TEs are enriched in dynamic genomic regions and are associated with structural variants and highly expressed pathogenicity-related genes. Collectively, our results provide evidence for the hypothesis that dynamic TEs contribute to increased genomic diversity, functional variation, and the evolution of dynamic genomic regions.

SiMiSnoRNA: Collection of siRNA, miRNA, and snoRNA database for RNA interference / SiMiSnoRNA: RNA Interferansı için siRNA, miRNA ve snoRNA veritabanında depolanan siRNA, miRNA, and snoRNA koleksiyonları

2015 ◽  
Vol 40 (6) ◽  
Author(s):  
Umesh Kalathiya ◽  
Monikaben Padariya ◽  
Maciej Baginski ◽  
Chintankumar Padariya
Keyword(s):  
Gene Expression ◽  
Rna Interference ◽  
Small Rna ◽  
Regulation Of Gene Expression ◽  
Specific Gene ◽  
Sequence Information ◽  
Rna Molecules ◽  
Inhibit Gene Expression ◽  
Considerable Impact ◽  
Interfering Rna

AbstractObjective: The discovery of sequence specific gene silencing which occurs due to the presence of double- stranded RNAs has considerable impact on biology, revealing an unknown level of regulation of gene expression. This process is known as RNA interference (RNAi) or RNA silencing in which RNA molecules inhibit gene expression, typically by causing the destruction of specific mRNA molecule. Two types of small RNA molecules-small interfering RNA (siRNA) and microRNA (miRNA) are central to RNA interference. Therefore, SMethods: SResults: A flexible web-based search engine is developed to obtain fast access to specific small RNA sequence information.Conclusion: BLAST search analysis within S

scholarly journals RNA Interference and mRNA Silencing, 2004: How Far Will They Reach?

2004 ◽  
Vol 15 (2) ◽  
pp. 407-410 ◽  
Author(s):  
Thoru Pederson
Keyword(s):  
Gene Expression ◽  
Rna Interference ◽  
Gene Silencing ◽  
Rna Silencing ◽  
Regulation Of Gene Expression ◽  
Clinical Impact ◽  
Posttranscriptional Gene Silencing ◽  
Highly Effective ◽  
The Future ◽  
Recent Developments

The discoveries of RNA interference and RNA-mediated posttranscriptional gene silencing have opened an unanticipated new window on the regulation of gene expression as well as a facile and highly effective tool for knocking down gene expression in many organisms and cells. In addition, RNA interference and RNA silencing may conceivably be exploited for human therapeutics sometime in the future, possibly bringing greater clinical impact than have the so far disappointing antisense endeavors. This essay summarizes recent developments and offers some personalized perspectives, with emphasis on what we do not yet know.

scholarly journals Application of small RNAs for plant protection

2020 ◽  
Vol 18 (4) ◽  
pp. 467-482
Author(s):  
Polina Ya. Tretiakova ◽  
Aleksandr A. Soloviev
Keyword(s):  
Rna Interference ◽  
Plant Pathogen ◽  
Small Rnas ◽  
Plant Protection ◽  
High Quality ◽  
Resistant Varieties ◽  
New Strategy ◽  
New Perspective ◽  
Plant Pathogen Interactions ◽  
Regulatory Functions

Double-stranded small RNAs (dsRNA) perform various regulatory functions via RNA-interference. Additionally, they can be transported between various plant species and their pathogens and pests via extracellular vesicles, protecting RNA from nucleases. Plants secrete short dsRNA molecules to defend themselves against pathogens. The latter also use small RNAs when infecting crops. Some dsRNAs of pathogens are known as ribonucleic effectors. Host-induced gene silencing (HIGS) was shown to be effective when breeding resistant varieties and analyzing plant-pathogen interactions. However, complexity of transgenesis and society fear of genetically modified products make HIGS application difficult. The appearance of a new strategy based on plant spraying with dsRNA gave a new perspective of plant protection. Currently such a strategy requires accurate studying as well as the development of efficient systems stably producing high-quality dsRNA.

scholarly journals Posttranslational interference of Ty1 retrotransposition by antisense RNAs

2009 ◽  
Vol 106 (37) ◽  
pp. 15657-15662 ◽  
Author(s):  
Emiko Matsuda ◽  
David J. Garfinkel
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Rna Interference ◽  
Transposable Elements ◽  
Reverse Transcription ◽  
Copy Number ◽  
Dramatic Decrease ◽  
Intrinsic Mechanism ◽  
In Trans ◽  
Ty1 Retrotransposition

Transposable elements impact genome function by altering gene expression and causing chromosome rearrangements. As a result, organisms have evolved mechanisms, such as RNA-interference, to minimize the level of transposition. However, organisms without the conserved RNAi pathways, likeSaccharomyces cerevisiae, must use other mechanisms to prevent transposon movement. Here, we provide evidence that antisense (AS) RNAs from the retrovirus-like element Ty1 inhibit retrotransposition posttranslationally inSaccharomyces. Multiple Ty1AS transcripts overlap Ty1 sequences necessary for copy number control (CNC) and inhibit transpositionin trans. Altering Ty1 copy number or deleting sequences in the CNC region that are required for reverse transcription affect Ty1AS RNA level and Ty1 movement. Ty1AS RNAs are enriched in virus-like particles, and are associated with a dramatic decrease in the level of integrase, less reverse transcriptase, and an inability to synthesize Ty1 cDNA. Thus, Ty1AS RNAs are part of an intrinsic mechanism that limits retrotransposition by reducing the level of proteins required for replication and integration.

scholarly journals Every cloud has a silver lining: how abiotic stresses affect gene expression in plant pathogen-interactions

2020 ◽  
Author(s):  
Marco Zarattini ◽  
Mahsa Farjad ◽  
Alban Launay ◽  
David Cannella ◽  
Marie-Christine Soulié ◽  
...  
Keyword(s):  
Gene Expression ◽  
Plant Defense ◽  
Plant Pathogen ◽  
Abiotic Stresses ◽  
Biotic Interactions ◽  
Mineral Nutrient ◽  
Transcriptional Level ◽  
Tissue Organization ◽  
Plant Pathogen Interactions ◽  
The Impact

Abstract The current context of environmental and climate changes deeply influences the outcome of plant-pathogen interactions. Indeed, nowadays it is clear that abiotic stresses strongly affect biotic interactions at various levels. For instance, physiological parameters such as plant architecture and tissue organization along with primary and specialized metabolism are affected by environmental constraints, thus making the plant a more or less worthy host for a given pathogen. Moreover, abiotic stresses can affect the timely expression of plant defense and pathogen virulence. Indeed, several studies have shown that variations in temperature, water and mineral nutrient availability impact plant defense gene expression. Virulence gene expression, known to be crucial for disease outbreak, is also affected by environmental conditions, potentially modifying existing pathosystems and paving the way for emerging pathogens. The present review summarizes the current knowledge on the impact of abiotic stress on biotic interactions at the transcriptional level in both the plant and the pathogen side of the interaction. We performed a meta-data analysis of four different combinations of abiotic and biotic stresses. 197 modulated genes were common to all four combinations, with a strong defense-related GO term enrichment. We also describe the multistress-specific responses of selected defense-related genes.

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