scholarly journals Subunit Compositions of the RNA-Silencing Enzymes Pol IV and Pol V Reveal Their Origins as Specialized Forms of RNA Polymerase II

2009 ◽  
Vol 33 (2) ◽  
pp. 192-203 ◽  
Author(s):  
Thomas S. Ream ◽  
Jeremy R. Haag ◽  
Andrzej T. Wierzbicki ◽  
Carrie D. Nicora ◽  
Angela D. Norbeck ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Rna Silencing ◽  
Pol Iv ◽  
Pol V

scholarly journals The Pol IV largest subunit CTD quantitatively affects siRNA levels guiding RNA-directed DNA methylation

2019 ◽  
Vol 47 (17) ◽  
pp. 9024-9036 ◽  
Author(s):  
Jered M Wendte ◽  
Jeremy R Haag ◽  
Olga M Pontes ◽  
Jasleen Singh ◽  
Sara Metcalf ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Catalytic Activity ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Cytosine Methylation ◽  
Transcriptional Gene Silencing ◽  
Rna Dependent Rna Polymerase ◽  
Pol Ii ◽  
Pol Iv ◽  
Non Coding Rnas

Abstract In plants, nuclear multisubunit RNA polymerases IV and V are RNA Polymerase II-related enzymes that synthesize non-coding RNAs for RNA-directed DNA methylation (RdDM) and transcriptional gene silencing. Here, we tested the importance of the C-terminal domain (CTD) of Pol IV’s largest subunit given that the Pol II CTD mediates multiple aspects of Pol II transcription. We show that the CTD is dispensable for Pol IV catalytic activity and Pol IV termination-dependent activation of RNA-DEPENDENT RNA POLYMERASE 2, which partners with Pol IV to generate dsRNA precursors of the 24 nt siRNAs that guide RdDM. However, 24 nt siRNA levels decrease ∼80% when the CTD is deleted. RNA-dependent cytosine methylation is also reduced, but only ∼20%, suggesting that siRNA levels typically exceed the levels needed for methylation of most loci. Pol IV-dependent loci affected by loss of the CTD are primarily located in chromosome arms, similar to loci dependent CLSY1/2 or SHH1, which are proteins implicated in Pol IV recruitment. However, deletion of the CTD does not phenocopy clsy or shh1 mutants, consistent with the CTD affecting post-recruitment aspects of Pol IV activity at target loci.

scholarly journals Genome Wide Identification of Key Components of RNA Silencing in Two Phaseolus vulgaris Genotypes of Contrasting Origin and Their Expression Analyses in Response to Fungal Infection

2021 ◽  
Author(s):  
Juan Camilo Alvarez-Diaz ◽  
Manon Richard ◽  
Vincent Thareau ◽  
Gianluca Teano ◽  
Christine Paysant-Le-Roux ◽  
...  
Keyword(s):  
Phaseolus Vulgaris ◽  
Stress Responses ◽  
Rna Silencing ◽  
Rna Binding ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Colletotrichum Lindemuthianum ◽  
Online Data ◽  
Pol Iv ◽  
Pol V

RNA silencing serves key roles in a multitude of cellular processes, including development, stress responses, metabolism, and maintenance of genome integrity. Dicer, Argonaute (AGO), double-stranded RNA binding (DRB), RNA-dependent RNA polymerase (RDR) and DNA-dependent RNA polymerases known as Pol IV and Pol V form core components to trigger RNA silencing. Common bean (Phaseolus vulgaris) is an important staple crop worldwide. In this study, we aimed to unravel the components of the RNA-guided silencing pathway in this non-model plant taking advantage of the availability of two genome assemblies of Andean and Meso-American origin. We identified six PvDCLs, thirteen PvAGOs, 10 PvDRB, 5 PvRDR, in both genotypes, suggesting no recent gene amplification or deletion after the gene pool separation. In addition, we identified one PvNRPD1 and one PvNRPE1 encoding the largest subunits of Pol IV and Pol V, respectively. These genes were categorized into subgroups based on phylogenetic analyses. Comprehensive analyses of gene structure, genomic localization and similarity among these genes were performed. Their expression patterns were investigated by means of expression models in different organs using online data and quantitative RT-PCR after pathogen infection. Several of the candidate genes were up-regulated after infection with the fungus Colletotrichum lindemuthianum.

scholarly journals The NRPD1 N-terminus contains a Pol IV-specific motif that is critical for genome surveillance in Arabidopsis

2019 ◽  
Vol 47 (17) ◽  
pp. 9037-9052 ◽  
Author(s):  
Laura Ferrafiat ◽  
David Pflieger ◽  
Jasleen Singh ◽  
Michael Thieme ◽  
Marcel Böhrer ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Surveillance Systems ◽  
Missense Mutations ◽  
Small Interfering Rnas ◽  
Mutant Genotype ◽  
Pol Iv ◽  
N Terminus

Abstract RNA-guided surveillance systems constrain the activity of transposable elements (TEs) in host genomes. In plants, RNA polymerase IV (Pol IV) transcribes TEs into primary transcripts from which RDR2 synthesizes double-stranded RNA precursors for small interfering RNAs (siRNAs) that guide TE methylation and silencing. How the core subunits of Pol IV, homologs of RNA polymerase II subunits, diverged to support siRNA biogenesis in a TE-rich, repressive chromatin context is not well understood. Here we studied the N-terminus of Pol IV’s largest subunit, NRPD1. Arabidopsis lines harboring missense mutations in this N-terminus produce wild-type (WT) levels of NRPD1, which co-purifies with other Pol IV subunits and RDR2. Our in vitro transcription and genomic analyses reveal that the NRPD1 N-terminus is critical for robust Pol IV-dependent transcription, siRNA production and DNA methylation. However, residual RNA-directed DNA methylation observed in one mutant genotype indicates that Pol IV can operate uncoupled from the high siRNA levels typically observed in WT plants. This mutation disrupts a motif uniquely conserved in Pol IV, crippling the enzyme's ability to inhibit retrotransposon mobilization. We propose that the NRPD1 N-terminus motif evolved to regulate Pol IV function in genome surveillance.

scholarly journals RNA-Silencing Enzymes Pol IV and Pol V in Maize: More than one Flavor?

PLoS Genetics ◽  
2009 ◽  
Vol 5 (11) ◽  
pp. e1000736 ◽  
Author(s):  
Craig S. Pikaard ◽  
Sarah Tucker
Keyword(s):  
Rna Silencing ◽  
Pol Iv ◽  
Pol V

An atypical RNA polymerase involved in RNA silencing shares small subunits with RNA polymerase II

2008 ◽  
Vol 16 (1) ◽  
pp. 91-93 ◽  
Author(s):  
Linfeng Huang ◽  
Alexandra M E Jones ◽  
Iain Searle ◽  
Kanu Patel ◽  
Hannes Vogler ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Rna Silencing

scholarly journals In Vitro Transcription Activities of Pol IV, Pol V, and RDR2 Reveal Coupling of Pol IV and RDR2 for dsRNA Synthesis in Plant RNA Silencing

2012 ◽  
Vol 48 (5) ◽  
pp. 811-818 ◽  
Author(s):  
Jeremy R. Haag ◽  
Thomas S. Ream ◽  
Michelle Marasco ◽  
Carrie D. Nicora ◽  
Angela D. Norbeck ◽  
...  
Keyword(s):  
Rna Silencing ◽  
In Vitro Transcription ◽  
Pol Iv ◽  
Pol V

scholarly journals Arabidopsis MED18 Interaction With RNA Pol IV and V Subunit NRPD2a in Transcriptional Regulation of Plant Immune Responses

2021 ◽  
Vol 12 ◽  
Author(s):  
Yan Zhang ◽  
Chengchen Shi ◽  
Weihong Fu ◽  
Xiaojing Gu ◽  
Ziyang Qi ◽  
...  
Keyword(s):  
Salicylic Acid ◽  
Jasmonic Acid ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Epigenetic Regulation ◽  
Plant Immunity ◽  
Critical Role ◽  
Regulation Of Gene Expression ◽  
Transcriptome Profiling ◽  
Pol Iv

Mediator is a conserved multiprotein complex important for transcription by RNA polymerase II (Pol II). Arabidopsis Mediator subunit MED18 regulates flowering, hormone signaling and plant immunity. Here we report that Arabidopsis MED18 interacted with NUCLEAR RNA POLYMERASE D2a (NRPD2a), the second largest subunit of the nuclear Pol IV and V, which function in RNA-directed DNA methylation and epigenetic regulation of gene expression. Mutants for both MED18 and NRPD2a were compromised in resistance to necrotrophic fungal pathogen Botrytis cinerea. Mutants for NRPD1a, the largest subunit of Pol IV, were also compromised in resistance to Botrytis, supporting a critical role of Pol IV and V in plant defense against Botrytis. Increased Botrytis susceptibility of both the med18 and nrpd2a mutants were associated with reduced accumulation of reactive oxygen species, which are known to promote resistance to Botrytis. Both the basal and pathogen-induced levels of salicylic acid and jasmonic acid were also significantly altered in the med18 and nrpd2a mutants. Transcriptome profiling found that MED18 and NRPD2a affected both unique and overlapping sets of genes in a broad spectrum of biological processes and pathways that influence plant–pathogen interaction. The genes altered in expression in the med18 and nrpd2a mutants include disease resistance proteins, salicylic acid and jasmonic acid signaling and responses, which are known to affect resistance to necrotrophic pathogens. The novel interaction between subunits of Mediator and plant-specific RNA polymerases provides a new mechanism for epigenetic regulation of resistance and expression of defense-related genes in plant immunity.

scholarly journals Genome-Wide Identification of Key Components of RNA Silencing in Two Phaseolus vulgaris Genotypes of Contrasting Origin and Their Expression Analyses in Response to Fungal Infection

Genes ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 64
Author(s):  
Juan C. Alvarez-Diaz ◽  
Manon M. S. Richard ◽  
Vincent Thareau ◽  
Gianluca Teano ◽  
Christine Paysant-Le-Roux ◽  
...  
Keyword(s):  
Phaseolus Vulgaris ◽  
Stress Responses ◽  
Rna Silencing ◽  
Rna Binding ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Colletotrichum Lindemuthianum ◽  
Online Data ◽  
Pol Iv ◽  
Pol V

RNA silencing serves key roles in a multitude of cellular processes, including development, stress responses, metabolism, and maintenance of genome integrity. Dicer, Argonaute (AGO), double-stranded RNA binding (DRB) proteins, RNA-dependent RNA polymerase (RDR), and DNA-dependent RNA polymerases known as Pol IV and Pol V form core components to trigger RNA silencing. Common bean (Phaseolus vulgaris) is an important staple crop worldwide. In this study, we aimed to unravel the components of the RNA-guided silencing pathway in this non-model plant, taking advantage of the availability of two genome assemblies of Andean and Meso-American origin. We identified six PvDCLs, thirteen PvAGOs, 10 PvDRBs, 5 PvRDRs, in both genotypes, suggesting no recent gene amplification or deletion after the gene pool separation. In addition, we identified one PvNRPD1 and one PvNRPE1 encoding the largest subunits of Pol IV and Pol V, respectively. These genes were categorized into subgroups based on phylogenetic analyses. Comprehensive analyses of gene structure, genomic localization, and similarity among these genes were performed. Their expression patterns were investigated by means of expression models in different organs using online data and quantitative RT-PCR after pathogen infection. Several of the candidate genes were up-regulated after infection with the fungus Colletotrichum lindemuthianum.

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