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Alternaria brassicicola infection regulates miRNAs in Arabidopsis thaliana [mRNA]

ABSTRACT: Plant microRNAs (miRNAs) have been implicated in plant immunity. These mainly focusing Arabidopsis thaliana threatened by (hemi-)biotrophic pathogens such as the bacterial pathogen Pseudomonas syringae. Here, we show that the Arabidopsis miRNA pathway is important for defense responses against the necrotrophic fungus Alternaria brassicicola. The miRNA pathway mutant ago1 exhibits an exaggerated response when treated with A. brassicicola, proposing that AGO1 is positive regulator. We found a subset of Arabidopsis miRNAs that quickly change their expression and their abundance in AGO1 complexes in plants exposed to A. brassicicola. The miRNAs responding to pathogen treatment are mainly targeting genes encoding metabolic enzymes, proteins involved protein degradation or transposons. In case of miR163, A. brassicicola infection results in increased levels of miRNA precursors and preferential accumulation of an unspliced form of pri-miR163, suggesting that A. brassicicola infection changes the transcriptional and post-regulation of pri-miRNAs. miR163 acts as a negative regulator of plant defense because mir163 mutants are more resistant when treated with A. brassicicola. Taken together, our results reveal the existence of positively and negatively acting Arabidopsis miRNA modulating the defense responses against A. brassicicola and highlight the importance of host miRNAs in the interaction between plants and necrotrophic pathogens.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE83478 | GEO | 2019/06/17

REPOSITORIES: GEO

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Alternaria brassicicola infection regulates miRNAs in Arabidopsis thaliana [sRNA]

Project description:Plant microRNAs (miRNAs) have been implicated in plant immunity. These mainly focusing Arabidopsis thaliana threatened by (hemi-)biotrophic pathogens such as the bacterial pathogen Pseudomonas syringae. Here, we show that the Arabidopsis miRNA pathway is important for defense responses against the necrotrophic fungus Alternaria brassicicola. The miRNA pathway mutant ago1 exhibits an exaggerated response when treated with A. brassicicola, proposing that AGO1 is positive regulator. We found a subset of Arabidopsis miRNAs that quickly change their expression and their abundance in AGO1 complexes in plants exposed to A. brassicicola. The miRNAs responding to pathogen treatment are mainly targeting genes encoding metabolic enzymes, proteins involved protein degradation or transposons. In case of miR163, A. brassicicola infection results in increased levels of miRNA precursors and preferential accumulation of an unspliced form of pri-miR163, suggesting that A. brassicicola infection changes the transcriptional and post-regulation of pri-miRNAs. miR163 acts as a negative regulator of plant defense because mir163 mutants are more resistant when treated with A. brassicicola. Taken together, our results reveal the existence of positively and negatively acting Arabidopsis miRNA modulating the defense responses against A. brassicicola and highlight the importance of host miRNAs in the interaction between plants and necrotrophic pathogens.

2019-06-17 | GSE83487 | GEO

Tight Regulation of the Interaction between Brassica napus and Sclerotinia sclerotiorum at the MicroRNA Level [array]

Project description:MicroRNAs are multifunctional non-coding short nucleotide molecules. Nevertheless, the role of miRNAs in the interactions between plants and necrotrophic pathogens is largely unknown. Here, we report the identification of the miRNA repertoire of the economically important oil crop oilseed rape (Brassica napus) and those involved in interacting with its most devastating necrotrophic pathogen Sclerotinia sclerotiorum. We identified 280 B. napus miRNA candidates, including 53 novel candidates and 227 canonical members or variants of known miRNA families, by high-throughput deep sequencing of small RNAs from both normal and S. sclerotiorum-inoculated leaves. Target genes of 15 novel candidates and 222 known miRNAs were further identified by sequencing of degradomes from the two types of samples. MicroRNA microarray analysis revealed that 68 miRNAs were differentially expressed between S. sclerotiorum-inoculated and uninoculated leaves. A set of these miRNAs target genes involved in plant defense to S. sclerotiorum and/or other pathogens such as NBS-LRR R genes and nitric oxygen and reactive oxygen species related genes. Additionally, three miRNAs target AGO1 and AGO2, key components of post-transcriptional gene silencing (PTGS). Expression of several viral PTGS suppressors reduced resistance to S. sclerotiorum. Arabidopsis mutants of AGO1 and AGO2 exhibited reduced resistance while transgenic lines over-expressing AGO1 displayed increased resistance to S. sclerotiorum in an AGO1 expression level-dependent manner. Moreover, transient over-expression of miRNAs targeting AGO1 and AGO2 decreased resistance to S. sclerotiorum in oilseed rape. Our results demonstrate that the interactions between B. napus and S. sclerotiorum are tightly regulated at miRNA level and probably involve PTGS.

2017-05-16 | GSE81560 | GEO

Tight Regulation of the Interaction between Brassica napus and Sclerotinia sclerotiorum at the MicroRNA Level [HTS]

2017-05-16 | GSE81561 | GEO

RACK1 function in the miRNA pathway

Project description:MicroRNAs (miRNAs) regulate plant development by post-transcriptional regulation of target genes. In Arabidopsis thaliana, DCL1 processes precursors (pri-miRNAs) to miRNA duplexes, which associate with AGO1. Additional proteins act in concert with DCL1 (e.g. HYL1 and SERRATE) or AGO1, respectively, to facilitate efficient and precise pri-miRNA processing and miRNA loading. In this study, we show that the accumulation of plant microRNAs depends on RECEPTOR FOR ACTIVATED C KINASE 1 (RACK1), a scaffold protein found in all higher eukaryotes. miRNA levels are reduced in rack1 mutants and our data suggest that RACK1 affects the microRNA pathway via several distinct mechanisms involving direct interactions with known microRNA factors: RACK1 ensures the accumulation and processing of some pri-miRNAs, directly interacts with SERRATE and is part of an AGO1 complex. As a result, mutations in RACK1 lead to misregulation of miRNA target genes, which is important for ABA responses and phyllotaxy. In conclusion, our study discovered complex functioning of RACK1 proteins in the Arabidopsis miRNA pathway, which are important for miRNA production and therefore plant development.

2013-07-01 | GSE40579 | GEO

RACK1 function in the miRNA pathway

Project description:MicroRNAs (miRNAs) regulate different aspects of plant development by post-transcriptional regulation of target genes. In Arabidopsis, DICER-LIKE 1 (DCL1) processes miRNA precursors (pri-miRNAs) to miRNA duplexes, which associate with ARGONAUTE 1 (AGO1). AGO1 together with the miRNA guide strand binds complementary RNA sequences within target mRNAs. Additional proteins act in concert with DCL1 (e.g. HYL1 and SERRATE) and AGO1, respectively, to facilitate efficient and precise pri-miRNA processing and loading into the effector protein. Here, we show that RECEPTOR OF ACTIVATED C KINASE 1 (RACK1) is a novel component of the Arabidopsis miRNA pathway. RACK1 is a seven-bladed WD-repeat protein that has previously been shown to act as a scaffold protein mediating multiple simultaneous protein-protein interactions. Our molecular analyses demonstrate that RACK1 function is required for controlling miRNA-mediated gene expression. rack1 mutants contain only low levels of mature miRNAs without affecting the first step of pri-miRNA processing. Physical and genetic interaction studies revealed that RACK1 acts in concert with AGO1 and also interacts with a SERRATE, a component of the miRNA processing machinery. These results suggest that RACK1 also functions as a scaffold protein in the miRNA pathway to orchestrates miRNA maturation steps after the initial events of pri-miRNA processing. sequencing of small RNAs from WT and rack1abc mutants (two biological replicates each)

2013-07-01 | E-GEOD-40579 | biostudies-arrayexpress

A quantitative map of human primary microRNA processing sites

Project description:Maturation of canonical microRNA (miRNA) is initiated by DROSHA that cleaves the primary transcript (pri-miRNA). Over 1,800 miRNA loci are annotated in humans, but it remains largely unknown if and at which sites the pri-miRNAs are cleaved by DROSHA. Here we performed in vitro processing on a full set of human pri-miRNAs (miRBase v21) followed by sequencing. This comprehensive profiling enabled us to classify miRNAs based on DROSHA-dependence and map their cleavage sites with respective processing efficiency measures. Only 758 pri-miRNAs are confidently processed by DROSHA, while the majority may be non-canonical or false entries. Analyses of the DROSHA-dependent pri-miRNAs show key cis-elements for processing. We observe widespread alternative processing as well as unproductive cleavage events such as “nick” or “inverse” processing. SRSF3 is a broad-acting auxiliary factor modulating alternative processing and suppressing unproductive processing. The profiling data and methods developed in this study will allow systematic analyses of miRNA regulation.

2021-07-28 | PXD025767 | Pride

Arabidopsis thaliana AGO1 immunoprecipitated small RNA from Col0 plants transformed with a transgene expressing wild-type or a nuclear localized form of AGO1 fused to GFP.

Project description:Plant microRNAs undergo stepwise-nuclear maturation before engaging cytosolic sequence-complementary transcripts in association with the silencing-effector protein ARGONAUTE1(AGO1). How plant miRNAs translocate to the cytosol remains mysterious as does their cellular loading site(s) into AGO1. Here, we show that the N-termini of plant AGO1s contain a nuclear-localization (NLS) and nuclear-export signal (NES), which, in Arabidopsis thaliana (At) enables AtAGO1 nucleo-cytosolic shuttling in a Leptomycin-B-inhibited manner, diagnostic of CRM1(Expo1)/NES-dependent nuclear export. Nuclear-only AtAGO1 contains the same 2’O-methylated miRNA cohort as its nucleo-cytosolic counterpart, but specifically interacts with the miRNA loading-chaperone HSP90. AtAGO1 nucleo-cytosolic shuttling is required for mature miRNA translocation and for miRNA-mediated silencing. We propose that plant miRNAs are matured, methylated, loaded into AGO1 in the nucleus, and exported cytoplasmically as AGO1:miRNA complexes in a CRM1(Expo1)/NES-dependent manner.

2018-01-04 | GSE100395 | GEO

Arabidopsis MOS4-associated complex promotes microRNA biogenesis and pre-mRNA splicing [ncRNA-seq]

Project description:The evolutionarily conserved, putative RNA helicase MAC7 exists in both animals and plants. The human MAC7 homolog, Aquarius, is part of the spliceosome and plays a role in pre-mRNA splicing in vitro. In Arabidopsis, MAC7 was shown to be part of the MOS4-associated complex (MAC), which is required for plant defense and development. Here through RNA-seq analysis we discover that down-regulated genes in MAC subunit mutants are mostly involved in plant defense and stimulus response, confirming a role of MAC in the regulation of biotic and abiotic stress responses. We also discover global intron retention defects in mutants in three members of MAC, thus linking the functions of MAC to splicing in Arabidopsis. In addition, we show that mac7-1, a partial loss-of-function mutant in MAC7, and two other MAC subunit mutants, mac3a mac3b and prl1 prl2, exhibit reduced microRNA levels in general, indicating that MAC promotes microRNA biogenesis. The mac7-1 mutant shows reduced primary miRNA (pri-miRNA) levels without affecting MIR promoter activity or the degradation of pri-miRNA transcripts, implicating functions of MAC7 during transcription elongation or maturation of pri-miRNAs. As a nuclear protein, MAC7 is not localized in dicing bodies, but it affects the localization of HYL1 to dicing bodies. We propose that MAC acts to link MIR transcription to pri-miRNA processing.

2017-12-08 | GSE103422 | GEO

Arabidopsis MOS4-associated complex promotes microRNA biogenesis and pre-mRNA splicing [RNA-seq]

2017-12-08 | GSE98035 | GEO

Responses of Arabidopsis immune signaling mutants to Alternaria brassicicola infection

Project description:A major part of plant immune response is mediated by signaling pathways controlled by three hormnes, jasmonate, ethylene, and salicylate. The involvement of each of these hormone signaling pathways in Arabidopsis thaliana was investigated in response to infection of a necrotrophic fungal pathogen, A. brassicicola. Arabideopsis mutants deficient in these hormone signaling pathways were compared to wild type.

2013-09-03 | GSE50526 | GEO

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