Evidence for involvement of Dicer‐like, Argonaute and histone deacetylase proteins in gene silencing in <i>Phytophthora infestans</i>

Vetukuri, Ramesh R.; Avrova, Anna O.; Grenville‐Briggs, Laura J.; West, Pieter van; Söderbom, Fredrik; Savenkov, Eugene I.; Whisson, Stephen C.; Dixelius, Christina

doi:10.1111/j.1364-3703.2011.00710.x

Cited by 60 publications

(90 citation statements)

References 70 publications

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“…The sorghum SbACTIN (Sb01g010030) and 18S rRNA genes were used for normalization of expression levels (Yang et al 2004;Shen et al 2010). All calculations and statistical analyses were performed as described in the ABI PRISM 7700 Sequence Detection System User Bulletin #2 (Applied Biosystems, USA) slightly modiWed by Vetukuri et al (2011).…”

Section: Quantitative Real-time Pcr (Qrt-pcr)mentioning

confidence: 99%

Two loci in sorghum with NB-LRR encoding genes confer resistance to Colletotrichum sublineolum

et al. 2011

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The aim of this work was to identify plant resistance genes to the sorghum anthracnose fungus Colletotrichum sublineolum. cDNA-AFLP transcript profiling on two contrasting sorghum genotypes inoculated with C. sublineolum generated about 3,000 informative fragments. In a final set of 126 sequenced genes, 15 were identified as biotic stress related. Seven of the plant-derived genes were selected for functional analysis using a Brome mosaic virus-based virus-induced gene silencing (VIGS) system followed by fungal inoculation and quantitative real-time PCR analysis. The candidate set comprised genes encoding resistance proteins (Cs1A, Cs2A), a lipid transfer protein (SbLTP1), a zinc finger-like transcription factor (SbZnTF1), a rice defensin-like homolog (SbDEFL1), a cell death related protein (SbCDL1), and an unknown gene harboring a casein kinase 2-like domain (SbCK2). Our results demonstrate that down-regulation of Cs1A, Cs2A, SbLTP1, SbZnF1 and SbCD1 via VIGS, significantly compromised the resistance response while milder effects were observed with SbDEFL1 and SbCK2. Expanded genome analysis revealed that Cs1A and Cs2A genes are located in two different loci on chromosome 9 closely linked with duplicated genes Cs1B and Cs2B, respectively. The nucleotide binding-leucine rich repeat (NB-LRR) encoding Cs gene sequence information is presently employed in regional breeding programs.

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Section: Quantitative Real-time Pcr (Qrt-pcr)mentioning

confidence: 99%

Two loci in sorghum with NB-LRR encoding genes confer resistance to Colletotrichum sublineolum

et al. 2011

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“…RNA silencing pathways in these unicellular eukaryotes have revealed some striking differences to several model organisms, such as atypical DCL proteins and unusual biogenesis of miRNAs [25], [26]. To advance the understanding of gene silencing processes operating in P. infestans , we have previously shown that P. infestans possesses the components of canonical gene silencing pathways similar to those of other eukaryotes [27]. However, genes encoding silencing-related proteins such as cytosine methyltransferases, RNA polymerase IV, Drosha and ERI1, present in other organisms, were not identified from its genome sequence.…”

Section: Introductionmentioning

confidence: 99%

Evidence for Small RNAs Homologous to Effector-Encoding Genes and Transposable Elements in the Oomycete Phytophthora infestans

et al. 2012

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Phytophthora infestans is the oomycete pathogen responsible for the devastating late blight disease on potato and tomato. There is presently an intense research focus on the role(s) of effectors in promoting late blight disease development. However, little is known about how they are regulated, or how diversity in their expression may be generated among different isolates. Here we present data from investigation of RNA silencing processes, characterized by non-coding small RNA molecules (sRNA) of 19–40 nt. From deep sequencing of sRNAs we have identified sRNAs matching numerous RxLR and Crinkler (CRN) effector protein genes in two isolates differing in pathogenicity. Effector gene-derived sRNAs were present in both isolates, but exhibited marked differences in abundance, especially for CRN effectors. Small RNAs in P. infestans grouped into three clear size classes of 21, 25/26 and 32 nt. Small RNAs from all size classes mapped to RxLR effector genes, but notably 21 nt sRNAs were the predominant size class mapping to CRN effector genes. Some effector genes, such as PiAvr3a, to which sRNAs were found, also exhibited differences in transcript accumulation between the two isolates. The P. infestans genome is rich in transposable elements, and the majority of sRNAs of all size classes mapped to these sequences, predominantly to long terminal repeat (LTR) retrotransposons. RNA silencing of Dicer and Argonaute genes provided evidence that generation of 21 nt sRNAs is Dicer-dependent, while accumulation of longer sRNAs was impacted by silencing of Argonaute genes. Additionally, we identified six microRNA (miRNA) candidates from our sequencing data, their precursor sequences from the genome sequence, and target mRNAs. These miRNA candidates have features characteristic of both plant and metazoan miRNAs.

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“…Previously, knowledge of epigenetic mechanisms in oomycetes was not available, except a few indirect evidences suggesting that histone acetylation may be involved in gene expression [8, 9, 74]. To our knowledge, this is the first study to identify and analyze the evolution and the express pattern of HATs and HDACs in oomycetes.…”

Section: Resultsmentioning

confidence: 97%

Diversity, evolution and expression profiles of histone acetyltransferases and deacetylases in oomycetes

et al. 2016

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BackgroundOomycetes are a group of fungus-like eukaryotes with diverse microorganisms living in marine, freshwater and terrestrial environments. Many of them are important pathogens of plants and animals, causing severe economic losses. Based on previous study, gene expression in eukaryotic cells is regulated by epigenetic mechanisms such as DNA methylation and histone modification. However, little is known about epigenetic mechanisms of oomycetes.ResultsIn this study, we investigated the candidate genes in regulating histone acetylation in oomycetes genomes through bioinformatics approaches and identified a group of diverse histone acetyltransferases (HATs) and histone deacetylases (HDACs), along with three putative novel HATs. Phylogenetic analyses suggested that most of these oomycetes HATs and HDACs derived from distinct evolutionary ancestors. Phylogenetic based analysis revealed the complex and distinct patterns of duplications and losses of HATs and HDACs in oomycetes. Moreover, gene expression analysis unveiled the specific expression patterns of the 33 HATs and 11 HDACs of Phytophthora infestans during the stages of development, infection and stress response.ConclusionsIn this study, we reveal the structure, diversity and the phylogeny of HATs and HDACs of oomycetes. By analyzing the expression data, we provide an overview of the specific biological stages of these genes involved. Our datasets provide useful inputs to help explore the epigenetic mechanisms and the relationship between genomes and phenotypes of oomycetes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3285-y) contains supplementary material, which is available to authorized users.

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Evidence for involvement of Dicer‐like, Argonaute and histone deacetylase proteins in gene silencing in Phytophthora infestans

Cited by 60 publications

References 70 publications

Two loci in sorghum with NB-LRR encoding genes confer resistance to Colletotrichum sublineolum

Two loci in sorghum with NB-LRR encoding genes confer resistance to Colletotrichum sublineolum

Evidence for Small RNAs Homologous to Effector-Encoding Genes and Transposable Elements in the Oomycete Phytophthora infestans

Diversity, evolution and expression profiles of histone acetyltransferases and deacetylases in oomycetes

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