Genome-wide identification of Dicer-like, Argonaute and RNA-dependent RNA polymerase gene families and their expression analyses in response to viral infection and abiotic stresses in Solanum lycopersicum

Miao, Bai; Gao, Yang; Chen, Wenting; Mao, Zhenchuan; Kang, Houxiang; Chen, Guohua; Yang, Youyou; Xie, Bingyan

doi:10.1016/j.gene.2012.02.009

Cited by 149 publications

(136 citation statements)

References 52 publications

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“…In the conserved DDH residues, H was replaced by aspartate in MrAGO1 and MrAGO2. Furthermore, all H798 sites in the MrAGO1/MrAGO2 group of fungi were replaced by proline, consistent with the previous studies that showed a variety of H798 residues in plants (5,(27)(28)(29) (Fig. S2).…”

supporting

confidence: 91%

Dicer and Argonaute Genes Involved in RNA Interference in the Entomopathogenic Fungus Metarhizium robertsii

Meng

Wang

et al. 2017

Appl Environ Microbiol

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RNA interference (RNAi) is a gene-silencing mechanism that plays an important role in gene regulation in a number of eukaryotic organisms. Two core components, Dicer and Argonaute, are central in the RNAi machinery. However, the physiological roles of Dicer and Argonaute in the entomopathogenic fungus Metarhizium robertsii have remained unclear. Here, the roles of genes encoding Dicer (M. robertsii dcl1 [Mrdcl1] and Mrdcl2) and Argonaute (Mrago1 and Mrago2) proteins in M. robertsii were investigated. The results showed that the Dicer-like protein MrDCL2 and Argonaute protein MrAGO1 are the major components of the RNAi process occurring in M. robertsii. The Dicer and Argonaute genes were not involved in the regulation of growth and diverse abiotic stress response in M. robertsii under the tested conditions. Moreover, our results showed that the Dicer and Argonaute gene mutants demonstrated reduced abilities to produce conidia, compared to the wild type (WT) and the gene-rescued mutant. In particular, the conidial yields in the Δdcl2 and Δago1 mutants were reduced by 55.8% and 59.3%, respectively, compared with those from the control strains. Subsequently, for the WT and Δdcl2 mutant strains, digital gene expression (DGE) profiling analysis of the stage of mycelium growth and conidiogenesis revealed that modest changes occur in development or metabolism processes, which may explain the reduction in conidiation in the Δdcl2 mutant. In addition, we further applied high-throughput sequencing technology to identify small RNAs (sRNAs) that are differentially expressed in the WT and the Δdcl2 mutant and found that 4 known microRNA-like small RNAs (milRNAs) and 8 novel milRNAs were Mrdcl2 dependent in M. robertsii. IMPORTANCEThe identification and characterization of components in RNAi have contributed significantly to our understanding of the mechanism and functions of RNAi in eukaryotes. Here, we found that Dicer and Argonaute genes play an important role in regulating conidiation in M. robertsii. Our study also demonstrates that diverse small RNA pathways exist in M. robertsii. The study provides a theoretical platform for exploration of the functions of Dicer and Argonaute genes involved in RNAi in fungi.KEYWORDS Argonaute, Dicer, Metarhizium robertsii, RNA interference R NA interference (RNAi) is a gene silencing mechanism that plays an important role in regulating gene expression from fungi, plants, and animals, and it has become a valuable molecular tool for analyzing the functions of many genes (1, 2). The 20-to 30-nucleotide (nt) small RNA (sRNA) molecules have emerged as powerful regulators of gene expression and genome stability via conserved eukaryotic RNAi-related pathways

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supporting

confidence: 91%

Dicer and Argonaute Genes Involved in RNA Interference in the Entomopathogenic Fungus Metarhizium robertsii

Meng

Wang

et al. 2017

Appl Environ Microbiol

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“…A search in the Sol Genomics Network database allowed us to obtain the tomato orthologous sequences of AtDCL1, AtDCL2, AtDCL4, AtRDR1, AtRDR2 and AtRDR6 which perfectly matched to the genes that have been very recently described (Bai et al, 2012). The expression of DCL endonucleases has been reported to be activated as a result of virus or viroid infections .…”

Section: Discussionmentioning

confidence: 99%

Salicylic acid and gentisic acid induce RNA silencing-related genes and plant resistance to RNA pathogens

Campos

Granell

Tárraga

et al. 2014

Plant Physiology and Biochemistry

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ElsevierCampos Beneyto, L.; Granell Albert, P.; Tarraga Herrero, S.; López Gresa, MP.; Conejero Tomás, V.; Belles Albert, JM.; Rodrigo Bravo, I.... (2014) AbstractWe have observed that treatments with salicylic acid (SA) or gentisic acid (GA) induced resistance to RNA pathogens such as ToMV and CEVd in tomato and Gynura auriantiaca, respectively. Accumulation of SA and GA has been found to occur in plants infected by these pathogens, thus pointing out a possible defence role of both molecules. To study the molecular basis of the observed induced resistance to RNA pathogens the induction of silencing-related genes by SA and GA was considered. For that purpose, we searched for tomato genes which were orthologous to those described in Arabidopsis thaliana, such as AtDCL1, AtDCL2, AtDCL4, AtRDR1, AtRDR2 and AtRDR6, and we tracked their induction in tomato along virus and viroid infections. We observed that CEVd significantly induced all these genes in tomato, with the exception of ToRDR6, being the induction of ToDCL4 the most outstanding. Regarding the ToMV asymptomatic infection, with the exception of ToRDR2, we observed a significant induction of all the indicated silencing-related genes, being ToDCL2 the most induced gene. Subsequently, we analyzed their transcriptional activation by SA and at the time when ToMV was inoculated on plants. ToDCL2, ToRDR1 and ToRDR2 were significantly induced by both SA and GA, whereas ToDCL1 was only induced by SA. Such an induction resulted more effective by SA treatment, which is in agreement with the stronger SA-induced resistance observed. Our results suggest that the observed delay in the RNA pathogen accumulation could be due to the pre-induction of RNA silencing-related genes by SA or GA. Highlights-Treatments with salicylic acid or gentisic acid induce resistance to RNA pathogens -Induction of tomato silencing-related genes by RNA pathogen infections is studied -Induction of RNA silencing by SA or GA treatments is analysed in tomato plants -New connexions between RNA silencing and the SA or GA response are proposed

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“…For RDRs, RDR2 converts ssRNAs generated from repetitive DNAs to precursor dsRNAs of ra-siRNAs (Xie et al, 2004), while RDR6 produces the ta-siRNA precursors (Yoshikawa et al, 2005). Gene families encoding these three key components of RNA silencing machinery have been identified only in several plant species such as A. thaliana, Oryza sativa (Kapoor et al, 2008), Zea mays (Qian et al, 2011), Solanum lycopersicum (Bai et al, 2012), Nicotiana benthamiana (Nakasugi et al, 2013), Setaria italica (Yadav et al, 2015), and Vitis vinifera (Zhao et al, 2015). Identification of these families in more plant species will enhance our understanding of RNA silencing.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification of Dicer-Like, Argonaute, and RNA-Dependent RNA Polymerase Gene Families in Brassica Species and Functional Analyses of Their Arabidopsis Homologs in Resistance to Sclerotinia sclerotiorum

Cao

Wen

et al. 2016

Front. Plant Sci.

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RNA silencing is an important mechanism to regulate gene expression and antiviral defense in plants. Nevertheless, RNA silencing machinery in the important oil crop Brassica napus and function in resistance to the devastating fungal pathogen Sclerotinia sclerotiorum are not well-understood. In this study, gene families of RNA silencing machinery in B. napus were identified and their role in resistance to S. sclerotiorum was revealed. Genome of the allopolyploid species B. napus possessed 8 Dicer-like (DCL), 27 Argonaute (AGO), and 16 RNA-dependent RNA polymerase (RDR) genes, which included almost all copies from its progenitor species B. rapa and B. oleracea and three extra copies of RDR5 genes, indicating that the RDR5 group in B. napus appears to have undergone further expansion through duplication during evolution. Moreover, compared with Arabidopsis, some AGO and RDR genes such as AGO1, AGO4, AGO9, and RDR5 had significantly expanded in these Brassica species. Twenty-one out of 51 DCL, AGO, and RDR genes were predicted to contain calmodulin-binding transcription activators (CAMTA)-binding site (CGCG box). S. sclerotiorum inoculation strongly induced the expression of BnCAMTA3 genes while significantly suppressed that of some CGCG-containing RNA silencing component genes, suggesting that RNA silencing machinery might be targeted by CAMTA3. Furthermore, Arabidopsis mutant analyses demonstrated that dcl4-2, ago9-1, rdr1-1, rdr6-11, and rdr6-15 mutants were more susceptible to S. sclerotiorum, while dcl1-9 was more resistant. Our results reveal the importance of RNA silencing in plant resistance to S. sclerotiorum and imply a new mechanism of CAMTA function as well as RNA silencing regulation.

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Genome-wide identification of Dicer-like, Argonaute and RNA-dependent RNA polymerase gene families and their expression analyses in response to viral infection and abiotic stresses in Solanum lycopersicum

Cited by 149 publications

References 52 publications

Dicer and Argonaute Genes Involved in RNA Interference in the Entomopathogenic Fungus Metarhizium robertsii

Dicer and Argonaute Genes Involved in RNA Interference in the Entomopathogenic Fungus Metarhizium robertsii

Salicylic acid and gentisic acid induce RNA silencing-related genes and plant resistance to RNA pathogens

Genome-Wide Identification of Dicer-Like, Argonaute, and RNA-Dependent RNA Polymerase Gene Families in Brassica Species and Functional Analyses of Their Arabidopsis Homologs in Resistance to Sclerotinia sclerotiorum

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