Nicotiana Benthamiana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA525845 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11939662_1.fastq.gz | Fastqsanger.gz | |||
| SRR11939662_2.fastq.gz | Fastqsanger.gz | |||
| SRR11939663_1.fastq.gz | Fastqsanger.gz | |||
| SRR11939663_2.fastq.gz | Fastqsanger.gz | |||
| SRR11939664_1.fastq.gz | Fastqsanger.gz |
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Project description:RNA interference (RNAi) is a conserved, RNA-mediated, regulatory mechanism in eukaryotes. In plants, it plays an important role in growth, development and resistance against viral infections. As a counter-defence, plant viruses, e.g. geminiviruses, encode RNAi suppressors, such as AC2, AC4 and AV2. To obtain Nicotiana tabacum virus resistant plants against Tomato leaf curl New Delhi virus (ToLCNDV), we employ the biogenesis pathway of a class of endogenous siRNAs, the trans-acting siRNAs (ta-siRNAs), by engineering artificial ta-siRNAs (ata-siRNAs) targeting the AC2 (TRiV-AC2) and AC4 (TRiV-AC4) RNAi suppressors using miRNA390 dual target sites. The mode of action of ta-siRNAs comprises of the cleavage of the target (similar to the miRNA targeting). Using degradome approaches, the abundance of the resulting 3' fragment of the cleaved transcript can be quantified and the precise localization of the cleavage on the target mRNA can be identified. We sequenced degradome libraries of Nicotiana tabacum plants infected with ToLCNDV which were treated with the ata-siRNA-AC2 construct; mock-treated plants were used as controls. Following quality checks, the abundance distributions of the degradation fragments were normalized. The transcripts with different cleavage patterns was the AC2, supporting the conclusion that an efficient cleavage of the target occurred, without significant off-target effects.
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Project description:RNA interference (RNAi) is a conserved, RNA-mediated, regulatory mechanism in eukaryotes. In plants, it plays an important role in growth, development and resistance against viral infections. As a counter-defence, plant viruses, e.g. geminiviruses, encode RNAi suppressors, such as AC2, AC4 and AV2. To obtain Nicotiana tabacum virus resistant plants against Tomato leaf curl New Delhi virus (ToLCNDV), we employ the biogenesis pathway of a class of endogenous siRNAs, the trans-acting siRNAs (ta-siRNAs), by engineering artificial ta-siRNAs (ata-siRNAs) targeting the AC2 (TRiV-AC2) and AC4 (TRiV-AC4) RNAi suppressors using miRNA390 dual target sites. The mode of action of ta-siRNAs comprises of the cleavage of the target (similar to the miRNA targeting). Using degradome approaches, the abundance of the resulting 3' fragment of the cleaved transcript can be quantified and the precise localization of the cleavage on the target mRNA can be identified. We sequenced degradome libraries of Nicotiana tabacum plants infected with ToLCNDV which were treated with the ata-siRNA-AC2 construct; mock-treated plants were used as controls. Following quality checks, the abundance distributions of the degradation fragments were normalized. The transcripts with different cleavage patterns was the AC2, supporting the conclusion that an efficient cleavage of the target occurred, without significant off-target effects.
2019-11-08 | GSE85816 | GEO
Project description:Co-infection of none-coding satellite RNAs (sat-RNAs) usually inhibits replication and attenuates disease symptoms of helper viruses. Here we find that the sat-RNA of Beet black scorch virus (BBSV) enhances both the accumulation and the systemic infection of its helper virus in the Nicotiana benthamiana (N. benthamiana). Besides, the infection of BBSV is higher efficient in low temperature (18ºC) than room temperature (25ºC), suggesting that BBSV is temperature sensitive. To explore the effect of temperature and sat-RNA on the silencing induced by BBSV, we cloned and sequenced the total small RNAs produced during infection of BBSV alone or with its sat-RNA under different temperature. Our results shows that the size profile of the siRNAs derived from either BBSV or coinfection with sat-RNA are 22 nucleotide (nt), followed by 21-nt reads and other length reads. Notably, more than 80% of the total small RNAs sequenced from plants infected with BBSV alone were BBSV-siRNAs, whereas the abundance of sat-RNA-derived siRNAs were higher than BBSV-siRNAs in the co-infected plants, indicating sat-RNA involved in gene silencing as a surrogacy of BBSV. Interestingly, the 5′ termini of siRNAs derived from BBSV and sat-RNA were dominated by Uridines (U) and Adenines (A), respectively. Consistently, the infection of BBSV alone or with sat-RNA induces high accumulation of Argonaute 1 (AGO1) and AGO2, respectively. Our work reveals the profiles of siRNAs of BBSV and sat-RNA and provides a new clue to investigate the complicated interaction between the helper virus and sat-RNA.
2017-02-09 | GSE80694 | GEO
Project description:To systematically investigate viral sRNA production and sRNA-target interaction, we sequenced sRNAs from Tobacco Rattle Virus (TRV)-infected Nicotiana benthamiana at an early (1 week post infection) and late time point (3 weeks post infection). The N. benthamiana 16c plants were infected with TGS-inducing viruses (TRV-35S and TRV-35-2M) and PTGS-inducing viruses (TRV-GFP and TRV-GFP-2M), respectively. TRV-35S is a recombinant TRV containing a 120 nt segment of the 35S promoter. Its derivative, TRV-35S-2M, carrying single nucleotide substitutions (SNS) at every 10 nt within the 120 nt 35S target segment. Same strategy was used to create recombinant TRV-GFP and TRV-GFP-2M targeting GFP coding sequence. According to SNS content, sRNAs from TRV-35S-2M/TRV-GFP-2M infected plants can be separated to yield primary (containing SNSs) and secondary sRNAs (lacking SNSs). Wild Type TRV was used along as viral infection control. Libraries were indexed during PCR amplification (16 cycles) according to the Illumina protocol. See individual sample information for specific index primers used.
2021-01-06 | E-MTAB-8342 | biostudies-arrayexpress
Project description:In order to find the miRNAs, target genes and signaling pathways related to the dwarf phenotype induced by NlCSP1, 35S-NlCSP1 and 35S-GFP control were infiltrated into Nicotiana benthamiana. We analyzed the differentially expressed miRNAs in the infiltrated leaves (NlCSP1_Z/GFP_Z) and the upper uninfiltrated leaves (NlCSP1_O/GFP_O) of N. benthamiana. A total of 106 and 97 differentially expressed miRNAs were identified in NlCSP1_Z/GFP_Z and NlCSP1_O/GFP_O, respectively. KEGG annotation revealed a large number of differentially expressed miRNAs involved in plant hormone signal transduction, indicating that NlCSP1 changed the hormone signal pathway in N. benthamiana.
2021-09-01 | GSE169282 | GEO
Project description:Nonsense mediated decay (NMD) is a translation termination coupled quality control system. NMD identifies and degrades aberrant mRNAs containing premature termination codons, thereby preventing the accumulation of detrimental truncated proteins. NMD also controls the expression of several normal mRNAs and non-coding transcripts. RNA-seq assays were conducted to identify the NMD regulated genes in Arabidopsis. However, NMD targets have not been studied in other plants. To identify the conserved NMD targets, we wanted to identify the NMD regulated genes in Nicotiana benthamiana model species. Virus induced gene silencing was used to inactivate UPF1 NMD key factor in N. benthamiana, and then comparative RNA-seq experiment was carried out using UPF1-silenced and control–silenced plants. We found that in N. benthamiana significantly more genes are controlled by NMD than in Arabidopsis and that, surprisingly few conserved NMD targets can be recognized. These results suggest that while the mechanism of NMD is highly conserved, the set of NMD controlled genes can be quickly changed in plants.
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Project description:We assessed the off-target effects of M2 expression on the leaf proteome of Nicotiana benthamiana infiltrated with the bacterial gene vector Agrobacterium tumefaciens. A iTRAQ quantitative proteomics procedure was followed to compare the leaf proteomes of plants agroinfiltrated with either an ‘empty’ vector or an M2-encoding vector. Leaves infiltrated with the empty vector had a low soluble protein content compared to non-infiltrated control leaves, associated with increased levels of stress-related proteins but decreased levels of photosynthesis-associated proteins. M2 expression partly compromised these effects of agroinfiltration to restore soluble protein content in leaf tissue, associated with restored levels of photosynthesis-associated proteins and reduced levels of stress-related proteins in the apoplast. These data illustrate the cell-wide influence of Golgi lumen pH homeostasis on the leaf proteome of N. benthamiana responding to microbial challenge.
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Project description:Small RNA expression from Nicotiana benthamiana leaves was profiled with the primary goal of ascertaining microRNA isoform diversity for known, conserved families. A secondary goal was to provide a baseline small RNA expression atlas for this species and tissue.
2014-02-10 | GSE48886 | GEO