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Nai1-1, ER body deficient mutant, vs wild-type Col-0

ABSTRACT: ER bodies are endoplasmic reticulum (ER)-derived organelles that might be involved in defense systems. The NAI1 gene regulates the development of ER bodies because mutation of NAI1 abolishes the formation of ER bodies. The nai1-1 mutant had a single nucleotide change at an intron acceptor site of At2g22770 (NAI1 gene). Because of this mutation, aberrant splicing of NAI1 mRNA occurs in the nai1-1 mutant. NAI1 encodes a transcription factor that has a basic-helix-loop-helix (bHLH) domain. Transient expression of NAI1 induced ER bodies in the nai1-1 mutant. To identify genes that are related to ER bodies, we compared the genome-wide expression profiles of Col-0 and the nai1-1 mutant using DNA microarrays. Twenty-nine genes were found to be expressed at least 2-fold more strongly in the nai1-1 mutant than in Col-0, and 341 genes were found to be expressed at least 2-fold more strongly in Col-0 than in the nai1-1 mutant. The 15 genes that showed the strongest expression in Col-0 compared to the expression in nai1-1 are shown in Table 1. Five of these genes are JAL genes (JAL22, JAL23, JAL31, JAL33 and PBP1/JAL30). The mRNA level of PYK10 was reduced in nai1-1 (4.3 fold larger in Col-0 than in nai1-1). The mRNA levels of GLL genes (GLL23 and GLL25) were also reduced in nai1-1. Keywords: mutant vs wt comparison

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE6446 | GEO | 2007/06/04

SECONDARY ACCESSION(S): PRJNA98641

REPOSITORIES: GEO

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Transcription profiling of Arabidopis nai1-1, ER body deficient mutant, vs wild-type Col-0

Project description:ER bodies are endoplasmic reticulum (ER)-derived organelles that might be involved in defense systems. The NAI1 gene regulates the development of ER bodies because mutation of NAI1 abolishes the formation of ER bodies. The nai1-1 mutant had a single nucleotide change at an intron acceptor site of At2g22770 (NAI1 gene). Because of this mutation, aberrant splicing of NAI1 mRNA occurs in the nai1-1 mutant. NAI1 encodes a transcription factor that has a basic-helix-loop-helix (bHLH) domain. Transient expression of NAI1 induced ER bodies in the nai1-1 mutant. To identify genes that are related to ER bodies, we compared the genome-wide expression profiles of Col-0 and the nai1-1 mutant using DNA microarrays. Twenty-nine genes were found to be expressed at least 2-fold more strongly in the nai1-1 mutant than in Col-0, and 341 genes were found to be expressed at least 2-fold more strongly in Col-0 than in the nai1-1 mutant. The 15 genes that showed the strongest expression in Col-0 compared to the expression in nai1-1 are shown in Table 1. Five of these genes are JAL genes (JAL22, JAL23, JAL31, JAL33 and PBP1/JAL30). The mRNA level of PYK10 was reduced in nai1-1 (4.3 fold larger in Col-0 than in nai1-1). The mRNA levels of GLL genes (GLL23 and GLL25) were also reduced in nai1-1. Experiment Overall Design: Total RNA was purified from the roots of 20-day-old plants (3 plants were pooled for each genotype). Arabidopsis plants were grown under continuous light condition at 22ËC on MS medium paltes. The control plants and the nai1-1 mutant were cultivated in the same plate. This was done to avoid any difference in plant growth conditions between the mutants and the control plants.

2008-06-14 | E-GEOD-6446 | biostudies-arrayexpress

Quantitative Proteomic Analysis of ER Stress Response Reveals both Common and Specific Features in Two Contrasting Ecotypes of Arabidopsis

Project description:Accumulation of unfolded/misfolded proteins in endoplasmic reticulum (ER) elicits a well conserved response called the Unfolded Protein Response (UPR), which triggers the up-regulation of downstream genes involved in protein folding, vesicle trafficking, and ER-Associated Degradation (ERAD). Although the dynamic transcriptomic responses and underlying major transcriptional regulators in ER stress response in plants have been well established, the proteome changes induced by ER stress have not been reported in plants. In the current study, we found that the Arabidopsis Ler ecotype is more sensitive to ER stress than the Col ecotype. Quantitative mass spectrometry analysis with Tandem Mass Tag (TMT) isobaric labeling showed that totally 7439 and 7035 proteins were identified from Col and Ler seedlings, with 88 and 113 differentially regulated (FC>1.3 or <0.7, P<0.05) proteins by ER stress in Col and Ler, respectively. Among them, 40 proteins were commonly up-regulated in Col and Ler, of which 10 were not up-regulated in bzip28 bzip60 double mutant (Col background) plants. Of the 19 specifically up-regulated proteins in Col comparing to that in Ler, components in ERAD, N-glycosylation, vesicle trafficking and molecular chaperones were represented. Quantitative RT-PCR showed that genes encoding 7 out of 19 proteins were not up-regulated (FC>1.3 or <0.7, P<0.05) by ER stress in both ecotypes while genes encoding 12 out of 19 proteins were up-regulated by ER stress with no obvious differences in fold change between Col and Ler. Our results experimentally demonstrated the robust ER stress response at proteome level in plants and revealed differentially regulated proteins that may contribute to differed ER stress sensitivity between Col and Ler ecotypes in Arabidopsis.

2021-09-09 | PXD022630 | Pride

Transformants of wheat GSK3/Shaggy-like kinase TaSK5 vs wild-type Col-0

Project description:A novel cold-inducible GSK3/Shaggy-like kinase cDNA (TaSK5) was isolated from winter wheat by a macroarray-based differential screening approach. Sequence analysis of TaSK5 revealed high similarity to Arabidopsis subgroup I GSK3/Shaggy-like kinases ASK-alpha, ASK-gamma and ASK-epsilon. Transgenic Arabidopsis plants overexpressing TaSK5 cDNA under the control of CaMV 35S promoter showed enhanced tolerance to salt and drought stresses. In contrast, the tolerance of the transgenic plants to freezing stress was not altered. To identify genes which are differentially regulated in the 35S:TaSK5 over-expressing Arabidopsis plants under non-stress conditions, we compared the genome-wide expression profiles of Col-0 and plants over-expressing TaSK5 using DNA microarrays. Sixty seven genes were found to be expressed at least 2-fold more strongly in 35S:TaSK5 plants than in Col-0, and 17 genes were found to be expressed at least 2-fold more strongly in Col-0 than in 35S:TaSK5 plants. Most of the TaSK5 up-regulated genes were also induced by abiotic stresses, including cold, salt and drought. These results support the involvement of TaSK5 in abiotic stress signal transduction. Keywords: transgenic vs wt Col.-0 comparison

2014-11-02 | GSE59556 | GEO

Endoplasmic reticulum-derived bodies enable a single-cell chemical defense in Brassicaceae plants

Project description:Brassicaceae plants have a dual-cell type of chemical defense against herbivory. Here we show a novel single-cell defense involving endoplasmic reticulum (ER)-derived organelles (ER bodies) and the vacuoles. We identify various glucosinolates as endogenous substrates of the ER-body β-glucosidases BGLU23 and BGLU21. Woodlice strongly prefer to eat seedlings of bglu23 bglu21 or a glucosinolate-deficient mutant over wild-type seedlings, confirming that the β-glucosidases have a role in chemical defense: production of toxic compounds upon organellar damage. Deficiency of the Brassicaceae-specific protein NAI2 prevents ER-body formation, which results in a loss of BGLU23 and a loss of resistance to woodlice. Hence, NAI2 that interacts with BGLU23 is essential for sequestering BGLU23 in ER bodies and preventing its degradation. Artificial expression of NAI2 and BGLU23 in non-Brassicaceae plants results in the formation of ER bodies, indicating that acquisition of NAI2 by Brassicaceae plants is a key step in developing their single-cell defense system.

2020-02-04 | MTBLS1383 | MetaboLights

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Project description:Arabidopsis DCP5, a homolog of human RNA-associated protein 55, is a nessary component of eukaryotic processing bodies (P-bodies). knockdown mutant of dcp5-1 showed compromised RNA decapping activity and reduced P-body size. Here we profiled Arabidopsis transcriptome of roots, shoots, and inflorensences in Col-0 and DCP5-1 mutant using strand-specific RNA-sequencing. Our analysis identified a large number of DCP5-regulatd transcripts in Arabidopsis.

2018-09-01 | GSE61812 | GEO

Total RNA sequencing of progenies of Col-0 grafted on msh1; Col-0 grafted on dcl2,3,4,msh1; Col-0 grafted on Col-0 in Arabidopsis [msh1_graft_leaf_RNA-seq]

2020-09-20 | GSE152565 | GEO

Bisulfite (methylome) sequencing of progenies of Col-0 grafted on msh1; Col-0 grafted on dcl2,3,4,msh1; Col-0 grafted on Col-0; msh1 mutant; dcl2,3,4,msh1 quadruple mutant in Arabidopsis [msh1_graft_BS-seq]

Project description:Col-0 floral stem was grafted on the msh1 mutant (Col-0/msh1); on the dcl2,3,4,msh1 quadruple mutant (Col-0/dcl2,3,4,msh1); on Col-0 (Col-0/Col-0). Seeds were collected from the grafted Col-0 scion after grafts were established. Seed coming from the graft then were grown on the peat mix, leaf tissue was collected at the bolting and used for the bisulfite sequencing (methylome). Tissue from the msh1 mutant and dcl2,3,4,msh1 quadruple mutants used as rootstocks was similarly collected at the bolting stage and used for the bisulfite sequencing.

2020-09-20 | GSE152564 | GEO

SPLICING FACTOR FOR PHYTOCHROME SIGNALING promotes photomorphogenesis by regulating alternative splicing in Arabidopsis

Project description:Purpose: The goals of this study are to compare the transcriptome profiling and alternative splicing (AS) profiling between Col-0 wild type and SFPS knockout mutant (sfps-2) through RNA-seq to determine the molecular mechanisms of how splicing factor SFPS regulates photomorphogenesis in Arabidopsis. Results: Using an optimized data analysis workflow, we mapped about 100 million sequence reads per sample to the Arabidopsis genome (TAIR10) and identified 1495 differentially expressed genes between Col-0 and mutant dark samples; 1361 differentially expressed genes between Col-0 and mutant red light treated samples; 4291 differentially expressed genes between Col-0 dark and red light treated samples; and 4479 differentially expressed genes between mutant dark and red light treated samples. Except for gene expression, we also discovered 788 differentially spliced bins between Col-0 and mutant dark samples; 827 differentially spliced bins between Col-0 and mutant red light treated samples; 610 differentially spliced bins between Col-0 dark and red light treated samples; and 405 differentially spliced bins between mutant dark and red light treated samples. Altered splicing of 9 genes was confirmed with qRT-PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Conclusions: Our study represents the first detailed analysis of SFPS mutant transcriptomes, with biologic replicates, generated by RNA-seq technology. Our results show that SFPS regulates photomorphogenesis in Arabidopisis through regulating the splicing activity of light signaling genes, which helps us.

2017-08-10 | GSE85883 | GEO

Transcriptomic analysis of regulatory gene expression profiles by DELLA and LEC1 during embryo development in Arabidopsis thaliana.

Project description:To understand how GA functions in regulating embryo development, a genome-wide transcriptomic analysis was carried out using 9DAF seeds dissected from siliques of dellaq (rga28 gai rgl1 rgl2) and the wild-type (col-0-2) grown in full-spectrum white fluorescent light at 22°C under long day conditions (16 h light/8 h dark). Then we found that GA regulates embryo development via DELLA-LEC1interaction, a subsequent genome-wide transcriptomic analysis was carried out using 9DAF seeds dissected from siliques of lec1-4 and the wild-type (col-0-1) in the same growth condition. Basing on the criteria of 1.5-fold cutoff for the genes with 5% false discovery rate, we first identified the differentially expressed genes in dellaq vs col-0-2, lec1-4 vs Col-0-1 subsets, which are referred to as DELLA and LEC1 regulated genes. These data reveal that DELLAs and LEC1 co-target a set of common genes in late embryogenesis, strongly supporting the role of DELLA-LEC1 in embryo development.

2018-02-15 | GSE108544 | GEO

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