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Expression data from shoots of rice seedlings after inoculation by Sinorhizobium meliloti 1021

ABSTRACT: Comparative transcriptome was profiled of rice seedling shoots in responding to live S. meliloti1021(LS) and dead S. meliloti1021 (DS) inoculation. The shoots with LS and DS were collected at 1, 2, 5 and 8 DAI respectively for microarry analysis. A total of 2413 differentially expressed genes (DEGs) were detected (q ≤ 0.05 and 1.5-fold change used as a cutoff), showing significantly differences between LS and DS. Enriched gene ontology terms and pathways analysis indicated that functions of these DEGs were observably involved in biotic stress, cellular regulation, plant hormone transduction, cell cycle and cell division. Among the classes of transcription factors, some key regulatory gene families such as WRKYs, NAC, bZIP, MYB and ZIM were involved in responding to defense. Others such as AUX, E2F/DP, BES1 and GASR were growth related. We used microarrays to profile the global view of gene expression underlying S. meliloti 1021 inoculation and identified regulated plant genes and pathway that likely key events in endophytic colonization and molecular promotion mechanism.

ORGANISM(S): Oryza sativa Oryza sativa Japonica Group

PROVIDER: GSE53535 | GEO | 2016/09/01

SECONDARY ACCESSION(S): PRJNA232307

REPOSITORIES: GEO

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Expression data from shoots of rice seedlings after inoculation by Sinorhizobium meliloti 1021

Project description:Comparative transcriptome was profiled of rice seedling shoots in responding to live S. meliloti1021(LS) and dead S. meliloti1021 (DS) inoculation. The shoots with LS and DS were collected at 1, 2, 5 and 8 DAI respectively for microarry analysis. A total of 2413 differentially expressed genes (DEGs) were detected (q â¤ 0.05 and 1.5-fold change used as a cutoff), showing significantly differences between LS and DS. Enriched gene ontology terms and pathways analysis indicated that functions of these DEGs were observably involved in biotic stress, cellular regulation, plant hormone transduction, cell cycle and cell division. Among the classes of transcription factors, some key regulatory gene families such as WRKYs, NAC, bZIP, MYB and ZIM were involved in responding to defense. Others such as AUX, E2F/DP, BES1 and GASR were growth related. We used microarrays to profile the global view of gene expression underlying S. meliloti 1021 inoculation and identified regulated plant genes and pathway that likely key events in endophytic colonization and molecular promotion mechanism. Surface sterilized seeds were germinated in petri plates with distilled water in the dark for 3 days at 28Â°C. And then transferred aseptically into sterilized glass bottle, which containing 175 cm3 of sterile vermiculite and 100 mL of 1/4 Kimura B solution. After 2 days transferred to sterilized glass bottle, the seedling were inoculation with live S. meliloti1021 (LS) as treatment and dead S. meliloti1021 (DS) as control. Shoots from inoculated by live S. meliloti1021 (LS) and dead bacteria as control (DS) were collected at 1, 2, 5 and 8 DAI respectively. Every RNA sample was derived from 5 independent seedlings. In sum, four time points were selected and three biological replicates were performed, totally 24 rice genome arrays were used.

2016-09-01 | E-GEOD-53535 | biostudies-arrayexpress

Transcriptome analysis provides insights into the mechanism of salt tolerance in rice colonized by arbuscular mycorrhizal fungi

Project description:Although previous studies have addressed the possible benefits of arbuscular mycorrhizal (AM) symbiosis for rice plants under salinity, the underlying molecular mechanisms are still unclear. Here, we showed that rice colonized with AM fungi had better growth performance and higher K+/Na+ ratio under salt stress. Differentially expressed genes (DEGs) responding to AM symbiosis especially under salt stress were obtained from RNA sequencing. AM-regulated DEGs in cell wall modification and peroxidases categories were mainly upregulated in shoots, suggesting AM symbiosis might assist in relaxing the cell wall and scavenging reactive oxygen species (ROS). AM symbiosis indeed improved ROS scavenging capacity in rice shoots under salt stress. In addition, genes involved in Calvin cycle and terpenoid synthesis were enhanced by AM symbiosis in shoots and roots under salt stress, respectively. AM-upregulated cation transporters and aquaporin in both shoots and roots were highlighted. Strikingly, “protein tyrosine kinase activity” subcategory was the most significantly over-represented GO term among all AM-upregulated and downregulated DEGs in both shoots and roots, highlighting the importance of kinase on AM-enhanced salinity tolerance. Overall, our results from the transcriptomic analyses indicate that AM symbiosis uses a multipronged approach to help plants achieve salt stress tolerance.

2022-04-18 | GSE200863 | GEO

RAV1 and BES1 mutually inhibit each other’s expression and oppositely co-regulate the genes for growth and defense in Arabidopsis

Project description:RAV1 (RELATED TO ABI3/VP1) is a plant-specific B3 domain and AP2 domain-containing transcription factor and acts as a negative regulator of growth in many plant species. Expression of the RAV1 was down-regulated by BR, and through the large-scale transcriptome analyses its expression was previously shown to be targeted by BES1 and BZR1 that are critical transcription factors for BR-signaling process. Using the RAV1-overexpressing transgenic plants, here we showed that RAV1 overexpression reduced BR signaling capacity, resulting in the up-regulation of BR biosynthetic genes and down regulation of BES1 expression. Furthermore, we demonstrated that BES1, not BZR1, directly bound to the RAV1 promoter and repressed RAV1 expression, and vice versa, RAV1 also bound to the BES1 promoter and repressed BES1 expression. This mutual inhibition was specific to between RAV1 and BES1, because RAV1 showed binding activity to BZR1 promoter but did not repressed BZR1 expression. To validate this mutual inhibition of RAV1 and BES1, we generated transgenic bes1-D plants overexpressing RAV1 and observed that constitutively activated BR-signaling phenotypes in bes1-D were attenuated due to the repression of endogenous BES1 expression. To investigate transcriptomic expressional changes that are regulated by RAV1 and BES1, we performed RNA-sequencing analysis from RAV1-overexpressing transgenic plants and bes1-D mutant plant. We identified differentially expressed genes (DEGs) by RAV1 and BES1, respectively, as well as the genes that are oppositely co-regulated by RAV1 and BES1. And we found that RAV1 and BES1 regulate different transcriptome but co-regulate a specific set of genes that are responsible for the balance between growth and defense. Taken together, these results suggested that mutual inhibitory transcriptional activities of the RAV1 and BES1 provide fine regulatory mechanisms for plants growth and development mediated by BR signaling.

2023-05-01 | GSE202679 | GEO

Analysis of BES1-PIF4 interdependency in gene expression

Project description:BES1 transcription factor is a master regulator of brassinosteroid signalling. Part of BES1 activity as a transcription factor is brought about upon dimerization with light-responsive PIF4 transcription factor. To analyse BES1-dependent transcriptional cascade, and to which extent BES1 requires PIF4/PIF5 for target gene regulation, we performed microarray analysis of the following phenotypes: Col-0, bes1-D, pif4pif5 and bes1-D;pif4pif5 in dark grown seedlings. Col-0, bes1-D, pif4pif5 and bes1-D;pif4pif5 5-days seedlings grown in the dark were used for RNA extraction. 3 independent biological samples were collected for each genoptye.

2016-08-05 | E-GEOD-85211 | biostudies-arrayexpress

Genome-wide mapping of BES1 binding sites in Arabidopsis thaliana

Project description:Brassinosteroids (BRs) are important regulators for plant growth and development. BRs signal to control the activities of the BES1 and BZR1 family transcription factors. In order to further understand the mechanism by which BES1/BZR1 regulates downstream genes, we performed chromatin immunoprecipitation coupled with tiling arrays (ChIP-chip) to identify BES1 binding sites in the genome. By combining ChIP-chip data with gene expression microarray data, we are able to discover genes that are directly regulated by BES1 (i.e. BES1 target genes). Chromatin from bes1-D Arabidopsis seedlings are immunoprecipitated by anti-BES1 antibody with anti-GFP antibody as control.

2011-01-02 | E-GEOD-24684 | biostudies-arrayexpress

Identification of drought stress-responsive transcription factor in ramie (Boehmeria nivea LM-oM-<M-^NGaud)

Project description:Drought is a main environment stress which severely inhibits the stem growth of ramie and lead to a decrease of the fiber yield. The mechanisms of ramie responding to drought stress are poorly understood. Using Illumina sequencing, approximately 4.8 million (M) 21-nt cDNA tags were sequenced in the cDNA library derived from the drought-stressed ramie (DS), and about 4.7 M were sequenced in the cDNA library constructed from the control ramie under well water condition (CO). The tags generated from two libraries were aligned with ramie transcriptome to annotate their function and a total of 23,912 and 22,826 ramie genes were matched by these tags of DS and CO library, respectively. Comparison of gene expression level between CO and DS ramie based on the differences of tag frequencies appearing in two libraries revealed that 1101 and 505 genes were respectively up- and down- regulated under drought stress. Pathway enrichment analysis identified a set of significantly enriched pathways of DEGs. A series of candidate genes and pathways that may contribute to drought tolerance in ramie will be helpful for further improving ramie drought tolerance ability. 3' tag-based DGE libraries were generated to exam the differentially expressed gene between drought-stressed and well-watered ramie

2013-04-23 | E-GEOD-46253 | biostudies-arrayexpress

Analysis of BES1-PIF4 interdependency in gene expression

2016-08-05 | GSE85211 | GEO

Genome-wide mapping of BES1 binding sites in Arabidopsis thaliana

2011-01-02 | GSE24684 | GEO

Transcriptome analysis of neural progenitor cells derived from Lowe Syndrome induced pluripotent stem cells

Project description:Lowe Syndrome (LS) is caused by loss-of-function mutations in the X-linked gene OCRL that codes for a 901 amino acid protein, inositol polyphosphate 5-phosphatase, which plays a key role in endosome recycling, clathrin coated pit formation and actin polymerization. It is characterized by congenital cataracts, intellectual and developmental disability, and renal proximal tubular dysfunction. Patients are also at high risk for developing glaucoma and seizures. We recently developed induced pluripotent stem cells (iPSCs) from three patients with LS who have hypomorphic variants affected the 3’ end of the gene, and their neurotypical brothers to serve as controls. In this study, we used RNA sequencing (RNA-seq) to obtain a transcriptome profile in neural progenitor cells (NPCs). Thirty-six differentially expressed genes (DEGs) were found in patient/control comparisons that were shared across all three sets of sibling pairs. Interestingly, two-thirds of these genes have previously been found to be involved in neuropsychiatric and neurodevelopmental disorders. Furthermore, 14 of the DEGs are strong candidate genes for a variety of eye disorders, including glaucoma development. The most notable example is EFEMP1, which was significantly increased in LS NPCs. These DEGs found in NPCs could reflect similar alterations occurring in eye tissues or their progenitor cells from LS. Overall, the RNA-seq findings present several molecular pathways that could explain the underlying basis for the neurodevelopmental and eye problems seen in boys with LS.

2020-05-21 | GSE129310 | GEO

BAF1 and Brassinosteroid related mutant in Arabidopsis

Project description:Brassinosteroids (BRs) regulate plant growth, development and stress responses by activating the core transcription factor BRI1-EMS-SUPPRESSOR1 (BES1). The E3 Ubiquitin ligase(s) that modify BES1 for autophagy-mediated degradation remain to be fully defined. In this study, we identified an F-box family E3 ubiquitin ligase termed BES1-ASSOCIATED F-BOX1 (BAF1). BAF1 interacts with and ubiquitinates BES1. Accordingly, BES1 stability and protein levels were reduced in BAF1 overexpression plants but increased in a baf1 loss-of-function mutant and in BAF1-DF (BAF1 with F-box deleted, dominant-negative form) overexpression lines. Selective autophagy of BES1, but not bulk autophagy, was significantly compromised in the baf1 mutant under sucrose starvation. BES1 degradation mediated by BAF1 could be blocked through autophagy but not proteasome inhibitors, suggesting that BAF1 mediates BES1 degradation largely through autophagy. baf1 and BAF1-DF overexpression plants had increased BR-regulated growth but were sensitive to long-term sucrose starvation, while BAF1 overexpression plants had decreased BR-regulated growth but were highly tolerant of sucrose starvation. Our results not only established BAF1 as a novel E3 ubiquitin ligase that targets BES1 for degradation through selective autophagy pathway, but also revealed a mechanism for plants to reduce growth during sucrose starvation by targeting this central growth regulator.

2022-08-01 | GSE155219 | GEO

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