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Transcriptome profiling reveals a genomewide role of G-proteins

ABSTRACT: Knock out mutants of GPA1 (gpa1-5), GCR1 (gcr1-5) as well as their double mutant (gpa1-5 gcr1-5) were used to obtain genomewide transcriptome profile to deduce genomewide effect of both the subunits alone or in combination. Heterotrimeric G-protein signaling pathways have been implicated in a variety of biological processes in plants. While an impressive range of important plant responses are known to be mediated by G-protein signaling pathways, the genes that respond through these pathways are not yet known completely. More importantly, the role of G-proteins in mediating plant metabolic regulation, which is well established in animal systems, has not received adequate attention. The availability of loss-of-function G_alpha (GPA1) and G-protein coupled receptor (GCR1) mutant(s) as well as their double mutant in Arabidopsis provided an opportunity for a genome-wide microarray analysis in the current study for the first time.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE40217 | GEO | 2015/02/25

SECONDARY ACCESSION(S): PRJNA173400

REPOSITORIES: GEO

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Transcriptome profiling reveals a genomewide role of G-proteins

Project description:Knock out mutants of GPA1 (gpa1-5), GCR1 (gcr1-5) as well as their double mutant (gpa1-5 gcr1-5) were used to obtain genomewide transcriptome profile to deduce genomewide effect of both the subunits alone or in combination. Heterotrimeric G-protein signaling pathways have been implicated in a variety of biological processes in plants. While an impressive range of important plant responses are known to be mediated by G-protein signaling pathways, the genes that respond through these pathways are not yet known completely. More importantly, the role of G-proteins in mediating plant metabolic regulation, which is well established in animal systems, has not received adequate attention. The availability of loss-of-function G_alpha (GPA1) and G-protein coupled receptor (GCR1) mutant(s) as well as their double mutant in Arabidopsis provided an opportunity for a genome-wide microarray analysis in the current study for the first time. transcriptome profile of mutants gpa1-5, gcr1-5 and double mutant gpa1-5 gcr1-5 were compared to that of the corresponding wild type, ws2. biological duplicates of each sample wa used and hybridized using single color array

2015-02-25 | E-GEOD-40217 | biostudies-arrayexpress

Genome-wide effect of cholera toxin and nitrate treatment in etiolated rice plants

2010-12-01 | GSE20924 | GEO

Transcriptome analysis of Arabidopsis thaliana G protein subunit mutants in response to abscisic acid (ABA)

Project description:Heterotrimeric G proteins mediate crucial and diverse signaling pathways in eukaryotes. To gain insights into the regulatory modes of the G protein and the co-regulatory modes of the G protein and the stress hormone abscisic acid (ABA), we generated and analyzed gene expression in G protein subunit single and double mutants of the model plant Arabidopsis thaliana. Through a Boolean modeling approach, our analysis reveals novel modes of heterotrimeric G protein action. Keywords: transcriptome analysis; G protein subunit mutants; abscisic acid (ABA) Microarray data were generated from four genotypes (wild type, gpa1-4 mutant, agb1-2 mutant, agb1-2 gpa1-4 double mutant) with or without ABA treatment. Arabidopsis plants were grown in growth chambers with an 8 hr light/16hr dark. Three hundred Arabidopsis leaves excised from 60-70 five-week-old plants were used as the starting material for each guard cell microarray. Ten mature leaves taken from 3-4 plants grown side-by side with the plants for guard cell isolation were used for each leaf sample. Excised leaf and isolated guard cell samples were treated with ABA (50 μM) or EtOH (solvent control) for 3 hrs. For each type of sample (guard cells or leaves), three independent biological replicates were performed, resulting in a total of 48 microarray hybridizations (2 sample types ´ 4 genotypes ´ two treatments ´3 replicates).

2010-12-06 | E-GEOD-19520 | biostudies-arrayexpress

Comparative transcriptome analysis between wild-type and gpa1 mutant in response to ABA

Project description:Mutations in the heterotrimeric G-protein a-subunit of Arabidopsis, GPA1, leads to deficiency in ABA-induced stomatal closure (Wang et al., 2001). To further investigate whether GPA1 is involved in the regulation of gene expression in response to ABA, we examined the induction of known ABA-inducible genes in the gpa1 mutant and compared it to wild-type. We found significant differences in levels of ABA-induced expression between wild-type and gpa1 mutant. In order to systematically investigate GPA1 involvement in ABA signalling leading to gene expression, we are requesting the transcriptome analysis of the gpa1 mutant in response to ABA.In detail, 2 week old wild-type and gpa1 plants grown in the 16/8 hrs light and dark cycle will be treated with either ABA or with a control solution for 3 hours. 10 plants will be used per sample to produce RNA, to give 4 samples, one for each chip: gpa1-1 mutant in the presence (chip1) or absence of ABA (chip2) and wild-type (WS2) in the presence (chip3) or absence of ABA (chip4). Keywords: strain_or_line_design

2007-01-22 | GSE6171 | GEO

Expression data from ozone-treated wild-type and G-protein null mutant Arabidopsis lines

Project description:Ozone pollution decreases plant growth and yield worldwide. Some of the effects are genetically-mediated and are reported to involve G-protein signaling pathways. Effects of ozone on gene expression were examined in wild-type and G-protein null mutants to determine affected genes and to determine differential responses that may help define affected pathways. We used microarrays to examine changes in gene expression in response to ozone exposure and identified distinct classes of up- and down-regulated genes in wild-type and G-protein null mutant genotypes. Columbia wild-type and G-protein null mutant gpa1-4/agb1-2 plants were exposed to 5 or 125 ppb ozone in controlled environment chambers for two days. Leaves were sampled after 3 h and 2 d of exposure to examine early and late gene expression changes.

2011-12-24 | E-GEOD-34667 | biostudies-arrayexpress

Transcription profiling of Arabidopsis wild type and gpa1 mutant in response to ABA

2022-11-21 | E-NASC-45 | biostudies-arrayexpress

Genome-wide effect of cholera toxin and nitrate treatment in etiolated rice plants

Project description:The present study used microarray approach to identify the genomewide response to cholera toxin in the presence of nitrate. Considering that fact that the possibility of the existence of multiple GM-NM-1 genes/proteins in plants has not been conclusively ruled out, analysis of the genomewide impact of RGA1 mutation in rice and GPA1 mutation in Arabidopsis reveal only those genes that are under their direct control. On the other hand, assuming that all those different GM-NM-1 subunits in any given plant are regulated by cholera toxin, analysis of the genomwide response to cholera toxin could capture the entire G-protein responsive transcriptome, beyond what can be revealed by the mutant approach. This could reveal even those genes that respond to other, as yet unidentified GM-NM-1 subunits, as well as reveal some genes that are non-specifically regulated by cholera toxin, independent of any G-proteins. Total RNA was isolated from 10 day old excised rice leaves treated with or without cholera toxin in the presence of nitrate.Total RNA was first converted into cDNA and then into cRNA labeled with Cy3 and Cy5 dyes. These were hybridized on the 44K 60-mer whole genome arrays on glass slides. The slides were washed and scanned on an Agilent scanner (G2565B) at 100 % laser power. Data extraction was carried out with Agilent Feature Exiraction software (version 9.1). The experiment was repeated with a biological-cum-technical replicate where total RNA samples were isolated from a fresh batch of rice plants and the cRNAs were labeled with opposite dyes (dye-swap).

2010-12-01 | E-GEOD-20924 | biostudies-arrayexpress

Transcription profiling of Arabidopsis wild-type and gpa1 mutant in response to ABA

2008-06-14 | E-GEOD-6171 | biostudies-arrayexpress

ChIP-seq for two forms of Gcr1, during exponential phase and diauxic shift

Project description:Gcr1, the most important transcription factor for glycolytic genes in Saccharomyces cerevisiae, was recently revealed to have two isoforms, Gcr1(U) and Gcr1(S), produced from unspliced and spliced transcripts, respectively. We generated strains expressing only Gcr1(U) or Gcr1(S) form using the CRISPR/Cas9 system, and added a TAP tag protein to the Gcr1(U) and Gcr1(S), using HIS3MX6 marker system. We conducted ChIP-seq for both strains during the glycolytic phase or after the diauxic shift.

2020-07-07 | GSE153841 | GEO

The role of the Ras- and cAMP-signaling pathways in stress response and sterol biosynthesis in Cryptococcus neoformans

Project description:The cAMP-pathway plays a central role in regulation of growth, differentiation, and virulence of human pathogenic fungi, including Cryptococcus neoformans. Three major upstream signaling regulators of the adenylyl cyclase (Cac1), Ras, Aca1 (Adenylyl cyclase-associated protein 1) and G-alpha subunit protein (Gpa1), have been identified to control the cAMP-pathway in C. neoformans, but their functional relationship remains elusive. Here we performed genome-wide transcriptome analysis with C. neoformans ras1, gpa1, cac1, aca1, and pka1 pka2 mutants by DNA microarray. The aca1, gpa1, cac1, and pka1 pka2 mutants displayed similar transcriptome patterns to each other whereas the ras1 mutant exhibited distinctive transcriptome patterns compared to WT and the cAMP mutants. Interestingly, a number of environmental stress response genes are differentially modulated in the ras1 and cAMP mutants. In fact, the Ras1-signaling pathway was found to be involved in osmotic and genotoxic stress response, and maintenance of cell wall integrity via the Cdc24-dependent signaling pathway. Through this microarray analysis, we have identified a number of cAMP-dependent genes, including GRE2, HSP12, ENA1, TCO2, PKP2, CAT1, in C. neoformans. Notably, a majority of ergosterol biosynthesis genes were found to be upregulated in the cAMP mutants. Interestingly, the gpa1, cac1, and pka1 mutants, but not the aca1 and pka2 mutants were hypersensitive to amphotericin B, but resistant to fluconazole. In conclusion, we demonstrated in this study that the Ras1- and cAMP-signaling pathways are involved in stress response and sterol biosynthesis of C. neoformans.

2009-09-26 | GSE17338 | GEO

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