Dataset Information

Differential gene expression patterns in the phosphate deficient mutant, pho 1

ABSTRACT: Background: The UK horticultural and agricultural industries routinely apply large amounts of inorganic fertiliser to maintain crop yield and quality, since chemical assays of soil nutrients are unreliable. Excessive fertiliser applications are costly and can lead to unnecessary pollution. A possible solution is to use sensor (GM or non-GM) technologies that exploit the changes in plant gene expression under incipient nutrient deficiency. Aim: The aim of this project is to use mutants with reduced leaf phosphate contents to identify genes upregulated in response to phosphate stress. Preliminary gene expression analysis has identified several phosphate responsive genes to be upregulated in the pho1 mutant. However, further replicates of the experiment are required to confirm these changes. Methods: Arabidopsis mutant pho1 (N8507) and its parent ecotype Columbia 2 (N907) will be grown on MS agar under identical conditions. RNA will be extracted from the rosette leaves of both parent and mutant and the same growth stage. By comparing the expression profiles, we will be able to differentiate between genes that are upregulated in leaves experiencing phosphate stress. Previously, two GeneChips have been used (mutant and parent) to provide preliminary data. A further two biological replicates are now required to confirm these results. Promoters and transcripts of these genes will underpin the development of novel sensor technologies, and knowledge of the gene expression profiles will improve our understanding of the physiology of plant mineral nutrition. Experimenter name = John Hammond Experimenter phone = 01789 470382 Experimenter fax = 01789 470552 Experimenter address = Plant Sciences Division Experimenter address = School of Biosciences Experimenter address = University of Nottingham Experimenter address = Sutton Bonington Campus Experimenter address = Loughborough Experimenter zip/postal_code = LE12 5RD Experimenter country = UK Keywords: genetic_modification_design

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE5611 | GEO | 2007/01/08

SECONDARY ACCESSION(S): PRJNA96901

REPOSITORIES: GEO

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Project description:Background: The UK horticultural and agricultural industries routinely apply large amounts of inorganic fertiliser to maintain crop yield and quality, since chemical assays of soil nutrients are unreliable. Excessive fertiliser applications are costly and can lead to unnecessary pollution. A possible solution is to use sensor (GM or non-GM) technologies that exploit the changes in plant gene expression under incipient nutrient deficiency. Aim: The aim of this project is to use mutants with reduced leaf phosphate contents to identify genes upregulated in response to phosphate stress. Preliminary gene expression analysis has identified several phosphate responsive genes to be upregulated in the pho1 mutant. However, further replicates of the experiment are required to confirm these changes. Methods: Arabidopsis mutant pho1 (N8507) and its parent ecotype Columbia 2 (N907) will be grown on MS agar under identical conditions. RNA will be extracted from the rosette leaves of both parent and mutant and the same growth stage. By comparing the expression profiles, we will be able to differentiate between genes that are upregulated in leaves experiencing phosphate stress. Previously, two GeneChips have been used (mutant and parent) to provide preliminary data. A further two biological replicates are now required to confirm these results. Promoters and transcripts of these genes will underpin the development of novel sensor technologies, and knowledge of the gene expression profiles will improve our understanding of the physiology of plant mineral nutrition. Experimenter name = John Hammond; Experimenter phone = 01789 470382; Experimenter fax = 01789 470552; Experimenter address = Plant Sciences Division; Experimenter address = School of Biosciences; Experimenter address = University of Nottingham; Experimenter address = Sutton Bonington Campus; Experimenter address = Loughborough; Experimenter zip/postal_code = LE12 5RD; Experimenter country = UK Experiment Overall Design: 6 samples were used in this experiment

Project description:The aim of this study is to study gene expression in Brassica oleracea in shoot tissues of plants grown under contrasting P supplies (see Hammond JP et al., 2003, Plant Physiology, 132, 578-596 for background). Seeds of B. oleracea (var. alboglabra, A12dH) were first washed in 70% (v/v) ethanol/water, rinsed in distilled water and surface sterilised using 50% (v/v) domestic bleach/water. Seeds were rinsed and imbibed for 3 to 5 days in sterile distilled water at 4°C to break dormancy. Following imbibition, B. oleracea seeds were sown in un-vented, polycarbonate culture boxes (Sigma-Aldrich Company Ltd., Dorset UK). Seedlings were grown for 21 days on perforated polycarbonate discs (diameter 91 mm by 5 mm) placed on 75 ml of 0.8% (w/v) agar containing 1% (w/v) sucrose and a basal salt mix. Roots grew into the agar, but shoots remained on the opposite side of the disc. After 21 days, seedlings were transferred, still on polycarbonate discs, to a hydroponics system situated in a Saxcil growth cabinet (16 h daylength, set to 22°C and 80% humidity). Each polycarbonate disc was placed on a light-proof 500 ml beaker over 450 ml of nutrient solution. After 7 days, half the plants were transferred to nutrient solution containing no phosphate and the other half remained on full nutrient solution (control plants). Shoots were harvested 100 h after the withdrawal of P. !Samples were snap frozen in liquid nitrogen. RNA was extracted using the TRIzol extraction method and cleaned through a Qiagen RNeasy column. Experimenter name = Martin Broadley Experimenter phone = 0115 951 6382 Experimenter fax = 0115 951 6334 Experimenter institute = University of Nottingham Experimenter address = Plant Sciences Division Experimenter address = School of Biosciences Experimenter address = University of Nottingham Experimenter address = Sutton Bonington Experimenter address = Loughborough Experimenter zip/postal_code = LE12 5RD Experimenter country = UK Keywords: growth_condition_design

Project description:The protein modules known as SH2 (Src-homology-2) domains are key players in the signal transduction of animals. Two questions arise: Do such modules exist in plants, and when did SH2 domains evolve? Here I show that the Arabidopsis genome contains three strong candidates for plant SH2 proteins (referred to as PASTA1, 2 and 3 : GI:25513455, At1g78540, At1g17040 respectively) with homology to the SH2 domains and the adjacent linker region of STAT proteins (Signal Transducer and Activator of Transcription). The three characteristics features of a STAT protein sequence1, namely, (i) the SH2 domain with a conserved arginine residue crucial for binding to a phospho-tyrosine residue (ii) a tyrosine residue outside the C-terminus of the SH2-domain for phosphorylation during signalling and (iii) a DNA-binding domain, are conserved in the PASTA3 protein. However, PASTA 1 and 2 proteins lack a tyrosine in a similar position. PASTA proteins are not homologous to STAT proteins outside the SH2 and linker regions. The three PASTA proteins are 70 to 80 % identical to one another. Gene expression studies with PASTA2 reveal that it is expressed in roots, stem, leaves, flowers and green siliques. Preliminary indications are that plants homozygous for PASTA2 do not have any obvious phenotype, most likely due to redundancies. This microarray experiment is an attempt to compare the gene expression of a mutant plant homozygous for PASTA2 with that of the wild type plant. This might give clues about the possible function of PASTA2 in Arabidopsis. Experimenter name = Latha Kadalayil; Experimenter phone = 023-8059 5512; Experimenter department = University of Southampton; Experimenter address = School of Biological Sciences; Experimenter address = Univ. Southampton; Experimenter address = Bassett Crescent East; Experimenter address = Southampton; Experimenter zip/postal_code = SO16 7PX; Experimenter country = UK Experiment Overall Design: 2 samples were used in this experiment

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Differential gene expression patterns in the phosphate deficient mutant, pho 1

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