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PiceaGenExpress database of transcription profiles

ABSTRACT: A small database of transcription profiles called PgGenExpress was developed from over 150 hybridizations spanning eight major tissue types. In total, transcripts were detected for 92% of the genes on the microarray, in at least one tissue. Non-annotated genes were predominantly expressed at low levels in fewer tissues than genes of known or predicted function. Diversity of expression within gene families may be rapidly assessed from PgGenExpress. In conifer trees, dehydrins and late embryogenesis (LEA) osmotic regulation proteins occur in large gene families compared to angiosperms. Strong contrasts and low diversity was observed in the dehydrin family, while diverse patterns suggested a greater degree of diversification among LEAs.

ORGANISM(S): Picea glauca Picea sitchensis Picea abies

PROVIDER: GSE35624 | GEO | 2012/02/08

SECONDARY ACCESSION(S): PRJNA152465

REPOSITORIES: GEO

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PgGenExpress database of transcription profiles

Project description:A small database of transcription profiles called PgGenExpress was developed from over 150 hybridizations spanning eight major tissue types. In total, transcripts were detected for 92% of the genes on the microarray, in at least one tissue. Non-annotated genes were predominantly expressed at low levels in fewer tissues than genes of known or predicted function. Diversity of expression within gene families may be rapidly assessed from PgGenExpress. In conifer trees, dehydrins and late embryogenesis (LEA) osmotic regulation proteins occur in large gene families compared to angiosperms. Strong contrasts and low diversity was observed in the dehydrin family, while diverse patterns suggested a greater degree of diversification among LEAs. This is a one-color meta-analysis of tissues from 5 separate experiments. There are 8 different tissue types. Each tissue is represented by a variable number of slides, each slide being a biological repetition, for a total of 149 slides.

2012-02-08 | E-GEOD-35624 | biostudies-arrayexpress

Spruce dehydrins analysis by LC-MS/MS

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The heat-stable proteome contains a tightly associated LEA protein network during seed germination in Arabidopsis

Project description:Seed germination involves transition from desiccation tolerance to sensitivity during early stages of seedling establishment accompanied by comprehensive changes of metabolome and proteome. Germination of Arabidopsis seeds was investigated over 72 h with special focus on the heat-stable proteome including late embryogenesis abundant (LEA) proteins together with changes of primary metabolites. Six metabolites in dry seeds important for seed longevity decreased during germination and seedling establishment, while all other metabolites increased simultaneously with activation of growth and development. In the heat stable proteome an almost equal fractioning of ordered and intrinsically disordered proteins (IDP) was discovered. Highly disordered proteins were assigned to functional bins development, protein, RNA and stress. Thermal stable proteins were related to a multitude of active biological processes. The majority of LEA proteins decreased during germination and seedling establishment in parallel to reduced desiccation tolerance. Five germination specific dehydrins were identified most likely providing stress tolerance. Network analysis of common proteins and metabolites over all time points revealed a tight network of LEA proteins with five hub LEAs with high connectivity. Connections to proteins such as Rubisco large subunit and seed storage proteins were discovered. Insights into the heat-stable proteome – metabolome network during seed germination are provided.

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Characterization of the heat-stable proteome during seed germination in Arabidopsis with special focus on LEA proteins

Project description:During seed germination, desiccation tolerance is lost in the radicle with progressing radicle protrusion and seedling establishment. This process is accompanied by comprehensive changes of the metabolome and proteome. Germination of Arabidopsis seeds was investigated over 72 h with special focus on the heat-stable proteome including late embryogenesis abundant (LEA) proteins together with changes of primary metabolites. Six metabolites in dry seeds known to be important for seed longevity decreased during germination and seedling establishment, while all other metabolites increased simultaneously with activation of growth and development. Thermo-stable proteins were associated with a multitude of biological processes. In the heat-stable proteome a relatively similar proportion of fully ordered and fully intrinsically disordered proteins (IDP) was discovered. Highly disordered proteins were found to be associated with functional categories development, protein, RNA and stress. As expected, the majority of LEA proteins decreased during germination and seedling establishment. However, four germination-specific dehydrins were identified, not present in dry seeds. A network analysis of proteins, metabolites and amino acids generated during the course of germination revealed a highly connected LEA protein network.

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Gene expression profiles during long-term low-temperature treatment and cold acclimation in synthetic wheat hexaploids

Project description:We conducted microarray analysis to study comprehensive changes of gene expression profile under long-term low-temperature (LT) treatment and to identify other LT-responsive genes related with cold acclimation in seedling leaves and crown tissues (shoots containing apical meristems) of a synthetic hexaploid wheat line. The microarray analysis revealed marked up-regulation of a number of Cor/Lea genes and fructan biosynthesis-related genes under the long-term LT treatment. For validation of the microarray data, we selected four synthetic wheat lines, which contained the A and B genomes from a tetraploid wheat cultivar Langdon and the diverse D genomes originating from the different Ae. tauschii accessions, with distinct levels of freezing tolerance after cold acclimation. Quantitative RT-PCR analyses showed that the transcription accumulated levels of the Cor/Lea, CBF, and fructan biosynthesis-related genes were higher in more freezing-tolerant lines than those in the sensitive lines. The fructan biosynthesis pathway would be associated with cold acclimation to develop wheat freezing tolerance and related with diversity of the freezing tolerance level in addition to the CBF-mediated Cor/Lea expression pathway.

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Gene expression profiles during long-term low-temperature treatment and cold acclimation in synthetic wheat hexaploids

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