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Expression data from Arabidopsis rosette leaves

ABSTRACT: The focus of this study was to identify changes in host gene expression induced by the transcription-dependent function of the viral AC2 protein, and induced by the interaction of AC2/C2 with SnRK1.2 (AtAKIN11). We used microarrays to identify changes in host gene expression induced by the transcription-dependent function of the geminivirus-encoded AC2 protein, and induced by the interaction of AC2 with a host serine-threonine kinase, SnRK1. Distinct classes of genes were up- and down regulated during this process. For experiment 1, Arabidopsis rosette leaves were infused with Agrobacterium capable of expressing full-length Cabbage leaf curl virus (CaLCuV) AC2 protein, a truncated version of AC2 lacking the C-terminal 29 amino acids (AC2del), or an empty vector control (530). In experiment 2, Arabidopsis rosette leaves were infused with Agrobacterium capable of expressing full-length Spinach curly top virus C2 protein, a truncated version of C2 lacking the C-terminal 29 amino acids (C2del), antisense (as) SnRK1.2 (AsAKIN11), or an empty vector control (530).

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE62180 | GEO | 2014/10/09

SECONDARY ACCESSION(S): PRJNA263380

REPOSITORIES: GEO

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Expression data from Arabidopsis rosette leaves

Project description:The focus of this study was to identify changes in host gene expression induced by the transcription-dependent function of the viral AC2 protein, and induced by the interaction of AC2/C2 with SnRK1.2 (AtAKIN11). We used microarrays to identify changes in host gene expression induced by the transcription-dependent function of the geminivirus-encoded AC2 protein, and induced by the interaction of AC2 with a host serine-threonine kinase, SnRK1. Distinct classes of genes were up- and down regulated during this process. For experiment 1, Arabidopsis rosette leaves were infused with Agrobacterium capable of expressing full-length Cabbage leaf curl virus (CaLCuV) AC2 protein, a truncated version of AC2 lacking the C-terminal 29 amino acids (AC2del), or an empty vector control (530). In experiment 2, Arabidopsis rosette leaves were infused with Agrobacterium capable of expressing full-length Spinach curly top virus C2 protein, a truncated version of C2 lacking the C-terminal 29 amino acids (C2del), antisense (as) SnRK1.2 (AsAKIN11), or an empty vector control (530). Infused Arabidopsis rosette leaves were selected at 1, 2 or 3 days post-infusion for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain homogeneous populations of plants at each time point in order to increase the temporal resolution of expression profiles. To that end, we isolated total RNA from four individual plants, for three independent sets of plants infused with the different constructs. This resulted in three independent samples per treatment per time point.

2014-10-09 | E-GEOD-62180 | biostudies-arrayexpress

Transcription profiling of hairy roots of M. trunculata transformed with TT2

Project description:M. truncatula was transformed with TT2 (transparent testa2 from Arabidopsis) using Agrobacterium rhizogene and the transgenic hairy roots were used for gene profiling in comparison with empty vector control.

2008-11-26 | E-MEXP-1115 | biostudies-arrayexpress

Transcriptional profiling on leaves of Pha21 (PATC144963) overexpressed Phalaenopsis aphrodite

Project description:To identify genes affected by Pha21, Pha21 was transiently overexpressed in leaves of P. aphrodite by agroinfiltration. The leaves of P. aphrodite infiltrated with agrobacterium carrying empty vector (without Pha21) was used as a control. Transcriptional profiling was analyzed using a customized oligonucleotide array with RNA extracted from Pha21 and empty vector overexpressed leaves of P. aphrodite. The sequences used for probe design were collected from the Orchidstra 2.0 database (http://orchidstra2.abrc.sinica.edu.tw/orchidstra2/index.php). Totally, 42,973 probes were designed on this oligonucleotide array.

2017-01-07 | GSE93247 | GEO

Transcriptional profiling on leaves of Pha13 (PATC148746) overexpressed Phalaenopsis aphrodite

Project description:To identify genes affected by Pha13, Pha13 was transiently overexpressed in leaves of P. aphrodite by agroinfiltration. The leaves of P. aphrodite infiltrated with agrobacterium carrying empty vector (without Pha13) was used as a control. Transcriptional profiling was analyzed using a customized oligonucleotide array with RNA extracted from Pha13 and empty vector overexpressed leaves of P. aphrodite. The sequences used for probe design were collected from the Orchidstra 2.0 database (http://orchidstra2.abrc.sinica.edu.tw/orchidstra2/index.php). Totally, 42,973 probes were designed on this oligonucleotide array.

2017-01-07 | GSE93246 | GEO

Differential gene expression profiling of MIHA cells transfected with C-terminal truncated HBx mutants

Project description:To compare the differentially expressed transcriptomes between MIHA cells transfected with empty vector control or different C-terminal truncated HBx mutants (14 or 35 amino acid carboxyl-terminal truncation - i.e. d14 and d35) mRNA profiles of MIHA cells stably overexpressing empty vector control or different C-terminal truncated HBx mutants (delta 14 and delta 35) were generated by PolyA mRNA sequencing using Illumina HiSeq 1500 platform

2016-08-02 | E-GEOD-71993 | biostudies-arrayexpress

Expression data from WT (Ws-2), CBF1,2,3, and CBF2M-NM-^Tc (a truncated CBF2) overexpression

Project description:CBF1, CBF2 and CBF3 regulons comprise nearly identical gene sets The vast majority of CBF2 regulon genes were down-regulated less that 50% by overexpression of CBF2M-NM-^Tc, a truncated version of CBF2 We used Affymetrix GeneChips to examine the CBF regulons of plants overexpressing CBF1, CBF2, CBF3 and a truncated version of CBF2, CBF2M-NM-^Tc.

2015-02-28 | E-GEOD-55906 | biostudies-arrayexpress

Over-expression of truncated FMRP with 295 amino acid residues: HEK293T cells

Project description:We used microarrays to detail the global gene expression in stably transfected HEK 293T cells of the over-expression of truncated FMRP containing 295 amino acid residues, which were compared with control (stably transfected HEK 293T cells of empty lentiviral vector (pLEX-MCS). Stably transfected HEK 293T cells of empty lentiviral vector (pLEX-MCS) and the over-expression of truncated FMRP were for RNA extraction and hybridization on Affymetrix microarrays.

2015-05-08 | E-GEOD-68668 | biostudies-arrayexpress

Differential gene expression profiling of MIHA cells transfected with C-terminal truncated HBx mutants

2016-08-02 | GSE71993 | GEO

Transcription profiling of Medicago truncatula with genetic modification 35S:bHLH1:EAR

Project description:Search of MtbHLH1 possible target genes by comparison of nodule transcriptomes from pPEX empty vector-transformed versus 35S:bHLH1:EAR Agrobacterium rhizogenes transformed plants, at 24 days post inoculation with wild-type Sinorhizobium meliloti 2011::lacZ (GMI6526)

2010-10-31 | E-TABM-719 | biostudies-arrayexpress

An allosteric switch between the activation loop and a c-terminal palindromic phospho-motif drives c-Src disfunction in cancer

Project description:The allosteric mechanisms that control the different functional and conformational states of oncogenic kinases, and how these molecular switches can be targeted and therapeutically exploited remains largely unexplored. Here we show that c-terminal Tyr 530 is a de facto c- Src auto-phosphorylation site with slow time-resolution kinetics and strong intermolecular component. On the contrary, activation-loop Tyr 419 undergoes fast kinetics and a cis-to-trans phosphorylation-switch that controls c-terminal Tyr 530 phosphorylation, enzyme specificity and strikingly, c-Src non-catalytic function as a substrate. In line with this, we visualize by X-ray crystallography a snapshot of c-terminal Tyr 530 intermolecular phosphorylation between the enzyme and susbtrate acting kinases, and identify a functionally relevant c-terminal palindromic phospho-motif flanking Tyr 530 making important contacts at the interface. Perturbation of this phospho-motif accounts for c-Src disfunction in cancer, as indicated by viral and a colorectal cancer (CRC) associated c-terminal deleted variants. We show that c-terminal residues 531 to 536 are required for c-Src Tyr 530 auto-phosphorylation and overall phospho-tyrosine activity. However, c-terminal truncated forms display a minor delay in the capacity to phosphorylate intact c-Src substrates surrogates. On the contrary, when these c-terminal variants were used as intact substrate surrogates themselves, they were equally and efficiently phosphorylated, but strikingly they resulted in the allosteric inhibition of the active kinase. Our work reveals a bi-directional crosstalk between activation and c-terminal segments driven by auto-phosphorylation that controls the allosteric interplay between enzyme and susbtrate acting kinases. These findings have important implications for the drug-design and development of next generation c-Src inhibitors targeting non-catalytic and/or allosteric vulnerabilities.

2023-09-04 | PXD037287 | Pride

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