Examination of the function of NtMYBGR1 and NtDC1B in tobacco BY-2 cells.
Ontology highlight
ABSTRACT:
ORGANISM(S): Nicotiana tabacum
SUBMITTER: Ken Matsuoka
PROVIDER: E-GEOD-6949 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
Comprehensive analysis of glucan elicitor-regulated gene expression in tobacco BY-2 cells reveals a novel MYB transcription factor involved in the regulation of phenylpropanoid metabolism.
Shinya Tomonori T Gális Ivan I Narisawa Tomoko T Sasaki Mami M Fukuda Hiroo H Matsuoka Hideaki H Saito Mikako M Matsuoka Ken K
Plant & cell physiology 20070830 10
We previously demonstrated that a beta-1,3-, 1,6-oligoglucan (AaGlucan) from the fungus Alternaria alternata 102 shows strong elicitor activity in tobacco BY-2 cells. We have used cDNA microarray analysis to monitor global changes in gene expression in tobacco cells treated with this A. alternata fraction or with laminarin. In total, we identified 265 genes that were induced 1 h after treatment with an AaGlucan-enriched fraction or laminarin. Among them, we characterized in detail a novel tobacc ...[more]
Similar Datasets
Project description:We have previously reported that the responses of tobacco tissues treated with AaGlucan are similar to those for laminarin [1]. To better understand the overall responses and signaling pathways in tobacco, we have identified here AaGlucan and laminarin early response genes, using a custom 16K BY-2 microarray [2,3]. BY-2 cells were treated with laminarin or an AaGlucan-enriched fraction prepared from A. alternata 102 culture-medium and subjected to microarray analysis. [1] Shinya, T., Menard, R., Kozone, I., Matsuoka, H., Shibuya, N., Kauffmann, S., Matsuoka, K. and Saito, M. (2006) Novel b-1,3-, 1,6-oligoglucan elicitor from Alternaria alternata 102 for defense responses in tobacco. FEBS J. 273: 2421-2431. [2] Matsuoka, K., Demura, T., Galis, I., Horiguchi, T., Sasaki, M., Tashiro, G. and Fukuda, H. (2004) A comprehensive gene expression analysis toward the understanding of growth and differentiation of tobacco BY-2 cells. Plant Cell Physiol. 45: 1280-1289. [3] Galis, I., Simek, P., Narisawa, T., Sasaki, M., Horiguchi, T., Fukuda, H. and Matsuoka, K. (2006) A novel R2R3 MYB transcription factor NtMYBJS1 is a methyl jasmonate-dependent regulator of phenylpropanoid-conjugate biosynthesis in tobacco. Plant J. 46: 573-592. AaGlucan was purified from Alternaria alternata 102 as a potent elicitor for tobacco [1] Four-day-old tobacco BY-2 cells after subculture were treated with 10 microg/ml AaGlucan enriched fraction for 1h. Total RNA was prepared from the control and treated samples and used for microarray experiment after reverse transcription and labeling with Cy5 fluorescent dye. [1] Shinya, T., Menard, R., Kozone, I., Matsuoka, H., Shibuya, N., Kauffmann, S., Matsuoka, K. and Saito, M. (2006) Novel b-1,3-, 1,6-oligoglucan elicitor from Alternaria alternata 102 for defense responses in tobacco. FEBS J. 273: 2421-2431.
2007-10-16 | E-GEOD-6948 | biostudies-arrayexpress
Project description:Boron (B) is an essential micronutrient for vascular plants. Boron works to build the cell wall structure by forming borate ester cross-links with pectin, and the deficiency of this element brings about oxidative damage and cell death. However, the process via which B deficiency leads to such serious damage has not been well understood. We investigated the temporal changes in metabolism of B-deprived cultured tobacco (Nicotiana tabacum) BY-2 cells by analyzing their gene expression using cDNA microarray. Three-day-old cells were deprived of B by washing with and transferred to B-free growth media ("-B" cells). Cells similarly treated with standard growth media were employed as a control for the effects of mechanical stress ("+B cells"). Cells were sampled at 1, 3, 6, 12 and 36 h after transfer to the B-free or standard media. Cells without washing treatment were also included in the analysis ("before-treatment cells"). Two independent sets of samples were analyzed (replicate 1 and 2).
2012-05-04 | E-GEOD-37649 | biostudies-arrayexpress
Project description:Promoters of many G2/M phase-specific genes in plants contain mitosis-specific activator (MSA) elements, which act as G2/M phase-specific enhancers and bind with R1R2R3-Myb transcription factors. A least three R1R2R3-Myb proteins are expressed in tobacco (Nicotiana tabacum). To examine the genome-wide effects of NtmybA2 overexpression, we constructed transgenic tobacco BY-2 cell lines overexpressing full-length NtmybA2 protein. In addition, we generated transgenic BY-2 cell lines that overexpress truncated hyperactive form of NtmybA2 (NtmybA2âC) lacking its C-terminal region which negatively regulates its own activity for transcriptional activation. We used a custom-made 16K cDNA microarray for comparative transcriptome analysis of these transgenic tobacco BY-2 cell lines. As control sample, BY-2 cells transformed with empty vector pPZP-35S were used. The transgenic cell lines were analyzed during stationary phase (i.e. day 7-8 after subculture into fresh media). Keywords: Genetic modification 1. pPZP-35S vector control, 2. NtmybA2 overexpressor, 3. C-truncated NtmybA2 (NtmyA2âC) overexpressor
2010-05-22 | E-GEOD-14251 | biostudies-arrayexpress
Project description:Tobacco BY-2 cells can be highly synchronized by treatment with an inhibitor of DNA synthesis, aphidicolin. For comprehensive understanding of cell cycle-regulated gene expression in tobacco, microarray analysis was conducted in synchronized cultures of BY-2 cells. Cells were treated with aphidicolin for 24 hours to block the entry into and progression through the S phase. After release from the aphidicolin block, cells were sampled every 2 h from 0â16 h. cDNA probes prepared from these samples were hybridised to a custom-made16K microarray. We performed this procedure twice independently to identify transcripts that reproducibly showed similar cell cycle-regulated expression. A total of 883 putative cell cycle-regulated transcripts were identified from 16,896 duplicated spots on the microarrays. These transcripts could be categorised into 10 classes on the basis of transcript expression patterns in the cell cycle. Keywords: time course Synchronization experiments were repeated twice (experiments A and B). In each experiment, cells were sampled every 2 h during the culture periods (0-16 h), and used for microarray analysis.
2010-05-22 | E-GEOD-14250 | biostudies-arrayexpress
Project description:Identification of underreplicated areas in drosophila polytene chromosomes Keywords: repeat sample
2010-06-10 | E-GEOD-2551 | biostudies-arrayexpress
Project description:Guanosine 3 ,5 -bispyrophosphate (ppGpp), also known as ‘‘magic spot,’’ has been shown to bind prokaryotic RNA polymerase to down-regulate ribosome production and increase transcription of amino acid biosynthesis genes during the stringent response to amino acid starvation. Because many environmental growth perturbations cause ppGpp to accumulate, we hypothesize ppGpp to have an overarching role in regulating the genetic program that coordinates transitions between logarithmic growth (feast) and growth arrest (famine). We used the classic glucose-lactose diauxie as an experimental system to investigate the temporal changes in transcription that accompany growth arrest and recovery in wildtype Escherichia coli and in mutants that lack RelA (ppGpp synthetase) and other global regulators, i.e., RpoS and Crp. When cultured on a mixture of glucose and lactose, E. coli grows preferentially on glucose until it is exhausted, resulting in growth arrest while the cells adjust to growth on lactose, i.e., diauxie. Diauxie was delayed in the relA mutant and was accompanied by a 15% decrease in the number of carbon sources used and a 3-fold overall decrease in the induction of RpoS and Crp regulon genes. Thus the data significantly expand the previously known role of ppGpp and support a model wherein the ppGpp-dependent redistribution of RNA polymerase across the genome is the driving force behind control of the stringent response, general stress response, and starvation-induced carbon scavenging. Our conceptual model of diauxie describes these global control circuits as dynamic, interconnected, and dependent upon ppGpp for the efficient temporal coordination of gene expression that programs the cell for transitions between feast and famine. E. coli MG1655 and isogenic mutants were cultured in a 2 l Biostat B fermentor (B. Braun Biotech International) containing 1 liter of Morpholinepropanesulfonic acid (MOPS) minimal medium with 0.5 g/l of glucose and 1.5 g/l of lactose. The temperature was maintained at 37 ºC and pH was kept constant at 7.2 by the addition of 2 M NaOH. The dissolved oxygen level was maintained above 20% of saturation by adjusting the agitation speeds in the range of 270-500 rpm with fixed 1 l/min air flow.
2007-03-17 | E-GEOD-7265 | biostudies-arrayexpress
Project description:Time series analysis of glucose-lactose diauxie; When cultured on a mixture of glucose and lactose, E. coli grows preferentially on glucose until it is exhausted, resulting in growth arrest while the cells adjust to growth on lactose, i.e., diauxie.
2006-11-27 | E-MEXP-918 | biostudies-arrayexpress
Project description:Enteric pathogens have developed several resistance mechanisms to survive the antimicrobial action of bile. We investigated the transcriptional profile of Vibrio cholerae O1 El Tor strain C6706 under virulence gene inducing conditions, in the presence and absence of bile. Microarray analysis revealed that the expression of 119 genes was affected by bile. The mRNA levels of genes encoding proteins involved in transport was increased in the presence of bile, whereas mRNA levels of genes encoding proteins involved in pathogenesis and chemotaxis was decreased. This study identified genes encoding transcriptional regulators from the TetR family (vexR and breR) and multidrug efflux pumps from the RND superfamily (vexB and vexD [here renamed breB]) that were induced in response to bile. Further analysis regarding vexAB and breAB expression in the presence of various antimicrobial compounds established that vexAB was induced in the presence of bile, SDS or novobiocin, whereas induction of breAB was specific to bile. BreR is a direct repressor of the breAB promoter and is able to autoregulate its own expression, as demonstrated by transcriptional and electrophoretic mobility shift assays (EMSA). Expression of breR and breAB is induced in the presence of the bile salts cholate, deoxycholate or chenodeoxycholate and EMSA showed that deoxycholate is able to abolish formation of BreR-PbreR complexes. We propose that deoxycholate is able to interact with BreR and induce a conformational change that will interfere with its DNA binding ability resulting in breAB and breR expression. These results provide new insight into a transcriptional regulator and a transport system that likely play an essential role in the ability of Vibrio cholerae to resist the action of bile in the host. Keywords: Vibrio cholerae response to bile Three independent experiments were performed for the microarray analysis. From each experiment, RNA was obtained from four different time points and was prepared for hybridization, therefore, a total of 3 slides were analyzed per time point. The growth conditions were as follows; C6706 str2 was grown 15 h in LB medium at 30 degrees C with aeration. The cultures were then diluted 100-fold into AKI medium with, or without, 0.4% crude bile (high bile concentration) and were grown at 37degrees C for 3.5 h stationary followed by 2 h with aeration to induce virulence gene expression. Then the cultures were diluted 100-fold into AKI medium with, or without, 0.02% crude bile (low bile concentration) and were grown at 37 degrees C for 2 h stationary. Samples were obtained from 4 different time points: 2, 4, and 5.5 h from the high bile cultures, and at 2 h from the low bile cultures.
2010-06-05 | E-GEOD-6468 | biostudies-arrayexpress
Project description:Background; The t(12;21)(p13;q22) translocation is found in 20 to 25% of cases of childhood B-lineage acute lymphoblastic leukemia (B-ALL). This rearrangement results in the fusion of ETV6 (TEL) and RUNX1 (AML1) genes and defines a relatively uniform category, although only some patients suffer very late relapse. TEL/AML1-positive patients are thus an interesting subgroup to study, and such studies should elucidate the biological processes underlying TEL/AML1 pathogenesis. We report an analysis of gene expression in 60 children with B-lineage ALL using Agilent whole genome oligo-chips (44K-G4112A) and/or real time RT-PCR. Results; We compared the leukemia cell gene expression profiles of 16 TEL/AML1-positive ALL patients to those of 44 TEL/AML1-negative patients, whose blast cells did not contain any additional recurrent translocation. Microarray analyses of 26 samples allowed the identification of genes differentially expressed between the TEL/AML1-positive and negative ALL groups. Gene enrichment analysis defined five enriched GO categories: cell differentiation, cell proliferation, apoptosis, cell motility and response to wounding, associated with 14 genes â??RUNX1, TCFL5, TNFRSF7, CBFA2T3, CD9, SCARB1, TP53INP1, ACVR1C, PIK3C3, EGFL7, SEMA6A, CTGF, LSP1, TFPIâ?? highlighting the biology of the TEL/AML1 sub-group. These results were first confirmed by the analysis of an additional microarray data-set (7 patient samples) and second by real-time RT-PCR quantification and clustering using an independent set (27 patient samples). Over-expression of RUNX1 (AML1) was further investigated and in one third of the patients correlated with cytogenetic findings. Conclusions; Gene expression analyses of leukemia cells from 60 children with TEL/AML1-positive and -negative B-lineage ALL led to the identification of five biological processes, associated with 14 validated genes characterizing and highlighting the biology of the TEL/AML1-positive ALL sub-group. Experiment Overall Design: We carried out a prospective multicentric study on childhood B-ALL leukemia to elucidate the molecular processes involved in TEL/AML1-positive leukemia. All the patients included in this study received treatment according to the French FRALLE 2000 trial. We used Agilent whole-genome oligo-chips (44K-G4112A) to compare the gene expression signatures of TEL/AML1-positive patients to those of TEL/AML1-negative patients with no recurrent chimeric products irrespective of their clinical risk category. Previous microarray gene expression studies had revealed the effect of chromosomal alteration on transcription profiles, so we excluded from our cohort those patients with other recurrent chromosomal translocations or fusion transcripts (BCR/ABL, E2A/PBX1, MLL rearrangements). We then searched for the biological pathways associated with genes differentially expressed in TEL/AML1-positive leukemia (ETV6/RUNX1).
2008-06-16 | E-GEOD-9170 | biostudies-arrayexpress
Project description:RSS1 is required for maintenance of meristematic activity under salinity conditions in rice. We carried out transcriptome analysis using shoot basal tissues in wild type and rss1-2 grown under non-stress and salt-stress conditions. WT (-NaCl), WT (+NaCl), rss1-2 (-NaCl), rss1-2 (+NaCl). Three biological replicates.
2011-03-11 | E-GEOD-27884 | biostudies-arrayexpress