Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

CYTOKININ HYPERSENSITIVE1 (CKH1) and CKH2 affect to cytokinin responses in tissue culture

ABSTRACT: Analysis of calli derived from the wild type (Ler), the ckh1 and ckh2 mutants cultured on media in the absence of cytokinin (control), in the presence of low (25 ng/ml kinetin) or high (200 ng/ml kinetin) levels of cytokinin, or in the presence of Trichostatin A (TSA). In these conditions, a constant 2,4-dichlorophenoxyacetic acid (2,4-D) was included as an auxin. Hypocotyl segments of the wild type (Ler), ckh1-1 and ckh2-1 mutants were cultured for 3 days on media containing 100 ng/ml 2,4-D in the absence of kinetin or in the presence of low (25 ng/ml) or high (200 ng/ml) kinetin or 100ng/ml TSA, and then collected and rapidly frozen by liquid nitrogen. Total RNA was extracted by using an RNeasy plant kit (Qiagen; USA), and 10 µg of total RNA was used for target preparation by using

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Minoru Kubo

PROVIDER: E-GEOD-26297 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

The CKH2/PKL chromatin remodeling factor negatively regulates cytokinin responses in Arabidopsis calli.

Furuta Kaori K Kubo Minoru M Sano Kiyomi K Demura Taku T Fukuda Hiroo H Liu Yao-Guang YG Shibata Daisuke D Kakimoto Tatsuo T

Plant & cell physiology 20110225 4

Cytokinins promote cell division and chloroplast development in tissue culture. We previously isolated two mutants of Arabidopsis thaliana, ckh1 (cytokinin-hypersensitive 1) and ckh2, which produce rapidly growing green calli in response to lower levels of cytokinins than those found in the wild type. Here we report that the product of the CKH2 gene is PICKLE, a protein resembling the CHD3 class of SWI/SNF chromatin remodeling factors. We also show that inhibition of histone deacetylase by trich ...[more]

PMID: 21357580

Publication: 1/2

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Project description:The cost of Carica papaya production through seed-based propagation is increased by sex segregation, making in vitro techniques a more appealing option for clonal propagation. Inducing embryogenic callus with 2,4-dichlorophenoxyacetic acid (2,4-D) hold the potential to large-scale cloning, although the molecular mechanisms underlying this process are still not well understood. In this study, we performed a temporal analysis in the proteome of C. papaya callus to identify the key players involved in embryogenic differentiation. Mature zygotic embryos were used as explants and treated with 20 μM 2,4-D to induce embryogenic callus. Total proteins were extracted at 0, 7, 14, and 21 days (T0, T7, T14, and T21), and 1407 proteins were identified using bottom-up proteomic approach. Comparative proteomics revealed 957 differentially accumulated proteins (DAPs) (p<0.05 and log2FC >0.585 or <-0.585) in at least one comparison between the analyzed induction times points. The clustering analysis revealed four clusters with distinct patterns of protein accumulation throughout the embryogenic callus induction treatment. The cluster 1 contains 386 DAPs that accumulated at all analyzed times after treatment with 2,4-D. In contrast, cluster 2 contains 165 DAPs that decrease in abundance during the induction. The cluster 3 contains 251 proteins that are most abundant just after the start of incubation in 2,4-D (T7) and cluster 4 grouped 155 proteins that accumulate after callus formation. Functional analysis revealed that proteins involved with reserve storage and seed maturation were more abundant in the explant at T0 and decreased as callus formation progressed. Biological processes involving carbohydrate and amino acid metabolism, aerobic respiration, and protein catabolic processes were enriched after induction treatment. Regulatory proteins, including histone deacetylase (HDT3) and argonaute 1, were more abundant after the start of induction treatment with 2,4-D, suggesting their role in acquisition of embryogenic competence. Predicted protein-protein networks revealed the regulatory role of proteins 14.3.3 accumulated during callus induction and the association of proteins involved in oxidative phosphorylation, hormone response, and SAM metabolism. Our findings emphasize the modulation of the proteome at different stages during embryogenic callus initiation and identify regulatory proteins that might be involved with the activation of this process.

Dataset Information

CYTOKININ HYPERSENSITIVE1 (CKH1) and CKH2 affect to cytokinin responses in tissue culture

Publications

The CKH2/PKL chromatin remodeling factor negatively regulates cytokinin responses in Arabidopsis calli.

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