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Age-related change of callus formation capability in Arabidopsis hypocotyls

ABSTRACT: Transcriptional profiling of age-related change of callus formation capability in Arabidopsis hypocotyls Organogenesis in vitro consists of many aspects such as phytohormone perception, dedifferentiation of differentiated cell to acquire organogenic competence, and re-entry of quiescent cells into cell cycle. In this study, we established an in vitro experimental system to study the age-dependent callus formation capacity in Arabidopsis. Interestingly, mature (35- to 38-day-old) hypocotyl explants exhibited better callus-forming potential than that of juvenile (7- to 10-day-old), determined by callus growth rates. To explore genome-wide expression changes underlying the phenomenon of age-dependent callus formation, a transcriptome-based analysis was performed. Gene expression profiling indicated that age-dependent callus formation capacity was associated with changes in phytohormone (auxins, cytokinins, abscisic acid, brassinosteroids and gibberellins) homeostasis, epigenetic mechanism and the cell cycle regulation. Besides, we identified two groups of genes involved in age-dependent callus formation capacity: (1) positive regulatory and (2) negative regulatory categories, i.e. genes that were significantly up- or down-regulated during callus formation derived from mature explants, respectively. One gene encoding DNA-binding protein (VARIANT IN METHYLATION 1, VIM1) belonging to the positive regulatory category was selected for functional analysis and assessment of age-dependent callus formation capacity. Indeed, vim1 reduced the efficiency of callus formation in mature explants, but not in juvenile. The result suggests that VIM1 plays an important role in regulating age-dependent callus formation capacity. Taken together, the investigation will help to better understand the molecular regulatory mechanism of age-dependent callus formation.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE27508 | GEO | 2011/06/19

SECONDARY ACCESSION(S): PRJNA138573

REPOSITORIES: GEO

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Project description:Transcriptional profiling of age-related change of callus formation capability in Arabidopsis hypocotyls Organogenesis in vitro consists of many aspects such as phytohormone perception, dedifferentiation of differentiated cell to acquire organogenic competence, and re-entry of quiescent cells into cell cycle. In this study, we established an in vitro experimental system to study the age-dependent callus formation capacity in Arabidopsis. Interestingly, mature (35- to 38-day-old) hypocotyl explants exhibited better callus-forming potential than that of juvenile (7- to 10-day-old), determined by callus growth rates. To explore genome-wide expression changes underlying the phenomenon of age-dependent callus formation, a transcriptome-based analysis was performed. Gene expression profiling indicated that age-dependent callus formation capacity was associated with changes in phytohormone (auxins, cytokinins, abscisic acid, brassinosteroids and gibberellins) homeostasis, epigenetic mechanism and the cell cycle regulation. Besides, we identified two groups of genes involved in age-dependent callus formation capacity: (1) positive regulatory and (2) negative regulatory categories, i.e. genes that were significantly up- or down-regulated during callus formation derived from mature explants, respectively. One gene encoding DNA-binding protein (VARIANT IN METHYLATION 1, VIM1) belonging to the positive regulatory category was selected for functional analysis and assessment of age-dependent callus formation capacity. Indeed, vim1 reduced the efficiency of callus formation in mature explants, but not in juvenile. The result suggests that VIM1 plays an important role in regulating age-dependent callus formation capacity. Taken together, the investigation will help to better understand the molecular regulatory mechanism of age-dependent callus formation. Comparison of young and mature Arabidopsis hypocotyls either with or without auxin treatment for 1 day

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.

Project description:Rooting capability is one of the economically traits lost during the juvenile to mature phase change in woody plants. A comprehensive microarray analysis was performed to compare the profiles of gene expression in juvenile and mature cuttings from E. grandis, either auxin treated or untreated on days, 0, 1, 3, 6, 9 and 12 post excision. At the end of the experiment, root primordia were observed only in auxin treated juvenile cuttings. Clustering the expression profiles revealed that the time after excision contributed to expression differences more than the age or auxin. Maximum differences contributed by the age and auxin occurred on day 6 which correlated with the kinetics of root primordia formation. These included genes related to the microtubules (MTs) system. Therefore, expression of 42 transcripts annotated as tubulin or MTs associated proteins (MAPs) was validated in the same RNA samples. The results suggest developmental and auxin regulation of MTs. To determine the relevance to adventitious root (AR) formation, subtle perturbations to MTs were performed with trifluralin during induction. While juvenile cuttings were not affected, improved rooting was obtained in mature cuttings. Taken together it suggests that specific MTs remodeling is required for AR formation in E. grandis. mRNA samlpes from mature and juvenile Eucalyptus sections immediately after cutting served as contorls. The rest of the samples were mature and juvenile sections, treated of not treated with Auxin, 1, 3, 6, 9 and 12 days after the prunning. At each time point, a loop design was performed consisting of a juvenile untreated vs. mature untreated array, a matrue untreated vs. mature auxin treated array, a matrue auxin treated vs. juvenile auxin treated array, and a juvenile auxin treated vs. juvenile untreated array. additional arrays connected between these loops, and between them and the time 0 controls. Most conditions had 3 replicates, but mature-untreated-day1 had 4 replicates, and three conditions had 2 replicates each: Juvenile-auxin-treated-day1, juvenile-untreated-day6, and mature-auxin-treated-day9.

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Age-related change of callus formation capability in Arabidopsis hypocotyls

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