Modeling protein destiny in developing tomato fruit
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ABSTRACT:
PROVIDER: PRJNA528656 | ENA |
REPOSITORIES: ENA
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Project description:Proteomics and transcriptomics data of tomato fruits at 9 developmental stages were used to calculate with a mathematical model the rate constants of synthesis and degradation for over 1,000 proteins.
2019-05-06 | PXD012877 | Pride
Project description:Proteomics and transcriptomics data of tomato fruits (Solanum lycopersicum L. var. Moneymaker) at 9 developmental stages were used to calculate with a mathematical model the rate constants of synthesis and degradation for over 1,000 proteins. Proteome and transcriptome were extracted from the pericarp tissue and analyzed using label-free LC-MS/MS (Orbitrap Q-Exactive) and RNA Sequencing (Illumina), respectively. Absolute quantification of transcriptome has been obtained by spiking-in internal standard before total-RNA extraction. Absolute quantification of the proteome has been approximated using the "Total Protein" approach. An OD equation defining the changes of protein content has been used to determine the synthesis and degradation rate constants (day -1). Almost 2,400 transcript-protein pairs were identified and the translation and degradation rate constants were determined for more than a thousand proteins. The model predicted median values of about 2 min for the translation and a lifetime of approximately 11 days. Proteins involved in protein synthesis had higher ks and kd values, indicating that the protein machinery is particularly flexible. None sequenced-based features were found that could be used to predict these rate constants.
2019-03-23 | GSE128739 | GEO
Project description:To evaluate the role of seeds in fruit quality, we induced parthenocarpy in tomato by regulating ovule-specific auxin synthesis or responsiveness using the INO promoter from A. thaliana, which is expressed in the outer layer of the integuments during early stages of ovule development. We compared these to fruit where the same coding regions were expressed from the DeFH9 promoter which is expressed in carpel tissues during early stages of ovule development. Expression of auxin synthesis or responsiveness genes by both of these promoters produced seedless parthenocarpic tomato fruit. We compared fruit samples using the Affymetrix tomato GeneChip (GPL4741) to determine how gene regulation and expression differed between wild-type and transgenic fruit. Keywords: genetic modification
2009-08-31 | GSE14358 | GEO
Project description:To evaluate the role of seeds in fruit quality, we induced parthenocarpy in tomato by regulating ovule-specific auxin synthesis or responsiveness using the INO promoter from A. thaliana, which is expressed in the outer layer of the integuments during early stages of ovule development. We compared these to fruit where the same coding regions were expressed from the DeFH9 promoter which is expressed in carpel tissues during early stages of ovule development. Expression of auxin synthesis or responsiveness genes by both of these promoters produced seedless parthenocarpic tomato fruit. We compared fruit samples using the Affymetrix tomato GeneChip (GPL4741) to determine how gene regulation and expression differed between wild-type and transgenic fruit. Experiment Overall Design: Wild-type fruit with seeds was compared with transgenic lines INO-IaaM, DefH9-IaaM, INO-RolB, and DefH9-RolB. To find genes with seed-specific expression, we also compared the control with wild-type fruit from which seeds had been manually removed. We had three biological replicates for each treatment and control except DefH9-RolB, for which only two replicates were available. Each CEL file from the microarray represents one plant from each line.
2009-09-15 | E-GEOD-14358 | biostudies-arrayexpress
Project description:Tomato fruit ripening is associated with a dramatic increase in susceptibility to the fungal pathogen Botrytis cinerea, the causal agent of gray mold. Mature green fruit, prior to ripening, are largely resistant to B. cinerea, whereas red fruit, at the end of ripening, are susceptible to B. cinerea infection. We used microarrays to detail the gene expression changes that are induced by B. cinerea when tomato fruit at unripe and ripe stages are infected. Experiment Overall Design: Tomato fruit at mature green and red ripe stages were wound inoculated with a water suspension of B. cinerea conidia. Twenty four hours post inoculation fruit pericarp and epicarp tissue around and including the inoculation sites was collected and the total RNA extracted. Total RNA was also collected from healthy and mock inoculated fruit.
2009-06-01 | E-GEOD-14637 | biostudies-arrayexpress
Project description:Tomato fruit ripening is associated with a dramatic increase in susceptibility to the fungal pathogen Botrytis cinerea, the causal agent of gray mold. Mature green fruit, prior to ripening, are largely resistant to B. cinerea, whereas red fruit, at the end of ripening, are susceptible to B. cinerea infection. We used microarrays to detail the gene expression changes that are induced by B. cinerea when tomato fruit at unripe and ripe stages are infected. Keywords: plant responses to pathogens
2009-05-22 | GSE14637 | GEO
Project description:To investigate the effects of transgenic lines L6 and L7 tomato fruits on total expression profile of MCF-7 breast cancer cells, we treated MCF-7 cells with 1 ug/ml of tomato fruit extract for 24 hours and compare it with wild type tomato fruit extract Objectives for this study included the identification of genes that were up or down-regulated at the transcriptional level in MCF-7 cells treated with transgenic lines L6 and L7 tomatofruit extract and compare it to wild type tomato fruit extract.
2017-06-12 | GSE94548 | GEO
Project description:Tomato phototropin1 mutant exhibits deep red color in the ripe fruits compared to the wild type. However, the mechanisms governing this intense fruit coloration in the mutant are largely unknown. Therefore, a proteomic approach combined with carotenoid profiling and carotenogenic gene expression was used to decipher the carotenogenesis in a tomato phototropin1 mutant with S. lycopersicum, cv. Ailsa Craig (tomato).
2021-02-24 | PXD018150 | Pride
Project description:In the present study, we demonstrated that application of CaCl2 to ‘Micro Tom’ tomato fruit (mature green stage) delayed fruit senescence and mature.
2017-09-28 | GSE73520 | GEO
Project description:Early fruit development is crucial for crop production in tomato. After fertilization, the ovary undergoes a cell division and a cell expansion stages before maturation. Although the roles of regulatory signals such as hormone and carbohydrate during early fruit development have been studied, the spatial distribution and the sequential initiation of these regulatory signals is still poorly understood. Using the cultivated tomato “Moneymaker” as materials, we analyzed the transcriptome of the ovule and the ovary wall dissected from the different stages of the early developing fruits. These datasets provide us the whole picture about the spatial and temporal signal distribution of fruit formation which has not been studied in such a detailed manner. Our results suggest that the hormone signal was initiated in both ovule and ovary wall after fertilization. After that, the different signals were activated in ovule and ovary wall due to their distinct developmental processes. By analyzing the global expression profiling of hormone related genes, we found that the auxin might be synthesized in both ovule and ovary wall after fertilization. The expression pattern of sugar related genes revealed the different carbohydrate metabolism events occurred in ovule and ovary wall. At last, we identified a gene showed tissue and stage specific expression pattern and localized in previously reported fruit weight locus which might be selected during tomato breeding.
2018-01-01 | GSE74827 | GEO