ITRAQ-based proteomic analysis of a chlorophyll-deficient mutant caused by single base change in RPS4 of Chinese cabbage (Brassica campestris L. ssp. pekinensis)
Ontology highlight
ABSTRACT:
ORGANISM(S): Brassica Rapa
SUBMITTER: 
Feng Hui
PROVIDER: PXD020683 | iProX | Mon Aug 03 00:00:00 BST 2020
REPOSITORIES: iProX
Similar Datasets
Project description:Even the latest generation of base editor (BE3) causes unwanted indels and non-C-to-T substitutions, compromising the fidelity of base editing outcome. Here we report a enhanced base editing system. The enhanced base edting system decreased the formation of unintended indels and C-to-A/C-to-G substitutions, and increased the frequency of desired C-to-T substitution, thereby improving both the accuracy and efficiency of base editing.
2017-08-29 | GSE98685 | GEO
Project description:The heme branch of tetrapyrrole biosynthesis contributes to the regulation of chlorophyll levels. However, the molecular mechanism underlying the balance between chlorophyll and heme synthesis remains elusive. Here, we identified a dark green leaf mutant dg, which contains high levels of chlorophyll b, from an ethyl methanesulfonate (EMS) -induced mutant library of Chinese cabbage. The dg phenotype is attributed to a nonsynonymous homozygous mutation in ferrochelatase 2 (BrFC2), leading to an arginine (R) to lysine (K) amino acid substitution in the conserved chlorophyll a/b-binding motif (CAB) of BrFC2. Overexpression of mutated BrFC2 (dBrFC2) in Chinese cabbage results in a pronounced phenotype associated with the dark green leaves, in contrast to transgenic lines overexpressing wild-type BrFC2 with a low-chlorophyll phenotype. Increased dBrFC2 homodimer formation stimulates heme production in dg compared with wildtype BrFC2. Moreover, we found that dBrFC2 interacts with protochlorophyllide oxidoreductase B1 and B2 (BrPORB1 and BrPORB2) to enhance their binding ability to substrate protochlorophyllide (Pchlide), thereby promoting BrPORBs-catalyzed production of chlorophyllide (Chlide) that can be directly converted into chlorophyll. Our results reveal that dBrFC2 is a strong gain-of-function mutation contributing to balancing heme and chlorophyll synthesis via a novel regulatory mechanism in which dBrFC2 promotes BrPORB enzymatic reaction to enhance chlorophyll synthesis.
2022-10-09 | PXD037223 |
Project description:Deoxyuridine (dU) in DNA can result from deamination of cytosine and dUMP misincorporation. The easy single-nucleotide resolution assay for dU are crucial to understanding its role in genome. Herein, we present a new concept of “base substitution” for accurate single-nucleotide resolution profiling of dU. The method termed AI-Seq (Artificial Incorporation of a modified nucleobase for sequencing) was developed using artificial cytosine (N3-C) to replace dU. After the artificial base construction, dU can read as cytosine during polymerase chain reaction assay. AI-seq was validated on synthetic DNA and then applied to the genome of HEK293T cell line. Collectively, the “base substitution” provides a novel approach for generating comprehensive information about the distribution of dU and can be potentially adapted to detect other epigenetic modifications.
2021-03-22 | GSE142071 | GEO
Project description:The leaf of Chinese cabbage is the major place of photosynthesis, the mutation of leaf may directly affect the rate of plant growth and development and the formation of leafy head, and ultimately influence the yield and quality of Chinese cabbage. We identified a developmentally retarded mutant (drm) exhibiting stable inheritance, which was derived from Chinese cabbage DH line âFTâ using a combination of isolated microspore culture and radiation treatment (60Co γ-rays). The drm exhibited slow growth and development at the seedling and heading stages, leading to the production of a tiny, leafy head, as well as chlorophyll-deficient leaves, especially in seedlings. Genetic analysis indicated that the phenotype of drm was controlled by a single recessive nuclear gene. Compared with wild-type line âFTâ, the drmâs chlorophyll content was significantly reduced and its chloroplast structure was abnormal. Moreover, the photosynthetic efficiency and chlorophyll fluorescence parameters were significantly decreased. The changes in leaf color, combined with these altered physiological characters may influence the growth and development of plant, ultimately resulting in the developmentally retarded phenotype of drm. To further understand the molecular regulatory mechanisms of phenotypic differences between âFTâ and drm, comparative transcriptome analysis were performed using RNA-Seq, a total of 338 differentially expressed genes (DEGs) were detected between âFTâ and drm. According to GO and KEGG pathway analysis, a number of DEGs which involved in the chlorophyll degradation and photosynthesis were identified, such as chlorophyllase and ribulose-1,5-bisphosphate carboxylase/oxygenase. In addition, the expression patterns of 12 DEGs, including three chlorophyll degradation- and photosynthesis-related genes and nine randomly selected genes, were confirmed by qRT-PCR. Numerous single nucleotide polymorphisms were also identified, providing a valuable resource for research and molecular marker-assistant breeding in Chinese cabbage. These results contribute to our understanding of the molecular regulatory mechanisms underlying growth and development and lay the foundation for future genetic and functional genomics studies in Chinese cabbage. The RNA from the third true leaves (day 15 to day 24 after the appearance of the third true leaves) of a developmentally retarded mutant (drm) and its wild type âFTâ in Chinese cabbage were sequenced by RNA-Seq, in triplicate.
2016-03-01 | E-GEOD-75464 | biostudies-arrayexpress
Project description:Chlorophyll production involves the synthesis of photoreactive intermediates that are toxic when in excess due to the production of reactive oxygen species (ROS). A novel activation tagged barley mutant is described that results from antisense suppression of a uroporphyrinogen III synthase (Uros) gene, the product of which catalyses the sixth step in the synthesis of chlorophyll and heme. In homozygous mutant plants uroporphyrin(ogen) I accumulates by spontaneous cyclization of hydroxyl methylbilane, the substrate of Uros. Accumulation of this tetrapyrrole intermediate results in photosensitive cell death due to the production of reactive oxygen species. The efficiency of Uros gene suppression is developmentally regulated, being most effective in mature seedling leaves compared with newly emergent leaves. A comparison of RNA from mutant and wild type seedlings grown under 30% and 3% light, shows reduced transcript accumulation of a number of nuclear-encoded photosynthesis genes occurs in the mutant even under 3% light conditions. This is consistent with a retrograde plastid-nuclear signalling mechanism arising from Uros gene suppression. No evidence for a direct signalling role by uroporphyrin I was observed suggesting that nuclear gene transcriptional suppression was mediated by ROS accumulation.
2009-04-23 | GSE11776 | GEO
Project description:Chlorophyll production involves the synthesis of photoreactive intermediates that are toxic when in excess due to the production of reactive oxygen species (ROS). A novel activation tagged barley mutant is described that results from antisense suppression of a uroporphyrinogen III synthase (Uros) gene, the product of which catalyses the sixth step in the synthesis of chlorophyll and heme. In homozygous mutant plants uroporphyrin(ogen) I accumulates by spontaneous cyclization of hydroxyl methylbilane, the substrate of Uros. Accumulation of this tetrapyrrole intermediate results in photosensitive cell death due to the production of reactive oxygen species. The efficiency of Uros gene suppression is developmentally regulated, being most effective in mature seedling leaves compared with newly emergent leaves. A comparison of RNA from mutant and wild type seedlings grown under 30% and 3% light, shows reduced transcript accumulation of a number of nuclear-encoded photosynthesis genes occurs in the mutant even under 3% light conditions. This is consistent with a retrograde plastid-nuclear signalling mechanism arising from Uros gene suppression. No evidence for a direct signalling role by uroporphyrin I was observed suggesting that nuclear gene transcriptional suppression was mediated by ROS accumulation. Two replicates samples were used for barley mutant 70a3 grown under 3% and 2 replicate sample of the mutant grown under 30% light, barley cv Golden Promise was used as the control.
2009-04-23 | E-GEOD-11776 | biostudies-arrayexpress
Project description:Chlorophyll plays critical roles in photosynthetic light harvesting, energy transduction and plant development. In this study, a novel wucai (Brassica campestris L.) germplasm with green outer leaves and yellow inner leaves at the adult stage (W7-2) was used to examine chlorophyll metabolism response to cold acclimation. A green leaf wucai genotype without leaf color changes named W7-1 was selected as the control to evaluate the chlorophyll metabolism changes of W7-2. Compared to W7-1, the contents of chlorophyll a (Chl a) and chlorophyll b (Chl b) in W7-2 were significantly reduced at five developmental stages (13, 21, 29, 37 and 45 days after planting (DAP). An iTRAQ-based quantitative proteomic analysis was carried out at 21 and 29 DAP according to the leaf color changes in both of genotypes. A total of 1409 proteins were identified, of which 218 showed differential accumulations between W7-2 and W7-1 during the two developmental stages.
2019-05-03 | PXD013323 | Pride