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Quantitative proteomics and transcriptomics analysis of fruit development and ripening in watermelon

ABSTRACT: Here, we used RNA sequencing and tandem mass tag (TMT)–based quantitative proteomics technology to study the comprehensive mRNA and protein expression changes during fruit development and ripening in watermelon. A total of 6,226 proteins were quantified, and the number of quantitative proteins is the largest in fruit proteome to date, comparable to studies in model organisms such as rice and Arabidopsis. Omics analysis showed that smaller changes occurred in protein abundance compared to mRNA abundance. Furthermore, protein and transcript abundance were poorly correlated, and the correlation coefficients decreased during fruit development and ripening. Our comprehensive transcriptomic and proteomic data offer a valuable resource for watermelon research, and provide new insights into the molecular mechanisms underlying complex regulatory networks of fruit ripening in watermelon.

INSTRUMENT(S): Q Exactive Plus

ORGANISM(S): Citrullus Lanatus

TISSUE(S): Egg Yolk

SUBMITTER: yu yongtao

LAB HEAD: Yongtao yu

PROVIDER: PXD024490 | Pride | 2022-04-10

REPOSITORIES: Pride

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			Action	DRS
	FA259TQ01_1.raw	Raw
	FA259TQ01_2.raw	Raw
	FA259TQ01_3.raw	Raw
	FA259TQ01_4.raw	Raw
	FA259TQ01_5.raw	Raw

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Comparative proteomic analysis provides novel insights into the regulation mechanism underlying the fruit ripening process in papaya (Carica papaya L.)

Project description:Papaya (Carica papaya L.) is a typical climacteric fruit, undergoing massive physico-chemical changes during ripening. Although papaya is widely cultivated and consumed, few studies have characterized the variations in metabolism during its ripening process at the proteasome level. Using an integrated approach involving Tandem Mass Tag labeling and liquid chromatography–mass spectrometry analysis, proteomes of papaya fruit at different ripening stages were investigated. A total of 3220 proteins were identified, of which 2818 were quantified. The differential accumulated proteins (DAPs) exhibited various biological functions and diverse subcellular localizations. Among the DEPs, most of the pathogen defense-related proteins were down-regulated, suggesting that disease resistance decreased during the ripening process. The Kyoto Encyclopedia of Genes and Genomes enrichment analysis revealed that various metabolic pathways were significantly altered, particularly in flavonoid and fatty acid metabolisms. The up-regulation of several flavonoid biosynthesis-related proteins may provide more raw materials for pigment biosynthesis, accelerating the color variation of papaya fruit. Thus, variations in the fatty acid metabolism-related enzymes were investigated. For example, a lipoxygenase, which catalyzes the conversion of ACC to ethylene, was significantly induced, suggesting a cross-talk between the lipoxygenase-mediated fatty acid metabolism and the hormone-controlled fruit ripening in papaya. Furthermore, the contents of several important fatty acids were determined, and increased unsaturated fatty acids may be associated with papaya fruit volatile formation. Our data may give an intrinsic explanation of the variations in metabolism during the ripening process of papaya fruit and serve as a comprehensive resource for investigating the regulation mechanism involved.

2019-11-12 | PXD008871 | Pride

Mass spectrometry analysis of RSV-induced RAW264.7 cells

Project description:In order to further explore the expression of proteins in RSV-infected macrophages, RSV type-L19 was used to stimulate RAW264.7 cells, and then mass spectrometry was conducted to detect the expression of different proteins after RSV infection. The results showed that there were different expression of proteins in RSV activated and inactive RAW264.7 cells.

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Quantitative proteomic analysis of pseudomonas aeruginosa samples

Project description:Ionizing irradiation kills pathogens by destroying nucleic acids while retaining the immunogenicity of pathogen proteins. However, the overall proteome of bacteria exposed to X-ray irradiation still remain unclear. This experiment was aimed to investigate the proteome changes of the laboratory Pseudomonas aeruginosa PAO1 strain after exposure to X-ray irradiation. A total of 2963 proteins were identified in this study, of which 2599 proteins contained quantitative information. If the differential expression change threshold is 2 times, and the statistical test t-test p-value <0.05 is the significance threshold, then among the quantified proteins, the expression of 48 proteins was up-regulated and 8 protein expression was down-regulated. Based on the above data, we performed a systematic bioinformatics analysis of all identified proteins, and performed functional classification, functional enrichment, and clustering analysis based on functional enrichment for all differentially expressed proteins. Combined with the above information, it provides a reference direction for further investigation in the biological effect on P. aeruginosa PAO1 and its MV formation under X-ray irradiation.

2020-12-14 | PXD019035 | Pride

Proteome-Wide Analyses Reveal Diverse Functions of Acylation Proteins in Neurospora crassa

Project description:Quantitative acetyl-proteomics, a newly identified post-translational modification, is known to regulate transcriptional activity in different organisms. Neurospora crassa is a model ascomycete fungus maintained for biochemistry and molecular biology research; however, extensive studies of the functions of its acylation proteins have yet to be performed. In this study, using LC-MS/MS qualitative proteomics strategies, we identified 1909 modification sites on 940 proteins in N. crassa and analysed the functions of these proteins using GO enrichment, KEGG pathway, and subcellular location experiments. We classified the acetylation protein involvement in diverse pathways, and protein-protein interaction (PPI) network analysis further demonstrated that these proteins participate in diverse biological processes. In summary, our study comprehensively profiles the crosstalk of modified sites, and PPI among these proteins may form a complex network with both similar and distinct regulatory mechanisms, providing improved understanding of their biological functions in N. crassa.

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Genotyping, generation and lysine 2-hydroxyisobutyrylation identification of the first human autosomal dominant osteopetrosis type II specific induced pluripotent stem cells

Project description:Background: Autosomal dominant osteopetrosis type II (ADO2) is a rare human genetic disease that has been broadly studied as an important osteopetrosis model; however, there are no disease-specific induced pluripotent stem cells (ADO2-iPSCs) that may be valuable for understanding the pathogenesis and may be a potential source of cells for autologous cell therapy. Methods: To generate the first human ADO2-iPSCs from a Chinese family with ADO2 and to identify their characteristics, blood samples were collected from the proband and his parents and were used for genotyping by whole-exome sequencing (WES); the urine-derived cells of the proband were reprogrammed with episomal plasmids that contained transcription factors, such as KLF4, OCT4, c-MYC, and SOX2. The proteome-wide analysis of lysine 2-hydroxyisobutyrylation in the ADO2-iPSCs and control cell lines was performed by high-resolution LC-MS/MS and a bioinformatics analysis. Results: WES with filtering strategies identified a mutation in CLCN7 (R286W) in the proband and his father, which was absent in the proband’s mother and the healthy controls; this was confirmed by Sanger sequencing. The ADO2-iPSCs were successfully generated, which carried the normal male karyotype (46, XY) and carried the mutation of CLCN7 (R286W); the ADO2-iPSCs positively expressed alkaline phosphatase and other surface markers; and no vector and transgene was detected. The ADO2-iPSCs could differentiate into all three germ cell layers, both in vitro and in vivo. Our proteomic profiling detected 7, 405 proteins and revealed 3,684 2-hydroxyisobutyrylated sites in 1,036 proteins in the ADO2-iPSCs. Conclusions: Our data indicated that mutation CLCN7 (R286W) may be a cause of the osteopetrosis family. The generated vector-free and transgene-free ADO2-iPSCs with identified lysine 2-hydroxyisobutyrylation may be valuable for personalized and cell-based regenerative medicine in the future.

2022-02-15 | PXD014227 | Pride

Proteomic Analysis of Liver in Diet-induced Hyperlipidemic Mice under Fructus Rosa roxburghii action

Project description:Fructus Rosae Roxburghii (FRR) has been considered as edible and medicinal fruit possessing antiatherosclerotic effect, but the mechanism is still unclear. Hyperlipidemia (HLP) is material basis for atherosclerosis (AS) formation. Under FRR action, TC, TG, LDL, HDL and ASI in serum were regulated to control level. Differentially expressed proteins in liver were analyzed by using TMT labeling and LC-MS/MS for better understanding the effect and molecular mechanism of FRR on diet-induced hyperlipidemic mice. In total, 4460 proteins were quantified, of which 469 proteins showed dramatic changes between each group. According to molecular functions, 25 differentially co-expressed proteins were divided into five categories: substance metabolism, energy transformation and signal transduction, transcription and translation, immune defense. 15 key proteins involved lipids metabolism, which were identified as Cyp7a1, Cyp3a11, Tm7sf2, COAT2, CSAD, RBP3, Lpin1, Dhrs4, Aldh1b1, GK, Acot 4, TSC22D1, PGFS, EHs, GSTM1. Their altered expression suggested that FRR could maintain the metabolism homeostasis by regulating the metabolism of fatty acids, biosynthesis of BAs and steroids, and production of lipid peroxides (LPOs) in mice. It’s first time potential antiatherosclerotic mechanism of FRR regulating blood lipids was explored from protein level, which is of great significance to explore new drug targets for AS.

2021-01-04 | PXD019962 | Pride

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Project description:Lysine acetylation of proteins is a dynamic and reversible post-translational modification that plays an important role in diverse cellular processes. Botrytis cinerea is the most thoroughly studied necrotrophic species due to its broad host range and huge economic impact. However, to date, little is known about the functions of lysine acetylation in this plant pathogen. In this study, we determined the lysine acetylome of B. cinerea through the combination of affinity enrichment and high-resolution LC-MS/MS analysis. Overall, 1582 lysine acetylation sites in 954 proteins were identified.

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