Proteome analysis of the differential analysis of terpenoids synthesis pathways in Fiucs triloba
Ontology highlight
ABSTRACT:
ORGANISM(S): Ficus Esquiroliana
SUBMITTER: 
Hui Yu
PROVIDER: PXD039978 | iProX | Thu Feb 09 00:00:00 GMT 2023
REPOSITORIES: iProX
Similar Datasets
Project description:We conducted a RNA-Seq analysis of MeJA-treated Chinese cabbage leaf transcriptome. Total 14,619,469 sequence reads were generated to produce 27,461 detected genes, among which 1,451 genes were up-regulated and 991 genes were down-regulated as differentially expressed genes (DEGs) (log2 ratio ≥1, false discovery rate ≤0.001). More than 90% of the DEGs (2,278) were between 1.0- and 3.0-fold (log2 ratio). The most highly represented pathways by 1,674 annotated DEGs were related to “metabolic pathways” (333 members), “ribosome” (314 members), “biosynthesis of secondary metabolites” (218 members), “plant-pathogen interaction” (146 members), and “plant hormone signal transduction” (99 members). Fourteen genes involved in JA biosynthesis pathway were up-regulated. As many as 182 genes for the biosynthesis of several secondary metabolites were induced, and the level of indole glucosinolate was highly increased by MeJA treatment. The genes encoding sugar catabolism and some amino acids synthesis were up-regulated, which could supply structural intermediates and energy for the biosynthesis of secondary metabolites. The results demonstrated a high degree of transcriptional complexity with dynamic coordinated changes in global gene expression of Chinese cabbage in response to MeJA treatment. It expands our understanding of the complex molecular events on JA-induced plant resistance and accumulation of secondary metabolites. It also provides a foundation for further studies on the molecular mechanisms of different pathways in other Brassica crops under MeJA treatment.
2015-12-31 | GSE51363 | GEO
Project description:We conducted a RNA-Seq analysis of MeJA-treated Chinese cabbage leaf transcriptome. Total 14,619,469 sequence reads were generated to produce 27,461 detected genes, among which 1,451 genes were up-regulated and 991 genes were down-regulated as differentially expressed genes (DEGs) (log2 ratio â¥1, false discovery rate â¤0.001). More than 90% of the DEGs (2,278) were between 1.0- and 3.0-fold (log2 ratio). The most highly represented pathways by 1,674 annotated DEGs were related to âmetabolic pathwaysâ (333 members), âribosomeâ (314 members), âbiosynthesis of secondary metabolitesâ (218 members), âplant-pathogen interactionâ (146 members), and âplant hormone signal transductionâ (99 members). Fourteen genes involved in JA biosynthesis pathway were up-regulated. As many as 182 genes for the biosynthesis of several secondary metabolites were induced, and the level of indole glucosinolate was highly increased by MeJA treatment. The genes encoding sugar catabolism and some amino acids synthesis were up-regulated, which could supply structural intermediates and energy for the biosynthesis of secondary metabolites. The results demonstrated a high degree of transcriptional complexity with dynamic coordinated changes in global gene expression of Chinese cabbage in response to MeJA treatment. It expands our understanding of the complex molecular events on JA-induced plant resistance and accumulation of secondary metabolites. It also provides a foundation for further studies on the molecular mechanisms of different pathways in other Brassica crops under MeJA treatment. Transcriptomic analysis of MeJA-treated Chinese cabbage leaf
2015-12-31 | E-GEOD-51363 | biostudies-arrayexpress
Project description:To explore the mechanisms of cotton response to this alkaline stress, we used next-generation sequencing (NGS) technology to study transcriptional changes of cotton under NaHCO3 alkaline stress. A total of 18,230 and 11,177 differentially expressed genes (DEGs) were identified in cotton roots and leaves, respectively. Gene ontology (GO) analysis indicated the enrichment of DEGs involved in various stimuli or stress responses. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that DEGs associated with plant hormone signal transduction, amino acid biosynthesis, and biosynthesis of secondary metabolites were regulated in response to the NaHCO3 stress. We further analyzed genes enriched in secondary metabolic pathways and found that secondary metabolites were regulated to eliminate the reactive oxygen species (ROS) and improve the cotton tolerance to the NaHCO3 stress. In this study, we learned that the toxic effect of NaHCO3 was more profound than that of NaOH at the same pH. Thus, Na+, HCO3- and pH had a great impact on the growth of cotton plant. The novel biological pathways and candidate genes for the cotton tolerance to NaHCO3 stress identified from the study would be useful in the genetic improvement of the alkaline tolerance in cotton.
2022-01-26 | GSE165472 | GEO
Project description:Cold tolerance of crop plants influences survival and productivity under low-temperature conditions. Elucidation of molecular mechanisms underlying low temperature tolerance could be helpful in breeding. In this study, based on transcriptome and metabolomic analysis, we successfully identified a number of candidate genes and metabolites involved in key biological pathways during cold stress response. During cold stress, a total of 22335 differentially expressed genes were detected in each group (093Cvs120C, 093Tvs120T, 093Cvs093T, 120Cvs120T), of which 12978 were up-regulated and 9357 were down-regulated. A total of 18,166 metabolites were detected and 7,670 metabolites were annotated, among which 654 were secondary metabolites with significant differences. Under cold stress, the petC gene in both common bean cultivars was down-regulated, which led to the decrease of photosynthetic efficiency. Transcriptome and metabolome results under cold stress showed that the synthesis pathways of various unsaturated fatty acids including alpha-linolenic acid were significantly up-regulated and their contents were enriched. In addition, leukotriene-A4 hydrolase in the catabolic pathway of 120 arachidonic acid was inhibited under cold stress. Furthermore, the content of arachidonic acid was increased. A variety of amino acids in both 093 and 120 were enriched under cold stress, which was beneficial to the resistance of bean to osmotic stress caused by cold stress. However, in addition to a few amino acids that were enriched together, 093 was mainly positively charged and 120 was negatively charged among the amino acids that were enriched differently. This is an interesting phenomenon that needs to be further studied. In addition, under cold stress, we found that genes in multiple metabolic pathways, including ABA, GA, JA and other hormone metabolism pathways, were differentially expressed in 093 and 120.
2022-01-05 | GSE192891 | GEO
Project description:Despite its necessity, manganese (Mn) can causes phytotoxicity when present in excess. Stylo (Stylosanthes) is a dominant tropical legume with high Mn adaptability, but its Mn tolerance mechanisms are not well documented. This study integrated both physiological and transcriptome analyses of stylo in response to excess Mn toxicity. Results showed that stylo growth was decreased by excess Mn higher than 200 µM, as reflected by reductions in leaf chlorophyll and plant dry weight. Increases in enzyme activities of peroxidase (POD), ascorbate peroxidase (APX) and phenylalanine ammonia-lyase (PAL) and concentrations of secondary metabolites, including total phenols, flavonoids, tannins and anthocyanidins, were observed in stylo leaves at high Mn stress. Transcriptome analysis in stylo leaves resulted in identification of 2,471 up-regulated and 1,623 down-regulated genes under excess Mn toxicity. Among them, a set of differentially expressed genes (DEGs) involved in secondary metabolism, including PAL, chalcone synthase (CHS), chalcone isomerase (CHI) and flavonol synthase (FLS), were up-regulated in stylo under Mn toxicity, which were closely associated with the accumulation of secondary metabolites, suggesting that activation of secondary metabolism and corresponding gene expression might be important for stylo adaptation to Mn toxicity. Furthermore, a group of DEGs encoding transcription factors, such as genes belonged to C2H2 zinc finger transcription factor, WRKY, MYB and AP2 family, may be involved in stylo responses to Mn toxicity. Taken together, this study suggests that enhancing defense response and secondary biosynthesis pathway is adaptive strategy of stylo during Mn exposure, which might be regulated by complex transcriptional regulatory networks.
2020-12-08 | GSE147431 | GEO
Project description:Dissolved oxygen (DO) in cultured water is one of the important environment factor in fish farming. Hypoxic environment affects fish growth, metabolism and immune system. Multi-omics integrative analysis helps to uncover the underlying molecular mechanisms. In this study, the 96h median lethal hypoxia (96h-LH50) for Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) was first analyzed by linear interpolation. We built control (5mg/l) and hypoxic stress (96h-LH50) groups, and extracted the liver tissues for high-throughput transcriptome and metabolome sequencing. The identification and quantification results of metabolites showed that a total of 19656 metabolites had been obtained, of which 10390 were annotated. There were 3028 differentially expressed (DE) metabolites, of which 1596 metabolites were up-regulated and 1432 metabolites were down-regulated. We obtained 2375 DE genes, of which 1201 genes were up-regulated and 1174 genes were down-regulated. We verified 8 DE genes by quantitative real-time PCR. Our finding reveals the changes in metabolites and genes expression of GIFT and facilitate the understanding of regulatory pathways under hypoxic stress, which will help reduce the damage caused by hypoxic stress during culture.
2021-01-12 | GSE146142 | GEO
Project description:Hickory (Carya cathayensis) is a woody plant with high nutritional and economic value, and is widely cultivated in China. It is different from herbaceous plants and undergoes a long vegetative stage before reaching floral transition. Hickory can be cultivated on a large scale using grafting. To reveal the response mechanisms to grafting, we employed a proteomics-based approach to identify differentially expressed proteins during the hickory grafting process. In our study, 3723 proteins were identified and 2518 proteins were quantified. A total of 710 differentially quantified proteins (DQPs) were identified and these were involved in various molecular functional and biological processes. Among these DQPs, 341 were up-regulated and 369 were down-regulated at 7 days after grafting compared to the control. The protein interaction networks of the DQPs indicated that there were two enriched interaction clusters. These were „ribosome‟ and „starch and sucrose metabolism‟. Four auxin-related proteins were down-regulated, which was in agreement with the transcription levels of their encoding genes. The Kyoto Encyclopedia of Genes and Genomes analysis showed that the „Flavonoid biosynthesis‟ pathway was significantly up-regulated. Further experiments verified a significant increase in the total flavonoid contents in scions, which suggested that graft union formation may activate flavonoid biosynthesis to increase the contents of a series of downstream secondary metabolites. This comprehensive analysis provides fundamental information on the candidate proteins and the secondary metabolism pathways involved in the grafting process for hickory.
2018-10-26 | PXD006025 | Pride
Project description:<p>This study integrated transcriptomics and metabolomics to analyse the molecular differences in the skin tissues of perennial long wool type (PT-LCG) and seasonal long wool type (ST-LCG) Liaoning cashmere goats to reveal the regulatory mechanisms underlying their differences in cashmere production. Histological observations showed no significant differences in the secondary hair follicle structure between the two types, but PT-LCG exhibited higher hair follicle activity during the catagen phase. Metabolomics analysis identified 92 differentially expressed metabolites (67 up-regulated and 25 down-regulated), primarily enriched in lipid metabolism, amino acid metabolism and energy metabolism pathways. The up-regulation of 3-hydroxypropionic acid and long-chain fatty acids may promote hair follicle growth through energy supply and membrane synthesis. Transcriptomic analysis revealed 145 differentially expressed genes (28 up-regulated and 117 down-regulated), significantly enriched in lipid metabolism, extracellular matrix (ECM), and inflammation-related pathways such as the PPAR and IL-17 signalling pathway. Multi-omics association analysis uncovered a synergistic regulatory network of ‘metabolite-receptor-gene’, indicating that lipid metabolism, energy supply and ECM remodelling are key factors in maintaining hair follicle activity in PT-LCG. This study provides potential targets for molecular breeding of cashmere goats and offers new insights into the regulatory mechanisms of mammalian hair follicle cycles.</p>
2025-11-27 | MTBLS13406 | MetaboLights
Project description:his study investigates the effects of sodium selenite on the yield, selenium content, and proteomic profile of Pleurotus pulmonarius (P. pulmonarius). Treatment with 2 μg/mL sodium selenite (PP-Se2) resulted in a 17.87% increase in the yield of P. pulmonarius. In contrast, treatment with 10 μg/mL sodium selenate (PP-Se10) caused a 23.58% reduction in yield. The selenium content exhibited a positive correlation with the sodium selenite concentration in the cultivation substrate. Based on data-independent acquisition (DIA) proteomics analysis, it was revealed that PP-Se2 and PP-Se10 contained 141 differential expressed proteins (DEPs) (64 up-regulated and 77 down-regulated) and 129 DEPs (73 up-regulated and 56 down-regulated), respectively. DEPs in PP-Se2 were predominantly involved in carbon metabolism, ribosomes, peroxisomes, and ABC transporters. In contrast, DEPs in PP-Se10 were primarily enriched in the biosynthesis of secondary metabolites and cysteine and methionine metabolism. These results suggest that P. pulmonarius exhibits distinct metabolic response mechanisms to varying levels of selenium treatment, with these pathways potentially being influenced by selenium concentration. These findings help to fill the gap in selenium proteomics research in edible fungi and provide new theoretical insights for the development of selenium-enriched functional foods.
2025-07-22 | PXD065347 | Pride