Browse
Submit Data
Databases
API
Help

Dataset Information

113 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparative Proteomic Analysis Reveals Elevated Capacity for Photosynthesis in Polyphenol Oxidase Expression-Silenced Clematis terniflora DC. Leaves

ABSTRACT: Comparitive proteomics on Clematis terniflora leaves with VIGS-CtPPO and VIGS-vector

INSTRUMENT(S): Q Exactive

ORGANISM(S): Clematis Terniflora (sweet Autumn Clematis)

TISSUE(S): Plant Cell, Leaf

SUBMITTER: Xi Chen

LAB HEAD: Jingkui Tian

PROVIDER: PXD011439 | Pride | 2018-12-21

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	VP.HUV-BD.1.msf	Msf
	VP.HUV-BD.1.raw	Raw
	VP.HUV-BD.1.xlsx	Xlsx
	VP.HUV-BD.2.msf	Msf
	VP.HUV-BD.2.raw	Raw

Items per page:

1 - 5 of 36

Publications

Comparative Proteomic Analysis Reveals Elevated Capacity for Photosynthesis in Polyphenol Oxidase Expression-Silenced <i>Clematis terniflora</i> DC. Leaves.

Chen Xi X Yang Bingxian B Huang Wei W Wang Tantan T Li Yaohan Y Zhong Zhuoheng Z Yang Lin L Li Shouxin S Tian Jingkui J

International journal of molecular sciences 20181205 12

Polyphenol oxidase (PPO) catalyzes the o-hydroxylation of monophenols and oxidation of o-diphenols to quinones. Although the effects of PPO on plant physiology were recently proposed, little has been done to explore the inherent molecular mechanisms. To explore the in vivo physiological functions of PPO, a model with decreased PPO expression and enzymatic activity was constructed on <i>Clematis terniflora</i> DC. using virus-induced gene silencing (VIGS) technology. Proteomics was performed to i ...[more]

PMID: 30563128

Similar Datasets

Distinct proteomic profile of extracellular vesicles from peritoneal exudates from WT and CD38-deficient mice 2 weeks after pristane injection (lupus disease model)

Project description:Extracellular vesicles (EVs) are present in all body fluids. Shed by cells, their molecular make-up reflects that of their cell of origin and/or tissue pathological situation. Our working hypothesis was that analyzing the protein composition, protein abundance, and functional clustering of EVs released by peritoneal exudate cells (PECs) in the pristane experimental lupus model would allow us to identify predictive or diagnostic biomarkers that might discriminate the autoimmunity process in lupus from inflammatory reactions and/or normal physiological processes. Three pools of PE-EVs were isolated from pristane-treated mice (WT versus Cd38-/- mice) by qEV size exclusion column methodology (F5-12, F5-10 and F11-12). Protein extracts were analyzed by LC-MS/MS. Protein identification was performed with ProteinScape, and MASCOT data searching using Swiss-Prot database. For relative quantification the emPAI-based method was used. The functional enrichment analysis was based on the latest publicly available data from multiple annotation and ontology resources that can be automatically accessed through ClueGO + CluePedia apps within Cytoscape environment. STRING app and EnrichR tools were also used. Gene Ontology (GO) and signaling pathways enrichment analyses of F5-10 and F11-12 PE-EVs via ClueGO analyses showed that the proteins clustered in functionally distinct GO terms and signaling pathways. Moreover, the predominance of given GO terms in PE-EVs seemed to vary with the extent of the inflammatory/autoimmune reaction to pristane. Compared with the protein content and protein abundance in PECs (mainly Ly6Chi inflammatory monocytes and neutrophils), PE-EVs showed an enrichment in neutrophil-associated functions, in particular in PE-EVs from Cd38-/- mice.

2022-10-20 | PXD035257 | Pride

Integrative proteomic and phosphoproteomic analyses revealed the regulation mechanism of Clematis terniflora DC. response to UV-B stress

Project description:Clematis terniflora DC. is used as traditional herb medicine since ancient China. The active substances in C.terniflora have been confirmed to be effective in treating disease like prostatitis. The UV light radiation is a common environmental factor that damage the plants and has an influence on the primary metabolism and secondary metabolism. Previous researches have shown that ultraviolet B (UV-B) radiation followed by dark stress acting on C.terniflora leaves，resulting in the accumulation of secondary metabolites. An in-depth understanding of how C.terniflora leaves respond to UV-B stress is crucial for improving medicinal plants value. Here, we conducted label-free proteomic and phosphoproteomic to explore the protein changes under UV-B and UV-B combined with dark treatment, respectively. A total of 2839 proteins and 1638 phosphorylated proteins were identified. Integrative omics revealed the photosynthetic system and carbohydrate balance were modulated in both stresses. The phosphoproteomic data indicated that, mitogen-activated protein kinase signaling pathway was triggered, meanwhile, the abundance of phosphorylated proteins related to the osmotic stress were increased under UV-B stress. Differential abundant phosphoproteins from UV-B followed by dark treatment were mainly enriched in response to stimulus including calcium-mediated proteins. This study dissects the impact of UV-B stress on C.terniflora and the plant molecular resistant mechanisms through proteomic and phosphoproteomic in a new sight.

2023-03-11 | PXD038136 | Pride

sRNA sequencing of TRV-infected Nicotiana benthamiana 16c at 29oC

Project description:To investigate how high temperature affects sRNA production during virus induced gene silencing (VIGS), we sequenced sRNAs from Tobacco Rattle Virus (TRV)-infected Nicotiana benthamiana kept at 29°C at an early (1 week post infection) and a late time point (3 weeks post infection). To compare sRNA production between virus induced transcriptional gene silencing (ViTGS) and virus induced post-translational gene silencing (ViPTGS) at 29°C, the N. benthamiana 16c plants were infected with TGS-inducing viruses (TRV-35S and TRV-35-2M) and PTGS-inducing viruses (TRV-GFP and TRV-GFP-2M). TRV-35S is a recombinant TRV containing a 120 nt segment of the 35S promoter. Its derivative, TRV-35S-2M, carrying single nucleotide substitutions (SNS) at every 10 nt within the 120 nt 35S target segment. Same strategy was used to create recombinant TRV-GFP and TRV-GFP-2M targeting GFP coding sequence. According to SNS content, sRNAs from TRV-35S-2M/TRV-GFP-2M infected plants can be separated to yield primary (containing SNSs) and secondary sRNAs (lacking SNSs). Wild Type TRV was used along as viral infection control. Libraries were indexed during PCR amplification (16 cycles) according to the Illumina protocol. See individual sample information for specific index primers used.

2021-06-28 | E-MTAB-9394 | biostudies-arrayexpress

Controlled hydroxylations of diterpenoids allow for plant chemical defense without autotoxicity

Project description:Disturbing the biosynthetic pathway of 17-hydroxylgeranyllinalool diterpene glycosides (HGL-DTGs), including silencing NaCYP736A, caused severe plant autotoxicity. This autotoxicity can be restored by co-silencing the upstream biosynthetic genes, like geranyllinalool synthase (GLS). Through comparing the transcriptome data of EV, VIGS-GLS, VIGS-CYP736A and VIGS-GLS&CYP736A, we tried to figure out the potential mechanism of this autotoxicity.

2020-11-17 | GSE160453 | GEO

Three-dimensional folding and functional organization principles of the Drosophila genome

Project description:Chromosomes are the physical realization of genetic information and thus form the basis for its reading, hindering and propagation. Here we present a high-resolution chromosomal contact map derived from a new genome-wide chromosome conformation capture approach (a simplified version of the Hi-C method) applied to Drosophila embryonic nuclei. The data show that the entire genome is linearly partitioned into well-demarcated physical domains that overlap extensively with active and repressive epigenetic marks. Chromosomal contacts are hierarchically organized between domains. Global modeling of compaction and clustering of domains show that inactive domains are condensed and confined to their chromosomal territories, while active domains reach out of the territory to form remote intra- and inter-chromosomal contacts. One pilot sample, comprising seven paired-end Illumina GA-II lanes; one deep-sequenced sample, comprising seven paired-end Illumina HiSeq lanes

2012-01-20 | E-GEOD-34453 | biostudies-arrayexpress

Expression analysis of gene silenced barley to identify the function of a novel LRR-RLK (leucine-rich repeat receptor-like kinase)

Project description:VIGS (virus-induced gene silencing) was used to silence a putative LRR-RLK, Affy ID Rbaal9i05_at, in barley. Expression patterns in leaves were compared between untreated control leaves, virus treated leaves, VIGS-Rbaal knockdown leaves and VIGS-Rbaal/PDS (phytoene desaturase) co-silenced leaves. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, David L Parrott. The equivalent experiment is BB108 at PLEXdb.] treatment: Untreated Control(3-replications); treatment: Empty Virus (no inserted plant sequences)(3-replications); treatment: Rbaal VIGS(3-replications); treatment: Co-silencing (Rbaal + PDS)(3-replications)

2011-12-03 | E-GEOD-34102 | biostudies-arrayexpress

Expression analysis of gene silenced barley to identify the function of a novel LRR-RLK (leucine-rich repeat receptor-like kinase)

2011-12-03 | GSE34102 | GEO

Pervasive Translation in Mycobacterium tuberculosis

Project description:The vast majority of bacterial open reading frames (ORFs) are identified by automated prediction algorithms. However, these algorithms fail to identify ORFs that deviate from the canonical features of ORFs such as a length of >50 codons, and the presence of an upstream Shine-Dalgarno sequence. Here, we use ribosome profiling approaches to experimentally identify actively translated ORFs in Mycobacterium tuberculosis. Most of the ORFs we identify have not been previously described, indicating that the M. tuberculosis transcriptome is pervasively translated. Moreover, the newly described ORFs are predominantly short, with many encoding proteins of ≤50 amino acids. The codon usage of the newly discovered ORFs suggests that most are not undergoing purifying selection, and hence are unlikely to contribute to cell fitness. Nevertheless, we identify ~90 new ORFs, with a median length of 52 codons, that bear the hallmarks of purifying selection. Thus, our data suggest that pervasive translation of short ORFs serves as a rich source for the evolution of new functional proteins

2021-06-30 | E-MTAB-10695 | biostudies-arrayexpress

Cellulomonas sp. B6 and C. fimi B-402 secretomes xylanases

Project description:We addressed the optimization of the xylanolytic activity in extracellular enzymatic extracts of Cellulomonas sp. B6 and C. fimi B-402 for their subsequent application in lignocellulosic biomass hydrolysis, by culture in several substrates. As demonstrated by secretomic profiling, wheat bran and waste paper resulted to be suitable inducers for the secretion of xylanases of Cellulomonas sp. B6 and C. fimi B-402, respectively. Both strains showed high xylanolytic activity in culture supernatant although Cellulomonas sp. B6 was the most efficient xylanolytic strain.

2021-09-09 | PXD022718 | Pride

Histone acetylation H2BK20ac marks cell-state specific active regulatory elements

Project description:Characterisation of different histone modifications is crucial to understand gene regulation. In order to study the most predictive histone modification for active enhancers we created unbiased set of enhancers and used machine learning approach. Our approach revealed an unconventional histone modification H2BK20ac as most efficient marker of active enhancers. H2BK20ac also showed superior coverage of tissue specific active enhancers in complex invivo samples. Adding H2BK20ac to set of conventional histone modifications lead to identification of new chromatin state which could be active enhancers. H2BK20ac tends to occur only at cell-type specific active promoters and showed higher specificity for related disease mutations than H3K27ac and other histone modifications. Using transient state of BV2 microglia cells after lipopolysaccharide based activation, we found that H2BK20ac also marks cell-state specific cis-regulatory elements. Further analysis using inhibition of TGF-beta pathway in BV2 cells and LPS stimulation, revealed differential patterns of H2BK20ac and H3K27ac at genome locations associated with opposite roles response to stmulation. Our study about H2BK20ac hints about a new mechanism of regulation of cell-type specificity and a distinct mode of action of pathways to maintain balance between cell-responses. Chip-seq of H2BK20ac and other histone modifcation was performed in 3 cell types and embryonic mouse forebrain. The sensitivity for active enhancers was compared for different histone modification ChIP-seq.The level of H2BK20ac at promoters and enhancers was assesed for relationship to cell-type specific expression. H2BK20ac signals were also analysed during cell-state transition when microgila are stimulated by LPS

2016-02-25 | E-GEOD-72886 | biostudies-arrayexpress