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Quantitative Analysis of Global Proteome in Aspergillus Flavus

ABSTRACT: In total, 4,563 protein groups were identified, among which 4128 proteins were quantified. The fold-change cutoff was set when proteins with quantitative ratios above 1.5 or below 1/1.5 are deemed significant. The bioinformatic analyses of protein annotation, functional classification, functional enrichment and cluster analyses were performed as listed below. For detailed information, please read the following report and the attached supplementary data.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Aspergillus Flavus Var. Flavus

TISSUE(S): Whole Body

SUBMITTER: Jones Macke

LAB HEAD: Jones macke

PROVIDER: PXD007706 | Pride | 2018-07-11

REPOSITORIES: Pride

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Publications

Insight into the global regulation of laeA in Aspergillus flavus based on proteomic profiling.

Lv Yangyong Y Lv Ang A Zhai Huanchen H Zhang Shuaibing S Li Lang L Cai Jingping J Hu Yuansen Y

International journal of food microbiology 20180702

In Aspergillus flavus, laeA affects cell morphology and contributes to the production of secondary metabolites (SMs) production including aflatoxin, cyclopiazonic acid, and aflatrem. Here, we investigated the function of this transcription factor by performing proteomics analysis of the wild-type (WT) and ΔlaeA mutant growing on corn. Notably, our proteomics profile confirmed the functions of extracellular hydrolases, conidial hydrophobin, and response to oxidative stress during the induction of ...[more]

PMID: 29990635

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Quantitative Analysis of Global Proteome in Arabidopsis thaliana

Project description:In total, 5,840 protein groups were identified, among which 5,188 proteins were quantified. The fold-change cutoff was set when proteins with quantitative ratios above 1.5 or below 0.667 are deemed significant. Among the quantified proteins, 95 proteins are up-regulated and 155 proteins are down-regulated in group gr1-seedling/WT-seedling.

2019-11-12 | PXD011814 | Pride

Morphological and proteomic analyses in petioles rigidity: evidence towards phenotypic plasticity in sacred lotus for aquatic environment

Project description:Very little is known about the mechanism controlling petiole rigidity in sacred lotus (Nelumbo nucifera Gaertn.). To investigate the mechanism controlling the lotus petiole rigidity, morphological and proteomic analyses were performed. Anatomically, there is a great variation between the petioles of floating and vertical leaves. The number of vascular bundles, ligneous cells and thickness of cell wall were higher in the initial vertical leaf petiole (IVP) compared to the initial floating leaf petiole (IFP). A total of 4855 proteins were quantified through comparative proteomic analysis, among which 421 proteins expressed 1.5 folds higher in IFP and 483 proteins expressed 1.5 folds higher in IVP. Protein function categories indicated hundreds of proteins involved in cell wall organization and biosynthesis, and cell wall assembly. Functional enrichment analysis for the differentially abundant proteins indicated the enrichment of 105 proteins in 6 different pathways, while 43 out the total proteins were enriched in lignin biosynthesis pathway. In consistent with genes and proteins expressions in lignin biosynthesis, the contents of lignin monomers precursors were significantly different in IFP and IVP. These findings support the involvement of lignin in lotus petioles rigidity.

2021-07-29 | PXD009136 | Pride

Proteome-wide identification of in vitro substrates for P. aeruginosa ClpXP

Project description:we treated the cell lysates of ΔclpX mutant with or without P. aeruginosa ClpXP protease and used Label-free quantitative techniques (LFQ) to identify and quantify the proteolytic targets of ClpXP (p.aeruginosa PAO1). As a result, 3338 proteins were identified and 2493 proteins were quantified. The abundance (LFQ intensity) of 44 proteins were decreased (≥1.5-fold, p < 0.05) by the treatment with ClpXP. Moreover, we observed that there are 31 proteins which have valid LFQ intensity values in all the three biological replicates of the control group but not in the experimental group (i.e., ClpXP-treated). These results suggest that exogenously added ClpXP has a profound effect on the abundance of proteins in our in vitro assays and that those 75 proteins may serve as potential substrates for the P. aeruginosa ClpXP.

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ChIP-chip from human and mouse fetal brain

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2015-01-30 | E-GEOD-57358 | biostudies-arrayexpress

Selective mRNA sequestration by OLIGOURIDYLATE BINDING PROTEIN 1 contributes to translational control during hypoxia in Arabidopsis

Project description:Low oxygen stress dynamically regulates the translation of cellular mRNAs as a means of energy conservation in seedlings of Arabidopsis thaliana. Most of the highly hypoxia-induced mRNAs are recruited to polysomes and actively translated, whereas other cellular mRNAs become translationally inactive and are either targeted for stabilization or degradation. Here we identify the involvement of OLIGOURIDYLATE BINDING PROTEIN 1 (UBP1), a triple RNA Recognition Motif protein, in dynamic and reversible aggregation of translationally repressed mRNAs during hypoxia. Mutation or downregulation of UBP1C interferes with seedling establishment and reduces survival of low oxygen stress. By use of messenger ribonucleoprotein immunopurification, we show that UBP1C constitutively binds a subpopulation of mRNAs characterized by U-rich 3M-bM-^@M-^Y-untranslated regions under normoxic conditions. During hypoxia, UBP1C association with non-U-rich mRNAs is enhanced concomitant with its aggregation into microscopically visible cytoplasmic foci, referred to as UBP1 stress granules (SGs). This UBP1C-mRNA association occurs as global levels of protein synthesis decline. Upon reoxygenation, rapid UBP1 SG disaggregation coincides with the return of the stabilized mRNAs to polysomes. The mRNAs that are highly induced and translated during hypoxia largely circumvent UBP1C sequestration. Thus, UBP1 is established as a component of dynamically assembled cytoplasmic mRNPs that sequester mRNAs that are poorly translated during a transient low energy stress. Immunoprecipated RNA associated with Arabidopsis UBP1C (IP) was compared with total cellular RNA from light (L), mock dark (D), 2 h hypoxia, and 2 h hypoxia + 20 min reoxygenation treated samples with duplicate hybridizations to the Affymetrix ATH1 Genechip array.

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Phosphoproteome analysis of petunia corolla treated with ethylene and air

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Selection for improved energy efficiency and drought tolerance in canola results in distinct transcriptome and epigenome changes

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the analysis of sus scrofa serum LC-MS/MS after african swine fever virus infection

Project description:African swine fever (ASF) is the most dangerous disease of pigs and causes enormous economic losses in the global pig industry. However, the mechanism of ASF virus (ASFV) infection is unclear. Hence, we wanted to understand the host response mechanism upon ASFV infection. We analyzed the differentially expressed proteins (DEPs) between ASFV-infected and un-infected serum samples using quantitative proteomics. Setting the p-value < 0.05 and |log2 (fold change)| > 1.5, we identified 173 DEPs, including 57 upregulated and 116 downregulated proteins, which belonged to various biological processes and pathways according to the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses. The enriched pathways include the immune system, metabolism, and inflammation.

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