Dataset Information

Chromosome 11-Centric Human Proteome Project

ABSTRACT: For the analysis of chromosome 11-centric human proteome, we analyzed the human brain hippocampal proteome. The samples from brain tissues were extensively off-gel fractionated by 12 fractions and analyzed by a high resolution mass spectrometer, Orbitrap XL ETD with collision induced dissociation, after LC separation using C18 column.

INSTRUMENT(S): instrument model

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Brain

SUBMITTER: Kyung-Hoon Kwon

LAB HEAD: Jinyoung Kim

PROVIDER: PXD000395 | Pride | 2016-10-10

REPOSITORIES: Pride

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Publications

Chromosome-Based Proteomic Study for Identifying Novel Protein Variants from Human Hippocampal Tissue Using Customized neXtProt and GENCODE Databases.

Hwang Heeyoun H Park Gun Wook GW Kim Kwang Hoe KH Lee Ju Yeon JY Lee Hyun Kyoung HK Ji Eun Sun ES Park Sung-Kyu Robin SK Xu Tao T Yates John R JR Kwon Kyung-Hoon KH Park Young Mok YM Lee Hyoung-Joo HJ Paik Young-Ki YK Kim Jin Young JY Yoo Jong Shin JS

Journal of proteome research 20151116 12

The goal of the Chromosome-Centric Human Proteome Project (C-HPP) is to fully provide proteomic information from each human chromosome, including novel proteoforms, such as novel protein-coding variants expressed from noncoding genomic regions, alternative splicing variants (ASVs), and single amino acid variants (SAAVs). In the 144 LC/MS/MS raw files from human hippocampal tissues of control, epilepsy, and Alzheimer's disease, we identified the novel proteoforms with a workflow including integra ...[more]

PMID: 26549206

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Project description:Sodium chloride is an important ionic-osmotic stressor in bulk and rhizosphere soils. Members of the alphaproteobacterial genus Methylocystis are known to have a low salt tolerance (≤ 1.0% NaCl),despite the fact that these methane oxidizers are soil inhabitants. We therefore tested various amino acids and other well-known osmolytes for their potential to act as a compatible solute or osmoprotectant under otherwise growth-inhibitory NaCl conditions. Besides ornithine, the addition of 10 mM asparagine to the medium had the greatest stress relief effect under severe salinity (1.50% NaCl), leading to a partial growth recovery of strain SC2. The analysis of its exo-metabolome revealed that asparagine was taken up quantitatively. This resulted in an intracellularconcentration of 264 ± 57 mM asparagine, with a certain portion hydrolyzed to aspartate (4.20 ± 1.41 mM). In addition to general and oxidative stress responses, the uptake of asparagine induced 34 major proteome rearrangements related to the KEGG level 2 categories energy metabolism, amino acid metabolism, and cell growth and death. In particular, various proteins involved in cell division (e.g., ChpT, CtrA, PleC, FtsA, FtsH1) and peptidoglycan synthesis showed a positive expression response. Asparagine-derived 13C-carbon was incorporated into nearly all amino acids. Both the exo-metabolome and the 13C-labeling degree suggests that in addition to aspartate, the amino acids glutamate, glycine, serine, and alanine, but also pyruvate and malate, were most crucially involved in the osmoprotective effect of asparagine, with glutamate being a major hub between the central carbon and amino acid pathways. In summary, asparagine induced significant proteome rearrangements, leading to major changes in the flux of central metabolites and free amino acids. In consequence, asparagine acted, in part, as a carbon and nitrogen source for the growth recovery of strain SC2 under severe salinity (1.50% NaCl).

Dataset Information

Chromosome 11-Centric Human Proteome Project

Publications

Chromosome-Based Proteomic Study for Identifying Novel Protein Variants from Human Hippocampal Tissue Using Customized neXtProt and GENCODE Databases.

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