Dataset Information

Characterization of the acetylome associated with rapamycin-induced autophagy in HeLa cells

ABSTRACT: Autophagy is a lysosomal-mediated catabolic process that degrades cytoplasmic components to help maintain cellular homeostasis and cell survival during exposure to stress. Lysine acetylation is a reversible post-translational modification that plays an important role in the regulation of diverse cellular processes.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: zhou lianqi

LAB HEAD: Shiping Ding

PROVIDER: PXD005793 | Pride | 2019-01-02

REPOSITORIES: Pride

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Publications

Comprehensive Analysis of Lysine Acetylome Reveals a Site-Specific Pattern in Rapamycin-Induced Autophagy.

Zhou Zhuo Z Chen Yu Y Jin Mengqi M He Jianqin J Guli Ayiding A Yan Chunlan C Ding Shiping S

Journal of proteome research 20190110 3

Protein acetylation reportedly acts as a key regulator of autophagy. However, up to now, the relationship between acetylome and autophagy has remained unclear. Here stable isotope labeling of amino acids in cell culture and high-throughput quantitative mass spectrometry were used to perform an acetylome analysis of rapamycin-induced autophagy in vitro. Our data revealed that 2135 sites were quantified on 1081 proteins. During autophagy, 421 sites were significantly regulated on 296 proteins, wit ...[more]

PMID: 30592415

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Project description:Metagenome-assembled genomes (MAGs) have revealed the existence of novel bacterial and archaeal groups and provided insight into their genetic potential. However, metagenomics and even metatranscriptomics cannot resolve how the genetic potential translates into metabolic functions and physiological activity. Here, we present a novel approach for the quantitative and organism-specific assessment of the carbon flux through microbial communities with stable isotope probing-metaproteomics and integration of temporal dynamics in 13C incorporation by Stable Isotope Cluster Analysis (SIsCA). We used groundwater microcosms labeled with 13CO2 and D2O as model systems and stimulated them with reduced sulfur compounds to determine the ecosystem role of chemolithoautotrophic primary production. Raman microspectroscopy detected rapid deuterium incorporation in microbial cells from 12 days onwards, indicating activity of the groundwater organisms. SIsCA revealed that groundwater microorganisms fell into five distinct carbon assimilation strategies. Only one of these strategies, comprising less than 3.5% of the community, consisted of obligate autotrophs (Thiobacillus), with a 13C incorporation of approximately 95%. Instead, mixotrophic growth was the most successful strategy, and was represented by 12 of the 15 MAGs expressing pathways for autotrophic CO2 fixation, including Hydrogenophaga, Polaromonas and Dechloromonas, with varying 13C incorporation between 5% and 90%. Within 21 days, 43% of carbon in the community was replaced by 13C, increasing to 80% after 70 days. Of the 31 most abundant MAGs, 16 expressed pathways for sulfur oxidation, including strict heterotrophs. We concluded that chemolithoautotrophy drives the recycling of organic carbon and serves as a fill-up function in the groundwater. Mixotrophs preferred the uptake of organic carbon over the fixation of CO2, and heterotrophs oxidize inorganic compounds to preserve organic carbon. Our study showcases how next-generation physiology approach like SIsCA can move beyond metagenomics studies by providing information about expression of metabolic pathways and elucidating the role of MAGs in ecosystem functioning.

Dataset Information

Characterization of the acetylome associated with rapamycin-induced autophagy in HeLa cells

Publications

Comprehensive Analysis of Lysine Acetylome Reveals a Site-Specific Pattern in Rapamycin-Induced Autophagy.

Similar Datasets

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