Dataset Information

Endogenous, in vivo, and site-specific characterization of the SUMO architecture across species and organs

ABSTRACT: Small ubiquitin-like modifiers (SUMOs) are post-translational modifications that play crucial roles in most cellular processes. While methods exist to study exogenous SUMOylation, large-scale characterization of endogenous SUMO has remained technically daunting. Here, we describe a proteomics approach facilitating system-wide and in vivo identification of lysines modified by endogenous and native SUMO2/3. We identified 14,869 endogenous SUMO sites in human cells during heat stress and proteasomal inhibition, and mapped 1,963 SUMO sites across eight mouse tissues; brain, heart, kidney, lung, liver, muscle, spleen, and testis. Quantification of the SUMO equilibrium highlighted striking differences in SUMO metabolism, between cells and tissues. Targeting preferences of SUMO varied across different organ types, coinciding with markedly differential SUMOylation states of all enzymes involved in the SUMO conjugation cascade. Collectively, our systemic investigation details the SUMOylation architecture across species and organs and provides a resource of endogenous SUMOylation sites on factors important in organ-specific functions and disease.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Homo Sapiens (human) Mus Musculus (mouse)

TISSUE(S): Spleen, Heart, Testis, Brain, Skeletal Muscle, Liver, Lung, Permanent Cell Line Cell, Cell Culture, Kidney

SUBMITTER: Ivo Hendriks

LAB HEAD: Michael Lund Nielsen

PROVIDER: PXD008003 | Pride | 2018-06-26

REPOSITORIES: Pride

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Publications

Site-specific characterization of endogenous SUMOylation across species and organs.

Hendriks Ivo A IA Lyon David D Su Dan D Skotte Niels H NH Daniel Jeremy A JA Jensen Lars J LJ Nielsen Michael L ML

Nature communications 20180625 1

Small ubiquitin-like modifiers (SUMOs) are post-translational modifications that play crucial roles in most cellular processes. While methods exist to study exogenous SUMOylation, large-scale characterization of endogenous SUMO2/3 has remained technically daunting. Here, we describe a proteomics approach facilitating system-wide and in vivo identification of lysines modified by endogenous and native SUMO2. Using a peptide-level immunoprecipitation enrichment strategy, we identify 14,869 endogeno ...[more]

PMID: 29942033

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Project description:Tuberculosis remains a major cause of death from an infectious disease worldwide, yet only 10% of people infected with Mycobacterium tuberculosis develop disease. Defining both necessary and sufficient immunologic determinants of protection remains a great scientific challenge. Analysis of peripheral blood gene expression profiles of active tuberculosis patients has identified correlates of risk for disease or pathogenesis. We sought to identify human potential candidate markers of host defense by studying gene expression profiles of macrophages, cells which, upon infection by M. tuberculosis, can mount an antimicrobial response. Weighted gene co-expression network analysis revealed an association between the cytokine, IL-32, and the vitamin D antimicrobial pathway in a network of IFN-γ and IL-15 induced ‘defense response’ genes. IL-32 was sufficient for induction of the vitamin D-dependent antimicrobial peptides, cathelicidin and DEFB4, and generation of antimicrobial activity in vitro, dependent on the presence of adequate 25-hydroxyvitamin D. The IL-15 induced ‘defense response’ macrophage gene network was integrated with ranked pairwise comparisons of gene expression from five different clinical data sets of latent vs. active tuberculosis or healthy controls, and a co-expression network derived from gene expression in patients with tuberculosis undergoing chemotherapy. Together, these analyses identified eight common genes, including IL-32, as molecular markers of latent tuberculosis and the IL-15 induced gene network. Inferring that maintaining M. tuberculosis in a latent state and preventing transition to active disease represents host resistance, we believe these results identify IL-32 as one functional marker and potential correlate of protection against active tuberculosis. Adherent peripheral blood monuclear cells were derived by Ficoll-Hypaque from the whole blood of four healthy donors. Cells adhered to tissue culture-treated plates for 2 h in 1% Fetal Bovine Serum (FBS) in RPMI. Cells were washed then stimulated with IL-10 (10ng/ml), IL-15 (10ng/ml) (R&D Systems), or IL-4 (1U/ml) in RPMI 1640 supplemented with 10% FBS at 37°C, 5% CO2. Cells were harvested at 6 h and 24 h after stimulation and monocytes purified by CD14 microbeads (Miltenyi Biotec) for a confirmed monocyte purity of at least 90%. RNA from purified monocytes extracted by Trizol and purified by Qiagen RNeasy Kit. RNA probe and microarray performed by UCLA Clinical Microarray Core using Ambion labeling kit and Affymetrix Human U133 Plus 2.0 array.

Dataset Information

Endogenous, in vivo, and site-specific characterization of the SUMO architecture across species and organs

Publications

Site-specific characterization of endogenous SUMOylation across species and organs.

Similar Datasets

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