Dataset Information

Comparative phosphoproteomic and acetylated proteomic analysis of intestine regeneration in the sea cucumber Apostichopus japonicus

ABSTRACT: Sea cucumbers have a striking capacity to regeneratemost of their viscera after evisceration, which has drawn theinterest ofmany researchers. In this study, we perform quantitative phosphoproteomics proteomic to analyze the proteinphosphorylation and acetylation changes between regenerative intestine at 3 days post evisceration (dpe) and normal intestine (intact intestine in normal situation) in A.japonicus. Altogether, 2,584 phosphorylation sites in 1,531 proteins were identified, among which 1862 phosphorylation site in 1169 proteins were quantified. When quantitative ratio of phosphorylation sites over 1.5 was considered up-regulation while quantitative ratio of phosphorylation sites below 0.67 (1/1.5) was considered as down-regulation. The amount of the up-regulatedphosphorylation quantified sites and proteins were 127 and 113; the amount of the down-regulatedphosphorylation quantified sites and proteins were 38 and 34. Totally, 886acetylation sites in 555 proteins were identified, among which 712acetylation site in 470 proteins were quantified (Table 1). When quantitative ratio of acetylation sites over 1.20 was considered up-regulation while quantitative ratio of acetylation sites below 0.83 (1/1.2) was considered as down-regulation. The amount of the up-regulatedacetylation quantified sites and proteins were 130 and 101; the amount of the down-regulatedacetylation quantified sites and proteins were 211 and 150.Our results suggest that intestine regeneration constitutes a complex lifeactivity regulated by the cooperation of various biological processes, including cytoskeletal changes, protein synthesis, signal recognition and transduction,energy production and conversion, and substance transport andmetabolism.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Stichopus Japonicus (sea Cucumber)

TISSUE(S): Intestine

SUBMITTER: Rachel Green

LAB HEAD: Lina Sun

PROVIDER: PXD008374 | Pride | 2018-10-22

REPOSITORIES: Pride

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Publications

Comparative Phospho- and Acetyl Proteomics Analysis of Posttranslational Modifications Regulating Intestine Regeneration in Sea Cucumbers.

Sun Lina L Lin Chenggang C Li Xiaoni X Xing Lili L Huo Da D Sun Jingchun J Zhang Libin L Yang Hongsheng H

Frontiers in physiology 20180703

Sea cucumbers exposed to stressful circumstances eviscerate most internal organs, and then regenerate them rapidly under favorable environments. Reversible protein phosphorylation and acetylation are major modifications regulating protein function. Herein, for the first time, we perform quantitative phospho- and acetyl proteomics analyses of intestine regeneration in a sea cucumber species <i>Apostichopus japonicus</i>. We identified 1,862 phosphorylation sites in 1,169 proteins, and 712 acetyla ...[more]

PMID: 30018572

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Project description:Background & Aims: Hierarchical organization of intestine relies on their stem cells by self-renew and producing committed progenitors. Although signals like Wnt are known to animate the continued renewal by maintaining intestinal stem cells (ISCs) activity, molecular mechanisms especially E3 ubiquitin ligases that modulate ISCs ‘stemness’ and supportive niche have not been well understood. Here, we investigated the role of Cullin 4B (Cul4b) in regulating ISC functions. Methods: We generated mice with intestinal epithelial-specific disruption of Cul4b (pVillin-cre; Cul4bfn/Y), inducible disruption of Cul4b (Lgr5-creERT2; Cul4bfn/Y, CAG-creERT2; Cul4bfn/Y) and their control (Cul4bfn/Y). Intestinal tissues were analyzed by histology, immunofluorescence, RNA sequencing and mass spectrum. Intestinal organoids deprived from mice with pVillin-Cre; Cul4bfn/Y, Lgr5-Cre; Cul4bfn/Y, Tg-Cul4b and their controls were used in assays to measure intestinal self-renewal, proliferation and differentiation. Wnt signaling and intestinal markers were analyzed by immunofluorescence and immunoblot assays. Differential proteins upon Cul4b ablation or Cul4b-interacting proteins were identified by mass spectrometry. Results: Cul4b specifically located at ISCs zone. Block of Cul4b impaired intestinal homeostasis maintenance by reduced self-renewal and proliferation. Transcriptome analysis revealed that Cul4b-null intestine lose ISC characterization and showed disturbed ISC niche. Mechanistically, reactivated Wnt pathway could recover intestinal dysfunction of Cul4b knockout mice. Analysis of differential total and ubiquitylated proteins uncovered the novel targeting substrate of Cullin-Ring ubiquitin ligase 4b (CRL4b), immunity-related GTPase family M member 1 (Irgm1) in intestine. Decreased Irgm1 rescued abnormally interferon signaling, overemphasized autophagy and downstream phosphate proteins in Cul4b knockout mice. Conclusion: We conclude that Cul4b is essential for ISC self-renewal and Paneth cell function by targeting Irgm1 and modulating Wnt signaling. Our results demonstrate that Cul4b is a novel ISC stemness and niche regulator.

Dataset Information

Comparative phosphoproteomic and acetylated proteomic analysis of intestine regeneration in the sea cucumber Apostichopus japonicus

Publications

Comparative Phospho- and Acetyl Proteomics Analysis of Posttranslational Modifications Regulating Intestine Regeneration in Sea Cucumbers.

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