The interactome and proteomic responses of ALKBH7 in cell lines by in-depth proteomics analysis.

IF 2.1 3区生物学 Q3 BIOCHEMICAL RESEARCH METHODS Proteome Science Pub Date : 2019-12-29 eCollection Date: 2019-01-01 DOI:10.1186/s12953-019-0156-x

Shu Meng, Shaohua Zhan, Wanchen Dou, Wei Ge

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引用次数: 6

Abstract

Background: ALKBH7 is a mitochondrial protein, involved in programmed necrosis, fatty acid metabolism, cell cycle regulation, and prostate cancer disease. However, the exact roles of ALKBH7 and the underlying molecular mechanisms remain mysterious. Thus, investigations of the interactome and proteomic responses of ALKBH7 in cell lines using proteomics strategies are urgently required.

Methods: In the present study, we investigated the interactome of ALKBH7 in mitochondria through immunoprecipitation-mass spectrometry/mass spectrometry (IP-MS/MS). Additionally, we established the ALKBH7 knockdown and overexpression cell lines and further identified the differentially expressed proteins (DEPs) in these cell lines by TMT-based MS/MS. Two DEPs (UQCRH and HMGN1) were validated by western blotting analysis.

Results: Through bioinformatic analysis the proteomics data, we found that ALKBH7 was involved in protein homeostasis and cellular immunity, as well as cell proliferation, lipid metabolism, and programmed necrosis by regulating the expression of PTMA, PTMS, UQCRH, HMGN1, and HMGN2. Knockdown of ALKBH7 resulted in upregulation of UQCRH and HMGN1 expression, and the opposite pattern of expression was detected in ALKBH7 overexpression cell lines; these results were consistent with our proteomics data.

Conclusion: Our findings indicate that the expression of UQCRH and HMGN1 is regulated by ALKBH7, which provides potential directions for future studies of ALKBH7. Furthermore, our results also provide comprehensive insights into the molecular mechanisms and pathways associated with ALKBH7.

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通过深入的蛋白质组学分析ALKBH7在细胞系中的相互作用和蛋白质组学反应。

背景:ALKBH7是一种线粒体蛋白，参与程序性坏死、脂肪酸代谢、细胞周期调节和前列腺癌疾病。然而，ALKBH7的确切作用和潜在的分子机制仍然是一个谜。因此，迫切需要利用蛋白质组学策略研究ALKBH7在细胞系中的相互作用和蛋白质组学反应。方法:采用免疫沉淀-质谱/质谱(IP-MS/MS)技术研究ALKBH7在线粒体中的相互作用。此外，我们建立了ALKBH7敲低和过表达细胞系，并利用基于tmt的质谱联用技术进一步鉴定了这些细胞系中的差异表达蛋白(DEPs)。2个DEPs (UQCRH和HMGN1)经western blotting分析验证。结果:通过蛋白质组学数据的生物信息学分析，我们发现ALKBH7通过调节PTMA、PTMS、UQCRH、HMGN1、HMGN2的表达，参与蛋白稳态和细胞免疫，以及细胞增殖、脂质代谢和程序性坏死。敲低ALKBH7可导致UQCRH和HMGN1表达上调，而ALKBH7过表达细胞系中则出现相反的表达模式;这些结果与我们的蛋白质组学数据一致。结论:我们的研究结果表明，UQCRH和HMGN1的表达受到ALKBH7的调控，这为ALKBH7的未来研究提供了可能的方向。此外，我们的研究结果还提供了与ALKBH7相关的分子机制和途径的全面见解。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Proteome Science 生物-生化研究方法

CiteScore

2.90

自引率

0.00%

发文量

审稿时长

4.5 months

期刊介绍： Proteome Science is an open access journal publishing research in the area of systems studies. Proteome Science considers manuscripts based on all aspects of functional and structural proteomics, genomics, metabolomics, systems analysis and metabiome analysis. It encourages the submissions of studies that use large-scale or systems analysis of biomolecules in a cellular, organismal and/or environmental context. Studies that describe novel biological or clinical insights as well as methods-focused studies that describe novel methods for the large-scale study of any and all biomolecules in cells and tissues, such as mass spectrometry, protein and nucleic acid microarrays, genomics, next-generation sequencing and computational algorithms and methods are all within the scope of Proteome Science, as are electron topography, structural methods, proteogenomics, chemical proteomics, stem cell proteomics, organelle proteomics, plant and microbial proteomics. In spite of its name, Proteome Science considers all aspects of large-scale and systems studies because ultimately any mechanism that results in genomic and metabolomic changes will affect or be affected by the proteome. To reflect this intrinsic relationship of biological systems, Proteome Science will consider all such articles.