Lysine Acetylation in the Proteome of Renal Tubular Epithelial Cells in Diabetic Nephropathy
Diabetic nephropathy is considered one of the most common microvascular complications of diabetes and the pathophysiology involves multiple factors. Progressive diabetic nephropathy is believed to be related to the structure and function of the tubular epithelial cells in the kidney. However, the ro...
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Frontiers Media S.A.
2021-11-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2021.767135/full |
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| author | Jiayi Wan Jiayi Wan Jiayi Wan Jiayi Wan Mingyang Hu Mingyang Hu Mingyang Hu Mingyang Hu Ziming Jiang Ziming Jiang Ziming Jiang Ziming Jiang Dongwei Liu Dongwei Liu Dongwei Liu Dongwei Liu Shaokang Pan Shaokang Pan Shaokang Pan Shaokang Pan Sijie Zhou Sijie Zhou Sijie Zhou Sijie Zhou Zhangsuo Liu Zhangsuo Liu Zhangsuo Liu Zhangsuo Liu |
| author_facet | Jiayi Wan Jiayi Wan Jiayi Wan Jiayi Wan Mingyang Hu Mingyang Hu Mingyang Hu Mingyang Hu Ziming Jiang Ziming Jiang Ziming Jiang Ziming Jiang Dongwei Liu Dongwei Liu Dongwei Liu Dongwei Liu Shaokang Pan Shaokang Pan Shaokang Pan Shaokang Pan Sijie Zhou Sijie Zhou Sijie Zhou Sijie Zhou Zhangsuo Liu Zhangsuo Liu Zhangsuo Liu Zhangsuo Liu |
| author_sort | Jiayi Wan |
| collection | DOAJ |
| description | Diabetic nephropathy is considered one of the most common microvascular complications of diabetes and the pathophysiology involves multiple factors. Progressive diabetic nephropathy is believed to be related to the structure and function of the tubular epithelial cells in the kidney. However, the role of lysine acetylation in lesions of the renal tubular epithelial cells arising from hyperglycemia is poorly understood. Consequently, in this study, we cultured mouse renal tubular epithelial cells in vitro under high glucose conditions and analyzed the acetylation levels of proteins by liquid chromatography-high-resolution mass spectrometry. We identified 48 upregulated proteins and downregulated 86 proteins. In addition, we identified 113 sites with higher acetylation levels and 374 sites with lower acetylation levels. Subcellular localization analysis showed that the majority of the acetylated proteins were located in the mitochondria (43.17%), nucleus (28.57%) and cytoplasm (16.19%). Enrichment analysis indicated that these acetylated proteins are primarily associated with oxidative phosphorylation, the citrate cycle (TCA cycle), metabolic pathways and carbon metabolism. In addition, we used the MCODE plug-in and the cytoHubba plug-in in Cytoscape software to analyze the PPI network and displayed the first four most compact MOCDEs and the top 10 hub genes from the differentially expressed proteins between global and acetylated proteomes. Finally, we extracted 37 conserved motifs from 4915 acetylated peptides. Collectively, this comprehensive analysis of the proteome reveals novel insights into the role of lysine acetylation in tubular epithelial cells and may make a valuable contribution towards the identification of the pathological mechanisms of diabetic nephropathy. |
| first_indexed | 2024-12-14T08:00:32Z |
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| id | doaj.art-c9084f39fab849168b9b2e9d58d2098e |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-14T08:00:32Z |
| publishDate | 2021-11-01 |
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| series | Frontiers in Genetics |
| spelling | doaj.art-c9084f39fab849168b9b2e9d58d2098e2022-12-21T23:10:25ZengFrontiers Media S.A.Frontiers in Genetics1664-80212021-11-011210.3389/fgene.2021.767135767135Lysine Acetylation in the Proteome of Renal Tubular Epithelial Cells in Diabetic NephropathyJiayi Wan0Jiayi Wan1Jiayi Wan2Jiayi Wan3Mingyang Hu4Mingyang Hu5Mingyang Hu6Mingyang Hu7Ziming Jiang8Ziming Jiang9Ziming Jiang10Ziming Jiang11Dongwei Liu12Dongwei Liu13Dongwei Liu14Dongwei Liu15Shaokang Pan16Shaokang Pan17Shaokang Pan18Shaokang Pan19Sijie Zhou20Sijie Zhou21Sijie Zhou22Sijie Zhou23Zhangsuo Liu24Zhangsuo Liu25Zhangsuo Liu26Zhangsuo Liu27Department of Nephrology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, ChinaResearch Institute of Nephrology, Zhengzhou University, Zhengzhou, ChinaHenan Province Research Center for Kidney Disease, Zhengzhou, ChinaKey Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, ChinaDepartment of Nephrology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, ChinaResearch Institute of Nephrology, Zhengzhou University, Zhengzhou, ChinaHenan Province Research Center for Kidney Disease, Zhengzhou, ChinaKey Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, ChinaDepartment of Nephrology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, ChinaResearch Institute of Nephrology, Zhengzhou University, Zhengzhou, ChinaHenan Province Research Center for Kidney Disease, Zhengzhou, ChinaKey Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, ChinaDepartment of Nephrology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, ChinaResearch Institute of Nephrology, Zhengzhou University, Zhengzhou, ChinaHenan Province Research Center for Kidney Disease, Zhengzhou, ChinaKey Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, ChinaDepartment of Nephrology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, ChinaResearch Institute of Nephrology, Zhengzhou University, Zhengzhou, ChinaHenan Province Research Center for Kidney Disease, Zhengzhou, ChinaKey Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, ChinaDepartment of Nephrology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, ChinaResearch Institute of Nephrology, Zhengzhou University, Zhengzhou, ChinaHenan Province Research Center for Kidney Disease, Zhengzhou, ChinaKey Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, ChinaDepartment of Nephrology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, ChinaResearch Institute of Nephrology, Zhengzhou University, Zhengzhou, ChinaHenan Province Research Center for Kidney Disease, Zhengzhou, ChinaKey Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, ChinaDiabetic nephropathy is considered one of the most common microvascular complications of diabetes and the pathophysiology involves multiple factors. Progressive diabetic nephropathy is believed to be related to the structure and function of the tubular epithelial cells in the kidney. However, the role of lysine acetylation in lesions of the renal tubular epithelial cells arising from hyperglycemia is poorly understood. Consequently, in this study, we cultured mouse renal tubular epithelial cells in vitro under high glucose conditions and analyzed the acetylation levels of proteins by liquid chromatography-high-resolution mass spectrometry. We identified 48 upregulated proteins and downregulated 86 proteins. In addition, we identified 113 sites with higher acetylation levels and 374 sites with lower acetylation levels. Subcellular localization analysis showed that the majority of the acetylated proteins were located in the mitochondria (43.17%), nucleus (28.57%) and cytoplasm (16.19%). Enrichment analysis indicated that these acetylated proteins are primarily associated with oxidative phosphorylation, the citrate cycle (TCA cycle), metabolic pathways and carbon metabolism. In addition, we used the MCODE plug-in and the cytoHubba plug-in in Cytoscape software to analyze the PPI network and displayed the first four most compact MOCDEs and the top 10 hub genes from the differentially expressed proteins between global and acetylated proteomes. Finally, we extracted 37 conserved motifs from 4915 acetylated peptides. Collectively, this comprehensive analysis of the proteome reveals novel insights into the role of lysine acetylation in tubular epithelial cells and may make a valuable contribution towards the identification of the pathological mechanisms of diabetic nephropathy.https://www.frontiersin.org/articles/10.3389/fgene.2021.767135/fullproteomelysine acetylationrenal tubular epithelial cellsdiabetic nephropathyacetyltransferase |
| spellingShingle | Jiayi Wan Jiayi Wan Jiayi Wan Jiayi Wan Mingyang Hu Mingyang Hu Mingyang Hu Mingyang Hu Ziming Jiang Ziming Jiang Ziming Jiang Ziming Jiang Dongwei Liu Dongwei Liu Dongwei Liu Dongwei Liu Shaokang Pan Shaokang Pan Shaokang Pan Shaokang Pan Sijie Zhou Sijie Zhou Sijie Zhou Sijie Zhou Zhangsuo Liu Zhangsuo Liu Zhangsuo Liu Zhangsuo Liu Lysine Acetylation in the Proteome of Renal Tubular Epithelial Cells in Diabetic Nephropathy Frontiers in Genetics proteome lysine acetylation renal tubular epithelial cells diabetic nephropathy acetyltransferase |
| title | Lysine Acetylation in the Proteome of Renal Tubular Epithelial Cells in Diabetic Nephropathy |
| title_full | Lysine Acetylation in the Proteome of Renal Tubular Epithelial Cells in Diabetic Nephropathy |
| title_fullStr | Lysine Acetylation in the Proteome of Renal Tubular Epithelial Cells in Diabetic Nephropathy |
| title_full_unstemmed | Lysine Acetylation in the Proteome of Renal Tubular Epithelial Cells in Diabetic Nephropathy |
| title_short | Lysine Acetylation in the Proteome of Renal Tubular Epithelial Cells in Diabetic Nephropathy |
| title_sort | lysine acetylation in the proteome of renal tubular epithelial cells in diabetic nephropathy |
| topic | proteome lysine acetylation renal tubular epithelial cells diabetic nephropathy acetyltransferase |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2021.767135/full |
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