101
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El-Mansi M, Phue JN, Shiloach J. Expression of the ace operon in Escherichia coli is triggered in response to growth rate-dependent flux-signal of ATP. FEMS Microbiol Lett 2021; 368:6070649. [PMID: 33417680 DOI: 10.1093/femsle/fnaa221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/31/2020] [Indexed: 01/06/2023] Open
Abstract
The signal that triggers the expression of the ace operon and, in turn, the transition of central metabolism's architecture from acetogenic to gluconeogenic in Escherichia coli remains elusive despite extensive research both in vivo and in vitro. Here, with the aid of flux analysis together with measurements of the enzymic activity of isocitrate lyase (ICL) and its aceA-messenger ribonucleuc acid (mRNA) transcripts, we provide credible evidence suggesting that the expression of the ace operon in E. coli is triggered in response to growth rate-dependent threshold flux-signal of adenosine triphosphate (ATP). Flux analysis revealed that the shortfall in ATP supply observed as the growth rate ($\mu $) diminishes from µmax to ≤ 0.43h-1 ($ \pm 0.02;n4)\ $is partially redressed by up-regulating flux through succinyl CoA synthetase. Unlike glycerol and glucose, pyruvate cannot feed directly into the two glycolytic ATP-generating reactions catalyzed by phosphoglycerokinase and pyruvate kinase. On the other hand, glycerol, which upon its conversion to D-glyceraldehyde, feeds into the phosphorylation and dephosphorylation parts of glycolysis including the substrate-level phosphorylation-ATP generating reactions, thus preventing ATP flux from dropping to the critical threshold signal required to trigger the acetate-diauxic switch until glycerol is fully consumed. The mRNA transcriptional patterns of key gluconeogenic enzymes, namely, ackA, acetate kinase; pta, phosphotransacetylase; acs, acetyl CoA synthetase and aceA, ICL, suggest that the pyruvate phenotype is better equipped than the glycerol phenotype for the switch from acetogenic to gluconeogenic metabolism.
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Affiliation(s)
- Mansi El-Mansi
- Bio-Ed, Scotland UK, 17/7 Watson Crescent, Edinburgh EGH11 1HA, Scotland, UK.,University of Africa, Toru-Orua, Department of Biotechnology, Faculty of Science, Sagbama L.G.A. Bayelsa State, Nigeria
| | - Je-Nie Phue
- Biotechnology Lab, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 14A, Room 173, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Joseph Shiloach
- Biotechnology Lab, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 14A, Room 173, 9000 Rockville Pike, Bethesda, MD 20892, USA
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102
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He J, Shangguan X, Zhou W, Cao Y, Zheng Q, Tu J, Hu G, Liang Z, Jiang C, Deng L, Wang S, Yang W, Zuo Y, Ma J, Cai R, Chen Y, Fan Q, Dong B, Xue W, Tan H, Qi Y, Gu J, Su B, Eugene Chin Y, Chen G, Wang Q, Wang T, Cheng J. Glucose limitation activates AMPK coupled SENP1-Sirt3 signalling in mitochondria for T cell memory development. Nat Commun 2021; 12:4371. [PMID: 34272364 PMCID: PMC8285428 DOI: 10.1038/s41467-021-24619-2] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 06/22/2021] [Indexed: 12/15/2022] Open
Abstract
Metabolic programming and mitochondrial dynamics along with T cell differentiation affect T cell fate and memory development; however, how to control metabolic reprogramming and mitochondrial dynamics in T cell memory development is unclear. Here, we provide evidence that the SUMO protease SENP1 promotes T cell memory development via Sirt3 deSUMOylation. SENP1-Sirt3 signalling augments the deacetylase activity of Sirt3, promoting both OXPHOS and mitochondrial fusion. Mechanistically, SENP1 activates Sirt3 deacetylase activity in T cell mitochondria, leading to reduction of the acetylation of mitochondrial metalloprotease YME1L1. Consequently, deacetylation of YME1L1 suppresses its activity on OPA1 cleavage to facilitate mitochondrial fusion, which results in T cell survival and promotes T cell memory development. We also show that the glycolytic intermediate fructose-1,6-bisphosphate (FBP) as a negative regulator suppresses AMPK-mediated activation of the SENP1-Sirt3 axis and reduces memory development. Moreover, glucose limitation reduces FBP production and activates AMPK during T cell memory development. These data show that glucose limitation activates AMPK and the subsequent SENP1-Sirt3 signalling for T cell memory development.
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Affiliation(s)
- Jianli He
- State Key Laboratory of Oncogenes and Related Genes, Renji Hospital Affiliated; Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xun Shangguan
- Department of Urology, Renji Hospital Affiliated, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Zhou
- State Key Laboratory of Oncogenes and Related Genes, Renji Hospital Affiliated; Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Urology, Renji Hospital Affiliated, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ying Cao
- State Key Laboratory of Oncogenes and Related Genes, Renji Hospital Affiliated; Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Quan Zheng
- State Key Laboratory of Oncogenes and Related Genes, Renji Hospital Affiliated; Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jun Tu
- State Key Laboratory of Oncogenes and Related Genes, Renji Hospital Affiliated; Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Gaolei Hu
- State Key Laboratory of Oncogenes and Related Genes, Renji Hospital Affiliated; Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zi Liang
- State Key Laboratory of Oncogenes and Related Genes, Renji Hospital Affiliated; Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Cen Jiang
- State Key Laboratory of Oncogenes and Related Genes, Renji Hospital Affiliated; Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Liufu Deng
- Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shengdian Wang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Wen Yang
- State Key Laboratory of Oncogenes and Related Genes, Renji Hospital Affiliated; Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yong Zuo
- State Key Laboratory of Oncogenes and Related Genes, Renji Hospital Affiliated; Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiao Ma
- State Key Laboratory of Oncogenes and Related Genes, Renji Hospital Affiliated; Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Rong Cai
- State Key Laboratory of Oncogenes and Related Genes, Renji Hospital Affiliated; Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yalan Chen
- State Key Laboratory of Oncogenes and Related Genes, Renji Hospital Affiliated; Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qiuju Fan
- State Key Laboratory of Oncogenes and Related Genes, Renji Hospital Affiliated; Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Baijun Dong
- Department of Urology, Renji Hospital Affiliated, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Xue
- Department of Urology, Renji Hospital Affiliated, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hongsheng Tan
- Clinical Research Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yitao Qi
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, China
| | - Jianmin Gu
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Bing Su
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Y Eugene Chin
- Institutes of Biology and Medical Sciences, Soochow University Medical College, Suzhou, Jiangsu, China
| | - Guoqiang Chen
- State Key Laboratory of Oncogenes and Related Genes, Renji Hospital Affiliated; Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qi Wang
- Department of Urology, Renji Hospital Affiliated, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Tianshi Wang
- State Key Laboratory of Oncogenes and Related Genes, Renji Hospital Affiliated; Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Jinke Cheng
- State Key Laboratory of Oncogenes and Related Genes, Renji Hospital Affiliated; Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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103
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Li Y, Quan J, Song H, Li D, Ma E, Wang Y, Ma C. Novel pyrrolo[2,1-c][1,4]benzodiazepine-3,11-dione (PBD) derivatives as selective HDAC6 inhibitors to suppress tumor metastasis and invasion in vitro and in vivo. Bioorg Chem 2021; 114:105081. [PMID: 34153811 DOI: 10.1016/j.bioorg.2021.105081] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 06/07/2021] [Accepted: 06/09/2021] [Indexed: 11/30/2022]
Abstract
Selective inhibition of histone deacetylase 6 (HDAC6) has been emerged as a promising approach to cancer treatment. As a pivotal strategy for drug discovery,molecular hybridization was introduced in this study and a series of pyrrolo[2,1-c][1,4] benzodiazepine-3,11-diones (PBDs) based hydroxamic acids was rationally designed and synthesizedas novel selective HDAC6 inhibitors. Preliminary in vitro enzyme inhibition assay and structure-activity relationship (SAR) discussion confirmed our design strategy and met the expectation. Several of the compounds showed high potent against HDAC6 enzyme in vitro, and compound A7 with a long aliphatic linker was revealed to have the similar activity as the positive control tubastatin A. Further in vitro characterization of A7 demonstrates the metastasis inhibitory potency in MDA-MB-231 cell line and western blotting showed that A7 could induce the upregulation of Ac-α-tubulin, but not induce the excessive acetylation of histone H3, which indicated that the compound had HDAC6 targeting effect in MDA-MB-231 cells. In vivo study revealed that compound A7 has satisfactory inhibitory effects onliver and lung metastasis of breast cancer in mice. Molecular docking released that A7 could fit well with the receptor and interact with some key residues, which lays a foundation for further structural modifications to elucidate the interaction mode between compounds and target protein. This pharmacological investigation workflow provided a reasonable and reference methodto examine the pharmacological effects of inhibiting HDAC6 with a single molecule, either in vitro or in vivo. All of these results suggested that A7 is a promising lead compound that could lead to the further development of novel selective HDAC6 inhibitors for the treatment of tumor metastasis.
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Affiliation(s)
- Yanchun Li
- School of Life Sciences and Biopharmaceutical Science, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, PR China
| | - Jishun Quan
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, PR China
| | - Haoxuan Song
- School of Life Sciences and Biopharmaceutical Science, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, PR China
| | - Dongzhu Li
- School of Life Sciences and Biopharmaceutical Science, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, PR China
| | - Enlong Ma
- School of Life Sciences and Biopharmaceutical Science, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, PR China
| | - Yanjuan Wang
- School of Pharmacy, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, PR China.
| | - Chao Ma
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang 110016, PR China.
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104
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Yuan B, Liu T, Cheng Y, Gao S, Li L, Cai L, Yang J, Chen J, Zhong K. Comprehensive Proteomic Analysis of Lysine Acetylation in Nicotiana benthamiana After Sensing CWMV Infection. Front Microbiol 2021; 12:672559. [PMID: 34084157 PMCID: PMC8166574 DOI: 10.3389/fmicb.2021.672559] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 04/15/2021] [Indexed: 11/13/2022] Open
Abstract
Protein lysine acetylation (Kac) is an important post-translational modification mechanism in eukaryotes that is involved in cellular regulation. To investigate the role of Kac in virus-infected plants, we characterized the lysine acetylome of Nicotiana benthamiana plants with or without a Chinese wheat mosaic virus (CWMV) infection. We identified 4,803 acetylated lysine sites on 1,964 proteins. A comparison of the acetylation levels of the CWMV-infected group with those of the uninfected group revealed that 747 sites were upregulated on 422 proteins, including chloroplast localization proteins and histone H3, and 150 sites were downregulated on 102 proteins. Nineteen conserved motifs were extracted and 51 percent of the acetylated proteins located on chloroplast. Nineteen Kac sites were located on histone proteins, including 10 Kac sites on histone 3. Bioinformatics analysis results indicated that lysine acetylation occurs on a large number of proteins involved in biological processes, especially photosynthesis. Furthermore, we found that the acetylation level of chloroplast proteins, histone 3 and some metabolic pathway-related proteins were significantly higher in CWMV-infected plants than in uninfected plants. In summary, our results reveal the regulatory roles of Kac in response to CWMV infection.
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Affiliation(s)
- Bowen Yuan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Tingting Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Ye Cheng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Shiqi Gao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China.,Yantai Academy of Agricultural Science, Yantai, China
| | - Linzhi Li
- Yantai Academy of Agricultural Science, Yantai, China
| | - Linna Cai
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jian Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Kaili Zhong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
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105
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Tappiban P, Ying Y, Xu F, Bao J. Proteomics and Post-Translational Modifications of Starch Biosynthesis-Related Proteins in Developing Seeds of Rice. Int J Mol Sci 2021; 22:5901. [PMID: 34072759 PMCID: PMC8199009 DOI: 10.3390/ijms22115901] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/26/2021] [Accepted: 05/28/2021] [Indexed: 12/25/2022] Open
Abstract
Rice (Oryza sativa L.) is a foremost staple food for approximately half the world's population. The components of rice starch, amylose, and amylopectin are synthesized by a series of enzymes, which are responsible for rice starch properties and functionality, and then affect rice cooking and eating quality. Recently, proteomics technology has been applied to the establishment of the differentially expressed starch biosynthesis-related proteins and the identification of posttranslational modifications (PTMs) target starch biosynthesis proteins as well. It is necessary to summarize the recent studies in proteomics and PTMs in rice endosperm to deepen our understanding of starch biosynthesis protein expression and regulation, which will provide useful information to rice breeding programs and industrial starch applications. The review provides a comprehensive summary of proteins and PTMs involved in starch biosynthesis based on proteomic studies of rice developing seeds. Starch biosynthesis proteins in rice seeds were differentially expressed in the developing seeds at different developmental stages. All the proteins involving in starch biosynthesis were identified using proteomics methods. Most starch biosynthesis-related proteins are basically increased at 6-20 days after flowering (DAF) and decreased upon the high-temperature conditions. A total of 10, 14, 2, 17, and 7 starch biosynthesis related proteins were identified to be targeted by phosphorylation, lysine acetylation, succinylation, lysine 2-hydroxyisobutyrylation, and malonylation, respectively. The phosphoglucomutase is commonly targeted by five PTMs types. Research on the function of phosphorylation in multiple enzyme complex formation in endosperm starch biosynthesis is underway, while the functions of other PTMs in starch biosynthesis are necessary to be conducted in the near future.
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Affiliation(s)
- Piengtawan Tappiban
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China; (P.T.); (Y.Y.); (F.X.)
| | - Yining Ying
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China; (P.T.); (Y.Y.); (F.X.)
| | - Feifei Xu
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China; (P.T.); (Y.Y.); (F.X.)
| | - Jinsong Bao
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China; (P.T.); (Y.Y.); (F.X.)
- Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Yazhou District, Sanya 572025, China
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106
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HBO1 overexpression is important for hepatocellular carcinoma cell growth. Cell Death Dis 2021; 12:549. [PMID: 34039960 PMCID: PMC8155027 DOI: 10.1038/s41419-021-03818-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 04/24/2021] [Accepted: 04/26/2021] [Indexed: 12/19/2022]
Abstract
Hepatocellular carcinoma (HCC) is a common primary liver malignancy lacking effective molecularly-targeted therapies. HBO1 (lysine acetyltransferase 7/KAT7) is a member of MYST histone acetyltransferase family. Its expression and potential function in HCC are studied. We show that HBO1 mRNA and protein expression is elevated in human HCC tissues and HCC cells. HBO1 expression is however low in cancer-surrounding normal liver tissues and hepatocytes. In HepG2 and primary human HCC cells, shRNA-induced HBO1 silencing or CRISPR/Cas9-induced HBO1 knockout potently inhibited cell viability, proliferation, migration, and invasion, while provoking mitochondrial depolarization and apoptosis induction. Conversely, ectopic overexpression of HBO1 by a lentiviral construct augmented HCC cell proliferation, migration and invasion. In vivo, xenografts-bearing HBO1-KO HCC cells grew significantly slower than xenografts with control HCC cells in severe combined immunodeficient mice. These results suggest HBO1 overexpression is important for HCC cell progression.
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107
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Sun L, Bhawal R, Xu H, Chen H, Anderson ET, Haroutunian V, Cross AC, Zhang S, Gibson GE. The human brain acetylome reveals that decreased acetylation of mitochondrial proteins associates with Alzheimer's disease. J Neurochem 2021; 158:282-296. [PMID: 33905124 DOI: 10.1111/jnc.15377] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 04/19/2021] [Indexed: 11/28/2022]
Abstract
Metabolic changes that correlate to cognitive changes are well-known in Alzheimer's disease (AD). Metabolism is often linked to functional changes in proteins by post-translational modifications. The importance of the regulation of transcription by acetylation is well documented. Advanced mass spectrometry reveals hundreds of acetylated proteins in multiple tissues, but the acetylome of human brain, its functional significance, and the changes with disease are unknown. Filling this gap is critical for understanding the pathophysiology and development of therapies. To fill this gap, we assessed the human brain acetylome in human brain and its changes with AD. More than 5% of the 4,442 proteins from the human brain global proteome were acetylated. Acetylated proteins were primarily found in the cytosol (148), mitochondria (100), nucleus (91), and plasma membrane (58). The comparison of the brain acetylome in controls to that of patients with AD revealed striking and selective differences in terms of its abundances of acetylated peptides/sites. Acetylation of 18 mitochondrial proteins decreased, while acetylation of two cytosolic proteins, tau and GFAP, increased. Our experiments demonstrate that acetylation at some specific lysine sites alters enzyme function. The results indicate that general activation of de-acetylases (i.e., sirtuins) is not an appropriate therapeutic approach for AD.
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Affiliation(s)
- Lidan Sun
- Brain and Mind Research Institute, Weill Cornell Medicine, Burke Neurological Institute, White Plains, NY, USA.,Integrated Medicine Research Center for Neurological Rehabilitation, College of Medicine, Jiaxing University, Jiaxing, China
| | - Ruchika Bhawal
- Proteomics and Metabolomics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, USA
| | - Hui Xu
- Brain and Mind Research Institute, Weill Cornell Medicine, Burke Neurological Institute, White Plains, NY, USA
| | - Huanlian Chen
- Brain and Mind Research Institute, Weill Cornell Medicine, Burke Neurological Institute, White Plains, NY, USA
| | - Elizabeth T Anderson
- Proteomics and Metabolomics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, USA
| | - Vahrum Haroutunian
- Department of Psychiatry, The Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Mental Illness Research, Education and Clinical Center, James J Peters VA Medical Center, Bronx, NY, USA.,Department of Neuroscience, The Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Abigail C Cross
- Brain and Mind Research Institute, Weill Cornell Medicine, Burke Neurological Institute, White Plains, NY, USA
| | - Sheng Zhang
- Proteomics and Metabolomics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, USA
| | - Gary E Gibson
- Brain and Mind Research Institute, Weill Cornell Medicine, Burke Neurological Institute, White Plains, NY, USA
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108
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Singh CK, George J, Chhabra G, Nihal M, Chang H, Ahmad N. Genetic Manipulation of Sirtuin 3 Causes Alterations of Key Metabolic Regulators in Melanoma. Front Oncol 2021; 11:676077. [PMID: 33937086 PMCID: PMC8085490 DOI: 10.3389/fonc.2021.676077] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 03/29/2021] [Indexed: 12/29/2022] Open
Abstract
The mitochondrial sirtuin SIRT3 plays key roles in cellular metabolism and energy production, which makes it an obvious target for the management of cancer, including melanoma. Previously, we have demonstrated that SIRT3 was constitutively upregulated in human melanoma and its inhibition resulted in anti-proliferative effects in vitro in human melanoma cells and in vivo in human melanoma xenografts. In this study, we expanded our data employing knockdown and overexpression strategies in cell culture and mouse xenografts to further validate and establish the pro-proliferative function of SIRT3 in melanocytic cells, and its associated potential mechanisms, especially focusing on the metabolic regulation. We found that short-hairpin RNA (shRNA) mediated SIRT3 knockdown in G361 melanoma cells showed diminished tumorigenesis in immunodeficient Nu/Nu mice. Conversely, SIRT3 overexpressing Hs294T melanoma cells showed increased tumor growth. These effects were consistent with changes in markers of proliferation (PCNA), survival (Survivin) and angiogenesis (VEGF) in xenografted tissues. Further, in in vitro culture system, we determined the effect of SIRT3 knockdown on glucose metabolism in SK-MEL-2 cells, using a PCR array. SIRT3 knockdown caused alterations in a total of 37 genes involved in the regulation and enzymatic pathways of glucose (32 genes) and glycogen (5 genes) metabolism. Functions annotation of these identified genes, using the ingenuity pathway analysis (IPA), predicted cumulative actions of decreased cell viability/proliferation, tumor growth and reactive oxygen species (ROS), and increased apoptosis in response to SIRT3 knockdown. Further, IPA gene network analysis of SIRT3 modulated genes revealed the interactions among these genes in addition to several melanoma-associated genes. Sirtuin pathway was identified as one of the top canonical pathways showing the interaction of SIRT3 with metabolic regulatory genes along with other sirtuins. IPA analysis also predicted the inhibition of HIF1α, PKM, KDM8, PPARGC1A, mTOR, and activation of P53 and CLPP; the genes involved in major cancer/melanoma-associated signaling events. Collectively, these results suggest that SIRT3 inhibition affects cellular metabolism, to impart an anti-proliferative response against melanoma.
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Affiliation(s)
- Chandra K Singh
- Department of Dermatology, University of Wisconsin, Madison, WI, United States
| | - Jasmine George
- Department of Dermatology, University of Wisconsin, Madison, WI, United States
| | - Gagan Chhabra
- Department of Dermatology, University of Wisconsin, Madison, WI, United States
| | - Minakshi Nihal
- Department of Dermatology, University of Wisconsin, Madison, WI, United States
| | - Hao Chang
- Department of Dermatology, University of Wisconsin, Madison, WI, United States
| | - Nihal Ahmad
- Department of Dermatology, University of Wisconsin, Madison, WI, United States.,William S. Middleton VA Medical Center, Madison, WI, United States
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109
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Cai Q, Tian L, Xie JT, Huang QY, Feng MG, Keyhani NO. A fungal sirtuin modulates development and virulence in the insect pathogen, Beauveria bassiana. Environ Microbiol 2021; 23:5164-5183. [PMID: 33817929 DOI: 10.1111/1462-2920.15497] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/25/2021] [Accepted: 03/30/2021] [Indexed: 01/02/2023]
Abstract
Chromatin transitions are mediated in part by acetylation/deacetylation post-translational modifications of histones. Histone deacetylases, e.g. sirtuins (Sir-proteins), repress transcription via promotion of heterochromatin formation. Here, we characterize the Sir2 class III histone deacetylase (BbSir2) in the environmentally and economically important fungal insect pathogen, Beauveria bassiana. BbSir2 is shown to contribute to the deacetylation of lysine residues on H3 and H4 histones. Targeted gene knockout of BbSir2 resulted in impaired asexual development, reduced abilities to utilize various carbon/nitrogen sources, reduced tolerance to oxidative, heat, and UV stress, and attenuated virulence. ΔBbSir2 cells showed disrupted cell cycle development and abnormal hyphal septation patterns. Proteomic protein acetylation analyses of wild type and ΔBbSir2 cells revealed the differential abundance of 462 proteins and altered (hyper- or hypo-) acetylation of 436 lysine residues on 350 proteins. Bioinformatic analyses revealed enrichment in pathways involved in carbon/nitrogen metabolism, cell cycle control and cell rescue, defence and mitochondrial functioning. Critical targets involved in virulence included LysM effector proteins and a benzoquinone oxidoreductase implicated in detoxification of cuticular compounds. These data indicate broad effects of BbSir2 on fungal development and stress response, with identification of discrete targets that can account for the observed (decreased) virulence phenotype.
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Affiliation(s)
- Qing Cai
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.,Department of Microbiology and Cell Science, University of Florida, Bldg. 981, Museum Road, Gainesville, FL, 32611, USA
| | - Li Tian
- Shandong Provincial Key Laboratory of Microbial Engineering, Department of Bioengineering, Qilu University of Technology, Jinan, Shandong, 250353, China
| | - Jia-Tao Xie
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Qiu-Ying Huang
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Ming-Guang Feng
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Nemat O Keyhani
- Department of Microbiology and Cell Science, University of Florida, Bldg. 981, Museum Road, Gainesville, FL, 32611, USA
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110
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Keenan EK, Zachman DK, Hirschey MD. Discovering the landscape of protein modifications. Mol Cell 2021; 81:1868-1878. [PMID: 33798408 DOI: 10.1016/j.molcel.2021.03.015] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 02/21/2021] [Accepted: 03/10/2021] [Indexed: 02/08/2023]
Abstract
Protein modifications modulate nearly every aspect of cell biology in organisms, ranging from Archaea to Eukaryotes. The earliest evidence of covalent protein modifications was found in the early 20th century by studying the amino acid composition of proteins by chemical hydrolysis. These discoveries challenged what defined a canonical amino acid. The advent and rapid adoption of mass-spectrometry-based proteomics in the latter part of the 20th century enabled a veritable explosion in the number of known protein modifications, with more than 500 discrete modifications counted today. Now, new computational tools in data science, machine learning, and artificial intelligence are poised to allow researchers to make significant progress in discovering new protein modifications and determining their function. In this review, we take an opportunity to revisit the historical discovery of key post-translational modifications, quantify the current landscape of covalent protein adducts, and assess the role that new computational tools will play in the future of this field.
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Affiliation(s)
- E Keith Keenan
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA; Department of Pharmacology & Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Derek K Zachman
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA
| | - Matthew D Hirschey
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC 27701, USA; Department of Pharmacology & Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA; Division of Endocrinology, Metabolism, & Nutrition, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA.
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111
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Kim Y, Lama S, Agrawal D, Kumar V, Park S. Acetate as a potential feedstock for the production of value-added chemicals: Metabolism and applications. Biotechnol Adv 2021; 49:107736. [PMID: 33781888 DOI: 10.1016/j.biotechadv.2021.107736] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 02/22/2021] [Accepted: 03/19/2021] [Indexed: 10/21/2022]
Abstract
Acetate is regarded as a promising carbon feedstock in biological production owing to its possible derivation from C1 gases such as CO, CO2 and methane. To best use of acetate, comprehensive understanding of acetate metabolisms from genes and enzymes to pathways and regulations is needed. This review aims to provide an overview on the potential of acetate as carbon feedstock for industrial biotechnology. Biochemical, microbial and biotechnological aspects of acetate metabolism are described. Especially, the current state-of-the art in the production of value-added chemicals from acetate is summarized. Challenges and future perspectives are also provided.
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Affiliation(s)
- Yeonhee Kim
- School of Energy and Chemical Engineering, UNIST, 50, UNIST-gil, Ulsan 44919, Republic of Korea
| | - Suman Lama
- School of Energy and Chemical Engineering, UNIST, 50, UNIST-gil, Ulsan 44919, Republic of Korea
| | - Deepti Agrawal
- Biochemistry and Biotechnology Area, Material Resource Efficiency Division, CSIR- Indian Institute of Petroleum, Mohkampur, Dehradun 248005, India
| | - Vinod Kumar
- Centre for Climate and Environmental Protection, School of Water, Energy and Environment, Cranfield University, Cranfield, MK430AL, United Kingdom.
| | - Sunghoon Park
- School of Energy and Chemical Engineering, UNIST, 50, UNIST-gil, Ulsan 44919, Republic of Korea.
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112
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Lv Y, Bu C, Meng J, Ward C, Volpe G, Hu J, Jiang M, Guo L, Chen J, Esteban MA, Bao X, Cheng Z. Global Profiling of the Lysine Crotonylome in Different Pluripotent States. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 19:80-93. [PMID: 33746086 PMCID: PMC8498919 DOI: 10.1016/j.gpb.2021.01.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 12/21/2020] [Accepted: 01/27/2021] [Indexed: 12/19/2022]
Abstract
Pluripotent stem cells (PSCs) can be expanded in vitro in different culture conditions, resulting in a spectrum of cell states with distinct properties. Understanding how PSCs transition from one state to another, ultimately leading to lineage-specific differentiation, is important for developmental biology and regenerative medicine. Although there is significant information regarding gene expression changes controlling these transitions, less is known about post-translational modifications of proteins. Protein crotonylation is a newly discovered post-translational modification where lysine residues are modified with a crotonyl group. Here, we employed affinity purification of crotonylated peptides and liquid chromatography–tandem mass spectrometry (LC–MS/MS) to systematically profile protein crotonylation in mouse PSCs in different states including ground, metastable, and primed states, as well as metastable PSCs undergoing early pluripotency exit. We successfully identified 3628 high-confidence crotonylated sites in 1426 proteins. These crotonylated proteins are enriched for factors involved in functions/processes related to pluripotency such as RNA biogenesis, central carbon metabolism, and proteasome function. Moreover, we found that increasing the cellular levels of crotonyl-coenzyme A (crotonyl-CoA) through crotonic acid treatment promotes proteasome activity in metastable PSCs and delays their differentiation, consistent with previous observations showing that enhanced proteasome activity helps to sustain pluripotency. Our atlas of protein crotonylation will be valuable for further studies of pluripotency regulation and may also provide insights into the role of metabolism in other cell fate transitions.
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Affiliation(s)
- Yuan Lv
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chen Bu
- Jingjie PTM BioLab (Hangzhou) Co. Ltd, Hangzhou 310018, China
| | - Jin Meng
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health and Guangzhou Medical University, Guangzhou 511436, China
| | - Carl Ward
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Giacomo Volpe
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Jieyi Hu
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mengling Jiang
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Lin Guo
- CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Jiekai Chen
- CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China; Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health and Guangzhou Medical University, Guangzhou 511436, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China
| | - Miguel A Esteban
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health and Guangzhou Medical University, Guangzhou 511436, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China; Institute of Stem Cells and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.
| | - Xichen Bao
- CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China; Laboratory of RNA Molecular Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
| | - Zhongyi Cheng
- Jingjie PTM BioLab (Hangzhou) Co. Ltd, Hangzhou 310018, China.
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113
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Martín JF, Liras P, Sánchez S. Modulation of Gene Expression in Actinobacteria by Translational Modification of Transcriptional Factors and Secondary Metabolite Biosynthetic Enzymes. Front Microbiol 2021; 12:630694. [PMID: 33796086 PMCID: PMC8007912 DOI: 10.3389/fmicb.2021.630694] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 01/04/2021] [Indexed: 12/20/2022] Open
Abstract
Different types of post-translational modifications are present in bacteria that play essential roles in bacterial metabolism modulation. Nevertheless, limited information is available on these types of modifications in actinobacteria, particularly on their effects on secondary metabolite biosynthesis. Recently, phosphorylation, acetylation, or phosphopantetheneylation of transcriptional factors and key enzymes involved in secondary metabolite biosynthesis have been reported. There are two types of phosphorylations involved in the control of transcriptional factors: (1) phosphorylation of sensor kinases and transfer of the phosphate group to the receiver domain of response regulators, which alters the expression of regulator target genes. (2) Phosphorylation systems involving promiscuous serine/threonine/tyrosine kinases that modify proteins at several amino acid residues, e.g., the phosphorylation of the global nitrogen regulator GlnR. Another post-translational modification is the acetylation at the epsilon amino group of lysine residues. The protein acetylation/deacetylation controls the activity of many short and long-chain acyl-CoA synthetases, transcriptional factors, key proteins of bacterial metabolism, and enzymes for the biosynthesis of non-ribosomal peptides, desferrioxamine, streptomycin, or phosphinic acid-derived antibiotics. Acetyltransferases catalyze acetylation reactions showing different specificity for the acyl-CoA donor. Although it functions as acetyltransferase, there are examples of malonylation, crotonylation, succinylation, or in a few cases acylation activities using bulky acyl-CoA derivatives. Substrates activation by nucleoside triphosphates is one of the central reactions inhibited by lysine acetyltransferases. Phosphorylation/dephosphorylation or acylation/deacylation reactions on global regulators like PhoP, GlnR, AfsR, and the carbon catabolite regulator glucokinase strongly affects the expression of genes controlled by these regulators. Finally, a different type of post-translational protein modification is the phosphopantetheinylation, catalized by phosphopantetheinyl transferases (PPTases). This reaction is essential to modify those enzymes requiring phosphopantetheine groups like non-ribosomal peptide synthetases, polyketide synthases, and fatty acid synthases. Up to five PPTases are present in S. tsukubaensis and S. avermitilis. Different PPTases modify substrate proteins in the PCP or ACP domains of tacrolimus biosynthetic enzymes. Directed mutations of genes encoding enzymes involved in the post-translational modification is a promising tool to enhance the production of bioactive metabolites.
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Affiliation(s)
- Juan F Martín
- Área de Microbiología, Departamento de Biología Molecular, Universidad de León, León, Spain
| | - Paloma Liras
- Área de Microbiología, Departamento de Biología Molecular, Universidad de León, León, Spain
| | - Sergio Sánchez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México, Mexico
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114
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Yu Y, Wang H, Rao X, Liu L, Zheng P, Li W, Zhou W, Chai T, Ji P, Song J, Wei H, Xie P. Proteomic Profiling of Lysine Acetylation Indicates Mitochondrial Dysfunction in the Hippocampus of Gut Microbiota-Absent Mice. Front Mol Neurosci 2021; 14:594332. [PMID: 33776647 PMCID: PMC7991600 DOI: 10.3389/fnmol.2021.594332] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 02/17/2021] [Indexed: 12/21/2022] Open
Abstract
Major depressive disorder (MDD) is a leading cause of disability around the world and contributes greatly to the global burden of disease. Mounting evidence suggests that gut microbiota dysbiosis may be involved in the pathophysiology of MDD through the microbiota–gut–brain axis. Recent research suggests that epigenetic modifications might relate to depression. However, our knowledge of the role of epigenetics in host–microbe interactions remains limited. In the present study, we used a combination of affinity enrichment and high-resolution liquid chromatography tandem mass spectrometry analysis to identify hippocampal acetylated proteins in germ-free and specific pathogen-free mice. In total, 986 lysine acetylation sites in 543 proteins were identified, of which 747 sites in 427 proteins were quantified. Motif analysis identified several conserved sequences surrounding the acetylation sites, including D∗Kac, DKac, KacY, KacD, and D∗∗Kac. Gene ontology annotations revealed that these differentially expressed acetylated proteins were involved in multiple biological functions and were mainly located in mitochondria. In addition, pathway enrichment analysis demonstrated that oxidative phosphorylation and the tricarboxylic acid cycle II (eukaryotic), both of which are exclusively localized to the mitochondria, were the primarily disturbed functions. Taken together, this study indicates that lysine acetylation alterations may play a pivotal role in mitochondrial dysfunction and may be a mechanism by which gut microbiota regulate brain function and behavioral phenotypes.
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Affiliation(s)
- Ying Yu
- The Ministry of Education, Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing, China.,National Health Commission, Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Haiyang Wang
- National Health Commission, Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,College of Stomatology and Affiliated Stomatological Hospital of Chongqing Medical University, Chongqing, China
| | - Xuechen Rao
- National Health Commission, Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,College of Biomedical Engineering, Chongqing Medical University, Chongqing, China
| | - Lanxiang Liu
- National Health Commission, Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,Department of Neurology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China.,Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Peng Zheng
- National Health Commission, Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Wenxia Li
- National Health Commission, Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Wei Zhou
- National Health Commission, Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Tingjia Chai
- National Health Commission, Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ping Ji
- College of Stomatology and Affiliated Stomatological Hospital of Chongqing Medical University, Chongqing, China
| | - Jinlin Song
- College of Stomatology and Affiliated Stomatological Hospital of Chongqing Medical University, Chongqing, China
| | - Hong Wei
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Third Military Medical University, Chongqing, China
| | - Peng Xie
- The Ministry of Education, Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing, China.,National Health Commission, Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,Department of Neurology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China.,Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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115
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Zhou F, Zhang L, Zhu K, Bai M, Zhang Y, Zhu Q, Wang S, Sheng C, Yuan M, Liu Y, Lu J, Shao L, Wang X, Zhou L. SIRT2 ablation inhibits glucose-stimulated insulin secretion through decreasing glycolytic flux. Am J Cancer Res 2021; 11:4825-4838. [PMID: 33754030 PMCID: PMC7978320 DOI: 10.7150/thno.55330] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 02/06/2021] [Indexed: 11/30/2022] Open
Abstract
Rationale: Sirtuins are NAD+-dependent protein deacylases known to have protective effects against age-related diseases such as diabetes, cancer, and neurodegenerative disease. SIRT2 is the only primarily cytoplasmic isoform and its overall role in glucose homeostasis remains uncertain. Methods: SIRT2-knockout (KO) rats were constructed to evaluate the role of SIRT2 in glucose homeostasis. The effect of SIRT2 on β-cell function was detected by investigating the morphology, insulin secretion, and metabolomic state of islets. The deacetylation and stabilization of GKRP in β-cells by SIRT2 were determined by western blot, adenoviral infection, and immunoprecipitation. Results: SIRT2-KO rats exhibited impaired glucose tolerance and glucose-stimulated insulin secretion (GSIS), without change in insulin sensitivity. SIRT2 deficiency or inhibition by AGK2 decreased GSIS in isolated rat islets, with lowered oxygen consumption rate. Adenovirus-mediated overexpression of SIRT2 enhanced insulin secretion from rat islets. Metabolomics analysis revealed a decrease in metabolites of glycolysis and tricarboxylic acid cycle in SIRT2-KO islets compared with control islets. Our study further demonstrated that glucokinase regulatory protein (GKRP), an endogenous inhibitor of glucokinase (GCK), was expressed in rat islets. SIRT2 overexpression deacetylated GKRP in INS-1 β-cells. SIRT2 knockout or inhibition elevated GKRP protein stability in islet β-cells, leading to an increase in the interaction of GKRP and GCK. On the contrary, SIRT2 inhibition promoted the protein degradation of ALDOA, a glycolytic enzyme. Conclusions: SIRT2 ablation inhibits GSIS through blocking GKRP protein degradation and promoting ALDOA protein degradation, resulting in a decrease in glycolytic flux.
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116
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Yang L, Miao S, Zhang J, Wang P, Liu G, Wang J. The growing landscape of succinylation links metabolism and heart disease. Epigenomics 2021; 13:319-333. [PMID: 33605156 DOI: 10.2217/epi-2020-0273] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Post-translational modification of proteins is an important biochemical process that occurs at the protein level. Succinylation is a newly discovered post-translational modification with the hallmark of a significant chemical and structural change. Succinylation has many similarities with other modifications, but succinylation may lead to more functional changes. Although the physiological significance of succinylation has not been well characterized, the lysine succinylation modification shows great potentials during disease processes. The discovery of SIRT5 has made great progress in exploring the role of succinylation in energy metabolism, heart disease and tumorigenesis. In this review, we focus on the discovery of succinylation in organisms and mechanism of succinylation. We are also concerned with the metabolic reactions and heart diseases associated with succinylation.
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Affiliation(s)
- Lanting Yang
- Department of Cardiovascular Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266000, China.,School of Basic Medicine, Qingdao University, Qingdao 266021, China
| | - Shuo Miao
- School of Basic Medicine, Qingdao University, Qingdao 266021, China
| | - Jing Zhang
- School of Basic Medicine, Qingdao University, Qingdao 266021, China
| | - Peiyan Wang
- School of Basic Medicine, Qingdao University, Qingdao 266021, China
| | - Gaoli Liu
- Department of Cardiovascular Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266000, China
| | - Jianxun Wang
- School of Basic Medicine, Qingdao University, Qingdao 266021, China
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117
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Changes of the Proteome and Acetylome during Transition into the Stationary Phase in the Organohalide-Respiring Dehalococcoides mccartyi Strain CBDB1. Microorganisms 2021; 9:microorganisms9020365. [PMID: 33673241 PMCID: PMC7918482 DOI: 10.3390/microorganisms9020365] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/06/2021] [Accepted: 02/08/2021] [Indexed: 11/17/2022] Open
Abstract
The strictly anaerobic bactGIerium Dehalococcoides mccartyi obligatorily depends on organohalide respiration for energy conservation and growth. The bacterium also plays an important role in bioremediation. Since there is no guarantee of a continuous supply of halogenated substrates in its natural environment, the question arises of how D. mccartyi maintains the synthesis and activity of dehalogenating enzymes under these conditions. Acetylation is a means by which energy-restricted microorganisms can modulate and maintain protein levels and their functionality. Here, we analyzed the proteome and Nε-lysine acetylome of D. mccartyi strain CBDB1 during growth with 1,2,3-trichlorobenzene as an electron acceptor. The high abundance of the membrane-localized organohalide respiration complex, consisting of the reductive dehalogenases CbrA and CbdbA80, the uptake hydrogenase HupLS, and the organohalide respiration-associated molybdoenzyme OmeA, was shown throughout growth. In addition, the number of acetylated proteins increased from 5% to 11% during the transition from the exponential to the stationary phase. Acetylation of the key proteins of central acetate metabolism and of CbrA, CbdbA80, and TatA, a component of the twin-arginine translocation machinery, suggests that acetylation might contribute to maintenance of the organohalide-respiring capacity of the bacterium during the stationary phase, thus providing a means of ensuring membrane protein integrity and a proton gradient.
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118
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Li X, Wang L, Wang M, Zhang Z, Ma C, Ma X, Na X, Liang W. Global analysis of protein succinylation modification of Nostoc flagelliforme in response to dehydration. J Proteomics 2021; 237:104149. [PMID: 33588108 DOI: 10.1016/j.jprot.2021.104149] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 01/13/2021] [Accepted: 02/02/2021] [Indexed: 11/29/2022]
Abstract
Nostoc flagelliforme is a type of terrestrial cyanobacteria that is distributed in arid or semi-arid steppes in China. To research the molecular mechanisms underlying the adaptation of N. flagelliforme to drought stress, the succinylated expression profile and changes in N. flagelliforme that resulted as a response to dehydration were analyzed by label-free proteomics. A total of 1149 succinylated sites, 1128 succinylated peptides, and 396 succinylated proteins were identified. Succinylated proteins were differentially involved in photosynthesis and energy metabolism, as well as in reactive oxygen species (ROS) scavenging. Motif-X analysis of succinylated sites determined a succinylation motif [KxxG]. N. flagelliforme adapts to dehydration by increasing glucose metabolism and pentose phosphate pathway flux, and decreasing photosynthetic rate, which some of the key proteins were succinylated. ROS scavenging was mainly involved in the regulation of the enzyme antioxidant defense system and non-enzymatic antioxidant defense system through succinylation modification, thus eliminating excessive ROS. Protein succinylation of N. flagelliforme may play an important regulatory role in response to dehydration. The results are foundational, as they can inform future research into the mechanisms involved in the succinylation regulation mechanism of N. flagelliforme in response to dehydration. SIGNIFICANCE: The global succinylation network involved in response to dehydration in N. flagelliforme has been established. We found that many succinylated proteins were involved in photosynthesis, glucose metabolism and antioxidation. The global survey of succinylated proteins and the changes of succinylated levels in response to dehydration provided effective information for the drought tolerance mechanism in N. flagelliforme.
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Affiliation(s)
- Xiaoxu Li
- School of Life Sciences, Ningxia University, Yinchuan 750021, PR China
| | - Lingxia Wang
- School of Life Sciences, Ningxia University, Yinchuan 750021, PR China
| | - Meng Wang
- School of Life Sciences, Ningxia University, Yinchuan 750021, PR China
| | - Zheng Zhang
- School of Life Sciences, Ningxia University, Yinchuan 750021, PR China
| | - Caixia Ma
- School of Life Sciences, Ningxia University, Yinchuan 750021, PR China
| | - Xiaorong Ma
- School of Life Sciences, Ningxia University, Yinchuan 750021, PR China
| | - Xiaofan Na
- School of Life Sciences, Lanzhou University, Lanzhou 730000, PR China.
| | - Wenyu Liang
- School of Life Sciences, Ningxia University, Yinchuan 750021, PR China.
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119
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Shi Y, Zhu J, Xu Y, Tang X, Yang Z, Huang A. Malonyl-proteome profiles of Staphylococcus aureus reveal lysine malonylation modification in enzymes involved in energy metabolism. Proteome Sci 2021; 19:1. [PMID: 33436009 PMCID: PMC7802289 DOI: 10.1186/s12953-020-00169-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 12/16/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Protein lysine malonylation, a novel post-translational modification (PTM), has been recently linked with energy metabolism in bacteria. Staphylococcus aureus is the third most important foodborne pathogen worldwide. Nonetheless, substrates and biological roles of malonylation are still poorly understood in this pathogen. RESULTS Using anti-malonyl-lysine antibody enrichment and high-resolution LC-MS/MS analysis, 440 lysine-malonylated sites were identified in 281 proteins of S. aureus strain. The frequency of valine in position - 1 and alanine at + 2 and + 4 positions was high. KEGG pathway analysis showed that six categories were highly enriched, including ribosome, glycolysis/gluconeogenesis, pentose phosphate pathway (PPP), tricarboxylic acid cycle (TCA), valine, leucine, isoleucine degradation, and aminoacyl-tRNA biosynthesis. In total, 31 malonylated sites in S. aureus shared homology with lysine-malonylated sites previously identified in E. coli, indicating malonylated proteins are highly conserved among bacteria. Key rate-limiting enzymes in central carbon metabolic pathways were also found to be malonylated in S. aureus, namely pyruvate kinase (PYK), 6-phosphofructokinase, phosphoglycerate kinase, dihydrolipoyl dehydrogenase, and F1F0-ATP synthase. Notably, malonylation sites were found at or near protein active sites, including KH domain protein, thioredoxin, alanine dehydrogenase (ALD), dihydrolipoyl dehydrogenase (LpdA), pyruvate oxidase CidC, and catabolite control protein A (CcpA), thus suggesting that lysine malonylation may affect the activity of such enzymes. CONCLUSIONS Data presented herein expand the current knowledge on lysine malonylation in prokaryotes and indicate the potential roles of protein malonylation in bacterial physiology and metabolism.
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Affiliation(s)
- Yanan Shi
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Jingjing Zhu
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Yan Xu
- Yunnan Center for Disease Control and Prevention, Kunming, 650201, Yunnan, China
| | - Xiaozhao Tang
- Yunnan Center for Disease Control and Prevention, Kunming, 650201, Yunnan, China
| | - Zushun Yang
- Yunnan Center for Disease Control and Prevention, Kunming, 650201, Yunnan, China
| | - Aixiang Huang
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan, China.
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Liu P, Wang Y, Yang G, Zhang Q, Meng L, Xin Y, Jiang X. The role of short-chain fatty acids in intestinal barrier function, inflammation, oxidative stress, and colonic carcinogenesis. Pharmacol Res 2021; 165:105420. [PMID: 33434620 DOI: 10.1016/j.phrs.2021.105420] [Citation(s) in RCA: 239] [Impact Index Per Article: 79.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 12/25/2020] [Accepted: 01/04/2021] [Indexed: 12/12/2022]
Abstract
Short-chain fatty acids (SCFAs), mainly including acetate, propionate, and butyrate, are metabolites produced during the bacterial fermentation of dietary fiber in the intestinal tract. They are believed to be essential factors affecting host health. Most in vitro and ex vivo studies have shown that SCFAs affect the regulation of inflammation, carcinogenesis, intestinal barrier function, and oxidative stress, but convincing evidence in humans is still lacking. Two major SCFA signaling mechanisms have been identified: promotion of histone acetylation and activation of G-protein-coupled receptors. In this review, we introduce the production and metabolic characteristics of SCFAs, summarize the potential effects of SCFAs on the four aspects mentioned above and the possible mechanisms. SCFAs have been reported to exert a wide spectrum of positive effects and have a high potential for therapeutic use in human-related diseases.
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Affiliation(s)
- Pinyi Liu
- Department of Radiation Oncology, The First Hospital of Jilin University, Changchun 130021, China; Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China; Jilin Provincial Key Laboratory of Radiation Oncology & Therapy, The First Hospital of Jilin University, Changchun 130021, China.
| | - Yanbing Wang
- Department of Orthopedic, The Second Hospital of Jilin University, Changchun, 130041, China.
| | - Ge Yang
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China.
| | - Qihe Zhang
- Department of Radiation Oncology, The First Hospital of Jilin University, Changchun 130021, China; Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China.
| | - Lingbin Meng
- Department of Hematology and Medical Oncology, Moffitt Cancer Center, Tampa, FL 33612, USA.
| | - Ying Xin
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China.
| | - Xin Jiang
- Department of Radiation Oncology, The First Hospital of Jilin University, Changchun 130021, China; Jilin Provincial Key Laboratory of Radiation Oncology & Therapy, The First Hospital of Jilin University, Changchun 130021, China.
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Hadj-Moussa H, Wade SC, Childers CL, Storey KB. Mind the GAP: Purification and characterization of urea resistant GAPDH during extreme dehydration. Proteins 2020; 89:544-557. [PMID: 33368595 DOI: 10.1002/prot.26038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 11/24/2020] [Accepted: 12/12/2020] [Indexed: 11/12/2022]
Abstract
The African clawed frog (Xenopus laevis) withstands prolonged periods of extreme whole-body dehydration that lead to impaired blood flow, global hypoxia, and ischemic stress. During dehydration, these frogs shift from oxidative metabolism to a reliance on anaerobic glycolysis. In this study, we purified the central glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) to electrophoretic homogeneity and investigated structural, kinetic, subcellular localization, and post-translational modification properties between control and 30% dehydrated X. laevis liver. GAPDH from dehydrated liver displayed a 25.4% reduction in maximal velocity and a 55.7% increase in its affinity for GAP, as compared to enzyme from hydrated frogs. Under dehydration mimicking conditions (150 mM urea and 1% PEG), GAP affinity was reduced with a Km value 53.8% higher than controls. Frog dehydration also induced a significant increase in serine phosphorylation, methylation, acetylation, beta-N-acetylglucosamination, and cysteine nitrosylation, post-translational modifications (PTMs). These modifications were bioinformatically predicted and experimentally validated to govern protein stability, enzymatic activity, and nuclear translocation, which increased during dehydration. These dehydration-responsive protein modifications, however, did not appear to affect enzymatic thermostability as GAPDH melting temperatures remained unchanged when tested with differential scanning fluorimetry. PTMs could promote extreme urea resistance in dehydrated GAPDH since the enzyme from dehydrated animals had a urea I50 of 7.3 M, while the I50 from the hydrated enzyme was 5.3 M. The physiological consequences of these dehydration-induced molecular modifications of GAPDH likely suppress GADPH glycolytic functions during the reduced circulation and global hypoxia experienced in dehydrated X. laevis.
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Affiliation(s)
- Hanane Hadj-Moussa
- Department of Biology and Institute of Biochemistry, Carleton University, Ottawa, Canada
| | - Steven C Wade
- Department of Biology and Institute of Biochemistry, Carleton University, Ottawa, Canada
| | - Christine L Childers
- Department of Biology and Institute of Biochemistry, Carleton University, Ottawa, Canada.,National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Kenneth B Storey
- Department of Biology and Institute of Biochemistry, Carleton University, Ottawa, Canada
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Bioenergetic Profiling of the Differentiating Human MDS Myeloid Lineage with Low and High Bone Marrow Blast Counts. Cancers (Basel) 2020; 12:cancers12123520. [PMID: 33255926 PMCID: PMC7759906 DOI: 10.3390/cancers12123520] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/19/2020] [Accepted: 11/20/2020] [Indexed: 12/20/2022] Open
Abstract
Simple Summary Myelodysplastic syndromes (MDS) encompass a very heterogeneous group of clonal hematopoietic stem cell differentiation disorders with malignant potential, an elusive pathobiology, and a poor prognosis. Given that the bioenergetic profile of the hematopoietic precursors is central to their effective differentiation, we investigated the metabolic status of a human differentiating MDS bone marrow-derived myeloid lineage. Our findings suggest that a perturbed metabolism underlies the syndrome’s pathogenesis and also determines the disease severity. We also propose that these bioenergetic alterations are essentially featured in and indeed drive the process of leukemic transformation. Our data not only offer novel insight into the elusive MDS pathophysiology, but also change our viewpoint on MDS-related acute myeloid leukemia biology. Abstract Myelodysplastic syndromes (MDS) encompass a very heterogeneous group of clonal hematopoietic stem cell differentiation disorders with malignant potential and an elusive pathobiology. Given the central role of metabolism in effective differentiation, we performed an untargeted metabolomic analysis of differentiating myeloid lineage cells from MDS bone marrow aspirates that exhibited <5% (G1) or ≥5% (G2) blasts, in order to delineate its role in MDS severity and malignant potential. Bone marrow aspirates were collected from 14 previously untreated MDS patients (G1, n = 10 and G2, n = 4) and age matched controls (n = 5). Following myeloid lineage cell isolation, untargeted mass spectrometry-based metabolomics analysis was performed. Data were processed and analyzed using Metabokit. Enrichment analysis was performed using Metaboanalyst v4 employing pathway-associated metabolite sets. We established a bioenergetic profile coordinated by the Warburg phenomenon in both groups, but with a massively different outcome that mainly depended upon its group mitochondrial function and redox state. G1 cells are overwhelmed by glycolytic intermediate accumulation due to failing mitochondria, while the functional electron transport chain and improved redox in G2 compensate for Warburg disruption. Both metabolomes reveal the production and abundance of epigenetic modifiers. G1 and G2 metabolomes differ and eventually determine the MDS clinical phenotype, as well as the potential for malignant transformation.
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Shurubor YI, Cooper AJL, Krasnikov AB, Isakova EP, Deryabina YI, Beal MF, Krasnikov BF. Changes of Coenzyme A and Acetyl-Coenzyme A Concentrations in Rats after a Single-Dose Intraperitoneal Injection of Hepatotoxic Thioacetamide Are Not Consistent with Rapid Recovery. Int J Mol Sci 2020; 21:E8918. [PMID: 33255464 PMCID: PMC7727790 DOI: 10.3390/ijms21238918] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/19/2020] [Accepted: 11/20/2020] [Indexed: 12/12/2022] Open
Abstract
Small biomolecules, such as coenzyme A (CoA) and acetyl coenzyme A (acetyl-CoA), play vital roles in the regulation of cellular energy metabolism. In this paper, we evaluated the delayed effect of the potent hepatotoxin thioacetamide (TAA) on the concentrations of CoA and acetyl-CoA in plasma and in different rat tissues. Administration of TAA negatively affects liver function and leads to the development of hepatic encephalopathy (HE). In our experiments, rats were administered a single intraperitoneal injection of TAA at doses of 200, 400, or 600 mg/kg. Plasma, liver, kidney, and brain samples were collected six days after the TAA administration, a period that has been suggested to allow for restoration of liver function. The concentrations of CoA and acetyl-CoA in the group of rats exposed to different doses of TAA were compared to those observed in healthy rats. The results obtained indicate that even a single administration of TAA to rats is sufficient to alter the physiological balance of CoA and acetyl-CoA in the plasma and tissues of rats for an extended period of time. The initial concentrations of CoA and acetyl-CoA were not restored even after the completion of the liver regeneration process.
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Affiliation(s)
- Yevgeniya I. Shurubor
- Center for Strategic Planning and Management of Medical and Biological Health Risks, Federal Medical-Biological Agency of The Russian Federation, 119121 Moscow, Russia;
| | - Arthur J. L. Cooper
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA
| | | | - Elena P. Isakova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (E.P.I.); (Y.I.D.)
| | - Yulia I. Deryabina
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (E.P.I.); (Y.I.D.)
| | - M. Flint Beal
- Department of Neurology, The Brain and Mind Research Institute, Weill Cornell Medical College, New York, NY 10021, USA;
| | - Boris F. Krasnikov
- Center for Strategic Planning and Management of Medical and Biological Health Risks, Federal Medical-Biological Agency of The Russian Federation, 119121 Moscow, Russia;
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA
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Di Francesco A, Choi Y, Bernier M, Zhang Y, Diaz-Ruiz A, Aon MA, Kalafut K, Ehrlich MR, Murt K, Ali A, Pearson KJ, Levan S, Preston JD, Martin-Montalvo A, Martindale JL, Abdelmohsen K, Michel CR, Willmes DM, Henke C, Navas P, Villalba JM, Siegel D, Gorospe M, Fritz K, Biswal S, Ross D, de Cabo R. NQO1 protects obese mice through improvements in glucose and lipid metabolism. NPJ Aging Mech Dis 2020; 6:13. [PMID: 33298924 PMCID: PMC7678866 DOI: 10.1038/s41514-020-00051-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 10/21/2020] [Indexed: 02/06/2023] Open
Abstract
Chronic nutrient excess leads to metabolic disorders and insulin resistance. Activation of stress-responsive pathways via Nrf2 activation contributes to energy metabolism regulation. Here, inducible activation of Nrf2 in mice and transgenesis of the Nrf2 target, NQO1, conferred protection from diet-induced metabolic defects through preservation of glucose homeostasis, insulin sensitivity, and lipid handling with improved physiological outcomes. NQO1-RNA interaction mediated the association with and inhibition of the translational machinery in skeletal muscle of NQO1 transgenic mice. NQO1-Tg mice on high-fat diet had lower adipose tissue macrophages and enhanced expression of lipogenic enzymes coincident with reduction in circulating and hepatic lipids. Metabolomics data revealed a systemic metabolic signature of improved glucose handling, cellular redox, and NAD+ metabolism while label-free quantitative mass spectrometry in skeletal muscle uncovered a distinct diet- and genotype-dependent acetylation pattern of SIRT3 targets across the core of intermediary metabolism. Thus, under nutritional excess, NQO1 transgenesis preserves healthful benefits.
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Affiliation(s)
- Andrea Di Francesco
- Translational Gerontology Branch, National Institute on Aging Intramural Program, National Institutes of Health, Baltimore, MD, 21224, USA
- Calico Life Sciences, South San Francisco, CA, USA
| | - Youngshim Choi
- Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
- University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Michel Bernier
- Translational Gerontology Branch, National Institute on Aging Intramural Program, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Yingchun Zhang
- Translational Gerontology Branch, National Institute on Aging Intramural Program, National Institutes of Health, Baltimore, MD, 21224, USA
- College of Pharmaceutical Sciences and Chinese Medicine, Southwest University, Chongqing, 475004, People's Republic of China
| | - Alberto Diaz-Ruiz
- Translational Gerontology Branch, National Institute on Aging Intramural Program, National Institutes of Health, Baltimore, MD, 21224, USA
- Nutritional Interventions Group, Precision Nutrition and Aging, Institute IMDEA Food, Crta. de Canto Blanco n° 8, 28049, Madrid, Spain
| | - Miguel A Aon
- Translational Gerontology Branch, National Institute on Aging Intramural Program, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Krystle Kalafut
- Translational Gerontology Branch, National Institute on Aging Intramural Program, National Institutes of Health, Baltimore, MD, 21224, USA
- Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Margaux R Ehrlich
- Translational Gerontology Branch, National Institute on Aging Intramural Program, National Institutes of Health, Baltimore, MD, 21224, USA
- Department Food Science, Cornell University, Ithaca, NY, 14850, USA
| | - Kelsey Murt
- Translational Gerontology Branch, National Institute on Aging Intramural Program, National Institutes of Health, Baltimore, MD, 21224, USA
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Ahmed Ali
- Translational Gerontology Branch, National Institute on Aging Intramural Program, National Institutes of Health, Baltimore, MD, 21224, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Kevin J Pearson
- Translational Gerontology Branch, National Institute on Aging Intramural Program, National Institutes of Health, Baltimore, MD, 21224, USA
- Pharmacology and Nutritional Sciences, University of Kentucky College of Medicine, Lexington, KY, 40536, USA
| | - Sophie Levan
- Translational Gerontology Branch, National Institute on Aging Intramural Program, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Joshua D Preston
- Pharmacology and Nutritional Sciences, University of Kentucky College of Medicine, Lexington, KY, 40536, USA
- Emory University School of Medicine (MD/PhD program), Atlanta, GA, USA
| | - Alejandro Martin-Montalvo
- Translational Gerontology Branch, National Institute on Aging Intramural Program, National Institutes of Health, Baltimore, MD, 21224, USA
- Department of Regeneration and Cell Therapy, Andalusian Center for Molecular Biology and Regenerative Medicine-CABIMER, Junta de Andalucia-University of Pablo de Olavide-University of Seville-CSIC, Seville, Spain
| | - Jennifer L Martindale
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Program, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Kotb Abdelmohsen
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Program, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Cole R Michel
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Diana M Willmes
- Molecular Diabetology, Paul Langerhans Institute Dresden of the Helmholtz German Center for Diabetes Research Munich, University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, 01307, Dresden, Germany
| | - Christine Henke
- Molecular Diabetology, Paul Langerhans Institute Dresden of the Helmholtz German Center for Diabetes Research Munich, University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, 01307, Dresden, Germany
| | - Placido Navas
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-CSIC-JA, 41013, Sevilla, Spain
| | - Jose Manuel Villalba
- Departamento de Biología Celular, Fisiología e Inmunología, Universidad de Córdoba, Campus de Excelencia Internacional Agroalimentario, ceiA3, Sevilla, Spain
| | - David Siegel
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Program, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Kristofer Fritz
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Shyam Biswal
- Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - David Ross
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Rafael de Cabo
- Translational Gerontology Branch, National Institute on Aging Intramural Program, National Institutes of Health, Baltimore, MD, 21224, USA.
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Regulation of gene expression by protein lysine acetylation in Salmonella. J Microbiol 2020; 58:979-987. [PMID: 33201432 DOI: 10.1007/s12275-020-0483-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/12/2020] [Accepted: 10/12/2020] [Indexed: 10/23/2022]
Abstract
Protein lysine acetylation influences many physiological functions, such as gene regulation, metabolism, and disease in eukaryotes. Although little is known about the role of lysine acetylation in bacteria, several reports have proposed its importance in various cellular processes. Here, we discussed the function of the protein lysine acetylation and the post-translational modifications (PTMs) of histone-like proteins in bacteria focusing on Salmonella pathogenicity. The protein lysine residue in Salmonella is acetylated by the Pat-mediated enzymatic pathway or by the acetyl phosphate-mediated non-enzymatic pathway. In Salmonella, the acetylation of lysine 102 and lysine 201 on PhoP inhibits its protein activity and DNA-binding, respectively. Lysine acetylation of the transcriptional regulator, HilD, also inhibits pathogenic gene expression. Moreover, it has been reported that the protein acetylation patterns significantly differ in the drug-resistant and -sensitive Salmonella strains. In addition, nucleoid-associated proteins such as histone-like nucleoid structuring protein (H-NS) are critical for the gene silencing in bacteria, and PTMs in H-NS also affect the gene expression. In this review, we suggest that protein lysine acetylation and the post-translational modifications of H-NS are important factors in understanding the regulation of gene expression responsible for pathogenicity in Salmonella.
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Teixeira CSS, Cerqueira NMFSA, Gomes P, Sousa SF. A Molecular Perspective on Sirtuin Activity. Int J Mol Sci 2020; 21:ijms21228609. [PMID: 33203121 PMCID: PMC7696986 DOI: 10.3390/ijms21228609] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/07/2020] [Accepted: 11/13/2020] [Indexed: 12/13/2022] Open
Abstract
The protein acetylation of either the α-amino groups of amino-terminal residues or of internal lysine or cysteine residues is one of the major posttranslational protein modifications that occur in the cell with repercussions at the protein as well as at the metabolome level. The lysine acetylation status is determined by the opposing activities of lysine acetyltransferases (KATs) and lysine deacetylases (KDACs), which add and remove acetyl groups from proteins, respectively. A special group of KDACs, named sirtuins, that require NAD+ as a substrate have received particular attention in recent years. They play critical roles in metabolism, and their abnormal activity has been implicated in several diseases. Conversely, the modulation of their activity has been associated with protection from age-related cardiovascular and metabolic diseases and with increased longevity. The benefits of either activating or inhibiting these enzymes have turned sirtuins into attractive therapeutic targets, and considerable effort has been directed toward developing specific sirtuin modulators. This review summarizes the protein acylation/deacylation processes with a special focus on the current developments in the sirtuin research field.
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Affiliation(s)
- Carla S. S. Teixeira
- UCIBIO/REQUIMTE, BioSIM - Department of Biomedicine, Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal; (C.S.S.T.); (N.M.F.S.A.C.)
| | - Nuno M. F. S. A. Cerqueira
- UCIBIO/REQUIMTE, BioSIM - Department of Biomedicine, Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal; (C.S.S.T.); (N.M.F.S.A.C.)
| | - Pedro Gomes
- Department of Biomedicine, Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal;
- Center for Health Technology and Services Research (CINTESIS), University of Porto, R. Dr. Plácido da Costa, 4200-450 Porto, Portugal
- Institute of Pharmacology and Experimental Therapeutics, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, Azinhaga Santa Comba, Celas, 3000-548 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, Azinhaga Santa Comba, Celas, 3000-548 Coimbra, Portugal
| | - Sérgio F. Sousa
- UCIBIO/REQUIMTE, BioSIM - Department of Biomedicine, Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal; (C.S.S.T.); (N.M.F.S.A.C.)
- Correspondence: ; Tel.: +351-22-551-3600
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Wang Y, Wondisford FE, Song C, Zhang T, Su X. Metabolic Flux Analysis-Linking Isotope Labeling and Metabolic Fluxes. Metabolites 2020; 10:metabo10110447. [PMID: 33172051 PMCID: PMC7694648 DOI: 10.3390/metabo10110447] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/03/2020] [Accepted: 11/04/2020] [Indexed: 01/02/2023] Open
Abstract
Metabolic flux analysis (MFA) is an increasingly important tool to study metabolism quantitatively. Unlike the concentrations of metabolites, the fluxes, which are the rates at which intracellular metabolites interconvert, are not directly measurable. MFA uses stable isotope labeled tracers to reveal information related to the fluxes. The conceptual idea of MFA is that in tracer experiments the isotope labeling patterns of intracellular metabolites are determined by the fluxes, therefore by measuring the labeling patterns we can infer the fluxes in the network. In this review, we will discuss the basic concept of MFA using a simplified upper glycolysis network as an example. We will show how the fluxes are reflected in the isotope labeling patterns. The central idea we wish to deliver is that under metabolic and isotopic steady-state the labeling pattern of a metabolite is the flux-weighted average of the substrates’ labeling patterns. As a result, MFA can tell the relative contributions of converging metabolic pathways only when these pathways make substrates in different labeling patterns for the shared product. This is the fundamental principle guiding the design of isotope labeling experiment for MFA including tracer selection. In addition, we will also discuss the basic biochemical assumptions of MFA, and we will show the flux-solving procedure and result evaluation. Finally, we will highlight the link between isotopically stationary and nonstationary flux analysis.
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Affiliation(s)
- Yujue Wang
- Department of Medicine, Rutgers-Robert Wood Johnson Medical School, New Brunswick, NJ 08901, USA; (Y.W.); (F.E.W.)
- Metabolomics Shared Resource, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
| | - Fredric E. Wondisford
- Department of Medicine, Rutgers-Robert Wood Johnson Medical School, New Brunswick, NJ 08901, USA; (Y.W.); (F.E.W.)
| | - Chi Song
- Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, OH 43210, USA;
| | - Teng Zhang
- Department of Mathematics, University of Central Florida, Orlando, FL 32816, USA;
| | - Xiaoyang Su
- Department of Medicine, Rutgers-Robert Wood Johnson Medical School, New Brunswick, NJ 08901, USA; (Y.W.); (F.E.W.)
- Metabolomics Shared Resource, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
- Correspondence: ; Tel.: +1-732-235-5447
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Pang R, Li Y, Liao K, Guo P, Li Y, Yang X, Zhang S, Lei T, Wang J, Chen M, Wu S, Xue L, Wu Q. Genome- and Proteome-Wide Analysis of Lysine Acetylation in Vibrio vulnificus Vv180806 Reveals Its Regulatory Roles in Virulence and Antibiotic Resistance. Front Microbiol 2020; 11:591287. [PMID: 33250879 PMCID: PMC7674927 DOI: 10.3389/fmicb.2020.591287] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/15/2020] [Indexed: 12/31/2022] Open
Abstract
Infection with Vibrio vulnificus is notorious for its atypical clinical manifestations and irreversible disease progression. Lysine acetylation is a conserved post-translational modification (PTM) that plays a critical regulatory role in diverse cellular processes. However, little is known about the role of lysine acetylation on the pathogenesis of V. vulnificus. Here, we report the complete genome sequence and a global profile for protein lysine acetylation of V. vulnificus Vv180806, a highly cefoxitin resistant strain isolated from a mortality case. The assembled genome comprised two circular chromosomes and one circular plasmid; it contained 4,770 protein-coding genes and 153 RNA genes. Phylogenetic analysis revealed genetic homology of this strain with other V. vulnificus strains from food sources. Of all the proteins in this strain, 1,924 (40.34%) were identified to be acetylated at 6,626 sites. The acetylated proteins were enriched in metabolic processes, binding functions, cytoplasm, and multiple central metabolic pathways. Moreover, the acetylation was found in most identified virulence factors of this strain, suggesting its potentially important role in bacterial virulence. Our work provides insights into the genomic and acetylomic features responsible for the virulence and antibiotic resistance of V. vulnificus, which will facilitate future investigations on the pathogenesis of this bacterium.
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Affiliation(s)
- Rui Pang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Ying Li
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Kang Liao
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Penghao Guo
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yanping Li
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xiaojuan Yang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Shuhong Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Tao Lei
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Juan Wang
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Moutong Chen
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Shi Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Liang Xue
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
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129
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Histone Deacetylase Inhibitors as Multitarget-Directed Epi-Drugs in Blocking PI3K Oncogenic Signaling: A Polypharmacology Approach. Int J Mol Sci 2020; 21:ijms21218198. [PMID: 33147762 PMCID: PMC7662987 DOI: 10.3390/ijms21218198] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 10/29/2020] [Accepted: 10/29/2020] [Indexed: 12/12/2022] Open
Abstract
Genetic mutations and aberrant epigenetic alterations are the triggers for carcinogenesis. The emergence of the drugs targeting epigenetic aberrations has provided a better outlook for cancer treatment. Histone deacetylases (HDACs) are epigenetic modifiers playing critical roles in numerous key biological functions. Inappropriate expression of HDACs and dysregulation of PI3K signaling pathway are common aberrations observed in human diseases, particularly in cancers. Histone deacetylase inhibitors (HDACIs) are a class of epigenetic small-molecular therapeutics exhibiting promising applications in the treatment of hematological and solid malignancies, and in non-neoplastic diseases. Although HDACIs as single agents exhibit synergy by inhibiting HDAC and the PI3K pathway, resistance to HDACIs is frequently encountered due to activation of compensatory survival pathway. Targeted simultaneous inhibition of both HDACs and PI3Ks with their respective inhibitors in combination displayed synergistic therapeutic efficacy and encouraged the development of a single HDAC-PI3K hybrid molecule via polypharmacology strategy. This review provides an overview of HDACs and the evolution of HDACs-based epigenetic therapeutic approaches targeting the PI3K pathway.
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130
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Yang F, Wang C. Profiling of post-translational modifications by chemical and computational proteomics. Chem Commun (Camb) 2020; 56:13506-13519. [PMID: 33084662 DOI: 10.1039/d0cc05447j] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Post-translational modifications (PTMs) diversify the molecular structures of proteins and play essential roles in regulating their functions. Abnormal PTM status has been linked to a variety of developmental disorders and human diseases, highlighting the importance of studying PTMs in understanding physiological processes and discovering novel nodes and links with therapeutic intervention potential. Classical biochemical methods are suitable for studying PTMs on individual proteins; however, global profiling of PTMs in proteomes remains a challenging task. In this feature article, we start with a brief review of the traditional affinity-based strategies and shift the emphasis to summarizing recent progress in the development and application of chemical and computational proteomic strategies to delineate the global landscapes of functional PTMs. Finally, we discuss current challenges in PTM detection and provide future perspectives on how the field can be further advanced.
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Affiliation(s)
- Fan Yang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
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131
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Rubisco lysine acetylation occurs at very low stoichiometry in mature Arabidopsis leaves: implications for regulation of enzyme function. Biochem J 2020; 477:3885-3896. [PMID: 32959870 PMCID: PMC7557146 DOI: 10.1042/bcj20200413] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 09/18/2020] [Accepted: 09/21/2020] [Indexed: 11/23/2022]
Abstract
Multiple studies have shown ribulose-1,5-bisphosphate carboxylase/oxygenase (E.C. 4.1.1.39; Rubisco) to be subject to Lys-acetylation at various residues; however, opposing reports exist about the biological significance of these post-translational modifications. One aspect of the Lys-acetylation that has not been addressed in plants generally, or with Rubisco specifically, is the stoichiometry at which these Lys-acetylation events occur. As a method to ascertain which Lys-acetylation sites on Arabidopsis Rubisco might be of regulatory importance to its catalytic function in the Calvin–Benson cycle, we purified Rubisco from leaves in both the day and night-time and performed independent mass spectrometry based methods to determine the stoichiometry of Rubisco Lys-acetylation events. The results indicate that Rubisco is acetylated at most Lys residues, but each acetylation event occurs at very low stoichiometry. Furthermore, in vitro treatments that increased the extent of Lys-acetylation on purified Rubisco had no effect on Rubisco maximal activity. Therefore, we are unable to confirm that Lys-acetylation at low stoichiometries can be a regulatory mechanism controlling Rubisco maximal activity. The results highlight the need for further use of stoichiometry measurements when determining the biological significance of reversible PTMs like acetylation.
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132
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Chen J, Liu Q, Zeng L, Huang X. Protein Acetylation/Deacetylation: A Potential Strategy for Fungal Infection Control. Front Microbiol 2020; 11:574736. [PMID: 33133044 PMCID: PMC7579399 DOI: 10.3389/fmicb.2020.574736] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 09/17/2020] [Indexed: 12/13/2022] Open
Abstract
Protein acetylation is a universal post-translational modification that fine-tunes the major cellular processes of many life forms. Although the mechanisms regulating protein acetylation have not been fully elucidated, this modification is finely tuned by both enzymatic and non-enzymatic mechanisms. Protein deacetylation is the reverse process of acetylation and is mediated by deacetylases. Together, protein acetylation and deacetylation constitute a reversible regulatory protein acetylation network. The recent application of mass spectrometry-based proteomics has led to accumulating evidence indicating that reversible protein acetylation may be related to fungal virulence because a substantial amount of virulence factors are acetylated. Additionally, the relationship between protein acetylation/deacetylation and fungal drug resistance has also been proven and the potential of deacetylase inhibitors as an anti-infective treatment has attracted attention. This review aimed to summarize the research progress in understanding fungal protein acetylation/deacetylation and discuss the mechanism of its mediation in fungal virulence, providing novel targets for the treatment of fungal infection.
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Affiliation(s)
- Junzhu Chen
- Department of Medical Microbiology, School of Medicine, Nanchang University, Nanchang, China
| | - Qiong Liu
- Department of Medical Microbiology, School of Medicine, Nanchang University, Nanchang, China
| | - Lingbing Zeng
- The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xiaotian Huang
- Department of Medical Microbiology, School of Medicine, Nanchang University, Nanchang, China
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133
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Min Z, Long X, Zhao H, Zhen X, Li R, Li M, Fan Y, Yu Y, Zhao Y, Qiao J. Protein Lysine Acetylation in Ovarian Granulosa Cells Affects Metabolic Homeostasis and Clinical Presentations of Women With Polycystic Ovary Syndrome. Front Cell Dev Biol 2020; 8:567028. [PMID: 33043000 PMCID: PMC7518144 DOI: 10.3389/fcell.2020.567028] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/13/2020] [Indexed: 12/11/2022] Open
Abstract
Polycystic ovary syndrome (PCOS) is one of the most common reproductive endocrine disorders accompanied by obvious metabolic abnormalities. Lower-quality oocytes and embryos are often found in PCOS women during assisted reproductive technology treatment. However, there is still no clarity about the mechanism of ovarian metabolic disorders and the impact on oocyte maturation in PCOS. The aim of this study was to understand the potential effect of the posttranslational modification on ovarian metabolic homeostasis and oocyte development potential in women with PCOS. A quantitative analysis of acetylated proteomics in ovarian granulosa cells of PCOS and control groups was carried out by mass spectrometry. There was widespread lysine acetylation of proteins, of which 265 proteins had increased levels of acetylation and 68 proteins had decreased levels of acetylation in the PCOS group. Most notably, differentially acetylated proteins were significantly enriched in the metabolic pathways of glycolysis, fatty acid degradation, TCA cycle, tryptophan metabolism, and branched-chain amino acid degradation. Acetyl-CoA acetyltransferase 1 (ACAT1) was an enzyme central to these metabolic pathways with increased acetylation level in the PCOS group, and there was a negative correlation of ACAT1 acetylation levels in PCOS granulosa cells with oocyte quality and embryo development efficiency in the clinic. Lysine acetylation changes of key enzymes in PCOS granulosa cells might attenuate their activities and alter metabolic homeostasis of follicular microenvironment for oocyte maturation and embryo development.
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Affiliation(s)
- Zheying Min
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.,National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Xiaoyu Long
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.,National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Hongcui Zhao
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.,National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Xiumei Zhen
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.,National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Rong Li
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.,National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Mo Li
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.,National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Yong Fan
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yang Yu
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.,National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Yue Zhao
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.,National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China.,Research Units of Comprehensive Diagnosis and Treatment of Oocyte Maturation Arrest, Chinese Academy of Medical Sciences, Beijing, China
| | - Jie Qiao
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.,National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Peking University, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China.,Research Units of Comprehensive Diagnosis and Treatment of Oocyte Maturation Arrest, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Beijing, China
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134
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Noonepalle S, Shen S, Ptáček J, Tavares MT, Zhang G, Stránský J, Pavlíček J, Ferreira GM, Hadley M, Pelaez G, Bařinka C, Kozikowski AP, Villagra A. Rational Design of Suprastat: A Novel Selective Histone Deacetylase 6 Inhibitor with the Ability to Potentiate Immunotherapy in Melanoma Models. J Med Chem 2020; 63:10246-10262. [PMID: 32815366 DOI: 10.1021/acs.jmedchem.0c00567] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Selective inhibition of histone deacetylase 6 (HDAC6) is being recognized as a therapeutic approach for cancers. In this study, we designed a new HDAC6 inhibitor, named Suprastat, using in silico simulations. X-ray crystallography and molecular dynamics simulations provide strong evidence to support the notion that the aminomethyl and hydroxyl groups in the capping group of Suprastat establish significant hydrogen bond interactions, either direct or water-mediated, with residues D460, N530, and S531, which play a vital role in regulating the deacetylase function of the enzyme and which are absent in other isoforms. In vitro characterization of Suprastat demonstrates subnanomolar HDAC6 inhibitory potency and a hundred- to a thousand-fold HDAC6 selectivity over the other HDAC isoforms. In vivo studies reveal that a combination of Suprastat and anti-PD1 immunotherapy enhances antitumor immune response, mediated by a decrease of protumoral M2 macrophages and increased infiltration of antitumor CD8+ effector and memory T-cells.
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Affiliation(s)
- Satish Noonepalle
- Department of Biochemistry and Molecular Medicine, The George Washington University, Washington, District of Columbia 20052, United States
| | - Sida Shen
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Jakub Ptáček
- Laboratory of Structural Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, Vestec 252 50, Czech Republic
| | - Maurício T Tavares
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Guiping Zhang
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Jan Stránský
- Centre of Molecular Structure, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, Vestec 252 50, Czech Republic
| | - Jiří Pavlíček
- Centre of Molecular Structure, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, Vestec 252 50, Czech Republic
| | - Glaucio M Ferreira
- Department of Pharmacy, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil
| | - Melissa Hadley
- Department of Biochemistry and Molecular Medicine, The George Washington University, Washington, District of Columbia 20052, United States
| | - Guido Pelaez
- Department of Biochemistry and Molecular Medicine, The George Washington University, Washington, District of Columbia 20052, United States
| | - Cyril Bařinka
- Laboratory of Structural Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, Vestec 252 50, Czech Republic
| | | | - Alejandro Villagra
- Department of Biochemistry and Molecular Medicine, The George Washington University, Washington, District of Columbia 20052, United States
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135
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Ceyssens PJ, De Smet J, Wagemans J, Akulenko N, Klimuk E, Hedge S, Voet M, Hendrix H, Paeshuyse J, Landuyt B, Xu H, Blanchard J, Severinov K, Lavigne R. The Phage-Encoded N-Acetyltransferase Rac Mediates Inactivation of Pseudomonas aeruginosa Transcription by Cleavage of the RNA Polymerase Alpha Subunit. Viruses 2020; 12:v12090976. [PMID: 32887488 PMCID: PMC7552054 DOI: 10.3390/v12090976] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/26/2020] [Accepted: 09/01/2020] [Indexed: 12/20/2022] Open
Abstract
In this study, we describe the biological function of the phage-encoded protein RNA polymerase alpha subunit cleavage protein (Rac), a predicted Gcn5-related acetyltransferase encoded by phiKMV-like viruses. These phages encode a single-subunit RNA polymerase for transcription of their late (structure- and lysis-associated) genes, whereas the bacterial RNA polymerase is used at the earlier stages of infection. Rac mediates the inactivation of bacterial transcription by introducing a specific cleavage in the α subunit of the bacterial RNA polymerase. This cleavage occurs within the flexible linker sequence and disconnects the C-terminal domain, required for transcription initiation from most highly active cellular promoters. To achieve this, Rac likely taps into a novel post-translational modification (PTM) mechanism within the host Pseudomonas aeruginosa. From an evolutionary perspective, this novel phage-encoded regulation mechanism confirms the importance of PTMs in the prokaryotic metabolism and represents a new way by which phages can hijack the bacterial host metabolism.
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Affiliation(s)
- Pieter-Jan Ceyssens
- Department of Biosystems, KU Leuven, 3000 Leuven, Belgium; (P.-J.C.); (J.D.S.); (J.W.); (M.V.); (H.H.); (J.P.)
| | - Jeroen De Smet
- Department of Biosystems, KU Leuven, 3000 Leuven, Belgium; (P.-J.C.); (J.D.S.); (J.W.); (M.V.); (H.H.); (J.P.)
| | - Jeroen Wagemans
- Department of Biosystems, KU Leuven, 3000 Leuven, Belgium; (P.-J.C.); (J.D.S.); (J.W.); (M.V.); (H.H.); (J.P.)
| | - Natalia Akulenko
- Institute of Molecular Genetics, Russian Academy of Sciences, 119334 Moscow, Russia; (N.A.); (E.K.); (K.S.)
| | - Evgeny Klimuk
- Institute of Molecular Genetics, Russian Academy of Sciences, 119334 Moscow, Russia; (N.A.); (E.K.); (K.S.)
| | - Subray Hedge
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY 10461, USA; (S.H.); (H.X.); (J.B.)
| | - Marleen Voet
- Department of Biosystems, KU Leuven, 3000 Leuven, Belgium; (P.-J.C.); (J.D.S.); (J.W.); (M.V.); (H.H.); (J.P.)
| | - Hanne Hendrix
- Department of Biosystems, KU Leuven, 3000 Leuven, Belgium; (P.-J.C.); (J.D.S.); (J.W.); (M.V.); (H.H.); (J.P.)
| | - Jan Paeshuyse
- Department of Biosystems, KU Leuven, 3000 Leuven, Belgium; (P.-J.C.); (J.D.S.); (J.W.); (M.V.); (H.H.); (J.P.)
| | - Bart Landuyt
- Department of Biology, KU Leuven, 3000 Leuven, Belgium;
| | - Hua Xu
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY 10461, USA; (S.H.); (H.X.); (J.B.)
| | - John Blanchard
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY 10461, USA; (S.H.); (H.X.); (J.B.)
| | - Konstantin Severinov
- Institute of Molecular Genetics, Russian Academy of Sciences, 119334 Moscow, Russia; (N.A.); (E.K.); (K.S.)
| | - Rob Lavigne
- Department of Biosystems, KU Leuven, 3000 Leuven, Belgium; (P.-J.C.); (J.D.S.); (J.W.); (M.V.); (H.H.); (J.P.)
- Correspondence: ; Tel.: +32-16-379-524
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136
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Luo L, Martin SC, Parkington J, Cadena SM, Zhu J, Ibebunjo C, Summermatter S, Londraville N, Patora-Komisarska K, Widler L, Zhai H, Trendelenburg AU, Glass DJ, Shi J. HDAC4 Controls Muscle Homeostasis through Deacetylation of Myosin Heavy Chain, PGC-1α, and Hsc70. Cell Rep 2020; 29:749-763.e12. [PMID: 31618641 DOI: 10.1016/j.celrep.2019.09.023] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 08/20/2019] [Accepted: 09/09/2019] [Indexed: 02/03/2023] Open
Abstract
HDAC4, a class IIa histone deacetylase, is upregulated in skeletal muscle in response to denervation-induced atrophy. When HDAC4 is deleted postnatally, mice are partially protected from denervation. Despite the name "histone" deacetylase, HDAC4 demonstrably deacetylates cytosolic and non-histone nuclear proteins. We developed potent and selective class IIa HDAC inhibitors. Using these tools and genetic knockdown, we identified three previously unidentified substrates of HDAC4: myosin heavy chain, peroxisome proliferator-activated receptor gamma co-activator 1alpha (PGC-1α), and heat shock cognate 71 kDa protein (Hsc70). HDAC4 inhibition almost completely prevented denervation-induced loss of myosin heavy chain isoforms and blocked the action of their E3 ligase, MuRF1. PGC-1α directly interacts with class IIa HDACs; selective inhibitors increased PGC-1α protein in muscles. Hsc70 deacetylation by HDAC4 affects its chaperone activity. Through these endogenous HDAC4 substrates, we identified several muscle metabolic pathways that are regulated by class IIa HDACs, opening up new therapeutic options to treat skeletal muscle disorders and potentially other disease where these specific pathways are affected.
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Affiliation(s)
- Liqing Luo
- Novartis Institute for Biomedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Sherry C Martin
- Novartis Institute for Biomedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Jascha Parkington
- Novartis Institute for Biomedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Samuel M Cadena
- Novartis Institute for Biomedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Jiang Zhu
- Novartis Institute for Biomedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Chikwendu Ibebunjo
- Novartis Institute for Biomedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | | | - Nicole Londraville
- Novartis Institute for Biomedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | | | - Leo Widler
- Novartis Institute for Biomedical Research, 4056 Basel, Switzerland
| | - Huili Zhai
- Novartis Institute for Biomedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | | | - David J Glass
- Novartis Institute for Biomedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Jun Shi
- Novartis Institute for Biomedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA.
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Abstract
Microbial CO2 fixation and conversion constitute a potential solution to both utilization of greenhouse gas or industrial waste gases and sustainable production of bulk chemicals and fuels. Autotrophic gas-fermenting bacteria play central roles in this bioprocess. This study provides new insights regarding the metabolic regulatory mechanisms underlying CO2 reduction in Clostridium ljungdahlii, a representative gas-fermenting bacterium. A critical formate dehydrogenase (FDH1) responsible for fixing CO2 and a dominant reversible lysine acetylation system, At2/Dat1, were identified. Furthermore, FDH1 was found to be interactively regulated by both the At2/Dat1 system and the global transcriptional factor CcpA, and the two regulatory systems are mutually restricted. Reconstruction of this multilevel metabolic regulatory module led to improved CO2 metabolism by C. ljungdahlii. These findings not only substantively expand our understanding but also provide a potentially useful metabolic engineering strategy for microbial carbon fixation. Protein lysine acetylation, a prevalent posttranslational modification, regulates numerous crucial biological processes in cells. Nevertheless, how lysine acetylation interacts with other types of regulation to coordinate metabolism remains largely unknown owing to the complexity of the process. Here, using a representative gas-fermenting bacterium, Clostridium ljungdahlii, we revealed a novel regulatory mechanism that employs both the lysine acetylation and transcriptional regulation systems to interactively control CO2 fixation, a key biological process for utilizing this one-carbon gas. A dominant lysine acetyltransferase/deacetylase system, At2/Dat1, was identified and found to regulate FDH1 (formate dehydrogenase responsible for CO2 fixation) activity via a crucial acetylation site (lysine-29). Notably, the global transcription factor CcpA was also shown to be regulated by At2/Dat1; in turn, CcpA could directly control At2 expression, thus indicating an unreported interaction mode between the acetylation system and transcription factors. Moreover, CcpA was observed to negatively regulate FDH1 expression, which, when combined with At2/Dat1, leads to the collaborative regulation of this enzyme. Based on this concept, we reconstructed the regulatory network related to FDH1, realizing significantly increased CO2 utilization by C. ljungdahlii.
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138
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Widespread protein lysine acetylation in gut microbiome and its alterations in patients with Crohn's disease. Nat Commun 2020; 11:4120. [PMID: 32807798 PMCID: PMC7431864 DOI: 10.1038/s41467-020-17916-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 07/27/2020] [Indexed: 02/06/2023] Open
Abstract
Lysine acetylation (Kac), an abundant post-translational modification (PTM) in prokaryotes, regulates various microbial metabolic pathways. However, no studies have examined protein Kac at the microbiome level, and it remains unknown whether Kac level is altered in patient microbiomes. Herein, we use a peptide immuno-affinity enrichment strategy coupled with mass spectrometry to characterize protein Kac in the microbiome, which successfully identifies 35,200 Kac peptides from microbial or human proteins in gut microbiome samples. We demonstrate that Kac is widely distributed in gut microbial metabolic pathways, including anaerobic fermentation to generate short-chain fatty acids. Applying to the analyses of microbiomes of patients with Crohn’s disease identifies 52 host and 136 microbial protein Kac sites that are differentially abundant in disease versus controls. This microbiome-wide acetylomic approach aids in advancing functional microbiome research. Intestinal microbiota is increasingly reported to influence human health, but little is known on how its functions are regulated. Here the authors characterize microbiome protein acetylation and demonstrate its potential roles in shaping gut microbial functions and the onset of Crohn’s disease.
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139
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Multiple stressor responses are regulated by sirtuins in Mytilus congeners. Comp Biochem Physiol A Mol Integr Physiol 2020; 246:110719. [DOI: 10.1016/j.cbpa.2020.110719] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 02/06/2023]
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140
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Proteomics analysis reveals the effect of Aeromonas hydrophila sirtuin CobB on biological functions. J Proteomics 2020; 225:103848. [DOI: 10.1016/j.jprot.2020.103848] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 05/09/2020] [Accepted: 05/24/2020] [Indexed: 02/07/2023]
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141
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Novak J, Fabrik I, Jurnecka D, Holubova J, Stanek O, Sebo P. Bordetella pertussis Acetylome is Shaped by Lysine Deacetylase Bkd1. J Proteome Res 2020; 19:3680-3696. [PMID: 32674575 DOI: 10.1021/acs.jproteome.0c00178] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Post-translational modifications of proteins enable swift physiological adaptation of cells to altered growth conditions and stress. Aside from protein phosphorylation, acetylation on ε-amino groups of lysine residues (N-ε-lysine acetylation) represents another important post-translational modification of proteins. For many bacterial pathogens, including the whooping cough agent Bordetella pertussis, the role and extent of protein acetylation remain to be defined. We expressed in Escherichia coli the BP0960 and BP3063 genes encoding two putative deacetylases of B. pertussis and show that BP0960 encodes a lysine deacetylase enzyme, named Bkd1, that regulates acetylation of a range of B. pertussis proteins. Comparison of the proteome and acetylome of a Δbkd1 mutant with the proteome and acetylome of wild-type B. pertussis (PRIDE ID. PXD016384) revealed that acetylation on lysine residues may modulate activities or stabilities of proteins involved in bacterial metabolism and histone-like proteins. However, increased acetylation of the BvgA response regulator protein of the B. pertussis master virulence-regulating BvgAS two-component system affected neither the total levels of produced BvgA nor its phosphorylation status. Indeed, the Δbkd1 mutant was not impaired in the production of key virulence factors and its survival within human macrophages in vitro was not affected. The Δbkd1 mutant exhibited an increased growth rate under carbon source-limiting conditions and its virulence in the in vivo mouse lung infection model was somewhat affected. These results indicate that the lysine deacetylase Bkd1 and N-ε-lysine acetylation primarily modulate the general metabolism rather than the virulence of B. pertussis.
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Affiliation(s)
- Jakub Novak
- Institute of Microbiology of the Czech Academy of Sciences, Prague 14220, Czech Republic.,Faculty of Science, Charles University, Prague 11636, Czech Republic
| | - Ivo Fabrik
- Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove 50005, Czech Republic
| | - David Jurnecka
- Institute of Microbiology of the Czech Academy of Sciences, Prague 14220, Czech Republic.,Faculty of Science, Charles University, Prague 11636, Czech Republic
| | - Jana Holubova
- Institute of Microbiology of the Czech Academy of Sciences, Prague 14220, Czech Republic
| | - Ondrej Stanek
- Institute of Microbiology of the Czech Academy of Sciences, Prague 14220, Czech Republic
| | - Peter Sebo
- Institute of Microbiology of the Czech Academy of Sciences, Prague 14220, Czech Republic
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142
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Li W, Yang L, Nan W, Lu J, Zhang S, Ujiroghene OJ, Pang X, Lv J. Whole-genome sequencing and genomic-based acid tolerance mechanisms of Lactobacillus delbrueckii subsp. bulgaricus LJJ. Appl Microbiol Biotechnol 2020; 104:7631-7642. [PMID: 32715364 DOI: 10.1007/s00253-020-10788-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 07/02/2020] [Accepted: 07/13/2020] [Indexed: 11/24/2022]
Abstract
The probiotic efficacy and fermentative ability of Lactobacillus delbrueckii subsp. bulgaricus (L. bulgaricus), a widely used probiotic, is majorly affected by its acid tolerance. Here, we conducted whole-genome sequencing of the high acid-tolerant L. bulgaricus LJJ stored in the laboratory. Compared with the whole genome of low acid-tolerant strain L. bulgaricus ATCC11842, the results show that 16 candidate acid-tolerant genes may be involved in the regulation of the acid tolerance of L. bulgaricus LJJ. Association analysis of candidate acid-tolerant genes and acid-tolerant traits of different L. bulgaricus strains revealed that the three genes dapA, dapH, and lysC are the main reasons for the strong acid tolerance of L. bulgaricus LJJ. The results of real-time quantitative PCR (RT-qPCR) supported this conclusion. KEGG pathway analysis showed that these three acid-tolerant genes are involved in the synthesis of lysine; the synthesis of lysine may confer L. bulgaricus LJJ strong acid tolerance. This study successfully revealed the acid tolerance mechanism of L. bulgaricus LJJ and provides a theoretical basis for the subsequent selection of strains with high acid tolerance for improved probiotic functions. KEY POINTS: • Three genes are identified as acid-tolerant genes, respectively, lysC, dapA, and dapH. • LysC and dapA are the major key genes in the synthesis of lysine. • The synthesis of lysine may confer L. bulgaricus LJJ strong acid tolerance.
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Affiliation(s)
- Weixun Li
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Lan Yang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Wenlong Nan
- China Animal Health and Epidemiology Center, Qingdao, 266032, China
| | - Jing Lu
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Shuwen Zhang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Obaroakpo Joy Ujiroghene
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,Department of Food Science and Technology, Auchi Polytechnic, Auchi, Edo State, Nigeria
| | - Xiaoyang Pang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Jiaping Lv
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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143
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Kruse R, Sahebekhtiari N, Højlund K. The Mitochondrial Proteomic Signatures of Human Skeletal Muscle Linked to Insulin Resistance. Int J Mol Sci 2020; 21:ijms21155374. [PMID: 32731645 PMCID: PMC7432338 DOI: 10.3390/ijms21155374] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/20/2020] [Accepted: 07/26/2020] [Indexed: 12/12/2022] Open
Abstract
Introduction: Mitochondria are essential in energy metabolism and cellular survival, and there is growing evidence that insulin resistance in chronic metabolic disorders, such as obesity, type 2 diabetes (T2D), and aging, is linked to mitochondrial dysfunction in skeletal muscle. Protein profiling by proteomics is a powerful tool to investigate mechanisms underlying complex disorders. However, despite significant advances in proteomics within the past two decades, the technologies have not yet been fully exploited in the field of skeletal muscle proteome. Area covered: Here, we review the currently available studies characterizing the mitochondrial proteome in human skeletal muscle in insulin-resistant conditions, such as obesity, T2D, and aging, as well as exercise-mediated changes in the mitochondrial proteome. Furthermore, we outline technical challenges and limitations and methodological aspects that should be considered when planning future large-scale proteomics studies of mitochondria from human skeletal muscle. Authors’ view: At present, most proteomic studies of skeletal muscle or isolated muscle mitochondria have demonstrated a reduced abundance of proteins in several mitochondrial biological processes in obesity, T2D, and aging, whereas the beneficial effects of exercise involve an increased content of muscle proteins involved in mitochondrial metabolism. Powerful mass-spectrometry-based proteomics now provides unprecedented opportunities to perform in-depth proteomics of muscle mitochondria, which in the near future is expected to increase our understanding of the complex molecular mechanisms underlying the link between mitochondrial dysfunction and insulin resistance in chronic metabolic disorders.
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Affiliation(s)
- Rikke Kruse
- Steno Diabetes Center Odense, Odense University Hospital, DK-5000 Odense C, Denmark; (R.K.); (N.S.)
- Department of Clinical Research & Department of Molecular Medicine, University of Southern Denmark, DK-5000 Odense C, Denmark
| | - Navid Sahebekhtiari
- Steno Diabetes Center Odense, Odense University Hospital, DK-5000 Odense C, Denmark; (R.K.); (N.S.)
- Department of Clinical Research & Department of Molecular Medicine, University of Southern Denmark, DK-5000 Odense C, Denmark
| | - Kurt Højlund
- Steno Diabetes Center Odense, Odense University Hospital, DK-5000 Odense C, Denmark; (R.K.); (N.S.)
- Department of Clinical Research & Department of Molecular Medicine, University of Southern Denmark, DK-5000 Odense C, Denmark
- Correspondence: ; Tel.: +45-2532-06-48
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144
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Contributions of Mass Spectrometry-Based Proteomics to Understanding Salmonella-Host Interactions. Pathogens 2020; 9:pathogens9070581. [PMID: 32708900 PMCID: PMC7400052 DOI: 10.3390/pathogens9070581] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/13/2020] [Accepted: 07/16/2020] [Indexed: 02/02/2023] Open
Abstract
As a model pathogen, Salmonella invades both phagocytic and non-phagocytic host cells and adopts an intracellular lifestyle in a membrane-bound compartment during infection. Therefore, a systemic overview of Salmonella adaptations to distinct host cells together with host remodeling will assist us in charting the landscape of host-pathogen interactions. Central to the Salmonella-host interplay are bacterial virulence factors (effectors) that are injected into host cells by type III secretion systems (T3SSs). Despite great progress, functional studies of bacterial effectors have experienced daunting challenges as well. In the last decade, mass spectrometry-based proteomics has evolved into a powerful technological platform that can quantitatively measure thousands of proteins in terms of their expression as well as post-translational modifications. Here, we will review the applications of high-throughput proteomic technologies in understanding the dynamic reprogramming of both Salmonella and host proteomes during the course of infection. Furthermore, we will summarize the progress in utilizing affinity purification-mass spectrometry to screen for host substrates of Salmonella T3SS effectors. Finally, we will critically discuss some limitations/challenges with current proteomic platforms in the context of host-pathogen interactions and highlight some emerging technologies that may offer the promise of tackling these problems.
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145
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Echlin H, Frank M, Rock C, Rosch JW. Role of the pyruvate metabolic network on carbohydrate metabolism and virulence in Streptococcus pneumoniae. Mol Microbiol 2020; 114:536-552. [PMID: 32495474 DOI: 10.1111/mmi.14557] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 04/27/2020] [Accepted: 05/22/2020] [Indexed: 11/30/2022]
Abstract
Streptococcus pneumoniae is a major human pathogen that must adapt to unique nutritional environments in several host niches. The pneumococcus can metabolize a range of carbohydrates that feed into glycolysis ending in pyruvate, which is catabolized by several enzymes. We investigated how the pneumococcus utilizes these enzymes to metabolize different carbohydrates and how this impacts survival in the host. Loss of ldh decreased bacterial burden in the nasopharynx and enhanced bacteremia in mice. Loss of spxB, pdhC or pfl2 decreased bacteremia and increased host survival. In glucose or galactose, loss of ldh increased capsule production, whereas loss of spxB and pdhC reduced capsule production. The pfl2 mutant exhibited reduced capsule production only in galactose. In glucose, pyruvate was metabolized primarily by LDH to generate lactate and NAD+ and by SpxB and PDHc to generate acetyl-CoA. In galactose, pyruvate metabolism was shunted toward acetyl-CoA production. The majority of acetyl-CoA generated by PFL was used to regenerate NAD+ with a subset used in capsule production, while the acetyl-CoA generated by SpxB and PDHc was utilized primarily for capsule biosynthesis. These data suggest that the pneumococcus can alter flux of pyruvate metabolism dependent on the carbohydrate present to succeed in distinct host niches.
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Affiliation(s)
- Haley Echlin
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Matthew Frank
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Charles Rock
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jason W Rosch
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
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146
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Kloehn J, Oppenheim RD, Siddiqui G, De Bock PJ, Kumar Dogga S, Coute Y, Hakimi MA, Creek DJ, Soldati-Favre D. Multi-omics analysis delineates the distinct functions of sub-cellular acetyl-CoA pools in Toxoplasma gondii. BMC Biol 2020; 18:67. [PMID: 32546260 PMCID: PMC7296777 DOI: 10.1186/s12915-020-00791-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 05/08/2020] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Acetyl-CoA is a key molecule in all organisms, implicated in several metabolic pathways as well as in transcriptional regulation and post-translational modification. The human pathogen Toxoplasma gondii possesses at least four enzymes which generate acetyl-CoA in the nucleo-cytosol (acetyl-CoA synthetase (ACS); ATP citrate lyase (ACL)), mitochondrion (branched-chain α-keto acid dehydrogenase-complex (BCKDH)) and apicoplast (pyruvate dehydrogenase complex (PDH)). Given the diverse functions of acetyl-CoA, we know very little about the role of sub-cellular acetyl-CoA pools in parasite physiology. RESULTS To assess the importance and functions of sub-cellular acetyl-CoA-pools, we measured the acetylome, transcriptome, proteome and metabolome of parasites lacking ACL/ACS or BCKDH. We demonstrate that ACL/ACS constitute a synthetic lethal pair. Loss of both enzymes causes a halt in fatty acid elongation, hypo-acetylation of nucleo-cytosolic and secretory proteins and broad changes in gene expression. In contrast, loss of BCKDH results in an altered TCA cycle, hypo-acetylation of mitochondrial proteins and few specific changes in gene expression. We provide evidence that changes in the acetylome, transcriptome and proteome of cells lacking BCKDH enable the metabolic adaptations and thus the survival of these parasites. CONCLUSIONS Using multi-omics and molecular tools, we obtain a global and integrative picture of the role of distinct acetyl-CoA pools in T. gondii physiology. Cytosolic acetyl-CoA is essential and is required for the synthesis of parasite-specific fatty acids. In contrast, loss of mitochondrial acetyl-CoA can be compensated for through metabolic adaptations implemented at the transcriptional, translational and post-translational level.
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Affiliation(s)
- Joachim Kloehn
- Department of Microbiology and Molecular Medicine, CMU, University of Geneva, Rue Michel-Servet 1, 1211, Geneva, Switzerland
| | - Rebecca D Oppenheim
- Department of Microbiology and Molecular Medicine, CMU, University of Geneva, Rue Michel-Servet 1, 1211, Geneva, Switzerland
| | - Ghizal Siddiqui
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville campus, Parkville, VIC, 3052, Australia
| | - Pieter-Jan De Bock
- University Grenoble Alpes, CEA, INSERM, IRIG, BGE, F-38000, Grenoble, France
| | - Sunil Kumar Dogga
- Department of Microbiology and Molecular Medicine, CMU, University of Geneva, Rue Michel-Servet 1, 1211, Geneva, Switzerland
| | - Yohann Coute
- University Grenoble Alpes, CEA, INSERM, IRIG, BGE, F-38000, Grenoble, France
| | - Mohamed-Ali Hakimi
- Epigenetic and Parasites Team, UMR5163/LAPM, Domaine de la Merci, Jean Roget Institute, 38700, La Tronche, France
| | - Darren J Creek
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville campus, Parkville, VIC, 3052, Australia
| | - Dominique Soldati-Favre
- Department of Microbiology and Molecular Medicine, CMU, University of Geneva, Rue Michel-Servet 1, 1211, Geneva, Switzerland.
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147
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Target genes directly regulated by Eha are required for Edwardsiella tarda survival within macrophages. Vet Microbiol 2020; 247:108739. [PMID: 32768240 DOI: 10.1016/j.vetmic.2020.108739] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 05/22/2020] [Accepted: 05/25/2020] [Indexed: 11/23/2022]
Abstract
Eha is a virulence regulator in Edwardsiella tarda (E. tarda). The present study examined how Eha regulated its target genes to affect the bacterial survival within the cells. We constructed the reporter a pGEX-4T-ehaflag plasmid expressing Eha tagged at its C terminus with the flag epitope, and introduced the plasmid into an eha mutant ET13 strain, and obtained a Cehaflag strain. The expression and activity of an EhaFlag fusion protein restored the survival of the Cehaflag as the wild type in macrophages by Western blotting and intracellular survival experiments. We used a monoclonal anti-Flag antibody to precipitate EhaFlag-DNA complexes using chromatic immunoprecipitation (ChIP). We then designed primers based on the differentially-expressed genes identified from RNA-sequencing, and identified ten Eha-interacting genes by qPCR. We amplified the promoter regions of the ten genes and the eha gene from ET13 strain by PCR, constructed pBD-PtargetlacZ and pBD-PehalacZ plasmids. The eha gene directly and positively regulated these target genes, and be negatively auto-regulated by Eha in E. tarda, as determined by comparing their β-Galactosidase activities. These target genes were distributed in the categories involved in the bacterial growth, movement and resistance to H2O2 or acid. We further constructed a ETATCC_RS15225 mutant (△dcuA1), a ETATCC_ RS14855 mutant (△flgK) anda ETATCC_RS07650 mutant (ΔtnaA), and a partial complementary strains of △eha-tnaA and △eha-flgK and the complementary strains of CΔflgK and CΔtnaA. The ETATCC_RS15225 gene probably encoded a transporter protein DcuA1 at outer membrane with SDS-PAGE and RT-PCR. The ETATCC _RS14855 gene probably encoded FlgK protein and affected the bacterial motility. The ETATCC_RS07650 gene encoded Tryptophanase, which affected the bacterial survival within macrophages. With the assistance of these above strains, our results showed that the eha gene was able to regulate the ETATCC_RS15225 gene to express its outer membrane protein DcuA1, the ETATCC _RS14855 gene to control the flagellar motility and the ETATCC_RS07650 to affect the bacterial survival within macrophages. With the combination of other functions of above three genes, our results suggested that Eha directly regulates the target genes to affect E. tarda to survive within the cells.
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148
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Mao M, Xue Y, He Y, Zhou X, Rafique F, Hu H, Liu J, Feng L, Yang W, Li X, Sun L, Huang Z, Ma J. Systematic identification and comparative analysis of lysine succinylation between the green and white parts of chimeric leaves of Ananas comosus var. bracteatus. BMC Genomics 2020; 21:383. [PMID: 32493214 PMCID: PMC7268518 DOI: 10.1186/s12864-020-6750-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 04/21/2020] [Indexed: 01/26/2023] Open
Abstract
Background Lysine succinylation, an important protein posttranslational modification (PTM), is widespread and conservative. The regulatory functions of succinylation in leaf color has been reported. The chimeric leaves of Ananas comosus var. bracteatus are composed of normal green parts and albino white parts. However, the extent and function of lysine succinylation in chimeric leaves of Ananas comosus var. bracteatus has yet to be investigated. Results Compared to the green (Gr) parts, the global succinylation level was increased in the white (Wh) parts of chimeric leaves according to the Western blot and immunohistochemistry analysis. Furthermore, we quantitated the change in the succinylation profiles between the Wh and Gr parts of chimeric leaves using label-free LFQ intensity. In total, 855 succinylated sites in 335 proteins were identified, and 593 succinylated sites in 237 proteins were quantified. Compared to the Gr parts, 232 (61.1%) sites in 128 proteins were quantified as upregulated targets, and 148 (38.9%) sites in 70 proteins were quantified as downregulated targets in the Wh parts of chimeric leaves using a 1.5-fold threshold (P < 0.05). These proteins with altered succinylation level were mainly involved in crassulacean acid metabolism (CAM) photosynthesis, photorespiration, glycolysis, the citric acid cycle (CAC) and pyruvate metabolism. Conclusions Our results suggested that the changed succinylation level in proteins might function in the main energy metabolism pathways—photosynthesis and respiration. Succinylation might provide a significant effect in the growth of chimeric leaves and the relationship between the Wh and Gr parts of chimeric leaves. This study not only provided a basis for further characterization on the function of succinylated proteins in chimeric leaves of Ananas comosus var. bracteatus but also provided a new insight into molecular breeding for leaf color chimera.
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Affiliation(s)
- Meiqin Mao
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Yanbin Xue
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Yehua He
- Horticultural Biotechnology College, South China Agricultural University, Guangzhou, China
| | - Xuzixing Zhou
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Fatima Rafique
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Hao Hu
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Jiawen Liu
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Lijun Feng
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Wei Yang
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Xi Li
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Lingxia Sun
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Zhuo Huang
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Jun Ma
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China.
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149
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Li P, Zhang H, Zhao GP, Zhao W. Deacetylation enhances ParB-DNA interactions affecting chromosome segregation in Streptomyces coelicolor. Nucleic Acids Res 2020; 48:4902-4914. [PMID: 32313947 PMCID: PMC7229854 DOI: 10.1093/nar/gkaa245] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 03/10/2020] [Accepted: 04/03/2020] [Indexed: 12/29/2022] Open
Abstract
Reversible lysine acetylation plays regulatory roles in diverse biological processes, including cell metabolism, gene transcription, cell apoptosis and ageing. Here, we show that lysine acetylation is involved in the regulation of chromosome segregation, a pivotal step during cell division in Streptomyces coelicolor. Specifically, deacetylation increases the DNA-binding affinity of the chromosome segregation protein ParB to the centromere-like sequence parS. Both biochemical and genetic experiments suggest that the deacetylation process is mainly modulated by a sirtuin-like deacetylase ScCobB1. The Lys-183 residue in the helix-turn-helix region of ParB is the major deacetylation site responsible for the regulation of ParB-parS binding. In-frame deletion of SccobB1 represses formation of ParB segregation complexes and leads to generation of abnormal spores. Taken together, these observations provide direct evidence that deacetylation participates in the regulation of chromosome segregation by targeting ParB in S. coelicolor.
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Affiliation(s)
- Peng Li
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.,Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.,Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai 200032, China
| | - Hong Zhang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Guo-Ping Zhao
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.,Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,State Key Lab of Genetic Engineering & Institutes of Biomedical Sciences, Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China.,Shanghai-MOST Key Laboratory of Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai 201203, China.,Department of Microbiology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Wei Zhao
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,College of Life Sciences, Shanghai Normal University, Shanghai 200232, China
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150
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Kim JE, Choi JS, Kim JS, Cho YH, Roe JH. Lysine acetylation of the housekeeping sigma factor enhances the activity of the RNA polymerase holoenzyme. Nucleic Acids Res 2020; 48:2401-2411. [PMID: 31970401 PMCID: PMC7049703 DOI: 10.1093/nar/gkaa011] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 12/28/2019] [Accepted: 01/04/2020] [Indexed: 02/03/2023] Open
Abstract
Protein lysine acetylation, one of the most abundant post-translational modifications in eukaryotes, occurs in prokaryotes as well. Despite the evidence of lysine acetylation in bacterial RNA polymerases (RNAPs), its function remains unknown. We found that the housekeeping sigma factor (HrdB) was acetylated throughout the growth of an actinobacterium, Streptomyces venezuelae, and the acetylated HrdB was enriched in the RNAP holoenzyme complex. The lysine (K259) located between 1.2 and 2 regions of the sigma factor, was determined to be the acetylated residue of HrdB in vivo by LC–MS/MS analyses. Specifically, the label-free quantitative analysis revealed that the K259 residues of all the HrdB subunits were acetylated in the RNAP holoenzyme. Using mutations that mimic or block acetylation (K259Q and K259R), we found that K259 acetylation enhances the interaction of HrdB with the RNAP core enzyme as well as the binding activity of the RNAP holoenzyme to target promoters in vivo. Taken together, these findings provide a novel insight into an additional layer of modulation of bacterial RNAP activity.
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Affiliation(s)
- Ji-Eun Kim
- Laboratory of Molecular Microbiology, School of Biological Sciences, and Institute of Microbiology, Seoul National University, Seoul 08826, Korea
| | - Joon-Sun Choi
- Laboratory of Molecular Microbiology, School of Biological Sciences, and Institute of Microbiology, Seoul National University, Seoul 08826, Korea
| | - Jong-Seo Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
| | - You-Hee Cho
- Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Gyeonggi-do 13488, Korea
| | - Jung-Hye Roe
- Laboratory of Molecular Microbiology, School of Biological Sciences, and Institute of Microbiology, Seoul National University, Seoul 08826, Korea
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