201
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Jiang S, Liu Y, Shen Z, Zhou B, Shen QW. Acetylome profiling reveals extensive involvement of lysine acetylation in the conversion of muscle to meat. J Proteomics 2019; 205:103412. [PMID: 31176012 DOI: 10.1016/j.jprot.2019.103412] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 04/25/2019] [Accepted: 06/04/2019] [Indexed: 12/17/2022]
Abstract
Protein lysine acetylation is an post-translational modification that regulates gene expression, metabolism, cell signaling, and diseases, but its implication in the postmortem (PM) meat quality development is basically unclear. In the present study, a quantitative proteomic analysis was conducted to profile acetylome in porcine muscle within 24 h PM. In total 595 acetylation sites assigned to 163 proteins were identified in porcine muscle, of which 460 sites distributing to 110 proteins significantly changed in acetylation levels in the conversion of muscle to meat. The dynamic acetylation/deacetylaion of muscle proteins was closely associated with critical chemical-biophysical changes in PM muscle. Bioinformatic analysis revealed that protein lysine acetylation likely regulated postmortem meat quality development by regulating glycolysis and muscle pH, cell stress reponse and apoptosis, muscle contraction and rigor mortis, calcium signaling and proteolysis, IMP synthesis and meat flavor development, and even the stability of pigment proteins and meat color. This study provided the first overview of protein lysine acetylation in PM muscle and revealed its significance in the conversion of muscle to meat. Future exploration of the exact role of protein lysine acetylation at specific sites will further our understanding regarding the underlying mechanisms and be helpful for meat quality control. SIGNIFICANCE: This is the first analysis of acetylome in farm animal and postmortem muscle. Our data showed that the dynamic acetylation/deacetylation of muscle proteins was closely related to the postmortem changes of muscle that affect the final quality of raw meat. Proteins related to glucose metabolism and muscle contraction were the two largest clusters of acetylproteins identified in postmortem porcine muscle. Networks of acetylproteins involved in apoptosis, calcium signaling and IMP synthesis were identified in postmortem porcine muscle at the same time. Our results revealed that protein lysine acetylation regulated the conversion of muscle to meat. It likely regulated meat quality development by regulating postmortem glycolysis, mitochondrion initiated cell apoptosis, calcium signaling, rigor mortis, meat flavor compound sysnthesis and meat tenderization. Our study broadened our understanding of the biochemistry regulating the postmortem conversion of muscle to meat and final meat quality development, which may be helpful for future meat quality control.
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Affiliation(s)
- Shengwang Jiang
- College of Food Science and Technology, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Yisong Liu
- College of Food Science and Technology, Hunan Agricultural University, Changsha, Hunan 410128, China
| | | | - Bing Zhou
- College of Food Science and Technology, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Qingwu W Shen
- College of Food Science and Technology, Hunan Agricultural University, Changsha, Hunan 410128, China.
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202
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Cao Y, Fan G, Wang Z, Gu Z. Phytoplasma-induced Changes in the Acetylome and Succinylome of Paulownia tomentosa Provide Evidence for Involvement of Acetylated Proteins in Witches' Broom Disease. Mol Cell Proteomics 2019; 18:1210-1226. [PMID: 30936209 PMCID: PMC6553929 DOI: 10.1074/mcp.ra118.001104] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 02/20/2019] [Indexed: 12/16/2022] Open
Abstract
Lysine acetylation and succinylation are post-translational modifications of proteins that have been shown to play roles in plants response to pathogen infection. Phytoplasma infection can directly alter multiple metabolic processes in the deciduous plant Paulownia and lead to Paulownia witches' broom (PaWB) disease, the major cause of Paulownia mortality worldwide. However, the extent and function of lysine aceylation and succinylation during phytoplasma infection have yet to be explored. Here, we investigated the changes in the proteome, acetylome, and succinylome of phytoplasma-infected Paulownia tomentosa seedlings using quantitative mass spectrometry. In total, we identified 8963 proteins, 2893 acetylated proteins (5558 acetylation sites), and 1271 succinylated proteins (1970 succinylation sites), with 425 (533 sites) simultaneously acetylated and succinylated. Comparative analysis revealed that 276 proteins, 546 acetylated proteins (741 acetylation sites) and 5 succinylated proteins (5 succinylation sites) were regulated in response to phytoplasma infection, suggesting that acetylation may be more important than succinylation in PaWB. Enzymatic assays showed that acetylation of specific sites in protochlorophyllide reductase and RuBisCO, key enzymes in chlorophyll and starch biosynthesis, respectively, modifies their activity in phytoplasma-infected seedlings. On the basis of these results, we propose a model to elucidate the molecular mechanism of responses to PaWB and offer a resource for functional studies on the effects of acetylation on protein function.
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Affiliation(s)
| | - Guoqiang Fan
- From the ‡Institute of Paulownia and
- §College of Forestry, Henan Agricultural University, Zhengzhou, Henan, 450002, P. R. China
| | - Zhe Wang
- From the ‡Institute of Paulownia and
| | - Zhibin Gu
- From the ‡Institute of Paulownia and
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203
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Olzscha H. Posttranslational modifications and proteinopathies: how guardians of the proteome are defeated. Biol Chem 2019; 400:895-915. [DOI: 10.1515/hsz-2018-0458] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 04/13/2019] [Indexed: 01/15/2023]
Abstract
Abstract
Protein folding is one of the fundamental processes in life and therefore needs to be tightly regulated. Many cellular quality control systems are in place to ensure that proteostasis is optimally adjusted for a changing environment, facilitating protein folding, translocation and degradation. These systems include the molecular chaperones and the major protein degradation systems, namely the ubiquitin proteasome system and autophagy. However, the capacity of the quality control systems can be exhausted and protein misfolding and aggregation, including the formation of amyloids, can occur as a result of ageing, mutations or exogenous influences. There are many known diseases in which protein misfolding and aggregation can be the underlying cause of the pathological condition; these are referred to as proteinopathies. Over the last decade, it has become clear that posttranslational modifications can govern and modulate protein folding, and that aberrant posttranslational modifications can cause or contribute to proteinopathies. This review provides an overview of protein folding and misfolding and the role of the major protein quality control systems. It focusses on different posttranslational modifications and gives examples of how these posttranslational modifications can alter protein folding and cause or accompany proteinopathies.
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Affiliation(s)
- Heidi Olzscha
- Institut für Physiologische Chemie , Medizinische Fakultät, Martin-Luther-Universität Halle-Wittenberg , Hollystr. 1 , D-06114 Halle/Saale , Germany
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204
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Lim CK, Villada JC, Chalifour A, Duran MF, Lu H, Lee PKH. Designing and Engineering Methylorubrum extorquens AM1 for Itaconic Acid Production. Front Microbiol 2019; 10:1027. [PMID: 31143170 PMCID: PMC6520949 DOI: 10.3389/fmicb.2019.01027] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 04/24/2019] [Indexed: 01/05/2023] Open
Abstract
Methylorubrum extorquens (formerly Methylobacterium extorquens) AM1 is a methylotrophic bacterium with a versatile lifestyle. Various carbon sources including acetate, succinate and methanol are utilized by M. extorquens AM1 with the latter being a promising inexpensive substrate for use in the biotechnology industry. Itaconic acid (ITA) is a high-value building block widely used in various industries. Given that no wildtype methylotrophic bacteria are able to utilize methanol to produce ITA, we tested the potential of M. extorquens AM1 as an engineered host for this purpose. In this study, we successfully engineered M. extorquens AM1 to express a heterologous codon-optimized gene encoding cis-aconitic acid decarboxylase. The engineered strain produced ITA using acetate, succinate and methanol as the carbon feedstock. The highest ITA titer in batch culture with methanol as the carbon source was 31.6 ± 5.5 mg/L, while the titer and productivity were 5.4 ± 0.2 mg/L and 0.056 ± 0.002 mg/L/h, respectively, in a scaled-up fed-batch bioreactor under 60% dissolved oxygen saturation. We attempted to enhance the carbon flux toward ITA production by impeding poly-β-hydroxybutyrate accumulation, which is used as carbon and energy storage, via mutation of the regulator gene phaR. Unexpectedly, ITA production by the phaR mutant strain was not higher even though poly-β-hydroxybutyrate concentration was lower. Genome-wide transcriptomic analysis revealed that phaR mutation in the ITA-producing strain led to complex rewiring of gene transcription, which might result in a reduced carbon flux toward ITA production. Besides poly-β-hydroxybutyrate metabolism, we found evidence that PhaR might regulate the transcription of many other genes including those encoding other regulatory proteins, methanol dehydrogenases, formate dehydrogenases, malate:quinone oxidoreductase, and those synthesizing pyrroloquinoline quinone and thiamine co-factors. Overall, M. extorquens AM1 was successfully engineered to produce ITA using acetate, succinate and methanol as feedstock, further supporting this bacterium as a feasible host for use in the biotechnology industry. This study showed that PhaR could have a broader regulatory role than previously anticipated, and increased our knowledge of this regulator and its influence on the physiology of M. extorquens AM1.
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Affiliation(s)
- Chee Kent Lim
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China
| | - Juan C Villada
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China
| | - Annie Chalifour
- Department of Chemistry, City University of Hong Kong, Hong Kong, China
| | - Maria F Duran
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China
| | - Hongyuan Lu
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China
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205
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Ogura M, Sato T, Abe K. Bacillus subtilis YlxR, Which Is Involved in Glucose-Responsive Metabolic Changes, Regulates Expression of tsaD for Protein Quality Control of Pyruvate Dehydrogenase. Front Microbiol 2019; 10:923. [PMID: 31118925 PMCID: PMC6504816 DOI: 10.3389/fmicb.2019.00923] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 04/11/2019] [Indexed: 01/09/2023] Open
Abstract
Glucose is the most favorable carbon source for many bacteria, which have several glucose-responsive gene networks. Recently, we found that in Bacillus subtilis glucose induces the expression of the extracellular sigma factor genes sigX and sigM through the acetylation of CshA (RNA helicase), which associates with RNA polymerase (RNAP). We performed a transposon mutagenesis screen for mutants with no glucose induction (GI) of sigX-lacZ. While screening for such mutants, we recently found that the GI of sigX/M involves YlxR, a nucleoid-associated protein (NAP) that regulates nearly 400 genes, including metabolic genes. It has been shown that acetylated CshA positively regulates expression of ylxR-containing operon. Here, we report additional mutations in yqfO or tsaD required for the GI of sigX. YqfO contains a universally conserved domain with unknown function. YqfO and YlxR were found to regulate expression of the tsaEBD-containing operon. Mutational analysis using lacZ fusions revealed the adenine-rich cis-element for YlxR. TsaD is a component of the TsaEBD enzyme required for the synthesis of threonylcarbamoyl adenosine (t6A). The t6A modification of tRNA is universal across the three domains of life. Western blot analysis showed that the tsaD mutation in the presence of glucose reduced levels of soluble PdhA, PdhB, and PdhD, which are subunits of the pyruvate dehydrogenase complex (PDHc). This resulted in severely defective PDHc function and thus reduced concentrations of cellular acetyl-CoA, a reaction product of PDHc and plausible source for CshA acetylation. Thus, we discuss a suggested glucose-responsive system (GRS) involving self-reinforcing CshA acetylation. This self-reinforcing pathway may contribute to the maintenance of the acetyl-CoA pool for protein acetylation.
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Affiliation(s)
- Mitsuo Ogura
- Institute of Oceanic Research and Development, Tokai University, Shizuoka, Japan
| | - Tsutomu Sato
- Department of Frontier Bioscience, Hosei University, Koganei, Japan
| | - Kimihiro Abe
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Japan
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206
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Li Y, Li H, Sui M, Li M, Wang J, Meng Y, Sun T, Liang Q, Suo C, Gao X, Li C, Li Z, Du W, Zhang B, Sai S, Zhang Z, Ye J, Wang H, Yue S, Li J, Zhong M, Chen C, Qi S, Lu L, Li D, Ding C. Fungal acetylome comparative analysis identifies an essential role of acetylation in human fungal pathogen virulence. Commun Biol 2019; 2:154. [PMID: 31069264 PMCID: PMC6494858 DOI: 10.1038/s42003-019-0419-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 04/08/2019] [Indexed: 11/09/2022] Open
Abstract
Lysine acetylation is critical in regulating important biological processes in many organisms, yet little is known about acetylome evolution and its contribution to phenotypic diversity. Here, we compare the acetylomes of baker's yeast and the three deadliest human fungal pathogens, Cryptococcus neoformans, Candida albicans, and Aspergillus fumigatus. Using mass spectrometry enriched for acetylated peptides together with public data from Saccharomyces cerevisiae, we show that fungal acetylomes are characterized by dramatic evolutionary dynamics and limited conservation in core biological processes. Notably, the levels of protein acetylation in pathogenic fungi correlate with their pathogenicity. Using gene knockouts and pathogenicity assays in mice, we identify deacetylases with critical roles in virulence and protein translation elongation. Finally, through mutational analysis of deactylation motifs we find evidence of positive selection at specific acetylation motifs in fungal pathogens. These results shed new light on the pathogenicity regulation mechanisms underlying the evolution of fungal acetylomes.
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Affiliation(s)
- Yanjian Li
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Hailong Li
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Mingfei Sui
- Software College, Northeastern University, Shenyang, China
| | - Minghui Li
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Jiamei Wang
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Yang Meng
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Tianshu Sun
- Department of Scientific Research, Central Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Qiaojing Liang
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Chenhao Suo
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Xindi Gao
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Chao Li
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Zhuoran Li
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Wei Du
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Baihua Zhang
- SINO-Dutch Biomedical and Information Engineering School, Northeastern University, Shenyang, China
| | - Sixiang Sai
- School of Medicine, Binzhou Medical University, Yantai, China
| | | | - Jing Ye
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Hongchen Wang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Shang Yue
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Jiayi Li
- College of Life and Health Sciences, Northeastern University, Shenyang, China
- Neural Plasticity and Repair Unit, Wallenberg Neuroscience Center, Lund University, Lund, Sweden
| | - Manli Zhong
- College of Life and Health Sciences, Northeastern University, Shenyang, China
| | - Changbin Chen
- Unit of Pathogenic Fungal Infection & Host Immunity, CAS Key Laboratory of Molecular Virology & Immunology, Institute Pasteur of Shanghai, Chinese Academy of Science, Shanghai, China
| | - Shouliang Qi
- SINO-Dutch Biomedical and Information Engineering School, Northeastern University, Shenyang, China
| | - Ling Lu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Dancheng Li
- Software College, Northeastern University, Shenyang, China
| | - Chen Ding
- College of Life and Health Sciences, Northeastern University, Shenyang, China
- Key Laboratory of Data Analytics and Optimization for Smart Industry, Northeastern University, Shenyang, China
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207
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Xu L, Li Y, Zhou L, Dorfman RG, Liu L, Cai R, Jiang C, Tang D, Wang Y, Zou X, Wang L, Zhang M. SIRT3 elicited an anti-Warburg effect through HIF1α/PDK1/PDHA1 to inhibit cholangiocarcinoma tumorigenesis. Cancer Med 2019; 8:2380-2391. [PMID: 30993888 PMCID: PMC6536927 DOI: 10.1002/cam4.2089] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 02/06/2019] [Accepted: 02/23/2019] [Indexed: 02/05/2023] Open
Abstract
Cholangiocarcinoma (CCA) is an extremely invasive malignancy with late diagnosis and unfavorable prognosis. Surgery and chemotherapy are still not effective in improving outcomes in CCA patients. It is crucial to explore a novel therapeutic target for treating CCA. An NAD‐dependent deacetylase also known as Sirtuin‐3 (SIRT3) has been shown to regulate cellular metabolism in various cancers dynamically. However, the biological function of SIRT3 in CCA remains unclear. In this study, bioinformatics analyses were performed to identify the differentially expressed genes and pathways enriched. CCA samples were collected for immunohistochemical analysis. Three human CCA cell lines (HuCCT1, RBE, and HCCC9810) were used to explore the molecular mechanism of SIRT3 regulation of metabolic reprogramming and malignant behavior in CCA. A CCA xenograft model was then established for further validation in vivo. The data showed that SIRT3 expression was decreased and glycolysis was enhanced in CCA. Similar metabolic reprogramming was also observed in SIRT3 knockout mice. Furthermore, we demonstrated that SIRT3 could play an anti‐Warburg effect by inhibiting the hypoxia‐inducible factor‐1α (HIF1α)/pyruvate dehydrogenase kinase 1 (PDK1)/pyruvate dehydrogenase (PDHA1) pathway in CCA cells. CCA cell proliferation and apoptosis were regulated by SIRT3‐mediated metabolic reprogramming. These findings were further confirmed in CCA clinical samples and the xenograft model. Collectively, this study suggests that in the inhibition of CCA progression, SIRT3 acts through an anti‐Warburg effect on the downstream pathway HIF1α/PDK1/PDHA1.
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Affiliation(s)
- Lei Xu
- Department of Gastroenterology, Drum Tower Clinical Medical College of Nanjing Medical University, Nanjing, China.,Department of Gastroenterology, Nanjing Drum Tower Hospital, Affiliated Hospital of Nanjing University Medical School, Nanjing University, Nanjing, China
| | - Yang Li
- Department of Gastroenterology, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Lixing Zhou
- The Center of Gerontology and Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | | | - Li Liu
- Department of Gastroenterology, Drum Tower Clinical Medical College of Nanjing Medical University, Nanjing, China
| | - Rui Cai
- Department of Gastroenterology, Drum Tower Clinical Medical College of Nanjing Medical University, Nanjing, China
| | - Chenfei Jiang
- Department of Gastroenterology, Nanjing Drum Tower Hospital, Affiliated Hospital of Nanjing University Medical School, Nanjing University, Nanjing, China
| | - Dehua Tang
- Department of Gastroenterology, Nanjing Drum Tower Hospital, Affiliated Hospital of Nanjing University Medical School, Nanjing University, Nanjing, China
| | - Yuming Wang
- Department of Gastroenterology, Nanjing Drum Tower Hospital, Affiliated Hospital of Nanjing University Medical School, Nanjing University, Nanjing, China
| | - Xiaoping Zou
- Department of Gastroenterology, Drum Tower Clinical Medical College of Nanjing Medical University, Nanjing, China.,Department of Gastroenterology, Nanjing Drum Tower Hospital, Affiliated Hospital of Nanjing University Medical School, Nanjing University, Nanjing, China
| | - Lei Wang
- Department of Gastroenterology, Drum Tower Clinical Medical College of Nanjing Medical University, Nanjing, China.,Department of Gastroenterology, Nanjing Drum Tower Hospital, Affiliated Hospital of Nanjing University Medical School, Nanjing University, Nanjing, China
| | - Mingming Zhang
- Department of Gastroenterology, Drum Tower Clinical Medical College of Nanjing Medical University, Nanjing, China.,Department of Gastroenterology, Nanjing Drum Tower Hospital, Affiliated Hospital of Nanjing University Medical School, Nanjing University, Nanjing, China
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208
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Chung S, Hwang JT, Park JH, Choi HK. Free fatty acid-induced histone acetyltransferase activity accelerates lipid accumulation in HepG2 cells. Nutr Res Pract 2019; 13:196-204. [PMID: 31214287 PMCID: PMC6548710 DOI: 10.4162/nrp.2019.13.3.196] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 12/18/2018] [Accepted: 02/12/2019] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND/OBJECTIVES Non-alcoholic fatty liver disease (NAFLD) is a common metabolic disease triggered by epigenetic alterations, including lysine acetylation at histone or non-histone proteins, affecting the stability or transcription of lipogenic genes. Although various natural dietary compounds have anti-lipogenic effects, their effects on the acetylation status and lipid metabolism in the liver have not been thoroughly investigated. MATERIALS/METHODS Following oleic-palmitic acid (OPA)-induced lipid accumulation in HepG2 cells, the acetylation status of histone and non-histone proteins, HAT activity, and mRNA expression of representative lipogenic genes, including PPARγ, SREBP-1c, ACLY, and FASN, were evaluated. Furthermore, correlations between lipid accumulation and HAT activity for 22 representative natural food extracts (NExs) were evaluated. RESULTS Non-histone protein acetylation increased following OPA treatment and the acetylation of histones H3K9, H4K8, and H4K16 was accelerated, accompanied by an increase in HAT activity. OPA-induced increases in the mRNA expression of lipogenic genes were down-regulated by C-646, a p300/CBP-specific inhibitor. Finally, we detected a positive correlation between HAT activity and lipid accumulation (Pearson's correlation coefficient = 0.604) using 22 NExs. CONCLUSIONS Our results suggest that NExs have novel applications as nutraceutical agents with HAT inhibitor activity for the prevention and treatment of NAFLD.
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Affiliation(s)
- Sangwon Chung
- Korea Food Research Institute, 245, Nongsaengmyeong-ro, Iseo-myeon, Wanju-gun, Jeonbuk 55365, Republic of Korea
| | - Jin-Taek Hwang
- Korea Food Research Institute, 245, Nongsaengmyeong-ro, Iseo-myeon, Wanju-gun, Jeonbuk 55365, Republic of Korea.,Department of Food Biotechnology, Korea University of Science & Technology, Daejeon 34113, Republic of Korea
| | - Jae Ho Park
- Korea Food Research Institute, 245, Nongsaengmyeong-ro, Iseo-myeon, Wanju-gun, Jeonbuk 55365, Republic of Korea
| | - Hyo-Kyoung Choi
- Korea Food Research Institute, 245, Nongsaengmyeong-ro, Iseo-myeon, Wanju-gun, Jeonbuk 55365, Republic of Korea
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209
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Christensen DG, Baumgartner JT, Xie X, Jew KM, Basisty N, Schilling B, Kuhn ML, Wolfe AJ. Mechanisms, Detection, and Relevance of Protein Acetylation in Prokaryotes. mBio 2019; 10:e02708-18. [PMID: 30967470 PMCID: PMC6456759 DOI: 10.1128/mbio.02708-18] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Posttranslational modification of a protein, either alone or in combination with other modifications, can control properties of that protein, such as enzymatic activity, localization, stability, or interactions with other molecules. N-ε-Lysine acetylation is one such modification that has gained attention in recent years, with a prevalence and significance that rival those of phosphorylation. This review will discuss the current state of the field in bacteria and some of the work in archaea, focusing on both mechanisms of N-ε-lysine acetylation and methods to identify, quantify, and characterize specific acetyllysines. Bacterial N-ε-lysine acetylation depends on both enzymatic and nonenzymatic mechanisms of acetylation, and recent work has shed light into the regulation of both mechanisms. Technological advances in mass spectrometry have allowed researchers to gain insight with greater biological context by both (i) analyzing samples either with stable isotope labeling workflows or using label-free protocols and (ii) determining the true extent of acetylation on a protein population through stoichiometry measurements. Identification of acetylated lysines through these methods has led to studies that probe the biological significance of acetylation. General and diverse approaches used to determine the effect of acetylation on a specific lysine will be covered.
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Affiliation(s)
- D G Christensen
- Department of Microbiology and Immunology, Loyola University Chicago, Health Sciences Division, Stritch School of Medicine, Maywood, Illinois, USA
| | - J T Baumgartner
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California, USA
| | - X Xie
- Buck Institute for Research on Aging, Novato, California, USA
| | - K M Jew
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California, USA
| | - N Basisty
- Buck Institute for Research on Aging, Novato, California, USA
| | - B Schilling
- Buck Institute for Research on Aging, Novato, California, USA
| | - M L Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California, USA
| | - A J Wolfe
- Department of Microbiology and Immunology, Loyola University Chicago, Health Sciences Division, Stritch School of Medicine, Maywood, Illinois, USA
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210
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Yoshida A, Yoshida M, Kuzuyama T, Nishiyama M, Kosono S. Protein acetylation on 2-isopropylmalate synthase from Thermus thermophilus HB27. Extremophiles 2019; 23:377-388. [PMID: 30919057 DOI: 10.1007/s00792-019-01090-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 03/14/2019] [Indexed: 12/23/2022]
Abstract
Protein lysine Nε-acetylation is one of the important factors regulating cellular metabolism. We performed a proteomic analysis to identify acetylated proteins in the extremely thermophilic bacterium, Thermus thermophilus HB27. A total of 335 unique acetylated lysine residues, including many metabolic enzymes and ribosomal proteins, were identified in 208 proteins. Enzymes involved in amino acid metabolism were the most abundant among acetylated metabolic proteins. 2-Isopropylmalate synthase (IPMS), which catalyzes the first step in leucine biosynthesis, was acetylated at four lysine residues. Acetylation-mimicking mutations at Lys332 markedly decreased IPMS activity in vitro, suggesting that Lys332, which is located in subdomain II, plays a regulatory role in IPMS activity. We also investigated the acetylation-deacetylation mechanism of IPMS and revealed that it was acetylated non-enzymatically by acetyl-CoA and deacetylated enzymatically by TT_C0104. The present results suggest that leucine biosynthesis is regulated by post-translational protein modifications, in addition to feedback inhibition/repression, and that metabolic enzymes are regulated by protein acetylation in T. thermophilus.
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Affiliation(s)
- Ayako Yoshida
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Minoru Yoshida
- RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198, Japan.,Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Tomohisa Kuzuyama
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Makoto Nishiyama
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Saori Kosono
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan. .,RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198, Japan. .,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
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211
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García-Roche M, Casal A, Mattiauda DA, Ceriani M, Jasinsky A, Mastrogiovanni M, Trostchansky A, Carriquiry M, Cassina A, Quijano C. Impaired hepatic mitochondrial function during early lactation in dairy cows: Association with protein lysine acetylation. PLoS One 2019; 14:e0213780. [PMID: 30870481 PMCID: PMC6417696 DOI: 10.1371/journal.pone.0213780] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 03/01/2019] [Indexed: 12/11/2022] Open
Abstract
Early lactation is an energy-demanding period for dairy cows which may lead to negative energy balance, threatening animal health and consequently productivity. Herein we studied hepatic mitochondrial function in Holstein-Friesian multiparous dairy cows during lactation, under two different feeding strategies. During the first 180 days postpartum the cows were fed a total mixed ration (70% forage: 30% concentrate) ad libitum (non-grazing group, G0) or grazed Festuca arundinacea or Mendicago sativa plus supplementation (grazing group, G1). From 180 to 250 days postpartum, all cows grazed Festuca arundinacea and were supplemented with total mixed ration. Mitochondrial function was assessed measuring oxygen consumption rate in liver biopsies and revealed that maximum respiratory rate decreased significantly in grazing cows during early lactation, yet was unchanged in non-grazing cows during the lactation curve. While no differences could be found in mitochondrial content or oxidative stress markers, a significant increase in protein lysine acetylation was found in grazing cows during early lactation but not in cows from the non-grazing group. Mitochondrial acetylation positively correlated with liver triglycerides and β-hydroxybutyrate plasma levels, well-known markers of negative energy balance, while a negative correlation was found with the maximum respiratory rate and sirtuin 3 levels. To our knowledge this is the first report of mitochondrial function in liver biopsies of dairy cows during lactation. On the whole our results indicate that mitochondrial function is impaired during early lactation in grazing cows and that acetylation may account for changes in mitochondrial function in this period. Additionally, our results suggest that feeding total mixed ration during early lactation may be an efficient protective strategy.
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Affiliation(s)
- Mercedes García-Roche
- Center for Free Radical and Biomedical Research (CEINBIO) and Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
- Departamento de Producción Animal y Pasturas, Facultad de Agronomía, Universidad de la República, Montevideo, Uruguay
| | - Alberto Casal
- Departamento de Producción Animal y Pasturas, Estación Experimental Mario A. Cassinoni, Facultad de Agronomía, Universidad de la República, Paysandú, Uruguay
| | - Diego A. Mattiauda
- Departamento de Producción Animal y Pasturas, Estación Experimental Mario A. Cassinoni, Facultad de Agronomía, Universidad de la República, Paysandú, Uruguay
| | - Mateo Ceriani
- Departamento de Producción Animal y Pasturas, Estación Experimental Mario A. Cassinoni, Facultad de Agronomía, Universidad de la República, Paysandú, Uruguay
| | - Alejandra Jasinsky
- Departamento de Producción Animal y Pasturas, Estación Experimental Mario A. Cassinoni, Facultad de Agronomía, Universidad de la República, Paysandú, Uruguay
| | - Mauricio Mastrogiovanni
- Center for Free Radical and Biomedical Research (CEINBIO) and Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Andrés Trostchansky
- Center for Free Radical and Biomedical Research (CEINBIO) and Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Mariana Carriquiry
- Departamento de Producción Animal y Pasturas, Facultad de Agronomía, Universidad de la República, Montevideo, Uruguay
- * E-mail: (CQ); (AC); (MC)
| | - Adriana Cassina
- Center for Free Radical and Biomedical Research (CEINBIO) and Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
- * E-mail: (CQ); (AC); (MC)
| | - Celia Quijano
- Center for Free Radical and Biomedical Research (CEINBIO) and Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
- * E-mail: (CQ); (AC); (MC)
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212
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Wu L, Gong T, Zhou X, Zeng J, Huang R, Wu Y, Li Y. Global analysis of lysine succinylome in the periodontal pathogen Porphyromonas gingivalis. Mol Oral Microbiol 2019; 34:74-83. [PMID: 30672658 DOI: 10.1111/omi.12255] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 12/22/2018] [Accepted: 01/21/2019] [Indexed: 02/05/2023]
Abstract
The gram-negative anaerobe Porphyromonas gingivalis is not only a keystone periodontal pathogen but also an emerging systemic pathogen. Although the newly discovered protein post-translational modification (PTM), lysine succinylation (Ksuc), appears to play an important role in modulating metabolic processes in bacteria, this PTM has not been investigated in P gingivalis. In this study, we used a highly sensitive proteomics approach combining affinity enrichment with high-resolution liquid chromatography coupled with tandem mass spectrometry to examine Ksuc in P gingivalis. In total, 345 Ksuc sites in 233 proteins were identified and determined to be involved in a variety of cellular processes. In the region surrounding Ksuc sites, lysine residues were drastically overrepresented and sequence motifs with succinyl-lysine flanked by a lysine at the +3 or +6 positions appear to be unique to this pathogen. Additionally, our results suggest a crosstalk between Ksuc and glycosylation, but the overlap between Ksuc and acetylation in P gingivalis is quite different from that observed in other organisms. Notably, Ksuc was observed in proteins associated with established virulence factors, including gingipains, fimbriae, RagB, and PorR. Moreover, products of the factors necessary for P gingivalis in vitro survival (18.5%) were found to be succinylated at lysine sites and the same was observed in products of fitness factors for P gingivalis survival in both abscess and epithelial cell colonization environments (12%). Collectively, these results suggest that Ksuc may be a new mechanism in modulating the virulence, adaptation, and fitness of P gingivalis.
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Affiliation(s)
- Leng Wu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China.,Department of Stomatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
| | - Tao Gong
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China
| | - Xuedong Zhou
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China
| | - Jumei Zeng
- Department of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ruijie Huang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China
| | - Yafei Wu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China
| | - Yuqing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China
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213
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Porter NJ, Christianson DW. Structure, mechanism, and inhibition of the zinc-dependent histone deacetylases. Curr Opin Struct Biol 2019; 59:9-18. [PMID: 30743180 DOI: 10.1016/j.sbi.2019.01.004] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/03/2019] [Accepted: 01/09/2019] [Indexed: 10/27/2022]
Affiliation(s)
- Nicholas J Porter
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, United States
| | - David W Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, United States.
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214
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Zhang Y, Zhou F, Bai M, Liu Y, Zhang L, Zhu Q, Bi Y, Ning G, Zhou L, Wang X. The pivotal role of protein acetylation in linking glucose and fatty acid metabolism to β-cell function. Cell Death Dis 2019; 10:66. [PMID: 30683850 PMCID: PMC6347623 DOI: 10.1038/s41419-019-1349-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 12/12/2018] [Accepted: 01/02/2019] [Indexed: 01/16/2023]
Abstract
Protein acetylation has a crucial role in energy metabolism. Here we performed the first large-scale profiling of acetylome in rat islets, showing that almost all enzymes in core metabolic pathways related to insulin secretion were acetylated. Label-free quantitative acetylome of islets in response to high glucose revealed hyperacetylation of enzymes involved in fatty acid β-oxidation (FAO), including trifunctional enzyme subunit alpha (ECHA). Acetylation decreased the protein stability of ECHA and its ability to promote FAO. The overexpression of SIRT3, a major mitochondrial deacetylase, prevented the degradation of ECHA via decreasing its acetylation level in β-cells. SIRT3 expression was upregulated in rat islets upon exposure to low glucose or fasting. SIRT3 overexpression in islets markedly decreased palmitate-potentiated insulin secretion, whereas islets from SIRT3 knockout mice secreted more insulin, with an opposite action on FAO. ECHA overexpression partially reversed SIRT3 deficiency-elicited insulin hypersecretion. Our study highlights the potential role of protein acetylation in insulin secretion.
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Affiliation(s)
- Yuqing Zhang
- Department of Endocrine and Metabolic Diseases, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China.,Center for Reproductive Medicine, Shandong University, Jinan, 250000, China.,Key Laboratory of Reproductive Endocrinology, Ministry of Education, Shandong University, Jinan, 250000, China
| | - Feiye Zhou
- Department of Endocrine and Metabolic Diseases, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Mengyao Bai
- Department of Endocrine and Metabolic Diseases, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Yun Liu
- Department of Endocrine and Metabolic Diseases, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Linlin Zhang
- Department of Endocrine and Metabolic Diseases, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Qin Zhu
- Department of Endocrine and Metabolic Diseases, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Yufang Bi
- Department of Endocrine and Metabolic Diseases, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Guang Ning
- Department of Endocrine and Metabolic Diseases, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China.
| | - Libin Zhou
- Department of Endocrine and Metabolic Diseases, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China.
| | - Xiao Wang
- Department of Endocrine and Metabolic Diseases, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China.
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215
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Li S, Fei Z, Xu Z, Wang J, Jiang Z, Xie Y, Wang Y, Huang W, Sun H. Enterococcus faecalis sir2-like gene enhances aerobic metabolism of themselves and mitochondrial respiration of mammal cells to bring about improving metabolic syndrome through the PGC-1α pathway. J Tissue Eng Regen Med 2019; 13:143-155. [PMID: 30512225 DOI: 10.1002/term.2775] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 08/23/2018] [Accepted: 11/19/2018] [Indexed: 01/31/2023]
Abstract
Recent studies showed that probiotics could improve metabolic syndrome, making the identification of factors affecting metabolic control more important than ever. The mammalian sirtuin protein family has received much attention for its regulatory role, especially in various mitochondrial ATP, glucose, and lipid metabolic pathways. However, compared with the mammalian sirtuin protein family, the function of prokaryotic sir2 protein is much less known. We studied the effects of probiotics sir2 protein on cell energy metabolize pathway, which showed that deletion of Enterococcus faecalis sir2 inhibited the aerobic oxidation of bacteria and increased the bacterial fermentation. The study of EF-sir2 (sir2 protein of E. faecalis) role of molecular targets demonstrated that deacetylation of EF-sir2 was via Rho upregulating in E. faecalis. When transfected into HEK293T cells, EF-sir2 could significantly facilitate aerobic oxidation of glucose, enhance the respiration to generate more ATP, and cause upregulation of NRF1 target gene. Then, we found EF-sir2 could increase activity of PGC-1α by deacetylation and PGC-1α inhibition decreased the expression of NRF1 target gene. Finally, we demonstrated that EF-sir2 could significantly improve the metabolic index of mammalian cells through insulin resistanced model in vitro and metabolic syndrome rat model in vivo. Our results first revealed that prokaryotic sir2 genes affect the molecular mechanism of cellular metabolism and the regulatory of cell homeostasis in prokaryotic and mammalian cells, suggesting that EF-sir2 has a positive regulatory effect on metabolic disturbance and may be used for the prevention and treatment of pathological processes related to metabolic syndrome.
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Affiliation(s)
- Shiyu Li
- Department of Anatomy, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Zhengbin Fei
- Institute of Genomic Medicine, College of Pharmacy, Jinan University, Guangzhou, China
| | - Zhenrui Xu
- Institute of Genomic Medicine, College of Pharmacy, Jinan University, Guangzhou, China
| | - Jiajia Wang
- Institute of Genomic Medicine, College of Pharmacy, Jinan University, Guangzhou, China
| | - Zhenyou Jiang
- Departments of Microbiology and Immunology, Jinan University, Guangzhou, China
| | - Yajie Xie
- Institute of Genomic Medicine, College of Pharmacy, Jinan University, Guangzhou, China
| | - Yuzhe Wang
- Institute of Genomic Medicine, College of Pharmacy, Jinan University, Guangzhou, China
| | - Wenhua Huang
- Department of Anatomy, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Hanxiao Sun
- Institute of Genomic Medicine, College of Pharmacy, Jinan University, Guangzhou, China
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216
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Chen G, Cao M, Yu J, Guo X, Shi S. Prediction and functional analysis of prokaryote lysine acetylation site by incorporating six types of features into Chou's general PseAAC. J Theor Biol 2019; 461:92-101. [DOI: 10.1016/j.jtbi.2018.10.047] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 10/09/2018] [Accepted: 10/22/2018] [Indexed: 12/12/2022]
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217
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Liu GT, Jiang JF, Liu XN, Jiang JZ, Sun L, Duan W, Li RM, Wang Y, Lecourieux D, Liu CH, Li SH, Wang LJ. New insights into the heat responses of grape leaves via combined phosphoproteomic and acetylproteomic analyses. HORTICULTURE RESEARCH 2019; 6:100. [PMID: 31666961 PMCID: PMC6804945 DOI: 10.1038/s41438-019-0183-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 06/03/2019] [Accepted: 06/04/2019] [Indexed: 05/04/2023]
Abstract
Heat stress is a serious and widespread threat to the quality and yield of many crop species, including grape (Vitis vinifera L.), which is cultivated worldwide. Here, we conducted phosphoproteomic and acetylproteomic analyses of leaves of grape plants cultivated under four distinct temperature regimes. The phosphorylation or acetylation of a total of 1011 phosphoproteins with 1828 phosphosites and 96 acetyl proteins with 148 acetyl sites changed when plants were grown at 35 °C, 40 °C, and 45 °C in comparison with the proteome profiles of plants grown at 25 °C. The greatest number of changes was observed at the relatively high temperatures. Functional classification and enrichment analysis indicated that phosphorylation, rather than acetylation, of serine/arginine-rich splicing factors was involved in the response to high temperatures. This finding is congruent with previous observations by which alternative splicing events occurred more frequently in grapevine under high temperature. Changes in acetylation patterns were more common than changes in phosphorylation patterns in photosynthesis-related proteins at high temperatures, while heat-shock proteins were associated more with modifications involving phosphorylation than with those involving acetylation. Nineteen proteins were identified with changes associated with both phosphorylation and acetylation, which is consistent with crosstalk between these posttranslational modification types.
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Affiliation(s)
- Guo-Tian Liu
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093 China
- College of Horticulture, Northwest A&F University, Yangling, 712100 China
- University of Chinese Academy of Sciences, Beijing, 100093 China
| | - Jian-Fu Jiang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009 China
| | - Xin-Na Liu
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100093 China
| | - Jin-Zhu Jiang
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100093 China
| | - Lei Sun
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009 China
| | - Wei Duan
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093 China
| | - Rui-Min Li
- College of Horticulture, Northwest A&F University, Yangling, 712100 China
| | - Yi Wang
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100093 China
| | - David Lecourieux
- Universite´ de Bordeaux, ISVV, Ecophysiologie et Ge´nomique Fonctionnelle de la Vigne, UMR 1287, F-33140 Villenave d’Ornon, France
- INRA, ISVV, Ecophysiologie et Ge´nomique Fonctionnelle de la Vigne, UMR 1287, F-33140 Villenave d’Ornon, France
| | - Chong-Huai Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009 China
| | - Shao-Hua Li
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100093 China
| | - Li-Jun Wang
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093 China
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218
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Abstract
Posttranslational modifications of proteins control many complex biological processes, including genome expression, chromatin dynamics, metabolism, and cell division through a language of chemical modifications. Improvements in mass spectrometry-based proteomics have demonstrated protein acetylation is a widespread and dynamic modification in the cell; however, many questions remain on the regulation and downstream effects, and an assessment of the overall acetylation stoichiometry is needed. In this chapter, we describe the determination of acetylation stoichiometry using data-independent acquisition mass spectrometry to expand the number of acetylation sites quantified. However, the increased depth of data-independent acquisition is limited by the spectral library used to deconvolute fragmentation spectra. We describe a powerful approach of subcellular fractionation in conjunction with offline prefractionation to increase the depth of the spectral library. This deep interrogation of subcellular compartments provides essential insights into the compartment-specific regulation and downstream functions of protein acetylation.
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219
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Xing T, Gao F, Tume RK, Zhou G, Xu X. Stress Effects on Meat Quality: A Mechanistic Perspective. Compr Rev Food Sci Food Saf 2018; 18:380-401. [PMID: 33336942 DOI: 10.1111/1541-4337.12417] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 10/31/2018] [Accepted: 11/12/2018] [Indexed: 12/16/2022]
Abstract
Stress inevitably occurs from the farm to abattoir in modern livestock husbandry. The effects of stress on the behavioral and physiological status and ultimate meat quality have been well documented. However, reports on the mechanism of stress effects on physiological and biochemical changes and their consequent effects on meat quality attributes have been somewhat disjointed and limited. Furthermore, the causes of variability in meat quality traits among different animal species, muscle fibers within an animal, and even positions within a piece of meat in response to stress are still not entirely clear. This review 1st summarizes the primary stress factors, including heat stress, preslaughter handling stress, oxidative stress, and other stress factors affecting animal welfare; carcass quality; and eating quality. This review further delineates potential stress-induced pathways or mediators, including AMP-activated protein kinase-mediated energy metabolism, crosstalk among calcium signaling pathways and reactive oxygen species, protein modification, apoptosis, calpain and cathepsin proteolytic systems, and heat shock proteins that exert effects that cause biochemical changes during the early postmortem period and affect the subsequent meat quality. To obtain meat of high quality, further studies are needed to unravel the intricate mechanisms involving the aforementioned signaling pathways or mediators and their crosstalk.
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Affiliation(s)
- Tong Xing
- College of Animal Science and Technology, Key Laboratory of Animal Products Processing, Ministry of Agriculture, Key Laboratory of Meat Processing and Quality Control, Ministry of Education, Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, Nanjing Agricultural Univ., Nanjing, 210095, China
| | - Feng Gao
- College of Animal Science and Technology, Key Laboratory of Animal Products Processing, Ministry of Agriculture, Key Laboratory of Meat Processing and Quality Control, Ministry of Education, Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, Nanjing Agricultural Univ., Nanjing, 210095, China
| | - Ronald K Tume
- College of Food Science and Technology, Nanjing Agricultural Univ., Nanjing, 210095, Jiangsu, China
| | - Guanghong Zhou
- College of Food Science and Technology, Nanjing Agricultural Univ., Nanjing, 210095, Jiangsu, China
| | - Xinglian Xu
- College of Food Science and Technology, Nanjing Agricultural Univ., Nanjing, 210095, Jiangsu, China
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220
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Diallo I, Seve M, Cunin V, Minassian F, Poisson JF, Michelland S, Bourgoin-Voillard S. Current trends in protein acetylation analysis. Expert Rev Proteomics 2018; 16:139-159. [PMID: 30580641 DOI: 10.1080/14789450.2019.1559061] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Acetylation is a widely occurring post-translational modification (PTM) of proteins that plays a crucial role in many cellular physiological and pathological processes. Over the last decade, acetylation analyses required the development of multiple methods to target individual acetylated proteins, as well as to cover a broader description of acetylated proteins that comprise the acetylome. Areas covered: This review discusses the different types of acetylation (N-ter/K-/O-acetylation) and then describes some major strategies that have been reported in the literature to detect, enrich, identify and quantify protein acetylation. The review highlights the advantages and limitations of these strategies, to guide researchers in designing their experimental investigations and analysis of protein acetylation. Finally, this review highlights the main applications of acetylomics (proteomics based on mass spectrometry) for understanding physiological and pathological conditions. Expert opinion: Recent advances in acetylomics have enhanced knowledge of the biological and pathological roles of protein acetylation and the acetylome. Besides, radiolabeling and western blotting remain also techniques-of-choice for targeted protein acetylation. Future challenges in acetylomics to analyze the N-ter and K-acetylome will most likely require enrichment/fractionation, MS instrumentation and bioinformatics. Challenges also remain to identify the potential biological roles of O-acetylation and cross-talk with other PTMs.
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Affiliation(s)
- Issa Diallo
- a Universite Grenoble Alpes - LBFA and BEeSy, PROMETHEE, Proteomic Platform , Saint-Martin-d'Heres , France.,b Inserm, U1055, PROMETHEE Proteomic Platform , Saint-Martin-d'Heres , France.,c CHU de Grenoble, Institut de Biologie et de Pathologie, PROMETHEE Proteomic Platform , La Tronche , France
| | - Michel Seve
- a Universite Grenoble Alpes - LBFA and BEeSy, PROMETHEE, Proteomic Platform , Saint-Martin-d'Heres , France.,b Inserm, U1055, PROMETHEE Proteomic Platform , Saint-Martin-d'Heres , France.,c CHU de Grenoble, Institut de Biologie et de Pathologie, PROMETHEE Proteomic Platform , La Tronche , France
| | - Valérie Cunin
- a Universite Grenoble Alpes - LBFA and BEeSy, PROMETHEE, Proteomic Platform , Saint-Martin-d'Heres , France.,b Inserm, U1055, PROMETHEE Proteomic Platform , Saint-Martin-d'Heres , France.,c CHU de Grenoble, Institut de Biologie et de Pathologie, PROMETHEE Proteomic Platform , La Tronche , France
| | | | | | - Sylvie Michelland
- a Universite Grenoble Alpes - LBFA and BEeSy, PROMETHEE, Proteomic Platform , Saint-Martin-d'Heres , France.,b Inserm, U1055, PROMETHEE Proteomic Platform , Saint-Martin-d'Heres , France.,c CHU de Grenoble, Institut de Biologie et de Pathologie, PROMETHEE Proteomic Platform , La Tronche , France
| | - Sandrine Bourgoin-Voillard
- a Universite Grenoble Alpes - LBFA and BEeSy, PROMETHEE, Proteomic Platform , Saint-Martin-d'Heres , France.,b Inserm, U1055, PROMETHEE Proteomic Platform , Saint-Martin-d'Heres , France.,c CHU de Grenoble, Institut de Biologie et de Pathologie, PROMETHEE Proteomic Platform , La Tronche , France
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221
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Matallana-Surget S, Werner J, Wattiez R, Lebaron K, Intertaglia L, Regan C, Morris J, Teeling H, Ferrer M, Golyshin PN, Gerogiorgis D, Reilly SI, Lebaron P. Proteogenomic Analysis of Epibacterium Mobile BBCC367, a Relevant Marine Bacterium Isolated From the South Pacific Ocean. Front Microbiol 2018; 9:3125. [PMID: 30622520 PMCID: PMC6308992 DOI: 10.3389/fmicb.2018.03125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 12/03/2018] [Indexed: 12/16/2022] Open
Abstract
Epibacterium mobile BBCC367 is a marine bacterium that is common in coastal areas. It belongs to the Roseobacter clade, a widespread group in pelagic marine ecosystems. Species of the Roseobacter clade are regularly used as models to understand the evolution and physiological adaptability of generalist bacteria. E. mobile BBCC367 comprises two chromosomes and two plasmids. We used gel-free shotgun proteomics to assess its protein expression under 16 different conditions, including stress factors such as elevated temperature, nutrient limitation, high metal concentration, and UVB exposure. Comparison of the different conditions allowed us not only to retrieve almost 70% of the predicted proteins, but also to define three main protein assemblages: 584 essential core proteins, 2,144 facultative accessory proteins and 355 specific unique proteins. While the core proteome mainly exhibited proteins involved in essential functions to sustain life such as DNA, amino acids, carbohydrates, cofactors, vitamins and lipids metabolisms, the accessory and unique proteomes revealed a more specific adaptation with the expression of stress-related proteins, such as DNA repair proteins (accessory proteome), transcription regulators and a significant predominance of transporters (unique proteome). Our study provides insights into how E. mobile BBCC367 adapts to environmental changes and copes with diverse stresses.
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Affiliation(s)
- Sabine Matallana-Surget
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom
| | - Johannes Werner
- Department of Biological Oceanography, Leibniz Institute of Baltic Sea Research, Rostock, Germany
| | - Ruddy Wattiez
- Department of Proteomics and Microbiology, Interdisciplinary Mass Spectrometry Center (CISMa), University of Mons, Mons, Belgium
| | - Karine Lebaron
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom
| | - Laurent Intertaglia
- Sorbonne Universites, UPMC Univ Paris 06, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), Observatoire Océanologique, Banyuls/Mer, France.,Sorbonne Universites, UPMC Univ Paris 06, CNRS, Observatoire Océanologique de Banyuls (OOB), Banyuls/Mer, France
| | - Callum Regan
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom
| | - James Morris
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom
| | - Hanno Teeling
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Manuel Ferrer
- Department of Applied Biocatalysis, Institute of Catalysis, CSIC, Madrid, Spain
| | - Peter N Golyshin
- School of Natural Sciences, University of Bangor, Bangor, United Kingdom
| | - Dimitrios Gerogiorgis
- Institute for Materials and Processes, School of Engineering, University of Edinburgh, The King's Buildings, Edinburgh, United Kingdom
| | - Simon I Reilly
- School of Natural Sciences, University of Bangor, Bangor, United Kingdom
| | - Philippe Lebaron
- Sorbonne Universites, UPMC Univ Paris 06, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), Observatoire Océanologique, Banyuls/Mer, France.,Sorbonne Universites, UPMC Univ Paris 06, CNRS, Observatoire Océanologique de Banyuls (OOB), Banyuls/Mer, France
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222
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Rittershaus ESC, Baek SH, Krieger IV, Nelson SJ, Cheng YS, Nambi S, Baker RE, Leszyk JD, Shaffer SA, Sacchettini JC, Sassetti CM. A Lysine Acetyltransferase Contributes to the Metabolic Adaptation to Hypoxia in Mycobacterium tuberculosis. Cell Chem Biol 2018; 25:1495-1505.e3. [PMID: 30318462 PMCID: PMC6309504 DOI: 10.1016/j.chembiol.2018.09.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 05/14/2018] [Accepted: 09/12/2018] [Indexed: 01/07/2023]
Abstract
Upon inhibition of respiration, which occurs in hypoxic or nitric oxide-containing host microenvironments, Mycobacterium tuberculosis (Mtb) adopts a non-replicating "quiescent" state and becomes relatively unresponsive to antibiotic treatment. We used comprehensive mutant fitness analysis to identify regulatory and metabolic pathways that are essential for the survival of quiescent Mtb. This genetic study identified a protein acetyltransferase (Mt-Pat/Rv0998) that promoted survival and altered the flux of carbon from oxidative to reductive tricarboxylic acid (TCA) reactions. Reductive TCA requires malate dehydrogenase (MDH) and maintains the redox state of the NAD+/NADH pool. Genetic or chemical inhibition of MDH resulted in rapid cell death in both hypoxic cultures and in murine lung. These phenotypic data, in conjunction with significant structural differences between human and mycobacterial MDH enzymes that could be exploited for drug development, suggest a new strategy for eradicating quiescent bacteria.
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Affiliation(s)
- Emily S. C. Rittershaus
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School. Worcester, MA. 01650 USA
| | - Seung-Hun Baek
- Department of Microbiology, Yonsei University College of Medicine, Seoul Korea
| | - Inna V. Krieger
- Department of Biochemistry and Biophysics. Texas A&M University. College Station, TX. 77843 USA
| | - Samantha J. Nelson
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School. Worcester, MA. 01650 USA
| | - Yu-Shan Cheng
- Department of Biochemistry and Biophysics. Texas A&M University. College Station, TX. 77843 USA
| | - Subhalaxmi Nambi
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School. Worcester, MA. 01650 USA
| | - Richard E. Baker
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School. Worcester, MA. 01650 USA
| | - John D. Leszyk
- Proteomics and Mass Spectrometry Facility, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA. 01650 USA
| | - Scott A. Shaffer
- Proteomics and Mass Spectrometry Facility, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA. 01650 USA
| | - James C. Sacchettini
- Department of Biochemistry and Biophysics. Texas A&M University. College Station, TX. 77843 USA
| | - Christopher M. Sassetti
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School. Worcester, MA. 01650 USA
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223
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Porter N, Shen S, Barinka C, Kozikowski AP, Christianson DW. Molecular Basis for the Selective Inhibition of Histone Deacetylase 6 by a Mercaptoacetamide Inhibitor. ACS Med Chem Lett 2018; 9:1301-1305. [PMID: 30613344 PMCID: PMC6295862 DOI: 10.1021/acsmedchemlett.8b00487] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 11/20/2018] [Indexed: 12/12/2022] Open
Abstract
Mercaptoacetamide histone deacetylase inhibitors are neuroprotective agents that do not exhibit the genotoxicity associated with more commonly used hydroxamate inhibitors. Here, we present the crystal structure of a selective mercaptoacetamide complexed with the C-terminal catalytic domain of HDAC6. When compared with the structure of a mercaptoacetamide bound to the class I isozyme HDAC8, different interactions are observed with the conserved tandem histidine pair in the active site. These differences likely contribute to the selectivity for inhibition of HDAC6, an important target for cancer chemotherapy and the treatment of neurodegenerative disease.
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Affiliation(s)
- Nicholas
J. Porter
- Roy
and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Sida Shen
- Department
of Medicinal Chemistry and Pharmacognosy, Drug Discovery Program, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Cyril Barinka
- Laboratory
of Structural Biology, Institute of Biotechnology
of the Czech Academy of Sciences, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Alan P. Kozikowski
- StarWise
Therapeutics LLC, 505
South Rosa Road, Madison, Wisconsin 53719, United States
| | - David W. Christianson
- Roy
and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
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224
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Lantier L, Williams AS, Hughey CC, Bracy DP, James FD, Ansari MA, Gius D, Wasserman DH. SIRT2 knockout exacerbates insulin resistance in high fat-fed mice. PLoS One 2018; 13:e0208634. [PMID: 30533032 PMCID: PMC6289500 DOI: 10.1371/journal.pone.0208634] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 11/20/2018] [Indexed: 01/26/2023] Open
Abstract
The NAD+-dependent deacetylase SIRT2 is unique amongst sirtuins as it is effective in the cytosol, as well as the mitochondria. Defining the role of cytosolic acetylation state in specific tissues is difficult since even physiological effects at the whole body level are unknown. We hypothesized that genetic SIRT2 knockout (KO) would lead to impaired insulin action, and that this impairment would be worsened in HF fed mice. Insulin sensitivity was tested using the hyperinsulinemic-euglycemic clamp in SIRT2 KO mice and WT littermates. SIRT2 KO mice exhibited reduced skeletal muscle insulin-induced glucose uptake compared to lean WT mice, and this impairment was exacerbated in HF SIRT2 KO mice. Liver insulin sensitivity was unaffected in lean SIRT2 KO mice. However, the insulin resistance that accompanies HF-feeding was worsened in SIRT2 KO mice. It was notable that the effects of SIRT2 KO were largely disassociated from cytosolic acetylation state, but were closely linked to acetylation state in the mitochondria. SIRT2 KO led to an increase in body weight that was due to increased food intake in HF fed mice. In summary, SIRT2 deletion in vivo reduces muscle insulin sensitivity and contributes to liver insulin resistance by a mechanism that is unrelated to cytosolic acetylation state. Mitochondrial acetylation state and changes in feeding behavior that result in increased body weight correspond to the deleterious effects of SIRT2 KO on insulin action.
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Affiliation(s)
- Louise Lantier
- Department of Molecular Physiology & Biophysics, Vanderbilt University School of Medicine, Nashville TN, United States of America
- Vanderbilt Mouse Metabolic Phenotyping Center, Nashville, TN, United States of America
| | - Ashley S. Williams
- Department of Molecular Physiology & Biophysics, Vanderbilt University School of Medicine, Nashville TN, United States of America
| | - Curtis C. Hughey
- Department of Molecular Physiology & Biophysics, Vanderbilt University School of Medicine, Nashville TN, United States of America
| | - Deanna P. Bracy
- Department of Molecular Physiology & Biophysics, Vanderbilt University School of Medicine, Nashville TN, United States of America
| | - Freyja D. James
- Department of Molecular Physiology & Biophysics, Vanderbilt University School of Medicine, Nashville TN, United States of America
| | - Muhammad A. Ansari
- Department of Molecular Physiology & Biophysics, Vanderbilt University School of Medicine, Nashville TN, United States of America
| | - David Gius
- Department of Radiation Oncology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States of America
| | - David H. Wasserman
- Department of Molecular Physiology & Biophysics, Vanderbilt University School of Medicine, Nashville TN, United States of America
- Vanderbilt Mouse Metabolic Phenotyping Center, Nashville, TN, United States of America
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225
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Jiang J, Gai Z, Wang Y, Fan K, Sun L, Wang H, Ding Z. Comprehensive proteome analyses of lysine acetylation in tea leaves by sensing nitrogen nutrition. BMC Genomics 2018; 19:840. [PMID: 30477445 PMCID: PMC6258439 DOI: 10.1186/s12864-018-5250-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 11/14/2018] [Indexed: 02/02/2023] Open
Abstract
Background Nε-Acetylation of lysine residues, a frequently occurring post-translational modification, plays important functions in regulating physiology and metabolism. However, the information of global overview of protein acetylome under nitrogen-starvation/resupply in tea (Camellia sinensis) leaves was limited. And the full function of lysine acetylated proteins of tea plants in nitrogen absorption and assimilation remains unclear. Results Here, we performed the global review of lysine acetylome in tea leaves under nitrogen (N)-starvation/resupply, using peptide prefractionation, immunoaffinity enrichment, and coupling with high sensitive LC-MS/MS combined with affinity purification analysis. Altogether, 2229 lysine acetylation sites on 1286 proteins were identified, of which 16 conserved motifs in E*KacK, Kac*K, Kac*R, Kac*HK, Kac*N, Kac*S, Kac*T, Kac*D, were extracted from 2180 acetylated peptides. Approximately, 36.76% of the acetylated lysines were located in the regions of ordered secondary structures. The most of the identified lysine acetylation proteins were located in the chloroplast (39%) and cytoplasm (29%). The largest group of acetylated proteins consisted of many enzymes, such as ATP synthase, ribosomal proteins and malate dehydrogenase [NADP], which were related to metabolism (38%) in the biological process. These acetylated proteins were mainly enriched in three primary protein complexes of photosynthesis: photosystem I, photosystem II and the cytochrome b6/f complex. And some acetylated proteins related to glycolysis and secondary metabolite biosynthesis were increased/decreased under N-resupply. Moreover, the PPI (protein-protein interaction) analysis revealed that the diverse interactions of identified acetylated proteins mainly involved in photosynthesis and ribosome. Conclusion The results suggested that lysine acetylated proteins might play regulating roles in metabolic process in tea leaves. The critical regulatory roles mainly involved in diverse aspects of metabolic processes, especially in photosynthesis, glycolysis and secondary metabolism. A lot of proteins related to the photosynthesis and glycolysis were found to be acetylated, including LHCA1, LHCA3, LHCB6, psaE, psaD, psaN, GAPDH, PEPC, ENL and petC. And some proteins related to flavonoids were also found to be acetylated, including PAL, DFR, naringenin 3-dioxygenase and CHI. The provided data may serve as important resources for exploring the physiological, biochemical, and genetic role of lysine acetylation in tea plants. Data are available via ProteomeXchange with identifier PXD008931. Electronic supplementary material The online version of this article (10.1186/s12864-018-5250-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jutang Jiang
- Tea Research Institute, Qingdao Agricultural University, 700 Changcheng road, Qingdao, 266109, Shandong, China
| | - Zhongshuai Gai
- College of Life Science, Yantai University, Yantai, Shandong, China
| | - Yu Wang
- Tea Research Institute, Qingdao Agricultural University, 700 Changcheng road, Qingdao, 266109, Shandong, China
| | - Kai Fan
- Tea Research Institute, Qingdao Agricultural University, 700 Changcheng road, Qingdao, 266109, Shandong, China
| | - Litao Sun
- Tea Research Institute, Qingdao Agricultural University, 700 Changcheng road, Qingdao, 266109, Shandong, China
| | - Hui Wang
- Rizhao Tea Research Institute of Shandong, Rizhao, Shandong, China
| | - Zhaotang Ding
- Tea Research Institute, Qingdao Agricultural University, 700 Changcheng road, Qingdao, 266109, Shandong, China.
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226
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Murray LA, Sheng X, Cristea IM. Orchestration of protein acetylation as a toggle for cellular defense and virus replication. Nat Commun 2018; 9:4967. [PMID: 30470744 PMCID: PMC6251895 DOI: 10.1038/s41467-018-07179-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 10/18/2018] [Indexed: 12/20/2022] Open
Abstract
Emerging evidence highlights protein acetylation, a prevalent lysine posttranslational modification, as a regulatory mechanism and promising therapeutic target in human viral infections. However, how infections dynamically alter global cellular acetylation or whether viral proteins are acetylated remains virtually unexplored. Here, we establish acetylation as a highly-regulated molecular toggle of protein function integral to the herpesvirus human cytomegalovirus (HCMV) replication. We offer temporal resolution of cellular and viral acetylations. By interrogating dynamic protein acetylation with both protein abundance and subcellular localization, we discover finely tuned spatial acetylations across infection time. We determine that lamin acetylation at the nuclear periphery protects against virus production by inhibiting capsid nuclear egress. Further studies within infectious viral particles identify numerous acetylations, including on the viral transcriptional activator pUL26, which we show represses virus production. Altogether, this study provides specific insights into functions of cellular and viral protein acetylations and a valuable resource of dynamic acetylation events. The dynamics of protein acetylation during infection remains unexplored. Here, Murray et al. characterize spatio-temporal acetylations of both cellular and viral proteins during HCMV infection, providing new functional insights into the host-virus acetylome that might help identify new antiviral targets.
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Affiliation(s)
- L A Murray
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ, 08544, USA
| | - X Sheng
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ, 08544, USA
| | - I M Cristea
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ, 08544, USA.
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227
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In-depth analysis of Bacillus subtilis proteome identifies new ORFs and traces the evolutionary history of modified proteins. Sci Rep 2018; 8:17246. [PMID: 30467398 PMCID: PMC6250715 DOI: 10.1038/s41598-018-35589-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 11/07/2018] [Indexed: 01/05/2023] Open
Abstract
Bacillus subtilis is a sporulating Gram-positive bacterium widely used in basic research and biotechnology. Despite being one of the best-characterized bacterial model organism, recent proteomics studies identified only about 50% of its theoretical protein count. Here we combined several hundred MS measurements to obtain a comprehensive map of the proteome, phosphoproteome and acetylome of B. subtilis grown at 37 °C in minimal medium. We covered 75% of the theoretical proteome (3,159 proteins), detected 1,085 phosphorylation and 4,893 lysine acetylation sites and performed a systematic bioinformatic characterization of the obtained data. A subset of analyzed MS files allowed us to reconstruct a network of Hanks-type protein kinases, Ser/Thr/Tyr phosphatases and their substrates. We applied genomic phylostratigraphy to gauge the evolutionary age of B. subtilis protein classes and revealed that protein modifications were present on the oldest bacterial proteins. Finally, we performed a proteogenomic analysis by mapping all MS spectra onto a six-frame translation of B. subtilis genome and found evidence for 19 novel ORFs. We provide the most extensive overview of the proteome and post-translational modifications for B. subtilis to date, with insights into functional annotation and evolutionary aspects of the B. subtilis genome.
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228
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Metabolite sensing and signaling in cell metabolism. Signal Transduct Target Ther 2018; 3:30. [PMID: 30416760 PMCID: PMC6224561 DOI: 10.1038/s41392-018-0024-7] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 05/27/2018] [Accepted: 05/31/2018] [Indexed: 02/07/2023] Open
Abstract
Metabolite sensing is one of the most fundamental biological processes. During evolution, multilayered mechanisms developed to sense fluctuations in a wide spectrum of metabolites, including nutrients, to coordinate cellular metabolism and biological networks. To date, AMPK and mTOR signaling are among the best-understood metabolite-sensing and signaling pathways. Here, we propose a sensor-transducer-effector model to describe known mechanisms of metabolite sensing and signaling. We define a metabolite sensor by its specificity, dynamicity, and functionality. We group the actions of metabolite sensing into three different modes: metabolite sensor-mediated signaling, metabolite-sensing module, and sensing by conjugating. With these modes of action, we provide a systematic view of how cells sense sugars, lipids, amino acids, and metabolic intermediates. In the future perspective, we suggest a systematic screen of metabolite-sensing macromolecules, high-throughput discovery of biomacromolecule-metabolite interactomes, and functional metabolomics to advance our knowledge of metabolite sensing and signaling. Most importantly, targeting metabolite sensing holds great promise in therapeutic intervention of metabolic diseases and in improving healthy aging. A simple, three-part model provides a systematic view of how cells sense sugars, lipids, amino acids and metabolic intermediates. Cells quickly and accurately perceive changes in intra- and extracellular molecules such as nutrients to respond to changing environments. Drawing on existing knowledge about AMPK and MTORC1 signaling, Yi-Ping Wang and Qun-Ying Lei at Fudan University in Shanghai propose a model in which three components: a sensor, transducer and effector enable metabolic sensing and signaling to proceed. The sensor detects the metabolite, and, through conjugation, conformational changes or protein–protein interactions, transmits this information to the transducer, which decides the appropriate response. The transducer then issues orders to effector proteins which coordinate the action. The future identification of novel metabolic sensors through systematic screening could lead to new therapeutic interventions for metabolic and age-related diseases.
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229
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Escherichia coli as a host for metabolic engineering. Metab Eng 2018; 50:16-46. [DOI: 10.1016/j.ymben.2018.04.008] [Citation(s) in RCA: 181] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 04/11/2018] [Accepted: 04/12/2018] [Indexed: 12/21/2022]
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230
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Hockenberry AM, Post DMB, Rhodes KA, Apicella M, So M. Perturbing the acetylation status of the Type IV pilus retraction motor, PilT, reduces Neisseria gonorrhoeae viability. Mol Microbiol 2018; 110:677-688. [PMID: 29719082 DOI: 10.1111/mmi.13979] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 04/29/2018] [Indexed: 02/07/2023]
Abstract
Post-translational acetylation is a common protein modification in bacteria. It was recently reported that Neisseria gonorrhoeae acetylates the Type IV pilus retraction motor, PilT. Here, we show recombinant PilT can be acetylated in vitro and acetylation does not affect PilT ultrastructure. To investigate the function of PilT acetylation, we mutated an acetylated lysine, K117, to mimic its acetylated or unacetylated forms. These mutations were not tolerated by wild-type N. gonorrhoeae, but they were tolerated by N. gonorrhoeae carrying an inducible pilE when grown without inducer. We identified additional mutations in pilT and pilU that suppress the lethality of K117 mutations. To investigate the link between PilE and PilT acetylation, we found the lack of PilE decreases PilT acetylation levels and increases the amount of PilT associated with the inner membrane. Finally, we found no difference between wild-type and mutant cells in transformation efficiency, suggesting neither mutation inhibits Type IV pilus retraction. Mutant cells, however, form microcolonies morphologically distinct from wt cells. We conclude that interfering with the acetylation status of PilTK117 greatly reduces N. gonorrhoeae viability, and mutations in pilT, pilU and pilE can overcome this lethality. We discuss the implications of these findings in the context of Type IV pilus retraction regulation.
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Affiliation(s)
- Alyson M Hockenberry
- Department of Immunobiology and BIO5 Institute, University of Arizona, Tucson, AZ, 85719, USA
| | | | - Katherine A Rhodes
- Department of Immunobiology and BIO5 Institute, University of Arizona, Tucson, AZ, 85719, USA
| | - Michael Apicella
- Department of Microbiology, The University of Iowa, Iowa City, IA, USA
| | - Magdalene So
- Department of Immunobiology and BIO5 Institute, University of Arizona, Tucson, AZ, 85719, USA
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231
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Vancura A, Nagar S, Kaur P, Bu P, Bhagwat M, Vancurova I. Reciprocal Regulation of AMPK/SNF1 and Protein Acetylation. Int J Mol Sci 2018; 19:ijms19113314. [PMID: 30366365 PMCID: PMC6274705 DOI: 10.3390/ijms19113314] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 10/22/2018] [Accepted: 10/24/2018] [Indexed: 12/31/2022] Open
Abstract
Adenosine monophosphate (AMP)-activated protein kinase (AMPK) serves as an energy sensor and master regulator of metabolism. In general, AMPK inhibits anabolism to minimize energy consumption and activates catabolism to increase ATP production. One of the mechanisms employed by AMPK to regulate metabolism is protein acetylation. AMPK regulates protein acetylation by at least five distinct mechanisms. First, AMPK phosphorylates and inhibits acetyl-CoA carboxylase (ACC) and thus regulates acetyl-CoA homeostasis. Since acetyl-CoA is a substrate for all lysine acetyltransferases (KATs), AMPK affects the activity of KATs by regulating the cellular level of acetyl-CoA. Second, AMPK activates histone deacetylases (HDACs) sirtuins by increasing the cellular concentration of NAD⁺, a cofactor of sirtuins. Third, AMPK inhibits class I and II HDACs by upregulating hepatic synthesis of α-hydroxybutyrate, a natural inhibitor of HDACs. Fourth, AMPK induces translocation of HDACs 4 and 5 from the nucleus to the cytoplasm and thus increases histone acetylation in the nucleus. Fifth, AMPK directly phosphorylates and downregulates p300 KAT. On the other hand, protein acetylation regulates AMPK activity. Sirtuin SIRT1-mediated deacetylation of liver kinase B1 (LKB1), an upstream kinase of AMPK, activates LKB1 and AMPK. AMPK phosphorylates and inactivates ACC, thus increasing acetyl-CoA level and promoting LKB1 acetylation and inhibition. In yeast cells, acetylation of Sip2p, one of the regulatory β-subunits of the SNF1 complex, results in inhibition of SNF1. This results in activation of ACC and reduced cellular level of acetyl-CoA, which promotes deacetylation of Sip2p and activation of SNF1. Thus, in both yeast and mammalian cells, AMPK/SNF1 regulate protein acetylation and are themselves regulated by protein acetylation.
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Affiliation(s)
- Ales Vancura
- Department of Biological Sciences, St. John's University, New York, NY 11439, USA.
| | - Shreya Nagar
- Department of Biological Sciences, St. John's University, New York, NY 11439, USA.
| | - Pritpal Kaur
- Department of Biological Sciences, St. John's University, New York, NY 11439, USA.
| | - Pengli Bu
- Department of Biological Sciences, St. John's University, New York, NY 11439, USA.
| | - Madhura Bhagwat
- Department of Biological Sciences, St. John's University, New York, NY 11439, USA.
| | - Ivana Vancurova
- Department of Biological Sciences, St. John's University, New York, NY 11439, USA.
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232
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Newly Identified Nucleoid-Associated-Like Protein YlxR Regulates Metabolic Gene Expression in Bacillus subtilis. mSphere 2018; 3:3/5/e00501-18. [PMID: 30355672 PMCID: PMC6200986 DOI: 10.1128/msphere.00501-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Expression of genes encoding NAPs is often temporally regulated. According to results from single-cell analysis, the ylxR gene is induced by glucose and expressed in a bistable mode. These characteristics have not previously been reported for NAP gene expression. Transcriptional profiling of the ylxR disruptant revealed a change in the expression levels of approximately 400 genes, including genes for synthesis of 12 amino acids and 4 nucleotides, in addition to the SigX/M regulons. Thus, YlxR is a critical regulator of glucose response in B. subtilis. Glucose is the most favorable carbon source for the majority of bacteria, which have several glucose-responsive gene networks. Recently, we found that in Bacillus subtilis, glucose induces expression of the extracellular sigma factor genes sigX/M. To explore the factors affecting this phenomenon, we performed a transposon mutagenesis screen for mutants with no glucose induction (GI) of sigX-lacZ and identified ylxR. YlxR is widely conserved in eubacteria. Further analysis revealed that ylxR is induced by glucose addition. In vitro DNA-binding and cytological studies suggested that YlxR is a nucleoid-associated protein (NAP) in B. subtilis. In many cases, NAPs influence transcription, recombination, and genome stability. Thus, we performed transcriptome sequencing (RNA-Seq) analysis to evaluate the impact of ylxR disruption on the transcriptome in the presence of glucose and observed that YlxR has a profound impact on metabolic gene expression in addition to that of four sigma factor genes. The wide fluctuations of gene expression may result in abolition of GI of sigX/M in the ylxR disruptant. IMPORTANCE Expression of genes encoding NAPs is often temporally regulated. According to results from single-cell analysis, the ylxR gene is induced by glucose and expressed in a bistable mode. These characteristics have not previously been reported for NAP gene expression. Transcriptional profiling of the ylxR disruptant revealed a change in the expression levels of approximately 400 genes, including genes for synthesis of 12 amino acids and 4 nucleotides, in addition to the SigX/M regulons. Thus, YlxR is a critical regulator of glucose response in B. subtilis.
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A Putative Acetylation System in Vibrio cholerae Modulates Virulence in Arthropod Hosts. Appl Environ Microbiol 2018; 84:AEM.01113-18. [PMID: 30143508 DOI: 10.1128/aem.01113-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 08/19/2018] [Indexed: 12/16/2022] Open
Abstract
Acetylation is a broadly conserved mechanism of covalently modifying the proteome to precisely control protein activity. In bacteria, central metabolic enzymes and regulatory proteins, including those involved in virulence, can be targeted for acetylation. In this study, we directly link a putative acetylation system to metabolite-dependent virulence in the pathogen Vibrio cholerae We demonstrate that the cobB and yfiQ genes, which encode homologs of a deacetylase and an acetyltransferase, respectively, modulate V. cholerae metabolism of acetate, a bacterially derived short-chain fatty acid with important physiological roles in a diversity of host organisms. In Drosophila melanogaster, a model arthropod host for V. cholerae infection, the pathogen consumes acetate within the gastrointestinal tract, which contributes to fly mortality. We show that deletion of cobB impairs growth on acetate minimal medium, delays the consumption of acetate from rich medium, and reduces virulence of V. cholerae toward Drosophila These impacts can be reversed by complementing cobB or by introducing a deletion of yfiQ into the ΔcobB background. We further show that cobB controls the accumulation of triglycerides in the Drosophila midgut, which suggests that cobB directly modulates metabolite levels in vivo In Escherichia coli K-12, yfiQ is upregulated by cAMP-cAMP receptor protein (CRP), and we identified a similar pattern of regulation in V. cholerae, arguing that the system is activated in response to similar environmental cues. In summary, we demonstrate that proteins likely involved in acetylation can modulate the outcome of infection by regulating metabolite exchange between pathogens and their colonized hosts.IMPORTANCE The bacterium Vibrio cholerae causes severe disease in humans, and strains can persist in the environment in association with a wide diversity of host species. By investigating the molecular mechanisms that underlie these interactions, we can better understand constraints affecting the ecology and evolution of this global pathogen. The Drosophila model of Vibrio cholerae infection has revealed that bacterial regulation of acetate and other small metabolites from within the fly gastrointestinal tract is crucial for its virulence. Here, we demonstrate that genes that may modify the proteome of V. cholerae affect virulence toward Drosophila, most likely by modulating central metabolic pathways that control the consumption of acetate as well as other small molecules. These findings further highlight the many layers of regulation that tune bacterial metabolism to alter the trajectory of interactions between bacteria and their hosts.
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234
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Xu Y, Li YX, Ye BC. Lysine propionylation modulates the transcriptional activity of phosphate regulator PhoP in Saccharopolyspora erythraea. Mol Microbiol 2018; 110:648-661. [PMID: 30303579 DOI: 10.1111/mmi.14122] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2018] [Indexed: 11/28/2022]
Abstract
Phosphate concentration extensively modulates the central physiological processes mediated by the two-component system PhoR-PhoP in actinobacteria. The system serves a role beyond phosphate metabolism, mediating crucial functions in nitrogen and carbon metabolism, and secondary metabolism in response to the nutritional states. Here, we found that the phosphate-sensing regulator PhoP was propionylated, and thus lost its DNA-binding activity in vivo and in vitro in Saccharopolyspora erythraea. Two key conserved lysine residues 198 and 203 (K198 and K203) in winged HTH motif at the C-terminal domain of PhoP are propionylated by protein acyltransferase AcuA (encoding by sace_5148). Single amino acid mutation of these two lysine residues resulted in severely impaired binding of PhoP to PHO box. The addition of propionate (to supply precursors for erythromycin biosynthesis) increases the intracellular propionylation level of PhoP, resulting in the loss of response to phosphate availability. Furthermore, simultaneous mutation of K198 and K203 of PhoP to arginine, mimicking the non-propionylated form, promotes the expression of the PhoP regulon under the condition of propionate addition. Together, these findings present a common regulatory mechanism of genes' expression mediated by posttranslational regulation of OmpR family transcriptional regulator PhoP and provide new insights into the multifaceted regulation of metabolism in response to nutritional signals.
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Affiliation(s)
- Ya Xu
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Yu-Xin Li
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Bang-Ce Ye
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.,Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, Zhejiang, 310014, China
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235
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Yeast two-hybrid screening reveals a dual function for the histone acetyltransferase GcnE by controlling glutamine synthesis and development in Aspergillus fumigatus. Curr Genet 2018; 65:523-538. [DOI: 10.1007/s00294-018-0891-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 09/25/2018] [Accepted: 10/08/2018] [Indexed: 01/20/2023]
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236
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Post-translational modification of nucleoid-associated proteins: an extra layer of functional modulation in bacteria? Biochem Soc Trans 2018; 46:1381-1392. [PMID: 30287510 DOI: 10.1042/bst20180488] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 08/31/2018] [Accepted: 09/04/2018] [Indexed: 01/08/2023]
Abstract
Post-translational modification (PTM) of histones has been investigated in eukaryotes for years, revealing its widespread occurrence and functional importance. Many PTMs affect chromatin folding and gene activity. Only recently the occurrence of such modifications has been recognized in bacteria. However, it is unclear whether PTM of the bacterial counterparts of eukaryotic histones, nucleoid-associated proteins (NAPs), bears a comparable significance. Here, we scrutinize proteome mass spectrometry data for PTMs of the four most abundantly present NAPs in Escherichia coli (H-NS, HU, IHF and FIS). This approach allowed us to identify a total of 101 unique PTMs in the 11 independent proteomic studies covered in this review. Combined with structural and genetic information on these proteins, we describe potential effects of these modifications (perturbed DNA-binding, structural integrity or interaction with other proteins) on their function.
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237
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Chen Y, Liu Y, Sarker MMR, Yan X, Yang C, Zhao L, Lv X, Liu B, Zhao C. Structural characterization and antidiabetic potential of a novel heteropolysaccharide from Grifola frondosa via IRS1/PI3K-JNK signaling pathways. Carbohydr Polym 2018; 198:452-461. [DOI: 10.1016/j.carbpol.2018.06.077] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 06/11/2018] [Accepted: 06/16/2018] [Indexed: 12/18/2022]
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238
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Li L, Wang W, Zhang R, Xu J, Wang R, Wang L, Zhao X, Li J. First acetyl-proteome profiling of Salmonella Typhimurium revealed involvement of lysine acetylation in drug resistance. Vet Microbiol 2018; 226:1-8. [PMID: 30389038 DOI: 10.1016/j.vetmic.2018.09.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 09/25/2018] [Accepted: 09/26/2018] [Indexed: 10/28/2022]
Abstract
Salmonella are becoming increasingly resistant to fluoroquinolones (FQs), therefore determining the resistance mechanism is very important. Recent studies have shown that protein post-translational modifications (PTM) play a role in bacterial antibiotic resistance. One such type of PTM, lysine acetylation, is a reversible and highly regulated PTM which has been found to be associated with antibiotic resistance in Mycobacterium and Acinetobacter species. Salmonella Typhimurium are major zoonotic pathogens, which are becoming increasingly resistant to FQs, the antibiotics of choice where therapy is indicated. To date, however, there have been no studies on the relationship between PTM and drug resistance in Salmonella. Therefore, in the present study, ciprofloxacin-resistant and susceptible strains of Salmonella were used as the research objects, and tandem mass tag labeling and acetylation enrichment techniques were used to screen for the different expression of actylated proteins between the two strains, and for quantitative and bioinformatics analysis. We identified a total of 631 acetylated proteins involving 1259 lysine acetylation sites. Among the quantified sites, compared with the susceptible strain, the expression of lysine acetylation was upregulated for 112 sites and downregulated for 149 sites in the resistant strain. Bioinformatic analyses showed that the main enrichment pathways for these differentially acetylated proteins are microbial metabolic process, biosynthesis of antibiotics, and bacterial chemotaxis. Among the differentially acetylated proteins, 14 proteins related to bacterial antibiotic resistance were identified (excluding metabolic and virulence-related proteins), and the lysine acetylation expression of these proteins was significantly different between the resistant and susceptible strains. These results indicated that protein lysine acetylation is not only related to metabolism and virulence, but also to antibiotic resistance. The results provide an important basis for in-depth studies of the relationship between protein lysine acetylation and bacterial antibiotic resistance.
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Affiliation(s)
- Lin Li
- Pharmacology and Toxicology Laboratory, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230026, PR China
| | - Wenjing Wang
- Pharmacology and Toxicology Laboratory, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230026, PR China
| | - Ruiliang Zhang
- Pharmacology and Toxicology Laboratory, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230026, PR China
| | - Jun Xu
- Pharmacology and Toxicology Laboratory, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230026, PR China
| | - Rui Wang
- Pharmacology and Toxicology Laboratory, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230026, PR China
| | - Lei Wang
- Pharmacology and Toxicology Laboratory, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230026, PR China
| | - Xia Zhao
- Pharmacology and Toxicology Laboratory, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230026, PR China
| | - Jinnian Li
- Anhui Province Key Lab of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei, Anhui 230036, PR China.
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239
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Porter NJ, Osko JD, Diedrich D, Kurz T, Hooker JM, Hansen FK, Christianson DW. Histone Deacetylase 6-Selective Inhibitors and the Influence of Capping Groups on Hydroxamate-Zinc Denticity. J Med Chem 2018; 61:8054-8060. [PMID: 30118224 PMCID: PMC6136958 DOI: 10.1021/acs.jmedchem.8b01013] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Four crystal structures are presented of histone deacetylase 6 (HDAC6) complexes with para-substituted phenylhydromaxamate inhibitors, including bulky peptoids. These structures provide insight regarding the design of capping groups that confer selectivity for binding to HDAC6, specifically with regard to interactions in a pocket formed by the L1 loop. Capping group interactions may also influence hydroxamate-Zn2+ coordination with monodentate or bidentate geometry.
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Affiliation(s)
- Nicholas J. Porter
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104-6323, United States
| | - Jeremy D. Osko
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104-6323, United States
| | - Daniela Diedrich
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Thomas Kurz
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Jacob M. Hooker
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts 02129, United States
| | - Finn K. Hansen
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
- Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Medical Faculty, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| | - David W. Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104-6323, United States
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240
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Gaviard C, Jouenne T, Hardouin J. Proteomics ofPseudomonas aeruginosa: the increasing role of post-translational modifications. Expert Rev Proteomics 2018; 15:757-772. [DOI: 10.1080/14789450.2018.1516550] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Charlotte Gaviard
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, PBS, 76000, Rouen, France
- PISSARO proteomic facility, IRIB, 76821 Mont-Saint-Aignan, France
| | - Thierry Jouenne
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, PBS, 76000, Rouen, France
- PISSARO proteomic facility, IRIB, 76821 Mont-Saint-Aignan, France
| | - Julie Hardouin
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, PBS, 76000, Rouen, France
- PISSARO proteomic facility, IRIB, 76821 Mont-Saint-Aignan, France
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241
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Abstract
2017 marks the 60th anniversary of Krebs’ seminal paper on the glyoxylate shunt (and coincidentally, also the 80th anniversary of his discovery of the citric acid cycle). Sixty years on, we have witnessed substantial developments in our understanding of how flux is partitioned between the glyoxylate shunt and the oxidative decarboxylation steps of the citric acid cycle. The last decade has shown us that the beautifully elegant textbook mechanism that regulates carbon flux through the shunt in E. coli is an oversimplification of the situation in many other bacteria. The aim of this review is to assess how this new knowledge is impacting our understanding of flux control at the TCA cycle/glyoxylate shunt branch point in a wider range of genera, and to summarize recent findings implicating a role for the glyoxylate shunt in cellular functions other than metabolism.
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Affiliation(s)
- Stephen K. Dolan
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom;,
| | - Martin Welch
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom;,
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242
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Latorre-Muro P, Baeza J, Armstrong EA, Hurtado-Guerrero R, Corzana F, Wu LE, Sinclair DA, López-Buesa P, Carrodeguas JA, Denu JM. Dynamic Acetylation of Phosphoenolpyruvate Carboxykinase Toggles Enzyme Activity between Gluconeogenic and Anaplerotic Reactions. Mol Cell 2018; 71:718-732.e9. [PMID: 30193097 PMCID: PMC6188669 DOI: 10.1016/j.molcel.2018.07.031] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 06/01/2018] [Accepted: 07/24/2018] [Indexed: 12/11/2022]
Abstract
Cytosolic phosphoenolpyruvate carboxykinase (PCK1) is considered a gluconeogenic enzyme; however, its metabolic functions and regulatory mechanisms beyond gluconeogenesis are poorly understood. Here, we describe that dynamic acetylation of PCK1 interconverts the enzyme between gluconeogenic and anaplerotic activities. Under high glucose, p300-dependent hyperacetylation of PCK1 did not lead to protein degradation but instead increased the ability of PCK1 to perform the anaplerotic reaction, converting phosphoenolpyruvate to oxaloacetate. Lys91 acetylation destabilizes the active site of PCK1 and favors the reverse reaction. At low energy input, we demonstrate that SIRT1 deacetylates PCK1 and fully restores the gluconeogenic ability of PCK1. Additionally, we found that GSK3β-mediated phosphorylation of PCK1 decreases acetylation and increases ubiquitination. Biochemical evidence suggests that serine phosphorylation adjacent to Lys91 stimulates SIRT1-dependent deacetylation of PCK1. This work reveals an unexpected capacity of hyperacetylated PCK1 to promote anaplerotic activity, and the intersection of post-translational control of PCK1 involving acetylation, phosphorylation, and ubiquitination.
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Affiliation(s)
- Pedro Latorre-Muro
- Departamento de Producción Animal y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), BIFIIQFR (CSIC) Joint Unit, Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - Josue Baeza
- Wisconsin Institute for Discovery and Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health-Madison, Madison, WI 53715, USA
| | - Eric A Armstrong
- Wisconsin Institute for Discovery and Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health-Madison, Madison, WI 53715, USA
| | - Ramón Hurtado-Guerrero
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), BIFIIQFR (CSIC) Joint Unit, Universidad de Zaragoza, 50018 Zaragoza, Spain; Fundación ARAID, Government of Aragón, Zaragoza, Spain
| | - Francisco Corzana
- Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja, 26006 Logroño, Spain
| | - Lindsay E Wu
- Department of Pharmacology, School of Medical Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
| | - David A Sinclair
- Department of Pharmacology, School of Medical Sciences, The University of New South Wales, Sydney, NSW 2052, Australia; Department of Genetics, Paul F. Glenn Laboratories for the Biological Mechanisms of Aging, Harvard Medical School, Boston, MA 02115, USA
| | - Pascual López-Buesa
- Departamento de Producción Animal y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), BIFIIQFR (CSIC) Joint Unit, Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - José A Carrodeguas
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), BIFIIQFR (CSIC) Joint Unit, Universidad de Zaragoza, 50018 Zaragoza, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; IIS Aragón, Zaragoza, Spain.
| | - John M Denu
- Wisconsin Institute for Discovery and Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health-Madison, Madison, WI 53715, USA; Morgridge Institute for Research, Madison, WI 53715, USA.
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243
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Šoštarić N, O'Reilly FJ, Giansanti P, Heck AJR, Gavin AC, van Noort V. Effects of Acetylation and Phosphorylation on Subunit Interactions in Three Large Eukaryotic Complexes. Mol Cell Proteomics 2018; 17:2387-2401. [PMID: 30181345 DOI: 10.1074/mcp.ra118.000892] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 08/27/2018] [Indexed: 01/18/2023] Open
Abstract
Protein post-translational modifications (PTMs) have an indispensable role in living cells as they expand chemical diversity of the proteome, providing a fine regulatory layer that can govern protein-protein interactions in changing environmental conditions. Here we investigated the effects of acetylation and phosphorylation on the stability of subunit interactions in purified Saccharomyces cerevisiae complexes, namely exosome, RNA polymerase II and proteasome. We propose a computational framework that consists of conformational sampling of the complexes by molecular dynamics simulations, followed by Gibbs energy calculation by MM/GBSA. After benchmarking against published tools such as FoldX and Mechismo, we could apply the framework for the first time on large protein assemblies with the aim of predicting the effects of PTMs located on interfaces of subunits on binding stability. We discovered that acetylation predominantly contributes to subunits' interactions in a locally stabilizing manner, while phosphorylation shows the opposite effect. Even though the local binding contributions of PTMs may be predictable to an extent, the long range effects and overall impact on subunits' binding were only captured because of our dynamical approach. Employing the developed, widely applicable workflow on other large systems will shed more light on the roles of PTMs in protein complex formation.
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Affiliation(s)
- Nikolina Šoštarić
- KU Leuven, Centre of Microbial and Plant Genetics, Kasteelpark Arenberg 20, Leuven, B-3001, Belgium
| | - Francis J O'Reilly
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany; Technical University of Berlin, Berlin, Germany
| | - Piero Giansanti
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Science4Life, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Centre, Utrecht, The Netherlands; Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Science4Life, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Centre, Utrecht, The Netherlands
| | - Anne-Claude Gavin
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Vera van Noort
- KU Leuven, Centre of Microbial and Plant Genetics, Kasteelpark Arenberg 20, Leuven, B-3001, Belgium; Leiden University, Institute of Biology Leiden, Leiden, The Netherlands.
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244
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Buffing MF, Link H, Christodoulou D, Sauer U. Capacity for instantaneous catabolism of preferred and non-preferred carbon sources in Escherichia coli and Bacillus subtilis. Sci Rep 2018; 8:11760. [PMID: 30082753 PMCID: PMC6079084 DOI: 10.1038/s41598-018-30266-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 07/26/2018] [Indexed: 02/08/2023] Open
Abstract
Making the right choice for nutrient consumption in an ever-changing environment is a key factor for evolutionary success of bacteria. Here we investigate the regulatory mechanisms that enable dynamic adaptation between non-preferred and preferred carbon sources for the model Gram-negative and -positive species Escherichia coli and Bacillus subtilis, respectively. We focus on the ability for instantaneous catabolism of a gluconeogenic carbon source upon growth on a glycolytic carbon source and vice versa. By following isotopic tracer dynamics on a 1–2 minute scale, we show that flux reversal from the preferred glucose to non-preferred pyruvate as the sole carbon source is primarily transcriptionally regulated. In the opposite direction, however, E. coli can reverse its flux instantaneously by means of allosteric regulation, whereas in B. subtilis this flux reversal is transcriptionally regulated. Upon removal of transcriptional regulation, B. subtilis assumes the ability of instantaneous glucose catabolism. Using an approach that combines quantitative metabolomics and kinetic modelling, we then identify the additionally necessary key metabolite-enzyme interactions that implement the instantaneous flux reversal in the transcriptionally deregulated B. subtilis, and validate the most relevant allosteric interactions.
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Affiliation(s)
- Marieke F Buffing
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,Life Science Zurich PhD Program on Systems Biology, Zurich, Switzerland
| | - Hannes Link
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Dimitris Christodoulou
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,Life Science Zurich PhD Program on Systems Biology, Zurich, Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
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245
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Zhu GR, Yan X, Zhu D, Deng X, Wu JS, Xia J, Yan YM. Lysine acetylproteome profiling under water deficit reveals key acetylated proteins involved in wheat grain development and starch biosynthesis. J Proteomics 2018; 185:8-24. [DOI: 10.1016/j.jprot.2018.06.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 06/06/2018] [Accepted: 06/18/2018] [Indexed: 01/17/2023]
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246
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Yao S, Udenigwe CC. Peptidomics of potato protein hydrolysates: implications of post-translational modifications in food peptide structure and behaviour. ROYAL SOCIETY OPEN SCIENCE 2018; 5:172425. [PMID: 30109062 PMCID: PMC6083715 DOI: 10.1098/rsos.172425] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 06/07/2018] [Indexed: 06/08/2023]
Abstract
Post-translational modifications (PTMs) often occur in proteins and play a regulatory role in protein function. There is an increasing interest in the bioactivity of food protein-derived peptides, but the occurrence of PTMs and their influence on food peptide structure and behaviour remain largely unknown. In this study, the shotgun-based peptidomics strategy was used to identify the occurrence of PTMs in peptides generated from potato protein hydrolysis using digestive proteases. Diverse PTMs were found in the potato peptides, including acetylation of lysine, N-terminal of proteins and peptides, C-terminal amidation, de-amidation of asparagine/glutamine, methylation and trimethylation, methionine oxidation and N-terminal pyro-glutamyl residue formation. The modifications may have been formed naturally or as a result of chemical reactions during isolation and enzymatic processing of the potato proteins. Most of the PTMs were calculated to decrease the isoelectric point and increase molecular hydrophobicity of the peptides, which will influence their bioactivity while also potentially altering their solubility in an aqueous environment. This is the first study to unravel that food-derived peptides can be widely modified by PTMs associated with notable changes in peptide chemical properties. The findings have broader implications on the bioavailability, biomolecular interactions and biological activities of food peptides.
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Affiliation(s)
- Shixiang Yao
- College of Food Science, Southwest University, Chongqing 400715, People's Republic of China
- School of Nutrition Sciences, University of Ottawa, Ottawa, Ontario, CanadaK1H 8L1
| | - Chibuike C. Udenigwe
- School of Nutrition Sciences, University of Ottawa, Ottawa, Ontario, CanadaK1H 8L1
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, CanadaK1N 6N5
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247
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Chen Y, Huang Q, Liu W, Zhu Q, Cui CP, Xu L, Guo X, Wang P, Liu J, Dong G, Wei W, Liu CH, Feng Z, He F, Zhang L. Mutually exclusive acetylation and ubiquitylation of the splicing factor SRSF5 control tumor growth. Nat Commun 2018; 9:2464. [PMID: 29942010 PMCID: PMC6018636 DOI: 10.1038/s41467-018-04815-3] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 05/18/2018] [Indexed: 12/30/2022] Open
Abstract
Most tumor cells take up more glucose than normal cells. Splicing dysregulation is one of the molecular hallmarks of cancer. However, the role of splicing factor in glucose metabolism and tumor development remains poorly defined. Here, we show that upon glucose intake, the splicing factor SRSF5 is specifically induced through Tip60-mediated acetylation on K125, which antagonizes Smurf1-mediated ubiquitylation. SRSF5 promotes the alternative splicing of CCAR1 to produce CCAR1S proteins, which promote tumor growth by enhancing glucose consumption and acetyl-CoA production. Conversely, upon glucose starvation, SRSF5 is deacetylated by HDAC1, and ubiquitylated by Smurf1 on the same lysine, resulting in proteasomal degradation of SRSF5. The CCAR1L proteins accumulate to promote apoptosis. Importantly, SRSF5 is hyperacetylated and upregulated in human lung cancers, which correlates with increased CCAR1S expression and tumor progression. Thus, SRSF5 responds to high glucose to promote cancer development, and SRSF5-CCAR1 axis may be valuable targets for cancer therapeutics.
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Affiliation(s)
- Yuhan Chen
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center of Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China.,Department of Genomics and Proteomics, Beijing Institute of Radiation Medicine, Beijing, 100850, China.,Affiliated BaYi Children's Hospital, PLA Army General Hospital, National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, Beijing Key Laboratory of Pediatric Organ Failure, Beijing, 100700, China
| | - Qingyang Huang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center of Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China.,Department of Genomics and Proteomics, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Wen Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center of Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China.,Department of Genomics and Proteomics, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Qiong Zhu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center of Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China.,Department of Genomics and Proteomics, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Chun-Ping Cui
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center of Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China.,Department of Genomics and Proteomics, Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Liang Xu
- Department of Genomics and Proteomics, Beijing Institute of Radiation Medicine, Beijing, 100850, China.,Department of Biochemistry and Molecular Biology, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Xing Guo
- Department of Genomics and Proteomics, Beijing Institute of Radiation Medicine, Beijing, 100850, China.,Department of Neurobiology, Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
| | - Ping Wang
- Department of Central Laboratory, Shanghai Tenth People's Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200072, China
| | - Jingwen Liu
- Department of General Surgery, Chinese People's Liberation Army General Hospital, Beijing, 100853, China
| | - Guanglong Dong
- Department of General Surgery, Chinese People's Liberation Army General Hospital, Beijing, 100853, China
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02115, USA
| | - Cui Hua Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhichun Feng
- Affiliated BaYi Children's Hospital, PLA Army General Hospital, National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, Beijing Key Laboratory of Pediatric Organ Failure, Beijing, 100700, China
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center of Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China. .,Department of Genomics and Proteomics, Beijing Institute of Radiation Medicine, Beijing, 100850, China.
| | - Lingqiang Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center of Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China. .,Department of Genomics and Proteomics, Beijing Institute of Radiation Medicine, Beijing, 100850, China. .,School of Life Science, Jiangsu Normal University, Xuzhou, 221116, Jiangsu, China.
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248
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Venkat S, Chen H, Stahman A, Hudson D, McGuire P, Gan Q, Fan C. Characterizing Lysine Acetylation of Isocitrate Dehydrogenase in Escherichia coli. J Mol Biol 2018; 430:1901-1911. [PMID: 29733852 PMCID: PMC5988991 DOI: 10.1016/j.jmb.2018.04.031] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 04/18/2018] [Accepted: 04/24/2018] [Indexed: 12/21/2022]
Abstract
The Escherichia coli isocitrate dehydrogenase (ICDH) is one of the tricarboxylic acid cycle enzymes, playing key roles in energy production and carbon flux regulation. E. coli ICDH was the first bacterial enzyme shown to be regulated by reversible phosphorylation. However, the effect of lysine acetylation on E. coli ICDH, which has no sequence similarity with its counterparts in eukaryotes, is still unclear. Based on previous studies of E. coli acetylome and ICDH crystal structures, eight lysine residues were selected for mutational and kinetic analyses. They were replaced with acetyllysine by the genetic code expansion strategy or substituted with glutamine as a classic approach. Although acetylation decreased the overall ICDH activity, its effects were different site by site. Deacetylation tests demonstrated that the CobB deacetylase could deacetylate ICDH both in vivo and in vitro, but CobB was only specific for lysine residues at the protein surface. On the other hand, ICDH could be acetylated by acetyl-phosphate chemically in vitro. And in vivo acetylation tests indicated that the acetylation level of ICDH was correlated with the amounts of intracellular acetyl-phosphate. This study nicely complements previous proteomic studies to provide direct biochemical evidence for ICDH acetylation.
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Affiliation(s)
- Sumana Venkat
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, United States; Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, United States
| | - Hao Chen
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, United States; Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, United States
| | - Alleigh Stahman
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, United States
| | - Denver Hudson
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, United States
| | - Paige McGuire
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, United States
| | - Qinglei Gan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, United States
| | - Chenguang Fan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, United States; Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, United States.
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249
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Li Y, Zhang M, Dorfman RG, Pan Y, Tang D, Xu L, Zhao Z, Zhou Q, Zhou L, Wang Y, Yin Y, Shen S, Kong B, Friess H, Zhao S, Wang L, Zou X. SIRT2 Promotes the Migration and Invasion of Gastric Cancer through RAS/ERK/JNK/MMP-9 Pathway by Increasing PEPCK1-Related Metabolism. Neoplasia 2018; 20:745-756. [PMID: 29925042 PMCID: PMC6005814 DOI: 10.1016/j.neo.2018.03.008] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/19/2018] [Accepted: 03/26/2018] [Indexed: 12/30/2022] Open
Abstract
Metastasis is the most important feature of gastric cancer (GC) and the most widely recognized reason for GC-related deaths. Unfortunately, the underlying mechanism behind this metastasis remains unknown. Mounting evidence suggests the dynamic regulatory role of sirtuin2 (SIRT2), a histone deacetylase (HDAC), in cell migration and invasion. The present study aims to evaluate the biological function of SIRT2 in GC and identify the target of SIRT2 as well as evaluate its therapeutic efficacy. We found that SIRT2 was upregulated in GC tissues compared to adjacent normal tissues, and this was correlated with reduced patient survival. Although CCK8 and colony-formation assays showed that SIRT2 overexpression marginally promoted proliferation in GC cell lines, SIRT2 knockdown or treatment with SirReal2 decreased the migration and invasion of GC cells. We demonstrated both in vitro and in vivo that SirReal2 could inhibit the deacetylation activity of SIRT2 and its downstream target PEPCK1, which is related to mitochondrial metabolism and RAS/ERK/JNK/MMP-9 pathway. Taken together, these results demonstrate for the first time that SirReal2 selectively targets SIRT2 and decreases migration as well as invasion in human GC cells. SirReal2 therefore shows promise as a new drug candidate for GC therapy.
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Affiliation(s)
- Yang Li
- Department of Gastroenterology, Drum Tower Clinical Medical College of Nanjing Medical University, Nanjing, China; Department of Gastroenterology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Mingming Zhang
- Department of Gastroenterology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing University, Nanjing, China; Key laboratory of Reproduction Regulation of NPFPC (SIPPR, IRD); School of Life Sciences, Fudan University, Shanghai, China
| | - Robert G Dorfman
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Yida Pan
- Department of Digestive Diseases of Huashan Hospital, Fudan University, Shanghai, China
| | - Dehua Tang
- Department of Gastroenterology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing University, Nanjing, China
| | - Lei Xu
- Department of Gastroenterology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing University, Nanjing, China
| | - Zhenguo Zhao
- Department of Gastroenterology, Drum Tower Clinical Medical College of Nanjing Medical University, Nanjing, China
| | - Qian Zhou
- School of Life Sciences, Fudan University, Shanghai, China
| | - Lixing Zhou
- Department of Gastroenterology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing University, Nanjing, China
| | - Yuming Wang
- Department of Gastroenterology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing University, Nanjing, China
| | - Yuyao Yin
- Department of Gastroenterology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing University, Nanjing, China
| | - Shanshan Shen
- Department of Gastroenterology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing University, Nanjing, China
| | - Bo Kong
- Department of Gastroenterology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing University, Nanjing, China; Department of Surgery, Technical University of Munich (TUM), Munich, Germany
| | - Helmut Friess
- Department of Surgery, Technical University of Munich (TUM), Munich, Germany
| | - Shimin Zhao
- Department of Gastroenterology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing University, Nanjing, China; Key laboratory of Reproduction Regulation of NPFPC (SIPPR, IRD); School of Life Sciences, Fudan University, Shanghai, China
| | - Lei Wang
- Department of Gastroenterology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing University, Nanjing, China.
| | - Xiaoping Zou
- Department of Gastroenterology, Drum Tower Clinical Medical College of Nanjing Medical University, Nanjing, China; Department of Gastroenterology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing University, Nanjing, China.
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250
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Xu JY, Xu Y, Xu Z, Zhai LH, Ye Y, Zhao Y, Chu X, Tan M, Ye BC. Protein Acylation is a General Regulatory Mechanism in Biosynthetic Pathway of Acyl-CoA-Derived Natural Products. Cell Chem Biol 2018; 25:984-995.e6. [PMID: 29887264 DOI: 10.1016/j.chembiol.2018.05.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 03/25/2018] [Accepted: 05/01/2018] [Indexed: 11/18/2022]
Abstract
Coenzyme A (CoA) esters of short fatty acids (acyl-CoAs) function as key precursors for the biosynthesis of various natural products and the dominant donors for lysine acylation. Herein, we investigated the functional interplay between beneficial and adverse effects of acyl-CoA supplements on the production of acyl-CoA-derived natural products in microorganisms by using erythromycin-biosynthesized Saccharopolyspora erythraea as a model: accumulation of propionyl-CoA benefited erythromycin biosynthesis, but lysine propionylation inhibited the activities of important enzymes involved in biosynthetic pathways of erythromycin. The results showed that the overexpression of NAD+-dependent deacylase could circumvent the inhibitory effects of high acyl-CoA concentrations. In addition, we demonstrated the similar lysine acylation mechanism in other acyl-CoA-derived natural product biosynthesis, such as malonyl-CoA-derived alkaloid and butyryl-CoA-derived bioalcohol. These observations systematically uncovered the important role of protein acylation on interaction between the accumulation of high concentrations of acyl-CoAs and the efficiency of their use in metabolic pathways.
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Affiliation(s)
- Jun-Yu Xu
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China; Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Ya Xu
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Zhen Xu
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Lin-Hui Zhai
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China
| | - Yang Ye
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China
| | - Yingming Zhao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China; Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, USA
| | - Xiaohe Chu
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China.
| | - Bang-Ce Ye
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China; Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.
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