1
|
Zhou JP, Tan YQ, Chen ZH, Zhao W, Liu T. Adenosine triphosphate can act as a determinant of lysine acetylation of non-native and native substrates. Microbiol Res 2023; 268:127296. [PMID: 36580869 DOI: 10.1016/j.micres.2022.127296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/20/2022] [Accepted: 12/23/2022] [Indexed: 12/25/2022]
Abstract
The protein lysine acetylation includes acetyl-CoA (AcCoA) or acetyl phosphate (AcP)-mediated nonenzymatic acetylation, and enzymatic acetylation. It is widespread in the proteomes but the acetylation levels of most sites are very low. A thorough understanding of the determinants of low acetylation levels is highly important for elucidating the physiological relevance of lysine acetylation. In this study, we constructed a non-native substrate library containing 24 synthesized polypeptides, and we showed that ATP could inhibit the AcCoA-mediated nonenzymatic acetylation of these polypeptides through LC-MS/MS analysis. The acetyltransferase PatZ could acetylated these non-native substrates, and the PatZ-catalyzed acetylation of the polypeptides was also inhibited by ATP. Furthermore, the Western blot showed that ATP also inhibited the nonenzymatic (AcCoA or AcP-mediated) and enzymatic (PatZ-catalyzed) acetylation of acetyl-CoA synthetase Acs, which is a native substrate for acetylation. ATP can also inhibit the autoacetylation of acetyltransferase PatZ. Besides, both ADP and AMP could enhance the AcP-mediated acetylation of Acs, but ADP slightly inhibited the AcCoA-mediated acetylation of Acs. However, both ADP and AMP had no evident inhibition on the PatZ-catalyzed acetylation of Acs. Based on these results, we proposed that ATP can act as an inhibitor of acetylation, and it may regulate the function of PatZ by inhibiting its autoacetylation and compensate for the function of deacetylase CobB.
Collapse
Affiliation(s)
- Jia-Peng Zhou
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Yu-Qing Tan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Zi-Hao Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Wei Zhao
- Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
| | - Tong Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China; The Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China.
| |
Collapse
|
2
|
Acetylation of Cyclic AMP Receptor Protein by Acetyl Phosphate Modulates Mycobacterial Virulence. Microbiol Spectr 2023; 11:e0400222. [PMID: 36700638 PMCID: PMC9927398 DOI: 10.1128/spectrum.04002-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The success of Mycobacterium tuberculosis (Mtb) as a pathogen is partly attributed to its ability to sense and respond to dynamic host microenvironments. The cyclic AMP (cAMP) receptor protein (CRP) is closely related to the pathogenicity of Mtb and plays an important role in this process. However, the molecular mechanisms guiding the autoregulation and downstream target genes of CRP while Mtb responds to its environment are not fully understood. Here, it is demonstrated that the acetylation of conserved lysine 193 (K193) within the C-terminal DNA-binding domain of CRP reduces its DNA-binding ability and inhibits transcriptional activity. The reversible acetylation status of CRP K193 was shown to significantly affect mycobacterial growth phenotype, alter the stress response, and regulate the expression of biologically relevant genes using a CRP K193 site-specific mutation. Notably, the acetylation level of K193 decreases under CRP-activating conditions, including the presence of cAMP, low pH, high temperature, and oxidative stress, suggesting that microenvironmental signals can directly regulate CRP K193 acetylation. Both cell- and murine-based infection assays confirmed that CRP K193 is critical to the regulation of Mtb virulence. Furthermore, the acetylation of CRP K193 was shown to be dependent on the intracellular metabolic intermediate acetyl phosphate (AcP), and deacetylation was mediated by NAD+-dependent deacetylases. These findings indicate that AcP-mediated acetylation of CRP K193 decreases CRP activity and negatively regulates the pathogenicity of Mtb. We believe that the underlying mechanisms of cross talk between transcription, posttranslational modifications, and metabolites are a common regulatory mechanism for pathogenic bacteria. IMPORTANCE Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis, and the ability of Mtb to survive harsh host conditions has been the subject of intensive research. As a result, we explored the molecular mechanisms guiding downstream target genes of CRP when Mtb responds to its environment. Our study makes a contribution to the literature because we describe the role of acetylated K193 in regulating its binding affinity to target DNA and influencing the virulence of mycobacteria. We discovered that mycobacteria can regulate their pathogenicity through the reversible acetylation of CRP K193 and that this reversible acetylation is mediated by AcP and a NAD+-dependent deacetylase. The regulation of CRPMtb by posttranslational modifications, at the transcriptional level, and by metabolic intermediates contribute to a better understanding of its role in the survival and pathogenicity of mycobacteria.
Collapse
|
3
|
Lassak J, Sieber A, Hellwig M. Exceptionally versatile take II: post-translational modifications of lysine and their impact on bacterial physiology. Biol Chem 2022; 403:819-858. [PMID: 35172419 DOI: 10.1515/hsz-2021-0382] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 01/05/2022] [Indexed: 01/16/2023]
Abstract
Among the 22 proteinogenic amino acids, lysine sticks out due to its unparalleled chemical diversity of post-translational modifications. This results in a wide range of possibilities to influence protein function and hence modulate cellular physiology. Concomitantly, lysine derivatives form a metabolic reservoir that can confer selective advantages to those organisms that can utilize it. In this review, we provide examples of selected lysine modifications and describe their role in bacterial physiology.
Collapse
Affiliation(s)
- Jürgen Lassak
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Großhaderner Straße 2-4, D-82152 Planegg, Germany
| | - Alina Sieber
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Großhaderner Straße 2-4, D-82152 Planegg, Germany
| | - Michael Hellwig
- Technische Universität Braunschweig - Institute of Food Chemistry, Schleinitzstraße 20, D-38106 Braunschweig, Germany
| |
Collapse
|
4
|
Dai X, Zhang X, Yin Q, Hu J, Guo J, Gao Y, Snell AH, Inuzuka H, Wan L, Wei W. Acetylation-dependent regulation of BRAF oncogenic function. Cell Rep 2022; 38:110250. [PMID: 35045286 PMCID: PMC8813213 DOI: 10.1016/j.celrep.2021.110250] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 11/02/2021] [Accepted: 12/21/2021] [Indexed: 12/21/2022] Open
Abstract
Aberrant BRAF activation, including the BRAFV600E mutation, is frequently observed in human cancers. However, it remains largely elusive whether other types of post-translational modification(s) in addition to phosphorylation and ubiquitination-dependent regulation also modulate BRAF kinase activity. Here, we report that the acetyltransferase p300 activates the BRAF kinase by promoting BRAF K601 acetylation, a process that is antagonized by the deacetylase SIRT1. Notably, K601 acetylation facilitates BRAF dimerization with RAF proteins and KSR1. Furthermore, K601 acetylation promotes melanoma cell proliferation and contributes to BRAFV600E inhibitor resistance in BRAFV600E harboring melanoma cells. As such, melanoma patient-derived K601E oncogenic mutation mimics K601 acetylation to augment BRAF kinase activity. Our findings, therefore, uncover a layer of BRAF regulation and suggest p300 hyperactivation or SIRT1 deficiency as potential biomarkers to determine ERK activation in melanomas. In tumor cells, hyperactivation of the BRAF protein kinase propels uncontrolled cell proliferation. BRAF hyperactivation is also achieved through several post-translational mechanisms. Dai et al. present an acetylation-dependent regulation of BRAF kinase function in melanoma cells, which serves to enhance BRAF oncogenic function and contributes to BRAF inhibitor resistance.
Collapse
Affiliation(s)
- Xiangpeng Dai
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA; Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun 130061, PR China; National-local Joint Engineering Laboratory of Animal Models for Human Diseases, Changchun, Jilin 130061, PR China.
| | - Xiaoling Zhang
- Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun 130061, PR China; National-local Joint Engineering Laboratory of Animal Models for Human Diseases, Changchun, Jilin 130061, PR China
| | - Qing Yin
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive, Tampa, FL 33612, USA
| | - Jia Hu
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA; Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Liberalization Avenue, No. 1095, Wuhan 430030, PR China
| | - Jianping Guo
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA; The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Yang Gao
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA; Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, PR China
| | - Aidan H Snell
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive, Tampa, FL 33612, USA
| | - Hiroyuki Inuzuka
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Lixin Wan
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive, Tampa, FL 33612, USA.
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.
| |
Collapse
|
5
|
Peng GX, Zhang Y, Wang QQ, Li QR, Xu H, Wang ED, Zhou XL. The human tRNA taurine modification enzyme GTPBP3 is an active GTPase linked to mitochondrial diseases. Nucleic Acids Res 2021; 49:2816-2834. [PMID: 33619562 PMCID: PMC7969015 DOI: 10.1093/nar/gkab104] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 02/03/2021] [Accepted: 02/09/2021] [Indexed: 01/03/2023] Open
Abstract
GTPBP3 and MTO1 cooperatively catalyze 5-taurinomethyluridine (τm5U) biosynthesis at the 34th wobble position of mitochondrial tRNAs. Mutations in tRNAs, GTPBP3 or MTO1, causing τm5U hypomodification, lead to various diseases. However, efficient in vitro reconstitution and mechanistic study of τm5U modification have been challenging, in part due to the lack of pure and active enzymes. A previous study reported that purified human GTPBP3 (hGTPBP3) is inactive in GTP hydrolysis. Here, we identified the mature form of hGTPBP3 and showed that hGTPBP3 is an active GTPase in vitro that is critical for tRNA modification in vivo. Unexpectedly, the isolated G domain and a mutant with the N-terminal domain truncated catalyzed GTP hydrolysis to only a limited extent, exhibiting high Km values compared with that of the mature enzyme. We further described several important pathogenic mutations of hGTPBP3, associated with alterations in hGTPBP3 localization, structure and/or function in vitro and in vivo. Moreover, we discovered a novel cytoplasm-localized isoform of hGTPBP3, indicating an unknown potential noncanonical function of hGTPBP3. Together, our findings established, for the first time, the GTP hydrolysis mechanism of hGTPBP3 and laid a solid foundation for clarifying the τm5U modification mechanism and etiology of τm5U deficiency-related diseases.
Collapse
Affiliation(s)
- Gui-Xin Peng
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China.,School of Life Science and Technology, ShanghaiTech University, 393 Middle Hua Xia Road, Shanghai 201210, China
| | - Yong Zhang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Qin-Qin Wang
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Hua Xia Road, Shanghai 201210, China
| | - Qing-Run Li
- CAS Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Sciences, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Hong Xu
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai Municipal Key Clinical Specialty, the International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, 910 Heng Shan Road, Shanghai 200030, China
| | - En-Duo Wang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China.,School of Life Science and Technology, ShanghaiTech University, 393 Middle Hua Xia Road, Shanghai 201210, China
| | - Xiao-Long Zhou
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| |
Collapse
|
6
|
Alreda Madhloom AA, Abd-Al-Hussan GF, Kadhim NJ, Abass MC, Header HR, Talib AHK, Alwan Al-Hussain MAT, Aziz DZ. The interaction effect of Salt stress and Lysine Concentrations in some properties of Fenugreek callus. JOURNAL OF PHYSICS: CONFERENCE SERIES 2020; 1660:012018. [DOI: 10.1088/1742-6596/1660/1/012018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Abstract
The callus induction by use 1.5mg/l of α-naphthalene acetic acid (NAA) as auxin and 2mg/l of BA as cytokinins were added to MS medium that prepared as above before sterilize step. Sodium Chloride and Lysine effect on callus induction and growth of Fenugreek (Trigonella foenum-graecum L.).Five concentration of Sodium Chloride Salts (0, 2, 4, 6 and 8) were added to the culture medium and five concentrations of lysine (0, 10, 20, 30and 40mg/l) added to cultured medium. Results showed that NaCl at (2g/l) increased callus induction, fresh weight, dry weight and potassium ions of callus. The study also showed that (2 g \l) of NaCl was signification increased Sodium and Chloride ions of callus. Lysine (Lys) effect on callus characteristics:-The treatment 40mg\l outperformed of the rest treatments including control by gave the highest values of callus fresh and dry weights, as well as ions, soluble carbohydrates
Collapse
|
7
|
Zheng WQ, Zhang Y, Yao Q, Chen Y, Qiao X, Wang ED, Chen C, Zhou XL. Nitrosative stress inhibits aminoacylation and editing activities of mitochondrial threonyl-tRNA synthetase by S-nitrosation. Nucleic Acids Res 2020; 48:6799-6810. [PMID: 32484546 PMCID: PMC7337905 DOI: 10.1093/nar/gkaa471] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/06/2020] [Accepted: 05/22/2020] [Indexed: 12/20/2022] Open
Abstract
Structure and/or function of proteins are frequently affected by oxidative/nitrosative stress via posttranslational modifications. Aminoacyl-tRNA synthetases (aaRSs) constitute a class of ubiquitously expressed enzymes that control cellular protein homeostasis. Here, we found the activity of human mitochondrial (mt) threonyl-tRNA synthetase (hmtThrRS) is resistant to oxidative stress (H2O2) but profoundly sensitive to nitrosative stress (S-nitrosoglutathione, GSNO). Further study showed four Cys residues in hmtThrRS were modified by S-nitrosation upon GSNO treatment, and one residue was one of synthetic active sites. We analyzed the effect of modification at individual Cys residue on aminoacylation and editing activities of hmtThrRS in vitro and found that both activities were decreased. We further confirmed that S-nitrosation of mtThrRS could be readily detected in vivo in both human cells and various mouse tissues, and we systematically identified dozens of S-nitrosation-modified sites in most aaRSs, thus establishing both mitochondrial and cytoplasmic aaRS species with S-nitrosation ex vivo and in vivo, respectively. Interestingly, a decrease in the S-nitrosation modification level of mtThrRS was observed in a Huntington disease mouse model. Overall, our results establish, for the first time, a comprehensive S-nitrosation-modified aaRS network and a previously unknown mechanism on the basis of the inhibitory effect of S-nitrosation on hmtThrRS.
Collapse
Affiliation(s)
- Wen-Qiang Zheng
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuying Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Qin Yao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuzhe Chen
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xinhua Qiao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - En-Duo Wang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chang Chen
- University of Chinese Academy of Sciences, Beijing 100049, China.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,Beijing Institute for Brain Disorders, Capital Medical University, Beijing 100069, China
| | - Xiao-Long Zhou
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
8
|
Christensen DG, Xie X, Basisty N, Byrnes J, McSweeney S, Schilling B, Wolfe AJ. Post-translational Protein Acetylation: An Elegant Mechanism for Bacteria to Dynamically Regulate Metabolic Functions. Front Microbiol 2019; 10:1604. [PMID: 31354686 PMCID: PMC6640162 DOI: 10.3389/fmicb.2019.01604] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 06/26/2019] [Indexed: 12/15/2022] Open
Abstract
Post-translational modifications (PTM) decorate proteins to provide functional heterogeneity to an existing proteome. The large number of known PTMs highlights the many ways that cells can modify their proteins to respond to diverse stimuli. Recently, PTMs have begun to receive increased interest because new sensitive proteomics workflows and structural methodologies now allow researchers to obtain large-scale, in-depth and unbiased information concerning PTM type and site localization. However, few PTMs have been extensively assessed for functional consequences, leaving a large knowledge gap concerning the inner workings of the cell. Here, we review understanding of N-𝜀-lysine acetylation in bacteria, a PTM that was largely ignored in bacteria until a decade ago. Acetylation is a modification that can dramatically change the function of a protein through alteration of its properties, including hydrophobicity, solubility, and surface properties, all of which may influence protein conformation and interactions with substrates, cofactors and other macromolecules. Most bacteria carry genes predicted to encode the lysine acetyltransferases and lysine deacetylases that add and remove acetylations, respectively. Many bacteria also exhibit acetylation activities that do not depend on an enzyme, but instead on direct transfer of acetyl groups from the central metabolites acetyl coenzyme A or acetyl phosphate. Regardless of mechanism, most central metabolic enzymes possess lysines that are acetylated in a regulated fashion and many of these regulated sites are conserved across the spectrum of bacterial phylogeny. The interconnectedness of acetylation and central metabolism suggests that acetylation may be a response to nutrient availability or the energy status of the cell. However, this and other hypotheses related to acetylation remain untested.
Collapse
Affiliation(s)
- David G. Christensen
- Health Sciences Division, Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
| | - Xueshu Xie
- Buck Institute for Research on Aging, Novato, CA, United States
| | - Nathan Basisty
- Buck Institute for Research on Aging, Novato, CA, United States
| | - James Byrnes
- Energy & Photon Sciences Directorate, National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, United States
| | - Sean McSweeney
- Energy & Photon Sciences Directorate, National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, United States
| | | | - Alan J. Wolfe
- Health Sciences Division, Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
| |
Collapse
|
9
|
Benoy V, Van Helleputte L, Prior R, d'Ydewalle C, Haeck W, Geens N, Scheveneels W, Schevenels B, Cader MZ, Talbot K, Kozikowski AP, Vanden Berghe P, Van Damme P, Robberecht W, Van Den Bosch L. HDAC6 is a therapeutic target in mutant GARS-induced Charcot-Marie-Tooth disease. Brain 2019; 141:673-687. [PMID: 29415205 PMCID: PMC5837793 DOI: 10.1093/brain/awx375] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 11/20/2017] [Indexed: 01/01/2023] Open
Abstract
Peripheral nerve axons require a well-organized axonal microtubule network for efficient transport to ensure the constant crosstalk between soma and synapse. Mutations in more than 80 different genes cause Charcot-Marie-Tooth disease, which is the most common inherited disorder affecting peripheral nerves. This genetic heterogeneity has hampered the development of therapeutics for Charcot-Marie-Tooth disease. The aim of this study was to explore whether histone deacetylase 6 (HDAC6) can serve as a therapeutic target focusing on the mutant glycyl-tRNA synthetase (GlyRS/GARS)-induced peripheral neuropathy. Peripheral nerves and dorsal root ganglia from the C201R mutant Gars mouse model showed reduced acetylated α-tubulin levels. In primary dorsal root ganglion neurons, mutant GlyRS affected neurite length and disrupted normal mitochondrial transport. We demonstrated that GlyRS co-immunoprecipitated with HDAC6 and that this interaction was blocked by tubastatin A, a selective inhibitor of the deacetylating function of HDAC6. Moreover, HDAC6 inhibition restored mitochondrial axonal transport in mutant GlyRS-expressing neurons. Systemic delivery of a specific HDAC6 inhibitor increased α-tubulin acetylation in peripheral nerves and partially restored nerve conduction and motor behaviour in mutant Gars mice. Our study demonstrates that α-tubulin deacetylation and disrupted axonal transport may represent a common pathogenic mechanism underlying Charcot-Marie-Tooth disease and it broadens the therapeutic potential of selective HDAC6 inhibition to other genetic forms of axonal Charcot-Marie-Tooth disease.
Collapse
Affiliation(s)
- Veronick Benoy
- KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology, and Leuven Research Institute for Neuroscience & Disease (LIND), Leuven, Belgium.,VIB - Center for Brain and Disease Research, Laboratory of Neurobiology, Leuven, Belgium
| | - Lawrence Van Helleputte
- KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology, and Leuven Research Institute for Neuroscience & Disease (LIND), Leuven, Belgium.,VIB - Center for Brain and Disease Research, Laboratory of Neurobiology, Leuven, Belgium
| | - Robert Prior
- KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology, and Leuven Research Institute for Neuroscience & Disease (LIND), Leuven, Belgium.,VIB - Center for Brain and Disease Research, Laboratory of Neurobiology, Leuven, Belgium
| | - Constantin d'Ydewalle
- KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology, and Leuven Research Institute for Neuroscience & Disease (LIND), Leuven, Belgium.,VIB - Center for Brain and Disease Research, Laboratory of Neurobiology, Leuven, Belgium
| | - Wanda Haeck
- KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology, and Leuven Research Institute for Neuroscience & Disease (LIND), Leuven, Belgium.,VIB - Center for Brain and Disease Research, Laboratory of Neurobiology, Leuven, Belgium
| | - Natasja Geens
- KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology, and Leuven Research Institute for Neuroscience & Disease (LIND), Leuven, Belgium.,VIB - Center for Brain and Disease Research, Laboratory of Neurobiology, Leuven, Belgium
| | - Wendy Scheveneels
- KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology, and Leuven Research Institute for Neuroscience & Disease (LIND), Leuven, Belgium.,VIB - Center for Brain and Disease Research, Laboratory of Neurobiology, Leuven, Belgium
| | - Begga Schevenels
- KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology, and Leuven Research Institute for Neuroscience & Disease (LIND), Leuven, Belgium.,VIB - Center for Brain and Disease Research, Laboratory of Neurobiology, Leuven, Belgium
| | - M Zameel Cader
- Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford, UK.,The Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Kevin Talbot
- Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Alan P Kozikowski
- Department of Medicinal Chemistry and Pharmacognosy, Drug Discovery Program, University of Illinois at Chicago, Chicago, USA
| | - Pieter Vanden Berghe
- Translational Research Center for Gastrointestinal Disorders, University of Leuven, Leuven, Belgium
| | - Philip Van Damme
- KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology, and Leuven Research Institute for Neuroscience & Disease (LIND), Leuven, Belgium.,VIB - Center for Brain and Disease Research, Laboratory of Neurobiology, Leuven, Belgium.,University Hospitals Leuven, Department of Neurology, Leuven, Belgium
| | - Wim Robberecht
- KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology, and Leuven Research Institute for Neuroscience & Disease (LIND), Leuven, Belgium.,VIB - Center for Brain and Disease Research, Laboratory of Neurobiology, Leuven, Belgium.,University Hospitals Leuven, Department of Neurology, Leuven, Belgium
| | - Ludo Van Den Bosch
- KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology, and Leuven Research Institute for Neuroscience & Disease (LIND), Leuven, Belgium.,VIB - Center for Brain and Disease Research, Laboratory of Neurobiology, Leuven, Belgium
| |
Collapse
|
10
|
Moruno Algara M, Kuczyńska‐Wiśnik D, Dębski J, Stojowska‐Swędrzyńska K, Sominka H, Bukrejewska M, Laskowska E. Trehalose protects
Escherichia coli
against carbon stress manifested by protein acetylation and aggregation. Mol Microbiol 2019; 112:866-880. [DOI: 10.1111/mmi.14322] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/01/2019] [Indexed: 12/22/2022]
Affiliation(s)
- María Moruno Algara
- Faculty of Biology, Department of General and Medical Biochemistry University of Gdansk Wita Stwosza 5980‐308Gdansk Poland
| | - Dorota Kuczyńska‐Wiśnik
- Faculty of Biology, Department of General and Medical Biochemistry University of Gdansk Wita Stwosza 5980‐308Gdansk Poland
| | - Janusz Dębski
- Mass Spectrometry Laboratory IBB PAS ul. Pawińskiego 5A02‐106Warsaw Poland
| | - Karolina Stojowska‐Swędrzyńska
- Faculty of Biology, Department of General and Medical Biochemistry University of Gdansk Wita Stwosza 5980‐308Gdansk Poland
| | - Hanna Sominka
- Faculty of Biology, Department of General and Medical Biochemistry University of Gdansk Wita Stwosza 5980‐308Gdansk Poland
| | - Małgorzata Bukrejewska
- Faculty of Biology, Department of General and Medical Biochemistry University of Gdansk Wita Stwosza 5980‐308Gdansk Poland
| | - Ewa Laskowska
- Faculty of Biology, Department of General and Medical Biochemistry University of Gdansk Wita Stwosza 5980‐308Gdansk Poland
| |
Collapse
|
11
|
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: 94] [Impact Index Per Article: 18.8] [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.
Collapse
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
| |
Collapse
|
12
|
Chen H, Venkat S, Hudson D, Wang T, Gan Q, Fan C. Site-Specifically Studying Lysine Acetylation of Aminoacyl-tRNA Synthetases. ACS Chem Biol 2019; 14:288-295. [PMID: 30642164 DOI: 10.1021/acschembio.8b01013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aminoacyl-tRNA synthetases (AARSs) charge their cognate tRNAs with corresponding amino acids, playing key roles in ribosomal protein synthesis. A series of proteomic studies have demonstrated that AARSs have levels of lysine acetylation much higher than those of other proteins in Escherichia coli. To study AARS acetylation, 25 site-specifically acetylated variants of four AARSs were generated by the genetic code expansion strategy. Kinetic analyses were performed to biochemically characterize the impact of site-specific acetylation on AARS functions, including amino acid activation, tRNA aminoacylation, and editing activities. The results showed that impacts of acetylation were different between class I and class II AARSs and also varied among the same class of AARSs. The results also showed that acetylation of threonyl-tRNA synthetase (ThrRS) could affect its editing function. Both in vivo and in vitro studies were further performed to explore the acetylation and deacetylation processes of ThrRS. Although nonenzymatic acetylation and CobB-dependent deacetylation were concluded, the results also indicated the existence of additional modifying enzymes or mechanisms for ThrRS acetylation and deacetylation.
Collapse
|
13
|
Suzuki S, Kondo N, Yoshida M, Nishiyama M, Kosono S. Dynamic changes in lysine acetylation and succinylation of the elongation factor Tu in Bacillus subtilis. MICROBIOLOGY-SGM 2018; 165:65-77. [PMID: 30394869 DOI: 10.1099/mic.0.000737] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Nε-lysine acetylation and succinylation are ubiquitous post-translational modifications in eukaryotes and bacteria. In the present study, we showed a dynamic change in acetylation and succinylation of TufA, the translation elongation factor Tu, from Bacillus subtilis. Increased acetylation of TufA was observed during the exponential growth phase in LB and minimal glucose conditions, and its acetylation level decreased upon entering the stationary phase, while its succinylation increased during the late stationary phase. TufA was also succinylated during vegetative growth under minimal citrate or succinate conditions. Mutational analysis showed that triple succinylation mimic mutations at Lys306, Lys308 and Lys316 in domain-3 of TufA had a negative effect on B. subtilis growth, whereas the non-acylation mimic mutations at these three lysine residues did not. Consistent with the growth phenotypes, the triple succinylation mimic mutant showed 67 % decreased translation activity in vitro, suggesting a possibility that succinylation at the lysine residues in domain-3 decreases the translation activity. TufA, including Lys308, was non-enzymatically succinylated by physiological concentrations of succinyl-CoA. Lys42 in the G-domain was identified as the most frequently modified acetylation site, though its acetylation was likely dispensable for TufA translation activity and growth. Determination of the intracellular levels of acetylating substrates and TufA acetylation revealed that acetyl phosphate was responsible for acetylation at several lysine sites of TufA, but not for Lys42 acetylation. It was speculated that acetyl-CoA was likely responsible for Lys42 acetylation, though AcuA acetyltransferase was not involved. Zn2+-dependent AcuC and NAD+-dependent SrtN deacetylases were responsible for deacetylation of TufA, including Lys42. These findings suggest the potential regulatory roles of acetylation and succinylation in controlling TufA function and translation in response to nutrient environments in B. subtilis.
Collapse
Affiliation(s)
- Shota Suzuki
- 1Biotechnology Research Center, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Naoko Kondo
- 1Biotechnology Research Center, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Minoru Yoshida
- 2Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.,3Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.,4RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Makoto Nishiyama
- 1Biotechnology Research Center, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.,2Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Saori Kosono
- 1Biotechnology Research Center, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.,4RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan.,2Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| |
Collapse
|
14
|
Umehara T, Kosono S, Söll D, Tamura K. Lysine Acetylation Regulates Alanyl-tRNA Synthetase Activity in Escherichia coli. Genes (Basel) 2018; 9:genes9100473. [PMID: 30274179 PMCID: PMC6209979 DOI: 10.3390/genes9100473] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 09/09/2018] [Accepted: 09/21/2018] [Indexed: 11/19/2022] Open
Abstract
Protein lysine acetylation is a widely conserved posttranslational modification in all three domains of life. Lysine acetylation frequently occurs in aminoacyl-tRNA synthetases (aaRSs) from many organisms. In this study, we determined the impact of the naturally occurring acetylation at lysine-73 (K73) in Escherichia coli class II alanyl-tRNA synthetase (AlaRS) on its alanylation activity. We prepared an AlaRS K73Ac variant in which Nε-acetyl-l-lysine was incorporated at position 73 using an expanded genetic code system in E. coli. The AlaRS K73Ac variant showed low activity compared to the AlaRS wild type (WT). Nicotinamide treatment or CobB-deletion in an E. coli led to elevated acetylation levels of AlaRS K73Ac and strongly reduced alanylation activities. We assumed that alanylation by AlaRS is affected by K73 acetylation, and the modification is sensitive to CobB deacetylase in vivo. We also showed that E. coli expresses two CobB isoforms (CobB-L and CobB-S) in vivo. CobB-S displayed the deacetylase activity of the AlaRS K73Ac variant in vitro. Our results imply a potential regulatory role for lysine acetylation in controlling the activity of aaRSs and protein synthesis.
Collapse
Affiliation(s)
- Takuya Umehara
- Biotechnology Research Center, The University of Tokyo, Tokyo 113-8657, Japan.
- Department of Biological Science and Technology, Tokyo University of Science, Tokyo 125-8585, Japan.
| | - Saori Kosono
- Biotechnology Research Center, The University of Tokyo, Tokyo 113-8657, Japan.
- Center for Sustainable Resource Science, RIKEN, Saitama 351-0198, Japan.
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
- Department of Chemistry, Yale University, New Haven, CT 06520, USA.
| | - Koji Tamura
- Department of Biological Science and Technology, Tokyo University of Science, Tokyo 125-8585, Japan.
- Research Institute for Science and Technology, Tokyo University of Science, Chiba 278-8510, Japan.
| |
Collapse
|
15
|
Liu YT, Pan Y, Lai F, Yin XF, Ge R, He QY, Sun X. Comprehensive analysis of the lysine acetylome and its potential regulatory roles in the virulence of Streptococcus pneumoniae. J Proteomics 2018; 176:46-55. [DOI: 10.1016/j.jprot.2018.01.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 01/18/2018] [Accepted: 01/25/2018] [Indexed: 12/28/2022]
|
16
|
Venkat S, Gregory C, Gan Q, Fan C. Biochemical Characterization of the Lysine Acetylation of Tyrosyl-tRNA Synthetase in Escherichia coli. Chembiochem 2017; 18:1928-1934. [PMID: 28741290 PMCID: PMC5629106 DOI: 10.1002/cbic.201700343] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Indexed: 12/21/2022]
Abstract
Aminoacyl-tRNA synthetases (aaRSs) play essential roles in protein synthesis. As a member of the aaRS family, the tyrosyl-tRNA synthetase (TyrRS) in Escherichia coli has been shown in proteomic studies to be acetylated at multiple lysine residues. However, these putative acetylation targets have not yet been biochemically characterized. In this study, we applied a genetic-code-expansion strategy to site-specifically incorporate Nϵ -acetyl-l-lysine into selected positions of TyrRS for in vitro characterization. Enzyme assays demonstrated that acetylation at K85, K235, and K238 could impair the enzyme activity. In vitro deacetylation experiments showed that most acetylated lysine residues in TyrRS were sensitive to the E. coli deacetylase CobB but not YcgC. In vitro acetylation assays indicated that 25 members of the Gcn5-related N-acetyltransferase family in E. coli, including YfiQ, could not acetylate TyrRS efficiently, whereas TyrRS could be acetylated chemically by acetyl-CoA or acetyl-phosphate (AcP) only. Our in vitro characterization experiments indicated that lysine acetylation could be a possible mechanism for modulating aaRS enzyme activities, thus affecting translation.
Collapse
Affiliation(s)
- Sumana Venkat
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Caroline Gregory
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 727011, USA
| | - Qinglei Gan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Chenguang Fan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, 72701, USA
| |
Collapse
|