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Dunkelmann DL, Chin JW. Engineering Pyrrolysine Systems for Genetic Code Expansion and Reprogramming. Chem Rev 2024. [PMID: 39235427 DOI: 10.1021/acs.chemrev.4c00243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2024]
Abstract
Over the past 16 years, genetic code expansion and reprogramming in living organisms has been transformed by advances that leverage the unique properties of pyrrolysyl-tRNA synthetase (PylRS)/tRNAPyl pairs. Here we summarize the discovery of the pyrrolysine system and describe the unique properties of PylRS/tRNAPyl pairs that provide a foundation for their transformational role in genetic code expansion and reprogramming. We describe the development of genetic code expansion, from E. coli to all domains of life, using PylRS/tRNAPyl pairs, and the development of systems that biosynthesize and incorporate ncAAs using pyl systems. We review applications that have been uniquely enabled by the development of PylRS/tRNAPyl pairs for incorporating new noncanonical amino acids (ncAAs), and strategies for engineering PylRS/tRNAPyl pairs to add noncanonical monomers, beyond α-L-amino acids, to the genetic code of living organisms. We review rapid progress in the discovery and scalable generation of mutually orthogonal PylRS/tRNAPyl pairs that can be directed to incorporate diverse ncAAs in response to diverse codons, and we review strategies for incorporating multiple distinct ncAAs into proteins using mutually orthogonal PylRS/tRNAPyl pairs. Finally, we review recent advances in the encoded cellular synthesis of noncanonical polymers and macrocycles and discuss future developments for PylRS/tRNAPyl pairs.
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Affiliation(s)
- Daniel L Dunkelmann
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England, United Kingdom
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England, United Kingdom
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2
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Qin C, Graf LG, Striska K, Janetzky M, Geist N, Specht R, Schulze S, Palm GJ, Girbardt B, Dörre B, Berndt L, Kemnitz S, Doerr M, Bornscheuer UT, Delcea M, Lammers M. Acetyl-CoA synthetase activity is enzymatically regulated by lysine acetylation using acetyl-CoA or acetyl-phosphate as donor molecule. Nat Commun 2024; 15:6002. [PMID: 39019872 PMCID: PMC11255334 DOI: 10.1038/s41467-024-49952-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 06/24/2024] [Indexed: 07/19/2024] Open
Abstract
The AMP-forming acetyl-CoA synthetase is regulated by lysine acetylation both in bacteria and eukaryotes. However, the underlying mechanism is poorly understood. The Bacillus subtilis acetyltransferase AcuA and the AMP-forming acetyl-CoA synthetase AcsA form an AcuA•AcsA complex, dissociating upon lysine acetylation of AcsA by AcuA. Crystal structures of AcsA from Chloroflexota bacterium in the apo form and in complex with acetyl-adenosine-5'-monophosphate (acetyl-AMP) support the flexible C-terminal domain adopting different conformations. AlphaFold2 predictions suggest binding of AcuA stabilizes AcsA in an undescribed conformation. We show the AcuA•AcsA complex dissociates upon acetyl-coenzyme A (acetyl-CoA) dependent acetylation of AcsA by AcuA. We discover an intrinsic phosphotransacetylase activity enabling AcuA•AcsA generating acetyl-CoA from acetyl-phosphate (AcP) and coenzyme A (CoA) used by AcuA to acetylate and inactivate AcsA. Here, we provide mechanistic insights into the regulation of AMP-forming acetyl-CoA synthetases by lysine acetylation and discover an intrinsic phosphotransacetylase allowing modulation of its activity based on AcP and CoA levels.
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Affiliation(s)
- Chuan Qin
- Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany
| | - Leonie G Graf
- Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany
| | - Kilian Striska
- Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany
| | - Markus Janetzky
- Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany
| | - Norman Geist
- Department of Biophysical Chemistry, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany
| | - Robin Specht
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany
| | - Sabrina Schulze
- Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany
| | - Gottfried J Palm
- Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany
| | - Britta Girbardt
- Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany
| | - Babett Dörre
- Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany
| | - Leona Berndt
- Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany
| | - Stefan Kemnitz
- Department for High Performance Computing, University Computing Center, University of Greifswald, 17489, Greifswald, Germany
| | - Mark Doerr
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany
| | - Uwe T Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany
| | - Mihaela Delcea
- Department of Biophysical Chemistry, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany
| | - Michael Lammers
- Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany.
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3
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Scarano N, Brullo C, Musumeci F, Millo E, Bruzzone S, Schenone S, Cichero E. Recent Advances in the Discovery of SIRT1/2 Inhibitors via Computational Methods: A Perspective. Pharmaceuticals (Basel) 2024; 17:601. [PMID: 38794171 PMCID: PMC11123952 DOI: 10.3390/ph17050601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 05/03/2024] [Accepted: 05/05/2024] [Indexed: 05/26/2024] Open
Abstract
Sirtuins (SIRTs) are classified as class III histone deacetylases (HDACs), a family of enzymes that catalyze the removal of acetyl groups from the ε-N-acetyl lysine residues of histone proteins, thus counteracting the activity performed by histone acetyltransferares (HATs). Based on their involvement in different biological pathways, ranging from transcription to metabolism and genome stability, SIRT dysregulation was investigated in many diseases, such as cancer, neurodegenerative disorders, diabetes, and cardiovascular and autoimmune diseases. The elucidation of a consistent number of SIRT-ligand complexes helped to steer the identification of novel and more selective modulators. Due to the high diversity and quantity of the structural data thus far available, we reviewed some of the different ligands and structure-based methods that have recently been used to identify new promising SIRT1/2 modulators. The present review is structured into two sections: the first includes a comprehensive perspective of the successful computational approaches related to the discovery of SIRT1/2 inhibitors (SIRTIs); the second section deals with the most interesting SIRTIs that have recently appeared in the literature (from 2017). The data reported here are collected from different databases (SciFinder, Web of Science, Scopus, Google Scholar, and PubMed) using "SIRT", "sirtuin", and "sirtuin inhibitors" as keywords.
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Affiliation(s)
- Naomi Scarano
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy; (N.S.); (F.M.); (S.S.)
| | - Chiara Brullo
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy; (N.S.); (F.M.); (S.S.)
| | - Francesca Musumeci
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy; (N.S.); (F.M.); (S.S.)
| | - Enrico Millo
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV 1, 16132 Genoa, Italy; (E.M.); (S.B.)
| | - Santina Bruzzone
- Department of Experimental Medicine, Section of Biochemistry, University of Genoa, Viale Benedetto XV 1, 16132 Genoa, Italy; (E.M.); (S.B.)
- IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Silvia Schenone
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy; (N.S.); (F.M.); (S.S.)
| | - Elena Cichero
- Department of Pharmacy, Section of Medicinal Chemistry, School of Medical and Pharmaceutical Sciences, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy; (N.S.); (F.M.); (S.S.)
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4
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Kremer M, Schulze S, Eisenbruch N, Nagel F, Vogt R, Berndt L, Dörre B, Palm GJ, Hoppen J, Girbardt B, Albrecht D, Sievers S, Delcea M, Baumann U, Schnetz K, Lammers M. Bacteria employ lysine acetylation of transcriptional regulators to adapt gene expression to cellular metabolism. Nat Commun 2024; 15:1674. [PMID: 38395951 PMCID: PMC10891134 DOI: 10.1038/s41467-024-46039-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
The Escherichia coli TetR-related transcriptional regulator RutR is involved in the coordination of pyrimidine and purine metabolism. Here we report that lysine acetylation modulates RutR function. Applying the genetic code expansion concept, we produced site-specifically lysine-acetylated RutR proteins. The crystal structure of lysine-acetylated RutR reveals how acetylation switches off RutR-DNA-binding. We apply the genetic code expansion concept in E. coli in vivo revealing the consequences of RutR acetylation on the transcriptional level. We propose a model in which RutR acetylation follows different kinetic profiles either reacting non-enzymatically with acetyl-phosphate or enzymatically catalysed by the lysine acetyltransferases PatZ/YfiQ and YiaC. The NAD+-dependent sirtuin deacetylase CobB reverses enzymatic and non-enzymatic acetylation of RutR playing a dual regulatory and detoxifying role. By detecting cellular acetyl-CoA, NAD+ and acetyl-phosphate, bacteria apply lysine acetylation of transcriptional regulators to sense the cellular metabolic state directly adjusting gene expression to changing environmental conditions.
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Affiliation(s)
- Magdalena Kremer
- Institute of Biochemistry, University of Cologne, Zülpicher Straße 47, 50674, Cologne, Germany
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Sabrina Schulze
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Nadja Eisenbruch
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Felix Nagel
- Institute of Biochemistry, Department of Biophysical Chemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Robert Vogt
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Leona Berndt
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Babett Dörre
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Gottfried J Palm
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Jens Hoppen
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Britta Girbardt
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Dirk Albrecht
- Institute of Microbiology, Department of Microbial Physiology and Molecular Biology, University of Greifswald, Felix-Hausdorff-Str. 8, 17489, Greifswald, Germany
| | - Susanne Sievers
- Institute of Microbiology, Department of Microbial Physiology and Molecular Biology, University of Greifswald, Felix-Hausdorff-Str. 8, 17489, Greifswald, Germany
| | - Mihaela Delcea
- Institute of Biochemistry, Department of Biophysical Chemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Ulrich Baumann
- Institute of Biochemistry, University of Cologne, Zülpicher Straße 47, 50674, Cologne, Germany
| | - Karin Schnetz
- Institute for Genetics, University of Cologne Zülpicher Straße 47a, 50674, Cologne, Germany
| | - Michael Lammers
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany.
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5
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Kaya SG, Eren G. Selective inhibition of SIRT2: A disputable therapeutic approach in cancer therapy. Bioorg Chem 2024; 143:107038. [PMID: 38113655 DOI: 10.1016/j.bioorg.2023.107038] [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: 11/13/2023] [Revised: 11/23/2023] [Accepted: 12/15/2023] [Indexed: 12/21/2023]
Abstract
Sirtuin 2 (SIRT2) is involved in a wide range of processes, from transcription to metabolism to genome stability. Dysregulation of SIRT2 has been associated with the pathogenesis and progression of different diseases, such as cancer and neurodegenerative disorders. In this context, targeting SIRT2 activity by small molecule inhibitors is a promising therapeutic strategy for treating related conditions, particularly cancer. This review summarizes the regulatory roles and molecular mechanisms of SIRT2 in cancer and the attempts to evaluate potential antitumor activities of SIRT2-selective inhibitors by in vitro and in vivo testing, which are expected to deepen our understanding of the role of SIRT2 in tumorigenesis and progression and may offer important clues or inspiration ideas for developing SIRT2 inhibitors with excellent affinity and selectivity.
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Affiliation(s)
- Selen Gozde Kaya
- SIRTeam Group, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Gazi University, 06330 Ankara, Türkiye.
| | - Gokcen Eren
- SIRTeam Group, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Gazi University, 06330 Ankara, Türkiye.
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6
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Yang J, Nicely NI, Weiser BP. Effects of Dimerization on the Deacylase Activities of Human SIRT2. Biochemistry 2023; 62:3383-3395. [PMID: 37966275 PMCID: PMC10702427 DOI: 10.1021/acs.biochem.3c00381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/05/2023] [Accepted: 10/25/2023] [Indexed: 11/16/2023]
Abstract
Human sirtuin isoform 2 (SIRT2) is an NAD+-dependent enzyme that functions as a lysine deacetylase and defatty-acylase. Here, we report that SIRT2 readily dimerizes in solution and in cells and that dimerization affects its ability to remove different acyl modifications from substrates. Dimerization of recombinant SIRT2 was revealed with analytical size exclusion chromatography and chemical cross-linking. Dimerized SIRT2 dissociates into monomers upon binding long fatty acylated substrates (decanoyl-, dodecanoyl-, and myristoyl-lysine). However, we did not observe dissociation of dimeric SIRT2 in the presence of acetyl-lysine. Analysis of X-ray crystal structures led us to discover a SIRT2 double mutant (Q142A/E340A) that is impaired in its ability to dimerize, which was confirmed with chemical cross-linking and in cells with a split-GFP approach. In enzyme assays, the SIRT2(Q142A/E340A) mutant had normal defatty-acylase activity and impaired deacetylase activity compared with the wild-type protein. These results indicate that dimerization is essential for optimal SIRT2 function as a deacetylase. Moreover, we show that SIRT2 dimers can be dissociated by a deacetylase and defatty-acylase inhibitor, ascorbyl palmitate. Our finding that its oligomeric state can affect the acyl substrate selectivity of SIRT2 is a novel mode of activity regulation by the enzyme that can be altered genetically or pharmacologically.
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Affiliation(s)
- Jie Yang
- Department
of Molecular Biology, Rowan University School
of Osteopathic Medicine, Stratford, New Jersey 08084, United States
| | - Nathan I. Nicely
- Department
of Pharmacology, University of North Carolina
at Chapel Hill, Chapel
Hill, North Carolina 27599, United States
| | - Brian P. Weiser
- Department
of Molecular Biology, Rowan University School
of Osteopathic Medicine, Stratford, New Jersey 08084, United States
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7
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Abstract
The silent information regulator (sirtuin) is a family of enzymes involved in epigenetic processes with lysine deacetylase activity, having as substrates histones and other proteins. They participate in a wide range of cellular and pathologic processes, such as gene expression, cell division and motility, oxidative-induced stress management, metabolic control and carcinogenesis, among others, thus presenting as interesting therapeutic targets. In this article, the authors describe the inhibitory mechanisms and binding modes of the human sirtuin 2 (hSIRT2) inhibitors, which had their complexes with the enzyme structurally characterized. The results help pave the way for the rational designing of new hSIRT2 inhibitors and the development of novel therapeutic agents targeting this epigenetic enzyme.
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8
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Fan Z, Bin L. Will Sirtuin 2 Be a Promising Target for Neuroinflammatory Disorders? Front Cell Neurosci 2022; 16:915587. [PMID: 35813508 PMCID: PMC9256990 DOI: 10.3389/fncel.2022.915587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Neuroinflammatory disorder is a general term that is associated with the progressive loss of neuronal structure or function. At present, the widely studied diseases with neuroinflammatory components are mainly divided into neurodegenerative and neuropsychiatric diseases, namely, Alzheimer’s disease, Parkinson’s disease, depression, stroke, and so on. An appropriate neuroinflammatory response can promote brain homeostasis, while excessive neuroinflammation can inhibit neuronal regeneration and damage the central nervous system. Apart from the symptomatic treatment with cholinesterase inhibitors, antidepressants/anxiolytics, and neuroprotective drugs, the treatment of neuroinflammation is a promising therapeutic method. Sirtuins are a host of class III histone deacetylases, that require nicotinamide adenine dinucleotide for their lysine residue deacetylase activity. The role of sirtuin 2 (SIRT2), one of the sirtuins, in modulating senescence, myelin formation, autophagy, and inflammation has been widely studied. SIRT2 is associated with many neuroinflammatory disorders considering it has deacetylation properties, that regulate the entire immune homeostasis. The aim of this review was to summarize the latest progress in regulating the effects of SIRT2 on immune homeostasis in neuroinflammatory disorders. The overall structure and catalytic properties of SIRT2, the selective inhibitors of SIRT2, the relationship between immune homeostasis and SIRT2, and the multitasking role of SIRT2 in several diseases with neuroinflammatory components were discussed.
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Affiliation(s)
- Zhang Fan
- Beijing Key Laboratory of Basic Research With Traditional Chinese Medicine (TCM) on Infectious Diseases, Beijing Institute of Chinese Medicine, Beijing Hospital of TCM, Capital Medical University, Beijing, China
| | - Li Bin
- Beijing Key Laboratory of Acupuncture Neuromodulation, Acupuncture and Moxibustion Department, Beijing Hospital of TCM, Capital Medical University, Beijing, China
- *Correspondence: Li Bin,
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Shao X, Kong W, Li Y, Zhang S. Quantitative structure-activity relationship modeling reveals the minimal sequence requirement and amino acid preference of sirtuin-1's deacetylation substrates in diabetes mellitus. J Bioinform Comput Biol 2022; 20:2250008. [PMID: 35451939 DOI: 10.1142/s0219720022500081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Sirtuin 1 (SIRT1) is a nicotinamide adenine dinucleotide (NAD[Formula: see text]-dependent deacetylase involved in multiple glucose metabolism pathways and plays an important role in the pathogenesis of diabetes mellitus (DM). The enzyme specifically recognizes its deacetylation substrates' peptide segments containing a central acetyl-lysine residue as well as a number of amino acids flanking the central residue. In this study, we attempted to ascertain the minimal sequence requirement (MSR) around the central acetyl-lysine residue of SIRT1 substrate-recognition sites as well as the amino acid preference (AAP) at different residues of the MSR window through quantitative structure-activity relationship (QSAR) strategy, which would benefit our understanding of SIRT1 substrate specificity at the molecular level and is also helpful to rationally design substrate-mimicking peptidic agents against DM by competitively targeting SIRT1 active site. In this procedure, a large-scale dataset containing 6801 13-mer acetyl-lysine peptides (and their SIRT1-catalyized deacetylation activities) were compiled to train 10 QSAR regression models developed by systematic combination of machine learning methods (PLS and SVM) and five amino acids descriptors (DPPS, T-scale, MolSurf, [Formula: see text]-score, and FASGAI). The two best QSAR models (PLS+FASGAI and SVM+DPPS) were then employed to statistically examine the contribution of residue positions to the deacetylation activity of acetyl-lysine peptide substrates, revealing that the MSR can be represented by 5-mer acetyl-lysine peptides that meet a consensus motif X[Formula: see text]X[Formula: see text]X[Formula: see text](AcK)0X[Formula: see text]. Structural analysis found that the X[Formula: see text] and (AcK)0 residues are tightly packed against the enzyme active site and confer both stability and specificity for the enzyme-substrate complex, whereas the X[Formula: see text], X[Formula: see text] and X[Formula: see text] residues are partially exposed to solvent but can also effectively stabilize the complex system. Subsequently, a systematic deacetylation activity change profile (SDACP) was created based on QSAR modeling, from which the AAP for each residue position of MSR was depicted. With the profile, we were able to rationally design an SDACP combinatorial library with promising deacetylation activity, from which nine MSR acetyl-lysine peptides as well as two known SIRT1 acetyl-lysine peptide substrates were tested by using SIRT1 deacetylation assay. It is revealed that the designed peptides exhibit a comparable or even higher activity than the controls, although the former is considerably shorter than the latter.
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Affiliation(s)
- X Shao
- Department of Nephrology, Suzhou Kowloon Hospital, Shanghai Jiao Tong University, School of Medicine, Suzhou 215000, P. R. China
| | - W Kong
- Department of Nephrology, Suzhou Kowloon Hospital, Shanghai Jiao Tong University, School of Medicine, Suzhou 215000, P. R. China
| | - Y Li
- Department of Nephrology, Suzhou Kowloon Hospital, Shanghai Jiao Tong University, School of Medicine, Suzhou 215000, P. R. China
| | - S Zhang
- Department of Nephrology, Suzhou Kowloon Hospital, Shanghai Jiao Tong University, School of Medicine, Suzhou 215000, P. R. China
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10
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Ogle MM, Trevino R, Schell J, Varmazyad M, Horikoshi N, Gius D. Manganese Superoxide Dismutase Acetylation and Regulation of Protein Structure in Breast Cancer Biology and Therapy. Antioxidants (Basel) 2022; 11:635. [PMID: 35453320 PMCID: PMC9024550 DOI: 10.3390/antiox11040635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 02/01/2023] Open
Abstract
The loss and/or dysregulation of several cellular and mitochondrial antioxidants' expression or enzymatic activity, which leads to the aberrant physiological function of these proteins, has been shown to result in oxidative damage to cellular macromolecules. In this regard, it has been surmised that the disruption of mitochondrial networks responsible for maintaining normal metabolism is an established hallmark of cancer and a novel mechanism of therapy resistance. This altered metabolism leads to aberrant accumulation of reactive oxygen species (ROS), which, under specific physiological conditions, leads to a potential tumor-permissive cellular environment. In this regard, it is becoming increasingly clear that the loss or disruption of mitochondrial oxidant scavenging enzymes may be, in specific tumors, either an early event in transformation or exhibit tumor-promoting properties. One example of such an antioxidant enzyme is manganese superoxide dismutase (MnSOD, also referred to as SOD2), which detoxifies superoxide, a ROS that has been shown, when its normal physiological levels are disrupted, to lead to oncogenicity and therapy resistance. Here, we will also discuss how the acetylation of MnSOD leads to a change in detoxification function that leads to a cellular environment permissive for the development of lineage plasticity-like properties that may be one mechanism leading to tumorigenic and therapy-resistant phenotypes.
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Affiliation(s)
- Meredith M. Ogle
- Department of Radiation Oncology, Mays Cancer Center at UT Health San Antonio MD Anderson, 7979 Wurzbach Road, San Antonio, TX 78229, USA; (M.M.O.); (R.T.J.); (J.S.); (M.V.); (N.H.)
- Joe R. & Teresa Lozano Long School of Medicine, University of Texas Health San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Rolando Trevino
- Department of Radiation Oncology, Mays Cancer Center at UT Health San Antonio MD Anderson, 7979 Wurzbach Road, San Antonio, TX 78229, USA; (M.M.O.); (R.T.J.); (J.S.); (M.V.); (N.H.)
- Joe R. & Teresa Lozano Long School of Medicine, University of Texas Health San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Joseph Schell
- Department of Radiation Oncology, Mays Cancer Center at UT Health San Antonio MD Anderson, 7979 Wurzbach Road, San Antonio, TX 78229, USA; (M.M.O.); (R.T.J.); (J.S.); (M.V.); (N.H.)
- Joe R. & Teresa Lozano Long School of Medicine, University of Texas Health San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Mahboubeh Varmazyad
- Department of Radiation Oncology, Mays Cancer Center at UT Health San Antonio MD Anderson, 7979 Wurzbach Road, San Antonio, TX 78229, USA; (M.M.O.); (R.T.J.); (J.S.); (M.V.); (N.H.)
- Joe R. & Teresa Lozano Long School of Medicine, University of Texas Health San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Nobuo Horikoshi
- Department of Radiation Oncology, Mays Cancer Center at UT Health San Antonio MD Anderson, 7979 Wurzbach Road, San Antonio, TX 78229, USA; (M.M.O.); (R.T.J.); (J.S.); (M.V.); (N.H.)
- Joe R. & Teresa Lozano Long School of Medicine, University of Texas Health San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - David Gius
- Department of Radiation Oncology, Mays Cancer Center at UT Health San Antonio MD Anderson, 7979 Wurzbach Road, San Antonio, TX 78229, USA; (M.M.O.); (R.T.J.); (J.S.); (M.V.); (N.H.)
- Joe R. & Teresa Lozano Long School of Medicine, University of Texas Health San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
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11
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Graf LG, Vogt R, Blasl AT, Qin C, Schulze S, Zühlke D, Sievers S, Lammers M. Assays to Study Enzymatic and Non-Enzymatic Protein Lysine Acetylation In Vitro. Curr Protoc 2021; 1:e277. [PMID: 34748287 DOI: 10.1002/cpz1.277] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Proteins can be lysine-acetylated both enzymatically, by lysine acetyltransferases (KATs), and non-enzymatically, by acetyl-CoA and/or acetyl-phosphate. Such modification can be reversed by lysine deacetylases classified as NAD+ -dependent sirtuins or by classical Zn2+ -dependent deacetylases (KDACs). The regulation of protein lysine acetylation events by KATs and sirtuins/KDACs, or by non-enzymatic processes, is often assessed only indirectly by mass spectrometry or by mutational studies in cells. Mutational approaches to study lysine acetylation are limited, as these often poorly mimic lysine acetylation. Here, we describe protocols to assess the direct regulation of protein lysine acetylation by both sirtuins/KDACs and KATs, as well as non-enzymatically. We first describe a protocol for the production of site-specific lysine-acetylated proteins using a synthetic biological approach, the genetic code expansion concept (GCEC). These natively folded, lysine-acetylated proteins can then be used as direct substrates for sirtuins and KDACs. This approach addresses various limitations encountered with other methods. First, results from sirtuin/KDAC-catalyzed deacetylation assays obtained using acetylated peptides as substrates can vary considerably compared to experiments using natively folded substrate proteins. In addition, producing lysine-acetylated proteins for deacetylation assays by using recombinantly expressed KATs is difficult, as these often do not yield proteins that are homogeneously and quantitatively lysine acetylated. Moreover, KATs are often huge multi-domain proteins, which are difficult to recombinantly express and purify in soluble form. We also describe protocols to study the direct regulation of protein lysine acetylation, both enzymatically, by sirtuins/KDACs and KATs, and non-enzymatically, by acetyl-CoA and/or acetyl-phosphate. The latter protocol also includes a section that explains how specific lysine acetylation sites can be detected by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). The protocols described here can be useful for providing a more detailed understanding of the enzymatic and non-enzymatic regulation of lysine acetylation sites, an important aspect to judge their physiological significance. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Preparation of N-(ε)-lysine-acetylated proteins using the genetic code expansion concept (GCEC) Basic Protocol 2: In vitro sirtuin (SIRT)-catalyzed deacetylation of lysine-acetylated proteins prepared by the GCEC Basic Protocol 3: In vitro KDAC/HDAC-catalyzed deacetylation of lysine-acetylated proteins Basic Protocol 4: In vitro lysine acetylation of recombinantly expressed proteins by lysine acetyltransferases (KATs) Basic Protocol 5: In vitro non-enzymatic lysine acetylation of proteins by acetyl-CoA and/or acetyl-phosphate.
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Affiliation(s)
- Leonie G Graf
- Department Synthetic and Structural Biochemistry, University of Greifswald, Institute for Biochemistry, Greifswald, Germany
| | - Robert Vogt
- Department Synthetic and Structural Biochemistry, University of Greifswald, Institute for Biochemistry, Greifswald, Germany
| | - Anna-Theresa Blasl
- Department Synthetic and Structural Biochemistry, University of Greifswald, Institute for Biochemistry, Greifswald, Germany
| | - Chuan Qin
- Department Synthetic and Structural Biochemistry, University of Greifswald, Institute for Biochemistry, Greifswald, Germany
| | - Sabrina Schulze
- Department Synthetic and Structural Biochemistry, University of Greifswald, Institute for Biochemistry, Greifswald, Germany
| | - Daniela Zühlke
- Department of Microbial Physiology and Molecular Biology, University of Greifswald, Institute of Microbiology, Greifswald, Germany
| | - Susanne Sievers
- Department of Microbial Physiology and Molecular Biology, University of Greifswald, Institute of Microbiology, Greifswald, Germany
| | - Michael Lammers
- Department Synthetic and Structural Biochemistry, University of Greifswald, Institute for Biochemistry, Greifswald, Germany
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12
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Lysine acetylation regulates the interaction between proteins and membranes. Nat Commun 2021; 12:6466. [PMID: 34753925 PMCID: PMC8578602 DOI: 10.1038/s41467-021-26657-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 09/30/2021] [Indexed: 11/23/2022] Open
Abstract
Lysine acetylation regulates the function of soluble proteins in vivo, yet it remains largely unexplored whether lysine acetylation regulates membrane protein function. Here, we use bioinformatics, biophysical analysis of recombinant proteins, live-cell fluorescent imaging and genetic manipulation of Drosophila to explore lysine acetylation in peripheral membrane proteins. Analysis of 50 peripheral membrane proteins harboring BAR, PX, C2, or EHD membrane-binding domains reveals that lysine acetylation predominates in membrane-interaction regions. Acetylation and acetylation-mimicking mutations in three test proteins, amphiphysin, EHD2, and synaptotagmin1, strongly reduce membrane binding affinity, attenuate membrane remodeling in vitro and alter subcellular localization. This effect is likely due to the loss of positive charge, which weakens interactions with negatively charged membranes. In Drosophila, acetylation-mimicking mutations of amphiphysin cause severe disruption of T-tubule organization and yield a flightless phenotype. Our data provide mechanistic insights into how lysine acetylation regulates membrane protein function, potentially impacting a plethora of membrane-related processes. Lysine acetylation regulates the function of soluble proteins in vivo, yet it remains largely unexplored whether lysine acetylation regulates the function of membrane proteins. Here, the authors map lysine acetylation predominantly in membrane-interaction regions in peripheral membrane proteins and show with three candidate proteins how lysine acetylation is a regulator of membrane protein function.
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13
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Lammers M. Post-translational Lysine Ac(et)ylation in Bacteria: A Biochemical, Structural, and Synthetic Biological Perspective. Front Microbiol 2021; 12:757179. [PMID: 34721364 PMCID: PMC8556138 DOI: 10.3389/fmicb.2021.757179] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 09/10/2021] [Indexed: 12/21/2022] Open
Abstract
Ac(et)ylation is a post-translational modification present in all domains of life. First identified in mammals in histones to regulate RNA synthesis, today it is known that is regulates fundamental cellular processes also in bacteria: transcription, translation, metabolism, cell motility. Ac(et)ylation can occur at the ε-amino group of lysine side chains or at the α-amino group of a protein. Furthermore small molecules such as polyamines and antibiotics can be acetylated and deacetylated enzymatically at amino groups. While much research focused on N-(ε)-ac(et)ylation of lysine side chains, much less is known about the occurrence, the regulation and the physiological roles on N-(α)-ac(et)ylation of protein amino termini in bacteria. Lysine ac(et)ylation was shown to affect protein function by various mechanisms ranging from quenching of the positive charge, increasing the lysine side chains’ size affecting the protein surface complementarity, increasing the hydrophobicity and by interfering with other post-translational modifications. While N-(ε)-lysine ac(et)ylation was shown to be reversible, dynamically regulated by lysine acetyltransferases and lysine deacetylases, for N-(α)-ac(et)ylation only N-terminal acetyltransferases were identified and so far no deacetylases were discovered neither in bacteria nor in mammals. To this end, N-terminal ac(et)ylation is regarded as being irreversible. Besides enzymatic ac(et)ylation, recent data showed that ac(et)ylation of lysine side chains and of the proteins N-termini can also occur non-enzymatically by the high-energy molecules acetyl-coenzyme A and acetyl-phosphate. Acetyl-phosphate is supposed to be the key molecule that drives non-enzymatic ac(et)ylation in bacteria. Non-enzymatic ac(et)ylation can occur site-specifically with both, the protein primary sequence and the three dimensional structure affecting its efficiency. Ac(et)ylation is tightly controlled by the cellular metabolic state as acetyltransferases use ac(et)yl-CoA as donor molecule for the ac(et)ylation and sirtuin deacetylases use NAD+ as co-substrate for the deac(et)ylation. Moreover, the accumulation of ac(et)yl-CoA and acetyl-phosphate is dependent on the cellular metabolic state. This constitutes a feedback control mechanism as activities of many metabolic enzymes were shown to be regulated by lysine ac(et)ylation. Our knowledge on lysine ac(et)ylation significantly increased in the last decade predominantly due to the huge methodological advances that were made in fields such as mass-spectrometry, structural biology and synthetic biology. This also includes the identification of additional acylations occurring on lysine side chains with supposedly different regulatory potential. This review highlights recent advances in the research field. Our knowledge on enzymatic regulation of lysine ac(et)ylation will be summarized with a special focus on structural and mechanistic characterization of the enzymes, the mechanisms underlying non-enzymatic/chemical ac(et)ylation are explained, recent technological progress in the field are presented and selected examples highlighting the important physiological roles of lysine ac(et)ylation are summarized.
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Affiliation(s)
- Michael Lammers
- Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Greifswald, Germany
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14
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Neumann-Staubitz P, Lammers M, Neumann H. Genetic Code Expansion Tools to Study Lysine Acylation. Adv Biol (Weinh) 2021; 5:e2100926. [PMID: 34713630 DOI: 10.1002/adbi.202100926] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 09/27/2021] [Accepted: 09/30/2021] [Indexed: 12/17/2022]
Abstract
Lysine acylation is a ubiquitous protein modification that controls various aspects of protein function, such as the activity, localization, and stability of enzymes. Mass spectrometric identification of lysine acylations has witnessed tremendous improvements in sensitivity over the last decade, facilitating the discovery of thousands of lysine acylation sites in proteins involved in all essential cellular functions across organisms of all domains of life. However, the vast majority of currently known acylation sites are of unknown function. Semi-synthetic methods for installing lysine derivatives are ideally suited for in vitro experiments, while genetic code expansion (GCE) allows the installation and study of such lysine modifications, especially their dynamic properties, in vivo. An overview of the current state of the art is provided, and its potential is illustrated with case studies from recent literature. These include the application of engineered enzymes and GCE to install lysine modifications or photoactivatable crosslinker amino acids. Their use in the context of central metabolism, bacterial and viral pathogenicity, the cytoskeleton and chromatin dynamics, is investigated.
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Affiliation(s)
- Petra Neumann-Staubitz
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Stephanstrasse 7, 64295, Darmstadt, Germany
| | - Michael Lammers
- Institute for Biochemistry, Department Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Heinz Neumann
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Stephanstrasse 7, 64295, Darmstadt, Germany
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15
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Blasl AT, Schulze S, Qin C, Graf LG, Vogt R, Lammers M. Post-translational lysine ac(et)ylation in health, ageing and disease. Biol Chem 2021; 403:151-194. [PMID: 34433238 DOI: 10.1515/hsz-2021-0139] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 06/18/2021] [Indexed: 12/13/2022]
Abstract
The acetylation/acylation (ac(et)ylation) of lysine side chains is a dynamic post-translational modification (PTM) regulating fundamental cellular processes with implications on the organisms' ageing process: metabolism, transcription, translation, cell proliferation, regulation of the cytoskeleton and DNA damage repair. First identified to occur on histones, later studies revealed the presence of lysine ac(et)ylation in organisms of all kingdoms of life, in proteins covering all essential cellular processes. A remarkable finding showed that the NAD+-dependent sirtuin deacetylase Sir2 has an impact on replicative lifespan in Saccharomyces cerevisiae suggesting that lysine acetylation has a direct role in the ageing process. Later studies identified sirtuins as mediators for beneficial effects of caloric/dietary restriction on the organisms' health- or lifespan. However, the molecular mechanisms underlying these effects are only incompletely understood. Progress in mass-spectrometry, structural biology, synthetic and semi-synthetic biology deepened our understanding of this PTM. This review summarizes recent developments in the research field. It shows how lysine ac(et)ylation regulates protein function, how it is regulated enzymatically and non-enzymatically, how a dysfunction in this post-translational machinery contributes to disease development. A focus is set on sirtuins and lysine acyltransferases as these are direct sensors and mediators of the cellular metabolic state. Finally, this review highlights technological advances to study lysine ac(et)ylation.
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Affiliation(s)
- Anna-Theresa Blasl
- Department Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487Greifswald, Germany
| | - Sabrina Schulze
- Department Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487Greifswald, Germany
| | - Chuan Qin
- Department Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487Greifswald, Germany
| | - Leonie G Graf
- Department Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487Greifswald, Germany
| | - Robert Vogt
- Department Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487Greifswald, Germany
| | - Michael Lammers
- Department Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487Greifswald, Germany
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16
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Hendler A, Akiva E, Sandhu M, Goldberg D, Arbely E, Jackson CJ, Aharoni A. Human SIRT1 Multispecificity Is Modulated by Active-Site Vicinity Substitutions during Natural Evolution. Mol Biol Evol 2021; 38:545-556. [PMID: 32956445 PMCID: PMC7826192 DOI: 10.1093/molbev/msaa244] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Many enzymes that catalyze protein post-translational modifications can specifically modify multiple target proteins. However, little is known regarding the molecular basis and evolution of multispecificity in these enzymes. Here, we used a combined bioinformatics and experimental approaches to investigate the evolution of multispecificity in the sirtuin-1 (SIRT1) deacetylase. Guided by bioinformatics analysis of SIRT1 orthologs and substrates, we identified and examined important amino acid substitutions that have occurred during the evolution of sirtuins in Metazoa and Fungi. We found that mutation of human SIRT1 at these positions, based on sirtuin orthologs from Fungi, could alter its substrate specificity. These substitutions lead to reduced activity toward K382 acetylated p53 protein, which is only present in Metazoa, without affecting the high activity toward the conserved histone substrates. Results from ancestral sequence reconstruction are consistent with a model in which ancestral sirtuin proteins exhibited multispecificity, suggesting that the multispecificity of some metazoan sirtuins, such as hSIRT1, could be a relatively ancient trait.
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Affiliation(s)
- Adi Hendler
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel.,National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Eyal Akiva
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA
| | - Mahakaran Sandhu
- Research School of Chemistry, Australian National University, Acton, ACT, Australia
| | - Dana Goldberg
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel.,National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Eyal Arbely
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel.,Department of Chemistry, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Acton, ACT, Australia
| | - Amir Aharoni
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel.,National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva, Israel
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17
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Gu H, Yang K, Wu Q, Shen Z, Li X, Sun C. A link between protein acetylation and mitochondrial dynamics under energy metabolism: A comprehensive overview. J Cell Physiol 2021; 236:7926-7937. [PMID: 34101176 DOI: 10.1002/jcp.30461] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/06/2021] [Accepted: 05/24/2021] [Indexed: 12/16/2022]
Abstract
Cells adjust mitochondrial morphologies to coordinate between the cellular demand for energy and the availability of resources. Mitochondrial morphology is regulated by the balance between two counteracting mitochondrial processes of fusion and fission. Fission and fusion are dynamic and reversible processes that depend on the coordination of a number of proteins and are primarily regulated by posttranslational modifications. In the mitochondria, more than 20% of proteins are acetylated in proteomic surveys, partly involved in the dynamic regulation of mitochondrial fusion and fission. This article focuses on the molecular mechanism of the mitochondrial dynamics of fusion and fission, and summarizes the related mechanisms and targets of mitochondrial protein acetylation to regulate the mitochondrial dynamics of fusion and fission in energy metabolism.
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Affiliation(s)
- Huihui Gu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Kun Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Qiong Wu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.,Department of Pathophysiology, Qinghai University Medical College, Xining, Qinghai, China
| | - Zhentong Shen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xinjian Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Chao Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
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18
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Gao Y, Zhu Y, Tran EL, Tokars V, Dean AE, Quan S, Gius D. MnSOD Lysine 68 acetylation leads to cisplatin and doxorubicin resistance due to aberrant mitochondrial metabolism. Int J Biol Sci 2021; 17:1203-1216. [PMID: 33867840 PMCID: PMC8040469 DOI: 10.7150/ijbs.51184] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 02/19/2021] [Indexed: 01/06/2023] Open
Abstract
Manganese superoxide dismutase (MnSOD) acetylation (Ac) has been shown to be a key post-translational modification important in the regulation of detoxification activity in various disease models. We have previously demonstrated that MnSOD lysine-68 (K68) acetylation (K68-Ac) leads to a change in function from a superoxide-scavenging homotetramer to a peroxidase-directed monomer. Here, we found that estrogen receptor positive (ER+) breast cancer cell lines (MCF7 and T47D), selected for continuous growth in cisplatin (CDDP) and doxorubicin (DXR), exhibited an increase in MnSOD-K68-Ac. In addition, MnSOD-K68-Ac, as modeled by the expression of a validated acetylation mimic mutant gene (MnSODK68Q ), also led to therapy resistance to CDDP and DXR, altered mitochondrial structure and morphology, and aberrant cellular metabolism. MnSODK68Q expression in mouse embryo fibroblasts (MEFs) induced an in vitro transformation permissive phenotype. Computerized molecular protein dynamics analysis of both MnSOD-K68-Ac and MnSOD-K68Q exhibited a significant change in charge distribution along the α1 and α2 helices, directly adjacent to the Mn2+ binding site, implying that this decrease in surface charge destabilizes tetrameric MnSOD, leading to an enrichment of the monomer. Finally, monomeric MnSOD, as modeled by amber codon substitution to generate MnSOD-K68-Ac or MnSOD-K68Q expression in mammalian cells, appeared to incorporate Fe to maximally induce its peroxidase activity. In summary, these findings may explain the mechanism behind the observed structural and functional change of MnSOD-K68-Ac.
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Affiliation(s)
- Yucheng Gao
- Department of Radiation Oncology and Northwestern University, Chicago, IL, USA
- Driskill Graduate Program in Life Sciences, Northwestern University, Chicago, IL, USA
| | - Yueming Zhu
- Department of Radiation Oncology and Northwestern University, Chicago, IL, USA
| | - Elizabeth L. Tran
- Department of Radiation Oncology and Northwestern University, Chicago, IL, USA
| | | | - Angela E. Dean
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign
| | - Songhua Quan
- Department of Radiation Oncology and Northwestern University, Chicago, IL, USA
| | - David Gius
- Department of Radiation Oncology and Northwestern University, Chicago, IL, USA
- Driskill Graduate Program in Life Sciences, Northwestern University, Chicago, IL, USA
- Department of Pharmacology, Robert H. Lurie Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Department of Radiation Oncology, Joe R. & Teresa Lozano Long School of Medicine, University of Texas Health San Antonio, TX, USA
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19
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Nielsen AL, Rajabi N, Kudo N, Lundø K, Moreno-Yruela C, Bæk M, Fontenas M, Lucidi A, Madsen AS, Yoshida M, Olsen CA. Mechanism-based inhibitors of SIRT2: structure-activity relationship, X-ray structures, target engagement, regulation of α-tubulin acetylation and inhibition of breast cancer cell migration. RSC Chem Biol 2021; 2:612-626. [PMID: 34458803 PMCID: PMC8341974 DOI: 10.1039/d0cb00036a] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 12/21/2020] [Indexed: 12/14/2022] Open
Abstract
Sirtuin 2 (SIRT2) is a protein deacylase enzyme that removes acetyl groups and longer chain acyl groups from post-translationally modified lysine residues. It affects diverse biological functions in the cell and has been considered a drug target in relation to both neurodegenerative diseases and cancer. Therefore, access to well-characterized and robust tool compounds is essential for the continued investigation of the complex functions of this enzyme. Here, we report a collection of chemical probes that are potent, selective, stable in serum, water-soluble, and inhibit SIRT2-mediated deacetylation and demyristoylation in cells. Compared to the current landscape of SIRT2 inhibitors, this is a unique ensemble of features built into a single compound. We expect the developed chemotypes to find broad application in the interrogation of SIRT2 functions in both healthy and diseased cells, and to provide a foundation for the development of future therapeutics. Sirtuin 2 (SIRT2) is a protein deacylase enzyme that removes acetyl groups and longer chain acyl groups from post-translationally modified lysine residues. Here, we developed small peptide-based inhibitors of its activity in living cells in culture.![]()
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Affiliation(s)
- Alexander L Nielsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen Universitetsparken 2 DK-2100 Copenhagen Denmark
| | - Nima Rajabi
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen Universitetsparken 2 DK-2100 Copenhagen Denmark
| | - Norio Kudo
- RIKEN Center for Sustainable Resource Science (S13) Hirosawa 2-1 Wako Saitama 351-0198 Japan
| | - Kathrine Lundø
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen Blegdamsvej 3B DK-2200 Copenhagen Denmark
| | - Carlos Moreno-Yruela
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen Universitetsparken 2 DK-2100 Copenhagen Denmark
| | - Michael Bæk
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen Universitetsparken 2 DK-2100 Copenhagen Denmark
| | - Martin Fontenas
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen Universitetsparken 2 DK-2100 Copenhagen Denmark
| | - Alessia Lucidi
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen Universitetsparken 2 DK-2100 Copenhagen Denmark
| | - Andreas S Madsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen Universitetsparken 2 DK-2100 Copenhagen Denmark
| | - Minoru Yoshida
- RIKEN Center for Sustainable Resource Science (S13) Hirosawa 2-1 Wako Saitama 351-0198 Japan
| | - Christian A Olsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen Universitetsparken 2 DK-2100 Copenhagen Denmark
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20
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Teixeira CSS, Cerqueira NMFSA, Gomes P, Sousa SF. A Molecular Perspective on Sirtuin Activity. Int J Mol Sci 2020; 21:ijms21228609. [PMID: 33203121 PMCID: PMC7696986 DOI: 10.3390/ijms21228609] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/07/2020] [Accepted: 11/13/2020] [Indexed: 12/13/2022] Open
Abstract
The protein acetylation of either the α-amino groups of amino-terminal residues or of internal lysine or cysteine residues is one of the major posttranslational protein modifications that occur in the cell with repercussions at the protein as well as at the metabolome level. The lysine acetylation status is determined by the opposing activities of lysine acetyltransferases (KATs) and lysine deacetylases (KDACs), which add and remove acetyl groups from proteins, respectively. A special group of KDACs, named sirtuins, that require NAD+ as a substrate have received particular attention in recent years. They play critical roles in metabolism, and their abnormal activity has been implicated in several diseases. Conversely, the modulation of their activity has been associated with protection from age-related cardiovascular and metabolic diseases and with increased longevity. The benefits of either activating or inhibiting these enzymes have turned sirtuins into attractive therapeutic targets, and considerable effort has been directed toward developing specific sirtuin modulators. This review summarizes the protein acylation/deacylation processes with a special focus on the current developments in the sirtuin research field.
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Affiliation(s)
- Carla S. S. Teixeira
- UCIBIO/REQUIMTE, BioSIM - Department of Biomedicine, Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal; (C.S.S.T.); (N.M.F.S.A.C.)
| | - Nuno M. F. S. A. Cerqueira
- UCIBIO/REQUIMTE, BioSIM - Department of Biomedicine, Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal; (C.S.S.T.); (N.M.F.S.A.C.)
| | - Pedro Gomes
- Department of Biomedicine, Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal;
- Center for Health Technology and Services Research (CINTESIS), University of Porto, R. Dr. Plácido da Costa, 4200-450 Porto, Portugal
- Institute of Pharmacology and Experimental Therapeutics, Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, Azinhaga Santa Comba, Celas, 3000-548 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, Azinhaga Santa Comba, Celas, 3000-548 Coimbra, Portugal
| | - Sérgio F. Sousa
- UCIBIO/REQUIMTE, BioSIM - Department of Biomedicine, Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal; (C.S.S.T.); (N.M.F.S.A.C.)
- Correspondence: ; Tel.: +351-22-551-3600
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21
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Bi D, Yang J, Hong JY, Parikh P, Hinds N, Infanti J, Lin H, Weiser BP. Substrate-Dependent Modulation of SIRT2 by a Fluorescent Probe, 1-Aminoanthracene. Biochemistry 2020; 59:3869-3878. [PMID: 32941003 PMCID: PMC7880049 DOI: 10.1021/acs.biochem.0c00564] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Sirtuin isoform 2 (SIRT2) is an enzyme that catalyzes the removal of acyl groups from lysine residues. SIRT2's catalytic domain has a hydrophobic tunnel where its substrate acyl groups bind. Here, we report that the fluorescent probe 1-aminoanthracene (AMA) binds within SIRT2's hydrophobic tunnel in a substrate-dependent manner. AMA's interaction with SIRT2 was characterized by its enhanced fluorescence upon protein binding (>10-fold). AMA interacted weakly with SIRT2 alone in solution (Kd = 37 μM). However, when SIRT2 was equilibrated with a decanoylated peptide substrate, AMA's affinity for SIRT2 was enhanced ∼10-fold (Kd = 4 μM). The peptide's decanoyl chain and AMA co-occupied SIRT2's hydrophobic tunnel when bound to the protein. In contrast, binding of AMA to SIRT2 was competitive with a myristoylated substrate whose longer acyl chain occluded the entire tunnel. AMA competitively inhibited SIRT2 demyristoylase activity with an IC50 of 21 μM, which was significantly more potent than its inhibition of other deacylase activities. Finally, binding and structural analysis suggests that the AMA binding site in SIRT2's hydrophobic tunnel was structurally stabilized when SIRT2 interacted with a decanoylated or 4-oxononanoylated substrate, but AMA's binding site was less stable when SIRT2 was bound to an acetylated substrate. Our use of AMA to explore changes in SIRT2's hydrophobic tunnel that are induced by interactions with specific acylated substrates has implications for developing ligands that modulate SIRT2's substrate specificity.
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Affiliation(s)
- David Bi
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, New Jersey 08084, United States
| | - Jie Yang
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, New Jersey 08084, United States
| | - Jun Young Hong
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Prashit Parikh
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, New Jersey 08084, United States
| | - Nicole Hinds
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, New Jersey 08084, United States
| | - Joseph Infanti
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, New Jersey 08084, United States
| | - Hening Lin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States.,Howard Hughes Medical Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Brian P Weiser
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, New Jersey 08084, United States
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22
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Zhou ZD, Tan EK. Oxidized nicotinamide adenine dinucleotide-dependent mitochondrial deacetylase sirtuin-3 as a potential therapeutic target of Parkinson's disease. Ageing Res Rev 2020; 62:101107. [PMID: 32535274 DOI: 10.1016/j.arr.2020.101107] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/18/2020] [Accepted: 06/05/2020] [Indexed: 12/11/2022]
Abstract
Mitochondrial impairment is associated with progressive dopamine (DA) neuron degeneration in Parkinson's disease (PD). Recent findings highlight that Sirtuin-3 (SIRT3), a mitochondrial protein, is an oxidized nicotinamide adenine dinucleotide (NAD+)-dependent deacetylase and a key modulator in maintaining integrity and functions of mitochondria. SIRT3 plays vital roles in regulation of mitochondrial functions, including mitochondrial ATP generation and energy metabolism, anti-oxidant defense, and cell death and proliferation. SIRT3 can deacetylate the transcriptional factors and crosstalk with different signaling pathways to cooperatively modulate mitochondrial functions and regulate defensive mitochondrial quality control (QC) systems. Down-regulated NAD+ level and decreased SIRT3 activity are related to aging process and has been pathologically linked to PD pathogenesis. Further, SIRT3 can bind and deacetylate PTEN-induced kinase 1 (PINK1) and PD protein 2 E3 ubiquitin protein ligase (Parkin) to facilitate mitophagy. Leucine Rich Repeat Kinase 2 (LRRK2)-G2019S mutation in PD is linked to SIRT3 impairment. Furthermore, SIRT3 is inversely associated with α-synuclein aggregation and DA neuron degeneration in PD. SIRT3 chemical activators and NAD+ precursors can up-regulate SIRT3 activity to protect against DA neuron degeneration in PD models. Taken together, SIRT3 is a promising PD therapeutic target and studies of SIRT3 functional modulators with neuroprotective capability will be of clinical interest.
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Affiliation(s)
- Zhi Dong Zhou
- National Neuroscience Institute, 11 Jalan Tan Tock Seng, 308433, Singapore; Duke-NUS Graduate Medical School, 8 College Road, 169857, Singapore.
| | - Eng King Tan
- National Neuroscience Institute, 11 Jalan Tan Tock Seng, 308433, Singapore; Department of Neurology, Singapore General Hospital, Outram Road, 169608, Singapore; Duke-NUS Graduate Medical School, 8 College Road, 169857, Singapore.
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23
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Chen G, Luo Y, Warncke K, Sun Y, Yu DS, Fu H, Behera M, Ramalingam SS, Doetsch PW, Duong DM, Lammers M, Curran WJ, Deng X. Acetylation regulates ribonucleotide reductase activity and cancer cell growth. Nat Commun 2019; 10:3213. [PMID: 31324785 PMCID: PMC6642173 DOI: 10.1038/s41467-019-11214-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 06/25/2019] [Indexed: 12/26/2022] Open
Abstract
Ribonucleotide reductase (RNR) catalyzes the de novo synthesis of deoxyribonucleoside diphosphates (dNDPs) to provide dNTP precursors for DNA synthesis. Here, we report that acetylation and deacetylation of the RRM2 subunit of RNR acts as a molecular switch that impacts RNR activity, dNTP synthesis, and DNA replication fork progression. Acetylation of RRM2 at K95 abrogates RNR activity by disrupting its homodimer assembly. RRM2 is directly acetylated by KAT7, and deacetylated by Sirt2, respectively. Sirt2, which level peak in S phase, sustains RNR activity at or above a threshold level required for dNTPs synthesis. We also find that radiation or camptothecin-induced DNA damage promotes RRM2 deacetylation by enhancing Sirt2-RRM2 interaction. Acetylation of RRM2 at K95 results in the reduction of the dNTP pool, DNA replication fork stalling, and the suppression of tumor cell growth in vitro and in vivo. This study therefore identifies acetylation as a regulatory mechanism governing RNR activity.
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Affiliation(s)
- Guo Chen
- Departments of Radiation Oncology, Emory University School of Medicine and Winship Cancer Institute of Emory University, 1365C Clifton Road NE, Atlanta, GA, 30322, USA
- Department of Medical Biochemistry and Molecular Biology, School of Medicine, Jinan University, 510632, Guangzhou, Guangdong, China
| | - Yin Luo
- Department of Pharmacology, Emory University School of Medicine and Winship Cancer Institute of Emory University, 1510 Clifton Rd. NE, Atlanta, GA, 30322, USA
| | - Kurt Warncke
- Department of Physics, Emory University, 400 Dowman Drive, Atlanta, GA, 30322, USA
| | - Youwei Sun
- Departments of Radiation Oncology, Emory University School of Medicine and Winship Cancer Institute of Emory University, 1365C Clifton Road NE, Atlanta, GA, 30322, USA
| | - David S Yu
- Departments of Radiation Oncology, Emory University School of Medicine and Winship Cancer Institute of Emory University, 1365C Clifton Road NE, Atlanta, GA, 30322, USA
| | - Haian Fu
- Department of Pharmacology, Emory University School of Medicine and Winship Cancer Institute of Emory University, 1510 Clifton Rd. NE, Atlanta, GA, 30322, USA
| | - Madhusmita Behera
- Department of Hematology and Medical Oncology, Emory University School of Medicine and Winship Cancer Institute of Emory University, 1365C Clifton Road NE, Atlanta, GA, 30322, USA
| | - Suresh S Ramalingam
- Department of Hematology and Medical Oncology, Emory University School of Medicine and Winship Cancer Institute of Emory University, 1365C Clifton Road NE, Atlanta, GA, 30322, USA
| | - Paul W Doetsch
- Laboratory of Genome Integrity and Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Duc M Duong
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Rd. NE, Atlanta, GA, 30322, USA
| | - Michael Lammers
- Institute of Biochemistry, Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, Greifswald, 17487, Germany
| | - Walter J Curran
- Departments of Radiation Oncology, Emory University School of Medicine and Winship Cancer Institute of Emory University, 1365C Clifton Road NE, Atlanta, GA, 30322, USA
| | - Xingming Deng
- Departments of Radiation Oncology, Emory University School of Medicine and Winship Cancer Institute of Emory University, 1365C Clifton Road NE, Atlanta, GA, 30322, USA.
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24
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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
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25
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Zhu Y, Zou X, Dean AE, Brien JO, Gao Y, Tran EL, Park SH, Liu G, Kieffer MB, Jiang H, Stauffer ME, Hart R, Quan S, Satchell KJF, Horikoshi N, Bonini M, Gius D. Lysine 68 acetylation directs MnSOD as a tetrameric detoxification complex versus a monomeric tumor promoter. Nat Commun 2019; 10:2399. [PMID: 31160585 PMCID: PMC6546705 DOI: 10.1038/s41467-019-10352-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 04/29/2019] [Indexed: 12/12/2022] Open
Abstract
Manganese superoxide dismutase (MnSOD) functions as a tumor suppressor; however, once tumorigenesis occurs, clinical data suggest MnSOD levels correlate with more aggressive human tumors, implying a potential dual function of MnSOD in the regulation of metabolism. Here we show, using in vitro transformation and xenograft growth assays that the MnSOD-K68 acetylation (Ac) mimic mutant (MnSODK68Q) functions as a tumor promoter. Interestingly, in various breast cancer and primary cell types the expression of MnSODK68Q is accompanied with a change of MnSOD's stoichiometry from a known homotetramer complex to a monomeric form. Biochemical experiments using the MnSOD-K68Q Ac-mimic, or physically K68-Ac (MnSOD-K68-Ac), suggest that these monomers function as a peroxidase, distinct from the established MnSOD superoxide dismutase activity. MnSODK68Q expressing cells exhibit resistance to tamoxifen (Tam) and cells selected for Tam resistance exhibited increased K68-Ac and monomeric MnSOD. These results suggest a MnSOD-K68-Ac metabolic pathway for Tam resistance, carcinogenesis and tumor progression.
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Affiliation(s)
- Yueming Zhu
- Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Xianghui Zou
- Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Driskill Graduate Program in Life Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Angela E Dean
- Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Joseph O' Brien
- Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Yucheng Gao
- Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Driskill Graduate Program in Life Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Elizabeth L Tran
- Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Seong-Hoon Park
- Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Department of General and Applied Toxicology, Innovative Toxicology Research Center, Korea Institute of Toxicology (KIT), Daejeon, 34114, Korea
| | - Guoxiang Liu
- Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Matthew B Kieffer
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Haiyan Jiang
- Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | | | - Robert Hart
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Songhua Quan
- Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Karla J F Satchell
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Nobuo Horikoshi
- Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Marcelo Bonini
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - David Gius
- Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
- Driskill Graduate Program in Life Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
- Department of Pharmacology, Robert H. Lurie Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
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26
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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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27
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Direct carborane-peptide conjugates: Synthesis and evaluation as non-natural lipopeptide mimetics. Chem Phys Lipids 2018; 213:62-67. [DOI: 10.1016/j.chemphyslip.2018.03.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/14/2018] [Accepted: 03/26/2018] [Indexed: 12/22/2022]
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28
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Kremer M, Kuhlmann N, Lechner M, Baldus L, Lammers M. Comment on 'YcgC represents a new protein deacetylase family in prokaryotes'. eLife 2018; 7:37798. [PMID: 29939131 PMCID: PMC6023612 DOI: 10.7554/elife.37798] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 06/18/2018] [Indexed: 11/13/2022] Open
Abstract
Lysine acetylation is a post-translational modification that is conserved from bacteria to humans. It is catalysed by the activities of lysine acetyltransferases, which use acetyl-CoA as the acetyl-donor molecule, and lysine deacetylases, which remove the acetyl moiety. Recently, it was reported that YcgC represents a new prokaryotic deacetylase family with no apparent homologies to existing deacetylases (Tu et al., 2015). Here we report the results of experiments which demonstrate that YcgC is not a deacetylase.
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Affiliation(s)
- Magdalena Kremer
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Nora Kuhlmann
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Marius Lechner
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Linda Baldus
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Michael Lammers
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Institute of Biochemistry, Synthetic and Structural Biochemistry, University of Greifswald, Greifswald, Germany
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29
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Abstract
Sirtuins (SIRT) are coenzyme NAD+-dependent histone deacetylases for the transfer of modified acetyl groups. Sirtuins are widely involved in various physiological processes and therefore associated with cardiovascular disease, diabetes, Parkinson's disease, cancer and beyond. Consequently, the development of modulators for sirtuins has considerable clinical value. To date, a variety of SIRT1/2 inhibitors have been reported and none has been approved for the market. This review summarizes the recent progress in the discovery and development of SIRT1/2 inhibitors including their inhibitory potency, structure–activity relationship and binding mode analysis as well as discusses the perspective for the future development of SIRT1/2 inhibitors.
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30
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Ali I, Conrad RJ, Verdin E, Ott M. Lysine Acetylation Goes Global: From Epigenetics to Metabolism and Therapeutics. Chem Rev 2018; 118:1216-1252. [PMID: 29405707 PMCID: PMC6609103 DOI: 10.1021/acs.chemrev.7b00181] [Citation(s) in RCA: 232] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Post-translational acetylation of lysine residues has emerged as a key regulatory mechanism in all eukaryotic organisms. Originally discovered in 1963 as a unique modification of histones, acetylation marks are now found on thousands of nonhistone proteins located in virtually every cellular compartment. Here we summarize key findings in the field of protein acetylation over the past 20 years with a focus on recent discoveries in nuclear, cytoplasmic, and mitochondrial compartments. Collectively, these findings have elevated protein acetylation as a major post-translational modification, underscoring its physiological relevance in gene regulation, cell signaling, metabolism, and disease.
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Affiliation(s)
- Ibraheem Ali
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158, United States
- University of California, San Francisco, Department of Medicine, San Francisco, California 94158, United States
| | - Ryan J. Conrad
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158, United States
- University of California, San Francisco, Department of Medicine, San Francisco, California 94158, United States
| | - Eric Verdin
- Buck Institute for Research on Aging, Novato, California 94945, United States
| | - Melanie Ott
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158, United States
- University of California, San Francisco, Department of Medicine, San Francisco, California 94158, United States
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31
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Identification of Bichalcones as Sirtuin Inhibitors by Virtual Screening and In Vitro Testing. Molecules 2018; 23:molecules23020416. [PMID: 29443909 PMCID: PMC6017733 DOI: 10.3390/molecules23020416] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 02/09/2018] [Accepted: 02/10/2018] [Indexed: 01/22/2023] Open
Abstract
Sirtuins are nicotinamide adenine dinucleotide (NAD+)-dependent class III histone deacetylases, which have been linked to the pathogenesis of numerous diseases, including HIV, metabolic disorders, neurodegeneration and cancer. Docking of the virtual pan-African natural products library (p-ANAPL), followed by in vitro testing, resulted in the identification of two inhibitors of sirtuin 1, 2 and 3 (sirt1–3). Two bichalcones, known as rhuschalcone IV (8) and an analogue of rhuschalcone I (9), previously isolated from the medicinal plant Rhus pyroides, were shown to be active in the in vitro assay. The rhuschalcone I analogue (9) showed the best activity against sirt1, with an IC50 value of 40.8 µM. Based on the docking experiments, suggestions for improving the biological activities of the newly identified hit compounds have been provided.
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32
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Lammers M. Expression and Purification of Site-Specifically Lysine-Acetylated and Natively-Folded Proteins for Biophysical Investigations. Methods Mol Biol 2018; 1728:169-190. [PMID: 29404998 DOI: 10.1007/978-1-4939-7574-7_11] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
N-(ε)-lysine-acetylation (short: lysine-acetylation) is a dynamic and powerful posttranslational modification to regulate protein function. Mutational approaches are often poor to access the real mechanistic impact of lysine-acetylation at the molecular level. Therefore, the ability to site-specifically incorporate N-(ε)-acetyl-L-lysine (short: AcK) into proteins dramatically increased our understanding how lysine-acetylation regulates protein function by using diverse molecular mechanisms going far beyond neutralizing a positive charge at the lysine-side chain. Genetically encoding AcK is a powerful way to introduce AcK into proteins, resulting in homogenously, quantitatively, and site-specifically lysine-acetylated proteins. Thereby, lysine-acetylated proteins can be produced in their natively-folded state in a high quality and in a yield sufficient to perform biophysical studies, including X-ray crystallography. This protocol describes the expression and purification of site-specifically lysine-acetylated proteins in Escherichia coli using the genetic-code expansion concept (GCEC) and subsequent steps to assess the successful incorporation of AcK by immunoblotting and mass-spectrometry.
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Affiliation(s)
- Michael Lammers
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.
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33
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Guillén C, Benito M. mTORC1 Overactivation as a Key Aging Factor in the Progression to Type 2 Diabetes Mellitus. Front Endocrinol (Lausanne) 2018; 9:621. [PMID: 30386301 PMCID: PMC6198057 DOI: 10.3389/fendo.2018.00621] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 09/27/2018] [Indexed: 01/06/2023] Open
Abstract
Type 2 Diabetes Mellitus (T2DM), a worldwide epidemics, is a progressive disease initially developing an insulin resistant state, with manifest pancreatic beta islet overwork and hyperinsulinemia. As the disease progresses, pancreatic β cells are overwhelmed and fails in their capacity to compensate insulin resistance. In addition, it is usually associated with other metabolic diseases such as hyperlipidemia, obesity and the metabolic syndrome. During the progression to T2DM there is a chronic activation of mTORC1 signaling pathway, which induces aging and acts as an endogenous inhibitor of autophagy. The complex 1 of mTOR (mTORC1) controls cell proliferation, cell growth as well as metabolism in a variety of cell types through a complex signaling network. Autophagy is involved in the recycling of cellular components for energy generation under nutrient deprivation, and serves as a complementary degradation system to the ubiquitin-proteasome pathway. Autophagy represents a protective mechanism for different cell types, including pancreatic β cells, and potentiates β cell survival across the progression to T2DM. Here, we focus our attention on the chronic overactivation of mTORC1 signaling pathway in β islets from prediabetics patients, making these cells more prone to trigger apoptosis upon several cellular stressors and allowing the progression from prediabetes to type 2 diabetes status.
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Affiliation(s)
- Carlos Guillén
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Complutense University of Madrid, Madrid, Spain
- Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain
- *Correspondence: Carlos Guillén
| | - Manuel Benito
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Complutense University of Madrid, Madrid, Spain
- Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain
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Gallego-Jara J, Écija Conesa A, de Diego Puente T, Lozano Terol G, Cánovas Díaz M. Characterization of CobB kinetics and inhibition by nicotinamide. PLoS One 2017; 12:e0189689. [PMID: 29253849 PMCID: PMC5734772 DOI: 10.1371/journal.pone.0189689] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 11/30/2017] [Indexed: 12/31/2022] Open
Abstract
Lysine acetylation has emerged as a global protein regulation system in all domains of life. Sirtuins, or Sir2-like enzymes, are a family of histone deacetylases characterized by their employing NAD+ as a co-substrate. Sirtuins can deacetylate several acetylated proteins, but a consensus substrate recognition sequence has not yet been established. Product inhibition of many eukaryotic sirtuins by nicotinamide and its analogues has been studied in vitro due to their potential role as anticancer agents. In this work, the kinetics of CobB, the main Escherichia coli deacetylase, have been characterized. To our knowledge, this is the first kinetic characterization of a sirtuin employing a fully acetylated and natively folded protein as a substrate. CobB deacetylated several acetyl-CoA synthetase acetylated lysines with a single kinetic rate. In addition, in vitro nicotinamide inhibition of CobB has been characterized, and the intracellular nicotinamide concentrations have been determined under different growth conditions. The results suggest that nicotinamide can act as a CobB regulator in vivo. A nicotinamidase deletion strain was thus phenotypically characterized, and it behaved similarly to the ΔcobB strain. The results of this work demonstrate the potential regulatory role of the nicotinamide metabolite in vivo.
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Affiliation(s)
- Julia Gallego-Jara
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence ‘‘Campus Mare Nostrum”, Murcia, Spain
- * E-mail:
| | - Ana Écija Conesa
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence ‘‘Campus Mare Nostrum”, Murcia, Spain
| | - Teresa de Diego Puente
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence ‘‘Campus Mare Nostrum”, Murcia, Spain
| | - Gema Lozano Terol
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence ‘‘Campus Mare Nostrum”, Murcia, Spain
| | - Manuel Cánovas Díaz
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence ‘‘Campus Mare Nostrum”, Murcia, Spain
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Kuhlmann N, Chollet C, Baldus L, Neundorf I, Lammers M. Development of Substrate-Derived Sirtuin Inhibitors with Potential Anticancer Activity. ChemMedChem 2017; 12:1703-1714. [DOI: 10.1002/cmdc.201700414] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Indexed: 12/17/2022]
Affiliation(s)
- Nora Kuhlmann
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, CECAD; University of Cologne; Joseph-Stelzmann-Str. 26 50931 Cologne Germany
| | - Constance Chollet
- Institute for Biochemistry; University of Cologne; Zülpicher Straße 47 50674 Cologne Germany
| | - Linda Baldus
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, CECAD; University of Cologne; Joseph-Stelzmann-Str. 26 50931 Cologne Germany
| | - Ines Neundorf
- Institute for Biochemistry; University of Cologne; Zülpicher Straße 47 50674 Cologne Germany
| | - Michael Lammers
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, CECAD; University of Cologne; Joseph-Stelzmann-Str. 26 50931 Cologne Germany
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Chao WCH, Wade BO, Bouchoux C, Jones AW, Purkiss AG, Federico S, O’Reilly N, Snijders AP, Uhlmann F, Singleton MR. Structural Basis of Eco1-Mediated Cohesin Acetylation. Sci Rep 2017; 7:44313. [PMID: 28290497 PMCID: PMC5349539 DOI: 10.1038/srep44313] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 02/06/2017] [Indexed: 12/11/2022] Open
Abstract
Sister-chromatid cohesion is established by Eco1-mediated acetylation on two conserved tandem lysines in the cohesin Smc3 subunit. However, the molecular basis of Eco1 substrate recognition and acetylation in cohesion is not fully understood. Here, we discover and rationalize the substrate specificity of Eco1 using mass spectrometry coupled with in-vitro acetylation assays and crystallography. Our structures of the X. laevis Eco2 (xEco2) bound to its primary and secondary Smc3 substrates demonstrate the plasticity of the substrate-binding site, which confers substrate specificity by concerted conformational changes of the central β hairpin and the C-terminal extension.
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Affiliation(s)
- William C. H. Chao
- Structural Biology of Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Benjamin O. Wade
- Structural Biology of Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Céline Bouchoux
- Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Andrew W. Jones
- Protein Analysis and Proteomics Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Andrew G. Purkiss
- Structural Biology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Stefania Federico
- Peptide Chemistry Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Nicola O’Reilly
- Peptide Chemistry Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Ambrosius P. Snijders
- Protein Analysis and Proteomics Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Martin R. Singleton
- Structural Biology of Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
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Schiedel M, Robaa D, Rumpf T, Sippl W, Jung M. The Current State of NAD + -Dependent Histone Deacetylases (Sirtuins) as Novel Therapeutic Targets. Med Res Rev 2017; 38:147-200. [PMID: 28094444 DOI: 10.1002/med.21436] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 10/24/2016] [Accepted: 11/14/2016] [Indexed: 12/19/2022]
Abstract
Sirtuins are NAD+ -dependent protein deacylases that cleave off acetyl, as well as other acyl groups, from the ε-amino group of lysines in histones and other substrate proteins. Seven sirtuin isotypes (Sirt1-7) have been identified in mammalian cells. As sirtuins are involved in the regulation of various physiological processes such as cell survival, cell cycle progression, apoptosis, DNA repair, cell metabolism, and caloric restriction, a dysregulation of their enzymatic activity has been associated with the pathogenesis of neoplastic, metabolic, infectious, and neurodegenerative diseases. Thus, sirtuins are promising targets for pharmaceutical intervention. Growing interest in a modulation of sirtuin activity has prompted the discovery of several small molecules, able to inhibit or activate certain sirtuin isotypes. Herein, we give an update to our previous review on the topic in this journal (Schemies, 2010), focusing on recent developments in sirtuin biology, sirtuin modulators, and their potential as novel therapeutic agents.
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Affiliation(s)
- Matthias Schiedel
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Dina Robaa
- Department of Pharmaceutical Chemistry, Martin-Luther Universität Halle-Wittenberg, Halle/Saale, Germany
| | - Tobias Rumpf
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Wolfgang Sippl
- Department of Pharmaceutical Chemistry, Martin-Luther Universität Halle-Wittenberg, Halle/Saale, Germany
| | - Manfred Jung
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
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Cao W, Jin H, Zhang L, Chen X, Qian H. Identification of miR-601 as a novel regulator in the development of pancreatic cancer. Biochem Biophys Res Commun 2016; 483:638-644. [PMID: 27993677 DOI: 10.1016/j.bbrc.2016.12.090] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 12/13/2016] [Indexed: 01/28/2023]
Abstract
Pancreatic cancer (PC) is one of the most aggressive malignancies, with a high mortality. Distant metastasis and recurrence are the main causes of PC-related deaths. MicroRNAs (miRNAs) have been reported in the serum or tumor tissue of cancer patients, including PC, which makes them potential biomarkers. The dysfunction of many miRNAs has been linked to PC occurrence and metastasis. In the current study, we found that miR-601 expression was significantly lower in PC samples, especially in metastatic compared to non-metastatic PC tissues. Gain-of-function and loss-of-function analysis showed that miR-601 suppressed PC cell proliferation and migration. One potential mechanism is that miR-601 inhibited the expression of Sirtuin 1 (SIRT1), which is a well-known regulator of PC development. We found that overexpression of SIRT1 could reverse the effect of miR-601 on PC cells. Our investigation therefore suggests that both miR-601 and SIRT1 are possible biomarkers for the early detection, and targets for the treatment of PC.
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Affiliation(s)
- Wenxi Cao
- Department of General Surgery, The First Affiliated Hospital of Soochow University, No.296, Shizi Road, Suzhou, 215006, China
| | - Huihan Jin
- Department of Heptabiliary Surgery, Wuxi No.2 People's Hospital, No.68, Zhongshan Road, Wuxi, 214001, China
| | - Lei Zhang
- Department of Heptabiliary Surgery, Wuxi No.2 People's Hospital, No.68, Zhongshan Road, Wuxi, 214001, China
| | - Xiao Chen
- Department of Heptabiliary Surgery, Wuxi No.2 People's Hospital, No.68, Zhongshan Road, Wuxi, 214001, China
| | - Haixin Qian
- Department of General Surgery, The First Affiliated Hospital of Soochow University, No.296, Shizi Road, Suzhou, 215006, China.
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