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Patil RS, Maloney ME, Lucas R, Fulton DJR, Patel V, Bagi Z, Kovacs-Kasa A, Kovacs L, Su Y, Verin AD. Zinc-Dependent Histone Deacetylases in Lung Endothelial Pathobiology. Biomolecules 2024; 14:140. [PMID: 38397377 PMCID: PMC10886568 DOI: 10.3390/biom14020140] [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: 12/31/2023] [Revised: 01/19/2024] [Accepted: 01/21/2024] [Indexed: 02/25/2024] Open
Abstract
A monolayer of endothelial cells (ECs) lines the lumen of blood vessels and, as such, provides a semi-selective barrier between the blood and the interstitial space. Compromise of the lung EC barrier due to inflammatory or toxic events may result in pulmonary edema, which is a cardinal feature of acute lung injury (ALI) and its more severe form, acute respiratory distress syndrome (ARDS). The EC functions are controlled, at least in part, via epigenetic mechanisms mediated by histone deacetylases (HDACs). Zinc-dependent HDACs represent the largest group of HDACs and are activated by Zn2+. Members of this HDAC group are involved in epigenetic regulation primarily by modifying the structure of chromatin upon removal of acetyl groups from histones. In addition, they can deacetylate many non-histone histone proteins, including those located in extranuclear compartments. Recently, the therapeutic potential of inhibiting zinc-dependent HDACs for EC barrier preservation has gained momentum. However, the role of specific HDAC subtypes in EC barrier regulation remains largely unknown. This review aims to provide an update on the role of zinc-dependent HDACs in endothelial dysfunction and its related diseases. We will broadly focus on biological contributions, signaling pathways and transcriptional roles of HDACs in endothelial pathobiology associated mainly with lung diseases, and we will discuss the potential of their inhibitors for lung injury prevention.
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Affiliation(s)
- Rahul S. Patil
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - McKenzie E. Maloney
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Rudolf Lucas
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - David J. R. Fulton
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Vijay Patel
- Department of Cardiothoracic Surgery, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Zsolt Bagi
- Department of Physiology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Anita Kovacs-Kasa
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Laszlo Kovacs
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Yunchao Su
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Alexander D. Verin
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
- Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
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2
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Zhang H, Lu F, Liu P, Qiu Z, Li J, Wang X, Xu H, Zhao Y, Li X, Wang H, Lu D, Qi R. A direct interaction between RhoGDIα/Tau alleviates hyperphosphorylation of Tau in Alzheimer's disease and vascular dementia. J Neuroimmune Pharmacol 2023; 18:58-71. [PMID: 35080740 DOI: 10.1007/s11481-021-10049-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 12/27/2021] [Indexed: 02/05/2023]
Abstract
RhoGDIα is an inhibitor of RhoGDP dissociation that involves in Aβ metabolism and NFTs production in Alzheimer's disease (AD) by regulating of RhoGTP enzyme activity. Our previous research revealed that RhoGDIα, as the target of Polygala saponin (Sen), might alleviate apoptosis of the nerve cells caused by hypoxia/reoxygenation (H/R). To further clarify the role of RhoGDIα in the generation of NFTs, we explored the relationship between RhoGDIα and Tau. We found out that RhoGDIα and Tau can bind with each other and interact by using coimmunoprecipitation (Co-IP) and GST pulldown methods in vitro. This RhoGDIα-Tau partnership was further verified by using immunofluorescence colocalization and fluorescence resonance energy transfer (FRET) approaches in PC12 cells. Using the RNA interference (RNAi) technique, we found that the RhoGDIα may be involved in an upstream signaling pathway for Tau. Subsequently, in Aβ25-35- and H/R-induced PC12 cells, forced expression of RhoGDIα via cDNA plasmid transfection was found to reduce the hyperphosphorylation of Tau, augment the expression of bcl-2 protein, and inhibit the expression of Bax protein (reducing the Bax/bcl-2 ratio) and the activity of caspase-3. In mouse AD and VaD models, forced expression of RhoGDIα via injection of a viral vector (pAAV-EGFP-RhoGDIα) into the lateral ventricle of the brain alleviated the pathological symptoms of AD and VaD. Finally, GST pulldown confirmed that the binding sites on RhoGDIα for Tau were located in the range of the ΔC33 fragment (aa 1-33). These results indicate that RhoGDIα is involved in the phosphorylation of Tau and apoptosis in AD and VaD. Overexpression of RhoGDIα can inhibit the generation of NFTs and delay the progress of these two types of dementia.
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Affiliation(s)
- Heping Zhang
- Department of Pathophysiology, Key Laboratory of State Administration of Traditional Chinese Medicine, School of Medicine, Jinan University, Guangzhou, 510632, Guangdong, China
| | - Fan Lu
- Department of Emergency, First Affiliated Hospital of Jinan University, Guangzhou, 510630, Guangdong, China
| | - Panhong Liu
- Department of Pathophysiology, Key Laboratory of State Administration of Traditional Chinese Medicine, School of Medicine, Jinan University, Guangzhou, 510632, Guangdong, China
- Department of Pathology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, 400010, China
| | - Zhaohui Qiu
- Department of Pathophysiology, Key Laboratory of State Administration of Traditional Chinese Medicine, School of Medicine, Jinan University, Guangzhou, 510632, Guangdong, China
- Department of Pathology, The Eighth Affiliated Hospital, Sun Yat-Sen University, ShenZhen, 518033, China
| | - Jianling Li
- Department of Pathophysiology, Key Laboratory of State Administration of Traditional Chinese Medicine, School of Medicine, Jinan University, Guangzhou, 510632, Guangdong, China
- Department of Anesthesiology, First Affiliated Hospital of Jinan University, Guangzhou, 510630, China
| | - Xiaotong Wang
- Department of Pathophysiology, Key Laboratory of State Administration of Traditional Chinese Medicine, School of Medicine, Jinan University, Guangzhou, 510632, Guangdong, China
| | - Hui Xu
- Department of Pathophysiology, Key Laboratory of State Administration of Traditional Chinese Medicine, School of Medicine, Jinan University, Guangzhou, 510632, Guangdong, China
| | - Yandong Zhao
- Department of Pathophysiology, Key Laboratory of State Administration of Traditional Chinese Medicine, School of Medicine, Jinan University, Guangzhou, 510632, Guangdong, China
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China
| | - Xuemin Li
- Department of Pathophysiology, Key Laboratory of State Administration of Traditional Chinese Medicine, School of Medicine, Jinan University, Guangzhou, 510632, Guangdong, China
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Anhui, 230031, China
| | - Huadong Wang
- Department of Pathophysiology, Key Laboratory of State Administration of Traditional Chinese Medicine, School of Medicine, Jinan University, Guangzhou, 510632, Guangdong, China
| | - Daxiang Lu
- Department of Pathophysiology, Key Laboratory of State Administration of Traditional Chinese Medicine, School of Medicine, Jinan University, Guangzhou, 510632, Guangdong, China
| | - Renbin Qi
- Department of Pathophysiology, Key Laboratory of State Administration of Traditional Chinese Medicine, School of Medicine, Jinan University, Guangzhou, 510632, Guangdong, China.
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3
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Significance of Pulmonary Endothelial Injury and the Role of Cyclooxygenase-2 and Prostanoid Signaling. BIOENGINEERING (BASEL, SWITZERLAND) 2023; 10:bioengineering10010117. [PMID: 36671689 PMCID: PMC9855370 DOI: 10.3390/bioengineering10010117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 01/19/2023]
Abstract
The endothelium plays a key role in the dynamic balance of hemodynamic, humoral and inflammatory processes in the human body. Its central importance and the resulting therapeutic concepts are the subject of ongoing research efforts and form the basis for the treatment of numerous diseases. The pulmonary endothelium is an essential component for the gas exchange in humans. Pulmonary endothelial dysfunction has serious consequences for the oxygenation and the gas exchange in humans with the potential of consecutive multiple organ failure. Therefore, in this review, the dysfunction of the pulmonary endothel due to viral, bacterial, and fungal infections, ventilator-related injury, and aspiration is presented in a medical context. Selected aspects of the interaction of endothelial cells with primarily alveolar macrophages are reviewed in more detail. Elucidation of underlying causes and mechanisms of damage and repair may lead to new therapeutic approaches. Specific emphasis is placed on the processes leading to the induction of cyclooxygenase-2 and downstream prostanoid-based signaling pathways associated with this enzyme.
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4
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A current overview of RhoA, RhoB, and RhoC functions in vascular biology and pathology. Biochem Pharmacol 2022; 206:115321. [DOI: 10.1016/j.bcp.2022.115321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 11/24/2022]
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5
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Song G, Jin F. RhoGDI1 interacts with PHLDA2, suppresses the proliferation, migration, and invasion of trophoblast cells, and participates in the pathogenesis of preeclampsia. Hum Cell 2022; 35:1440-1452. [PMID: 35841528 DOI: 10.1007/s13577-022-00746-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 07/03/2022] [Indexed: 11/28/2022]
Abstract
Preeclampsia (PE) is a pregnancy-associated disease, which is the major cause of mortality on maternity and perinatal infants. It is hypothesized that PE is a consequence of the dysfunction of the trophoblast cells. Pleckstrin homology-like domain, family A, member 2 (PHLDA2) was shown to inhibit the proliferation, migration, and invasion of trophoblast cells in our previous studies. However, the mechanism by which PHLDA2 affects trophoblast cell function has not been clarified. In the current study, co-immunoprecipitation (Co-IP) with mass spectroscopy analysis was used to explore the proteins that interacted with PHLDA2. A total of 291 candidate proteins were found to be associated with PHLDA2. The interaction between PHLDA2 and Rho guanine nucleotide dissociation inhibitor (RhoGDI) 1 was identified by Co-IP and immunofluorescence staining. Western blot analysis indicated that overexpression of PHLDA2 resulted in upregulation of the RhoGDI1 protein levels, which were stabilized in the presence of cycloheximide. Similarly, overexpression of RhoGDI1 promoted PHLDA2 expression and its stability. Furthermore, pull-down and Co-IP results indicated that PHLDA2 repressed the activity of Rho guanosine triphosphate hydrolase family proteins by regulating RhoGDI1 expression. In addition, RhoGDI1 expression was upregulated in the placental tissues of patients with PE. The effects of the suppression of PHLDA2 expression on proliferation, migration, and invasion of trophoblast cells were partly abrogated following knockdown of RhoGDI1. Taken together, the data indicated that RhoGDI1 mediated regulation of PHLDA2 on the biological behavior of trophoblast cells and may participate in the pathophysiology of PE.
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Affiliation(s)
- Guiyu Song
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, No. 36, Sanhao Street, Shenyang, 110004, Liaoning, China
| | - Feng Jin
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, No. 36, Sanhao Street, Shenyang, 110004, Liaoning, China.
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6
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Kowluru A, Gleason NF. Underappreciated roles for Rho GDP dissociation inhibitors (RhoGDIs) in cell function: Lessons learned from the pancreatic islet β-cell. Biochem Pharmacol 2022; 197:114886. [PMID: 34968495 PMCID: PMC8858860 DOI: 10.1016/j.bcp.2021.114886] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/10/2021] [Accepted: 12/13/2021] [Indexed: 11/02/2022]
Abstract
Rho subfamily of G proteins (e.g., Rac1) have been implicated in glucose-stimulated insulin secretion from the pancreatic β-cell. Interestingly, metabolic stress (e.g., chronic exposure to high glucose) results in sustained activation of Rac1 leading to increased oxidative stress, impaired insulin secretion and β-cell dysfunction. Activation-deactivation of Rho G proteins is mediated by three classes of regulatory proteins, namely the guanine nucleotide exchange factors (GEFs), which facilitate the conversion of inactive G proteins to their active conformations; the GTPase-activating proteins (GAPs), which convert the active G proteins to their inactive forms); and the GDP-dissociation inhibitors (GDIs), which prevent the dissociation of GDP from G proteins. Contrary to a large number of GEFs (82 members) and GAPs (69 members), only three members of RhoGDIs (RhoGDIα, RhoGDIβ and RhoGDIγ) are expressed in mammalian cells.Even though relatively smaller in number, the GDIs appear to play essential roles in G protein function (e.g., subcellular targeting) for effector activation and cell regulation. Emerging evidence also suggests that the GDIs are functionally regulated via post-translational modification (e.g., phosphorylation) and by lipid second messengers, lipid kinases and lipid phosphatases. We highlight the underappreciated regulatory roles of RhoGDI-Rho G protein signalome in islet β-cell function in health and metabolic stress. Potential knowledge gaps in the field, and directions for future research for the identification of novel therapeutic targets to loss of functional β-cell mass under the duress of metabolic stress are highlighted.
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Affiliation(s)
- Anjaneyulu Kowluru
- Biomedical Research Service, John D. Dingell VA Medical Center and Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI 48201, USA.
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7
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Martins VF, LaBarge SA, Stanley A, Svensson K, Hung CW, Keinan O, Ciaraldi TP, Banoian D, Park JE, Ha C, Hetrick B, Meyer GA, Philp A, David LL, Henry RR, Aslan JE, Saltiel AR, McCurdy CE, Schenk S. p300 or CBP is required for insulin-stimulated glucose uptake in skeletal muscle and adipocytes. JCI Insight 2021; 7:141344. [PMID: 34813504 PMCID: PMC8765050 DOI: 10.1172/jci.insight.141344] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 11/19/2021] [Indexed: 11/17/2022] Open
Abstract
While current thinking posits that insulin signaling to GLUT4 exocytic translocation and glucose uptake in skeletal muscle and adipocytes is controlled by phosphorylation-based signaling, many proteins in this pathway are acetylated on lysine residues. However, the importance of acetylation and lysine acetyltransferases to insulin-stimulated glucose uptake is incompletely defined. Here, we demonstrate that combined loss of the acetyltransferases E1A binding protein p300 (p300) and cAMP response element binding protein binding protein (CBP) in mouse skeletal muscle causes a complete loss of insulin-stimulated glucose uptake. Similarly, brief (i.e. 1 h) pharmacological inhibition of p300/CBP acetyltransferase activity recapitulates this phenotype in human and rodent myotubes, 3T3-L1 adipocytes, and mouse muscle. Mechanistically, these effects are due to p300/CBP-mediated regulation of GLUT4 exocytic translocation and occurs downstream of Akt signaling. Taken together, we highlight a fundamental role for acetylation and p300/CBP in the direct regulation of insulin-stimulated glucose transport in skeletal muscle and adipocytes.
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Affiliation(s)
- Vitor F Martins
- Department of Orthopedic Surgery, University of California, San Diego, La Jolla, United States of America
| | - Samuel A LaBarge
- Department of Orthopedic Surgery, University of California, San Diego, La Jolla, United States of America
| | - Alexandra Stanley
- Department of Orthopedic Surgery, University of California, San Diego, La Jolla, United States of America
| | - Kristoffer Svensson
- Department of Orthopedic Surgery, University of California, San Diego, La Jolla, United States of America
| | - Chao-Wei Hung
- Department of Medicine, University of California, San Diego, La Jolla, United States of America
| | - Omer Keinan
- Department of Medicine, University of California, San Diego, La Jolla, United States of America
| | - Theodore P Ciaraldi
- Department of Medicine, University of California, San Diego, La Jolla, United States of America
| | - Dion Banoian
- Department of Orthopedic Surgery, University of California, San Diego, La Jolla, United States of America
| | - Ji E Park
- Department of Orthopedic Surgery, University of California, San Diego, La Jolla, United States of America
| | - Christina Ha
- Department of Orthopedic Surgery, University of California, San Diego, La Jolla, United States of America
| | - Byron Hetrick
- Department of Human Physiology, University of Oregon, Eugene, United States of America
| | - Gretchen A Meyer
- Program in Physical Therapy, Washington University in St. Louis, St. Louis, United States of America
| | - Andrew Philp
- Mitochondrial Metabolism and Ageing, Garvan Institute of Medical Research, Darlinghurst, Australia
| | - Larry L David
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, United States of America
| | - Robert R Henry
- Division of Endocrinology & Metabolism, VA San Diego Healthcare System, San Diego, United States of America
| | - Joseph E Aslan
- Knight Cardiovascular Institute, Oregon Health & Science University, Portland, United States of America
| | - Alan R Saltiel
- University of California, San Diego, La Jolla, United States of America
| | - Carrie E McCurdy
- Department of Human Physiology, University of Oregon, Eugene, United States of America
| | - Simon Schenk
- Department of Orthopedic Surgery, University of California, San Diego, La Jolla, United States of America
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8
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Electrostatic Forces Mediate the Specificity of RHO GTPase-GDI Interactions. Int J Mol Sci 2021; 22:ijms222212493. [PMID: 34830380 PMCID: PMC8622166 DOI: 10.3390/ijms222212493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/15/2021] [Accepted: 11/16/2021] [Indexed: 01/13/2023] Open
Abstract
Three decades of research have documented the spatiotemporal dynamics of RHO family GTPase membrane extraction regulated by guanine nucleotide dissociation inhibitors (GDIs), but the interplay of the kinetic mechanism and structural specificity of these interactions is as yet unresolved. To address this, we reconstituted the GDI-controlled spatial segregation of geranylgeranylated RHO protein RAC1 in vitro. Various biochemical and biophysical measurements provided unprecedented mechanistic details for GDI function with respect to RHO protein dynamics. We determined that membrane extraction of RHO GTPases by GDI occurs via a 3-step mechanism: (1) GDI non-specifically associates with the switch regions of the RHO GTPases; (2) an electrostatic switch determines the interaction specificity between the C-terminal polybasic region of RHO GTPases and two distinct negatively-charged clusters of GDI1; (3) a non-specific displacement of geranylgeranyl moiety from the membrane sequesters it into a hydrophobic cleft, effectively shielding it from the aqueous milieu. This study substantially extends the model for the mechanism of GDI-regulated RHO GTPase extraction from the membrane, and could have implications for clinical studies and drug development.
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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: 0] [Impact Index Per Article: 0] [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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10
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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: 20] [Impact Index Per Article: 6.7] [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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11
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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: 10] [Impact Index Per Article: 3.3] [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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12
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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: 3] [Impact Index Per Article: 1.0] [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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13
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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: 14] [Impact Index Per Article: 4.7] [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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14
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Satpathy S, Krug K, Jean Beltran PM, Savage SR, Petralia F, Kumar-Sinha C, Dou Y, Reva B, Kane MH, Avanessian SC, Vasaikar SV, Krek A, Lei JT, Jaehnig EJ, Omelchenko T, Geffen Y, Bergstrom EJ, Stathias V, Christianson KE, Heiman DI, Cieslik MP, Cao S, Song X, Ji J, Liu W, Li K, Wen B, Li Y, Gümüş ZH, Selvan ME, Soundararajan R, Visal TH, Raso MG, Parra ER, Babur Ö, Vats P, Anand S, Schraink T, Cornwell M, Rodrigues FM, Zhu H, Mo CK, Zhang Y, da Veiga Leprevost F, Huang C, Chinnaiyan AM, Wyczalkowski MA, Omenn GS, Newton CJ, Schurer S, Ruggles KV, Fenyö D, Jewell SD, Thiagarajan M, Mesri M, Rodriguez H, Mani SA, Udeshi ND, Getz G, Suh J, Li QK, Hostetter G, Paik PK, Dhanasekaran SM, Govindan R, Ding L, Robles AI, Clauser KR, Nesvizhskii AI, Wang P, Carr SA, Zhang B, Mani DR, Gillette MA. A proteogenomic portrait of lung squamous cell carcinoma. Cell 2021; 184:4348-4371.e40. [PMID: 34358469 PMCID: PMC8475722 DOI: 10.1016/j.cell.2021.07.016] [Citation(s) in RCA: 156] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 04/26/2021] [Accepted: 07/12/2021] [Indexed: 02/07/2023]
Abstract
Lung squamous cell carcinoma (LSCC) remains a leading cause of cancer death with few therapeutic options. We characterized the proteogenomic landscape of LSCC, providing a deeper exposition of LSCC biology with potential therapeutic implications. We identify NSD3 as an alternative driver in FGFR1-amplified tumors and low-p63 tumors overexpressing the therapeutic target survivin. SOX2 is considered undruggable, but our analyses provide rationale for exploring chromatin modifiers such as LSD1 and EZH2 to target SOX2-overexpressing tumors. Our data support complex regulation of metabolic pathways by crosstalk between post-translational modifications including ubiquitylation. Numerous immune-related proteogenomic observations suggest directions for further investigation. Proteogenomic dissection of CDKN2A mutations argue for more nuanced assessment of RB1 protein expression and phosphorylation before declaring CDK4/6 inhibition unsuccessful. Finally, triangulation between LSCC, LUAD, and HNSCC identified both unique and common therapeutic vulnerabilities. These observations and proteogenomics data resources may guide research into the biology and treatment of LSCC.
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Affiliation(s)
- Shankha Satpathy
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.
| | - Karsten Krug
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Pierre M Jean Beltran
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Sara R Savage
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Francesca Petralia
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Yongchao Dou
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Boris Reva
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - M Harry Kane
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Shayan C Avanessian
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Suhas V Vasaikar
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Azra Krek
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jonathan T Lei
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric J Jaehnig
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Yifat Geffen
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Erik J Bergstrom
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Vasileios Stathias
- Sylvester Comprehensive Cancer Center and Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Karen E Christianson
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - David I Heiman
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Marcin P Cieslik
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Song Cao
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Xiaoyu Song
- Department of Population Health Science and Policy, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jiayi Ji
- Department of Population Health Science and Policy, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Wenke Liu
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Kai Li
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Bo Wen
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yize Li
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Zeynep H Gümüş
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Myvizhi Esai Selvan
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rama Soundararajan
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Tanvi H Visal
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Maria G Raso
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Edwin Roger Parra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Özgün Babur
- Computer Science Department, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Pankaj Vats
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shankara Anand
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Tobias Schraink
- Institute for Systems Genetics and Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - MacIntosh Cornwell
- Institute for Systems Genetics and Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | | | - Houxiang Zhu
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Chia-Kuei Mo
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Yuping Zhang
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Chen Huang
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Arul M Chinnaiyan
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Gilbert S Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Stephan Schurer
- Sylvester Comprehensive Cancer Center and Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Kelly V Ruggles
- Institute for Systems Genetics and Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - David Fenyö
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Scott D Jewell
- Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Mathangi Thiagarajan
- Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Sendurai A Mani
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Namrata D Udeshi
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Gad Getz
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - James Suh
- Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Qing Kay Li
- Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins Medical Institutions, Baltimore, MD 21224, USA
| | | | - Paul K Paik
- Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | - Ramaswamy Govindan
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Li Ding
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Karl R Clauser
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Steven A Carr
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
| | - D R Mani
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.
| | - Michael A Gillette
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA 02115, USA.
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15
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Ahmad Mokhtar AM, Ahmed SBM, Darling NJ, Harris M, Mott HR, Owen D. A Complete Survey of RhoGDI Targets Reveals Novel Interactions with Atypical Small GTPases. Biochemistry 2021; 60:1533-1551. [PMID: 33913706 PMCID: PMC8253491 DOI: 10.1021/acs.biochem.1c00120] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/16/2021] [Indexed: 01/07/2023]
Abstract
There are three RhoGDIs in mammalian cells, which were initially defined as negative regulators of Rho family small GTPases. However, it is now accepted that RhoGDIs not only maintain small GTPases in their inactive GDP-bound form but also act as chaperones for small GTPases, targeting them to specific intracellular membranes and protecting them from degradation. Studies to date with RhoGDIs have usually focused on the interactions between the "typical" or "classical" small GTPases, such as the Rho, Rac, and Cdc42 subfamily members, and either the widely expressed RhoGDI-1 or the hematopoietic-specific RhoGDI-2. Less is known about the third member of the family, RhoGDI-3 and its interacting partners. RhoGDI-3 has a unique N-terminal extension and is found to localize in both the cytoplasm and the Golgi. RhoGDI-3 has been shown to target RhoB and RhoG to endomembranes. In order to facilitate a more thorough understanding of RhoGDI function, we undertook a systematic study to determine all possible Rho family small GTPases that interact with the RhoGDIs. RhoGDI-1 and RhoGDI-2 were found to have relatively restricted activity, mainly binding members of the Rho and Rac subfamilies. RhoGDI-3 displayed wider specificity, interacting with the members of Rho, Rac, and Cdc42 subfamilies but also forming complexes with "atypical" small Rho GTPases such as Wrch2/RhoV, Rnd2, Miro2, and RhoH. Levels of RhoA, RhoB, RhoC, Rac1, RhoH, and Wrch2/RhoV bound to GTP were found to decrease following coexpression with RhoGDI-3, confirming its role as a negative regulator of these small Rho GTPases.
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Affiliation(s)
| | | | | | | | - Helen R. Mott
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Darerca Owen
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
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16
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Kovacs-Kasa A, Kovacs L, Cherian-Shaw M, Patel V, Meadows ML, Fulton DJ, Su Y, Verin AD. Inhibition of Class IIa HDACs improves endothelial barrier function in endotoxin-induced acute lung injury. J Cell Physiol 2021; 236:2893-2905. [PMID: 32959895 PMCID: PMC9946131 DOI: 10.1002/jcp.30053] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 08/31/2020] [Accepted: 09/03/2020] [Indexed: 12/21/2022]
Abstract
Acute lung injury (ALI) is an acute inflammatory process arises from a wide range of lung insults. A major cause of ALI is dysfunction of the pulmonary vascular endothelial barrier but the mechanisms involved are incompletely understood. The therapeutic potential of histone deacetylase (HDAC) inhibitors for the treatment of cardiovascular and inflammatory diseases is increasingly apparent, but the mechanisms by which HDACs regulate pulmonary vascular barrier function remain to be resolved. We found that specific Class IIa HDACs inhibitor, TMP269, significantly attenuated the lipopolysaccharide (LPS)-induced human lung microvascular endothelial cells (HLMVEC) barrier compromise in vitro and improved vascular barrier integrity and lung function in murine model of ALI in vivo. TMP269 decreased LPS-induced myosin light chain phosphorylation suggesting the role for Class IIa HDACs in LPS-induced cytoskeleton reorganization. TMP269 did not affect microtubule structure and tubulin acetylation in contrast to the HDAC6-specific inhibitor, Tubastatin A suggesting that Class IIa HDACs and HDAC6 (Class IIb) regulate endothelial cytoskeleton and permeability via different mechanisms. Furthermore, LPS increased the expression of ArgBP2 which has recently been attributed to HDAC-mediated activation of Rho. Depletion of ArgBP2 abolished the ability of LPS to disrupt barrier function in HLMVEC and both TMP269 and Tubastatin A decreased the level of ArgBP2 expression after LPS stimulation suggesting that both Class IIa and IIb HDACs regulate endothelial permeability via ArgBP2-dependent mechanism. Collectively, our data strongly suggest that Class IIa HDACs are involved in LPS-induced ALI in vitro and in vivo via specific mechanism which involved contractile responses, but not microtubule reorganization.
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Affiliation(s)
- Anita Kovacs-Kasa
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
| | - Laszlo Kovacs
- Department of Pharmacology and Toxicology, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
| | - Mary Cherian-Shaw
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
| | - Vijay Patel
- Department of Cardiothoracic Surgery, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
| | - Mary L. Meadows
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
| | - David J. Fulton
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
- Department of Pharmacology and Toxicology, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
| | - Yunchao Su
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
- Department of Pharmacology and Toxicology, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
- Department of Medicine, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
- Research Service, Charlie Norwood Veterans Affairs Medical Center, Augusta, Georgia, USA
| | - Alexander D. Verin
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
- Department of Medicine, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
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17
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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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18
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Toro TB, Watt TJ. Critical review of non-histone human substrates of metal-dependent lysine deacetylases. FASEB J 2020; 34:13140-13155. [PMID: 32862458 DOI: 10.1096/fj.202001301rr] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/29/2020] [Accepted: 08/03/2020] [Indexed: 12/15/2022]
Abstract
Lysine acetylation is a posttranslational modification that occurs on thousands of human proteins, most of which are cytoplasmic. Acetylated proteins are involved in numerous cellular processes and human diseases. Therefore, how the acetylation/deacetylation cycle is regulated is an important question. Eleven metal-dependent lysine deacetylases (KDACs) have been identified in human cells. These enzymes, along with the sirtuins, are collectively responsible for reversing lysine acetylation. Despite several large-scale studies which have characterized the acetylome, relatively few of the specific acetylated residues have been matched to a proposed KDAC for deacetylation. To understand the function of lysine acetylation, and its association with diseases, specific KDAC-substrate pairs must be identified. Identifying specific substrates of a KDAC is complicated both by the complexity of assaying relevant activity and by the non-catalytic interactions of KDACs with cellular proteins. Here, we discuss in vitro and cell-based experimental strategies used to identify KDAC-substrate pairs and evaluate each for the purpose of directly identifying non-histone substrates of metal-dependent KDACs. We propose criteria for a combination of reproducible experimental approaches that are necessary to establish a direct enzymatic relationship. This critical analysis of the literature identifies 108 proposed non-histone substrate-KDAC pairs for which direct experimental evidence has been reported. Of these, five pairs can be considered well-established, while another thirteen pairs have both cell-based and in vitro evidence but lack independent replication and/or sufficient cell-based evidence. We present a path forward for evaluating the remaining substrate leads and reliably identifying novel KDAC substrates.
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Affiliation(s)
- Tasha B Toro
- Department of Chemistry, Xavier University of Louisiana, New Orleans, LA, USA
| | - Terry J Watt
- Department of Chemistry, Xavier University of Louisiana, New Orleans, LA, USA
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19
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Structural Insights into the Regulation Mechanism of Small GTPases by GEFs. Molecules 2019; 24:molecules24183308. [PMID: 31514408 PMCID: PMC6767298 DOI: 10.3390/molecules24183308] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/09/2019] [Accepted: 09/10/2019] [Indexed: 12/12/2022] Open
Abstract
Small GTPases are key regulators of cellular events, and their dysfunction causes many types of cancer. They serve as molecular switches by cycling between inactive guanosine diphosphate (GDP)-bound and active guanosine triphosphate (GTP)-bound states. GTPases are deactivated by GTPase-activating proteins (GAPs) and are activated by guanine-nucleotide exchange factors (GEFs). The intrinsic GTP hydrolysis activity of small GTPases is generally low and is accelerated by GAPs. GEFs promote GDP dissociation from small GTPases to allow for GTP binding, which results in a conformational change of two highly flexible segments, called switch I and switch II, that enables binding of the gamma phosphate and allows small GTPases to interact with downstream effectors. For several decades, crystal structures of many GEFs and GAPs have been reported and have shown tremendous structural diversity. In this review, we focus on the latest structural studies of GEFs. Detailed pictures of the variety of GEF mechanisms at atomic resolution can provide insights into new approaches for drug discovery.
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20
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Cho HJ, Kim JT, Baek KE, Kim BY, Lee HG. Regulation of Rho GTPases by RhoGDIs in Human Cancers. Cells 2019; 8:cells8091037. [PMID: 31492019 PMCID: PMC6769525 DOI: 10.3390/cells8091037] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/02/2019] [Accepted: 09/03/2019] [Indexed: 12/15/2022] Open
Abstract
Rho GDP dissociation inhibitors (RhoGDIs) play important roles in various cellular processes, including cell migration, adhesion, and proliferation, by regulating the functions of the Rho GTPase family. Dissociation of Rho GTPases from RhoGDIs is necessary for their spatiotemporal activation and is dynamically regulated by several mechanisms, such as phosphorylation, sumoylation, and protein interaction. The expression of RhoGDIs has changed in many human cancers and become associated with the malignant phenotype, including migration, invasion, metastasis, and resistance to anticancer agents. Here, we review how RhoGDIs control the function of Rho GTPases by regulating their spatiotemporal activity and describe the regulatory mechanisms of the dissociation of Rho GTPases from RhoGDIs. We also discuss the role of RhoGDIs in cancer progression and their potential uses for therapeutic intervention.
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Affiliation(s)
- Hee Jun Cho
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea.
| | - Jong-Tae Kim
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea.
| | - Kyoung Eun Baek
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea.
| | - Bo-Yeon Kim
- Anticancer Cancer Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea.
| | - Hee Gu Lee
- Immunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea.
- Department of Biomolecular Science, University of Science and Technology (UST), Daejeon 34141, Korea.
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21
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Ding Y, Kang A, Tang Q, Zhao Y. Inhibition of HDAC6 expression decreases brain injury induced by APOE4 and Aβ co‑aggregation in rats. Mol Med Rep 2019; 20:3363-3370. [PMID: 31432127 DOI: 10.3892/mmr.2019.10571] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Accepted: 07/11/2019] [Indexed: 11/06/2022] Open
Abstract
The present study aimed to explore the effects of histone deacetylase 6 (HDAC6) on brain injury in rats induced by apolipoprotein E4 (APOE4) and amyloid β protein alloform 1‑40 (Aβ1‑40) copolymerization. The rats were randomly divided into four groups: Control group, sham group, APOE4 + Aβ1‑40 co‑injection group (model group) and HDAC6 inhibitor group (HDAC6 group). The brain injury model was established by co‑injection of APOE4 + Aβ1‑40. Morris water maze experiment was used to observe the spatial memory and learning the ability of rats. Histological changes of the hippocampus were observed by hematoxylin and eosin staining. The mRNA expression levels of choline acetyltransferase (ChAT) and HDAC6 were detected by reverse transcription‑quantitative PCR. Immunohistochemistry was used to detect the protein expression of HDAC6. Western blotting was used to detect the protein expression levels of HDAC6, microtubule‑associated protein tau and glycogen synthase kinase 3β (GSK3β). APOE4 and Aβ1‑40 co‑aggregation decreased the short‑term spatial memory and learning ability of rats, whereas inhibition of HDAC6 activity attenuated the injury. Inhibition of HDAC6 activity resulted in an attenuation of the APOE4 and Aβ1‑40 co‑aggregation‑induced increase in the number of dysplastic hippocampal cells. Further experiments demonstrated that APOE4 and Aβ1‑40 co‑aggregation decreased the expression levels of ChAT mRNA, and the phosphorylation levels of tau GSK3β protein in the hippocampus, whereas inhibition of HDAC6 activity resulted in increased expression of ChAT mRNA, tau protein and GSK3β phosphorylation. The inhibition of HDAC6 activity was also demonstrated to reduce brain injury induced by APOE4 and Aβ1‑40 co‑aggregation in model rats.
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Affiliation(s)
- Yuexia Ding
- Department of Pharmacy, Yantai Yuhuangding Hospital, Yantai, Shandong 264000, P.R. China
| | - Airong Kang
- Department of Respiration, Yantai Yuhuangding Hospital, Yantai, Shandong 264000, P.R. China
| | - Qiling Tang
- Department of Pharmacy, Yantai Yuhuangding Hospital, Yantai, Shandong 264000, P.R. China
| | - Ying Zhao
- Department of Pharmacy, Yantai Yuhuangding Hospital, Yantai, Shandong 264000, P.R. China
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22
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Martins VF, Dent JR, Svensson K, Tahvilian S, Begur M, Lakkaraju S, Buckner EH, LaBarge SA, Hetrick B, McCurdy CE, Schenk S. Germline or inducible knockout of p300 or CBP in skeletal muscle does not alter insulin sensitivity. Am J Physiol Endocrinol Metab 2019; 316:E1024-E1035. [PMID: 30888860 PMCID: PMC6620570 DOI: 10.1152/ajpendo.00497.2018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Akt is a critical mediator of insulin-stimulated glucose uptake in skeletal muscle. The acetyltransferases, E1A binding protein p300 (p300) and cAMP response element-binding protein binding protein (CBP) are phosphorylated and activated by Akt, and p300/CBP can acetylate and inactivate Akt, thus giving rise to a possible Akt-p300/CBP axis. Our objective was to determine the importance of p300 and CBP to skeletal muscle insulin sensitivity. We used Cre-LoxP methodology to generate mice with germline [muscle creatine kinase promoter (P-MCK and C-MCK)] or inducible [tamoxifen-activated, human skeletal actin promoter (P-iHSA and C-iHSA)] knockout of p300 or CBP. A subset of P-MCK and C-MCK mice were switched to a calorie-restriction diet (60% of ad libitum intake) or high-fat diet at 10 wk of age. For P-iHSA and C-iHSA mice, knockout was induced at 10 wk of age. At 13-15 wk of age, we measured whole-body energy expenditure, oral glucose tolerance, and/or ex vivo skeletal muscle insulin sensitivity. Although p300 and CBP protein abundance and mRNA expression were reduced 55%-90% in p300 and CBP knockout mice, there were no genotype differences in energy expenditure or fasting glucose and insulin concentrations. Moreover, neither loss of p300 or CBP impacted oral glucose tolerance or skeletal muscle insulin sensitivity, nor did their loss impact alterations in these parameters in response to a calorie restriction or high-fat diet. Muscle-specific loss of either p300 or CBP, be it germline or in adulthood, does not impact energy expenditure, glucose tolerance, or skeletal muscle insulin action.
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Affiliation(s)
- Vitor F Martins
- Department of Orthopaedic Surgery, University of California, San Diego, La Jolla, California
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, California
| | - Jessica R Dent
- Department of Orthopaedic Surgery, University of California, San Diego, La Jolla, California
| | - Kristoffer Svensson
- Department of Orthopaedic Surgery, University of California, San Diego, La Jolla, California
| | - Shahriar Tahvilian
- Department of Orthopaedic Surgery, University of California, San Diego, La Jolla, California
| | - Maedha Begur
- Department of Orthopaedic Surgery, University of California, San Diego, La Jolla, California
| | - Shivani Lakkaraju
- Department of Orthopaedic Surgery, University of California, San Diego, La Jolla, California
| | - Elisa H Buckner
- Department of Orthopaedic Surgery, University of California, San Diego, La Jolla, California
| | - Samuel A LaBarge
- Department of Orthopaedic Surgery, University of California, San Diego, La Jolla, California
| | - Byron Hetrick
- Department of Human Physiology, University of Oregon , Eugene, Oregon
| | - Carrie E McCurdy
- Department of Human Physiology, University of Oregon , Eugene, Oregon
| | - Simon Schenk
- Department of Orthopaedic Surgery, University of California, San Diego, La Jolla, California
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, California
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23
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GEF mechanism revealed by the structure of SmgGDS-558 and farnesylated RhoA complex and its implication for a chaperone mechanism. Proc Natl Acad Sci U S A 2018; 115:9563-9568. [PMID: 30190425 DOI: 10.1073/pnas.1804740115] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
SmgGDS has dual functions in cells and regulates small GTPases as both a guanine nucleotide exchange factor (GEF) for the Rho family and a molecular chaperone for small GTPases possessing a C-terminal polybasic region followed by four C-terminal residues called the CaaX motif, which is posttranslationally prenylated at its cysteine residue. Our recent structural work revealed that SmgGDS folds into tandem copies of armadillo-repeat motifs (ARMs) that are not present in other GEFs. However, the precise mechanism of GEF activity and recognition mechanism for the prenylated CaaX motif remain unknown because SmgGDS does not have a typical GEF catalytic domain and lacks a pocket to accommodate a prenyl group. Here, we aimed to determine the crystal structure of the SmgGDS/farnesylated RhoA complex. We found that SmgGDS induces a significant conformational change in the switch I and II regions that opens up the nucleotide-binding site, with the prenyl group fitting into the cryptic pocket in the N-terminal ARMs. Taken together, our findings could advance the understanding of the role of SmgGDS and enable drug design strategies for targeting SmgGDS and small GTPases.
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24
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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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25
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Matera MG, Calzetta L, Gritti G, Gallo L, Perfetto B, Donnarumma G, Cazzola M, Rogliani P, Donniacuo M, Rinaldi B. Role of statins and mevalonate pathway on impaired HDAC2 activity induced by oxidative stress in human airway epithelial cells. Eur J Pharmacol 2018; 832:114-119. [PMID: 29782855 DOI: 10.1016/j.ejphar.2018.05.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 05/17/2018] [Accepted: 05/17/2018] [Indexed: 01/04/2023]
Abstract
In patients with chronic obstructive pulmonary disease (COPD) the inflammatory response is often steroid-resistant, likely since oxidative stress and cigarette smoking impair histone deacetylase 2 (HDAC2) activity. Since it has been demonstrated that statins may restore the HDAC2 activity in cultured human endothelial cells, the aim of this study was to investigate the effects of statins in reversing the steroid-resistance induced by oxidative stress. We evaluated the effects of simvastatin and dexamethasone on HDAC2 expression and activity, and the role of mevalonate and Rho/ROCK pathways in A549 cells, a human lung type II epithelial cell line stressed with H2O2. Our results documented that H2O2 significantly reduced the HDAC2 expression and activity. In H2O2 treated cells dexamethasone was unable to restore the activity of HDAC2, whereas simvastatin restored both the expression and the activity of this enzyme. Our data also showed that mevalonate reduced the activity of HDAC2 whereas Y27632, a Rho/ROCK inhibitor, had no effect on HDAC2 activity when co-administered with simvastatin. Our data suggest that statins could have the potential to restore corticosteroid sensitivity in A549 cells. The evidences of this study suggest that, although both mevalonate and Rho/ROCK pathways are involved in the detrimental effect elicited by oxidative stress, statins may restore the function and expression of depleted HDAC2 via modulating the mevalonate cascade, at least in A549 cells. In conclusion, the modulation of histone acetyltransferase/deacetylase activity may lead to the development of novel anti-inflammatory approaches to inflammatory lung diseases that are currently difficult to treat.
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Affiliation(s)
- Maria Gabriella Matera
- Department of Experimental Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Luigino Calzetta
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy.
| | - Giulia Gritti
- Department of Experimental Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Laura Gallo
- Department of Experimental Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Brunella Perfetto
- Department of Experimental Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Giovanna Donnarumma
- Department of Experimental Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Mario Cazzola
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
| | - Paola Rogliani
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
| | - Maria Donniacuo
- Department of Experimental Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Barbara Rinaldi
- Department of Experimental Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
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26
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Weykamp M, Nikolian VC, Dennahy IS, Higgins GA, Georgoff PE, Remmer H, Ghandour MH, Alam HB. Rapid valproic acid-induced modulation of the traumatic proteome in a porcine model of traumatic brain injury and hemorrhagic shock. J Surg Res 2018; 228:84-92. [PMID: 29907235 DOI: 10.1016/j.jss.2018.02.046] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 01/10/2018] [Accepted: 02/22/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND Histone deacetylase inhibitors such as valproic acid (VPA) improve survival in lethal models of hemorrhagic shock and polytrauma. Although VPA is known to modulate transcription, its ability to reduce mortality within minutes of administration suggests involvement of a rapid, posttranslational mechanism. We hypothesized that VPA treatment would cause proteomic changes within minutes of treatment including quantitative and/or posttranslational differences in structural and/or effector proteins. MATERIALS AND METHODS We used a porcine model of traumatic brain injury (computer-controlled cortical impact, 12 mm depth) and hemorrhagic shock (40% hemorrhage). Animals were kept in shock for 2 h and randomized to two groups (n = 3): normal saline (volume = 3:1 hemorrhage volume) or normal saline + VPA (150 mg/kg, single dose). Peripheral blood mononuclear cells were collected at baseline, postshock, and postresuscitation. Intracellular protein profiles were assessed using 1 dimensional gel electrophoresis, liquid chromatography, mass spectrometry, and analyzed with Ingenuity Pathway Analysis software. RESULTS Animals treated with VPA demonstrated significant proteomic changes. Quantitative differences were found in over 200 proteins including effector, regulatory, and structural proteins in critical cell signaling pathways. Posttranslational modification analysis demonstrated differential VPA-induced acetylation of lysine residues in histone and nonhistone proteins. Pathway analysis correlated these changes with significant increases in numerous prosurvival and cytoskeletal intracellular pathways, including Rho GTPase signaling (P = 1.66E-11), integrin signaling (P = 4.19E-21), and a decrease in Rho guanosine nucleotide dissociation inhibitor signaling (P = 4.83E-12). CONCLUSIONS In a porcine model of severe injuries, a single dose of VPA is associated with protective changes in the proteome that are measurable within minutes of treatment.
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Affiliation(s)
- Michael Weykamp
- Department of Surgery, University of Michigan Medical School, Ann Arbor, Michigan
| | - Vahagn C Nikolian
- Department of Surgery, University of Michigan Medical School, Ann Arbor, Michigan
| | - Isabel S Dennahy
- Department of Surgery, University of Michigan Medical School, Ann Arbor, Michigan
| | - Gerald A Higgins
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Patrick E Georgoff
- Department of Surgery, University of Michigan Medical School, Ann Arbor, Michigan
| | - Henriette Remmer
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan
| | - Mohamed H Ghandour
- Department of Surgery, University of Michigan Medical School, Ann Arbor, Michigan
| | - Hasan B Alam
- Department of Surgery, University of Michigan Medical School, Ann Arbor, Michigan.
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27
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Abstract
Exciting new technological developments have pushed the boundaries of structural biology, and have enabled studies of biological macromolecules and assemblies that would have been unthinkable not long ago. Yet, the enhanced capabilities of structural biologists to pry into the complex molecular world have also placed new demands on the abilities of protein engineers to reproduce this complexity into the test tube. With this challenge in mind, we review the contents of the modern molecular engineering toolbox that allow the manipulation of proteins in a site-specific and chemically well-defined fashion. Thus, we cover concepts related to the modification of cysteines and other natural amino acids, native chemical ligation, intein and sortase-based approaches, amber suppression, as well as chemical and enzymatic bio-conjugation strategies. We also describe how these tools can be used to aid methodology development in X-ray crystallography, nuclear magnetic resonance, cryo-electron microscopy and in the studies of dynamic interactions. It is our hope that this monograph will inspire structural biologists and protein engineers alike to apply these tools to novel systems, and to enhance and broaden their scope to meet the outstanding challenges in understanding the molecular basis of cellular processes and disease.
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28
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Kim JG, Islam R, Cho JY, Jeong H, Cap KC, Park Y, Hossain AJ, Park JB. Regulation of RhoA GTPase and various transcription factors in the RhoA pathway. J Cell Physiol 2018; 233:6381-6392. [PMID: 29377108 DOI: 10.1002/jcp.26487] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 01/11/2018] [Indexed: 12/11/2022]
Abstract
RhoA GTPase plays a variety of functions in regulation of cytoskeletal proteins, cellular morphology, and migration along with various proliferation and transcriptional activity in cells. RhoA activity is regulated by guanine nucleotide exchange factors (GEFs), GTPase activating proteins (GAPs), and the guanine nucleotide dissociation factor (GDI). The RhoA-RhoGDI complex exists in the cytosol and the active GTP-bound form of RhoA is located to the membrane. GDI displacement factors (GDFs) including IκB kinase γ (IKKγ) dissociate the RhoA-GDI complex, allowing activation of RhoA through GEFs. In addition, modifications of Tyr42 phosphorylation and Cys16/20 oxidation in RhoA and Tyr156 phosphorylation and oxidation of RhoGDI promote the dissociation of the RhoA-RhoGDI complex. The expression of RhoA is regulated through transcriptional factors such as c-Myc, HIF-1α/2α, Stat 6, and NF-κB along with several reported microRNAs. As the role of RhoA in regulating actin-filament formation and myosin-actin interaction has been well described, in this review we focus on the transcriptional activity of RhoA and also the regulation of RhoA message itself. Of interest, in the cytosol, activated RhoA induces transcriptional changes through filamentous actin (F-actin)-dependent ("actin switch") or-independent means. RhoA regulates the activity of several transcription regulators such as serum response factor (SRF)/MAL, AP-1, NF-κB, YAP/TAZ, β-catenin, and hypoxia inducible factor (HIF)-1α. Interestingly, RhoA also itself is localized to the nucleus by an as-yet-undiscovered mechanism.
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Affiliation(s)
- Jae-Gyu Kim
- Department of Biochemistry, Hallym University College of Medicine, Chuncheon, Kangwon-do, Republic of Korea
| | - Rokibul Islam
- Department of Biochemistry, Hallym University College of Medicine, Chuncheon, Kangwon-do, Republic of Korea
| | - Jung Y Cho
- Department of Biochemistry, Hallym University College of Medicine, Chuncheon, Kangwon-do, Republic of Korea.,Department of Biochemistry, Institute of Cell Differentiation and Aging, Hallym University College of Medicine, Chuncheon, Kangwon-do, Republic of Korea
| | - Hwalrim Jeong
- Department of Paediatrics, Chuncheon Sacred Hospital Hallym University, Chuncheon, Kangwon-do, Republic of Korea
| | - Kim-Cuong Cap
- Department of Biochemistry, Hallym University College of Medicine, Chuncheon, Kangwon-do, Republic of Korea
| | - Yohan Park
- Department of Biochemistry, Hallym University College of Medicine, Chuncheon, Kangwon-do, Republic of Korea
| | - Abu J Hossain
- Department of Biochemistry, Hallym University College of Medicine, Chuncheon, Kangwon-do, Republic of Korea.,Department of Biochemistry, Institute of Cell Differentiation and Aging, Hallym University College of Medicine, Chuncheon, Kangwon-do, Republic of Korea
| | - Jae-Bong Park
- Department of Biochemistry, Hallym University College of Medicine, Chuncheon, Kangwon-do, Republic of Korea.,Department of Biochemistry, Institute of Cell Differentiation and Aging, Hallym University College of Medicine, Chuncheon, Kangwon-do, Republic of Korea
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29
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Acevedo A, González-Billault C. Crosstalk between Rac1-mediated actin regulation and ROS production. Free Radic Biol Med 2018; 116:101-113. [PMID: 29330095 DOI: 10.1016/j.freeradbiomed.2018.01.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 01/03/2018] [Accepted: 01/05/2018] [Indexed: 02/08/2023]
Abstract
The small RhoGTPase Rac1 is implicated in a variety of events related to actin cytoskeleton rearrangement. Remarkably, another event that is completely different from those related to actin regulation has the same relevance; the Rac1-mediated production of reactive oxygen species (ROS) through NADPH oxidases (NOX). Each outcome involves different Rac1 downstream effectors; on one hand, events related to the actin cytoskeleton require Rac1 to bind to WAVEs proteins and PAKs that ultimately promote actin branching and turnover, on the other, NOX-derived ROS production demands active Rac1 to be bound to a cytosolic activator of NOX. How Rac1-mediated signaling ends up promoting actin-related events, NOX-derived ROS, or both is poorly understood. Rac1 regulators, including scaffold proteins, are known to exert tight control over its functions. Hence, evidence of Rac1 regulatory events leading to both actin remodeling and NOX-mediated ROS generation are discussed. Moreover, cellular functions linked to physiological and pathological conditions that exhibit crosstalk between Rac1 outcomes are analyzed, while plausible roles in neuronal functions (and dysfunctions) are highlighted. Together, discussed evidence shed light on cellular mechanisms which requires Rac1 to direct either actin- and/or ROS-related events, helping to understand crucial roles of Rac1 dual functionality.
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Affiliation(s)
- Alejandro Acevedo
- FONDAP Geroscience Center for Brain Health and Metabolism, Santiago, Chile.
| | - Christian González-Billault
- FONDAP Geroscience Center for Brain Health and Metabolism, Santiago, Chile; Department of Biology, Faculty of Sciences, Universidad de Chile, 7800024, Chile; The Buck Institute for Research on Aging, Novato, USA.
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30
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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: 9] [Impact Index Per Article: 1.5] [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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31
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Hughes A, Greene NDE, Copp AJ, Galea GL. Valproic acid disrupts the biomechanics of late spinal neural tube closure in mouse embryos. Mech Dev 2017; 149:20-26. [PMID: 29225143 PMCID: PMC5846844 DOI: 10.1016/j.mod.2017.12.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 11/22/2017] [Accepted: 12/06/2017] [Indexed: 01/26/2023]
Abstract
Failure of neural tube closure in the early embryo causes neural tube defects including spina bifida. Spina bifida lesions predominate in the distal spine, particularly after exposure to the anticonvulsant valproic acid (VPA). How VPA specifically disturbs late stages of neural tube closure is unclear, as neurulation is usually viewed as a uniform 'zippering' process along the spine. We recently identified a novel closure site ("Closure 5") which forms at the caudal extremity of the mouse posterior neuropore (PNP) when completion of closure is imminent. Here we investigated whether distal spina bifida in VPA-exposed embryos involves disruption of Closure 5. Exposure of E8.5 mouse embryos to VPA in whole embryo culture had marked embryotoxic effects, whereas toxic effects were less pronounced in more developmentally advanced (E9) embryos. Only 33% of embryos exposed to VPA from E9 to E10.5 achieved PNP closure (control=90%). Short-term (8h) VPA treatment diminished supra-cellular F-actin cables which normally run along the lateral neural folds, and prevented caudal PNP narrowing normally characteristic of Closure 5 formation. Laser ablation of Closure 5 caused rapid neuropore widening. Equivalent ablations of the caudal PNP in VPA treated embryos resulted in significantly less widening, suggesting VPA prevents formation of Closure 5 as a biomechanically active structure. Thus, VPA exposure prevents morphological and biomechanical conversion of the caudal extreme of the PNP during late spinal closure. Closure 5 facilitates neural fold apposition when completion of closure is imminent, such that its disruption in VPA-exposed embryos may lead to distal spina bifida.
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Affiliation(s)
- Amy Hughes
- Developmental Biology of Birth Defects, UCL GOS Institute of Child Health, London, UK
| | - Nicholas D E Greene
- Developmental Biology of Birth Defects, UCL GOS Institute of Child Health, London, UK
| | - Andrew J Copp
- Developmental Biology of Birth Defects, UCL GOS Institute of Child Health, London, UK
| | - Gabriel L Galea
- Developmental Biology of Birth Defects, UCL GOS Institute of Child Health, London, UK.
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32
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Choi EK, Kim JG, Kim HJ, Cho JY, Jeong H, Park Y, Islam R, Cap CK, Park JB. Regulation of RhoA GTPase and novel target proteins for ROCK. Small GTPases 2017; 11:95-102. [PMID: 29199510 DOI: 10.1080/21541248.2017.1364831] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Rho GTPases play significant roles in cellular function and their activity is regulated by guanine nucleotide exchange factors (GEFs) and GTPase activating proteins (GAPs), providing activation and inactivation of these GTPases, respectively. Active GTP-bound form of RhoA activates its effector proteins while the inactive GDP-bound form of RhoA exists in a RhoA-RhoGDI (guanine nucleotide dissociation inhibitor) complex in the cytosol. In particular, IκB kinase γ IKKγ/NF-κB essential modulator (NEMO) plays a role as a GDI displacement factor (GDF) for RhoA activation through binding to RhoA-RhoGDI complex. Meanwhile, prion protein inactivates RhoA despite RhoA/RhoGDI association. Novel target proteins for Rho-associated kinase (ROCK) such as glycogen synthase kinase (GSK)-3β and IKKβ are recently discovered. Here, we elaborate on a post-translationally modified version of RhoA, phosphorylated at Tyr42 and oxidized at Cys16/20. This form of RhoA dissociates from RhoA-RhoGDI complex and activates IKKβ on IKKγ/NEMO, thus providing possibly a critical role for tumourigenesis.
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Affiliation(s)
- Eun-Kyoung Choi
- Ilsong Institute of Life Science, Hallym University, Ahnyang, Gyeonggi-do, South Korea
| | - Jae-Gyu Kim
- Department of Biochemistry, College of Medicine, Hallym University, Chuncheon, Kangwon-do, Republic of Korea
| | - Hee-Jun Kim
- Ilsong Institute of Life Science, Hallym University, Ahnyang, Gyeonggi-do, South Korea.,Department of Biochemistry, College of Medicine, Hallym University, Chuncheon, Kangwon-do, Republic of Korea
| | - Jung-Yoon Cho
- Department of Biochemistry, College of Medicine, Hallym University, Chuncheon, Kangwon-do, Republic of Korea.,Institute of Cell Differentiation and Ageing, College of Medicine, Hallym University, Chuncheon, South Korea
| | - Hwalrim Jeong
- Department of Paediatrics, Chuncheon Sacred Hospital, Hallym University, Chuncheon, Kangwon-do, Republic of Korea
| | - Yohan Park
- Department of Biochemistry, College of Medicine, Hallym University, Chuncheon, Kangwon-do, Republic of Korea
| | - Rokibul Islam
- Department of Biochemistry, College of Medicine, Hallym University, Chuncheon, Kangwon-do, Republic of Korea
| | - Cuong Kim Cap
- Department of Biochemistry, College of Medicine, Hallym University, Chuncheon, Kangwon-do, Republic of Korea
| | - Jae-Bong Park
- Department of Biochemistry, College of Medicine, Hallym University, Chuncheon, Kangwon-do, Republic of Korea.,Institute of Cell Differentiation and Ageing, College of Medicine, Hallym University, Chuncheon, South Korea
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33
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Edler E, Stein M. Recognition and stabilization of geranylgeranylated human Rab5 by the GDP Dissociation Inhibitor (GDI). Small GTPases 2017; 10:227-242. [PMID: 29065764 PMCID: PMC6548291 DOI: 10.1080/21541248.2017.1371268] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The small GTPase Rab5 is the key regulator of early endosomal fusion. It is post-translationally modified by covalent attachment of two geranylgeranyl (GG) chains to adjacent cysteine residues of the C-terminal hypervariable region (HVR). The GDP dissociation inhibitor (GDI) recognizes membrane-associated Rab5(GDP) and serves to release it into the cytoplasm where it is kept in a soluble state. A detailed new structural and dynamic model for human Rab5(GDP) recognition and binding with human GDI at the early endosome membrane and in its dissociated state is presented. In the cytoplasm, the GDI protein accommodates the GG chains in a transient hydrophobic binding pocket. In solution, two different binding modes of the isoprenoid chains inserted into the hydrophobic pocket of the Rab5(GDP):GDI complex can be identified. This equilibrium between the two states helps to stabilize the protein-protein complex in solution. Interprotein contacts between the Rab5 switch regions and characteristic patches of GDI residues from the Rab binding platform (RBP) and the C-terminus coordinating region (CCR) reveal insight on the formation of such a stable complex. GDI binding to membrane-anchored Rab5(GDP) is initially mediated by the solvent accessible switch regions of the Rab-specific RBP. Formation of the membrane-associated Rab5(GDP):GDI complex induces a GDI reorientation to establish additional interactions with the Rab5 HVR. These results allow to devise a detailed structural model for the process of extraction of GG-Rab5(GDP) by GDI from the membrane and the dissociation from targeting factors and effector proteins prior to GDI binding.
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Affiliation(s)
- Eileen Edler
- a Molecular Simulations and Design Group, Max Planck Institute for Dynamics of Complex Technical Systems , Magdeburg , Germany
| | - Matthias Stein
- a Molecular Simulations and Design Group, Max Planck Institute for Dynamics of Complex Technical Systems , Magdeburg , Germany
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34
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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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35
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Shimizu H, Toma-Fukai S, Saijo S, Shimizu N, Kontani K, Katada T, Shimizu T. Structure-based analysis of the guanine nucleotide exchange factor SmgGDS reveals armadillo-repeat motifs and key regions for activity and GTPase binding. J Biol Chem 2017; 292:13441-13448. [PMID: 28630045 PMCID: PMC5555202 DOI: 10.1074/jbc.m117.792556] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 06/14/2017] [Indexed: 01/15/2023] Open
Abstract
Small GTPases are molecular switches that have critical biological roles and are controlled by GTPase-activating proteins and guanine nucleotide exchange factors (GEFs). The smg GDP dissociation stimulator (SmgGDS) protein functions as a GEF for the RhoA and RhoC small GTPases. SmgGDS has various regulatory roles, including small GTPase trafficking and localization and as a molecular chaperone, and interacts with many small GTPases possessing polybasic regions. Two SmgGDS splice variants, SmgGDS-558 and SmgGDS-607, differ in GEF activity and binding affinity for RhoA depending on the lipidation state, but the reasons for these differences are unclear. Here we determined the crystal structure of SmgGDS-558, revealing a fold containing tandem copies of armadillo repeats not present in other GEFs. We also observed that SmgGDS harbors distinct positively and negatively charged regions, both of which play critical roles in binding to RhoA and GEF activity. This is the first report demonstrating a relationship between the molecular function and atomic structure of SmgGDS. Our findings indicate that the two SmgGDS isoforms differ in GTPase binding and GEF activity, depending on the lipidation state, thus providing useful information about the cellular functions of SmgGDS in cells.
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Affiliation(s)
- Hikaru Shimizu
- From the Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Sachiko Toma-Fukai
- From the Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shinya Saijo
- the Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan, and
| | - Nobutaka Shimizu
- the Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan, and
| | - Kenji Kontani
- the Meiji Pharmaceutical University, 2-522-1 Noshio, Kiyose-shi, Tokyo 204-8588, Japan
| | - Toshiaki Katada
- From the Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Toshiyuki Shimizu
- From the Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan,
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36
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The interplay between histone deacetylases and rho kinases is important for cancer and neurodegeneration. Cytokine Growth Factor Rev 2017; 37:29-45. [PMID: 28606734 DOI: 10.1016/j.cytogfr.2017.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 05/18/2017] [Accepted: 05/21/2017] [Indexed: 12/24/2022]
Abstract
Rho associated coiled-coil containing kinases (ROCKs) respond to defined extra- and intracellular stimuli to control cell migration, cell proliferation, and apoptosis. Histone deacetylases (HDACs) are epigenetic modifiers that regulate nuclear and cytoplasmic signaling through the deacetylation of histones and non-histone proteins. ROCK and HDAC functions are important compounds of basic and applied research interests. Recent evidence suggests a physiologically important interplay between HDACs and ROCKs in various cells and organisms. Here we summarize the crosstalk between these enzymatic families and its implications for cancer and neurodegeneration.
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37
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Ngo ATP, Thierheimer MLD, Babur Ö, Rocheleau AD, Huang T, Pang J, Rigg RA, Mitrugno A, Theodorescu D, Burchard J, Nan X, Demir E, McCarty OJT, Aslan JE. Assessment of roles for the Rho-specific guanine nucleotide dissociation inhibitor Ly-GDI in platelet function: a spatial systems approach. Am J Physiol Cell Physiol 2017; 312:C527-C536. [PMID: 28148498 PMCID: PMC5407014 DOI: 10.1152/ajpcell.00274.2016] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 01/25/2017] [Accepted: 01/25/2017] [Indexed: 12/29/2022]
Abstract
On activation at sites of vascular injury, platelets undergo morphological alterations essential to hemostasis via cytoskeletal reorganizations driven by the Rho GTPases Rac1, Cdc42, and RhoA. Here we investigate roles for Rho-specific guanine nucleotide dissociation inhibitor proteins (RhoGDIs) in platelet function. We find that platelets express two RhoGDI family members, RhoGDI and Ly-GDI. Whereas RhoGDI localizes throughout platelets in a granule-like manner, Ly-GDI shows an asymmetric, polarized localization that largely overlaps with Rac1 and Cdc42 as well as microtubules and protein kinase C (PKC) in platelets adherent to fibrinogen. Antibody interference and platelet spreading experiments suggest a specific role for Ly-GDI in platelet function. Intracellular signaling studies based on interactome and pathways analyses also support a regulatory role for Ly-GDI, which is phosphorylated at PKC substrate motifs in a PKC-dependent manner in response to the platelet collagen receptor glycoprotein (GP) VI-specific agonist collagen-related peptide. Additionally, PKC inhibition diffuses the polarized organization of Ly-GDI in spread platelets relative to its colocalization with Rac1 and Cdc42. Together, our results suggest a role for Ly-GDI in the localized regulation of Rho GTPases in platelets and hypothesize a link between the PKC and Rho GTPase signaling systems in platelet function.
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Affiliation(s)
- Anh T P Ngo
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon
| | - Marisa L D Thierheimer
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon.,School of Chemical, Biological and Environmental Engineering, Oregon State University, Corvallis, Oregon; and
| | - Özgün Babur
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon.,Computational Biology Program, Oregon Health & Science University, Portland, Oregon
| | - Anne D Rocheleau
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon
| | - Tao Huang
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon
| | - Jiaqing Pang
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon
| | - Rachel A Rigg
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon
| | - Annachiara Mitrugno
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon
| | - Dan Theodorescu
- Department of Surgery, Department of Pharmacology, and Comprehensive Cancer Center University of Colorado, Aurora, Colorado
| | - Julja Burchard
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon
| | - Xiaolin Nan
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon
| | - Emek Demir
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon.,Computational Biology Program, Oregon Health & Science University, Portland, Oregon
| | - Owen J T McCarty
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon.,Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, Oregon.,Division of Hematology & Medical Oncology, Oregon Health & Science University, Portland, Oregon
| | - Joseph E Aslan
- Knight Cardiovascular Institute, School of Medicine, Oregon Health & Science University, Portland, Oregon;
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38
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Knyphausen P, Lang F, Baldus L, Extra A, Lammers M. Insights into K-Ras 4B regulation by post-translational lysine acetylation. Biol Chem 2016; 397:1071-85. [DOI: 10.1515/hsz-2016-0118] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 05/03/2016] [Indexed: 11/15/2022]
Abstract
Abstract
Ras is a molecular switch cycling between an active, GTP-bound and an inactive, GDP-bound state. Mutations in Ras, mostly affecting the off-switch, are found in many human tumours. Recently, it has been shown that K-Ras 4B is targeted by lysine acetylation at K104. Based on results obtained for an acetylation mimetic Ras mutant (K104Q), it was hypothesised that K104-acetylation might interfere with its oncogenicity by impairing SOS-catalysed guanine-nucleotide exchange. We prepared site-specifically K104-acetylated K-Ras 4B and the corresponding oncogenic mutant protein G12V using the genetic-code expansion concept. We found that SOS-catalysed nucleotide exchange, also of allosterically activated SOS, was neither affected by acetylation of K104 in wildtype K-Ras 4B nor in the G12V mutant, suggesting that glutamine is a poor mimetic for acetylation at this site. In vitro, the lysine-acetyltransferases CBP and p300 were able to acetylate both, wildtype and G12V K-Ras 4B. In addition to K104 we identified further acetylation sites in K-Ras 4B, including K147, within the important G5/SAK-motif. However, the intrinsic and the SOS-catalysed nucleotide exchange was not affected by K147-acetylation of K-Ras 4B. Finally, we show that Sirt2 and HDAC6 do neither deacetylate K-Ras 4B if acetylated at K104 nor if acetylated at K147 in vitro.
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Panten U, Früh E, Reckers K, Rustenbeck I. Acute metabolic amplification of insulin secretion in mouse islets: Role of cytosolic acetyl-CoA. Metabolism 2016; 65:1225-9. [PMID: 27506729 DOI: 10.1016/j.metabol.2016.05.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 04/20/2016] [Accepted: 05/05/2016] [Indexed: 01/10/2023]
Abstract
OBJECTIVE Stimulation of the ß-cell metabolism by glucose and other fuels triggers insulin release by enhancing the mitochondrial ATP production and acutely amplifies the secretory response by increase in mitochondrial export of metabolites. We aimed to narrow down the uniform final reaction steps mediating fuel-induced acute amplification of insulin secretion. MATERIAL/METHODS Insulin secretion and metabolic parameters were measured in isolated mouse islets exposed to the sulfonylurea glipizide in high concentration (closing all ATP-sensitive K(+) channels) during the entire experiment. Fuel-induced effects were examined after treating the islets for one hour with medium devoid of fuels. This experimental design prevented acute amplification, but only when glucose was the sole fuel. RESULTS Strong amplification of insulin secretion by α-ketoisocaproate or glucose combined with α-ketoisovalerate (supplying mitochondrial oxaloacetate) was abolished within 14min after transition to medium devoid of fuels. After transition from medium containing glucose plus α-ketoisovalerate to medium containing solely glucose or α-ketoisovalerate, amplification (strong or weak, respectively) occurred until the end of the experiment. Glucose (alone or combined with α-ketoisovalerate) increased the total acetyl-CoA content as intensely as α-ketoisocaproate. Low concentrations of α-ketoisovalerate or α-ketoisocaproate were sufficient for saturation of acetyl-CoA increase, but caused no or only weak amplification, respectively. No acetyl-CoA increases occurred in the absence of glipizide. CONCLUSIONS Glucose and other fuels regulate acute amplification of insulin secretion by controlling the supply of acetyl-CoA to the ß-cell cytosol. Cytosolic acetyl-CoA does not amplify by serving as substrate for syntheses of metabolic intermediates, but amplifies by acting as substrate for cytosolic protein acetylation.
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Affiliation(s)
- Uwe Panten
- Institute of Pharmacology, Toxicology and Clinical Pharmacy, Technical University of Braunschweig, Mendelssohnstrasse 1, D-38106 Braunschweig, Germany.
| | - Eike Früh
- Institute of Pharmacology, Toxicology and Clinical Pharmacy, Technical University of Braunschweig, Mendelssohnstrasse 1, D-38106 Braunschweig, Germany
| | - Kirstin Reckers
- Institute of Pharmacology, Toxicology and Clinical Pharmacy, Technical University of Braunschweig, Mendelssohnstrasse 1, D-38106 Braunschweig, Germany
| | - Ingo Rustenbeck
- Institute of Pharmacology, Toxicology and Clinical Pharmacy, Technical University of Braunschweig, Mendelssohnstrasse 1, D-38106 Braunschweig, Germany
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40
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Neumann-Staubitz P, Neumann H. The use of unnatural amino acids to study and engineer protein function. Curr Opin Struct Biol 2016; 38:119-28. [DOI: 10.1016/j.sbi.2016.06.006] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 06/02/2016] [Accepted: 06/04/2016] [Indexed: 12/21/2022]
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41
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Knyphausen P, de Boor S, Kuhlmann N, Scislowski L, Extra A, Baldus L, Schacherl M, Baumann U, Neundorf I, Lammers M. Insights into Lysine Deacetylation of Natively Folded Substrate Proteins by Sirtuins. J Biol Chem 2016; 291:14677-94. [PMID: 27226597 DOI: 10.1074/jbc.m116.726307] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Indexed: 11/06/2022] Open
Abstract
Sirtuins are NAD(+)-dependent lysine deacylases, regulating a variety of cellular processes. The nuclear Sirt1, the cytosolic Sirt2, and the mitochondrial Sirt3 are robust deacetylases, whereas the other sirtuins have preferences for longer acyl chains. Most previous studies investigated sirtuin-catalyzed deacylation on peptide substrates only. We used the genetic code expansion concept to produce natively folded, site-specific, and lysine-acetylated Sirt1-3 substrate proteins, namely Ras-related nuclear, p53, PEPCK1, superoxide dismutase, cyclophilin D, and Hsp10, and analyzed the deacetylation reaction. Some acetylated proteins such as Ras-related nuclear, p53, and Hsp10 were robustly deacetylated by Sirt1-3. However, other reported sirtuin substrate proteins such as cyclophilin D, superoxide dismutase, and PEPCK1 were not deacetylated. Using a structural and functional approach, we describe the ability of Sirt1-3 to deacetylate two adjacent acetylated lysine residues. The dynamics of this process have implications for the lifetime of acetyl modifications on di-lysine acetylation sites and thus constitute a new mechanism for the regulation of proteins by acetylation. Our studies support that, besides the primary sequence context, the protein structure is a major determinant of sirtuin substrate specificity.
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Affiliation(s)
- Philipp Knyphausen
- From the Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), Joseph-Stelzmann-Strasse 26, University of Cologne, 50931 Cologne and
| | - Susanne de Boor
- From the Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), Joseph-Stelzmann-Strasse 26, University of Cologne, 50931 Cologne and
| | - Nora Kuhlmann
- From the Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), Joseph-Stelzmann-Strasse 26, University of Cologne, 50931 Cologne and
| | - Lukas Scislowski
- From the Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), Joseph-Stelzmann-Strasse 26, University of Cologne, 50931 Cologne and
| | - Antje Extra
- From the Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), Joseph-Stelzmann-Strasse 26, University of Cologne, 50931 Cologne and
| | - Linda Baldus
- From the Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), Joseph-Stelzmann-Strasse 26, University of Cologne, 50931 Cologne and
| | - Magdalena Schacherl
- the Institute for Biochemistry, Zülpicher Strasse 47b, University of Cologne, 50674 Cologne, Germany
| | - Ulrich Baumann
- the Institute for Biochemistry, Zülpicher Strasse 47b, University of Cologne, 50674 Cologne, Germany
| | - Ines Neundorf
- the Institute for Biochemistry, Zülpicher Strasse 47b, University of Cologne, 50674 Cologne, Germany
| | - Michael Lammers
- From the Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), Joseph-Stelzmann-Strasse 26, University of Cologne, 50931 Cologne and
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Abstract
Rho GTPases regulate cell motility in a large part through control of actin cytoskeletal organization. The activation state of Rho proteins is regulated by a wide variety of guanine nucleotide exchange factors (GEFs) and GTPase activating proteins that are differentially expressed among cell types and disease states. The RhoA specific GEF neuroepithelial transforming gene 1 (Net1) is highly expressed in many cancer cells and stimulates cell motility, invasion and cell spreading in response to a variety of ligands. A key feature of Net1 proteins is that they are sequestered in the nucleus in the absence of a motility stimulus. We have recently found that accumulation of the Net1A isoform outside the nucleus, which is the primary Net1 isoform controlling cell motility, is regulated by its acetylation status. Here, we describe acetylation as a novel mechanism of RhoGEF regulation in cell motility that can be targeted in cancer and metastasis.
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Affiliation(s)
- Arzu Ulu
- a Department of Integrative Biology and Pharmacology , University of Texas Health Science Center at Houston , Houston , TX , USA
| | - Jeffrey A Frost
- a Department of Integrative Biology and Pharmacology , University of Texas Health Science Center at Houston , Houston , TX , USA
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