1
|
Simmons ZR, Sharma S, Wayne J, Li S, Vander Kooi CW, Gentry MS. Generation and characterization of a laforin nanobody inhibitor. Clin Biochem 2021; 93:80-89. [PMID: 33831386 PMCID: PMC8217207 DOI: 10.1016/j.clinbiochem.2021.03.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/05/2021] [Accepted: 03/29/2021] [Indexed: 02/06/2023]
Abstract
OBJECTIVES Mutations in the gene encoding the glycogen phosphatase laforin result in the fatal childhood dementia Lafora disease (LD). A cellular hallmark of LD is cytoplasmic, hyper-phosphorylated, glycogen-like aggregates called Lafora bodies (LBs) that form in nearly all tissues and drive disease progression. Additional tools are needed to define the cellular function of laforin, understand the pathological role of laforin in LD, and determine the role of glycogen phosphate in glycogen metabolism. In this work, we present the generation and characterization of laforin nanobodies, with one being a laforin inhibitor. DESIGN AND METHODS We identify multiple classes of specific laforin-binding nanobodies and determine their binding epitopes using hydrogen deuterium exchange (HDX) mass spectrometry. Using para-nitrophenyl phosphate (pNPP) and a malachite gold-based assay specific for glucan phosphatase activity, we assess the inhibitory effect of one nanobody on laforin's catalytic activity. RESULTS Six families of laforin nanobodies are characterized and their epitopes mapped. One nanobody is identified and characterized that serves as an inhibitor of laforin's phosphatase activity. CONCLUSIONS The six generated and characterized laforin nanobodies, with one being a laforin inhibitor, are an important set of tools that open new avenues to define unresolved glycogen metabolism questions.
Collapse
Affiliation(s)
- Zoe R Simmons
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY 40536, United States
| | - Savita Sharma
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY 40536, United States
| | - Jeremiah Wayne
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY 40536, United States
| | - Sheng Li
- Department of Medicine, University of California at San Diego, La Jolla, CA 92093, United States
| | - Craig W Vander Kooi
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY 40536, United States; Lafora Epilepsy Cure Initiative, University of Kentucky College of Medicine, Lexington, KY 40536, United States
| | - Matthew S Gentry
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY 40536, United States; Lafora Epilepsy Cure Initiative, University of Kentucky College of Medicine, Lexington, KY 40536, United States.
| |
Collapse
|
2
|
Garcia-Gimeno MA, Rodilla-Ramirez PN, Viana R, Salas-Puig X, Brewer MK, Gentry MS, Sanz P. A novel EPM2A mutation yields a slow progression form of Lafora disease. Epilepsy Res 2018; 145:169-177. [PMID: 30041081 DOI: 10.1016/j.eplepsyres.2018.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/11/2018] [Accepted: 07/13/2018] [Indexed: 12/19/2022]
Abstract
Lafora disease (LD, OMIM 254780) is a rare disorder characterized by epilepsy and neurodegeneration leading patients to a vegetative state and death, usually within the first decade from the onset of the first symptoms. In the vast majority of cases LD is related to mutations in either the EPM2A gene (encoding the glucan phosphatase laforin) or the EPM2B gene (encoding the E3-ubiquitin ligase malin). In this work, we characterize the mutations present in the EPM2A gene in a patient displaying a slow progression form of the disease. The patient is compound heterozygous with Y112X and N163D mutations in the corresponding alleles. In primary fibroblasts obtained from the patient, we analyzed the expression of the mutated alleles by quantitative real time PCR and found slightly lower levels of expression of the EPM2A gene respect to control cells. However, by Western blotting we were unable to detect endogenous levels of the protein in crude extracts from patient fibroblasts. The Y112X mutation would render a truncated protein lacking the phosphatase domain and likely degraded. Since minute amounts of laforin-N163D might still play a role in cell physiology, we analyzed the biochemical characteristics of the N163D mutation. We found that recombinant laforin N163D protein was as stable as wild type and exhibited near wild type phosphatase activity towards biologically relevant substrates. On the contrary, it showed a severe impairment in the interaction profile with previously identified laforin binding partners. These results lead us to conclude that the slow progression of the disease present in this patient could be either due to the specific biochemical properties of laforin N163D or to the presence of alternative genetic modifying factors separate from pathogenicity.
Collapse
Affiliation(s)
| | | | - Rosa Viana
- IBV-CSIC. Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Xavier Salas-Puig
- Epilepsy Unit, Neurology Dept., Hospital Vall Hebron, Barcelona, Spain
| | - M Kathryn Brewer
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, USA
| | - Matthew S Gentry
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, USA; Lafora Epilepsy Cure Initiative, USA
| | - Pascual Sanz
- IBV-CSIC. Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain; CIBERER. Centro de Investigación Biomédica en Red de Enfermedades Raras, Valencia, Spain; Lafora Epilepsy Cure Initiative, USA.
| |
Collapse
|
3
|
Yu ZH, Zhang ZY. Regulatory Mechanisms and Novel Therapeutic Targeting Strategies for Protein Tyrosine Phosphatases. Chem Rev 2018; 118:1069-1091. [PMID: 28541680 PMCID: PMC5812791 DOI: 10.1021/acs.chemrev.7b00105] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
An appropriate level of protein phosphorylation on tyrosine is essential for cells to react to extracellular stimuli and maintain cellular homeostasis. Faulty operation of signal pathways mediated by protein tyrosine phosphorylation causes numerous human diseases, which presents enormous opportunities for therapeutic intervention. While the importance of protein tyrosine kinases in orchestrating the tyrosine phosphorylation networks and in target-based drug discovery has long been recognized, the significance of protein tyrosine phosphatases (PTPs) in cellular signaling and disease biology has historically been underappreciated, due to a large extent to an erroneous assumption that they are largely constitutive and housekeeping enzymes. Here, we provide a comprehensive examination of a number of regulatory mechanisms, including redox modulation, allosteric regulation, and protein oligomerization, that control PTP activity. These regulatory mechanisms are integral to the myriad PTP-mediated biochemical events and reinforce the concept that PTPs are indispensable and specific modulators of cellular signaling. We also discuss how disruption of these PTP regulatory mechanisms can cause human diseases and how these diverse regulatory mechanisms can be exploited for novel therapeutic development.
Collapse
Affiliation(s)
- Zhi-Hong Yu
- Department of Medicinal Chemistry and Molecular Pharmacology, Department of Chemistry, Center for Cancer Research, and Institute for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, IN 47907
| | - Zhong-Yin Zhang
- Department of Medicinal Chemistry and Molecular Pharmacology, Department of Chemistry, Center for Cancer Research, and Institute for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, IN 47907
| |
Collapse
|
4
|
Emanuelle S, Brewer MK, Meekins DA, Gentry MS. Unique carbohydrate binding platforms employed by the glucan phosphatases. Cell Mol Life Sci 2016; 73:2765-2778. [PMID: 27147465 PMCID: PMC4920694 DOI: 10.1007/s00018-016-2249-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 04/22/2016] [Indexed: 12/19/2022]
Abstract
Glucan phosphatases are a family of enzymes that are functionally conserved at the enzymatic level in animals and plants. These enzymes bind and dephosphorylate glycogen in animals and starch in plants. While the enzymatic function is conserved, the glucan phosphatases employ distinct mechanisms to bind and dephosphorylate glycogen or starch. The founding member of the family is a bimodular human protein called laforin that is comprised of a carbohydrate binding module 20 (CBM20) followed by a dual specificity phosphatase domain. Plants contain two glucan phosphatases: Starch EXcess4 (SEX4) and Like Sex Four2 (LSF2). SEX4 contains a chloroplast targeting peptide, dual specificity phosphatase (DSP) domain, a CBM45, and a carboxy-terminal motif. LSF2 is comprised of simply a chloroplast targeting peptide, DSP domain, and carboxy-terminal motif. SEX4 employs an integrated DSP-CBM glucan-binding platform to engage and dephosphorylate starch. LSF2 lacks a CBM and instead utilizes two surface binding sites to bind and dephosphorylate starch. Laforin is a dimeric protein in solution and it utilizes a tetramodular architecture and cooperativity to bind and dephosphorylate glycogen. This chapter describes the biological role of glucan phosphatases in glycogen and starch metabolism and compares and contrasts their ability to bind and dephosphorylate glucans.
Collapse
Affiliation(s)
- Shane Emanuelle
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, KY 40536 USA
| | - M. Kathryn Brewer
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, KY 40536 USA
| | - David A. Meekins
- Division of Biology, Kansas State University, Manhattan, KS 66506 USA
| | - Matthew S. Gentry
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, KY 40536 USA
| |
Collapse
|
5
|
Romá-Mateo C, Raththagala M, Gentry MS, Sanz P. Assessing the Biological Activity of the Glucan Phosphatase Laforin. Methods Mol Biol 2016; 1447:107-119. [PMID: 27514803 PMCID: PMC5339740 DOI: 10.1007/978-1-4939-3746-2_7] [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] [Indexed: 06/06/2023]
Abstract
Glucan phosphatases are a recently discovered family of enzymes that dephosphorylate either starch or glycogen and are essential for proper starch metabolism in plants and glycogen metabolism in humans. Mutations in the gene encoding the only human glucan phosphatase, laforin, result in the fatal, neurodegenerative, epilepsy known as Lafora disease. Here, we describe phosphatase assays to assess both generic laforin phosphatase activity and laforin's unique glycogen phosphatase activity.
Collapse
Affiliation(s)
- Carlos Romá-Mateo
- Department of Physiology, School of Medicine and Dentistry, University of Valencia and FIHCUV-INCLIVA, Valencia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Jaime Roig 11, 46010, Valencia, Spain
| | - Madushi Raththagala
- Department of Molecular and Cellular Biochemistry, Center for Structural Biology, University of Kentucky, Lexington, KY, USA
| | - Mathew S Gentry
- Department of Molecular and Cellular Biochemistry, Center for Structural Biology, University of Kentucky, Lexington, KY, USA
| | - Pascual Sanz
- Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Jaime Roig 11, 46010, Valencia, Spain.
| |
Collapse
|
6
|
Liu T, Yang Y, Wang D, Xiao Y, Du G, Wu L, Ding M, Li L, Wu C. Human eukaryotic elongation factor 1A forms oligomers through specific cysteine residues. Acta Biochim Biophys Sin (Shanghai) 2015; 47:1011-7. [PMID: 26515794 DOI: 10.1093/abbs/gmv113] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Accepted: 08/15/2015] [Indexed: 12/29/2022] Open
Abstract
Eukaryotic elongation factor 1A (eEF1A) is a multifunctional protein involved in bundling actin, severing microtubule, activating the phosphoinositol-4 kinase, and recruiting aminoacyl-tRNAs to ribosomes during protein biosynthesis. Although evidence has shown the presence of the isoform eEF1A1 oligomers, the substantial mechanism of the self-association remains unclear. Herein, we found that human eEF1A1 could spontaneously form oligomers. Specifically, mutagenesis screen on cysteine residues demonstrated that Cys(234) was essential for eEF1A1 oligomerization. In addition, we also found that hydrogen peroxide treatment could induce the formation of eEF1A oligomers in cells. By cysteine replacement, eEF1A2 isoform displayed the ability to oligomerize in cells under the oxidative environment. In summary, in this study we characterized eEF1A1 oligomerization and demonstrated that specific cysteine residues are required for this oligomerization activity.
Collapse
Affiliation(s)
- Tao Liu
- School of Life Sciences and Key Laboratory of Bio-Resources and Eco-Environment, Sichuan University, Ministry of Education, Chengdu 610064, China
| | - Yu Yang
- School of Life Sciences and Key Laboratory of Bio-Resources and Eco-Environment, Sichuan University, Ministry of Education, Chengdu 610064, China
| | - Di Wang
- School of Life Sciences and Key Laboratory of Bio-Resources and Eco-Environment, Sichuan University, Ministry of Education, Chengdu 610064, China
| | - Yan Xiao
- School of Life Sciences and Key Laboratory of Bio-Resources and Eco-Environment, Sichuan University, Ministry of Education, Chengdu 610064, China
| | - Guangshi Du
- School of Life Sciences and Key Laboratory of Bio-Resources and Eco-Environment, Sichuan University, Ministry of Education, Chengdu 610064, China
| | - Lei Wu
- School of Life Sciences and Key Laboratory of Bio-Resources and Eco-Environment, Sichuan University, Ministry of Education, Chengdu 610064, China
| | - Muran Ding
- School of Life Sciences and Key Laboratory of Bio-Resources and Eco-Environment, Sichuan University, Ministry of Education, Chengdu 610064, China
| | - Ling Li
- School of Life Sciences and Key Laboratory of Bio-Resources and Eco-Environment, Sichuan University, Ministry of Education, Chengdu 610064, China
| | - Chuanfang Wu
- School of Life Sciences and Key Laboratory of Bio-Resources and Eco-Environment, Sichuan University, Ministry of Education, Chengdu 610064, China
| |
Collapse
|
7
|
Romá-Mateo C, Aguado C, García-Giménez JL, Knecht E, Sanz P, Pallardó FV. Oxidative stress, a new hallmark in the pathophysiology of Lafora progressive myoclonus epilepsy. Free Radic Biol Med 2015; 88:30-41. [PMID: 25680286 DOI: 10.1016/j.freeradbiomed.2015.01.034] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 01/16/2015] [Accepted: 01/28/2015] [Indexed: 12/12/2022]
Abstract
Lafora disease (LD; OMIM 254780, ORPHA501) is a devastating neurodegenerative disorder characterized by the presence of glycogen-like intracellular inclusions called Lafora bodies and caused, in most cases, by mutations in either the EPM2A or the EPM2B gene, encoding respectively laforin, a phosphatase with dual specificity that is involved in the dephosphorylation of glycogen, and malin, an E3-ubiquitin ligase involved in the polyubiquitination of proteins related to glycogen metabolism. Thus, it has been reported that laforin and malin form a functional complex that acts as a key regulator of glycogen metabolism and that also plays a crucial role in protein homeostasis (proteostasis). Regarding this last function, it has been shown that cells are more sensitive to ER stress and show defects in proteasome and autophagy activities in the absence of a functional laforin-malin complex. More recently, we have demonstrated that oxidative stress accompanies these proteostasis defects and that various LD models show an increase in reactive oxygen species and oxidative stress products together with a dysregulated antioxidant enzyme expression and activity. In this review we discuss possible connections between the multiple defects in protein homeostasis present in LD and oxidative stress.
Collapse
Affiliation(s)
- Carlos Romá-Mateo
- Fundación Investigación Clinico de Valencia, Instituto de Investigación Sanitaria, Valencia, Spain; Department of Physiology, School of Medicine and Dentistry, University of Valencia, E46010 Valencia, Spain
| | - Carmen Aguado
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Valencia, Spain; Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - José Luis García-Giménez
- Fundación Investigación Clinico de Valencia, Instituto de Investigación Sanitaria, Valencia, Spain; Department of Physiology, School of Medicine and Dentistry, University of Valencia, E46010 Valencia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras, Valencia, Spain
| | - Erwin Knecht
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Valencia, Spain; Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Pascual Sanz
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Valencia, Spain; Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Federico V Pallardó
- Fundación Investigación Clinico de Valencia, Instituto de Investigación Sanitaria, Valencia, Spain; Department of Physiology, School of Medicine and Dentistry, University of Valencia, E46010 Valencia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras, Valencia, Spain.
| |
Collapse
|
8
|
Sankhala RS, Koksal AC, Ho L, Nitschke F, Minassian BA, Cingolani G. Dimeric quaternary structure of human laforin. J Biol Chem 2015; 290:4552-4559. [PMID: 25538239 PMCID: PMC4335197 DOI: 10.1074/jbc.m114.627406] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 12/17/2014] [Indexed: 01/01/2023] Open
Abstract
The phosphatase laforin removes phosphate groups from glycogen during biosynthetic activity. Loss-of-function mutations in the gene encoding laforin is the predominant cause of Lafora disease, a fatal form of progressive myoclonic epilepsy. Here, we used hybrid structural methods to determine the molecular architecture of human laforin. We found that laforin adopts a dimeric quaternary structure, topologically similar to the prototypical dual specificity phosphatase VH1. The interface between the laforin carbohydrate-binding module and the dual specificity phosphatase domain generates an intimate substrate-binding crevice that allows for recognition and dephosphorylation of phosphomonoesters of glucose. We identify novel molecular determinants in the laforin active site that help decipher the mechanism of glucan phosphatase activity.
Collapse
Affiliation(s)
- Rajeshwer S Sankhala
- From the Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
| | - Adem C Koksal
- the Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
| | - Lan Ho
- From the Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
| | - Felix Nitschke
- the Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada, and
| | - Berge A Minassian
- the Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada, and; the Institute of Medical Sciences, Department of Pediatrics, University of Toronto, Ontario M5S 1A8, Canada
| | - Gino Cingolani
- From the Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107,.
| |
Collapse
|
9
|
Structural mechanism of laforin function in glycogen dephosphorylation and lafora disease. Mol Cell 2014; 57:261-72. [PMID: 25544560 DOI: 10.1016/j.molcel.2014.11.020] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 11/13/2014] [Accepted: 11/18/2014] [Indexed: 01/30/2023]
Abstract
Glycogen is the major mammalian glucose storage cache and is critical for energy homeostasis. Glycogen synthesis in neurons must be tightly controlled due to neuronal sensitivity to perturbations in glycogen metabolism. Lafora disease (LD) is a fatal, congenital, neurodegenerative epilepsy. Mutations in the gene encoding the glycogen phosphatase laforin result in hyperphosphorylated glycogen that forms water-insoluble inclusions called Lafora bodies (LBs). LBs induce neuronal apoptosis and are the causative agent of LD. The mechanism of glycogen dephosphorylation by laforin and dysfunction in LD is unknown. We report the crystal structure of laforin bound to phosphoglucan product, revealing its unique integrated tertiary and quaternary structure. Structure-guided mutagenesis combined with biophysical and biochemical analyses reveal the basis for normal function of laforin in glycogen metabolism. Analyses of LD patient mutations define the mechanism by which subsets of mutations disrupt laforin function. These data provide fundamental insights connecting glycogen metabolism to neurodegenerative disease.
Collapse
|