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      Loss of Catalytically Inactive Lipid Phosphatase Myotubularin-related Protein 12 Impairs Myotubularin Stability and Promotes Centronuclear Myopathy in Zebrafish

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          Abstract

          X-linked myotubular myopathy (XLMTM) is a congenital disorder caused by mutations of the myotubularin gene, MTM1. Myotubularin belongs to a large family of conserved lipid phosphatases that include both catalytically active and inactive myotubularin-related proteins (i.e., “MTMRs”). Biochemically, catalytically inactive MTMRs have been shown to form heteroligomers with active members within the myotubularin family through protein-protein interactions. However, the pathophysiological significance of catalytically inactive MTMRs remains unknown in muscle. By in vitro as well as in vivo studies, we have identified that catalytically inactive myotubularin-related protein 12 (MTMR12) binds to myotubularin in skeletal muscle. Knockdown of the mtmr12 gene in zebrafish resulted in skeletal muscle defects and impaired motor function. Analysis of mtmr12 morphant fish showed pathological changes with central nucleation, disorganized Triads, myofiber hypotrophy and whorled membrane structures similar to those seen in X-linked myotubular myopathy. Biochemical studies showed that deficiency of MTMR12 results in reduced levels of myotubularin protein in zebrafish and mammalian C2C12 cells. Loss of myotubularin also resulted in reduction of MTMR12 protein in C2C12 cells, mice and humans. Moreover, XLMTM mutations within the myotubularin interaction domain disrupted binding to MTMR12 in cell culture. Analysis of human XLMTM patient myotubes showed that mutations that disrupt the interaction between myotubularin and MTMR12 proteins result in reduction of both myotubularin and MTMR12. These studies strongly support the concept that interactions between myotubularin and MTMR12 are required for the stability of their functional protein complex in normal skeletal muscles. This work highlights an important physiological function of catalytically inactive phosphatases in the pathophysiology of myotubular myopathy and suggests a novel therapeutic approach through identification of drugs that could stabilize the myotubularin-MTMR12 complex and hence ameliorate this disorder.

          Author Summary

          Congenital myopathies are a group of heredity diseases characterized by muscle weakness and impaired locomotion that manifest in both children and adults. X-linked myotubular myopathy (XLMTM) is a subtype of congenital myopathy that predominantly affects males and is caused by mutations in the myotubularin ( MTM1) gene. To date, more than 200 pathogenic mutations have been identified in MTM1. However, no effective therapy is available to treat patients presenting with XLMTM. This is largely due to a lack of understanding of molecular processes perturbed in the XLMTM disease state, thereby limiting the availability of suitable therapeutic targets. In this study, we show that catalytically inactive MTMR12 interacts with myotubularin in skeletal muscle. This complex formation is required to provide stability to myotubularin in the normal functioning of skeletal muscle and these interactions appear to be disrupted in XLMTM. This work therefore offers a novel direction for therapy development, both in XLMTM and other genetic diseases, by identifying crucial protein interactors of disease-causing proteins whose complexes might be stabilized in the disease state to restore normal function.

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          Most cited references35

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          Predicting disease genes using protein-protein interactions.

          The responsible genes have not yet been identified for many genetically mapped disease loci. Physically interacting proteins tend to be involved in the same cellular process, and mutations in their genes may lead to similar disease phenotypes. To investigate whether protein-protein interactions can predict genes for genetically heterogeneous diseases. 72,940 protein-protein interactions between 10,894 human proteins were used to search 432 loci for candidate disease genes representing 383 genetically heterogeneous hereditary diseases. For each disease, the protein interaction partners of its known causative genes were compared with the disease associated loci lacking identified causative genes. Interaction partners located within such loci were considered candidate disease gene predictions. Prediction accuracy was tested using a benchmark set of known disease genes. Almost 300 candidate disease gene predictions were made. Some of these have since been confirmed. On average, 10% or more are expected to be genuine disease genes, representing a 10-fold enrichment compared with positional information only. Examples of interesting candidates are AKAP6 for arrythmogenic right ventricular dysplasia 3 and SYN3 for familial partial epilepsy with variable foci. Exploiting protein-protein interactions can greatly increase the likelihood of finding positional candidate disease genes. When applied on a large scale they can lead to novel candidate gene predictions.
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            A gene mutated in X-linked myotubular myopathy defines a new putative tyrosine phosphatase family conserved in yeast.

            X-linked recessive myotubular myopathy (MTM1) is characterized by severe hypotonia and generalized muscle weakness, with impaired maturation of muscle fibres. We have restricted the candidate region to 280 kb and characterized two candidate genes using positional cloning strategies. The presence of frameshift or missense mutations (of which two are new mutations) in seven patients proved that one of these genes is indeed implicated in MTM1. The protein encoded by the MTM1 gene is highly conserved in yeast, which is surprising for a muscle specific disease. The protein contains the consensus sequence for the active site of tyrosine phosphatases, a wide class of proteins involved in signal transduction. At least three other genes, one located within 100 kb distal from the MTM1 gene, encode proteins with very high sequence similarities and define, together with the MTM1 gene, a new family of putative tyrosine phosphatases in man.
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              Charcot-Marie-Tooth type 4B is caused by mutations in the gene encoding myotubularin-related protein-2.

              A gene mutated in Charcot-Marie-Tooth disease type 4B (CMT4B), an autosomal recessive demyelinating neuropathy with myelin outfoldings, has been mapped on chromosome 11q22. Using a positional-cloning strategy, we identified in unrelated CMT4B patients mutations occurring in the gene MTMR2, encoding myotubularin-related protein-2, a dual specificity phosphatase (DSP).
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS Genet
                PLoS Genet
                plos
                plosgen
                PLoS Genetics
                Public Library of Science (San Francisco, USA )
                1553-7390
                1553-7404
                June 2013
                June 2013
                20 June 2013
                : 9
                : 6
                : e1003583
                Affiliations
                [1 ]Genomics Program and Division of Genetics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
                [2 ]Department of Translational Medicine and Neurogenetics, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Inserm U964, CNRS UMR7104, Université de Strasbourg, Collège de France, Chaire de Génétique Humaine, Illkirch, France
                The Jackson Laboratory, United States of America
                Author notes

                The authors have declared that no competing interests exist.

                Conceived and designed the experiments: VAG KH JL AHB. Performed the experiments: VAG KH LLS SRG JEM LA JS JRB EAT NEG. Analyzed the data: VAG KH JL AHB. Wrote the paper: VAG AHB.

                Article
                PGENETICS-D-12-03175
                10.1371/journal.pgen.1003583
                3688503
                23818870
                930b3c80-8ffe-4d83-807b-597b5aad3810
                Copyright @ 2013

                This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 20 December 2012
                : 7 May 2013
                Page count
                Pages: 16
                Funding
                This work was supported by the Muscular Dystrophy Association (MDA201302 to AHB and MDA186985 to JL); National Institutes of Health grant from the National Institute of Arthritis and Musculoskeletal and Skin Diseases R01 AR044345; P50 NS040828; by the Joshua Frase Foundation; and the William Randolph Hearst Fund, by grants from Institut National de la Santé et de la Recherche Médicale (INSERM); Centre National de la Recherche Scientifique (CNRS); University of Strasbourg (UdS); ERA-NET E-rare program; and Association Française contre les Myopathies (AFM). VAG is supported by K01 AR062601 from the National Institute of Arthritis and Musculoskeletal and Skin Diseases and LLS is supported by F31 NS081928 from the National Institute of Neurological Disorders and Stroke of National Institutes of Health. LA was supported in part by a Region Alsace fellowship. DNA sequencing was performed by the Boston Children's Hospital Molecular Genetics Core supported in part by National Institute of Child Health and Human Development grant P30 HD18655. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.
                Categories
                Research Article
                Biology
                Medicine

                Genetics
                Genetics

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