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Dai N, Groenendyk J, Michalak M. Interplay between myotubularins and Ca 2+ homeostasis. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119739. [PMID: 38710289 DOI: 10.1016/j.bbamcr.2024.119739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 05/08/2024]
Abstract
The myotubularin family, encompassing myotubularin 1 (MTM1) and 14 myotubularin-related proteins (MTMRs), represents a conserved group of phosphatases featuring a protein tyrosine phosphatase domain. Nine members are characterized by an active phosphatase domain C(X)5R, dephosphorylating the D3 position of PtdIns(3)P and PtdIns(3,5)P2. Mutations in myotubularin genes result in human myopathies, and several neuropathies including X-linked myotubular myopathy and Charcot-Marie-Tooth type 4B. MTM1, MTMR6 and MTMR14 also contribute to Ca2+ signaling and Ca2+ homeostasis that play a key role in many MTM-dependent myopathies and neuropathies. Here we explore the evolving roles of MTM1/MTMRs, unveiling their influence on critical aspects of Ca2+ signaling pathways.
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Affiliation(s)
- Ning Dai
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Jody Groenendyk
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Marek Michalak
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.
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2
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Lin M, Chen Y, Xia S, He Z, Yu X, Huang L, Lin S, Liang B, Huang Z, Mei S, Liu D, Zheng L, Luo Y. Integrative profiling of extrachromosomal circular DNA in placenta and maternal plasma provides insights into the biology of fetal growth restriction and reveals potential biomarkers. Front Genet 2023; 14:1128082. [PMID: 37476414 PMCID: PMC10354665 DOI: 10.3389/fgene.2023.1128082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 02/24/2023] [Indexed: 07/22/2023] Open
Abstract
Introduction: Fetal growth restriction (FGR) is a placenta-mediated pregnancy complication that predisposes fetuses to perinatal complications. Maternal plasma cell-free DNA harbors DNA originating from placental trophoblasts, which is promising for the prenatal diagnosis and prediction of pregnancy complications. Extrachromosomal circular DNA (eccDNA) is emerging as an ideal biomarker and target for several diseases. Methods: We utilized eccDNA sequencing and bioinformatic pipeline to investigate the characteristics and associations of eccDNA in placenta and maternal plasma, the role of placental eccDNA in the pathogenesis of FGR, and potential plasma eccDNA biomarkers of FGR. Results: Using our bioinformatics pipelines, we identified multi-chromosomal-fragment and single-fragment eccDNA in placenta, but almost exclusively single-fragment eccDNA in maternal plasma. Relative to that in plasma, eccDNA in placenta was larger and substantially more abundant in exons, untranslated regions, promoters, repetitive elements [short interspersed nuclear elements (SINEs)/Alu, SINEs/mammalian-wide interspersed repeats, long terminal repeats/endogenous retrovirus-like elements, and single recognition particle RNA], and transcription factor binding motifs. Placental multi-chromosomal-fragment eccDNA was enriched in confident enhancer regions predicted to pertain to genes in apoptosis, energy, cell growth, and autophagy pathways. Placental eccDNA-associated genes whose abundance differed between the FGR and control groups were associated with immunity-related gene ontology (GO) terms. The combined analysis of plasma and placental eccDNA-associated genes in the FGR and control groups led to the identification of potential biomarkers that were assigned to the GO terms of the epigenetic regulation of gene expression and nutrient-related processes, respectively. Conclusion: Together, our results highlight links between placenta functions and multi-chromosomal-fragment and single-fragment eccDNA. The integrative analysis of placental and plasma eccDNA confirmed the potential of these molecules as disease-specific biomarkers of FGR.
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Affiliation(s)
- Minhuan Lin
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yiqing Chen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Shuting Xia
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Zhiming He
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xuegao Yu
- Clinical Laboratory, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Linhuan Huang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Shaobin Lin
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Binrun Liang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ziliang Huang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shiqiang Mei
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Dong Liu
- Clinical Laboratory, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Lingling Zheng
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yanmin Luo
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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3
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Volpatti JR, Ghahramani-Seno MM, Mansat M, Sabha N, Sarikaya E, Goodman SJ, Chater-Diehl E, Celik A, Pannia E, Froment C, Combes-Soia L, Maani N, Yuki KE, Chicanne G, Uusküla-Reimand L, Monis S, Alvi SA, Genetti CA, Payrastre B, Beggs AH, Bonnemann CG, Muntoni F, Wilson MD, Weksberg R, Viaud J, Dowling JJ. X-linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition. Acta Neuropathol 2022; 144:537-563. [PMID: 35844027 PMCID: PMC9381459 DOI: 10.1007/s00401-022-02468-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 07/04/2022] [Accepted: 07/04/2022] [Indexed: 12/29/2022]
Abstract
X-linked myotubular myopathy (XLMTM) is a fatal neuromuscular disorder caused by loss of function mutations in MTM1. At present, there are no directed therapies for XLMTM, and incomplete understanding of disease pathomechanisms. To address these knowledge gaps, we performed a drug screen in mtm1 mutant zebrafish and identified four positive hits, including valproic acid, which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model, and showed that valproic acid ameliorates the murine phenotype. These observations led us to interrogate the epigenome in Mtm1 knockout mice; we found increased DNA methylation, which is normalized with valproic acid, and likely mediated through aberrant 1-carbon metabolism. Finally, we made the unexpected observation that XLMTM patients share a distinct DNA methylation signature, suggesting that epigenetic alteration is a conserved disease feature amenable to therapeutic intervention.
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MESH Headings
- Animals
- Disease Models, Animal
- Epigenesis, Genetic
- Mice
- Muscle, Skeletal/metabolism
- Myopathies, Structural, Congenital/drug therapy
- Myopathies, Structural, Congenital/genetics
- Myopathies, Structural, Congenital/metabolism
- Protein Tyrosine Phosphatases, Non-Receptor/genetics
- Protein Tyrosine Phosphatases, Non-Receptor/metabolism
- Valproic Acid/metabolism
- Valproic Acid/pharmacology
- Zebrafish/metabolism
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Affiliation(s)
- Jonathan R Volpatti
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A1, Canada
- Program for Genetics and Genome Biology, The Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 0A4, Canada
| | - Mehdi M Ghahramani-Seno
- Program for Genetics and Genome Biology, The Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 0A4, Canada
| | - Mélanie Mansat
- Institute of Cardiovascular and Metabolic Diseases (I2MC), INSERM, UMR-S U1297 and University of Toulouse III, CHU-Rangueil, Toulouse, France
| | - Nesrin Sabha
- Program for Genetics and Genome Biology, The Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 0A4, Canada
| | - Ege Sarikaya
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A1, Canada
- Program for Genetics and Genome Biology, The Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 0A4, Canada
| | - Sarah J Goodman
- Program for Genetics and Genome Biology, The Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 0A4, Canada
- Institute of Medical Sciences, University of Toronto, Toronto, ON, M5S 1A1, Canada
| | - Eric Chater-Diehl
- Program for Genetics and Genome Biology, The Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 0A4, Canada
| | - Alper Celik
- Program for Genetics and Genome Biology, The Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 0A4, Canada
| | - Emanuela Pannia
- Program for Genetics and Genome Biology, The Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 0A4, Canada
| | - Carine Froment
- Institut de Pharmacologie Et Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Lucie Combes-Soia
- Institut de Pharmacologie Et Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Nika Maani
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A1, Canada
- Program for Genetics and Genome Biology, The Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 0A4, Canada
| | - Kyoko E Yuki
- Program for Genetics and Genome Biology, The Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 0A4, Canada
| | - Gaëtan Chicanne
- Institute of Cardiovascular and Metabolic Diseases (I2MC), INSERM, UMR-S U1297 and University of Toulouse III, CHU-Rangueil, Toulouse, France
| | - Liis Uusküla-Reimand
- Program for Genetics and Genome Biology, The Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 0A4, Canada
| | - Simon Monis
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A1, Canada
- Program for Genetics and Genome Biology, The Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 0A4, Canada
| | - Sana Akhtar Alvi
- Program for Genetics and Genome Biology, The Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 0A4, Canada
| | - Casie A Genetti
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Bernard Payrastre
- Institute of Cardiovascular and Metabolic Diseases (I2MC), INSERM, UMR-S U1297 and University of Toulouse III, CHU-Rangueil, Toulouse, France
- Laboratoire d'Hématologie, Centre Hospitalier Universitaire (CHU) de Toulouse, Toulouse Cedex, France
| | - Alan H Beggs
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Carsten G Bonnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, NINDS, NIH, Bethesda, MD, USA
| | - Francesco Muntoni
- Dubowitz Neuromuscular Centre, NIHR Great Ormond Street Hospital Biomedical Research Centre, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Michael D Wilson
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A1, Canada
- Program for Genetics and Genome Biology, The Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 0A4, Canada
- Program for Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Rosanna Weksberg
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A1, Canada
- Program for Genetics and Genome Biology, The Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 0A4, Canada
- Department of Paediatrics, University of Toronto, Toronto, ON, M5S 1A1, Canada
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Julien Viaud
- Institute of Cardiovascular and Metabolic Diseases (I2MC), INSERM, UMR-S U1297 and University of Toulouse III, CHU-Rangueil, Toulouse, France
| | - James J Dowling
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A1, Canada.
- Program for Genetics and Genome Biology, The Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 0A4, Canada.
- Department of Paediatrics, University of Toronto, Toronto, ON, M5S 1A1, Canada.
- Division of Neurology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.
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4
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Chua JP, Bedi K, Paulsen MT, Ljungman M, Tank EMH, Kim ES, McBride JP, Colón-Mercado JM, Ward ME, Weisman LS, Barmada SJ. Myotubularin-related phosphatase 5 is a critical determinant of autophagy in neurons. Curr Biol 2022; 32:2581-2595.e6. [PMID: 35580604 PMCID: PMC9233098 DOI: 10.1016/j.cub.2022.04.053] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 02/18/2022] [Accepted: 04/20/2022] [Indexed: 12/12/2022]
Abstract
Autophagy is a conserved, multi-step process of capturing proteolytic cargo in autophagosomes for lysosome degradation. The capacity to remove toxic proteins that accumulate in neurodegenerative disorders attests to the disease-modifying potential of the autophagy pathway. However, neurons respond only marginally to conventional methods for inducing autophagy, limiting efforts to develop therapeutic autophagy modulators for neurodegenerative diseases. The determinants underlying poor autophagy induction in neurons and the degree to which neurons and other cell types are differentially sensitive to autophagy stimuli are incompletely defined. Accordingly, we sampled nascent transcript synthesis and stabilities in fibroblasts, induced pluripotent stem cells (iPSCs), and iPSC-derived neurons (iNeurons), thereby uncovering a neuron-specific stability of transcripts encoding myotubularin-related phosphatase 5 (MTMR5). MTMR5 is an autophagy suppressor that acts with its binding partner, MTMR2, to dephosphorylate phosphoinositides critical for autophagy initiation and autophagosome maturation. We found that MTMR5 is necessary and sufficient to suppress autophagy in iNeurons and undifferentiated iPSCs. Using optical pulse labeling to visualize the turnover of endogenously encoded proteins in live cells, we observed that knockdown of MTMR5 or MTMR2, but not the unrelated phosphatase MTMR9, significantly enhances neuronal degradation of TDP-43, an autophagy substrate implicated in several neurodegenerative diseases. Our findings thus establish a regulatory mechanism of autophagy intrinsic to neurons and targetable for clearing disease-related proteins in a cell-type-specific manner. In so doing, our results not only unravel novel aspects of neuronal biology and proteostasis but also elucidate a strategy for modulating neuronal autophagy that could be of high therapeutic potential for multiple neurodegenerative diseases.
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Affiliation(s)
- Jason P. Chua
- Department of Neurology, Johns Hopkins Medicine, Baltimore, MD, USA
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Lead contact
| | - Karan Bedi
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Michelle T. Paulsen
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, USA
| | - Mats Ljungman
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, USA
| | | | - Erin S. Kim
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
| | - Jonathon P. McBride
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
- Medical Scientist Training Program, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - Michael E. Ward
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Lois S. Weisman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Sami J. Barmada
- Department of Neurology, University of Michigan, Ann Arbor, MI, USA
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5
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Gómez-Oca R, Cowling BS, Laporte J. Common Pathogenic Mechanisms in Centronuclear and Myotubular Myopathies and Latest Treatment Advances. Int J Mol Sci 2021; 22:11377. [PMID: 34768808 PMCID: PMC8583656 DOI: 10.3390/ijms222111377] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 10/18/2021] [Indexed: 01/18/2023] Open
Abstract
Centronuclear myopathies (CNM) are rare congenital disorders characterized by muscle weakness and structural defects including fiber hypotrophy and organelle mispositioning. The main CNM forms are caused by mutations in: the MTM1 gene encoding the phosphoinositide phosphatase myotubularin (myotubular myopathy), the DNM2 gene encoding the mechanoenzyme dynamin 2, the BIN1 gene encoding the membrane curvature sensing amphiphysin 2, and the RYR1 gene encoding the skeletal muscle calcium release channel/ryanodine receptor. MTM1, BIN1, and DNM2 proteins are involved in membrane remodeling and trafficking, while RyR1 directly regulates excitation-contraction coupling (ECC). Several CNM animal models have been generated or identified, which confirm shared pathological anomalies in T-tubule remodeling, ECC, organelle mispositioning, protein homeostasis, neuromuscular junction, and muscle regeneration. Dynamin 2 plays a crucial role in CNM physiopathology and has been validated as a common therapeutic target for three CNM forms. Indeed, the promising results in preclinical models set up the basis for ongoing clinical trials. Another two clinical trials to treat myotubular myopathy by MTM1 gene therapy or tamoxifen repurposing are also ongoing. Here, we review the contribution of the different CNM models to understanding physiopathology and therapy development with a focus on the commonly dysregulated pathways and current therapeutic targets.
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Affiliation(s)
- Raquel Gómez-Oca
- Department of Translational Medicine and Neurogenetics, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France;
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67400 Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR7104, 67400 Illkirch, France
- Strasbourg University, 67081 Strasbourg, France
- Dynacure, 67400 Illkirch, France;
| | | | - Jocelyn Laporte
- Department of Translational Medicine and Neurogenetics, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France;
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67400 Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR7104, 67400 Illkirch, France
- Strasbourg University, 67081 Strasbourg, France
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6
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Horn RL, Kamphaus C, Murdoch K, Narum SR. Detecting genomic variation underlying phenotypic characteristics of reintroduced Coho salmon (Oncorhynchus kisutch). CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01307-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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7
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Wu SY, Tong XL, Li CL, Ding X, Zhang ZL, Fang CY, Tan D, Hu H, Liu H, Dai FY. BmBlimp-1 gene encoding a C2H2 zinc finger protein is required for wing development in the silkworm Bombyx mori. Int J Biol Sci 2019; 15:2664-2675. [PMID: 31754338 PMCID: PMC6854374 DOI: 10.7150/ijbs.34743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 07/28/2019] [Indexed: 11/05/2022] Open
Abstract
Cys2-His2 zinc finger (C2H2-ZF) proteins represent the most common class of transcription factors. These factors have great potential for the management of developmental progression by regulating the specific spatiotemporal expression of genes. In this study, we cloned one C2H2-ZF protein gene of Bombyx mori, BGIBMGA000319, that is orthologous to B-lymphocyte-induced maturation protein-1 (Blimp-1); we thus named it as Bombyx mori Blimp-1 (BmBlimp-1). In the silkworm, the BmBlimp-1 gene is specifically upregulated during day 2 of the pupal to adult stage and is highly expressed in wing discs on day 3 of the pupa. Knockdown of its expression level in the pupal stage results in a crumpled-winged silkworm moth. Using the predicted DNA-binding sequences of BmBlimp-1 to search the silkworm genome to screen target genes of BmBlimp-1, 7049 genes were identified to have at least one binding site of BmBlimp-1 on their 1 kb upstream and downstream genome regions. Comparisons of those genes with a reported pupal wing disc transcriptome data resulted in 4065 overlapping genes being retrieved. GO enrichment analysis of the overlapping genes showed that most of the genes were enriched in the binding term. Combining functional annotation and real-time quantitative PCR, 15 genes were identified as the candidate target genes of BmBlimp-1, including several wing cuticular protein genes, chitin synthase A, and wing disc development genes, such as Wnt1, cubitus interruptus (ci) and engrailed (en). Moreover, the amino acid sequence of the zinc finger motif of Blimp-1 gene was highly conserved among the 15 insect species. We propose that BmBlimp-1 is an important regulatory factor in silkworm wing development.
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Affiliation(s)
- Song-Yuan Wu
- State Key Laboratory of Silkworm Genome Biology; Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs; College of Biotechnology, Southwest University, Chongqing 400715, China.,College of Plant Protection, Southwest University, Chongqing 400716, China
| | - Xiao-Ling Tong
- State Key Laboratory of Silkworm Genome Biology; Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs; College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Chun-Lin Li
- State Key Laboratory of Silkworm Genome Biology; Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs; College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Xin Ding
- State Key Laboratory of Silkworm Genome Biology; Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs; College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Zhu-Lin Zhang
- State Key Laboratory of Silkworm Genome Biology; Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs; College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Chun-Yan Fang
- State Key Laboratory of Silkworm Genome Biology; Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs; College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Duan Tan
- State Key Laboratory of Silkworm Genome Biology; Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs; College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Hai Hu
- State Key Laboratory of Silkworm Genome Biology; Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs; College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Huai Liu
- College of Plant Protection, Southwest University, Chongqing 400716, China
| | - Fang-Yin Dai
- State Key Laboratory of Silkworm Genome Biology; Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs; College of Biotechnology, Southwest University, Chongqing 400715, China
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8
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Frey S, Eichler A, Stonawski V, Kriebel J, Wahl S, Gallati S, Goecke TW, Fasching PA, Beckmann MW, Kratz O, Moll GH, Heinrich H, Kornhuber J, Golub Y. Prenatal Alcohol Exposure Is Associated With Adverse Cognitive Effects and Distinct Whole-Genome DNA Methylation Patterns in Primary School Children. Front Behav Neurosci 2018; 12:125. [PMID: 29997484 PMCID: PMC6028559 DOI: 10.3389/fnbeh.2018.00125] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 06/06/2018] [Indexed: 12/22/2022] Open
Abstract
Prenatal alcohol exposure (PAE) is known to elicit a broad range of systemic effects, including neurophysiological alterations that result in adverse behavioral and cognitive outcomes. However, molecular pathways underlying these long-term intrauterine effects remain to be investigated. Here, we tested a hypothesis that PAE may lead to epigenetic alterations to the DNA resulting in attentional and cognitive alterations of the children. We report the results of the study that included 156 primary school children of the Franconian Cognition and Emotion Studies (FRANCES) cohort which were tested for an objective marker of PAE, ethyl glucuronide (EtG) in meconium at birth. Thirty-two newborns were found to be exposed to alcohol with EtG values above 30 ng/g (EtG+). Previously we described PAE being associated with lower IQ and smaller amplitude of the event-related potential component P3 in go trials (Go-P3), which indicates a reduced capacity of attentional resources. Whole-genome methylation analysis of the buccal cell DNA revealed 193 differentially methylated genes in children with positive meconium EtG, that were clustered into groups involved in epigenetic modifications, neurodegeneration, neurodevelopment, axon guidance and neuronal excitability. Furthermore, we detected mediation effects of the methylation changes in DPP10 and SLC16A9 genes on the EtG related cognitive and attention-related deficits. Our results suggest that system-wide epigenetic changes are involved in long-term effects of PAE. In particular, we show an epigenetic mediation of PAE effects on cognition and attention-related processes.
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Affiliation(s)
- Stefan Frey
- Department of Child and Adolescent Mental Health, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Anna Eichler
- Department of Child and Adolescent Mental Health, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Valeska Stonawski
- Department of Child and Adolescent Mental Health, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Jennifer Kriebel
- Research Unit of Molecular Epidemiology, German Research Center for Environmental Health - Institute of Epidemiology II, Helmholtz Zentrum München, Munich, Germany
| | - Simone Wahl
- Research Unit of Molecular Epidemiology, German Research Center for Environmental Health - Institute of Epidemiology II, Helmholtz Zentrum München, Munich, Germany
| | - Sabina Gallati
- Division of Human Genetics, Department of Paediatrics, Inselspital University of Bern, Bern, Switzerland
| | - Tamme W Goecke
- Department of Obstetrics and Gynecology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany.,Department of Obstetrics and Gynecology, RWTH Aachen University, Aachen, Germany
| | - Peter A Fasching
- Department of Obstetrics and Gynecology, RWTH Aachen University, Aachen, Germany
| | - Matthias W Beckmann
- Department of Obstetrics and Gynecology, RWTH Aachen University, Aachen, Germany
| | - Oliver Kratz
- Department of Child and Adolescent Mental Health, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Gunther H Moll
- Department of Child and Adolescent Mental Health, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Hartmut Heinrich
- Department of Child and Adolescent Mental Health, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany.,kbo-Heckscher-Klinikum, Munich, Germany
| | - Johannes Kornhuber
- Department of Psychiatry and Psychotherapy, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Yulia Golub
- Department of Child and Adolescent Mental Health, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany.,Department of Child and Adolescent Psychiatry, Faculty of Medicine of the TU Dresden, Dresden, Germany
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9
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Aguti S, Malerba A, Zhou H. The progress of AAV-mediated gene therapy in neuromuscular disorders. Expert Opin Biol Ther 2018; 18:681-693. [DOI: 10.1080/14712598.2018.1479739] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Sara Aguti
- The Dubowitz Neuromuscular Centre, Developmental Neurosciences Programme, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Alberto Malerba
- School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey, UK
| | - Haiyan Zhou
- The Dubowitz Neuromuscular Centre, Developmental Neurosciences Programme, Great Ormond Street Institute of Child Health, University College London, London, UK
- Genetics and Genomic Medicine Programme, Great Ormond Street Institute of Child Health, University College London, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, London, UK
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10
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Abstract
Modern genomics has shed light on many entomopathogenic fungi and expanded our knowledge widely; however, little is known about the genomic features of the insect-commensal fungi. Harpellales are obligate commensals living in the digestive tracts of disease-bearing insects (black flies, midges, and mosquitoes). In this study, we produced and annotated whole-genome sequences of nine Harpellales taxa and conducted the first comparative analyses to infer the genomic diversity within the members of the Harpellales. The genomes of the insect gut fungi feature low (26% to 37%) GC content and large genome size variations (25 to 102 Mb). Further comparisons with insect-pathogenic fungi (from both Ascomycota and Zoopagomycota), as well as with free-living relatives (as negative controls), helped to identify a gene toolbox that is essential to the fungus-insect symbiosis. The results not only narrow the genomic scope of fungus-insect interactions from several thousands to eight core players but also distinguish host invasion strategies employed by insect pathogens and commensals. The genomic content suggests that insect commensal fungi rely mostly on adhesion protein anchors that target digestive system, while entomopathogenic fungi have higher numbers of transmembrane helices, signal peptides, and pathogen-host interaction (PHI) genes across the whole genome and enrich genes as well as functional domains to inactivate the host inflammation system and suppress the host defense. Phylogenomic analyses have revealed that genome sizes of Harpellales fungi vary among lineages with an integer-multiple pattern, which implies that ancient genome duplications may have occurred within the gut of insects. Insect guts harbor various microbes that are important for host digestion, immune response, and disease dispersal in certain cases. Bacteria, which are among the primary endosymbionts, have been studied extensively. However, fungi, which are also frequently encountered, are poorly known with respect to their biology within the insect guts. To understand the genomic features and related biology, we produced the whole-genome sequences of nine gut commensal fungi from disease-bearing insects (black flies, midges, and mosquitoes). The results show that insect gut fungi tend to have low GC content across their genomes. By comparing these commensals with entomopathogenic and free-living fungi that have available genome sequences, we found a universal core gene toolbox that is unique and thus potentially important for the insect-fungus symbiosis. This comparative work also uncovered different host invasion strategies employed by insect pathogens and commensals, as well as a model system to study ancient fungal genome duplication within the gut of insects.
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11
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Piao L, Nakakido M, Suzuki T, Dohmae N, Nakamura Y, Hamamoto R. Automethylation of SUV39H2, an oncogenic histone lysine methyltransferase, regulates its binding affinity to substrate proteins. Oncotarget 2017; 7:22846-56. [PMID: 26988914 PMCID: PMC5008405 DOI: 10.18632/oncotarget.8072] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 02/25/2016] [Indexed: 12/14/2022] Open
Abstract
We previously reported that the histone lysine methyltransferase SUV39H2, which is overexpressed in various types of human cancer, plays a critical role in the DNA repair after double strand breakage, and possesses oncogenic activity. Although its biological significance in tumorigenesis has been elucidated, the regulatory mechanism of SUV39H2 activity through post-translational modification is not well known. In this study, we demonstrate in vitro and in vivo automethylation of SUV39H2 at lysine 392. Automethylation of SUV39H2 led to impairment of its binding affinity to substrate proteins such as histone H3 and LSD1. Furthermore, we observed that hyper-automethylated SUV39H2 reduced methylation activities to substrates through affecting the binding affinity to substrate proteins. Our finding unveils a novel autoregulatory mechanism of SUV39H2 through lysine automethylation.
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Affiliation(s)
- Lianhua Piao
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Makoto Nakakido
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Yusuke Nakamura
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Ryuji Hamamoto
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA.,Division of Molecular Modification and Cancer Biology, National Cancer Center, Chuo-ku, Tokyo 104-0045, Japan
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12
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Sun M, Jia B, Yang J, Cui N, Zhu Y, Sun X. Genome-Wide Identification of the PHD-Finger Family Genes and Their Responses to Environmental Stresses in Oryza sativa L. Int J Mol Sci 2017; 18:ijms18092005. [PMID: 32961651 PMCID: PMC5618654 DOI: 10.3390/ijms18092005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/25/2017] [Accepted: 09/14/2017] [Indexed: 11/16/2022] Open
Abstract
The PHD-finger family has been demonstrated to be involved in regulating plant growth and development. However, little information is given for its role in environmental stress responses. Here, we identified a total of 59 PHD family genes in the rice genome. These OsPHDs genes were located on eleven chromosomes and synteny analysis only revealed nine duplicated pairs within the rice PHD family. Phylogenetic analysis of all OsPHDs and PHDs from other species revealed that they could be grouped into two major clusters. Furthermore, OsPHDs were clustered into eight groups and members from different groups displayed a great divergence in terms of gene structure, functional domains and conserved motifs. We also found that with the exception of OsPHD6, all OsPHDs were expressed in at least one of the ten tested tissues and OsPHDs from certain groups were expressed in specific tissues. Moreover, our results also uncovered differential responses of OsPHDs expression to environmental stresses, including ABA (abscisic acid), water deficit, cold and high Cd. By using quantitative real-time PCR, we further confirmed the differential expression of OsPHDs under these stresses. OsPHD1/7/8/13/33 were differentially expressed under water deficit and Cd stresses, while OsPHD5/17 showed altered expression under water deficit and cold stresses. Moreover, OsPHD3/44/28 displayed differential expression under ABA and Cd stresses. In conclusion, our results provide valuable information on the rice PHD family in plant responses to environmental stress, which will be helpful for further characterizing their biological roles in responding to environmental stresses.
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Affiliation(s)
- Mingzhe Sun
- Key Laboratory of Agricultural Biological Functional Gene, College of Life Science, Northeast Agricultural University, Harbin 150038, China; (M.S.); (B.J.)
- Crop Stress Molecular Biology Laboratory, College of Agronomy, Heilongjiang Bayi Agricultural University, Daqing 163319, China;
| | - Bowei Jia
- Key Laboratory of Agricultural Biological Functional Gene, College of Life Science, Northeast Agricultural University, Harbin 150038, China; (M.S.); (B.J.)
- Crop Stress Molecular Biology Laboratory, College of Agronomy, Heilongjiang Bayi Agricultural University, Daqing 163319, China;
| | - Junkai Yang
- Crop Stress Molecular Biology Laboratory, College of Agronomy, Heilongjiang Bayi Agricultural University, Daqing 163319, China;
| | - Na Cui
- LGPM, CentraleSupélec, Université Paris-Saclay, SFR Condorcet FR CNRS 3417, Centre Européen de Biotechnologie et de Bioéconomie (CEBB), 3 rue des Rouges Terres, 51110 Pomacle, France;
| | - Yanming Zhu
- Key Laboratory of Agricultural Biological Functional Gene, College of Life Science, Northeast Agricultural University, Harbin 150038, China; (M.S.); (B.J.)
- Crop Stress Molecular Biology Laboratory, College of Agronomy, Heilongjiang Bayi Agricultural University, Daqing 163319, China;
- Correspondence: (Y.Z.); (X.S.); Tel.: +86-451-55190025 (Y.Z.); +86-459-6819185 (X.S.)
| | - Xiaoli Sun
- Crop Stress Molecular Biology Laboratory, College of Agronomy, Heilongjiang Bayi Agricultural University, Daqing 163319, China;
- Correspondence: (Y.Z.); (X.S.); Tel.: +86-451-55190025 (Y.Z.); +86-459-6819185 (X.S.)
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13
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WANTED - Dead or alive: Myotubularins, a large disease-associated protein family. Adv Biol Regul 2016; 63:49-58. [PMID: 27666502 DOI: 10.1016/j.jbior.2016.09.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 09/13/2016] [Accepted: 09/13/2016] [Indexed: 11/21/2022]
Abstract
Myotubularins define a large family of proteins conserved through evolution. Several members are mutated in different neuromuscular diseases including centronuclear myopathies and Charcot-Marie-Tooth (CMT) neuropathies, or are linked to a predisposition to obesity and cancer. While some members have phosphatase activity against the 3-phosphate of phosphoinositides, regulating the phosphorylation status of PtdIns3P and PtdIns(3,5)P2 implicated in membrane trafficking and autophagy, and producing PtdIns5P, others lack key residues in the catalytic site and are classified as dead-phosphatases. However, these dead phosphatases regulate phosphoinositide-dependent cellular pathways by binding to catalytically active myotubularins. Here we review previous studies on the molecular regulation and physiological roles of myotubularins. We also used the recent myotubularins three-dimensional structures to underline key residues that are mutated in neuromuscular diseases and required for enzymatic activity. In addition, through database mining and analysis, expression profile and specific isoforms of the different myotubularins are described in depth, as well as a revisited protein interaction network. Comparison of the interactome and expression data for each myotubularin highlights specific protein complexes and tissues where myotubularins should have a key regulatory role.
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14
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Rudge SA, Wakelam MJO. Phosphatidylinositolphosphate phosphatase activities and cancer. J Lipid Res 2015; 57:176-92. [PMID: 26302980 DOI: 10.1194/jlr.r059154] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Indexed: 12/13/2022] Open
Abstract
Signaling through the phosphoinositide 3-kinase pathways mediates the actions of a plethora of hormones, growth factors, cytokines, and neurotransmitters upon their target cells following receptor occupation. Overactivation of these pathways has been implicated in a number of pathologies, in particular a range of malignancies. The tight regulation of signaling pathways necessitates the involvement of both stimulatory and terminating enzymes; inappropriate activation of a pathway can thus result from activation or inhibition of the two signaling arms. The focus of this review is to discuss, in detail, the activities of the identified families of phosphoinositide phosphatase expressed in humans, and how they regulate the levels of phosphoinositides implicated in promoting malignancy.
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Affiliation(s)
- Simon A Rudge
- Signalling Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Michael J O Wakelam
- Signalling Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom
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15
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Kondo H. Complex genetics of familial exudative vitreoretinopathy and related pediatric retinal detachments. Taiwan J Ophthalmol 2015; 5:56-62. [PMID: 29018668 PMCID: PMC5602728 DOI: 10.1016/j.tjo.2015.04.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 03/31/2015] [Accepted: 04/13/2015] [Indexed: 11/19/2022] Open
Abstract
Familial exudative vitreoretinopathy (FEVR) is a hereditary vitreoretinal disorder that can cause various types of retinal detachments. The abnormalities in eyes with FEVR are caused by poor vascularization in the peripheral retina. The genetics of FEVR is highly heterogeneous, and mutations in the genes for Wnt signaling and a transcription factor have been reported to be responsible for FEVR. These factors have been shown to be the regulators of the pathophysiological pathways of retinal vascular development. Studies conducted to identify the causative genes of FEVR have uncovered a diverse and complex relationship between FEVR and other diseases; for example, Norrie disease, a Mendelian-inherited disease; retinopathy of prematurity, a multifactorial genetic disease; and Coats disease, a nongenetic disease, associated with pediatric retinal detachments.
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Affiliation(s)
- Hiroyuki Kondo
- Department of Ophthalmology, University of Occupational and Environmental Health, Kitakyushu, Japan
- Corresponding author. Department of Ophthalmology, University of Occupational and Environmental Health, Number 1-1, Iseigaoka, Yahatanishiku, Kitakyushu 807-8555, Japan. E-mail address:
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16
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Chen YC, Auer-Grumbach M, Matsukawa S, Zitzelsberger M, Themistocleous AC, Strom TM, Samara C, Moore AW, Cho LTY, Young GT, Weiss C, Schabhüttl M, Stucka R, Schmid AB, Parman Y, Graul-Neumann L, Heinritz W, Passarge E, Watson RM, Hertz JM, Moog U, Baumgartner M, Valente EM, Pereira D, Restrepo CM, Katona I, Dusl M, Stendel C, Wieland T, Stafford F, Reimann F, von Au K, Finke C, Willems PJ, Nahorski MS, Shaikh SS, Carvalho OP, Nicholas AK, Karbani G, McAleer MA, Cilio MR, McHugh JC, Murphy SM, Irvine AD, Jensen UB, Windhager R, Weis J, Bergmann C, Rautenstrauss B, Baets J, De Jonghe P, Reilly MM, Kropatsch R, Kurth I, Chrast R, Michiue T, Bennett DLH, Woods CG, Senderek J. Transcriptional regulator PRDM12 is essential for human pain perception. Nat Genet 2015; 47:803-8. [PMID: 26005867 DOI: 10.1038/ng.3308] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 04/27/2015] [Indexed: 12/12/2022]
Abstract
Pain perception has evolved as a warning mechanism to alert organisms to tissue damage and dangerous environments. In humans, however, undesirable, excessive or chronic pain is a common and major societal burden for which available medical treatments are currently suboptimal. New therapeutic options have recently been derived from studies of individuals with congenital insensitivity to pain (CIP). Here we identified 10 different homozygous mutations in PRDM12 (encoding PRDI-BF1 and RIZ homology domain-containing protein 12) in subjects with CIP from 11 families. Prdm proteins are a family of epigenetic regulators that control neural specification and neurogenesis. We determined that Prdm12 is expressed in nociceptors and their progenitors and participates in the development of sensory neurons in Xenopus embryos. Moreover, CIP-associated mutants abrogate the histone-modifying potential associated with wild-type Prdm12. Prdm12 emerges as a key factor in the orchestration of sensory neurogenesis and may hold promise as a target for new pain therapeutics.
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Affiliation(s)
- Ya-Chun Chen
- 1] Department of Medical Genetics, University of Cambridge, Cambridge, UK. [2] Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | | | - Shinya Matsukawa
- Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Tokyo, Japan
| | | | - Andreas C Themistocleous
- 1] Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK. [2] Brain Function Research Group, School of Physiology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tim M Strom
- 1] Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany. [2] Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Chrysanthi Samara
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
| | - Adrian W Moore
- Disease Mechanism Research Core, RIKEN Brain Science Institute, Saitama, Japan
| | | | | | - Caecilia Weiss
- Friedrich-Baur-Institute, Ludwig Maximilians University Munich, Munich, Germany
| | - Maria Schabhüttl
- Department of Orthopaedics, Medical University Vienna, Vienna, Austria
| | - Rolf Stucka
- Friedrich-Baur-Institute, Ludwig Maximilians University Munich, Munich, Germany
| | - Annina B Schmid
- 1] Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK. [2] School of Health and Rehabilitation Sciences, The University of Queensland, St. Lucia, Australia
| | - Yesim Parman
- Department of Neurology, Istanbul University, Istanbul, Turkey
| | - Luitgard Graul-Neumann
- Ambulantes Gesundheitszentrum der Charité Campus Virchow (Humangenetik), Universitätsmedizin Berlin, Berlin, Germany
| | - Wolfram Heinritz
- 1] Praxis für Humangenetik Cottbus, Cottbus, Germany. [2] Institut für Humangenetik, Universitätsklinikum Leipzig, Leipzig, Germany
| | - Eberhard Passarge
- 1] Institut für Humangenetik, Universitätsklinikum Leipzig, Leipzig, Germany. [2] Institut für Humangenetik, Universitätsklinikum Essen, Essen, Germany
| | - Rosemarie M Watson
- Department of Dermatology, Our Lady's Children's Hospital, Dublin, Ireland
| | - Jens Michael Hertz
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Ute Moog
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Manuela Baumgartner
- Neuropädiatrische Ambulanz, Krankenhaus der Barmherzigen Schwestern Linz, Linz, Austria
| | - Enza Maria Valente
- Neurogenetics Unit, Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Diego Pereira
- Departamento de Cirugía Plástica, Hospital Infantil Universitario de San José, Bogotá, Colombia
| | | | - Istvan Katona
- Institut für Neuropathologie, Uniklinik RWTH Aachen, Aachen, Germany
| | - Marina Dusl
- Friedrich-Baur-Institute, Ludwig Maximilians University Munich, Munich, Germany
| | - Claudia Stendel
- 1] Friedrich-Baur-Institute, Ludwig Maximilians University Munich, Munich, Germany. [2] German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Thomas Wieland
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Fay Stafford
- 1] Department of Medical Genetics, University of Cambridge, Cambridge, UK. [2] Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Frank Reimann
- Department of Clinical Biochemistry, University of Cambridge, Cambridge, UK
| | - Katja von Au
- SPZ Neuropädiatrie Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Christian Finke
- CharitéCentrum für Zahn-, Mund- und Kieferheilkunde, Arbeitsbereich Kinderzahnmedizin, Universitätsmedizin Berlin, Berlin, Germany
| | | | - Michael S Nahorski
- 1] Department of Medical Genetics, University of Cambridge, Cambridge, UK. [2] Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Samiha S Shaikh
- 1] Department of Medical Genetics, University of Cambridge, Cambridge, UK. [2] Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Ofélia P Carvalho
- 1] Department of Medical Genetics, University of Cambridge, Cambridge, UK. [2] Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Adeline K Nicholas
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Gulshan Karbani
- Yorkshire Regional Genetics Service, Chapel Allerton Hospital, Leeds, UK
| | - Maeve A McAleer
- Department of Dermatology, Our Lady's Children's Hospital, Dublin, Ireland
| | - Maria Roberta Cilio
- 1] Department of Neurology, University of California San Francisco, San Francisco, California, USA. [2] Department of Neuroscience, Bambino Gesù Children's Hospital and Research Institute, Rome, Italy
| | - John C McHugh
- Department of Neurology and Neurophysiology, Our Lady's Children's Hospital, Dublin, Ireland
| | - Sinead M Murphy
- 1] Department of Neurology, Adelaide &Meath Hospital, Dublin, Ireland. [2] Academic Unit of Neurology, Trinity College, Dublin, Ireland
| | - Alan D Irvine
- 1] Department of Dermatology, Our Lady's Children's Hospital, Dublin, Ireland. [2] Clinical Medicine, Trinity College, Dublin, Ireland
| | - Uffe Birk Jensen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | | | - Joachim Weis
- Institut für Neuropathologie, Uniklinik RWTH Aachen, Aachen, Germany
| | - Carsten Bergmann
- 1] Center for Human Genetics, Bioscientia, Ingelheim, Germany. [2] Department of Medicine, Renal Division, Freiburg University Medical Center, Freiburg, Germany. [3] Center for Clinical Research, Freiburg University Medical Center, Freiburg, Germany
| | - Bernd Rautenstrauss
- 1] Friedrich-Baur-Institute, Ludwig Maximilians University Munich, Munich, Germany. [2] Medizinisch Genetisches Zentrum, Munich, Germany
| | - Jonathan Baets
- 1] Neurogenetics Group, VIB Department of Molecular Genetics, University of Antwerp, Antwerp, Belgium. [2] Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium. [3] Department of Neurology, Antwerp University Hospital, Antwerp, Belgium
| | - Peter De Jonghe
- 1] Neurogenetics Group, VIB Department of Molecular Genetics, University of Antwerp, Antwerp, Belgium. [2] Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium. [3] Department of Neurology, Antwerp University Hospital, Antwerp, Belgium
| | - Mary M Reilly
- MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, National Hospital for Neurology, London, UK
| | - Regina Kropatsch
- Department of Human Genetics, Ruhr-University Bochum, Bochum, Germany
| | - Ingo Kurth
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Roman Chrast
- 1] Institute of Human Genetics, Technische Universität München, Munich, Germany. [2] Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden. [3] Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Tatsuo Michiue
- Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Tokyo, Japan
| | - David L H Bennett
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - C Geoffrey Woods
- 1] Department of Medical Genetics, University of Cambridge, Cambridge, UK. [2] Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Jan Senderek
- Friedrich-Baur-Institute, Ludwig Maximilians University Munich, Munich, Germany
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17
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18
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Ma AN, Wang H, Guo R, Wang YX, Li W, Cui J, Wang G, Hoffman AR, Hu JF. Targeted gene suppression by inducing de novo DNA methylation in the gene promoter. Epigenetics Chromatin 2014; 7:20. [PMID: 25184003 PMCID: PMC4150861 DOI: 10.1186/1756-8935-7-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Accepted: 08/01/2014] [Indexed: 11/16/2022] Open
Abstract
Background Targeted gene silencing is an important approach in both drug development and basic research. However, the selection of a potent suppressor has become a significant hurdle to implementing maximal gene inhibition for this approach. We attempted to construct a ‘super suppressor’ by combining the activities of two suppressors that function through distinct epigenetic mechanisms. Results Gene targeting vectors were constructed by fusing a GAL4 DNA-binding domain with a epigenetic suppressor, including CpG DNA methylase Sss1, histone H3 lysine 27 methylase vSET domain, and Kruppel-associated suppression box (KRAB). We found that both Sss1 and KRAB suppressors significantly inhibited the expression of luciferase and copGFP reporter genes. However, the histone H3 lysine 27 methylase vSET did not show significant suppression in this system. Constructs containing both Sss1 and KRAB showed better inhibition than either one alone. In addition, we show that KRAB suppressed gene expression by altering the histone code, but not DNA methylation in the gene promoter. Sss1, on the other hand, not only induced de novo DNA methylation and recruited Heterochromatin Protein 1 (HP1a), but also increased H3K27 and H3K9 methylation in the promoter. Conclusions Epigenetic studies can provide useful data for the selection of suppressors in constructing therapeutic vectors for targeted gene silencing.
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Affiliation(s)
- Ai-Niu Ma
- King's Lab, Shanghai Jiao Tong University School of Pharmacy, 800 Dongchuan Road, Shanghai 200240, China.,Stanford University Medical School, VA Palo Alto Health Care System, 3801 Miranda Avenue, Palo Alto, CA 94304, USA
| | - Hong Wang
- King's Lab, Shanghai Jiao Tong University School of Pharmacy, 800 Dongchuan Road, Shanghai 200240, China.,Stem Cell and Cancer Center, First Affiliated Hospital, Jilin University, 519 Dongminzhu Blvd, Changchun 130021, China
| | - Rui Guo
- King's Lab, Shanghai Jiao Tong University School of Pharmacy, 800 Dongchuan Road, Shanghai 200240, China.,Stem Cell and Cancer Center, First Affiliated Hospital, Jilin University, 519 Dongminzhu Blvd, Changchun 130021, China
| | - Yong-Xiang Wang
- King's Lab, Shanghai Jiao Tong University School of Pharmacy, 800 Dongchuan Road, Shanghai 200240, China
| | - Wei Li
- Stem Cell and Cancer Center, First Affiliated Hospital, Jilin University, 519 Dongminzhu Blvd, Changchun 130021, China
| | - Jiuwei Cui
- Stem Cell and Cancer Center, First Affiliated Hospital, Jilin University, 519 Dongminzhu Blvd, Changchun 130021, China
| | - Guanjun Wang
- Stem Cell and Cancer Center, First Affiliated Hospital, Jilin University, 519 Dongminzhu Blvd, Changchun 130021, China
| | - Andrew R Hoffman
- Stanford University Medical School, VA Palo Alto Health Care System, 3801 Miranda Avenue, Palo Alto, CA 94304, USA
| | - Ji-Fan Hu
- Stem Cell and Cancer Center, First Affiliated Hospital, Jilin University, 519 Dongminzhu Blvd, Changchun 130021, China.,Stanford University Medical School, VA Palo Alto Health Care System, 3801 Miranda Avenue, Palo Alto, CA 94304, USA
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19
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McElroy KA, Kang H, Kuroda MI. Are we there yet? Initial targeting of the Male-Specific Lethal and Polycomb group chromatin complexes in Drosophila. Open Biol 2014; 4:140006. [PMID: 24671948 PMCID: PMC3971409 DOI: 10.1098/rsob.140006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Chromatin-binding proteins must navigate the complex nuclear milieu to find their sites of action, and a constellation of protein factors and other properties are likely to influence targeting specificity. Despite considerable progress, the precise rules by which binding specificity is achieved have remained elusive. Here, we consider early targeting events for two groups of chromatin-binding complexes in Drosophila: the Male-Specific Lethal (MSL) and the Polycomb group (PcG) complexes. These two serve as models for understanding targeting, because they have been extensively studied and play vital roles in Drosophila, and their targets have been documented at high resolution. Furthermore, the proteins and biochemical properties of both complexes are largely conserved in multicellular organisms, including humans. While the MSL complex increases gene expression and PcG members repress genes, the two groups share many similarities such as the ability to modify their chromatin environment to create active or repressive domains, respectively. With legacies of in-depth genetic, biochemical and now genomic approaches, the MSL and PcG complexes will continue to provide tractable systems for understanding the recruitment of multiprotein chromatin complexes to their target loci.
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Affiliation(s)
- Kyle A McElroy
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
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Celá P, Balková SM, Bryjová A, Horáková D, Míšek I, Richman J, Buchtová M. Expression, function and regulation of Evi-1 during embryonic avian development. Gene Expr Patterns 2013; 13:343-53. [DOI: 10.1016/j.gep.2013.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 06/15/2013] [Accepted: 06/19/2013] [Indexed: 12/14/2022]
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ZNF408 is mutated in familial exudative vitreoretinopathy and is crucial for the development of zebrafish retinal vasculature. Proc Natl Acad Sci U S A 2013; 110:9856-61. [PMID: 23716654 DOI: 10.1073/pnas.1220864110] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Familial exudative vitreoretinopathy (FEVR) is a genetically heterogeneous disorder characterized by abnormal vascularization of the peripheral retina, which can result in retinal detachment and severe visual impairment. In a large Dutch FEVR family, we performed linkage analysis, exome sequencing, and segregation analysis of DNA variants. We identified putative disease-causing DNA variants in proline-alanine-rich ste20-related kinase (c.791dup; p.Ser265ValfsX64) and zinc finger protein 408 (ZNF408) (c.1363C>T; p.His455Tyr), the latter of which was also present in an additional Dutch FEVR family that subsequently appeared to share a common ancestor with the original family. Sequence analysis of ZNF408 in 132 additional individuals with FEVR revealed another potentially pathogenic missense variant, p.Ser126Asn, in a Japanese family. Immunolocalization studies in COS-1 cells transfected with constructs encoding the WT and mutant ZNF408 proteins, revealed that the WT and the p.Ser126Asn mutant protein show complete nuclear localization, whereas the p.His455Tyr mutant protein was localized almost exclusively in the cytoplasm. Moreover, in a cotransfection assay, the p.His455Tyr mutant protein retains the WT ZNF408 protein in the cytoplasm, suggesting that this mutation acts in a dominant-negative fashion. Finally, morpholino-induced knockdown of znf408 in zebrafish revealed defects in developing retinal and trunk vasculature, that could be rescued by coinjection of RNA encoding human WT ZNF408 but not p.His455Tyr mutant ZNF408. Together, our data strongly suggest that mutant ZNF408 results in abnormal retinal vasculogenesis in humans and is associated with FEVR.
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Rincon-Arano H, Parkhurst SM, Groudine M. UpSET-ting the balance: modulating open chromatin features in metazoan genomes. Fly (Austin) 2013; 7:153-60. [PMID: 23649046 DOI: 10.4161/fly.24732] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Appropriate gene expression relies on the sophisticated interplay between genetic and epigenetic factors. Histone acetylation and an open chromatin configuration are key features of transcribed regions and are mainly present around active promoters. Our recent identification of the SET-domain containing protein UpSET established a new functional link between the modulation of open chromatin features and active recruitment of well-known co-repressors in metazoans. Structurally, the SET domain of UpSET resembles H3K4 and H3K36 methyltransferases; however, it is does not confer histone methyltransferase activity. Rather than methylating histones to regulate gene expression like other SET domain-containing proteins, UpSET fine-tunes transcription by modulating the chromatin structure around active promoters resulting in suppression of expression of off-target genes or nearby repetitive elements. Chromatin modulation by UpSET occurs in part through its interaction with histone deacetylases. Here, we discuss the different scenarios in which UpSET could play key roles in modulating gene expression.
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Affiliation(s)
- Hector Rincon-Arano
- Basic Sciences Division; Fred Hutchinson Cancer Research Center; Seattle, WA USA
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Roffers-Agarwal J, Hutt KJ, Gammill LS. Paladin is an antiphosphatase that regulates neural crest cell formation and migration. Dev Biol 2012; 371:180-90. [PMID: 22926139 DOI: 10.1016/j.ydbio.2012.08.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2012] [Revised: 08/05/2012] [Accepted: 08/15/2012] [Indexed: 12/31/2022]
Abstract
Although a network of transcription factors that specifies neural crest identity in the ectoderm has been defined, expression of neural crest transcription factors does not guarantee eventual migration as a neural crest cell. While much work has gone into determining regulatory relationships within the transcription factor network, the ability of protein modifications like phosphorylation to modulate the function of neural crest regulatory factors and determine when and where they are active also has crucial implications. Paladin, which was previously classified as a phosphatase based on sequence similarity, is expressed in chick neural crest precursors and is maintained throughout their epithelial to mesenchymal transition and migration. Loss of Paladin delays the expression of transcription factors Snail2 and Sox10 in premigratory neural crest cells, but does not affect accumulation of FoxD3, Cad6B or RhoB, indicating that Paladin differentially modulates the expression of genes previously thought to be coregulated within the neural crest gene regulatory network. Both gain and loss of Paladin function result in disrupted neural crest migration, reinforcing the importance of precisely regulated phosphorylation for neural crest migration. Mutation of critical, catalytic cysteine residues within Paladin's predicted phosphatase active site motifs did not abolish the function of Paladin in the neural crest. Collectively, these data indicate that Paladin is an antiphosphatase that modulates the activity of specific neural crest regulatory factors during neural crest development. Our work identifies a novel regulator of phosphorylation status that provides an additional layer of regulation in the neural crest.
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Affiliation(s)
- Julaine Roffers-Agarwal
- Department of Genetics, Cell Biology and Development, 6-160 Jackson Hall, 321 Church Street SE, University of Minnesota, Minneapolis, MN 55455, USA
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Myotubularin phosphoinositide phosphatases: cellular functions and disease pathophysiology. Trends Mol Med 2012; 18:317-27. [DOI: 10.1016/j.molmed.2012.04.004] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Revised: 04/10/2012] [Accepted: 04/12/2012] [Indexed: 11/23/2022]
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Berger P, Tersar K, Ballmer-Hofer K, Suter U. The CMT4B disease-causing proteins MTMR2 and MTMR13/SBF2 regulate AKT signalling. J Cell Mol Med 2012; 15:307-15. [PMID: 19912440 PMCID: PMC3822797 DOI: 10.1111/j.1582-4934.2009.00967.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Charcot-Marie-Tooth disease type 4B is caused by mutations in the genes encoding either the lipid phosphatase myotubularin-related protein-2 (MTMR2) or its regulatory binding partner MTMR13/SBF2. Mtmr2 dephosphorylates PI-3-P and PI-3,5-P2 to form phosphatidylinositol and PI-5-P, respectively, while Mtmr13/Sbf2 is an enzymatically inactive member of the myotubularin protein family. We have found altered levels of the critical signalling protein AKT in mouse mutants for Mtmr2 and Mtmr13/Sbf2. Thus, we analysed the influence of Mtmr2 and Mtmr13/Sbf2 on signalling processes. We found that overexpression of Mtmr2 prevents the degradation of the epidermal growth factor receptor (EGFR) and leads to sustained Akt activation whereas Erk activation is not affected. Mtmr13/Sbf2 counteracts the blockage of EGFR degradation without affecting prolonged Akt activation. Our data indicate that Mtmr2 and Mtmr13/Sbf2 play critical roles in the sorting and modulation of cellular signalling which are likely to be disturbed in CMT4B.
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Affiliation(s)
- Philipp Berger
- Molecular Cell Biology, Paul Scherrer Institut, Villigen, Switzerland
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Abstract
Proteins involved in membrane remodeling play an essential role in a plethora of cell functions including endocytosis and intracellular transport. Defects in several of them lead to human diseases. Myotubularins, amphiphysins, and dynamins are all proteins implicated in membrane trafficking and/or remodeling. Mutations in myotubularin, amphiphysin 2 (BIN1), and dynamin 2 lead to different forms of centronuclear myopathy, while mutations in myotubularin-related proteins cause Charcot-Marie-Tooth neuropathies. In addition to centronuclear myopathy, dynamin 2 is also mutated in a dominant form of Charcot-Marie-Tooth neuropathy. While several proteins from these different families are implicated in similar diseases, mutations in close homologues or in the same protein in the case of dynamin 2 lead to diseases affecting different tissues. This suggests (1) a common molecular pathway underlying these different neuromuscular diseases, and (2) tissue-specific regulation of these proteins. This review discusses the pathophysiology of the related neuromuscular diseases on the basis of animal models developed for proteins of the myotubularin, amphiphysin, and dynamin families. A better understanding of the common mechanisms between these neuromuscular disorders will lead to more specific health care and therapeutic approaches.
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Tronchère H, Bolino A, Laporte J, Payrastre B. Myotubularins and associated neuromuscular diseases. ACTA ACUST UNITED AC 2012. [DOI: 10.2217/clp.12.7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Cabrera CP, Dunn IC, Fell M, Wilson PW, Burt DW, Waddington D, Talbot R, Hocking PM, Law A, Knott S, Haley CS, de Koning DJ. Complex traits analysis of chicken growth using targeted genetical genomics. Anim Genet 2011; 43:163-71. [PMID: 22404352 DOI: 10.1111/j.1365-2052.2011.02223.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Dissecting the genetic control of complex trait variation remains very challenging, despite many advances in technology. The aim of this study was to use a major growth quantitative trait locus (QTL) in chickens mapped to chromosome 4 as a model for a targeted approach to dissect the QTL. We applied a variant of the genetical genomics approach to investigate genome-wide gene expression differences between two contrasting genotypes of a marked QTL. This targeted approach allows the direct quantification of the link between the genotypes and the genetic responses, thus narrowing the QTL-phenotype gap using fewer samples (i.e. microarrays) compared with the genome-wide genetical genomics studies. Four differentially expressed genes were localized under the region of the QTL. One of these genes is a potential positional candidate gene (AADAT) that affects lysine and tryptophan metabolism and has alternative splicing variants between the two genotypes. In addition, the lysine and glycolysis metabolism pathways were significantly enriched for differentially expressed genes across the genome. The targeted approach provided a complementary route to fine mapping of QTL by characterizing the local and the global downstream effects of the QTL and thus generating further hypotheses about the action of that QTL.
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Affiliation(s)
- C P Cabrera
- Medical Research Council, Human Genetics Unit, Edinburgh, UK.
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Abstract
The MTM (myotubularin)/MTMR (myotubularin-related) protein family is comprised of 15 lipid phosphatases, of which nine members are catalytically active. MTMs are known to play a fundamental role in human physiology as gene mutations can give rise to X-linked myotubular myopathy or Charcot-Marie-Tooth disease, which manifest in skeletal muscle or in peripheral neurons respectively. Interestingly, studies have shown MTMR2 and MTMR5, two MTM family members, to be highly expressed in the testis, particularly in Sertoli and germ cells, and knockout of either gene resulted in spermatogenic defects. Other studies have shown that MTMR2 functions in endocytosis and membrane trafficking. In the testis, MTMR2 interacts and co-localizes with c-Src/phospho-Src-(Tyr⁴¹⁶), a non-receptor protein tyrosine kinase that regulates the phosphorylation state of proteins at the apical ES (ectoplasmic specialization), a unique type of cell junction found between Sertoli cells and elongating/elongated spermatids. In the present review, we highlight recent findings that have made a significant impact on our understanding of this protein family in normal cell function and in disease, with the emphasis on the role of MTMs and MTMRs in spermatogenesis. We also describe a working model to explain how MTMR2 interacts with other proteins such as c-Src, dynamin 2, EPS8 (growth factor receptor pathway substrate 8) and ARP2/3 (actin-related protein 2/3) at the apical ES and the apical TBC (tubulobulbar complex; tubular-like invaginations that function in the disassembly of the apical ES and in the recycling of its components) to regulate spermiation at late stage VIII of the seminiferous epithelial cycle.
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Ndamukong I, Jones DR, Lapko H, Divecha N, Avramova Z. Phosphatidylinositol 5-phosphate links dehydration stress to the activity of ARABIDOPSIS TRITHORAX-LIKE factor ATX1. PLoS One 2010; 5:e13396. [PMID: 20967218 PMCID: PMC2954176 DOI: 10.1371/journal.pone.0013396] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Accepted: 09/17/2010] [Indexed: 11/18/2022] Open
Abstract
Background Changes in gene expression enable organisms to respond to environmental stress. Levels of cellular lipid second messengers, such as the phosphoinositide PtdIns5P, change in response to a variety of stresses and can modulate the localization, conformation and activity of a number of intracellular proteins. The plant trithorax factor (ATX1) tri-methylates the lysine 4 residue of histone H3 (H3K4me3) at gene coding sequences, which positively correlates with gene transcription. Microarray analysis has identified a target gene (WRKY70) that is regulated by both ATX1 and by the exogenous addition of PtdIns5P in Arabidopsis. Interestingly, ATX1 contains a PtdIns5P interaction domain (PHD finger) and thus, phosphoinositide signaling, may link environmental stress to changes in gene transcription. Principal Findings Using the plant Arabidopsis as a model system, we demonstrate a link between PtdIns5P and the activity of the chromatin modifier ATX1 in response to dehydration stress. We show for the first time that dehydration leads to an increase in cellular PtdIns5P in Arabidopsis. The Arabidopsis homolog of myotubularin (AtMTM1) is capable of generating PtdIns5P and here, we show that AtMTM1 is essential for the induced increase in PtdIns5P upon dehydration. Furthermore, we demonstrate that the ATX1-dependent gene, WRKY70, is downregulated during dehydration and that lowered transcript levels are accompanied by a drastic reduction in H3K4me3 of its nucleosomes. We follow changes in WRKY70 nucleosomal K4 methylation as a model to study ATX1 activity at chromatin during dehydration stress. We found that during dehydration stress, the physical presence of ATX1 at the WRKY70 locus was diminished and that ATX1 depletion resulted from it being retained in the cytoplasm when PtdIns5P was elevated. The PHD of ATX1 and catalytically active AtMTM1 are required for the cytoplasmic localization of ATX1. Conclusions/Significance The novelty of the manuscript is in the discovery of a mechanistic link between a chromatin modifying activity (ATX1) and a lipid (PtdIns5P) synthesis in a signaling pathway that ultimately results in altered expression of ATX1 dependent genes downregulated in response to dehydration stress.
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Affiliation(s)
- Ivan Ndamukong
- School of Biological Sciences, University of Nebraska at Lincoln, Lincoln, Nebraska, United States of America
| | - David R. Jones
- Inositide Laboratory, Paterson Institute for Cancer Research, The University of Manchester, Manchester, United Kingdom
| | - Hanna Lapko
- School of Biological Sciences, University of Nebraska at Lincoln, Lincoln, Nebraska, United States of America
| | - Nullin Divecha
- Inositide Laboratory, Paterson Institute for Cancer Research, The University of Manchester, Manchester, United Kingdom
- * E-mail: (ZA); (ND)
| | - Zoya Avramova
- School of Biological Sciences, University of Nebraska at Lincoln, Lincoln, Nebraska, United States of America
- * E-mail: (ZA); (ND)
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Ding Y, Lapko H, Ndamukong I, Xia Y, Al-Abdallat A, Lalithambika S, Sadder M, Saleh A, Fromm M, Riethoven JJ, Lu G, Avramova Z. The Arabidopsis chromatin modifier ATX1, the myotubularin-like AtMTM and the response to drought. PLANT SIGNALING & BEHAVIOR 2009; 4:1049-58. [PMID: 19901554 PMCID: PMC2819512 DOI: 10.4161/psb.4.11.10103] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Accepted: 09/15/2009] [Indexed: 05/19/2023]
Abstract
Plants respond to environmental stresses by altering transcription of genes involved in the response. The chromatin modifier ATX1 regulates expression of a large number of genes; consequently, factors that affect ATX1 activity would also influence expression from ATX1-regulated genes. Here, we demonstrate that dehydration is such a factor implicating ATX1 in the plant's response to drought. In addition, we report that a hitherto unknown Arabidopsis gene, At3g10550, encodes a phosphoinositide 3'-phosphatase related to the animal myotubularins (AtMTM1). Myotubularin activities in plants have not been described and herein, we identify an overlapping set of genes co-regulated by ATX1 and AtMTM under drought conditions. We propose that these shared genes represent the ultimate targets of partially overlapping branches of the pathways of the nuclear ATX1 and the cytoplasmic AtMTM1. Our analyses offer first genome-wide insights into the relationship of an epigenetic factor and a lipid phosphatase from the other end of a shared drought responding pathway in Arabidopsis.
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Affiliation(s)
- Yong Ding
- UNL Center for Biotechnology and Plant Science Initiative; UNL; Lincoln, NE USA
| | - Hanna Lapko
- School of Biological Sciences; UNL; Lincoln, NE USA
| | | | - Yuannan Xia
- Genomics Core Research Facility; Center for Biotechnology UNL; Lincoln, NE USA
| | - Ayed Al-Abdallat
- UNL Center for Biotechnology and Plant Science Initiative; UNL; Lincoln, NE USA
- Faculty of Agriculture; University of Jordan; Amman, Jordan
| | | | - Monther Sadder
- School of Biological Sciences; UNL; Lincoln, NE USA
- Faculty of Agriculture; University of Jordan; Amman, Jordan
| | | | - Michael Fromm
- UNL Center for Biotechnology and Plant Science Initiative; UNL; Lincoln, NE USA
| | - Jean-Jack Riethoven
- Bioinformatics Core Research Facility; Center for Biotechnology UNL; Lincoln, NE USA
| | - Guoqing Lu
- Department of Biology; University of Nebraska at Omaha; Omaha, NE USA
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Sasaki T, Takasuga S, Sasaki J, Kofuji S, Eguchi S, Yamazaki M, Suzuki A. Mammalian phosphoinositide kinases and phosphatases. Prog Lipid Res 2009; 48:307-43. [PMID: 19580826 DOI: 10.1016/j.plipres.2009.06.001] [Citation(s) in RCA: 190] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Phosphoinositides are lipids that are present in the cytoplasmic leaflet of a cell's plasma and internal membranes and play pivotal roles in the regulation of a wide variety of cellular processes. Phosphoinositides are molecularly diverse due to variable phosphorylation of the hydroxyl groups of their inositol rings. The rapid and reversible configuration of the seven known phosphoinositide species is controlled by a battery of phosphoinositide kinases and phosphoinositide phosphatases, which are thus critical for phosphoinositide isomer-specific localization and functions. Significantly, a given phosphoinositide generated by different isozymes of these phosphoinositide kinases and phosphatases can have different biological effects. In mammals, close to 50 genes encode the phosphoinositide kinases and phosphoinositide phosphatases that regulate phosphoinositide metabolism and thus allow cells to respond rapidly and effectively to ever-changing environmental cues. Understanding the distinct and overlapping functions of these phosphoinositide-metabolizing enzymes is important for our knowledge of both normal human physiology and the growing list of human diseases whose etiologies involve these proteins. This review summarizes the structural and biological properties of all the known mammalian phosphoinositide kinases and phosphoinositide phosphatases, as well as their associations with human disorders.
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Affiliation(s)
- Takehiko Sasaki
- Department of Pathology and Immunology, Akita University, Graduate School of Medicine, Akita 010-8543, Japan.
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Jungbluth H, Wallgren-Pettersson C, Laporte J. Centronuclear (myotubular) myopathy. Orphanet J Rare Dis 2008; 3:26. [PMID: 18817572 PMCID: PMC2572588 DOI: 10.1186/1750-1172-3-26] [Citation(s) in RCA: 223] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2008] [Accepted: 09/25/2008] [Indexed: 01/23/2023] Open
Abstract
Centronuclear myopathy (CNM) is an inherited neuromuscular disorder characterised by clinical features of a congenital myopathy and centrally placed nuclei on muscle biopsy. The incidence of X-linked myotubular myopathy is estimated at 2/100000 male births but epidemiological data for other forms are not currently available. The clinical picture is highly variable. The X-linked form usually gives rise to a severe phenotype in males presenting at birth with marked weakness and hypotonia, external ophthalmoplegia and respiratory failure. Signs of antenatal onset comprise reduced foetal movements, polyhydramnios and thinning of the ribs on chest radiographs; birth asphyxia may be the present. Affected infants are often macrosomic, with length above the 90th centile and large head circumference. Testes are frequently undescended. Both autosomal-recessive (AR) and autosomal-dominant (AD) forms differ from the X-linked form regarding age at onset, severity, clinical characteristics and prognosis. In general, AD forms have a later onset and milder course than the X-linked form, and the AR form is intermediate in both respects. Mutations in the myotubularin (MTM1) gene on chromosome Xq28 have been identified in the majority of patients with the X-linked recessive form, whilst AD and AR forms have been associated with mutations in the dynamin 2 (DNM2) gene on chromosome 19p13.2 and the amphiphysin 2 (BIN1) gene on chromosome 2q14, respectively. Single cases with features of CNM have been associated with mutations in the skeletal muscle ryanodine receptor (RYR1) and the hJUMPY (MTMR14) genes. Diagnosis is based on typical histopathological findings on muscle biopsy in combination with suggestive clinical features; muscle magnetic resonance imaging may complement clinical assessment and inform genetic testing in cases with equivocal features. Genetic counselling should be offered to all patients and families in whom a diagnosis of CNM has been made. The main differential diagnoses include congenital myotonic dystrophy and other conditions with severe neonatal hypotonia. Management of CNM is mainly supportive, based on a multidisciplinary approach. Whereas the X-linked form due to MTM1 mutations is often fatal in infancy, dominant forms due to DNM2 mutations and some cases of the recessive BIN1-related form appear to be associated with an overall more favourable prognosis.
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Affiliation(s)
- Heinz Jungbluth
- Department of Paediatric Neurology, Neuromuscular Service, Evelina Children's Hospital, St Thomas' Hospital, London, UK.
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Abstract
The Class III PI3K (phosphoinositide 3-kinase), Vps34 (vacuolar protein sorting 34), was first described as a component of the vacuolar sorting system in Saccharomyces cerevisiae and is the sole PI3K in yeast. The homologue in mammalian cells, hVps34, has been studied extensively in the context of endocytic sorting. However, hVps34 also plays an important role in the ability of cells to respond to changes in nutrient conditions. Recent studies have shown that mammalian hVps34 is required for the activation of the mTOR (mammalian target of rapamycin)/S6K1 (S6 kinase 1) pathway, which regulates protein synthesis in response to nutrient availability. In both yeast and mammalian cells, Class III PI3Ks are also required for the induction of autophagy during nutrient deprivation. Finally, mammalian hVps34 is itself regulated by nutrients. Thus Class III PI3Ks are implicated in the regulation of both autophagy and, through the mTOR pathway, protein synthesis, and thus contribute to the integration of cellular responses to changing nutritional status.
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Pulido R, van Huijsduijnen RH. Protein tyrosine phosphatases: dual-specificity phosphatases in health and disease. FEBS J 2008; 275:848-66. [DOI: 10.1111/j.1742-4658.2008.06250.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Krouwels IM, Wiesmeijer K, Abraham TE, Molenaar C, Verwoerd NP, Tanke HJ, Dirks RW. A glue for heterochromatin maintenance: stable SUV39H1 binding to heterochromatin is reinforced by the SET domain. ACTA ACUST UNITED AC 2007; 170:537-49. [PMID: 16103223 PMCID: PMC2171490 DOI: 10.1083/jcb.200502154] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Trimethylation of histone H3 lysine 9 and the subsequent binding of heterochromatin protein 1 (HP1) mediate the formation and maintenance of pericentromeric heterochromatin. Trimethylation of H3K9 is governed by the histone methyltransferase SUV39H1. Recent studies of HP1 dynamics revealed that HP1 is not a stable component of heterochromatin but is highly mobile (Cheutin, T., A.J. McNairn, T. Jenuwein, D.M. Gilbert, P.B. Singh, and T. Misteli. 2003. Science. 299:721–725; Festenstein, R., S.N. Pagakis, K. Hiragami, D. Lyon, A. Verreault, B. Sekkali, and D. Kioussis. 2003. Science. 299:719–721). Because the mechanism by which SUV39H1 is recruited to and interacts with heterochromatin is unknown, we studied the dynamic properties of SUV39H1 in living cells by using fluorescence recovery after photobleaching and fluorescence resonance energy transfer. Our results show that a substantial population of SUV39H1 is immobile at pericentromeric heterochromatin, suggesting that, in addition to its catalytic activity, SUV39H1 may also play a structural role at pericentromeric regions. Analysis of SUV39H1 deletion mutants indicated that the SET domain mediates this stable binding. Furthermore, our data suggest that the recruitment of SUV39H1 to heterochromatin is at least partly independent from that of HP1 and that HP1 transiently interacts with SUV39H1 at heterochromatin.
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Affiliation(s)
- Ilke M Krouwels
- Department of Molecular Cell Biology, Leiden University Medical Center, 2333 AL, Leiden, Netherlands
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Cao C, Laporte J, Backer JM, Wandinger-Ness A, Stein MP. Myotubularin lipid phosphatase binds the hVPS15/hVPS34 lipid kinase complex on endosomes. Traffic 2007; 8:1052-67. [PMID: 17651088 DOI: 10.1111/j.1600-0854.2007.00586.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Myotubularins constitute a ubiquitous family of phosphatidylinositol (PI) 3-phosphatases implicated in several neuromuscular disorders. Myotubularin [myotubular myopathy 1 (MTM1)] PI 3-phosphatase is shown associated with early and late endosomes. Loss of endosomal phosphatidylinositol 3-phosphate [PI(3)P] upon overexpression of wild-type MTM1, but not a phosphatase-dead MTM1C375S mutant, resulted in altered early and late endosomal PI(3)P levels and rapid depletion of early endosome antigen-1. Membrane-bound MTM1 was directly complexed to the hVPS15/hVPS34 [vacuolar protein sorting (VPS)] PI 3-kinase complex with binding mediated by the WD40 domain of the hVPS15 (p150) adapter protein and independent of a GRAM-domain point mutation that blocks PI(3,5)P(2) binding. The WD40 domain of hVPS15 also constitutes the binding site for Rab7 and, as shown previously, contributes to Rab5 binding. In vivo, the hVPS15/hVPS34 PI 3-kinase complex forms mutually exclusive complexes with the Rab GTPases (Rab5 or Rab7) or with MTM1, suggesting a competitive binding mechanism. Thus, the Rab GTPases together with MTM1 likely serve as molecular switches for controlling the sequential synthesis and degradation of endosomal PI(3)P. Normal levels of endosomal PI(3)P and PI(3,5)P(2) are crucial for both endosomal morphology and function, suggesting that disruption of endosomal sorting and trafficking in skeletal muscle when MTM1 is mutated may be a key factor in precipitating X-linked MTM.
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Affiliation(s)
- Canhong Cao
- Molecular Trafficking Laboratory, Department of Pathology, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA
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38
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Previtali SC, Quattrini A, Bolino A. Charcot-Marie-Tooth type 4B demyelinating neuropathy: deciphering the role of MTMR phosphatases. Expert Rev Mol Med 2007; 9:1-16. [PMID: 17880751 DOI: 10.1017/s1462399407000439] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Charcot-Marie-Tooth type 4B (CMT4B) is a severe autosomal recessive neuropathy with demyelination and myelin outfoldings of the nerve. This disorder is genetically heterogeneous, but thus far, mutations in myotubularin-related 2 (MTMR2) and MTMR13 genes have been shown to underlie CMT4B1 and CMT4B2, respectively. MTMR2 and MTMR13 belong to a family of ubiquitously expressed proteins sharing homology with protein tyrosine phosphatases (PTPs). The MTMR family, which has 14 members in humans, comprises catalytically active proteins, such as MTMR2, and catalytically inactive proteins, such as MTMR13. Despite their homology with PTPs, catalytically active MTMR phosphatases dephosphorylate both PtdIns3P and PtdIns(3,5)P2 phosphoinositides. Thus, MTMR2 and MTMR13 may regulate vesicular trafficking in Schwann cells. Loss of these proteins could lead to uncontrolled folding of myelin and, ultimately, to CMT4B. In this review, we discuss recent findings on this interesting protein family with the main focus on MTMR2 and MTMR13 and their involvement in the biology of Schwann cell and CMT4B neuropathies.
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Affiliation(s)
- Stefano C Previtali
- Neuropathology Unit, Department of Neurology, San Raffaele Scientific Institute, Milan, Italy
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39
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Chojnowski A, Ravisé N, Bachelin C, Depienne C, Ruberg M, Brugg B, Laporte J, Baron-Van Evercooren A, LeGuern E. Silencing of the Charcot–Marie–Tooth associated MTMR2 gene decreases proliferation and enhances cell death in primary cultures of Schwann cells. Neurobiol Dis 2007; 26:323-31. [PMID: 17336078 DOI: 10.1016/j.nbd.2006.12.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2006] [Revised: 11/30/2006] [Accepted: 12/05/2006] [Indexed: 01/12/2023] Open
Abstract
Loss of function of the myotubularin (MTM)-related protein 2 (MTMR2) in Schwann cells causes Charcot-Marie-Tooth disease type 4B1, a severe demyelinating neuropathy, but the consequences of MTMR2 disruption in Schwann cells are unknown. We established the expression profile of MTMR2 by real-time RT-PCR during rat myelination and showed it to be preferentially expressed at the onset of the myelination period. We developed a model in which MTMR2 loss of function was reproduced in primary cultures of Schwann cells by RNA interference. We found that depletion of MTMR2 in Schwann cells decreased their rate of proliferation. Furthermore, when cultivated in serum-free medium, MTMR2 depletion increased the number of Schwann cells that died by a caspase-dependent process. These results support the hypothesis that loss of MTMR2 in patients, by decreasing Schwann cells proliferation and survival, may impair the first stages of myelination of the peripheral nervous system.
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Affiliation(s)
- Alexandre Chojnowski
- UMR 679 INSERM (formely U289)-Université Pierre et Marie Curie, IFR70, Faculté de Médecine Pierre et Marie Curie, Paris, France.
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40
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Ng DWK, Wang T, Chandrasekharan MB, Aramayo R, Kertbundit S, Hall TC. Plant SET domain-containing proteins: structure, function and regulation. ACTA ACUST UNITED AC 2007; 1769:316-29. [PMID: 17512990 PMCID: PMC2794661 DOI: 10.1016/j.bbaexp.2007.04.003] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2006] [Revised: 04/03/2007] [Accepted: 04/04/2007] [Indexed: 01/01/2023]
Abstract
Modification of the histone proteins that form the core around which chromosomal DNA is looped has profound epigenetic effects on the accessibility of the associated DNA for transcription, replication and repair. The SET domain is now recognized as generally having methyltransferase activity targeted to specific lysine residues of histone H3 or H4. There is considerable sequence conservation within the SET domain and within its flanking regions. Previous reviews have shown that SET proteins from Arabidopsis and maize fall into five classes according to their sequence and domain architectures. These classes generally reflect specificity for a particular substrate. SET proteins from rice were found to fall into similar groupings, strengthening the merit of the approach taken. Two additional classes, VI and VII, were established that include proteins with truncated/interrupted SET domains. Diverse mechanisms are involved in shaping the function and regulation of SET proteins. These include protein-protein interactions through both intra- and inter-molecular associations that are important in plant developmental processes, such as flowering time control and embryogenesis. Alternative splicing that can result in the generation of two to several different transcript isoforms is now known to be widespread. An exciting and tantalizing question is whether, or how, this alternative splicing affects gene function. For example, it is conceivable that one isoform may debilitate methyltransferase function whereas the other may enhance it, providing an opportunity for differential regulation. The review concludes with the speculation that modulation of SET protein function is mediated by antisense or sense-antisense RNA.
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Affiliation(s)
| | | | | | | | | | - Timothy C. Hall
- Corresponding author. Tel: 1-979-845-7728; fax: 1-979-862-4098,
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41
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Da Costa M, Bach L, Landrieu I, Bellec Y, Catrice O, Brown S, De Veylder L, Lippens G, Inzé D, Faure JD. Arabidopsis PASTICCINO2 is an antiphosphatase involved in regulation of cyclin-dependent kinase A. THE PLANT CELL 2006; 18:1426-37. [PMID: 16698944 PMCID: PMC1475488 DOI: 10.1105/tpc.105.040485] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2005] [Revised: 04/12/2006] [Accepted: 04/22/2006] [Indexed: 05/09/2023]
Abstract
PASTICCINO2 (PAS2), a member of the protein Tyr phosphatase-like family, is conserved among all eukaryotes and is characterized by a mutated catalytic site. The cellular functions of the Tyr phosphatase-like proteins are still unknown, even if they are essential in yeast and mammals. Here, we demonstrate that PAS2 interacts with a cyclin-dependent kinase (CDK) that is phosphorylated on Tyr and not with its unphosphorylated isoform. Phosphorylation of the conserved regulatory Tyr-15 is involved in the binding of CDK to PAS2. Loss of the PAS2 function dephosphorylated Arabidopsis thaliana CDKA;1 and upregulated its kinase activity. In accordance with its role as a negative regulator of the cell cycle, overexpression of PAS2 slowed down cell division in suspension cell cultures at the G2-to-M transition and early mitosis and inhibited Arabidopsis seedling growth. The latter was accompanied by altered leaf development and accelerated cotyledon senescence. PAS2 was localized in the cytoplasm of dividing cells but moved into the nucleus upon cell differentiation, suggesting that the balance between cell division and differentiation is regulated through the interaction between CDKA;1 and the antiphosphatase PAS2.
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Affiliation(s)
- Marco Da Costa
- Laboratoire de Biologie Cellulaire, Institut National de la Recherche Agronomique, F-78026 Versailles Cedex, France
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42
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Alvarez-Venegas R, Sadder M, Hlavacka A, Baluška F, Xia Y, Lu G, Firsov A, Sarath G, Moriyama H, Dubrovsky JG, Avramova Z. The Arabidopsis homolog of trithorax, ATX1, binds phosphatidylinositol 5-phosphate, and the two regulate a common set of target genes. Proc Natl Acad Sci U S A 2006; 103:6049-54. [PMID: 16585509 PMCID: PMC1458695 DOI: 10.1073/pnas.0600944103] [Citation(s) in RCA: 140] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2005] [Indexed: 01/04/2023] Open
Abstract
The Arabidopsis homolog of trithorax, ATX1, regulates numerous functions in Arabidopsis beyond the homeotic genes. Here, we identified genome-wide targets of ATX1 and showed that ATX1 is a receptor for a lipid messenger, phosphatidylinositol 5-phosphate, PI5P. PI5P negatively affects ATX1 activity, suggesting a regulatory pathway connecting lipid-signaling with nuclear functions. We propose a model to illustrate how plants may respond to stimuli (external or internal) that elevate cellular PI5P levels by altering expression of ATX1-controlled genes.
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Affiliation(s)
| | - Monther Sadder
- *School of Biological Sciences, University of Nebraska, Lincoln, NE 68588-0118
| | - Andrej Hlavacka
- Department of Plant Cell Biology, Institute of Botany, University of Bonn, Kirschallee 1, D-53115 Bonn, Germany
| | - František Baluška
- Department of Plant Cell Biology, Institute of Botany, University of Bonn, Kirschallee 1, D-53115 Bonn, Germany
| | | | - Guoqing Lu
- *School of Biological Sciences, University of Nebraska, Lincoln, NE 68588-0118
- Bioinformatics Core Research Facility, Center for Biotechnology, University of Nebraska, Lincoln, NE 68588-0665
| | - Alexey Firsov
- *School of Biological Sciences, University of Nebraska, Lincoln, NE 68588-0118
| | - Gautam Sarath
- United States Department of Agriculture, Agricultural Research Service Unit, East Campus, University of Nebraska, Lincoln, NE 68583-0939
| | - Hideaki Moriyama
- **Department of Chemistry, University of Nebraska, Lincoln, NE 68588-0304; and
| | - Joseph G. Dubrovsky
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apartado Postal 510-3, Cuernavaca Morelos, CP 62250, Mexico
| | - Zoya Avramova
- *School of Biological Sciences, University of Nebraska, Lincoln, NE 68588-0118
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43
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Duex JE, Tang F, Weisman LS. The Vac14p-Fig4p complex acts independently of Vac7p and couples PI3,5P2 synthesis and turnover. ACTA ACUST UNITED AC 2006; 172:693-704. [PMID: 16492811 PMCID: PMC2063702 DOI: 10.1083/jcb.200512105] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Phosphoinositide-signaling lipids function in diverse cellular pathways. Dynamic changes in the levels of these signaling lipids regulate multiple processes. In particular, when Saccharomyces cerevisiae cells are exposed to hyperosmotic shock, PI3,5P2 (phosphatidylinositol [PI] 3,5-bisphosphate) levels transiently increase 20-fold. This causes the vacuole to undergo multiple acute changes. Control of PI3,5P2 levels occurs through regulation of both its synthesis and turnover. Synthesis is catalyzed by the PI3P 5-kinase Fab1p, and turnover is catalyzed by the PI3,5P2 5-phosphatase Fig4p. In this study, we show that two putative Fab1p activators, Vac7p and Vac14p, independently regulate Fab1p activity. Although Vac7p only regulates Fab1p, surprisingly, we find that Vac14 regulates both Fab1p and Fig4p. Moreover, Fig4p itself functions in both PI3,5P2 synthesis and turnover. In both the absence and presence of Vac7p, the Vac14p-Fig4p complex controls the hyperosmotic shock-induced increase in PI3,5P2 levels. These findings suggest that the dynamic changes in PI3,5P2 are controlled through a tight coupling of synthesis and turnover.
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Affiliation(s)
- Jason E Duex
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
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44
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Abstract
The myotubularins (MTMs) constitute a large family of phosphoinositide lipid 3-phosphatases with specificity for PtdIns3P and PtdIns (3,5)P2. Mutations in MTM proteins are associated with inherited conditions such as myotubular myopathy and Charcot-Marie-Tooth syndrome. The substrate lipids are known to be regulators of the endosomal pathway through recruitment of specific effector proteins. Hydrolysis of PtdIns (3,5)P2 provides a biosynthetic pathway to the production of PtdIns5P, which itself can allosterically activate MTMs. We review the properties of this intriguing family of proteins and discuss potential physiological functions that include regulation of the endocytic pathway.
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Affiliation(s)
- Michael J Clague
- Physiological Laboratory, University of Liverpool, Crown St., Liverpool, L69 3BX, UK.
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45
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Begley MJ, Taylor GS, Brock MA, Ghosh P, Woods VL, Dixon JE. Molecular basis for substrate recognition by MTMR2, a myotubularin family phosphoinositide phosphatase. Proc Natl Acad Sci U S A 2006; 103:927-32. [PMID: 16410353 PMCID: PMC1347996 DOI: 10.1073/pnas.0510006103] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Myotubularins, a large family of catalytically active and inactive proteins, belong to a unique subgroup of protein tyrosine phosphatases that use inositol phospholipids, rather than phosphoproteins, as physiological substrates. Here, by integrating crystallographic and deuterium-exchange mass spectrometry studies of human myotubularin-related protein-2 (MTMR2) in complex with phosphoinositides, we define the molecular basis for this unique substrate specificity. Phosphoinositide substrates bind in a pocket located on a positively charged face of the protein, suggesting an electrostatic mechanism for membrane targeting. A flexible, hydrophobic helix makes extensive interactions with the diacylglycerol moieties of substrates, explaining the specificity for membrane-bound phosphoinositides. An extensive H-bonding network and charge-charge interactions within the active site pocket determine phosphoinositide headgroup specificity. The conservation of these specificity determinants within the active, but not the inactive, myotubularins provides insight into the functional differences between the active and inactive members.
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Affiliation(s)
- Michael J Begley
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
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46
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Berger P, Berger I, Schaffitzel C, Tersar K, Volkmer B, Suter U. Multi-level regulation of myotubularin-related protein-2 phosphatase activity by myotubularin-related protein-13/set-binding factor-2. Hum Mol Genet 2006; 15:569-79. [PMID: 16399794 DOI: 10.1093/hmg/ddi473] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Mutations in myotubularin-related protein-2 (MTMR2) or MTMR13/set-binding factor-2 (SBF2) genes are responsible for the severe autosomal recessive hereditary neuropathies, Charcot-Marie-Tooth disease (CMT) types 4B1 and 4B2, both characterized by reduced nerve conduction velocities, focally folded myelin sheaths and demyelination. MTMRs form a large family of conserved dual-specific phosphatases with enzymatically active and inactive members. We show that homodimeric active Mtmr2 interacts with homodimeric inactive Sbf2 in a tetrameric complex. This association dramatically increases the enzymatic activity of the complexed Mtmr2 towards phosphatidylinositol 3-phosphate and phosphatidylinositol 3,5-bisphosphate. Mtmr2 and Sbf2 are considerably, but not completely, co-localized in the cellular cytoplasm. On membranes of large vesicles formed under hypo-osmotic conditions, Sbf2 favorably competes with Mtmr2 for binding sites. Our data are consistent with a model suggesting that, at a given cellular location, Mtmr2 phosphatase activity is highly regulated, being high in the Mtmr2/Sbf2 complex, moderate if Mtmr2 is not associated with Sbf2 or functionally blocked by competition through Sbf2 for membrane-binding sites.
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Affiliation(s)
- Philipp Berger
- Institute of Cell Biology, Dept. of Biology, Swiss Federal Institute of Technology ETH-Hönggerberg, CH-8093 Zürich, Switzerland
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47
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Begley MJ, Dixon JE. The structure and regulation of myotubularin phosphatases. Curr Opin Struct Biol 2005; 15:614-20. [PMID: 16289848 DOI: 10.1016/j.sbi.2005.10.016] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2005] [Revised: 10/17/2005] [Accepted: 10/21/2005] [Indexed: 11/18/2022]
Abstract
The human neuromuscular diseases X-linked myotubular myopathy and Charcot-Marie-Tooth disease type 4B are caused by mutations in myotubularin family proteins. The myotubularins are a unique subfamily of protein tyrosine phosphatases that utilize inositol phospholipids, rather than phosphoproteins, as substrates. Recent structural studies, including the first crystal structure of a myotubularin family protein, have defined the structural features that are characteristic of the family and revealed the molecular basis of their unique substrate specificity. Interestingly, the myotubularin family contains a subgroup of proteins that are catalytically inactive. Recent biochemical studies have established that the inactive myotubularins function as adaptors for the active members and play an important regulatory role within the family.
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Affiliation(s)
- Michael J Begley
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 2093-0721, USA
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48
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Howell GR, Munroe RJ, Schimenti JC. Transgenic rescue of the mouse t complex haplolethal locus Thl1. Mamm Genome 2005; 16:838-46. [PMID: 16284799 DOI: 10.1007/s00335-005-0045-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2005] [Accepted: 07/07/2005] [Indexed: 10/25/2022]
Abstract
Chromosomal deletions can uncover haploinsufficient or imprinted regions of the genome. Previously, the haploinsufficient locus t haplolethal 1 (Thl1) was identified and localized to a 1.3-Mb region using overlapping deletions around the Sod2 and D17Leh94 loci of the mouse t complex on Chr 17. Germline chimeric mice, produced from embryonic stem (ES) cells containing radiation-induced deletions of the Thl1 locus, never produced viable deletion-bearing progeny when mated to C57BL/6J (B6) females. However, deletion-bearing offspring could be obtained by mating to females of other strains. In this article we describe a transgenic approach to narrow the critical region for Thl1. BAC clones were introduced into a deletion-bearing ES cell line and one was shown to rescue the Thl1 phenotype, reducing the critical region to 140 kb. Analysis of the gene content of this region suggests two strong Thl1 candidates, Pdcd2 and a novel SET domain-containing gene termed Tset1. A more detailed analysis using mice carrying overlapping deletions identified subregions that influence the phenotypic characteristics of Thl1 hemizygotes.
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Affiliation(s)
- Gareth R Howell
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine 04660, USA
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49
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Zhang J, Mruk DD, Cheng CY. Myotubularin phosphoinositide phosphatases, protein phosphatases, and kinases: their roles in junction dynamics and spermatogenesis. J Cell Physiol 2005; 204:470-83. [PMID: 15690393 DOI: 10.1002/jcp.20303] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Spermatogenesis in the seminiferous epithelium of the mammalian testis is a dynamic cellular event. It involves extensive restructuring at the Sertoli-germ cell interface, permitting germ cells to traverse the epithelium from basal to adluminal compartment. As such, Sertoli-germ cell actin-based adherens junctions (AJ), such as ectoplasmic specializations (ES), must disassemble and reassemble to facilitate this event. Recent studies have shown that AJ dynamics are regulated by intricate interactions between AJ integral membrane proteins (e.g., cadherins, alpha6beta1 integrins and nectins), phosphatases, kinases, adaptors, and the underlying cytoskeleton network. For instance, the myotubularin (MTM) phosphoinositide (PI) phosphatases, such as MTM related protein 2 (MTMR2), can form a functional complex with c-Src (a non-receptor protein tyrosine kinase). In turn, this phosphatase/kinase complex associates with beta-catenin, a constituent of the N-cadherin/beta-catenin functional unit at the AJ site. This MTMR2-c-Src-beta-catenin complex apparently regulates the phosphorylation status of beta-catenin, which determines cell adhesive function conferred by the cadherin-catenin protein complex in the seminiferous epithelium. In this review, we discuss the current status of research on selected phosphatases and kinases, and how these proteins potentially interact with adaptors at AJ in the seminiferous epithelium to regulate cell adhesion in the testis. Specific research areas that are open for further investigation are also highlighted.
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Affiliation(s)
- Jiayi Zhang
- Population Council, Center for Biomedical Research, New York, New York, USA
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50
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Pierson CR, Tomczak K, Agrawal P, Moghadaszadeh B, Beggs AH. X-linked myotubular and centronuclear myopathies. J Neuropathol Exp Neurol 2005; 64:555-64. [PMID: 16042307 DOI: 10.1097/01.jnen.0000171653.17213.2e] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Recent work has significantly enhanced our understanding of the centronuclear myopathies and, in particular, myotubular myopathy. These myopathies share similar morphologic appearances with other diseases, namely the presence of hypotrophic myofibers with prominent internalized or centrally placed nuclei. Early workers suggested that this alteration represented an arrest in myofiber maturation, while other hypotheses implicated either failure in myofiber maturation or neurogenic causes. Despite similarities in morphology, distinct patterns of inheritance and some differences in clinical features have been recognized among cases. A severe form, known as X-linked myotubular myopathy (XLMTM), presents at or near birth. Affected males have profound global hypotonia and weakness, accompanied by respiratory difficulties that often require ventilation. Most of these patients die in infancy or early childhood, but some survive into later childhood or even adulthood. The responsible gene (MTM1) has been cloned; it encodes a phosphoinositide lipid phosphatase known as myotubularin that appears to be important in muscle maintenance. In autosomal recessive centronuclear myopathy (AR CNM), the onset of weakness typically occurs in infancy or early childhood. Some investigators have divided AR CNM into 3 subgroups: 1) an early-onset form with ophthalmoparesis, 2) an early-onset form without ophthalmoparesis, and 3) a late-onset form without ophthalmoparesis. Clinically, autosomal dominant CNM (AD CNM) is relatively mild and usually presents in adults with a diffuse weakness that is slowly progressive and may be accompanied by muscle hypertrophy. Overall, the autosomal disorders are not as clinically uniform as XLMTM, which has made their genetic characterization more difficult. Currently the responsible gene(s) remain unknown. This review will explore the historical evolution in understanding of these myopathies and give an update on their histopathologic features, genetics and pathogenesis.
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MESH Headings
- Adult
- Diagnosis, Differential
- Female
- Genetic Diseases, X-Linked/genetics
- Genetic Diseases, X-Linked/pathology
- Genetic Diseases, X-Linked/physiopathology
- Humans
- Male
- Muscle, Skeletal/pathology
- Myopathies, Structural, Congenital/genetics
- Myopathies, Structural, Congenital/pathology
- Myopathies, Structural, Congenital/physiopathology
- Protein Tyrosine Phosphatases/genetics
- Protein Tyrosine Phosphatases, Non-Receptor
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