Human Molecular Genetics Advance Access originally published online on August 12, 2003
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Human Molecular Genetics, 2003, Vol. 12, Review Issue 2 R285-R292
DOI: 10.1093/hmg/ddg273
© 2003 Oxford University Press
Myotubularins, a large disease-associated family of cooperating catalytically active and inactive phosphoinositides phosphatases
1IGBMC, CNRS/INSERM/ULP, Illkirch, France and 2Dulbecco Telethon Institute, DIBIT, San Raffaele Scientific Institute, Milan, Italy
Received July 28, 2003; Accepted August 4, 2003
| ABSTRACT |
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The myotubularin family is a large eukaryotic group within the tyrosine/dual-specificity phosphatase super-family (PTP/DSP). Among the 14 human members, three are mutated in genetic diseases: myotubular myopathy and two forms of CharcotMarieTooth neuropathy. We present an analysis of the myotubularin family in sequenced genomes. The myotubularin family encompasses catalytically active and inactive phosphatases, and both classes are well conserved from nematode to man. Catalytically active myotubularins dephosphorylate phosphatidylinositol 3-phosphate (PtdIns3P) and PtdIns3,5P2, leading to the production of PtdIns and PtdIns5P. This activity may be modulated by direct interaction with catalytically inactive myotubularins. These phosphoinositides are signaling molecules that are notably involved in vacuolar transport and membrane trafficking. Myotubularins are thus proposed to be implicated in these cellular mechanisms, and recent observations on myotubularins homologues in the nematode Caenorhabditis elegans indicate a role in endocytosis.
| INTRODUCTION |
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The myotubularin family constitutes a large group within the tyrosine/dual-specificity phosphatase super-family (PTP/DSP) and members are present in almost all eukaryotic organisms (see below), including yeasts and plants. The founder member, myotubularin (encoded by the MTM1 gene), was shown to be mutated in X-linked myotubular myopathy (XLMTM) by positional cloning. Two other members were more recently found mutated in two forms of demyelinating CharcotMarieTooth (CMT) neuropathy type 4B. These ubiquitously expressed myotubularins are thus implicated in diseases affecting different tissues. The myotubularin family encompasses catalytically active and inactive phosphatases. Surprisingly, recent data suggest that there is a functional cooperation between members of these two classes. This review focuses on recent advances concerning the biochemical and putative cellular functions of myotubularins and the associated human diseases or phenotypes in model organisms. We also present an overview of the evolution of this family based on the analysis of sequenced genomes.
| THE MYOTUBULARIN FAMILY |
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The myotubularin family contains 14 genes in human, named MTM1 and MTMRelated 1 to 13, and at least two pseudogenes (see legend to Fig. 1). In Metazoa, it can be divided into six subgroups, each with one member in Caenorhabditis elegans and Drosophila melanogaster (14) (Figs 1 and 2). They all share homologies with the active site of tyrosine and dual-specificity phosphatases (5). Interestingly, three of the subgroups encompass catalytically inactive myotubularins bearing conserved mutations of the residues essential for the phosphatase activity (cysteine and arginine in the CX5R motif present in all PTP/DSP; Fig. 1). However, the overall homology with PTP/DSP remains and the aspartate at position 380 in human MTM1 is conserved in all members.
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Protein domains
Myotubularins all share the same protein domains core. Sequences alignment, domain prediction and functional analysis suggest that they all consist of the four following domains: GRAM, RID, PTP/DSP active site homology and SID (Fig. 1). In addition, some members bear phosphoinositides binding and protein interaction domains.
The GRAM domain (Glucosyltransferase, Rab-like GTPase Activator and Myotubularins) is also found in a number of proteins implicated in the regulation of membrane processes (6). It represents a divergent PH (Pleckstrin Homology) domain and may have the capacity to bind phosphoinositides (4,7).
The RID (Rac-Induced recruitment Domain) was defined as necessary for the recruitment of myotubularin and homologues (MTMR2, MTMR3 and MTMR9) to plasma membrane ruffles induced by constitutively activated Rac GTPase (8,9). This region may also mediate interaction with the neurofilament light chain (NF-L) protein in the case of MTMR2 (amino acids 160300) (10).
The catalytic activity of myotubularins should implicate, as for the PTP/DSPs, three essential amino acids. The cysteine and arginine residues of the CX5R motif in the catalytic pocket form a covalent thiophosphate intermediate and stabilize the phosphoryl group respectively (5). An aspartate residue participates in the release of the substrate. Although this amino acid has not been unambiguously identified, mutation of aspartate 278 in MTM1, conserved in all active members from yeast to human, leads to complete loss of phosphatase activity and to specific localization at plasma membrane extensions (11). Whether the degenerated phosphatase consensus of the catalytically inactive myotubularins can still bind the substrates is not known.
The SET-interacting domain (SID) consists of a pair of amphipatic helices and was initially described as mediating interaction of the catalytically inactive myotubularin homologue MTMR5 with the SET (Su(var), Enhancer of zeste, Trithorax) domain of ALL1, the human orthologue of trithorax implicated in leukaemias (12,13). The SET domain has a histone methyltransferase activity (13,14). While myotubularins appear in general to have a cytoplasmic or plasma membrane localization in transfection studies, nuclear localization has been reported in some studies (10,15). For instance, while MTMR5 is cytoplasmic, deletion of part of its DENN domain leads to localization in the nucleus and acquisition of transforming properties (16). Thus, although a role of myotubularins in the nucleus has not yet been directly demonstrated, they could participate in the regulation of chromatin remodeling. The SID has also been recently proposed to mediate interaction between myotubularin (MTM1) and the catalytically inactive phosphatase MTMR12 (3-PAP) (see below) (17).
Disease-causing missense mutations have been found in each of these domains, suggesting that they all participate in the function of myotubularins (1822). Missense mutations are, however, predominant in the RID and in the PTP/DSP homology region of MTM1, in myotubular myopathy.
Other domains are found only in a subset of myotubularins but are interestingly related to phosphoinositides and membrane-trafficking pathways. FYVE (Fab1p, YO1B, Vac1p and EEA1) and PH domains are proposed to bind either specifically to PtdIns3P or to various phosphoinositides, respectively (23). Only the PH domain of MTMR5 was confirmed to bind to PtdIns3,4P2 and PtdIns3,4,5P3 (24). The MTMR5/R13 subgroup also contains a DENN (differentially expressed in neoplastic versus normal cells) domain found in some regulators of GTPases (for example, Rab3GEF involved in exocytosis), which could represent a new GTPase effector domain (25). Additional domains include predicted coiled-coil domains at the C-terminus of nearly all myotubularins, which appear important for heterodimerization between MTMR2 and MTMR5 and between MTMR7 and MTMR9 (see below) (26,27), and a PDZ (PSD-95/Dlg/ZO-1) binding site at the C-terminus of human proteins of the MTM1 and MTMR5 subgroups (28).
Phylogenetic relationship and evolution
As numerous genomes have been recently sequenced, the phylogeny and timescale evoution of gene families are becoming better understood (29). We looked for the appearance and possible co-evolution of myotubularins subgroups. Procaryotes do not contain clear myotubularin homologues. Fungi genomes contains one myotubularin with a consensus active site, except the fully sequenced Aspergillus terreus, which has no myotubularin. The obligate intracellular parasite Encephalitozoon cuniculi (Microsporidia) does not have myotubularins, also suggesting that these proteins appeared in yeast. In both budding yeast (S. cerevisiae) and fission yeast (S. pombe), deletion of the single myotubularin gene does not cause an obvious phenotype, indicating that in these unicellular organisms, myotubularin function is dispensable at least under laboratory conditions (11,30).
Catalytically inactive myotubularins appear very early in evolution, as they are found in Giardia lamblia, Dictyostelium discoideum and Entamoeba histolytica. These organisms also have several myotubularins with CX5R consensus active sites, like in the kinetoplastida (leshmania and trypanosoma). In contrast, absence of myotubularins in the apicomplexa Plasmodium vivax suggests that its functions have been lost or replaced in this intracellular parasitic organism. No catalytically inactive myotubularins have been found in plants to date and Arabidopsis thaliana contains only two putatively active myotubularins.
In all metazoa, the myotubularin family is divided into three catalytically active and three catalytically inactive subgroups (Fig. 2), except in the urochordate Ciona intestinalis where we have found no MTMR3 subgroup member to date. The functional separation of MTM1, MTMR1 and MTMR2, and of MTMR5 and MTMR13 appeared with the vertebrates, as individual orthologues of these genes are found in fugu and zebrafish. At present, it is uncertain whether the three catalytically inactive phosphatase subgroups evolved from a single inactive ancestor or by recurrent very ancient events from active phosphatases. The HsMTMR6/7/8 subgroup appears the most closely related to the yeast orthologues and has lost its FYVE domain in vertebrates (present in C. elegans and drosophila but absent in human and fishes).
| FUNCTIONS AND REGULATION |
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Biochemical functions
Although catalytically active myotubularins share extensive conservation with the active site of PTP/DSP, it was surprising to find that they dephosphorylate phosphoinositides instead of phosphoaminoacids (11,30). Phosphoinositides are second messengers implicated in a wide range of cellular processes from growth factor response and proliferation to differentiation and transport. In vitro, catalytically active myotubularins (MTM1, MTMR2, MTMR3, MTMR4, MTMR6 and MTMR7) are specific 3-phosphatases for phosphatidylinositol 3-monophosphate (PtdIns3P) (9,11,27,3034) and phosphatidylinositol 3,5-biphosphate (PtdIns3,5P2) (7,31,33) (see Fig. 3A for the structure of phosphatidylinositol and metabolism of phosphoinositides). Dephosphorylation of PtdIns3P has also been shown in yeast and mammalian cells. PtdIns3P and Rab GTPases are the two key players that regulate endosome trafficking and fusion (35,36). The activated state of Rab GTPases (GTP-bound) is regulated by Rab GAP (GTPase activating proteins) and GEF (GTPases effectors) while PtdIns3P is synthetized by the type III PI 3-kinase homologue of yeast VPS (vacuolar protein sorting) (35). Thus myotubularins could represent a fourth type of regulator of endosome trafficking, by dephosphorylating PtdIns3P.
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The role of PtdIns3,5P2 has mainly been studied in yeast and it was shown to be important for vacuolar homeostasis and membrane trafficking (37,38). PtdIns3,5P2 dephosphorylation by myotubularins produces PtdIns5P, a recently discovered phosphoinositide of unknown function (39). Lately, the PtdIns5P binding property of the nuclear protein ING2, a modulator of histone acetyl transferase and deacetylase activities, has been shown to be required for its ability to activate p53-dependent apoptotic pathways (40). It has also been proposed that PtdIns5P acts as a positive allosteric regulator of myotubularin enzymatic activity, and addition of PtdIns3P and PtdIns5P in vitro promotes oligomerization of myotubularin into a ring heptameric structure (7). The physiological action of catalytically active myotubularins (regulation of PtdIns3P and/or PtdIns3,5P2 levels, or production of PtdIns5P) remains to be discovered (Fig. 3A). For some myotubularins, the same phosphoinositide can act both as a ligand and as a substrate. For example, MTMR3 contains a FYVE domain and dephosphorylates PtdIns3P, which is also a substrate for the formation of PtdIns3,5P2 by PtdIns3P 5-kinase (39).
Putative cellular functions
Catalytically active myotubularins are cytoplasmic proteins that do not co-localize with PtdIns3P onto endosomes in transfected cells (8). Thus there should be some mechanisms to target these enzymes to their site of action, either directly through a phosphoinositides binding domain (such as the GRAM or FYVE domains), or indirectly through protein interactors. MTMR2 (the gene mutated in CMT4B) interacts with NF-L, the neurofilament light chain protein specifically expressed in the nervous system both in Schwann cells and in neurons (10). NF-L is one of the major component of the neuronal cytoskeleton. Membrane trafficking is very important for the plasma membrane remodeling of myelin forming Schwann cells.
Overexpression of human myotubularins in yeast (MTM1, MTMR2 and MTMR3) or mammalian cells (MTMR3 inactive mutant) leads to enlarged vacuoles (9,11,31), suggesting that endogenous myotubularins could be implicated in vacuolar transport or fusion. Ablation of the mouse orthologues of MTM1 and MTMR5 also leads to the formation of abnormal vacuoles respectively in muscle (41) and Sertoli cells (42). In the nematode C. elegans, decreased expression of the orthologue of the human MTMR6 subgroup (called F53a2.8) compensates for the loss-of-function of the VPS34 PI 3-kinase homologue, strongly suggesting that this myotubularin subgroup indeed participates in the regulation of PtdIns3P level (43). RNA inhibition of orthologues of human MTMR3/4, MTMR6/7/8 and MTMR9 subgroups (T24a11.1, F53a2.8 and Y39h10a.3) disrupts endocytosis by C. elegans coelomocytes, scavenger cells (43,44). Interestingly, these experiments suggest that both catalytically active (MTMR6/7/8) and inactive (MTMR9) myotubularins are implicated in the same uptake pathway. The mechanisms by which myotubularins may regulate endocytosis have not been reported yet.
A role of myotubularins at the plasma membrane is also suspected as overexpression of the MTM1 protein in mammalian cells lead to altered shape and plasma membrane projections (8,34). Moreover, constitutively activated Rac1 GTPase leads to recruitment of myotubularins and homologues to plasma membrane ruffles independent of catalytic activity (8,9).
Functional redundancy and specificity
One can wonder why there are so many myotubularins in human and mouse. The catalytically active ones show identical substrate specificity in vitro, high sequence homology (especially within a subgroup) and an overall ubiquitous expression. The fact that loss-of-function of MTM1, MTMR2 or MTMR13 leads to observable and rather severe phenotypes (myotubular myopathy and CMT4B neuropathies) indicates that they possess some tissue-specific role that cannot be compensated by other members of the family. Lack of MTM1 causes a very similar muscle phenotype in man and mouse (41,45) indicating that this specificity is indeed a characteristic of the gene (muscle-specific regulation) and/or of the protein (muscle-specific function). MTM1 is increased at the RNA and protein level during myoblasts fusion in culture (34,46). In contrast, expression of Mtmr2 mRNA is stronger in peripheral nervous system, the tissue affected in CMT4B, with high level in neurons (33,47). In vivo, MTMR2 protein is both cytoplasmic and nuclear in Schwann cells and motor neurons and only cytoplasmic in sensory neurons (10). Further suggestions for a specific protein function is the observation that subcellular localization differs slightly between myotubularins when co-localization is performed in transfected cells. MTMR2 and MTMR3 are more concentrated around the nucleus compared to MTM1 and MTMR1 (9,34,48). Such results suggest that different myotubularins may regulate different phosphoinositides subcellular pools.
Functional regulation and cooperation
The fact that two forms of demyelinating CMT4B neuropathy are due to loss-of-function mutations in either a catalytically active phosphatase, MTMR2 (18), or inactive phosphatase, MTMR13 (49,50), is not in accordance with the hypothesis that the so-called dead-phosphatases would compete with their active homologues for the substrate (12,51) (competition model in Fig. 3B). Recent studies have shown that catalytically inactive myotubularins can heterodimerize with active homologues. This might promote a higher substrate turnover either by increasing the enzymatic activity or by recruitment to specific phosphoinositides subpools (cooperation model in Fig. 3B). Physical interactions have been reported to date between MTMR2 and MTMR5 (26) and between MTM1 and MTMR12 (17,52) and between MTMR7 and MTMR9 (27). Interaction of MTM1 and MTMR2 with inactive homologues appears to promote their recruitment to specific subcellular localizations while MTMR7 in vitro enzymatic activity is increased in the heterodimer MTMR7/MTMR9. The heterodimers might also have a modified substrate specificity, as the MTM1MTMR12 heterodimer purified from platelets can dephosphorylate PtdIns3,4P2 (52). However, isolated MTM1 activity on this substrate was not tested in this report. Heterodimers might also acquire new functions (Fig. 3B). These results suggest that there might be complex interactions between the 14 human myotubularin proteins. The formation of these heterodimers might have a key role in the regulation of the function of myotubularins in different tissues.
| ASSOCIATED DISEASES AND PHENOTYPES |
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Congenital myopathies
Myotubular myopathy (XLMTM) is a usually very severe congenital myopathy associated with major hypotonia at birth (45,53). The histopathology of skeletal muscle reveals small rounded fibers with central nuclei. The nuclei are surrounded by a region devoid of contractile apparatus but with a high density of mitochondria and other organites. This pattern is somewhat similar to the structure of fetal myotubes, while mature muscle fibers have peripherally located nuclei. Central nuclei can also be observed in regenerating muscle (for instance in the mdx mouse model of Duchenne muscular dystrophy). MTM1 mutations have been reported in more than 300 patients, including more than 60 different missense mutations that affect conserved domains of myotubularin (2022,54). Some of these missense mutations are found in patients with a mild phenotype. The oldest surviving patient reported, a 67-year-old male, carries a N180K missense affecting a residue between the GRAM and the RID domains. Involvement of nonmuscle tissues has been observed in some patients with prolonged survival (55), such as hepatic peliosis, an internal bleeding disorder. The Mtm1 knockout mice recapitulate the histopathological signs of XLMTM and show a progressive myopathy starting a few weeks after birth while muscle histology appears normal at birth. This suggests that the disorganized appearance of the muscle fibers is due to a defect in structural maintenance rather than an impairment in myogenesis as previously hypothesized. No signs of active regeneration were observed in the mouse model. Specific ablation of the gene in skeletal muscle showed that it is the primary tissue involved in the pathology (41). The MTMR1 gene is adjacent to MTM1 on the X chromosome. No mutations associated to MTMR1 have been found to date in myotubular myopathy (56). However, a muscle-specific transcript, which appears after myoblasts fusion, is decreased in cells and muscle from patients with the congenital form of myotonic dystrophy (cDM1) (48). The cause of cDM1 is a large CTG expansion in the 3'UTR of the DMPK gene and is believed to interfere with transcription and splicing of other genes (57). MTMR1 altered splicing might thus account for part of the cDM1 phenotype, which is clinically close to myotubular myopathy.
CharcotMarieTooth neuropathies
CharcotMarieTooth (CMT) disease is the most frequent class of inherited disorder of the peripheral nervous system and is classified into demyelinating and axonal neuropathies. Of the 30 mapped loci, 15 disease genes have been identified so far (58) and code for structural proteins of myelin (PMP22, MPZ, GJB1, periaxin), of axons (neurofilament light chain and kinesin 1B), and of the nuclear envelope (lamin A/C) (59), for the EGR2 transcription factor, the Rab7 GTPase (60), GDAP1 (61,62), LITAF/SIMPLE (63), the glycyl tRNA synthetase (64) and the N-myc downstream regulated protein 1.
Recently, a catalytically active and an inactive member of the myotubularin family (MTMR2 and MTMR13/Sbf2 respectively) have been identified as mutated in two demyelinating recessive forms of CMT type 4B (CMT4B). CMT4B1 is caused by MTMR2 loss-of-function mutations (18), while mutations in MTMR13/Sbf2 are responsible for CMT4B2 associated or not with infantile glaucoma (49,50). This disease is characterized by childhood onset, symmetrical distal and proximal muscular weakness starting at the lower extremities, sensory loss and severely decreased nerve conduction velocity. A hallmark of this disorder is the presence of myelin outfoldings in peripheral nerves. The fact that CMT4B2 phenotype is very similar to CMT4B1, and that MTMR5 (the closest homologue of MTMR13) interacts with MTMR2, strongly suggests that MTMR13 may directly regulate MTMR2 activity. The interaction between MTMR2 and NF-L support the notion that hereditary demyelinating and axonal neuropathies may represent different clinical manifestations of a common pathological mechanism.
MTMR13 is the first catalytically inactive phosphatase mutated in a human disorder. Loss-of-function of other dead-phosphatases have been achieved recently in mouse for STYX (65) and MTMR5. For the latter, mice demonstrate impaired spermatogenesis and azoospermia (42). Interestingly, expression of the rat Mtmr2 gene is high in testis and increases when inter-Sertoli junctions are formed in vitro (66). Moreover, the follow-up of one CMT4B male patient has revealed the presence of azoospermia (Dr Paola Mandich, personal communication), suggesting that MTMR2, in association with MTMR5, also has a role in spermatogenesis and/or spermiogenesis.
Candidate diseases
Myotubularin homologues are very good candidate genes for other forms of CMT neuropathies, DejerineSottas syndrome, and congenital hypomyelinating neuropathies (58,67), centronuclear myopathies with histopathology related to XLMTM (68) and glaucomas (69). The role of the murine MTMR5 gene in spermatogenesis makes the human gene a good candidate for male infertility on chromosome 22qter. The chromosomal localization of the genes encoding myotubularins (Fig. 1) and the nascent understanding of their cellular functions provide good candidates for disease with intracellular transport anomalies.
| CONCLUSION |
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Future studies of the myotubularin family should decipher the physiological functions and tissue-specificity of the different members. The hypothesis that catalytically inactive phosphatases could regulate phosphorylation level by cooperating with active phosphatases is a new concept and brings a third player into the opposing couple kinase/phosphatase. Myotubularins could also be responsible for the production of PtdIns5P, the function of which remains unknown. Their action on PtdIns3P and PtdIns3,5P2 suggests that anomalies of membrane trafficking and protein transport are the cause of the associated human disorders. However, the relationship between such mechanisms and the tissue phenotype observed in myotubular myopathy and type 4B CharcotMarieTooth neuropathy remains mysterious.
| ACKNOWLEDGEMENTS |
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We wish to thank Harshal Nandurkar, Hanna Fares and Paola Mandich for sharing unpublished results and Laurent Bianchetti and Olivier Poch for help with bio-informatics analysis. This work was supported by INSERM, CNRS, Hôpital Universitaire de Strasbourg and by grants from the Association Francaise contre les Myopathies. A.B. is supported by Telethon-Italy and is an Assistant Telethon Scientist from the Dulbecco Telethon Institute.
| FOOTNOTES |
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* To whom correspondence should be addressed at: IGBMC, 1 rue Laurent Fries, BP 10142, 67404 Illkirch, France. Tel: +33 388653244; Fax: +33 388653246; Email: mtm{at}titus.u-strasbg.fr
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