A sea urchin gene encoding dystrophin-related proteins

Farewell to Professor David Yaffe - A pillar of the myogenesis field

It is with great sadness that we have learned about the passing of Professor David Yaffe (1929-2020, Israel). Yehi Zichro Baruch - May his memory be a blessing. David was a man of family, science and nature. A native of Israel, David grew up in the historic years that preceded the birth of the State of Israel. He was a member of the group that established Kibbutz Revivim in the Negev desert, and in 1948 participated in Israel's War of Independence. David and Ruth eventually joined Kibbutz Givat Brenner by Rehovot, permitting David to be both a kibbutz member and a life-long researcher at the Weizmann Institute of Science, where David received his PhD in 1959. David returned to the Institute after his postdoc at Stanford. Here, after several years of researching a number of tissues as models for studying the process of differentiation, David entered the myogenesis field and stayed with it to his last day. With his dedication to the field of myogenesis and his commitment to furthering the understanding of the People and the Land of Israel throughout the international scientific community, David organized the first ever myogenesis meeting that took place in Shoresh, Israel in 1975. This was followed by the 1980 myogenesis meeting at the same place and many more outstanding meetings, all of which brought together myogenesis, nature and scenery. Herein, through the preparation and publication of this current manuscript, we are meeting once again at a "David Yaffe myogenesis meeting". Some of us have been members of the Yaffe lab, some of us have known David as his national and international colleagues in the myology field. One of our contributors has also known (and communicates here) about David Yaffe's earlier years as a kibbutznick in the Negev. Our collective reflections are a tribute to Professor David Yaffe. We are fortunate that the European Journal of Translational Myology has provided us with tremendous input and a platform for holding this 2020 distance meeting "Farwell to Professor David Yaffe - A Pillar of the Myogenesis Field".

Dystrophin gene expression and intracellular calcium changes in the giant freshwater prawn, Macrobrachium rosenbergii, in response to white spot symptom disease infection

Background

Dystrophin, an essential protein functional in the maintenance of muscle structural integrity is known to be responsible for muscle deterioration during white spot syndrome virus (WSSV) infection among prawn species. Previous studies have shown the upregulation of dystrophin protein in Macrobrachium rosenbergii (the giant freshwater prawn) upon white spot syndrome virus (WSSV) infection. The literature has also suggested the important role of calcium ion alterations in causing such muscle diseases. Thus, the interest of this study lies within the linkage between dystrophin functioning, intracellular calcium and white spot syndrome virus (WSSV) infection condition.

Methods

In this study, the dystrophin gene from M. rosenbergii (MrDys) was first characterised followed by the characterization of dystrophin gene from a closely related shrimp species, Penaeus monodon (PmDys). Dystrophin sequences from different phyla were then used for evolutionary comparison through BLAST analysis, conserved domain analysis and phylogenetic analysis. The changes in mRNA expression levels of dystrophin and the alteration of intracellular calcium concentrations in WSSV infected muscle cells were then studied.

Results

A 1246 base pair long dystrophin sequence was identified in the giant freshwater prawn, Macrobrachium rosenbergii (MrDys) followed by 1082 base pair long dystrophin sequence in P. monodon (PmDys). Four conserved domains were identified from the thirteen dystrophin sequences compared which were classified into 5 different phyla. From the phylogenetic analysis, aside from PmDys, the characterised MrDys was shown to be most similar to the invertebrate phylum of Nematoda. In addition, an initial down-regulation of dystrophin gene expression followed by eventual up-regulation, together with an increase in intracellular calcium concentration [Ca²⁺]_i were shown upon WSSV experimental infection.

Discussion

Both the functionality of the dystrophin protein and the intracellular calcium concentration were affected by WSSV infection which resulted in progressive muscle degeneration. An increased understanding of the role of dystrophin-calcium in MrDys and the interactions between these two components is necessary to prevent or reduce occurrences of muscle degeneration caused by WSSV infection, thereby reducing economic losses in the prawn farming industry from such disease.

Apoptosis: Focus on sea urchin development

It has been proposed that the apoptosis is an essential requirement for the evolution of all animals, in fact the apoptotic program is highly conserved from nematodes to mammals. Throughout development, apoptosis is employed by multicellular organisms to eliminate damaged or unnecessary cells. Here, we will discuss both developmental programmed cell death (PCD) under normal conditions and stress induced apoptosis, in sea urchin embryos. Sea urchin represent an excellent model system for studying embryogenesis and cellular processes involved in metamorphosis. PCD plays an essential role in sculpting and remodelling the embryos and larvae undergoing metamorphosis. Moreover, this marine organism directly interacts with its environment, and is susceptible to effects of several aquatic contaminants. Apoptosis can be adopted as a defence mechanism against any environmental chemical, physical and mechanical stress, for removing irreversibly damaged cells. This review, while not comprehensive in its reporting, aims to provide an overview of current knowledge on mechanisms to regulate physiological and the induced apoptotic program in sea urchin embryos.

The dystrotelin, dystrophin and dystrobrevin superfamily: new paralogues and old isoforms

BACKGROUND

Dystrophins and dystrobrevins are distantly related proteins with important but poorly understood roles in the function of metazoan muscular and neuronal tissues. Defects in them and their associated proteins cause a range of neuromuscular disorders. Members of this superfamily have been discovered in a relatively serendipitous way; we set out to compile a comprehensive description of dystrophin- and dystrobrevin-related sequences from available metazoan genome sequences, validated in representative organisms by RT-PCR, or acquired de novo from key species.

RESULTS

Features of the superfamily revealed by our survey include: a) Dystrotelin, an entirely novel branch of the superfamily, present in most vertebrates examined. Dystrotelin is expressed in the central nervous system, and is a possible orthologue of Drosophila DAH. We describe the preliminary characterisation of its function, evolution and expression. b) A novel vertebrate member of the dystrobrevin family, gamma-dystrobrevin, an ancient branch now extant only in fish, but probably present in our own ancestors. Like dystrophin, zebrafish gamma-dystrobrevin mRNA is localised to myosepta. c) The extent of conservation of alternative splicing and alternative promoter use in the dystrophin and dystrobrevin genes; alternative splicing of dystrophin exons 73 and 78 and alpha-dystrobrevin exon 13 are conserved across vertebrates, as are the use of the Dp116, Dp71 and G-utrophin promoters; the Dp260 and Dp140 promoters are tetrapod innovations. d) The evolution of the unique N-terminus of DRP2 and its relationship to Dp116 and G-utrophin. e) A C-terminally truncated common ancestor of dystrophin and utrophin in cyclostomes. f) A severely restricted repertoire of dystrophin complex components in ascidians.

CONCLUSION

We have refined our understanding of the evolutionary history and isoform diversity of the five previously reported vertebrate superfamily members and describe two novel members, dystrotelin and gamma-dystrobrevin. Dystrotelins, dystrophins and dystrobrevins are roughly equally related to each other. Vertebrates therefore have a repertoire of seven superfamily members (three dystrophins, three dystrobevins, and one dystrotelin), with one lost in tetrapods. Most invertebrates studied have one member from each branch. Although the basic shared function which is implied by the common architecture of these distantly related proteins remains unclear, it clearly permeates metazoan biology.

The proteome of the developing tooth of the sea urchin,Lytechinus variegatus: mortalin is a constituent of the developing cell syncytium

Echinoderm teeth are continuously growing calcite-mineralized tissues of complex structure. Two features are of special interest: (1) cell division takes place in a restricted aboral domain, the plumula, and the cells immediately merge into multinucleated syncytial layers; (2) the major part of the heavily mineralized tooth elongates and moves towards the adoral incisal tip continuously as the syncytial cells actively expand the syncytium and intermembrane mineral phase. As the first step to understanding the nature of the mineralization processes, we have isolated the proteins of the plumula and of the mature mineralized portions of the tooth, and begun their characterization. Peptide sequences were used to screen a plumula cDNA library by polymerase chain reaction. One primer set yielded a prominent amplified product which was cloned, and sequenced. Comparison with the nucleotide and protein data banks revealed the protein to be Mortalin, a member of the hsp-70 family, with >75% of its sequences identical to that of human mortalin. Immunocytochemical localization of mortalin within the plumula, using Anti-human Grp75, showed staining of the odontoblast cytosol and matrix at the point where syncytial formation was occurring. The cytosol of the syncytial layers was weakly stained. The nuclei within the syncytia were stained at their periphery. In the mature part of the tooth, the perinuclear staining of the nuclei was more prominent. We conclude that mortalin is involved in syncytium formation and maintenance. The urchin mortalin has a distinctive aspartic acid and serine-rich C-terminal domain that may link it to the mineralization process.

The Drosophila homologue of the dystrophin gene - introns containing promoters are the major contributors to the large size of the gene

We show that the drosophila gene encoding the dystrophin-like protein (DLP) is as complex as the mammalian dystrophin gene. Three 5' promoters and three internal promoters regulate the expression of three full-length and three truncated products, respectively. The existence of this complex gene structure in such evolutionary remote organisms suggests that both types of products have diverse important functions. The promoters of both the DLP gene and the mammalian dystrophin gene are located in very large introns. These introns contribute significantly to the large size of the genes. The possible relevance of the conservation of the large size of introns containing promoters to the regulation of promoter activity is discussed.

Invertebrate Muscles: Muscle Specific Genes and Proteins

This is the first of a projected series of canonic reviews covering all invertebrate muscle literature prior to 2005 and covers muscle genes and proteins except those involved in excitation-contraction coupling (e.g., the ryanodine receptor) and those forming ligand- and voltage-dependent channels. Two themes are of primary importance. The first is the evolutionary antiquity of muscle proteins. Actin, myosin, and tropomyosin (at least, the presence of other muscle proteins in these organisms has not been examined) exist in muscle-like cells in Radiata, and almost all muscle proteins are present across Bilateria, implying that the first Bilaterian had a complete, or near-complete, complement of present-day muscle proteins. The second is the extraordinary diversity of protein isoforms and genetic mechanisms for producing them. This rich diversity suggests that studying invertebrate muscle proteins and genes can be usefully applied to resolve phylogenetic relationships and to understand protein assembly coevolution. Fully achieving these goals, however, will require examination of a much broader range of species than has been heretofore performed.

Cell adhesion and communication: a lesson from echinoderm embryos for the exploitation of new therapeutic tools

In this chapter, we summarise fundamental findings concerning echinoderms as well as research interests on this phylum for biomedical and evolutionary studies. We discuss how current knowledge of echinoderm biology, in particular of the sea urchin system, can shed light on the understanding of important biological phenomena and in dissecting them at the molecular level. The general principles of sea urchin embryo development are summarised, mainly focusing on cell communication and interactions, with particular attention to the cell-extracellular matrix and cell-cell adhesion molecules and related proteins. Our purpose is not to review all the work done over the years in the field of cellular interaction in echinoderms. On the contrary, we will rather focus on a few arguments in an effort to re-examine some ideas and concepts, with the aim of promoting discussion in this rapidly growing field and opening new routes for research on innovative therapeutic tools.

Comparative analysis of vertebrate dystrophin loci indicate intron gigantism as a common feature

The human DMD gene is the largest known to date, spanning > 2000 kb on the X chromosome. The gene size is mainly accounted for by huge intronic regions. We sequenced 190 kb of Fugu rubripes (pufferfish) genomic DNA corresponding to the complete dystrophin gene (FrDMD) and provide the first report of gene structure and sequence comparison among dystrophin genomic sequences from different vertebrate organisms. Almost all intron positions and phases are conserved between FrDMD and its mammalian counterparts, and the predicted protein product of the Fugu gene displays 55% identity and 71% similarity to human dystrophin. In analogy to the human gene, FrDMD presents several-fold longer than average intronic regions. Analysis of intron sequences of the human and murine genes revealed that they are extremely conserved in size and that a similar fraction of total intron length is represented by repetitive elements; moreover, our data indicate that intron expansion through repeat accumulation in the two orthologs is the result of independent insertional events. The hypothesis that intron length might be functionally relevant to the DMD gene regulation is proposed and substantiated by the finding that dystrophin intron gigantism is common to the three vertebrate genes.

The 3'-untranslated region of the dystrophin gene - conservation and consequences of loss

The 3'-untranslated region (3'UTR) of some vertebrate dystrophin genes shows an extraordinary degree and extent of conservation (better than that of many coding regions), a phenomenon that remains unexplained. We examine novel sequence and mutational data to explore the possible reasons for this. We show that loss of the human dystrophin 3'UTR is sufficient to cause Becker muscular dystrophy with pronounced reduction in dystrophin protein levels. The acquisition of dystrophin 3'UTR sequence from an amphibian and a cartilaginous fish allows us to refine previously identified functionally constrained regions which might account for the observed phenotype. These comprise (a) the open reading frame encoding the ancestral 'alternative' amphipathic C-terminal alpha-helix, normally removed from adult dystrophin by inclusion of a poorly conserved frameshifting penultimate exon, and (b) two highly conserved untranslated regions ('Lemaire A', 350 nucleotides and 'Lemaire D', 250 nucleotides) separated by a non-conserved 700-2000-nucleotide spacer. We consider the possibility that the 3'UTR may represent a significant target for pathogenic mutations.

Molecular cloning and characterization of dystrophin and Dp71, two products of the Duchenne Muscular Dystrophy gene, in zebrafish

Dystrophin, the protein responsible for Duchenne Muscular Dystrophy (DMD), plays a critical role in the maintenance of the muscle membrane integrity. There are several forms of dystrophin derived from the DMD gene by alternative promoter usage. In addition to full-length dystrophin (Dp427), four shorter transcripts have been identified: Dp260, Dp140, Dp116 and Dp71. The functional role played by the different products of the DMD gene is not yet determined. To get insight into the function of dystrophin and related products, we have investigated the presence of dystrophin in zebrafish. This choice takes advantage of large-scale mutagenesis screens in zebrafish, which have led to the identification of several mutants with motility defects. The identification and characterization of the genes affected by these mutations is likely to provide relevant information for the understanding of the molecular mechanisms of muscle development and function. Two cDNA clones encoding the homologues of dystrophin and Dp71 in zebrafish were identified and characterized. Both transcripts exhibit a high degree of sequence homology with the dystrophin and Dp71 proteins described in higher vertebrates. In addition, three alternative spliced transcripts that occur at the C-terminal end of the zebrafish DMD gene have been identified. These transcripts exhibit different patterns of tissue expression. We have also determined the chromosomal localization of dystrophin on the radiation hybrid map of the zebrafish genome. Our results indicate that the dystrophin gene is localized to linkage group one. Altogether, these results give new insights on the physiological role played by dystrophin and related proteins, and provide new tools for the identification of mutated genes associated with muscle defects in zebrafish.

Variations in dystrophin complex in red and white caudal muscles from Torpedo marmorata

We present an up-to-date study on the nature, at the protein level, of various members of the dystrophin complex at the muscle cell membrane by comparing red and white caudal muscles from Torpedo marmorata. Our investigations involved immunodetection approaches and Western blotting analysis. We determined the presence or absence of different molecules belonging to the dystrophin family complex by analyzing their localization and molecular weight. Specific antibodies directed against dystrophin, i.e., DRP2 alpha-dystrobrevin, beta-dystroglycan, alpha-syntrophin, alpha-, beta-, gamma-, and delta-sarcoglycan, and sarcospan, were used. The immunofluorescence study (confocal microscopy) showed differences in positive immunoreactions at the sarcolemmal membrane in these slow-type and fast-type skeletal muscle fibers. Protein extracts from T. marmorata red and white muscles were analyzed by Western blotting and confirmed the presence of dystrophin and associated proteins at the expected molecular weights. Differences were confirmed by comparative immunoprecipitation analysis of enriched membrane preparations with anti-beta-dystroglycan polyclonal antibody. These experiments revealed clear complex or non-complex formation between members of the dystrophin system, depending on the muscle type analyzed. Differences in the potential function of these various dystrophin complexes in fast or slow muscle fibers are discussed in relation to previous data obtained in corresponding mammalian tissues. (J Histochem Cytochem 49:857-865, 2001)

Dystrophin-associated proteins in obliquely striated muscle of the leech Pontobdella muricata (Annelida, Hirudinea)

The distribution of dystrophin-associated proteins (beta-dystroglycan, alpha-, beta-, gamma- and delta-sarcoglycan, alpha-syntrophin and sarcospan) were studied in obliquely striated muscle of the leech Pontobdella muricata. Western blot analysis and immunohistochemical electron microscopy, using various polyclonal antibodies, were employed. Western blot analysis of all of these antibodies showed a single band, with approximately the same molecular weights as similar proteins detected in vertebrate muscles. The immunoelectron microscopy study confirmed specific immunogold labelling in the membrane of muscle cells. Since all dystrophin complex components have similar molecular weights and the same localisation in leech as in vertebrate skeletal muscle, we assume that these proteins have similar properties in leech and vertebrate muscle. The presence of these molecules in annelid muscles, together with a short version of dystrophin (previously described as IDLp-140) is of particular interest since phylogenetic and functional studies on this material could help to shed new light on the role and function of this complex in the muscle membrane.

The dystrophin / utrophin homologues in Drosophila and in sea urchin

The gene which is defective in Duchenne muscular dystrophy (DMD) is the largest known gene containing at least 79 introns, some of which are extremely large. The product of the gene in muscle, dystrophin, is a 427 kDa protein. The same gene encodes at least two additional non-muscle full length dystrophin isoforms transcribed from different promoters located in the 5'-end region of the gene, and four smaller proteins transcribed from internal promoters located further downstream, and lack important domains of dystrophin. Several other genes, encoding evolutionarily related proteins, have been identified. To study the evolution of the DMD gene and the significance of its various products, we have searched for genes encoding dystrophin-like proteins in sea urchin and in Drosophila. We previously reported on the characterization of a sea urchin gene encoding a protein which is an evolutionary homologue of Dp116, one of the small products of the mammalian DMD gene, and on the partial sequencing of a large product of the same gene. Here we describe the full-length product which shows strong structural similarity and sequence identity to human dystrophin and utrophin. We also describe a Drosophila gene closely related to the human dystrophin gene. Like the human gene, the Drosophila gene encodes at least three isoforms of full length dystrophin-like proteins (dmDLP1, dmDLP2 and dmDLP3,), regulated by different promoters located at the 5' end of the gene, and a smaller product regulated by an internal promoter (dmDp186). As in mammals, dmDp186 and the dmDLPs share the same C-terminal and cysteine-rich domains which are very similar to the corresponding domains in human dystrophin and utrophin. In addition, dmDp186 contains four of the spectrin-like repeats of the dmDLPs and a unique N-terminal region of 512 amino acids encoded by a single exon. The full length products and the small product have distinct patterns of expression. Thus, the complex structure of the dystrophin gene, encoding several large dystrophin-like isoforms and smaller truncated products with different patterns of expression, existed before the divergence between the protostomes and deuterostomes. The conservation of this gene structure in such distantly related organisms, points to important distinct functions of the multiple products.

Mitochondrial expression of a short dystrophin-like product with molecular weight of 71 kDa

In the brain, Dp71 is the most abundant protein product of the DMD gene and by alternative splicing of exon 78 two isoforms can be expressed, Dp71d and Dp71f. To explore the subcellular distribution of these Dp71 isoforms, specific monoclonal antibodies were used. Dp71d (with exon 78) was found in microsomes, while Dp71f (without exon 78) was detected in mitochondria. To determine the alterations which the absence of dystrophin proteins induces, we compared the expression of Dp71d in microsomes and Dp71f in mitochondria from mdx and mdx(3CV) mice. Dp71d in microsomes of mdx was similar to that of wild-type mice and, as expected, in mdx(3CV) this protein was undetectable. However, in mitochondria from mdx(3CV), Dp71f was overexpressed in comparison to mitochondria from mdx mice. Because in mdx(3CV) mice all the dystrophin proteins are mutated or diminished, we concluded that the protein detected in mitochondria is not a Dp71f but a novel product named Dp71f-like protein.

Presence of invertebrate dystrophin-like products in obliquely striated muscle of the leech, Pontobdella muricata (Annelida, Hirudinea)

Dystrophin is a 427-kDa cytoskeletal protein, which occurs in scant amounts in vertebrate muscle and nerve cells. No previous references to dystrophin or associated proteins in invertebrates at the protein level have been found, while two recent studies investigated the presence of genes encoding proteins homologous to dystrophin in sea urchin and other invertebrates such as Drosophila melanogaster. In this study, the possible presence and distribution of dystrophin-like proteins were studied in different invertebrate muscle cell types and species through Western blot analysis and light and electron microscope immunohistochemistry using a panel of antibodies whose specificities have been determined in vertebrates. Crude protein extracts of leech Pontobdella muricata were analysed by Western blotting. The revealed protein band, with 140 kDa molecular weight, was related to dystrophin, utrophin or dystrophin-related protein-2 (DRP2) according to the specificities of the antibodies used to detect them. The immunofluorescence study showed positive immunoreactions in obliquely striated muscle of this hyrudinean. The immunoelectron microscopy study confirmed specific immunogold labelling beneath the sarcolemma of muscle cells. We thus assume that this protein is an invertebrate dystrophin-like product that is referred to as IDLp140. The potential functions of this invertebrate dystrophin-like protein in invertebrate muscles are discussed relative to previous data in vertebrate tissues.