Independent evolution of striated muscles in cnidarians and bilaterians

Abstract

Results and discussion

Cnidarians and bilaterians^{1, 3-5}, as well as a single ctenophore species⁶, share smooth and striated muscle cell types, which are absent in other non-bilaterian phyla (i.e. sponges and placozoans). The characteristic striation is due to the reiteration of a contractile unit, the sarcomere, composed of alternating assemblies of myosin-based thick filaments and actin-based thin filaments, bordered by the supporting z-discs^{3, 7, 8}. The strong ultrastructural similarities of striated muscles are highly suggestive of a common evolutionary origin^{1, 2} but independent origins have been discussed^{4, 5}. We have reassessed muscle evolution by genome mining and molecular phylogenetic approaches coupled with expression analysis in sponges and cnidarians. A comparative analysis of 47 bilaterian muscle components in 22 completely sequenced genomes of species representing metazoans, closest-related protists, fungi, and representatives of other eukaryotic groups allowed us to reconstruct key steps in muscle evolution (Fig.1, Supplementary Fig.1). First, we identified a core set of contractile proteins that predates muscle evolution and is conserved amongst metazoans, holozoan protists, fungi and amoebozoans (Fig. 1a and Supplementary Fig. 1a,b). This set comprises actin, myosin type II heavy chain (MyHC) and their associated proteins (Myosin light chains, Tropomyosin and Calmodulin). Presumably, this actomyosin machinery fulfilled basic cytoskeletal roles (e.g. cell division or shape changes) in the common ancestor of these various multi- and unicellular organisms before adopting additional roles in muscle contraction during animal evolution. Second, we identified Myosin light chain kinase (MLCK) as a metazoan innovation, which allowed for the tight regulation of actomyosin contraction by coupling Regulatory Light Chain (RLC) phosphorylation to elevated cytoplasmic Ca²⁺ concentrations in muscle and non-muscle cells^{9, 10} (Supplementary Fig. 1b,d). Notably, all associated regulatory components, except Caldesmon, are present in all animals (Fig.1a, Supplementary Fig. 1b). Hence, of the different known modes of muscle contraction regulation⁹, MLCK-dependent RLC phosphorylation appears most ancient. A third major finding is that not one of the 47 structural or regulatory proteins we analysed is uniquely shared between cnidarians and bilaterians, i.e. no protein correlates with the evolutionary origin of muscle. These observations suggest that the core contractile apparatus in eumetazoan muscles antedates the origin of the animal kingdom and that lineage-specific innovations underlie muscle evolution in cnidarians and bilaterians.

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Figure 1

Complex phylogenomic distribution of contractile machinery (a) and z-disc interactome (b) components

Rows: gene names of vertebrate and/or D. melanogaster contractile machinery (a) or z-disc complex (b) components. Columns: species and their phylogenetic relationship^{29, 30}. Asterisk: only a preliminary assembly without gene predictions was available for M. leidyi. Row labels in (a): site of predominant gene expression; in (b): species with reported z-disc localization of the gene product. Multifamily protein and uncertain orthologies supported by further molecular phylogenetic and protein domain analyses (Supplementary Figs. 2, 6, 7). All abbreviations in Supplementary Table 1.

Previous studies suggested that a gene duplication event gave rise to two distinct phylogenetic groups of myhc orthologues in bilaterian animals, each having a distinct function and pattern of expression^11-13. Bilaterian “non-muscle” orthologues (MyHC-nm) function during common cellular processes (e.g. cell division or migration) and during vertebrate smooth muscle contraction¹⁴, while bilaterian “muscle” orthologues (MyHC-st) function specifically in vertebrate striated muscles and in both smooth and striated muscles of protostomes¹⁵. Counter-intuitively, our analyses demonstrate that the gene duplication that generated the two MyHC orthology groups occurred much earlier than the origin of muscle cells (Fig.2, Supplementary Fig.2). Bilaterians, cnidarians, ctenophores, placozoans and sponges (the latter two lacking muscles) each possess at least one of each MyHC-nm and MyHC-st orthologues with specific coiled-coil domain structures, while the unicellular organisms Capsaspora owczarzaki, Sphaeroforma arctica and choanoflagellates possess a clear member of the MyHC-nm group, characterized by a specific coiled-coil structure (except in the reduced choanoflagellate MyHCs) (Fig.2, Supplementary Fig.2). The tree topology strongly indicates that the myhc-st and myhc-nm genes had already separated in the last common ancestor of all animals and the aforementioned protists, with the latter having later lost myhc-st (Fig.2, Supplementary Figs. 1d, 2).

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Figure 2

Ancient myhc gene duplication predated animal radiation

Maximum likelihood phylogenetic tree of MyHC type II proteins with nodes collapsed if they diverged between neighbour-joining, maximum likelihood, or Bayesian inference. The nesting of protist MyHCs within the MyHC-nm orthology group supports a myhc duplication event in the common ancestor of Metazoa, Choanoflagellata, Filasterea and Ichthyosporea, but also assumes secondary losses of myhc-st genes in protist phyla. Diagrams: MyHC domain structures. Final alignment length: 1730 a.a. Scale bar: 0.2 changes per site. Coloured numbers: positions of non-canonical coiled-coil domains. a.a.: amino acid. Species abbreviations, sequence accession and protein model numbers in Supplementary Table 1.

To address how myhc-st and myhc-nm are used in non-bilaterian animals, we investigated their deployment in two sponges, generally considered to lack muscles, as well as two cnidarian species harbouring striated and smooth muscles (Fig.3, Supplementary Figs. 3-6). In Tethya wilhelma, a demosponge, myhc-nm expression was detected in a wide variety of cell types (Supplementary Fig. 3a-g) including the pinacocytes, primarily responsible for the peristalsis-like contractions of the adult sponge¹⁶ (Supplementary Fig. 3e). In contrast, Tw-myhc-st expression is restricted to the outlet pore (apopyle) of the current-producing choanocyte chambers (Fig. 3a,c, Supplementary Fig. 3h-k), the site of a sieve-like cell type (Fig. 3b,c and Supplementary Fig. 4) proposed to regulate the water flow¹⁷. In larvae of the demosponge Amphimedon queenslandica, the myhc orthologues were found differentially expressed in regions of presumptive cell shape change or migration¹⁸, with Aq-myhc-nm more broadly expressed than Aq-myhc-st (Supplementary Fig.5). We conclude that the segregation of a “general function” myhc-nm orthologue, and a more specialised myhc-st orthologue had already occurred in the last common ancestor of demosponges and all other animals, accounting for their evolutionary retention over long times.

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Figure 3

Expression of myhc-st in a demosponge, and in anthozoan and hydrozoan cnidarians

In situ hybridisations (a, d-g, l-o) and schematic representations (c, h-k, p-r) of myhc-st expression in the adult demosponge Tethya wilhelma (a,c), the anthozoan Nematostella vectensis (d-k), and the hydrozoan Clytia hemisphaerica (l-r). Scanning electron microscopy image (b) and schematic representation (c) of a sectionned choanocyte chambers of T. wilhelma. Tw-myhc-st-expressing multi-porous cells (b, white arrows, inlet; c, red) are likely involved in water flow (blue dotted arrows) regulation through choanocyte chambers (within dotted white lines). (o) Velum of a young medusa was lifted. Developmental stages: (d-e, h-i) 4 days old planula; (f,k) 9 days old primary polyps; (l-m, p-q) medusal buds; (n-o, r) young medusae; (a-c, g) adults. (a,g) Cross-sections of stained animals; (d-g, l-o) whole-mount micrographs. Views: (d,f,h,k-l,p,r) lateral; (e,i, m-o,q) oral. Aboral towards top (d,h,r) or lower-right (f, k-l, p). Asterisk: mouth. ap: apopyle, cc: choanocyte chamber; exc: excurrent channel; inc: incurrent channel; mh: mesohyl; pp: prosopyle; rc: ring canal; rm: retractor muscle; su: subumbrella; tb: tentacle bulb; tm: tentacle muscle; v: velum. Scale bar: 10μm.

In cnidarians, we found myhc-st orthologs prominently expressed in fast-contracting muscle cells, but also in a few non-muscle cell types. In the sea anemone Nematostella vectensis (with smooth muscles only), myhc-st (formerly termed Nv-myhc1¹⁹) is strongly expressed in the tentacle and body column retractor muscles that contract oral-aborally during escape response (Fig. 3d-k). Nv-myhc-nm on the other hand is broadly expressed in the whole endoderm, hence in all endodermal epitheliomuscular cells (Supplementary Fig. 6a-c). In the hydrozoan Clytia hemisphaerica, myhc-st expression is detected in the developing striated ring muscles of the velum and the subumbrella (Fig. 3l-r; Supplementary Fig. 6g-k) that propel the medusa by fast contractions. It is further detected in the tentacles and the mouth tube ectoderm (manubrium)(Fig. 3n,r), which both include longitudinal smooth muscles. Ch-myhc-nm, like Nv-myhc-nm, is expressed broadly in the endoderm including the smooth muscle-rich gastrovascular system, and in non-muscle cells of the tentacle bulb nematocyte precursor region (Supplementary Fig. 6d-f). Thus, in both cnidarian species examined, myhc-st is predominantly expressed in fast-contracting muscles while the broad myhc-nm expression includes smooth and non-muscle cell types. A clear segregation of function between a muscle- and a more general-purpose MyHC is thus observed, albeit less pronounced than in bilaterians.

MyHC-st is the predominant motor protein in all striated muscles so far investigated, but its deployment in smooth retractor muscles in Nematostella shows that it is not sufficient to confer striation. We therefore examined the presence of other striated muscle components in cnidarians. A hallmark of striated muscle regulation and formation in bilaterians is the Troponin complex, comprising Troponin I, C and T^{9, 20}. To our surprise, none of the corresponding genes could be found in the genome sequences of the non-bilaterian species, the cnidarians Nematostella vectensis, Acropora digitifera or Hydra magnipapillata, the ctenophore Mnemiopsis leidyi, the placozoan Trichoplax adherens, or in the deeply sequenced transcriptome of Clytia hemisphaerica medusae (Fig. 1a, Supplementary Fig. 1a,d), indicating that muscle striation or the regulation of contraction are not Troponin-dependent in these organisms.

Concerning components of the z-disc^21-23, a marked lack of conservation was discovered even within the Bilateria. Nearly half of the known vertebrate (13 out of 28) and a quarter of the known Drosophila melanogaster (2 out of 8) z-disc proteins^21-23 are uniquely present (Fig. 1b) or have unique protein domain structures (Supplementary Fig. 7a,e; 8a) in either chordates or D. melanogaster. Of the remaining proteins, only 4 orthologue groups localise to the z-disc in both taxa: the actin-scaffolding protein α-Actinin, its binding partners Muscle-Lim and Ldb3/Zasp, and the giant Titin proteins, which regulate sarcomeric length and integrity (Fig. 1b). Thus, a considerable part of the complex vertebrate and insect z-disc interactomes evolved by the recruitment of novel, lineage-specific proteins to a “proto-z-disc” complex of only 4 proteins present in their last common ancestor (Supplementary Fig. 1c).

Of the four “proto-z-disc” components, only the general, hence uninformative, cellular actin cross-linker α-actinin is expressed during striated muscle formation in jellyfish MuscleLim and ldb3/zasp, like α-actinin, originated before animal evolution (Fig. 1b, Supplementary Figs.1c, 7b-d). Their expression was not, however, detected in developing or differentiated striated muscles in C. hemisphaerica medusae (compare Fig. 4a-f and Fig. 3m,n,q,r), but rather was concentrated in endodermal radial canals and other endodermal structures (Fig.4). Similarly, Nv-ldb3/zasp and Nv-muscleLim²⁴ gene expression was detected throughout the endoderm (Supplementary Fig. 10) and therefore in all types of smooth epithelial muscle cells except the ectodermal tentacle retractor muscles. Titin appears absent in non-bilaterians, as Immunglobulin / Fibronectin type III (Fn)-domain super-repeats, characteristic of the giant Titin proteins^{25, 26} were not identified in any predicted proteins from non-bilaterian genomes (Fig.1b, Supplementary Figs. 8b,c).

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Figure 4

Absence of Clytia hemisphaerica muscleLim and Ch-ldb3/zasp expression in striated muscles

In situ hybridisation (a-d) and schematic representation (e-f) of Ch-muscleLim (a, b), Ch-ldb3/zasp (c, d) expression mainly restricte to the developing radial canal endoderm (a-f). Ch-myhc-st-positive subumbrella striated muscle precursor cells (arrows, compare with Fig. 3m) do not show muscleLim- or ldb3/zasp-expression. Stages: medusal bud (a,c,e), young medusa (b,d,f). All oral views.

Proteins found in the z-discs of Drosophila melanogaster but so far not in the vertebrate z-discs appear to be absent outside Bilateria. Amongst vertebrate z-disc components not detected in D. melanogaster z-discs, many play general roles in the cytoskeleton (capZ-α, capZ-β, lasp), signal transduction (calcineurin A and calcineurin B) or protein degradation (trim9/67 ubiquitin ligase). Orthologues of these genes are expressed ubiquitously in C. hemisphaerica (Supplementary Fig.9) and in N. vectensis (Supplementary Fig.11). Finally, Obscurin, a giant sarcomeric protein anchored in vertebrate but not the Drosophila z-discs and predominantly expressed in striated muscles of vertebrates, flies and nematodes²⁷ is expressed throughout all tissue layers of C. hemisphaerica (Supplementary Fig.9g) and in the smooth muscle-forming N. vectensis endoderm (Supplementary Fig. 11kk-mm), suggesting a more general role in cnidarians.

To conclude, we have shown that cnidarians lack all molecular hallmarks of bilaterian striated muscles except myhc-st expression, and thus striated muscles in Bilateria and Hydrozoa are very likely to have evolved convergently from cells with an ancient contractile machinery (Supplementary Fig.1d). This may also apply to the striated muscles of the ctenophore Euplokamis sp.^{4, 6}, as suggested by their isolated occurence within the ctenophores. We suggest that the observed correlation between myhc-st expression and striated muscles in bilaterians and hydrozoan jellyfish is due to functional constraints: MyHC-st-based “bipolar” thick filaments (as found in vertebrate and protostome striated muscles) may favour a faster contraction and reiteration of the acto-myosin machinery when compared with MyHC-nm-based “side-polar” thick filaments (as found in vertebrate smooth and non-muscle cells)²⁸. Our work revealed that the origin of many components integral to muscle cell function (notably MyHC-st) predates that of muscle cells, while others (such as the Troponin complex, Paramyosin or Titin) were acquired progressively during muscle specialisations in different animal groups (Supplementary Fig. 1d). A similar scenario may also apply to other complex cell types. Our analysis of striated muscle evolution therefore highlights that ultrastructural similarity alone is not a reliable indication of common evolutionary origin, but can be achieved independently by different sets of proteins.

Methods summary

Details of animal husbandry, genome mining, protein domain structure, phylogenetic and expression analyses, cloning, microscopy and image processing are found in Methods.

Methods

Supplementary Material

Acknowledgements

Footnotes

References

Supplementary References