Demosponge and sea anemone fibrillar collagen diversity reveals the early emergence of A/C clades and the maintenance of the modular structure of type V/XI collagens from sponge to human

Abstract

Collagens are often considered a metazoan hallmark, with the fibril-forming fibrillar collagens present from sponges to human. From evolutionary studies, three fibrillar collagen clades (named A, B, and C) have been defined and shown to be present in mammals, whereas the emergence of the A and B clades predates the protostome/deuterostome split. Moreover, several C clade fibrillar collagen chains are present in some invertebrate deuterostome genomes but not in protostomes whose genomes have been sequenced. The newly sequenced genomes of the choanoflagellate Monosiga brevicollis, the demosponge Amphimedon queenslandica, and the cnidarians Hydra magnipapillata (Hydra) and Nematostella vectensis (sea anemone) allow us to have a better understanding of the origin and evolution of fibrillar collagens. Analysis of these genomes suggests that an ancestral fibrillar collagen gene arose at the dawn of the Metazoa, before the divergence of sponge and eumetazoan lineages. The duplication events leading to the formation of the three fibrillar collagen clades (A, B, and C) occurred before the eumetazoan radiation. Interestingly, only the B clade fibrillar collagens preserved their characteristic modular structure from sponge to human. This observation is compatible with the suggested primordial function of type V/XI fibrillar collagens in the initiation of the formation of the collagen fibrils.

FIGURE 1.

Modular structure of sponge and sea anemone fibrillar collagens and of choanoflagellate collagen-like proteins. A–C, the general modular architecture of human members of the three fibrillar collagen clades (A), sponge (B), and sea anemone (C) α chains is depicted. For each α chain, the Arabic numbers under their domain architecture indicate the lengths in amino acids of the major triple helices. For the sponge fibrillar collagens chains, the Arabic numbers above the glycine substitutions and Gly-Xaa-Yaa-Zaa imperfections represent their precise location according to their numbering in the major triple helix. Under the A. queenslandica α chains, the solid lines represent regions confirmed by EST and RT-PCR sequences, and the dashed lines indicate that these sequences were deduced from genomic analysis. Amq, marine demosponge A. queenslandica; Emu, freshwater demosponge E. mülleri; Nve, starlet sea anemone N. vectensis;?, undetermined sequence. D, putative proteins including triple helical or COLF1 (C-propeptide) modules present in the choanoflagellate M. brevicollis. The accession numbers of the predicted M. brevicollis proteins are indicated below their modular representation. The Arabic numbers under the triple helix indicate their lengths in amino acids. In this figure, the different modules are not represented to scale.

FIGURE 2.

Gene-specific RT-PCR of 5 collagen genes during the Amphimedon life cycle. Columns correspond to the different stages. E, embryogenesis; L, larva; M, metamorphosis; A, adult. The embryogenesis, larva, and metamorphosis stages correspond to a pool of embryos, larvae, and postlarvae of different ages, respectively.

FIGURE 3.

Representative multiple alignments of the TSPN module from sponge, starlet sea anemone, and human fibrillar collagen chains. The alignments were generated with ClustalW, and gray boxes denote sequence identity (Threshold = 0.75). See Table 1 for abbreviations.

FIGURE 4.

Representative multiple alignments of the COLF1 module from choanoflagellate, sponge, and sea anemone proteins. The alignments were generated with ClustalW. The gray boxes and asterisks denote sequence identity (Threshold = 0.66) and perfectly conserved amino acids between the proteins analyzed, respectively. Numbering of the cysteine residues is indicated above the multiple alignments. See Table 1 and Fig. 1D for abbreviations.

FIGURE 5.

Phylogenetic analyses of metazoan fibrillar collagen chains. Representative Bayesian and ML trees are shown for metazoan (A) and sponge/bilaterian (B) fibrillar collagen chains. These trees are inferred from the major triple helical sequences. The numbers above branches indicate percentage of Bayesian posterior probability ≥95, whereas the numbers below indicate ML bootstrap support ≥65 and ML/NJ bootstrap support ≥65 in trees represented in A and B, respectively. The different clusters discussed in the text are indicated on the right-hand side of each tree. Nodes observed in both Bayesian and ML trees are highlighted by open circles. For the sponge/bilaterian fibrillar collagen analysis, closed circles indicated nodes observed in ML, NJ, and Bayesian trees. A T indicates the presence of a TSPN module in the N-propeptide of the fibrillar collagen chains. Stars indicate Bayesian posterior probabilities and ML bootstrap supports below the cut-off but discussed in the text. In B, the tree was rooted using the midpoint rooting method and the retree editor from the PHYLIP package (32).

FIGURE 6.

Early evolution of the fibrillar collagen family. In this model, we propose that an ancestral fibrillar collagen gene arose in the lineage leading up to the Metazoa. Indeed, the choanoflagellate M. brevicollis possesses genes encoding either triple helical or COLF1 module, whereas in demosponges several fibrillar collagen genes are present. From modular structure comparison and phylogenetic analysis, we propose that the split into the three fibrillar collagen clades occurred before the Parazoa/Eumetazoa split. Regarding the A clade, demosponges and cnidarians have several fibrillar collagen chains related to this clade. The acquisition of a VWC module in the N-propeptide domain of an A clade-related chain occurred at the base of the Bilateria, possibly evolving from a WAP module present in cnidarians. Some protostomes have lost gene(s) encoding A clade collagens. Regarding the B/C clade, two different scenarios (H1 and H2) are proposed. In hypothesis H1, demosponges possess fibrillar collagen chains descended from an ancestral B/C clade fibrillar collagen chain containing a TSPN module in its N-propeptide. In this scenario, the emergence of B and C clades occurred between Parazoa-Eumetazoa and Cnidaria-Bilateria splits. In hypothesis H2, the divergence of B and C clades from an ancestral B/C clade α chain predated metazoan cladogenesis. Whatever the scenario, the B clade seems to correspond to the most conserved fibrillar collagen family, whether it is at the modular level (from sponge to human) or at the sequence level (from sea anemone to human).