The evolution of the vertebrate metzincins; insights from Ciona intestinalis and Danio rerio

Abstract

Background: The metzincins are a large gene superfamily of proteases characterized by the presence of a zinc protease domain, and include the ADAM, ADAMTS, BMP1/TLL, meprin and MMP genes. Metzincins are involved in the proteolysis of a wide variety of proteins, including those of the extracellular matrix. The metzincin gene superfamily comprises eighty proteins in the human genome and ninety-three in the mouse. When and how the level of complexity apparent in the vertebrate metzincin gene superfamily arose has not been determined in detail. Here we present a comprehensive analysis of vertebrate metzincins using genes from both Ciona intestinalis and Danio rerio to provide new insights into the complex evolution of this gene superfamily.

Results: We have identified 19 metzincin genes in the ciona genome and 83 in the zebrafish genome. Phylogenetic analyses reveal that the expansion of the metzincin gene superfamily in vertebrates has occurred predominantly by the simple duplication of pre-existing genes rather than by the appearance and subsequent expansion of new metzincin subtypes (the only example of which is the meprin gene family). Despite the number of zebrafish metzincin genes being relatively similar to that of tetrapods (e.g. man and mouse), the pattern of gene retention and loss within these lineages is markedly different. In addition, we have studied the evolution of the related TIMP gene family and identify a single ciona and four zebrafish TIMP genes.

Conclusion: The complexity seen in the vertebrate metzincin gene families was mainly acquired during vertebrate evolution. The metzincin gene repertoire in protostomes and invertebrate deuterostomes has remained relatively stable. The expanded metzincin gene repertoire of extant tetrapods, such as man, has resulted largely from duplication events associated with early vertebrate evolution, prior to the sarcopterygian-actinopterygian split. The teleost repertoire of metzincin genes in part parallels that of tetrapods but has been significantly modified, perhaps as a consequence of a teleost-specific duplication event.

Figure 1

The metzincin gene family. A. Schematic representation of subdivisions within the Metzincin superfamily. B. Domain structure of generic metzincin genes. All ADAM, BMP/TLL, Meprin and TIMP genes have the same domain structure as that shown on the figure. * The ADAMTSL domain structure shown is ADAMTSL2. ADAMTS, ADAMTSL and MMMP genes have a variable C-terminal domain structure. The domain structures shown are ADAMTS10, ADAMTSL2 and MMP1.

Figure 2

Phylogenetic relationships of the ADAM gene family. The ADAM gene family was separated into three sub-analyses, indicated A, B and C, based upon the clades produced and independent phylogenetic analyses performed. The trees shown were inferred by Neighbor Joining from a gapped alignment. The values on the tree nodes are neighbor joining percentage bootstrap values (black), maximum parsimony bootstrap values (blue) and Bayesian clade credibility values (brown). Nodes also present in the tree generated by Maximum Likelihood are indicated (*). The trees are mid-point rooted. The scale bar corresponds to 0.1 amino acid replacements per site (horizontal axis). Where both mouse and human orthologues are present only the human gene is shown. † There is no mouse ADAM20. Ψ D. rerio ADAM12b and ADAM12c group with ADAM12a (Fig. S3). Ω D.rerio ADAML genes based on location in Fig. S1. The full phylogenetic guide tree is available in Fig. S1. The full phylogenetic trees for the A, B and C subgroups, containing all mouse ADAM orthologues, are presented in Figs. S2-S4. Accession numbers for used in the analyses can be obtained from additional file 1. Further analysis on individual sub-fragments of the B-clade, indicated in Fig. S3, found zebrafish ADAM19b (LOC571252) to group with H. sapiens ADAM19 at α; zebrafish ADAM12b (LOC558872) and ADAM12c (LOC561244) to group with D. rerio ADAM12A at β and zebrafish ADAM9 (zgc101824) at χ.

Figure 3

Phylogenetic relationships of metzincin gene families. A. ADAMTS, B. ADAMTS like, C. BMP1/Tolloid-like, D. Meprin and E. TIMP gene families. The trees summarise the phylogenetic analysis. The trees shown were inferred by Neighbor Joining. The values on the tree nodes are Neighbor Joining percentage bootstrap values (black), maximum parsimony bootstrap values (blue) and Bayesian clade credibility values (brown). Nodes also present in the tree generated by Maximum Likelihood are indicated (*). The trees are rooted on the protostome lineage. The scale bars correspond to the number of amino acid replacements per site (horizontal axis). Accession numbers for used in the analyses can be obtained from additional file 1.

Figure 4

Phylogenetic relationships of the MMP gene family. The MMP gene family was separated into six sub-analyses, indicated A – F, based upon the clades produced and independent phylogenetic analyses performed. The trees shown were inferred by Neighbor Joining from a gapped alignment. The values on the tree nodes are neighbor joining percentage bootstrap values (black), maximum parsimony bootstrap values (blue) and Bayesian clade credibility values (brown). Nodes also present in the tree generated by Maximum Likelihood are indicated (*). The trees are mid-point rooted. The scale bar corresponds to 0.05 amino acid replacements per site (horizontal axis). The MMP gene family was separated into six sub-analyses, indicated A to F, based upon the clades produced and independent phylogenetic analyses performed. The full phylogenetic guide tree is available in Fig. S5. Accession numbers for used in the analyses can be obtained from additional file 1.