Conservation and divergence of ADAM family proteins in the Xenopus genome

Abstract

Background: Members of the disintegrin metalloproteinase (ADAM) family play important roles in cellular and developmental processes through their functions as proteases and/or binding partners for other proteins. The amphibian Xenopus has long been used as a model for early vertebrate development, but genome-wide analyses for large gene families were not possible until the recent completion of the X. tropicalis genome sequence and the availability of large scale expression sequence tag (EST) databases. In this study we carried out a systematic analysis of the X. tropicalis genome and uncovered several interesting features of ADAM genes in this species.Results: Based on the X. tropicalis genome sequence and EST databases, we identified Xenopus orthologues of mammalian ADAMs and obtained full-length cDNA clones for these genes. The deduced protein sequences, synteny and exon-intron boundaries are conserved between most human and X. tropicalis orthologues. The alternative splicing patterns of certain Xenopus ADAM genes, such as adams 22 and 28, are similar to those of their mammalian orthologues. However, we were unable to identify an orthologue for ADAM7 or 8. The Xenopus orthologue of ADAM15, an active metalloproteinase in mammals, does not contain the conserved zinc-binding motif and is hence considered proteolytically inactive. We also found evidence for gain of ADAM genes in Xenopus as compared to other species. There is a homologue of ADAM10 in Xenopus that is missing in most mammals. Furthermore, a single scaffold of X. tropicalis genome contains four genes encoding ADAM28 homologues, suggesting genome duplication in this region. Conclusions:Our genome-wide analysis of ADAM genes in X. tropicalis revealed both conservation and evolutionary divergence of these genes in this amphibian species. On the one hand, all ADAMs implicated in normal development and health in other species are conserved in X. tropicalis. On the other hand, some ADAM genes and ADAM protease activities are absent, while other novel ADAM proteins in this species are predicted by this study. The conservation and unique divergence of ADAM genes in Xenopus probably reflect the particular selective pressures these amphibian species faced during evolution. BackgroundADAMs belong to the M12B subfamily of metalloproteinases and metalloproteinase-like proteins [1]. A prototype ADAM is a type I transmembrane protein, but some ADAMs are also present as soluble forms, either due to alternative splicing or protease-mediated cleavage ("shedding") from the cell surface [2,3]. ADAMs are multidomain proteins with an extracellular metalloproteinase domain, a disintegrin domain and a cysteine-rich domain; therefore they are also called MDC (metalloproteinase/

Extracellular metalloproteinases in neural crest development and craniofacial morphogenesis

“…Phylogenetic analysis of non-testis-specific human and Xenopus tropicalis ADAMs showed that there are several subfamilies, which remained consistent when other vertebrate ADAMs were analyzed (Wei et al, 2010a). Of these ADAMs, four clades were described.…”

“…Our phylogenetic and syntenic (gene linkage) analyses suggest that Xenopus ADAM13 is the ortholog of mammalian ADAM33 (Wei et al, 2010a), although the proteins have some key differences. For example, ADAM13 has multiple intracellular SH3-binding motifs and can bind to proteins such as Src and PACSIN2 (Cousin et al, 2000), whereas mouse ADAM33 does not contain any SH3-binding motifs (Gunn et al, 2002).…”

Roles of ADAM13-regulated Wnt activity in early Xenopus eye development

“…A further question is whether these mechanisms are conserved during vertebrate evolution. In mammals, ADAMs 12, 19 and 33 form a subfamily, and our phylogenetic and syntenic analyses suggest that mammalian ADAM33 is the orthologue of frog ADAM13 (Wei et al, 2010a). However, mammalian ADAMs 19 and 33 have nearly equal similarity to Xenopus ADAM13 in protein sequence, raising the possibility that functions of ADAM13 could be shared between ADAMs 19 and 33 in mammals.…”

“…X. tropicalis cDNA clones for snail2 (in pCS107; clone ID: Ttba075D05; from Geneservice) and cerberus (in pCS108; clone ID: 7579004; from OpenBiosystems) were identified by bioinformatics and used directly for expression (sequences of all clones were confirmed by DNA sequencing). Cloning of X. tropicalis adam13 has been described previously (Wei et al, 2010a). The coding sequence for ADAM13 was then subcloned into a pCS2+ expression vector modified to append a C-terminal myc 6 -tag.…”

“…With the aid of bioinformatics tools, we have identified more than a dozen ADAM genes in the X. tropicalis genome (Wei et al, 2010a). Loss-of-function studies suggest that ADAM13, one of the proteolytically active ADAMs, is essential for early CNC induction in X. tropicalis .…”