The molecular evolution of the collagen X (C1q/TNFα) supergene family
Authors: Huxley‐Jones Julie , Robertson David L. , Boot‐Handford Raymond P. 
Published: August 2004

Introduction  Collagen X is a nonfibrillar short‐chain collagen that contains a globular domain at the C‐terminus (NC1 domain) responsible for trimerization of the protein (Marks et al. 1999). Homologous NC1 domains are found in an extensive family of trimeric proteins (often referred to as the C1q/TNF super‐family) including C1q and TNF (Shapiro & Scherer 1998). This family may have radiated during vertebrate evolution (Kishore et al. 2002), but how and when the family first evolved has not been determined. We report here that Ciona intestinalis, a urochordate that represents one of the closest invertebrate relatives of vertebrates, has two genes containing the C1q/TNFα NC1 domain. Using these sequences to root a detailed phylogenetic analysis of the supergene family members found in mammals allows us to describe not only the relationships between family members but also the temporal order with which family members evolved in vertebrates.

Materials and methods  A variety of human NC1 domain amino acid sequences (e.g. type X collagen, TNFα, Clq) were used to BLAST the Ciona genome. Two sequences (Ciona 247 & 377) were identified. Sequences with homology to the NC1 domains of the Ciona proteins, and human type X collagen and TNFα were identified by BLAST using the nonredundant protein and human genome databases. The NC1 sequences were aligned using ClustalX and trees produced by three independent methods: Neighbor Joining, Bayesian and Maximum Likelihood. Information on protein expression was obtained from the scientific literature and EST databases.

Results  Extensive BLAST analyses of the Ciona genome identified two genes that contained domains with significant sequence homology to the trimerizing NC1 domain of the C1q/TNFα supergene family. The human genome contained 27 genes with such a domain and in addition, three chipmunk‐specific hibernation proteins were identified using the nonredundant protein database. A striking feature of identified genes is that most (22 out of 32), including one of the Ciona genes (377), encode a collagenous domain just N‐terminal to the NC1 domain. Phylogenetic analyses demonstrated that specific subgroupings or clades have evolved within this highly divergent family including the TNF/emilin clade, the collagen X/VIII clade, the C1q clade and the hibernation protein clade. Comparisons of the domain structures of the encoded proteins, and the exon structures encoding the NC1 domains, strongly supports the majority of the phylogenetic groupings of genes even where statistical support is not high. The majority of the vertebrate genes encoding C1q/TNF NC1 domains have lost the intron apparent in both Ciona genes although a subset of vertebrate genes, including precerebellins, that phylogenetically cluster appear to have conserved this intron.

Discussion  We have identified, for the first time, invertebrate sequences from which the C1q/TNF supergene family of proteins, including types VIII and X collagen have evolved and demonstrated that this super‐gene family has radiated extensively during vertebrate evolution. The precise clustering of genes, based on phylogenetic analyses and supported by the overall gene and domain structures of the encoded proteins, provides new insights into the evolution of the vertebrate extracellular matrix, the versatility of the collagen triple helical domain and potential functions of novel genes