Abstract
The type XXVII collagen gene codes for a novel vertebrate fibrillar collagen that is highly conserved in man, mouse, and fish (Fugu rubripes). The pro(alpha)1(XXVII) chain has a domain structure similar to that of the type B clade chains (alpha1(V), alpha3(V), alpha1(XI), and alpha2(XI)). However, compared with other vertebrate fibrillar collagens (types I, II, III, V, and XI), type XXVII collagen has unusual molecular features such as no minor helical domain, a major helical domain that is short and interrupted, and a short chain selection sequence within the NC1 domain. Pro(alpha)1(XXVII) mRNA is 9 kb and expressed by chondrocytes but also by a variety of epithelial cell layers in developing tissues including stomach, lung, gonad, skin, cochlear, and tooth. By Western blotting, type XXVII antisera recognized multiple bands of 240-110 kDa in tissue extracts and collagenous bands of 150-140 kDa in the conditioned medium of the differentiating chondrogenic ATDC5 cell line. Phylogenetic analyses revealed that type XXVII, together with the closely related type XXIV collagen gene, form a new, third clade (type C) within the vertebrate fibrillar collagen family. Furthermore, the exon structure of the type XXVII collagen gene is similar to, but distinct from, those of the genes coding for the type A or B clade pro(alpha) chains.
Highlights
The type XXVII collagen gene codes for a novel vertebrate fibrillar collagen that is highly conserved in man, mouse, and fish (Fugu rubripes)
The N terminus of type XXVII collagen pro␣ chains has a similar domain structure to that exhibited by the type B clade vertebrate fibrillar collagens including a TSPN domain of ϳ150 residues and a variable domain ranging in size from 403 residues in man to 226 residues in the Fugu pro␣1(XXVII) chain (Fig. 1A and Table I)
That unlike the pro␣ chains of classical vertebrate fibrillar collagens, pro␣1(XXVII) contains a short chain selection sequence, a feature previously only found in fibrillar collagens of invertebrates (Fig. 1B and Ref. 7)
Summary
Sequence Determination—Sequences from the collagen XXVII gene were originally identified by blast searches of the F. rubripes genome data base looking for amino acid sequence homologies with C-terminal noncollagenous domains of human fibrillar collagens. The Fugu sequences identified in this fashion were compared directly with the human to identify the collagen chain and type. In this way, F. rubripes sequences matching a previously uncharacterized fibrillar collagen conserved in both human and mouse genomes were identified and assembled by standard bioinformatics approaches including the use of available expressed sequence tags. Most parsimonious trees were identified using PROTPARS with input order jumbled 10 times. 100 bootstrap replicates were generated using SEQBOOT and analyzed by PROTPARS, and bootstrap values were calculated using CONSENSE
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