The triple-helical domain of alpha 2(VI) collagen is encoded by 19 short exons that are multiples of 9 base pairs

A new FACIT of the collagen family: COL21A1

Interrogation of the Human Genome data for sequences related to the von Willebrand factor A-domain module identified a previously unreported 4.1 kb full-length cDNA that is predicted to encode a new member of the collagen superfamily of extracellular matrix proteins, collagen XXI. The domain organization of collagen XXI comprised an N-terminal signal sequence, followed by single von Willebrand factor A-domain and thrombospondin domains, and an interrupted collagen triple helix. The organization of these motifs predict that collagen XXI is a new member of the FACIT collagen sub-family. Expression analysis indicated that COL21A1 mRNA is present in many tissues including heart, stomach, kidney, skeletal muscle and placenta, and radiation hybrid mapping localized the COL21A1 gene to 6p11-12.

Murine alpha 1(VI) collagen chain. Complete amino acid sequence and identification of the gene promoter region

The entire primary structure of the murine alpha 1(VI) collagen chain was deduced from cloned cDNA. The predicted polypeptide consists of 1025 amino acids and shows extensive homology with the corresponding human and chicken chains. A genomic clone isolated with a cDNA probe was found to contain about 13 kilobases of the 5'-flanking region and the first and second exon, coding for the 5'-untranslated sequence and signal peptide and part of the N-terminal portion of the mature protein, respectively. Polymerase chain reaction and primer extension analyses revealed two major and several minor transcription start sites distributed over 76 base pairs (bp). The region just upstream of the transcription initiation sites lacks canonical TATA and CAAT boxes and Sp1 binding sites, but contains putative binding sites for other transcription factors and a 90-bp polypyrimidine tract with elements of dyad symmetry. Chimeric constructs were derived from different fragments of the 5'-flanking genomic region and the chloramphenicol acetyltransferase (CAT) gene and expression of the reporter gene was assayed following transfection of various cell types. A construct containing sequences extending from -215 to +41 directed high levels of CAT expression. The data indicate that this region harbours a functional promoter.

Characterization of the chicken alpha 1(VI) collagen promoter

The promoter of the chicken alpha 1(VI) collagen gene resembles the 5'-flanking regions of many housekeeping genes. It lacks a canonical TATAA box but contains potential binding sites for transcription factors AP1 and SP1. The promoter region has a relatively high GC content and forms a typical CpG island. In accordance with the absence of a TATAA element, the gene contains multiple transcription-initiation sites distributed over 80 bp genomic DNA. A 621-bp fragment derived from the 5' end of the alpha 1(VI) collagen gene is able to direct transcription of a heterologous reporter gene in transient-expression assays. Other DNA fragments that are either shorter or longer than the 621-bp fragment show markedly reduced promoter activity. Thus, the basic promoter element of the alpha 1(VI) collagen gene must reside within this 621-bp fragment.

Type XIV collagen is a variant of undulin

We have isolated undulin, an extracellular matrix protein associated with the surface of collagen fibrils, from chicken embryos. The protein showed a molecular mass of about 600 kDa and is composed of three 210-kDa subunits linked by reducible as well as non-reducible bonds. In contrast to human undulin which reportedly is devoid of collagenous sequences, the chicken protein contained a short triple-helical segment that was sensitive to digestion by bacterial collagenase. Screening of an expression library with affinity-purified antibodies yielded two cDNA clones specific for chicken undulin. Analysis of the amino acid sequence deduced from the nucleotide sequence of these clones showed that the human and the chicken protein shared 71% sequence identity. At the amino-terminus both polypeptides contained several similar repeats related to the type III modules found in fibronectin. Towards the carboxyl terminus, however, the two sequences diverged substantially from each other. While the human sequence terminated in a proline-rich segment, the chicken sequence continued with a domain related to von Willebrand factor, with a domain similar to the noncollagenous domain NC4 of type IX collagen and with a typical collagenous triple helix. A short segment of this sequence was found to be identical with the published sequence of a bovine peptide derived from type XIV collagen. Our protein must therefore represent chicken type XIV collagen. One way to explain these results is the possibility that undulin exists in at least two alternatively spliced variants, one lacking the collagenous domain, as described initially for human undulin, and one containing the triple-helical domain, as found in type XIV collagen.

Structural comparison of the chicken genes for alpha 1(VI) and alpha 2(VI) collagen

The chicken alpha 1(VI) polypeptide is encoded by a single gene spanning 21 kbp of genomic DNA. This gene is composed of 34 exons and 33 introns. Its structure is closely related to that of the alpha 2(VI) collagen gene, suggesting that the two genes evolved by gene duplication. Both genes contain 19 exons coding for the triple-helical domain. These exons are multiples of 9 bp (27, 36, 45, 54, 63 and 90 bp) and encode an integral number of collagenous Gly-Xaa-Yaa triplets. Since there is no convincing correlation to a building block of 54 bp, it is unlikely that type VI collagen has evolved from a primordial 54-bp module as suggested for all fibrillar collagens.

The exon organization of the triple-helical coding regions of the human alpha 1(VI) and alpha 2(VI) collagen genes is highly similar

The alpha 1(VI) and alpha 2(VI) chains, two of the three constituent chains of type VI collagen, are highly similar in size and domain structure. They are encoded by single-copy genes residing in close proximity on human chromosome 21. To study the evolution of the type VI collagen genes, we have isolated and characterized genomic clones coding for the triple-helical domains of the human alpha 1(VI) and alpha 2(VI) chains, which consist of 336 and 335 amino acid residues, respectively. Nucleotide sequencing indicates that, in both genes, the exons are multiples of 9 bp in length (including 27, 36, 45, 54, 63, and 90 bp) except for those encoding for regions with triple-helical interruptions. In addition, the introns are positioned between complete codons. The most predominant exon size is 63 bp, instead of 54 bp as seen in the fibrillar collagen genes. Of particular interest is the finding that the exon structures of the alpha 1(VI) and alpha 2(VI) genes are almost identical. A significant deviation is that a segment of 30 amino acid residues is encoded by two exons of 54 and 36 bp in the alpha 1(VI) gene, but by a single exon of 90 bp in the alpha 2(VI) gene. The exon arrangement therefore provides further evidence that the two genes have evolved from tandem gene duplication. Furthermore, comparison with the previously reported gene structure of the chick alpha 2(VI) chain indicates that the exon structure for the triple-helical domain of the alpha 2(VI) collagen is strictly conserved between human and chicken.

Complete structure of the chicken alpha 2(VI) collagen gene

Type VI collagen is a hybrid molecule consisting of a short triple helix flanked by two large globular domains. These globular domains are composed of several homologous repeats which show a striking similarity to the collagen-binding motifs found in von Willebrand factor. The alpha 2(VI) subunit contains three of these homologous repeats termed D1, D2 and D3. We have isolated and characterized the entire gene for chicken alpha 2(VI) collagen. This gene, which is present as a single copy in the chicken genome, is 26 kbp long and comprises 28 exons. All exons can be classified in three groups. (a) The triple-helical domain is encoded by 19 short exons (27-90 bp) separated by introns of phase class 0. These exons are multiples of 9 bp and encode an integral number of collagenous Gly-Xaa-Yaa triplets. (b) The homologous repeats D1-D3 are encoded by one or two very long exons each (153-1578 bp). These exons are separated by introns of phase class 1. (c) The homologous repeats and the collagen sequence are linked to each other by three short adapter segments which are each encoded by a single exon (21-46 bp). The modular nature of the polypeptide is thus clearly reflected by the mosaic structure of its gene. The size of the exons and the phase class of the introns suggest that the alpha 2(VI) gene evolved by duplication and shuffling of two different primordial exons, one of 9 bp encoding a collagen Gly-Xaa-Yaa triplet and one of 600 bp encoding the precursor of the homologous repeats.