Structural and functional analysis of the genes for alpha 2(I) and alpha 1(III) collagens

Characterization of the 3' half of the human type IV collagen alpha 5 gene that is affected in the Alport syndrome

We have determined the exon-intron structure of the 3' half of the gene for the human type IV collagen alpha 5 chain that is affected in X-chromosome-linked Alport syndrome. Six overlapping lambda phage genomic clones containing exons 1-14 (as counted from the 3' end) and two additional overlapping genomic clones containing exons 16-19 spanned a total of 60 kb, 9.5 kb of which were the 3' flanking region. The exon-intron structure was elucidated by restriction enzyme mapping, nucleotide sequencing, and heteroduplex analyses. The sequences of all of the 19 most 3' exons and their flanking sequences were determined from the genomic clones, with the exception of exon 15, which was sequenced after amplification from genomic DNA with the polymerase chain reaction. The results show that the genes for the alpha 5(IV) and alpha 1(IV) chains have an almost identical exon size pattern in the 3' half. In contrast, there is not a clear conservation of intron sizes between the two genes, although both genes may have a similar total size. The current results have allowed the identification of three mutations in the alpha 5(IV) gene in three kindreds with Alport syndrome, and the gene structure and sequencing data presented should facilitate the analysis of other as yet unidentified mutations in this heterogeneous genetic disease.

Characterization of a fibrillar collagen gene in sponges reveals the early evolutionary appearance of two collagen gene families

We have characterized cDNA and genomic clones coding for a sponge collagen. The partial cDNA has an open reading frame encoding 547 amino acid residues. The conceptual translation product contains a probably incomplete triple-helical domain (307 amino acids) with one Gly-Xaa-Yaa-Zaa imperfection in the otherwise perfect Gly-Xaa-Yaa repeats and a carboxyl propeptide (240 amino acids) that includes 7 cysteine residues. Amino acid sequence comparisons indicate that this sponge collagen is homologous to vertebrate and sea urchin fibrillar collagens. Partial characterization of the corresponding gene reveals an intron-exon organization clearly related to the fibrillar collagen gene family. The exons coding for the triple-helical domain are 54 base pairs (bp) or multiples thereof, except for a 57-bp exon containing the Gly-Xaa-Yaa-Zaa coding sequence and for two unusual exons of 126 and 18 bp, respectively. This latter 18-bp exon marks the end of the triple-helical domain, contrary to the other known fibrillar collagen genes that contain exons coding for the junction between the triple-helical domain and the carboxyl propeptide. Compared to other fibrillar collagen genes, the introns are remarkably small. Hybridization to blotted RNAs established that the gene transcript is 4.9 kilobases. Together with previous results that showed the existence of a nonfibrillar collagen in the same species, these data demonstrate that at least two collagen gene families are represented in the most primitive metazoa.

Assignment of the human collagen alpha 1 (XIII) chain gene (COL13A1) to the q22 region of chromosome 10

Type XIII collagen is a recently described collagen that resembles in structure the short-chain collagens of types IX, X, and XII. Unlike any other collagen, the type XIII is found in several different forms generated through alternative splicing. A 2.0-kb genomic fragment from the human alpha 1 (XIII) collagen gene was isolated and shown by DNA sequencing to contain exon 12 as counted from the 3' end. This fragment was used as a probe to localize the gene. The gene (COL13A1) was assigned to chromosome 10 by hybridization of the probe to DNA isolated from a panel of human-mouse somatic cell hybrids containing different human chromosomes. Furthermore, the gene was mapped to the q22 region by in situ hybridization to metaphase chromosomes.

Organization of the exons coding for pro alpha 1(II) collagen N-propeptide confirms a distinct evolutionary history of this domain of the fibrillar collagen genes

The organization of the exons coding for the N-terminal portion of human type II procollagen has been determined. Aside from inferring the previously unknown primary structure of type II N-propeptide, this study has revealed that this coding domain of the gene exhibits an organization uniquely distinct from those of type I and type III collagens. This finding substantiates the notion that the N-propeptide coding domains of the fibrillar collagen genes evolved under less stringent selection than those encoding the C-propeptide and triple helical regions.

Domain organization and intron positions in Caenorhabditis elegans collagen genes: the 54-bp module hypothesis revisited

The amino acid (aa) sequences of the polypeptides encoded by five collagen genes of the nematode Caenorhabditis elegans, col-6, col-7 (partial), col-8, col-14, and col-19, were determined. These collagen polypeptides, as well as those encoded by the previously sequenced C. elegans collagen genes col-1 and col-2, share a common organization into five domains: an amino-terminal leader, a short (30-33 aa) (Gly-X-Y)n domain, a non(Gly-X-Y) spacer, a long (127-132 aa) (Gly-X-Y)n domain, and a short carboxyl-terminal domain. The domain organizations and intron positions of these polypeptides were compared with those of the polypeptides encoded by Drosophila and Strongylocentrotus type IV, and vertebrate types I, II, III, IV, and IX collagen genes; the C. elegans collagen polypeptides are most similar to the vertebrate type IX collagens. It is suggested that the collagen gene family comprises two divergent subfamilies, one of which includes the vertebrate interstitial collagen genes, and the other of which includes the invertebrate collagen genes and the vertebrate type IV and type IX collagen genes. Only the vertebrate interstitial collagen genes display clear evidence of evolution via the tandem duplication of a 54-bp exon.

Gene structure for the alpha 1 chain of a human short-chain collagen (type XIII) with alternatively spliced transcripts and translation termination codon at the 5' end of the last exon

Two overlapping human genomic clones that encode a short-chain collagen, designated alpha 1(XIII), were isolated by using recently described cDNA clones. Characterization of the cosmid clones that span approximately equal to 65,000 base pairs (bp) of the 3' end of the gene established several unusual features of this collagen gene. The last exon encodes solely the 3' untranslated region and it begins with a complete stop codon. The 10 adjacent exons vary in size from 27 to 87 bp and two of them are 54 bp. Therefore, the alpha 1-chain gene of type XIII collagen has some features found in genes for fibrillar collagens but other features that are distinctly different. Previous analysis of overlapping cDNA clones and nuclease S1 mapping of mRNAs indicated one alternative splicing site causing a deletion of 36 bp from the mature mRNA. The present study showed that the 36 bp is contained within the gene as a single exon and also that the gene has a 45-bp -Gly-Xaa-Xaa- repeat coding exon not found in the cDNA clones previously characterized. Nuclease S1 mapping experiments indicated that this 45-bp exon is found in normal human skin fibroblast mRNAs. Accordingly, the data demonstrate that there is alternative splicing of at least two exons of the type alpha 1(XIII)-chain gene.

Extensive structural differences between genes for the alpha 1 and alpha 2 chains of type IV collagen despite conservation of coding sequences

Analysis of the structure of the 3'-end of the human alpha 2(IV) gene demonstrated that the alpha 1(IV) and alpha 2(IV) genes have diverged extensively in spite of the apparent homology of the respective gene products. The NC-1 domain and the 3'-untranslated region are encoded by three exons in the alpha 2(IV) gene but five exons in the alpha 1(IV) gene. The two introns present in the NC-1 domain coding part of the alpha 2(IV) gene had the same location as two of the introns of the alpha 1(IV) gene. The junction exon in the alpha 2(IV) gene contains 53 bp coding for Gly-X-Y sequences whereas there are 71 bp in the alpha 1(IV) gene. Three other Gly-X-Y coding exons studied from the human alpha 2(IV) gene have sizes that differ from corresponding exons in the alpha 1(IV) gene and only one intron location matches here between the two genes. None of the exons studied has 54 bp or multiples thereof.

The pro alpha 2(V) collagen gene is evolutionarily related to the major fibrillar-forming collagens

A number of overlapping cDNA clones, covering 5.2 kb of sequences which code for the human pro alpha 2(V) collagen chain, have been isolated. Analysis of the structural data have indicated a close evolutionary kinship between the pro alpha 2(V) chain and the major fibrillar collagen types. Isolation and analysis of an 8 kb genomic fragment has further supported this notion by revealing a homologous arrangement of nine triple-helical domain exons. These studies have therefore provided conclusive evidence which categorizes the Type V collagen as a member of the Group 1 molecules, or fibrillar-forming collagens.