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

The collagen binding domain of gelatinase A modulates degradation of collagen IV by gelatinase B

Type IV collagen remodeling plays a critical role in inflammatory responses, angiogenesis and metastasis. Its remodeling is executed by a family of matrix metalloproteinases (MMPs), of which the constitutive gelatinase A (MMP2) and the inducible gelatinase B (MMP9) are key examples. Thus, in many pathological conditions, both gelatinases act together. Kinetic data are reported for the enzymatic processing at 37 degrees C of type IV collagen from human placenta by MMP9 and its modulation by the fibronectin-like collagen binding domain (CBD) of MMP2. The alpha1 and alpha2 chain components of type IV collagen were cleaved by gelatinases and identified by mass spectrometry as well as Edman sequencing. Surface plasmon resonance interaction assays showed that CBD bound type IV collagen at two topologically distinct sites. On the basis of linked-function analysis, we demonstrated that CBD of MMP2 tuned the cleavage of collagen IV by MMP9, presumably by inducing a ligand-linked structural change on the type IV collagen. At low concentrations, the CBD bound the first site and thereby allosterically modulated the binding of MMP9 to collagen IV, thus enhancing the collagenolytic activity of MMP9. At high concentrations, CBD binding to the second site interfered with MMP9 binding to collagen IV, acting as a competitive inhibitor. Interestingly, modulation of collagen IV degradation by inactive forms of MMP2 also occurred in a cell-based system, revealing that this interrelationship affected neutrophil migration across a collagen IV membrane. The regulation of the proteolytic processing by a catalytically inactive domain (i.e., CBD) suggests that the two gelatinases might cooperate in degrading substrates even when either one is inactive. This observation reinforces the idea of exosite targets for MMP inhibitors, which should include all macromolecular substrate recognition sites.

Enzymatic processing of collagen IV by MMP-2 (gelatinase A) affects neutrophil migration and it is modulated by extracatalytic domains

Proteolytic degradation of basement membrane influences the cell behavior during important processes, such as inflammations, tumorigenesis, angiogenesis, and allergic diseases. In this study, we have investigated the action of gelatinase A (MMP-2) on collagen IV, the major constituent of the basement membrane. We have compared quantitatively its action on the soluble forms of collagen IV extracted with or without pepsin (from human placenta and from Engelbreth-Holm-Swarm [EHS] murine sarcoma, respectively). The catalytic efficiency of MMP-2 is dramatically reduced in the case of the EHS murine sarcoma with respect to the human placenta, probably due to the much tighter packing of the network which renders very slow the speed of the rate-limiting step. We have also enquired on the role of MMP-2 domains in processing collagen IV. Addition of the isolated collagen binding domain, corresponding to the fibronectin-like domain of whole MMP-2, greatly in hibits the cleavage process, demonstrating that MMP-2 interacts with collagen type IV preferentially through its fibronectin-like domain. Conversely, the removal of the hemopexin-like domain, using only the catalytic domain of MMP-2, has only a limited effect on the catalytic efficiency toward collagen IV, indicating that the missing domain does not have great relevance for the overall mechanism. Finally, we have investigated the effect of MMP-2 proteolytic activity ex vivo. MMP-2 action negatively affects the neutrophils' migration across type IV coated membranes and this is likely related to the production of lower molecular weight fragments that impair the cellular migration.

The clinical spectrum of type IV collagen mutations

Clinical manifestations of type IV collagen mutations can vary from the severe, clinically and genetically heterogeneous renal disorder, Alport syndrome, to autosomal dominant familial benign hematuria. The predominant form of Alport syndrome is X-linked; more than 160 different mutations have yet been identified in the type IV collagen alpha 5 chain (COL4A5) gene, located at Xq22-24 head to head to the COL4A6 gene. The autosomal recessive form of Alport syndrome is caused by mutations in the COL4A3 and COL4A4 genes, located at 2q35-37. Recently, the first mutation in the COL4A4 gene was identified in familial benign hematuria. This paper presents an overview of type IV collagen mutations, including eight novel COL4A5 mutations from our own group in patients with Alport syndrome. The spectrum of mutations is broad and provides insight into the clinical heterogeneity of Alport syndrome with respect to age at renal failure and accompanying features such as deafness, leiomyomatosis, and anti-GBM nephritis.

Structure of the human type XIX collagen (COL19A1) gene, which suggests it has arisen from an ancestor gene of the FACIT family

Type XIX collagen is a newly discovered member of the FACIT (fibril-associated collagens with interrupted triple helices) group of extracellular matrix proteins. Based on the primary structure, type XIX collagen is thought to act as a cross-bridge between fibrils and other extracellular matrix molecules. Here we describe the complete exon/intron organization of COL19A1 and show that it contains 51 exons, spanning more than 250 kb of genomic DNA. The comparison of exon structures of COL19A1 and other FACIT family genes revealed several similarities among these genes. The structure of exons encoding the noncollagenous (NC) 1-collagenous (COL) 1-NC 2-COL 2-NC 3-COL 3-NC 4 domain of the alpha1(XIX) chain is similar to that of the NC 1-COL 1-NC 2-COL 3-NC 3 domain of the alpha2(IX) chain except for the NC 3 domain of alpha1(XIX). The exons encoding the COL 5-NC 6 domain of alpha1(XIX) are also similar to those of the COL 3-NC 4 domain of alpha1(IX) chain. Previously, COL19A1 was mapped to human chromosome 6q12-q14, where COL9A1 is also located. Likewise, the present work shows that the mouse Col19a1 gene is located on mouse chromosome 1, region A3, where Col9a1 has also been mapped. Taken together, the data suggest that COL19A1 and COL9A1 (Col19a1 and Col9a1) were duplicated from the same ancestor gene of the FACIT family. Three CA repeat markers with high heterozygosity were found in COL19A1. These markers may be useful for linkage analysis of age-related inheritable diseases involved in eyes and/or brain.

Isolation and structure of the COL4A6 gene encoding the human alpha 6(IV) collagen chain and comparison with other type IV collagen genes

The genes COL4A5 and COL4A6, coding for the basement membrane collagen chains, alpha 5(IV) and alpha 6(IV), respectively, are located head-to-head in close proximity on human chromosome Xq22, and COL4A6 is transcribed from two alternative promoters in a tissue-specific fashion (Sugimoto M., Oohashi T., and Ninomiya Y. (1994) Proc. Natl. Acad. Sci. U.S.A. 91, 11679-11683). Immunofluorescence studies using alpha chain-specific antibodies demonstrated that the two genes are expressed in a tissue-specific manner (Ninomiya, Y., Kagawa, M., Iyama, K., Naito, L., Kishiro, Y., Seyer, J. M., Sugimoto, M., Oohashi, T., and Sado, Y. (1995) J. Cell Biol. 130, 1219-1229). We report here for the first time the isolation and the structural organization of the human COL4A6 gene. The entire gene presumably exceeds 200 kilobase pairs and contains 46 exons. Exons 1' and 1 encode the two different 5'-UTRs and the two amino-terminal parts of of the signal peptide. The carboxyl part of the signal peptide and the 7 S domain are coded for by the following 6 different exons, 2-7, whereas the exons 7-42 encode the central COL 1 domain, which contains the Gly-X-Y repeats. The last three exons, 43-45, encode the carboxyl-terminal NC1 domain. Sizes of more than a half of the exons of the gene are the same as those of Col4a2 but quite different from those of COL4A5. Within the COL4A6 gene we found three CA repeat markers that can be used for allele detection. The detailed structure of the COL4A6 gene and the high heterozygosity microsatellite markers located within the gene will be useful for linkage analysis and familial diagnosis of diseases caused by mutations of this gene.

Comparative distribution of the alpha 1(IV), alpha 5(IV), and alpha 6(IV) collagen chains in normal human adult and fetal tissues and in kidneys from X-linked Alport syndrome patients

We have shown previously that the 5' ends of the genes for the alpha 5(IV) and alpha 6(IV) collagen chains lie head-to-head on Xq22 and are deleted in patients with Alport syndrome (AS)-associated diffuse leiomyomatosis. In this study, we raised a rabbit anti-human alpha 6(IV)chain antibody, demonstrated its specificity by the analysis of recombinant NC1 domains af all six type IV chains, and studied the distribution of the alpha 6(IV) chain in relation to the alpha 1(IV) and alpha 5(IV) chains in human adult and fetal tissues involved in AS and diffuse leiomyomatosis. The alpha 6(IV) chain colocalizes with the alpha 5(IV) chain in basement membranes (BMs) of many tissues, but not in glomerular BM. These data exclude the alpha 6(IV) chain as a site for AS mutations. The head-to-head genomic pairing of the alpha 5(IV) and alpha 6 (IV) genes implies coordinate transcription of the two genes. Differential localization of the alpha 5(IV) and alpha 6(IV) chains shows that the two chains are not always coordinately regulated. The alpha 6(IV) chain, together with the alpha 3(IV)-alpha 5(IV) chains, was absent from all renal BMs in eight patients with X-linked AS while the alpha 1(IV) and alpha 2(IV) chains were increased. The data support the existence of two independent collagen networks, one for the alpha 3(IV)-alpha 6(IV) chains and one for the alpha 1(IV) and alpha 2(IV) chains.

Genetic identification, sequence, and alternative splicing of the Caenorhabditis elegans alpha 2(IV) collagen gene

The nematode Caenorhabditis elegans has two type IV collagen genes homologous to the mammalian alpha 1(IV) and alpha 2(IV) collagen genes. We demonstrate by transgenic rescue of mutant animals that the genetic locus encoding the C. elegans alpha 2(IV) collagen gene is let-2 on the X chromosome. The most severe effect of mutations in let-2 is temperature-sensitive embryonic lethality. The embryonic lethal phenotype is similar to that seen in animals with mutations in the alpha 1(IV) collagen gene, emb-9. The sequence of the entire C. elegans alpha 2(IV) collagen gene is presented. Comparisons with mammalian type IV collagen sequences show high amino acid sequence conservation in the C-terminal NCl domain and of crosslinking residues (Cys and Lys) in the N-terminal 7S domain. RT-PCR analysis shows that transcripts of the C. elegans alpha 2(IV) collagen gene are alternatively spliced. Transcripts contain one of two mutually exclusive exons, exon 9 or 10. These exons encode very similar products, differing primarily in the sequence of a 9-10 amino acid Gly-X-Y interruption. The expression of these alternatively spliced alpha 2(IV) collagen transcripts is developmentally regulated. In embryos over 90% of the alpha 2(IV) collagen mRNA contains exon 9, while larval and adult RNAs contain 80-90% exon 10. This shift in expression of alternative alpha 2(IV) collagen transcripts suggests that C. elegans embryos may require a different form of alpha 2(IV) collagen than do larvae and adults.

cDNA isolation and partial gene structure of the human alpha 4(IV) collagen chain

A novel collagen IV chain, alpha 4(IV), has recently been identified in basement membranes. We describe part of the primary structure of the human alpha 4(IV) polypeptide for the first time, which has been determined by cloning and sequencing of cDNAs encoding 241 amino acid residues of the COL domain and 231 residues of the NC1 domain. We also characterized a genomic DNA fragment containing 4 exons coding for the entire NC1 domain. Among five known alpha chains of collagen IV, the alpha 4(IV) chain is distinct from the other four chains. However, it is more similar to the alpha 2(IV) chain than to the alpha 1(IV), alpha 3(IV) and alpha 5(IV) chains in terms of amino acid sequence homology, domain structure of polypeptides and exon/intron structure of the genes, suggesting the presence of two phylogenetically distinct subclasses of collagen IV alpha chains; one composed of alpha 2 and alpha 4 chains and the other of alpha 1, alpha 3 and alpha 5 chains.

Identification of a novel sequence element in the common promoter region of human collagen type IV genes, involved in the regulation of divergent transcription

The expression of the heterotrimeric collagen IV molecule alpha 1(IV)2 alpha 2(IV) is essential for the structural integrity and functional properties of all basement membranes. The two genes COL4A1 and COL4A2 that code for the subunits are found closely linked on chromosome 13 in a head-to-head arrangement and are transcribed in divergent directions. We have identified a novel trans-acting factor that binds in vitro to a unique homopyrimidine/homopurine stretch within the shared promoter region of the two collagen IV genes. Additional binding sites have been identified within the first introns of both genes and the consensus sequence CCCTYCCCC for efficient binding has been deduced; the factor was named therefore 'CTC-binding factor' or 'CTCBF'. Mutations in the binding site of CTC-binding factor within the promoter inhibited binding in vitro and resulted in reduced transcription from both genes. The effect of mutations on the transcription of COL4A2 is more pronounced than on the transcription of COL4A1. CTC-binding factor is a nuclear factor that binds dominantly in vitro to the collagen IV promoter and is involved in regulating the expression of both collagen IV genes.

Molecular genetics of Alport syndrome

Alport syndrome is a progressive hereditary kidney disease characterized by hematuria, sensorineural hearing loss and ocular lesions with structural defects in the glomerular basement membrane (GBM). The gene frequency has been estimated to be 1:5000. The disease is primarily X chromosome-linked, but autosomal forms have also been reported. The X-linked form has been shown to be caused by mutations in a recently identified alpha 5(IV) collagen chain gene (COL4A5). We have isolated cDNA clones for providing the entire primary structure of the human alpha 5(IV) chain. The gene has been located to the Xq22 region. Using antibodies against synthetic peptides, the alpha 5(IV) chain was shown to be located in the kidney only in the glomerular basement membrane. Thus far, the exon-intron structure has been determined for a large portion of the gene which probably has a size of over 200 kb. Numerous different mutations have been identified in the COL4A5 gene. The mutations include single base mutations, large deletions and other major rearrangements such as inversion and duplication. The consequences of the mutations observed can be considered sufficient to cause structural and functional defects in the type IV collagen molecule and, therefore, also the GBM network. This, in turn can explain the disruption of the GBM and hematuria occurring in these Alport patients. Alport syndrome is the first genetic basement membrane and kidney disease whose gene has been cloned. These recent results have enabled the development of antibodies and DNA probes for accurate diagnosis of Alport syndrome.

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.

Identification of mutations in the COL4A5 collagen gene in Alport syndrome

X-linked Alport syndrome is a hereditary glomerulonephritis in which progressive loss of kidney function is often accompanied by progressive loss of hearing. Ultrastructural defects in glomerular basement membranes (GBM) of Alport syndrome patients implicate an altered structural protein as the cause of nephritis. The product of COL4A5, the alpha 5(IV) collagen chain, is a specific component of GBM within the kidney, and the gene maps to the same X chromosomal region as does Alport syndrome. Three structural aberrations were found in COL4A5, in intragenic deletion, a Pst I site variant, and an uncharacterized abnormality, which appear to cause nephritis and deafness, with allele-specific severity, in three Alport syndrome kindreds in Utah.

Regulation of divergent transcription of the genes coding for basement membrane type IV collagen

The genes coding for the two polypeptide chains, alpha 1(IV) and alpha 2(IV), which form together the molecule of the basement membrane type IV collagen, were found to have a special and unusual genomic arrangement. The two genes are very closely linked, they are transcribed in opposite directions, and they apparently use a common and bidirectional promoter with a length of 127 bp. This region is characterized by a symmetrical arrangement of typical elements and by the palindromic structure of the sequence. In accordance with the symmetry of the promoter itself, a symmetrical organization of sequence motifs (SP1, CCAAT) was also observed in flanking regions. For the promoter and the flanking regions we could detect specific binding of nuclear factors that indicates their involvement in transcriptional activation. This suggests that the intrinsic symmetry of the type IV collagen promoter and its flanking regions may be a structural prerequisite for its bidirectional function. In transient gene expression systems no significant activity of the type IV collagen promoter was observed in either direction. This implies that additional enhancing elements are essential for the efficient and tissue-specific transcription of both type IV collagen genes. The screening for such controlling elements within the alpha 1(IV) and the alpha 2(IV) gene led to the observation that the transcription in direction of the alpha 2(IV) gene is activated by an element located in the first intron of the alpha 2 gene. Its enhancing effect is strictly dependent on the intact genomic structure of this region. Alternation of orientation and distance to the promoter destroys its activity completely. This element, located about 100-600 bp downstream from the start site of alpha 2(IV) transcription, seems to form a synergistically acting unit with the common promoter, essential for transcriptional activity in alpha 2 direction. We have not found additional enhancing elements in other regions of both genes. Explanations for the discrepancy with previous data, which define an enhancing element within the first intron of the alpha 1(IV) gene of mouse, are only speculative at present.

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.

Structure and biological activity of basement membrane proteins

Collagen type IV, laminin, heparan sulfate proteoglycans, nidogen (entactin) and BM-40 (osteonectin, SPARC) represent major structural proteins of basement membranes. They are well-characterized in their domain structures, amino acid sequences and potentials for molecular interactions. Such interactions include self-assembly processes and heterotypic binding between individual constituents, as well as binding of calcium (laminin, BM-40) and are likely to be used for basement membrane assembly. Laminin, collagen IV and nidogen also possess several cell-binding sites which interact with distinct cellular receptors. Some evidence exists that those interactions are involved in the control of cell behaviour. These observations have provided a more defined understanding of basement membrane function and the definition of new research goals in the future.

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.