Physical and linkage mapping of the gene for the alpha3 chain of type IX collagen, COL9A3, to human chromosome 20q13.3

Type IX collagen is a minor cartilage component which associates with mixed fibrils of types II/XI collagen. We have determined the precise physical and genetic locations for the gene encoding the alpha3 chain of type IX collagen, COL9A3. Utilizing fluorescence in situ hybridization, radiation hybrid mapping, and multipoint linkage analysis, we have mapped COL9A3 to human chromosome 20q13.3, 13 cM telomeric to D20S173.

Complete sequence of the 23-kilobase human COL9A3 gene. Detection of Gly-X-Y triplet deletions that represent neutral variants

We report the complete sequence of the human COL9A3 gene that encodes the alpha3 chain of heterotrimeric type IX collagen, a member of the fibril-associated collagens with interrupted triple helices family of collagenous proteins. Nucleotide sequencing defined over 23,000 base pairs (bp) of the gene and about 3000 bp of the 5'-flanking sequences. The gene contains 32 exons. The domain and exon organization of the gene is almost identical to a related gene, the human COL9A2 gene. However, exon 2 of the COL9A3 gene codes for one -Gly-X-Y- triplet less than exon 2 of the COL9A2 gene. The difference is compensated by an insertion of 9 bp coding for an additional triplet in exon 4 of the COL9A3 gene. As a result, the number of -Gly-X-Y- repeats in the third collagenous domain remains the same in both genes and ensures the formation of an in-register triple helix. In the course of screening this gene for mutations, heterozygosity for separate 9-bp deletions within the COL1 domain were identified in two kindreds. In both instances, the deletions did not co-segregate with any disease phenotype, suggesting that they were neutral variants. In contrast, similar deletions in triple helical domain of type I collagen are lethal. To study whether alpha3(IX) chains with the deletion will participate in the formation of correctly folded heterotrimeric type IX collagen, we expressed mutant alpha3 chains together with normal alpha1 and alpha2 chains in insect cells. We show here that despite the deletion, mutant alpha3 chains were secreted as heterotrimeric, triple helical molecules consisting of three alpha chains in a 1:1:1 ratio. The results suggest that the next noncollagenous domain (NC2) is capable of correcting the alignment of the alpha chains, and this ensures the formation of an in-register triple helix.

Primary structure and expression of a chicken laminin beta chain: evidence for four beta chains in birds

Characterization of a full length cDNA sequence for a chicken laminin beta chain is described which is most closely related to the mammalian beta 2 chain. Comparison with published sequences shows that the chicken beta 2-like chain corresponds to a fragment of a previously described laminin beta chain called B1-2 (O'Rear, 1992). The sequence of the chicken beta 2-like chain differed from fragments of two other chicken laminin beta chains that were previously described and designated B1-1 (now called beta 1; O'Rear, 1992) and beta x (Ybot-Gonzalez et a1.,1995). In addition, the beta 2- like chain does not appear to be the chicken equivalent of the mammalian laminin beta 3 chain, since it differs markedly in cDNA sequence, possesses domain IV and has a transcript size of 6 kb. We therefore propose that there are at least four laminin beta chains in the chicken. Sequence comparison of the beta 2-like laminin chain with previously cloned beta 1 and beta 2 chains shows a somewhat closer relationship to rat and human beta 2 than to mouse and human beta 1, especially in domains I, II and alpha. In addition, two expressed fragments of the chicken beta 2-like chain were recognized by a monoclonal antibody (C4) regarded as specific for the rat beta 2 chain (Hunter et al., 1989a). The results therefore suggest that the laminin chain previously described as a potentially novel chain called B1-2 (O'Rear, 1992) is likely to be the chicken equivalent of the mammalian beta 2 chain.

Molecular cloning of the alpha 3 chain of human type IX collagen: linkage of the gene COL9A3 to chromosome 20q13.3

Type IX collagen is composed of three polypeptides derived from the human genes COL9A1, COL9A2, and COL9A3 that assemble to form a mature collagen molecule with the structure alpha 1(IX)alpha 2(IX)alpha 3(IX). We have identified overlapping cDNA and genomic clones that encode for the entire alpha 3 chain of human type IX collagen. Tryptic peptides from the human alpha 3(IX) collagen chain were subjected to N-terminal amino acid sequencing, and a stretch of 124 contiguous amino acids that included the NC1, COL1, and NC2 domains was obtained. Degenerate oligonucleotide primers were designed based on the amino acid sequences of the human tryptic peptides as well as bovine peptides and sequences from chicken cDNA clones. These primers were used to amplify three overlapping PCR products that covered the majority of the human alpha 3(IX) collagen. PCR products were then used to identify overlapping cDNA clones from a human chondrocyte library. A lambda genomic clone was identified that contained the 5'-most exon that encodes the signal peptide to complete the entire structure of the human alpha 3(IX) collagen chain. Genomic amplification identified a single-strand conformational polymorphism in COL1 that was used to map COL9A3 to chromosome 20q13.3 by linkage analysis. The present study completes the structure of human type IX collagen, and linkage for COL9A3 completes the genomic mapping of cartilage collagen genes. These data will greatly assist the genetic screening of families with degenerative cartilage and eye diseases by allowing investigators to screen for a complete set of candidate collagen gene markers.

New members of the collagen superfamily

During the past year, several novel collagenous clones have been isolated from cDNA libraries and designated as new collagen types. Recent research has been concerned with describing these new collagens and their potential relationships to other previously described collagen types.

Molecular cloning of PARP (proline/arginine-rich protein) from human cartilage and subsequent demonstration that PARP is a fragment of the NH2-terminal domain of the collagen alpha 2(XI) chain

We report the molecular cloning of a proline/arginine-rich protein (called PARP) from human cartilage using the polymerase chain reaction (PCR) and degenerate oligonucleotides based on the previously published amino acid sequence of bovine PARP [1]. Subsequently, a reverse transcription-polymerase chain reaction (RT-PCR) was performed with poly(A)-rich RNA from human cartilage using a sense oligonucleotide derived from PARP and an anti-sense oligonucleotide derived from the known sequence of the human collagen alpha 2(XI) chain [2]. Nucleotide sequencing of the PCR product demonstrated that PARP is a fragment of the NH2-terminal non-collagenous (NC3) domain of the collagen alpha 2(XI) chain.

Isolation and characterization of the chains of type V/type XI collagen present in bovine vitreous

Previous studies show that the collagen fibrils of the mammalian vitreous humor are assembled largely from type II collagen with smaller amounts of type IX collagen and either type V or type XI collagen. In this paper, we report the separation of two chains of type V/type XI collagen from type II collagen by heparin-Sepharose chromatography. These chains were characterized by sequencing of selected cyanogen bromide or tryptic peptides with subsequent comparison of these sequences with cDNA-derived amino acid sequences of the alpha 1(V), alpha 1(XI), alpha 2(V), and alpha 2(XI) chains. The results show that vitreous fibrils are assembled from molecules containing the alpha 1(XI) and alpha 2(V) chains. These results, together with recent results from other laboratories, indicate that type V and type XI collagens are not separate collagen types but are part of a larger collagen family in which chains of both type V and type XI collagens participate in the formation of a variety of native molecules.

Cloning of the chicken alpha 3(IX) collagen chain completes the primary structure of type IX collagen

Type IX collagen is composed of three genetically distinct polypeptides that contain several collagenous and non-collagenous domains. The alpha 2(IX) chain also contains a covalently bound glycosaminoglycan side chain. Type IX collagen is located on the surface of collagen fibrils of both hyaline cartilage and vitreous humor, such that one of the collagenous domains (COL3) projects from the surface of the fibril in a periodic manner. We have cloned and sequenced a full-length cDNA for the chicken alpha 3(IX) collagen chain from a cartilage cDNA library. Together with the sequence of the alpha 1(IX) and alpha 2(IX) chains, this completes the primary structure of type IX collagen for one species. These sequences will be useful to better understand the mechanism of triple-helix formation in type IX collagen and the nature of type II and type IX collagen interactions in fibril formation.

Mammalian vitreous humor contains networks of hyaluronan molecules: electron microscopic analysis using the hyaluronan-binding region (G1) of aggrecan and link protein

Vitreous humor from human, bovine, and chicken eyes was analyzed by rotary shadowing to characterize further the supramolecular organization of the gel-like matrix which forms this tissue. Extensive filamentous networks, distinct from collagen fibrils, were found in both human and bovine vitreous but not in chicken vitreous. The networks consisted of branching structures of various diameters, due to variable numbers of hyaluronan molecules being laterally associated with each other and apparently giving rise to a three-dimensional lattice. These networks could be decorated in a specific and regular manner by the hyaluronan-binding region called G1 purified from bovine nasal septum cartilage. The extent of decoration of hyaluronan was dependent on the relative concentration of G1. In the presence of an excess of G1 the networks were destabilized giving rise to individual unbranched hyaluronan chains of varying length that were saturated with G1. One or more globular proteins, as yet uncharacterized, were seen interacting with the hyaluronan networks, often at branch points. These proteins may serve to stabilize the three-dimensional structure of the matrix although highly ordered networks were also observed without globular proteins. Link protein, which also binds to hyaluronan, bound to the networks in a fashion clearly distinct from G1. Neither G1 nor link protein bound directly to human or bovine vitreous collagen fibrils. However, link protein did bind extensively to the glycosaminoglycan coat of chicken vitreous collagen fibrils described previously (D. W. Wright, and R. Mayne J. Ultrastruct. Mol. Struct. Res. 100, 224-234, 1988), while G1 did not. Digestion of the chicken vitreous collagen fibrils with Streptomyces hyaluronidase did not result in the removal of the glycosaminoglycan coat of the collagen fibrils nor did it affect the binding of G1 or link protein to the fibrils, indicating that hyaluronan is not a component of this structure. These studies demonstrate that proteins with specific binding properties can be used as probes to investigate the structure of the native vitreous humor gel from several species and suggest that this method potentially can be used for structural studies of other connective tissue matrices.

Characterization of protein production by ovine placental membranes: identification of a placental retinol-binding protein

Ovine chorion, allantois, and amnion from days 23, 26, 28, 35, 45, 53, 62, and 72 and yolk sac from day 23 of pregnancy were isolated by dissection and cultured for 24 h in modified minimum essential medium in the presence of [35S] methionine to characterize in vitro synthesis and release of proteins. Proteins synthesized and released into medium were analyzed by two-dimensional polyacrylamide gel electrophoresis and fluorography. Patterns of protein production by these isolated membranes remained relatively unchanged from days 23-72 with the exception of the products of yolk sac, which regress by day 35 of pregnancy. In general, chorion was the source of a number of basic-to-neutral proteins; allantois and amnion were the sources of more acidic proteins; and yolk sac was the source of serum-like proteins. A major low mol wt acidic protein, D4, was produced by all membranes and present in fetal membrane fluids. Protein D4 consisted of three isoelectric variants (isoelectric point 5.3-6.1) with identical mol wts (23,000 +/- 800) and was shown to react immunologically with antibovine placental retinol-binding protein (RBP) serum. Hence, protein D4 is a putative ovine placental RBP. The present study is the first to characterize and compare protein production by isolated ovine chorionic, allantoic, amniotic, and yolk sac membranes from day 23 through midpregnancy and identify the major low mol wt acidic protein produced by each membrane as a placental RBP.

An analysis by rotary shadowing of the structure of the mammalian vitreous humor and zonular apparatus

An electron microscopic analysis of human and bovine vitreous humor after rotary shadowing showed the presence of both collagen fibrils and an extensive loose network of hyaluronan molecules. No interaction between the collagen fibrils and the hyaluronan molecules was observed under the conditions used for rotary shadowing. Periodic "struts" were present on the surface of the collagen fibrils. These struts showed an organization the same as that previously observed for type IX collagen on the surface of collagen fibrils from chicken cartilage and vitreous. However, the knob of the noncollagenous NC4 domain of cartilage type IX collagen was not observed at the ends of the struts in a manner identical to that of chicken vitreous humor. Zonular fibrils were dissected out from bovine eyes and shown by rotary shadowing to contain a beaded fibril which is similar in morphology to the "elastin-associated" microfibrils of many connective tissues. Experiments in which the zonular fibrils were stretched and fixed prior to rotary shadowing showed that the distance between each bead is variable and can be accounted for by the bowing out of overlapping filaments which connect each bead.

Studies of methotrexate-induced limb dysplasias utilizing a 51chromium release assay

The folate antagonist methotrexate (MTX), widely used in chemotherapy, is a well-documented teratogen. However, the mechanism by which it exerts its effects is still unclear. Specifically, we have examined the cytotoxicity of MTX in vivo and in vitro and have looked at the relationship between cytotoxicity and teratogenesis. The chick embryo was utilized to examine the effects of the drug administered to carefully staged embryos. Embryos were exposed at stages 18-22 and examined on day 11 of incubation. Wings were malformed in a stage-dependent manner while legs were affected similarly at each stage used. A modification of the 51chromium-release assay was used to test the toxicity of MTX to limb cells in vitro. None of the tissues tested showed measurable toxicity in vitro even though the drug kills cells in vivo, thereby suggesting that MTX may be metabolized differently in vitro. Malformations induced by MTX do not seem to be due to changes in the amount of cell death taking place in the limb but may be caused by a transient inhibition of cell division.

Ectodermal influence on physiological cell death in the posterior necrotic zone of the chick wing bud

The phenomenon of "programmed cell death" in the posterior necrotic zone (PNZ) of the chick wing bud was reexamined. Prospective PNZs (pPNZs) were excised from stage 18-21 donor wings and observed for signs of necrosis in vitro. Cell death was quantified by a chromium-51 release assay. Prospective PNZs from the youngest donors (stage 18) showed no signs of death above control levels, while necrosis increased in vitro with increasing donor age. Cell death in the PNZ at stage 24 could be inhibited by removing the overlying ridge at stage 20 or 21. These results suggest that cell death in the PNZ is not rigidly determined early in development as previous studies suggest, but remains responsive to the cellular environment until shortly before the cells die.

In vitro effects of calmodulin antagonists on macrophage function in the posterior necrotic zone of the chick wing

Excised tissues from the prospective posterior necrotic zone (pPNZ) of the stage 21 chick wing were cultured in the presence of the calmodulin antagonists/protein kinase C inhibitors trifluoperazine (TFP) or chlorpromazine (CPZ). The appearance of cell death in vitro was not affected by the drugs. Macrophages differentiated normally and were competent to engulf debris. Lysosomal fusion with phagosomes and the digestion of most debris also occurred in the presence of the drugs. However, the macrophages were unable to process internalized cell membranes properly and continued accumulating membrane until they were grossly distended. The effect was reversible upon removal of the drugs. The results suggest a role for calmodulin and/or protein kinase C in the proper recycling of internalized membrane in embryonic macrophages.