An NcoI RFLP associated with the gene encoding the alpha-3 chain of human type VI collagen (COL6A3).
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Chromosomes, Human, Pair 2↗
Biomedical subjects
M L Chu
Publications and source records attributed to M L Chu.
Amino acid sequence of mouse nidogen, a multidomain basement membrane protein with binding activity for laminin, collagen IV and cells.
The whole amino acid sequence of nidogen was deduced from cDNA clones isolated from expression libraries and confirmed to approximately 50% by Edman degradation of peptides. The protein consists of some 1217 amino acid residues and a 28-residue signal peptide. The data support a previously proposed dumb-bell model of nidogen by demonstrating a large N-terminal globular domain (641 residues), five EGF-like repeats constituting the rod-like domain (248 residues) and a smaller C-terminal globule (328 residues). Two more EGF-like repeats interrupt the N-terminal and terminate the C-terminal sequences. Weak sequence homologies (25%) were detected between some regions of nidogen, the LDL receptor, thyroglobulin and the EGF precursor. Nidogen contains two consensus sequences for tyrosine sulfation and for asparagine beta-hydroxylation, two N-linked carbohydrate acceptor sites and, within one of the EGF-like repeats an Arg-Gly-Asp sequence. The latter was shown to be functional in cell attachment to nidogen. Binding sites for laminin and collagen IV are present on the C-terminal globule but not yet precisely localized.
Amino Acid Sequence↗
Sequence analysis of alpha 1(VI) and alpha 2(VI) chains of human type VI collagen reveals internal triplication of globular domains similar to the A domains of von Willebrand factor and two alpha 2(VI) chain variants that differ in the carboxy terminus.
Amino acid sequences of human collagen alpha 1(VI) and alpha 2(VI) chains were completed by cDNA sequencing and Edman degradation demonstrating that the mature polypeptides contain 1009 and 998 amino acid residues respectively. In addition, they contain small signal peptide sequences. Both chains show 31% identity in the N-terminal (approximately 235 residues) and C-terminal (approximately 430 residues) globular domains which are connected by a triple helical segment (335-336 residues). Internal alignment of the globular sequences indicates a repetitive 200-residue structure (15-23% identity) occurring three times (N1, C1, C2) in each chain. These repeating subdomains are connected to each other and to the triple helix by short (15-30 residues) cysteine-rich segments. The globular domains possess several N-glycosylation sites but no cell-binding RGD sequences, which are exclusively found in the triple helical segment. Sequencing of alpha 2(VI) cDNA clones revealed two variant chains with a distinct C2 subdomain and 3' non-coding region. The repetitive segments C1, C2 and, to a lesser extent, N1 show significant identity (15-18%) to the collagen-binding A domains of von Willebrand factor (vWF) and they are also similar to some integrin receptors, complement components and a cartilage matrix protein. Since the globular domains of collagen VI come into close contact with triple helical segments during the formation of tissue microfibrils it suggests that the globular domains bind to collagenous structures in a manner similar to the binding of vWF to collagen I.
Amino Acid Sequence↗
Expression of extracellular matrix genes by cultured human cells: localization of messenger RNAs and antigenic epitopes.
Simplified and expedient methodologies for examination of cellular gene expression at the mRNA and protein levels, utilizing in situ hybridization and peroxidase-anti-peroxidase immunodetection, were developed. These techniques were first optimized for the detection of extracellular matrix genes expressed by cultured human skin fibroblasts and keratinocytes, the two principal cell types of human skin. In situ hybridizations and Northern transfer analyses with human-sequence-specific cDNAs encoding collagenous and noncollagenous protein sequences demonstrated selective expression of different matrix genes by these two cell types, indicating different biosynthetic capacities of these cells and attesting to the specificity of the hybridizations. The utility of in situ hybridization was also demonstrated in mixed primary cell cultures established from cutaneous neurofibromas consisting of Schwann cells, perineurial cells, and fibroblasts. The methodologies developed here were further utilized for simultaneous detection of fibronectin mRNA and immunoreactive protein in fibroblast cultures. This procedure allowed detection of grains representative of radioactively labeled cDNA-mRNA hybrids and protein epitopes, as visualized by peroxidase-anti-peroxidase immunodetection on the same cells. This methodology, with appropriate modifications, may be applicable to other cell types as well as tissue specimens.
Cells, Cultured↗
Human laminin A chain (LAMA) gene: chromosomal mapping to locus 18p11.3.
Laminin, an integral component of basement membranes, consists of three subunit polypeptides, A, B1, and B2 chains. We have recently isolated cDNAs corresponding to human laminin A chain. These cDNAs were utilized for chromosomal in situ hybridizations to establish the genomic location of the laminin A chain gene. Metaphase chromosomes of PHA-stimulated human peripheral blood leukocytes were examined by in situ hybridization with 3H-labeled cDNAs, and the chromosomes were identified by R-banding (fluorochrome-photolysis-Giemsa method). The results indicated that the human laminin A chain is at locus 18p11.3. Since human laminin B1 and B2 chain genes have been previously mapped to chromosomes 7 and 1, respectively, the results indicate that genes encoding human laminin chains reside in separate chromosomes.
Blotting, Southern↗
Human nidogen: complete amino acid sequence and structural domains deduced from cDNAs, and evidence for polymorphism of the gene.
Nidogen, a multifunctional glycoprotein, is an integral part of all basement membranes. In this study, human nidogen cDNAs were isolated and characterized from human placental and skin fibroblast cDNA libraries by hybridization with a mouse nidogen cDNA probe. Six overlapping clones covering 4.9 kb were characterized. The composite cDNA contained a 3,741-nucleotide open reading frame which coded for a 1,247-amino-acid peptide that included a hydrophobic signal sequence. The deduced amino acid sequence contains seven epidermal growth factor-like cysteine-rich repeats, one possible tyrosine O-sulfation site, and a possible N-glycosylation site. The tripeptide sequence -Arg-Gly-Asp- (RGD), a potential cell attachment site, was also present. Human and mouse nidogen sequences were 84% homologous at the nucleotide level and 85% homologous at the deduced amino acid level. Southern blotting of human leukocyte DNA from 23 individuals indicated that nidogen probably is a single-copy gene and shows multiple restriction fragment length polymorphisms when cleaved with Eco RI, Pvu II, Taq I, and Msp I. In particular, digestions with Pvu II revealed polymorphism in four discrete DNA fragments, which could be discriminated by hybridizations with nidogen subclones. One of the polymorphisms revealed an allelic frequency of 0.52/0.48. Thus, human nidogen gene displays RFLPs which provide analytical tools to establish genetic linkage between the nidogen gene and a clinical phenotype.
Amino Acid Sequence↗
Collagen gene expression by cultured human skin fibroblasts. Abundant steady-state levels of type VI procollagen messenger RNAs.
Previous studies have suggested that procollagen types I and III are the major collagenous gene products of cultured human skin fibroblasts. In this study the expression of 10 different genes, encoding the subunit polypeptides for collagen types I-VI, by human skin fibroblasts in culture was analyzed by molecular hybridizations. Northern transfer analysis demonstrated the presence of specific mRNA transcripts for collagen types I, III, IV, V, and VI, but not for type II collagen. Quantitation of the abundance of these mRNAs by slot blot hybridizations revealed that type I, III, and VI procollagens were the major collagenous gene products of skin fibroblasts in culture. The mRNAs for type IV and V collagens represented only a small percentage of the total collagenous mRNA transcripts. Further analysis by in situ hybridization demonstrated that the majority of the cultured cells coexpressed the genes for type I, III, and VI procollagen pro-alpha chains. Further in situ hybridization analyses revealed the expression of type VI collagen genes in normal human skin. These data demonstrate that human skin fibroblast cultures can be used to study the transcriptional regulation of at least nine genetically distinct procollagen genes. The data further suggest that type VI collagen, in addition to types I and III, may be a major collagenous component of human skin.
Cells, Cultured↗
Type 1 neurofibromatosis: selective expression of extracellular matrix genes by Schwann cells, perineurial cells, and fibroblasts in mixed cultures.
Cutaneous neurofibromas, characteristic lesions of neurofibromatosis 1, are composed of an abundant extracellular matrix and nerve connective tissue-derived cell types: Schwann cells, perineurial cells, and fibroblasts. In this study, the extracellular matrix gene expression by these cells was examined under culture conditions that allowed them to be metabolically active and readily identifiable by morphologic and immunocytochemical criteria. Northern hybridizations demonstrated expression of genes for type I, III, IV, and VI collagens, as well as for fibronectin, laminin, and elastin. In situ hybridizations revealed that all three cell types expressed pro alpha 1 (I), pro alpha 2 (VI), and laminin B1 chain genes. However, fibroblasts did not contain [35S]cDNA-mRNA hybrids specific for type IV collagen, whereas both Schwann cells and perineurial cells expressed these genes. Perineurial cells and fibroblasts readily expressed the fibronectin gene whereas Schwann cells were essentially devoid of the corresponding mRNA. Perineurial cells also expressed the gene for laminin A chain. The results indicate that the extracellular matrix gene expression profiles of Schwann cells, perineurial cells, and fibroblasts are distinct: all three cell types are capable of expressing some of the genes for extracellular matrix components, such as type I and VI collagens, whereas Schwann cells and perineurial cells may have the primary role in synthesizing basement membrane zone components, type IV collagen and laminin. These observations potentially relate to the mechanisms of growth and development of human neurofibromas. The results attest to the applicability of the methodology utilized here to study other human tumors with mixed cell populations.
Blotting, Northern↗
Human nidogen: cDNA cloning, cellular expression, and mapping of the gene to chromosome Iq43.
A human placental lambda gt11 expression cDNA library was screened for nidogen cDNAs by hybridizations with a heterologous mouse nidogen cDNA. A total of four positive overlapping clones were identified, and the sizes of the inserts were shown to vary from 0.8 to 2.8 kb. Nucleotide sequencing of the human cDNAs revealed that the largest clone, cHPN-16, contained both a 5' open reading frame encoding 582 amino acids and a 3' untranslated region of 1,063 nucleotides. Comparison of human cDNA sequences with mouse nidogen sequences revealed 84% identity on the nucleotide level and 88% identity with the deduced amino acid sequence. The deduced amino acid sequence of the human cDNAs revealed the presence of cysteine-rich epidermal growth factor-like repeats and the sequence Arg-Gly-Asp (RGD), a potential cell binding site, two features previously identified in mouse nidogen. The sequence Asn-Pro-Ser, a consensus sequence for N-linked glycosylation, was also noted. The newly isolated human cDNAs were utilized to analyze the expression of the nidogen gene by cultured human cells. Northern hybridizations revealed a single mRNA transcript of approximately 6.0 kb in human skin fibroblast and in HT 1080 fibrosarcoma cell cultures. However, the human choriocarcinoma cell line JEG-3, which expressed laminin genes, did not contain detectable levels of nidogen mRNAs. Quantitation of the relative nidogen mRNA abundance in HT 1080 fibrosarcoma cells indicated that nidogen mRNA levels were approximately the same as those for the laminin B2 chain. Finally, one of the nidogen cDNAs was used to map the nidogen gene onto locus q43 of chromosome 1.
Amino Acid Sequence↗
[Epidemiological characterization of Neisseria gonorrhoeae isolates from Taiwan. Part II: Distribution of auxotyping, serogrouping and plasmid profile].
Epidemiology of gonococcal infection in Taiwan was investigated. Six hundred twelve isolates from 7 cities in 1983-1984 were examined for auxotyping by Hendry and Stewart's method, for serotyping by coagglutination of monoclonal antibodies with the antigenic specificity of gonococcal protein I molecules and for plasmid profile by the alkaline quick method. The results are described below: (1) Thirty-six auxotypes were found. Prototropic (Prototype) 45.4% (284/612) and Proline type (Pro) 38.7% (237/612) were the two dominant auxotypes. Arg- Hyp- Ura- which was thought to be correlated with disseminated gonococcal infection was not found. (2) Fifty-five percent penicillinase producing Neisseria gonorrheal (PPNG) were prototype and 48.8% non-PPNG were Pro. (3) Sixteen serotypes were identified among 56 strains. There was 17.8 (10/56 which belonged to the IA group and 82.2% (46/56) to the IB group. (4) Five molecular weight plasmids were found. They were 2.6 Mdal, 3.05 Mdal, 4.7 Mdal, 7.8 Mdal and 24.5 Mdal. (5) There were 7 plasmid profiles including 2.6 Mdal (26.4%); 2.6 Mdal +24.5 Mdal (23.2%); 2.6 Mdal+7.8 Mdal+24.5 Mdal (0.4%); 2.6 Mdal+4.7 Mdal (8.9%); 2.6 Mdal+4.7 Mdal+24.5 Mdal (38.2%); 2.6 Mdal+4.7 Mdal+24.5 Mdal (0.2%) and 2.6 Mdal+3.05 Mdal+24.5 Mdal (2.4%). (6) All the isolates harbored cryptic 2.6 Mdal plasmid. Eighty three percent of the PPNG and 48.6% of the non-PPNG harbored 24.5 Mdal plasmid. Twelve out of 305 PPNG isolates were "Toronto" type 3.05 Mdal plasmid. Others were "Asian" 4.7 Mdal plasmid. There were no "African" type 3.2 Mdal plasmids found.
Neisseria gonorrhoeae↗
[Clinical analysis and study of hypospadias].
We did a retrospective survey on 117 patients with hypospadias to determine what other congenital anomalies were present. We confirm the increasing incidence of chordee with severity of hypospadias. There were many other systemic anomalies associated with hypospadias. We found nongenitourinary tract malformations as follows: neuromuscular 1.7%, gastrointestinal 4.3%, cardiovascular 3.4%, ENT 0.8%, eye 0.8%. The incidence of genitourinary tract anomalies associated with hypospadias was 24.8% (undescended testis 11.1% and hernia 6.0%). Intravenous pyelography should be reserved for a selected group of children with hypospadias with abnormal ultrasonograms or urologic symptomatology. The primary therapeutic approach is surgical. Urethra-cutaneous fistula requiring additional surgery may occur following hypospadias repair in about 29.0% of cases in this paper.
Adolescent↗
Human laminin: cloning and sequence analysis of cDNAs encoding A, B1 and B2 chains, and expression of the corresponding genes in human skin and cultured cells.
A human placental lambdagt11 expression cDNA library was probed for laminin cDNAs by a combination of immunoscreening using polyclonal anti-human laminin antibody, and plaque hybridizations using a mouse laminin A chain cDNA. A total of 36 recombinant clones were isolated and characterized. Northern blot hybridizations with poly(A)+RNA, isolated from cultured human skin fibroblasts, revealed hybridization either to (a) a single 10 kb transcript consistent with A chain; (b) a single 5.7 kb transcript consistent with B1 chain; or (c) polymorphic 5.6 and 8.2 kb transcripts consistent with B2 chain of human laminin. Nucleotide sequencing of representative cDNA clones (approximately 2.5 kb in size) confirmed that these three groups of cDNAs encoded C-terminal sequences of laminin A, B1 and B2 chains, respectively. Deduced amino acid sequences for both B1 and B2 chains contained epidermal growth factor-like sequences and alpha-helical heptad repeats, as found previously for mouse laminin. Partial laminin A chain cDNA encoded 680 amino acid residues characterized by several internal repeats. This portion of the peptide accounted for a large part of the globular domain (fragment 3), the whole length of a second (T2) and portions of a third (T1) globular domain. The human A chain also contained an Arg-Gly-Asp sequence, a potential cell-binding site, which is not found in the same segment of mouse laminin. The newly isolated cDNAs were also utilized to analyze expression of laminin mRNAs by cultured human cells and tissues. The results demonstrated that the laminin A, B1, and B2 chain genes were expressed in an uncoordinate manner in both cultured cells and tissues, with a particularly low level of the A chain mRNA being present.
Amino Acid Sequence↗
Amino acid sequence of the triple-helical domain of human collagen type VI.
The complete amino acid sequence of the triple-helical domain of human collagen VI was deduced from sequences of appropriate cDNA clones and confirmed to about 50% by Edman degradation of tryptic peptides. This domain consists of three different peptide segments containing some 335-336 amino acid residues originating from central portions of the alpha 1 (VI), alpha 2(VI), and alpha 3(VI) chains, respectively. Sequence identity in the X/Y positions of the Gly-X-Y repeats is rather low (10-15%) between the chains. Peculiar features of these sequences include 3 cysteine residues about 50 (alpha 3(VI)) and 89 (alpha 1(VI), alpha 2(VI)) residues away from the N-terminus and several Gly-X-Y interruptions clustered in the C-terminal two-thirds of the triple helix. These structures are presumably required for cross-linking collagen VI oligomers and for super-coiling of triple helices in the dimers. Other features include 11 Arg-Gly-Asp sequences, some of which are likely to be used as cell-binding sites, and four Asn-X-Thr sequences, allowing N-linked glycosylation along the triple helix. Junctional areas close to the helix contain short, cysteine-rich segments which may seal the triple-helical domain through disulfide bond formation, endowing it with high stability. These features, together with a low sequence homology to fiber-forming and basement-membrane collagens, document the unique character of collagen VI, whose triple helix is specifically adjusted for forming microfibrils in tissues.
Amino Acid Sequence↗
A BglI polymorphism in the type VI (alpha 3) procollagen gene [COL6A3].
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Deoxyribonucleases, Type II Site-Specific↗
Structure of a full-length cDNA clone for the prepro alpha 2(I) chain of human type I procollagen. Comparison with the chicken gene confirms unusual patterns of gene conservation.
A cDNA clone from a human placental library was found to consist of an essentially full-length cDNA of 4.6 kb for the prepro alpha 2(I) chain of type I procollagen. Nucleotide sequencing of the 5'-end of the cDNA provided a sequence of 1617 nucleotide residues and codons for 539 amino acid residues not previously defined. Comparison of the complete structure of the prepro alpha 2(I) cDNA with previously reported sequences for the chicken pro alpha 2(I) gene indicated that 83% of 1366 total amino acid residues were conserved. In the alpha-chain domain 84% of 1014 amino acid residues were conserved. Also, there was conservation of the previously noted preference for U and C in the third position of codons for glycine, proline and alanine. One major difference between the human and the chicken prepro alpha 2(I) chain was that the human chain contained 21 fewer proline residues, an observation that probably explains why the triple helix of human type I procollagen unfolds at temperatures that are 1-2 degrees C lower. In parallel experiments, sequencing of intron-exon boundaries for nine exons of genomic subclones confirmed and extended previous observations that the pro alpha 2(I) gene, like other genes from fibrillar collagens, has an unusual 54-base pattern of exon sizes that is highly conserved through evolution.
Amino Acid Sequence↗
Modulation of collagen metabolism by glucocorticoids. Receptor-mediated effects of dexamethasone on collagen biosynthesis in chick embryo fibroblasts and chondrocytes.
The steroid modulation of collagen metabolism was studied by injecting chick embryos with dexamethasone in vivo, and collagen synthesis was subsequently assayed by pulse-labeling the tissue with [14C]proline in vitro. The synthesis of [14C]hydroxyproline in tendons and sterna from chick embryos treated with dexamethasone was markedly reduced as compared with untreated controls. The inhibition of [3H]hydroxyproline synthesis was accompanied by a similar reduction in type I and II procollagen mRNA levels, as detected by Northern blot and dot blot hybridizations with chick pro alpha 1(I), pro alpha 2(I) and pro alpha 1(II) sequence specific cDNAs. The reduction in type II procollagen mRNA level was shown to be dose dependent. Control experiments indicated that the post-translational hydroxylation of prolyl residues was only slightly decreased in dexamethasone treated animals, and that the specific activity of the intracellular free proline pool and the intracellular degradation of collagen were unchanged. To address the mechanisms of the inhibition of collagen biosynthesis, specific binding of dexamethasone to glucocorticoid receptors in chick embryo tendon and cartilage cells was studied in a whole cell assay using [3H]dexamethasone as the ligand. Matrix-free tendon and cartilage cells had approximately 19,000 and 15,000 receptor sites per cell, respectively, and the binding affinities (Kd) for dexamethasone in tendon and cartilage cells were 2.9 x 10(-9) and 2.3 x 10(-9) M. Comparable values were obtained using a cytosol binding assay. The nuclear binding of dexamethasone in tendon and cartilage cells were similar. The results suggest that the dexamethasone-induced inhibition of collagen production is primarily due to decreased levels of functional procollagen mRNA, possibly resulting from receptor-mediated inhibition of the gene expression on the transcriptional level.
Animals↗
cDNA cloning, expression and mapping of human laminin B2 gene to chromosome 1q31.
A laminin B2 chain cDNA clone was isolated from a human lung cDNA library by screening with antibody against mouse laminin. The authenticity of the human cDNA clone was established by comparison of the nucleotide and deduced amino acid sequences of the cDNA insert with those of the previously reported mouse laminin cDNA clones. The human clone (LC7) contained an insert of 0.75 kb (kilobase pair) that corresponded to the last 232 amino acid residues in the carboxyl terminus of the B2 chain. Northern blot analyses with the LC7 probe detected two mRNA transcripts of 8.2 and 5.6 kb in both normal human skin fibroblasts and three human tumor cell lines. The cDNA probe was also used in Southern blot analysis of DNA from human rodent somatic cell hybrids to localize the gene to human chromosome 1. In situ hybridization of the cDNA with metaphase chromosome spreads confirmed the assignment and further mapped the human laminin B2 chain gene to the long arm of chromosome 1 in the band q31.
Amino Acid Sequence↗
Expression of basement membrane zone genes coding for type IV procollagen and laminin by human skin fibroblasts in vitro: elevated alpha 1 (IV) collagen mRNA levels in lipoid proteinosis.
Basement membrane zone gene expression by fibroblast cultures established from adult human skin was examined by molecular hybridizations with human sequence-specific cDNAs corresponding to pro-alpha 1 (IV) chain of type IV collagen and B2 chain of laminin. Northern transfer analysis of poly(A)+RNA isolated from fibroblast cultures clearly revealed the presence of specific mRNA transcripts, indicating the expression of the genes coding for pro-alpha 1 (IV) and laminin B2 polypeptides. Quantitative estimates of the relative levels of these mRNAs coding for basement membrane zone components indicated that they are of relatively low abundance in control fibroblasts, as compared with mRNAs coding for fibronectin or pro-alpha 1 (I) chain of type I procollagen. In fibroblast cultures established from the lesional skin of a 32-year-old patient with lipoid proteinosis, the levels of mRNA coding for pro-alpha 1 (IV) polypeptides were increased approximately 4.5-fold, as compared with age- and passage-matched control cultures. This increase was selective in that the levels of fibronectin, pro-alpha 1 (I), and beta-actin mRNAs were unaltered in the same cultures. The increase in pro-alpha 1 (IV) mRNA level was also uncoordinate with the expression of the laminin B2 chain gene, which was unaltered in lipoid proteinosis. The selective increase in pro-alpha 1 (IV) mRNA may have relevance to the accumulation of this basement membrane component in the skin in lipoid proteinosis.
Adult↗