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F Ramirez

Publications and source records attributed to F Ramirez.

At least 163 records · Page 9Linked to original sources
PubMed1985

Analysis of the promoter region and the N-propeptide domain of the human pro alpha 2(I) collagen gene.

We have located the exon coding for the start site of transcription of the human pro alpha 2(I) collagen gene. Comparison with the homologous region of other fibrillar collagen genes has confirmed the existence of a consensus sequence (CATGTCTA-n-TAGACATG) capable of forming a hairpin secondary structure possibly involved in the regulation of collagen biosynthesis. Sequence comparison of the chromosomal regions at the 5' end of the pro alpha 1(I) and pro alpha 2(I) collagen genes failed to identify unique DNA elements potentially mediating common regulatory signals. Sequencing of four exons coding for the N-terminal propeptide has determined most of its structure and it has implied the existence of smaller coding units similar to the 11 and 18 bp exons originally described in the avian gene.

Animals↗
PubMed1985

Analysis of cDNA and genomic clones coding for the pro alpha 1 chain of calf type II collagen.

A bovine cDNA library constructed from fetal cartilage RNA was screened with a pro alpha 1(II) collagen specific chicken cDNA. A recombinant clone (Bc 7), with an insert of 1 kb, was identified and shown to contain sequences exhibiting 85% homology with the chicken pro alpha 1(II) collagen C-propeptide. Interspecies comparison strongly suggested that one potential glycosylation site present in the avian C-propeptide is not utilized, since this site is absent in the bovine chain. In addition, two overlapping genomic clones (Pal 3 and Pal 4) were isolated and partially characterized. These clones span 23 kb of DNA and contain approximately 17 kb of the pro alpha 1(II) calf gene. Sequencing of exon 1 has determined the length of the 3' untranslated region and the exact location of the polyadenylation attachment site.

Amino Acid Sequence↗
PubMed1985

Isolation and partial characterization of the entire human pro alpha 1(II) collagen gene.

Using a cDNA probe specific for the bovine Type II procollagen, a series of overlapping genomic clones containing 45 kb of contiguous human DNA have been isolated. Sequencing of a 54 bp exon, number 29, provided direct evidence that the recombinant clones bear human Type II collagen sequences. Localization of the 5' and 3' ends of the gene indicated that the human Type II collagen gene is 30 kb in size. This value is significantly higher than that of the homologous avian gene. The segregation of a polymorphic restriction site in informative families conclusively demonstrated that the Type II gene is found in a single copy in the human haploid genome. Finally, sequencing of a triple helical domain exon has confirmed that a rearrangement leading to the fusion of two exons occurred in the pro alpha 1(I) gene, following the divergence of the fibrillar collagens.

Amino Acid Sequence↗
PubMed1985

Isolation of cDNA and genomic clones encoding human pro-alpha 1 (III) collagen. Partial characterization of the 3' end region of the gene.

A cDNA library constructed from human fibroblast poly(A+) RNA was screened for the identification of chimeric molecules bearing collagen-specific sequences. Analysis of three of the resulting positive clones showed that they encoded for the COOH-terminal propeptide region of the human Type III collagen. In addition, three overlapping clones covering more than 21 kilobases of the Type III gene were isolated from Charon 4A libraries of human genomic fragments. Identity between these and the cDNA clones was obtained by direct DNA sequencing. Establishment of the exon/intron arrangement of the Type III gene was obtained by electron microscopic analysis in conjunction with sequencing of selected genomic regions. Sequence comparison with other collagen genes confirmed some evolutionary features of this important family of proteins. Finally, the collinearity of two mRNA transcripts with 3' noncoding region length polymorphism was established.

Amino Acid Sequence↗
PubMed1985

Fine structural analysis of the human pro-alpha 1 (I) collagen gene. Promoter structure, AluI repeats, and polymorphic transcripts.

The human pro-alpha 1(I) collagen gene is 18 kilobases long, and its coding information is subdivided in 51 exons. We have recently reported a detailed analysis of this elaborate structure. Here we describe the exact termini of the gene as well as its 5' flanking sequences (promoter region). Sequence comparison between the human and mouse pro-alpha 1(I) gene showed an unusual highly conserved region 5' to the initiation site of transcription, which may be important for pro-alpha 1(I) collagen expression. Sequence comparison between the pro-alpha 1(I) and other collagen genes revealed the presence of a conserved secondary structure possibly implicated in the regulation of collagen mRNA translation and/or collagen secretion. Two short repetitive sequences closely associated with the pro-alpha 1(I) gene have been identified to be different members of the AluI family of repeats. Like the independently co-expressed pro-alpha 2(I) collagen gene, the analysis of the last exon has revealed that the pro-alpha 1(I) gene transcribes two different mRNAs in cultured fibroblasts. The colinearity and exact location of the termini of these transcripts, as well as their monogenic nature, have been conclusively determined.

Base Sequence↗
PubMed1985

Multiexon deletion in an osteogenesis imperfecta variant with increased type III collagen mRNA.

Recently, the dermal fibroblasts (ATCC CRL 1262) of a lethal perinatal variant of osteogenesis imperfecta have been used for the first molecular characterization of a collagen gene defect (Chu, M. L., Williams, C. J., Pepe, G., Hirsch, J. L., Prockop, D. J., and Ramirez, F. (1983) Nature (Lond.) 304, 78-80). These studies revealed that the patient was heterozygous for an internal deletion of approximately 500 base pairs in the pro-alpha 1(I) collagen gene, consistent with previous investigations indicating that CRL 1262 fibroblasts equally synthesized a normal and a shortened pro-alpha 1(I) chain (Barsh, G. S., and Byers, P. H. (1981) Proc. Natl. Acad. Sci. U.S.A. 78, 5142-5146). Cloning and analysis of the affected allele of CRL 1262 has now indicated that the deletion is contained between two introns of the pro-alpha 1(I) gene and results in the elimination of three exons of the triple helical domain. Furthermore, the termini of the rearrangement are located within two short inverted repeats suggesting that the self-complementary nature of these DNA elements may have favored the formation of a DNA secondary structure intermediate which, in turn, served as substrate for the deletion. Evidence are also presented for an elevated Type III collagen mRNA content in the patient fibroblasts.

Base Sequence↗
PubMed1985

Altered steady-state ratio of type I/III procollagen mRNAs correlates with selectively increased type I procollagen biosynthesis in cultured keloid fibroblasts.

Regulation of collagen gene expression was studied in fibroblast cultures established from patients with keloids, fibrotic lesions of the skin. In selected keloid fibroblast cultures, an overproduction of type I procollagen was observed. This increase was accompanied by a parallel increase in type I procollagen-specific mRNA levels, as detected by dot-blot and RNA transfer hybridizations, without concomitant change in type I procollagen gene copy number. At the same time, type III procollagen mRNA levels were unaltered, resulting in markedly elevated type I/III procollagen mRNA ratios. Thus, keloid fibroblasts offer a unique model to study the independent regulation of the gene expression of two genetically distinct procollagens, type I and type III.

Cells, Cultured↗
PubMed1985

Isolation and characterization of the human fibrillar collagen genes.

In order to elucidate some of the mechanisms leading to the pathological expression of the human fibrillar collagens, as well as to understand the evolution of these loci, specific cDNA and genomic clones have been isolated. The primary structure of the COOH-terminal propeptide of the four collagen chains and either part or the entire exon/intron arrangement of the genes have been determined. Interspecies and pairwise comparison revealed that the four loci have evolved at slightly different rates, maintaining, however, remarkably similar exon/intron arrangement. The fibrillar genes, albeit sharing the same elaborate structure, exhibit different sizes that correlate with the average length of their intron sequences, possibly because of their different chromosomal origin.

Animals↗
PubMed1984

Lateral interaction of cholesterol in diacylphosphatidylcholesterol bilayers.

Thermotropic phase-transition properties of the aqueous dispersions of several diacylphosphatidylcholesterol (DRCh) analogs are examined. The aqueous dispersions of their calcium salts exhibit characteristic endothermic thermotropic transitions due to a change in the conformation of acyl chains. These dispersions consist of osmotically intact liposomes that trap ions, and at the transition temperature there is anomalous increase in the ion leakage. Wide-angle electron diffraction studies of DPCh . Ca monolayers also exhibit a transition from a sharp 4.25 A band to a broad one centering at 4.7 A, reflecting an order-disorder transition in the acyl chains. The long-range order in the organization of acyl chains of DRCh molecules could arise from intermolecular interactions between the cholesterol moieties to form a functional dimer, and such dimers are apparently cross-linked by Ca2+ to form a long-range interacting lattice of acyl chains. Evidence for this model is adduced from the fluorescence properties of the dispersions of dimyristoylphosphatidylcholesta-5,7,9-trienol. The phase-transition properties of DRCh are an ideal illustration of calcium-induced isothermal phase transition.

Cholestanes↗
PubMed1984

Evidence from oxygen exchange studies that the two heads of myosin are functionally different.

Recent studies of oxygen exchange have shown that there are two normal pathways for the hydrolysis of MgATP by myosin in the presence of actin, each producing Pi at the same rate. These two apparent pathways for actin-activated hydrolysis differ greatly in the extent of oxygen exchange they support. This is revealed by an analysis of the distribution of [18O]Pi species produced by the hydrolysis of [gamma-18O]ATP. We have extended these studies to certain abnormal substrates, using Mn2+ in place of Mg2+, and dATP or ITP in place of ATP. The results, together with past findings, lead to the proposal that the two heads of myosin are functionally different. One of these (Head 1) is able to reversibly cleave bound MgATP and thereby support oxygen exchange while it is free of actin; the other (Head 2) cannot cleave bound MgATP at its active site while free of actin. However, in the presence of actin, both Head 1 and Head 2 cleave bound MgATP, support some oxygen exchange, and produce Pi at the same rapid actin-activated rate. Apparently, MgATP is positioned differently on the two heads when they are free of actin, with Mg2+ and the 6-amino group of ATP playing an important role in the orientation. This proposed difference between the heads could serve to make Head 1 react first with the actin filament, followed by Head 2. Thus, in muscle, the two heads on a myosin cross-bridge would interact with an actin filament and exert their pull in a fixed sequence.

Actins↗
PubMed1984

Amine fluorescamine compounds inhibit oxidative phosphorylation in rat liver mitochondria.

The reaction of fluorescamine with ammonia, benzylamine, o,p-dimethylbenzylamine, 2-phenylethylamine, p-aminobenzoic acid, and the mycosamine-containing macrolide antibiotic, amphotericin B, yield compounds which induce significant effects on mitochondrial activities. From their effects on energy-yielding processes which lead to transmembranous proton movements, the compounds may be divided into three classes. While all modifiers significantly inhibit proton movement induced by both ATP hydrolysis and electron transfer in mitochondria, their influence on the primary energy yielding steps are quite different. Class I modifiers, e.g., the compound made from amphotericin B, inhibit electron transfer but have no effect on the Pi release associated with ATP hydrolysis. Class II modifiers, e.g., the compound made from benzylamine, inhibit respiration but stimulate Pi release. Class III modifiers, e.g., the compound made from p-aminobenzoic acid, on the other hand, only slightly increase Pi release but have no effect on redox reactions. These and other effects of the modifiers are taken to mean that the proton movements and their associated energy-yielding processes are only linked indirectly. The effects of the modifiers on State 3 mitochondrial activities were also investigated. Although all the modifiers decrease the rates of both State 3 respiration and its coupled ATP synthesis, the efficiency of energy conversion measured by the P/O ratio remains unaltered.

Adenosine Triphosphatases↗
PubMed1984

Molecular heterogeneity in the mild autosomal dominant forms of osteogenesis imperfecta.

Mild osteogenesis imperfecta (OI type I and OI type IV) is characterized by postnatal onset of fractures, absence of skeletal deformity, presenile hearing loss with or without blue sclerae, and dentinogenesis imperfecta. Using one common DNA polymorphism associated with the pro alpha 2(I) human collagen gene, we found genetic heterogeneity in this disorder. In three families, the OI phenotype segregated independently of the DNA polymorphism, whereas in one family, the OI phenotype cosegregated with a DNA polymorphism in a manner suggesting linkage. Use of DNA polymorphisms associated with both type I procollagen genes should provide a tool to unravel the molecular heterogeneity of various heritable disorders of the connective tissue.

DNA Restriction Enzymes↗
PubMed1983

Nucleotide sequences of complementary deoxyribonucleic acids for the pro alpha 1 chain of human type I procollagen. Statistical evaluation of structures that are conserved during evolution.

Nucleotide sequences were determined for two cloned cDNAs encoding for over three-fourths of the pro alpha 1 (I) chain of type I procollagen from man. Comparison with previously published data on amino acid sequences of the alpha 1 (I) chain of type I collagen made it possible to examine mutations in the transcribed products of the gene which have occurred during the evolution of man, calf, rat, mouse, and chick. Comparison of the nucleotide sequences with the corresponding sequences of cDNAs from chick [Fuller, F., & Boedtker, H. (1981) Biochemistry 20, 996] and with cDNAs for the pro alpha 2(I) chain from man [Bernard, M.P., Myers, J. C., Chu, M.-L., Ramirez, F., Eikenberry, E. F., & Prockop, D. J. (1983) Biochemistry 22, 1139] demonstrated that selective pressure during evolution for 250 million or more years acted more strongly on the structure of the pro alpha 1 (I) chain than on the pro alpha 2(I) chain. To improve the reliability of the comparison, the nucleotide sequences were examined with a modification of previous procedures for evaluating mutations in replacement sites and silent sites. The corrected divergence for replacement sites between the alpha 1 (I) chains was 6 +/- 0.8% whereas it was 15 +/- 1.9% for the alpha 2(I) chains. The C-propeptide domain of the pro alpha 1 (I) chain was also highly conserved with a corrected divergence at replacement sites of 5 +/- 0.9%, a value that was not distinguishable from the value previously found for the C-propeptide of the pro alpha 2(I) chain. Therefore, a large part of the structure of both C-propeptides appears to be under selective pressure. Inspection of changes in the C-propeptide of the pro alpha 1 (I) chain suggested that there was a highly conserved region around the carbohydrate attachment site similar to the highly conserved region of 37 amino acids previously found in the C-propeptide of the pro alpha 2(I) chain. Two statistical tests, however, were unable to confirm nonrandom distribution of changes in the C-propeptide of the pro alpha 1(I) chain. The same tests established the presence of a nonrandom distribution in nucleotide changes of the C-propeptide of the pro alpha 2(I) chain. The 3'-noncoding region of the cDNA for pro alpha 1(I) of human type I procollagen showed no homology with the same region in the chick.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗
PubMed1983

Oxygen-exchange studies on the pathways for magnesium adenosine 5'-triphosphate hydrolysis by actomyosin.

At an intermediate stage in the hydrolysis of magnesium adenosine 5'-phosphate (MgATP) by myosin or actomyosin, there is an exchange of oxygen between water and the P gamma group of enzyme-bound nucleotide. Starting with [P gamma-18O]ATP as substrate, the exchange is revealed in the [18O]Pi species that are ultimately released as product into the reaction medium. An analysis of the distribution of these labeled Pi species, which contain 3, 2, 1, or none of the 18O atoms originally on the P gamma of ATP, is used to probe intermediate stages of the hydrolytic mechanism. In recent years, studies of this kind by several groups have shown that more than one pathway of hydrolysis operates. The work reported here demonstrates that two of these pathways are spurious; one is a "nonexchanging MgATPase" that is present in fresh myosin preparations; the other is an induced slow exchange that develops in myosin during storage (-20 degrees C) and subsequent aging (4 degrees C). However, after correction for these artifacts, two normal pathways for actomyosin hydrolysis remain. These normal pathways differ in the mode of interaction between actin and myosin in the course of hydrolysis; one is the Lymn-Taylor pathway where oxygen exchange occurs at a stage when actin and myosin are dissociated; the other is a pathway in which actin and myosin are associated during oxygen exchange. Each of these two pathways contributes an equal amount of Pi to the product pool. Thus, on average, each myosin head uses each of these pathways half the time. The findings suggest, e.g., that during contraction, myosin can dissociate from the actin filament only during every other cycle of MgATP hydrolysis or that only half the heads, at any one time, can exchange oxygen while free of the actin filament.

Actomyosin↗
PubMed1983

Analysis of the 3' end of the human pro-alpha 2(I) collagen gene. Utilization of multiple polyadenylation sites in cultured fibroblasts.

Three overlapping genomic clones covering 28 kilobases of the human pro-alpha 2(I) collagen gene have been isolated from a lambda phage library. The analysis of 12 introns and 12 exons in the 3' end region has shown that the human gene has a structure remarkably similar to that reported for the homologous chicken gene. One large intron, in the alpha-chain domain, contains an AluI sequence flanked by short direct repeats; a second AluI sequence is present 4 kilobases downstream from the termination codon. The analysis of the exon coding for the 3'-untranslated region has revealed that the pro-alpha 2(I) collagen gene transcribes at least four different mRNAs in cultured fibroblasts. The colinearity and exact location of the termini of these transcripts was determined by Northern blots, R-looping analysis, S1 protection, and DNA sequencing. The ends of two transcripts are closely preceded by the canonical polyadenylation signal (AAUAAA), whereas two of its variations (AUUAAA and AUUAA) precede the ends of the other two transcripts.

Base Sequence↗