Structural and functional studies on the interstitial collagen genes

An understanding of the molecular mechanisms which control expression of the type I and III collagen genes may provide a rational basis for the design of more effective therapeutic approaches to fibrotic diseases. The structure of the interstitial collagen genes is reviewed and potential sites which could control their expression are examined. One approach to the study of the regulation of these genes consists in DNA-mediated gene transfection experiments and is discussed in this paper.

Crystallization and preliminary X-ray characterization of rat liver acyl-CoA oxidase

A recombinant form of the flavoenzyme acyl-CoA oxidase from rat liver has been crystallized by the hanging-drop vapour-diffusion technique using PEG 20 000 as a precipitating agent. The crystals grew as yellow prisms, with unit-cell parameters a = 71.05, b = 87.29, c = 213.05 A, alpha = beta = gamma = 90 degrees. The crystals exhibit the symmetry of space group P2(1)2(1)2(1) and are most likely to contain a dimer in the asymmetric unit, with a V(M) value of 2.21 A(3) Da(-1). The crystals diffract to a resolution of 2.5 A at beamline BL6A of the Photon Factory. Two heavy-atom derivatives have been identified.

On the ligands in charge-transfer complexes of porcine kidney flavoenzyme D-amino acid oxidase in three redox states: a resonance Raman study

To investigate the structural modulation of ligands and their interaction in the active-site nanospace when they form charge-transfer (CT) complexes with D-amino acid oxidase (DAO) in three redox states, we compared Raman bands of the ligands in complex with DAO with those of ligands free in solution. Isotope-labeled ligands were synthesized for assignments of observed bands. The COO(-) stretching of ligands observed around, 1,370 cm(-1) downshifted by about 17 cm(-1) upon complexation with oxidized, semiquinoid and reduced DAO, except for the case of reduced DAO-N-methylisonicotinate complex (8 cm(-1) downward shift); the interaction mode of the carboxylate group with the guanidino group of Arg283 and the hydroxy moiety of Tyr228 of DAO is similar in the three redox states. The C=N stretching mode (1,704 cm(-1)) of Delta(1)-piperideine-2-carboxylate (D1PC) downshifted to 1,675 and 1,681 cm(-1) upon complexation with reduced and semiquinoid DAO, respectively. The downward shifts indicate that the C=N bond is weakened upon the complexation. This is probably due mainly to charge-transfer (CT) interaction between D1PC and semiquinoid or reduced flavin, i.e., the partial electron donation from the highest occupied molecular orbital (HOMO) of reduced flavin or a singly occupied molecular orbital (SOMO) of semiquinoid flavin to the lowest unoccupied molecular orbital (LUMO), an antibonding orbital, of D1PC. This speculation was supported by the finding that the magnitude of the shift is smaller by 5 cm(-1) (observed at 1,680 cm(-1)) in the case of reduced DAO reconstituted with 7,8-Cl(2)-FAD, whose reduced form has lower electron-donating ability than natural reduced FAD. The amount of electron flow was estimated by applying the theory of Friedrich and Person [(1966) J. Chem. Phys. 44, 2166-2170] to these complexes; the amounts of charge transfer from reduced FAD and reduced 7,8-Cl(2)-FAD to D1PC were estimated to be about 10 and 8% of one electron, respectively, in the CT complexes of reduced DAO with D1PC.

Three-dimensional structure of the purple intermediate of porcine kidney D-amino acid oxidase. Optimization of the oxidative half-reaction through alignment of the product with reduced flavin

The three-dimensional structure of the purple intermediate of porcine kidney D-amino acid oxidase (DAO) was solved by cryo-X-ray crystallography; the purple intermediate is known to comprise a complex between the dehydrogenated product, an imino acid, and the reduced form of DAO. The crystalline purple intermediate was obtained by anaerobically soaking crystals of oxidized DAO in a buffer containing excess D-proline as the substrate. The dehydrogenated product, delta(1)-pyrrolidine-2-carboxylate (DPC), is found sandwiched between the phenol ring of Tyr 224 and the planar reduced flavin ring. The cationic protonated imino nitrogen is within hydrogen-bonding distance of the backbone carbonyl oxygen of Gly 313. The carboxyl group of DPC is recognized by the Arg 283 guanidino and Tyr 228 hydroxyl groups through ion-pairing and hydrogen-bonding, respectively. The (+)HN=C double bond of DPC overlaps the N(5)-C(4a) bond of reduced flavin. The electrostatic effect of the cationic nitrogen of DPC is suggested to shift the resonance hybridization of anionic reduced flavin toward a canonical form with a negative charge at C(4a), thereby augmenting the electron density at C(4a), from which electrons are transferred to molecular oxygen during reoxidation of reduced flavin. The reactivity of reduced flavin in the purple intermediate, therefore, is enhanced through the alignment of DPC with respect to reduced flavin.

[Chemical and functional properties of flavin coenzymes]

The yellow-colored compounds with the basic structural frame work of 7,8-dimethyl-10-alkylisoalloxazine are generally termed as flavins. The 10-ribityl derivative, riboflavin, is the most abundant flavin found in nature and is known as vitamin B2. Riboflavin is a precursor of the flavocoenzymes, FMN (flavin mononucleotide) and FAD (flavin adenine dinucleotide) which function as prosthetic groups of flavocoenzymes. While flavocoenzymes are usually bound noncovalently to apoproteins of flavoenzymes, covalently-bound flavocoenzymes also occur in nature, though much less often. Flavin molecules can exist in three different redox states, i.e., oxidized, one-electron reduced and two-electron reduced states, and therefore can participate in redox reactions as either one- or two-electron mediator, making the flavoenzymes extremely versatile in terms of substrate and type of reactions catalyzed. We classified flavoenzymes according to the electron-transfer process in their reductive and oxidative half-reactions and the mechanism of each class of flavoenzymes is discussed in detail.

Unusually high standard redox potential of acrylyl-CoA/propionyl-CoA couple among enoyl-CoA/acyl-CoA couples: a reason for the distinct metabolic pathway of propionyl-CoA from longer acyl-CoAs

The standard redox potential of acrylyl-CoA/propionyl-CoA couple (C(3)) was determined to be 69 mV (vs. standard hydrogen electrode) at pH 7 and 25 degrees C. This value implies that the 2, 3-dehydrogenation of propionyl-CoA is thermodynamically much more unfavorable than that of longer acyl-CoAs because the standard redox potentials of crotonyl-CoA/butyryl-CoA (C(4)), octenoyl-CoA/octanoyl-CoA (C(8)), and hexadecenoyl-CoA/palmitoyl-CoA (C(16)) are all about -10 mV. The unusually high standard redox potential of the acrylyl-CoA/propionyl-CoA couple is thought to be one of the reasons that in mammals propionyl-CoA is not metabolized by beta-oxidation as in the case of longer acyl-CoAs, but by a methylmalonyl-CoA pathway. The obvious structural difference between C(3) and C(4) (and longer) is whether an H or the C(4) atom is connected to -C(3)H=C(2)H-C(1)O-S-CoA. The molecular orbital calculations (MOPAC) for the enoyl and acyl forms of C(3) and C(4) revealed that this structural feature is the main cause for the higher standard redox potential of the C(3) couple. That is, the C(4)-C(3) bond is stabilized by the dehydrogenation to a greater degree than the H-C(3) bond.

C-terminal tripeptide Ser-Asn-Leu (SNL) of human D-aspartate oxidase is a functional peroxisome-targeting signal

The functionality of the C-terminus (Ser-Asn-Leu; SNL) of human d-aspartate oxidase, an enzyme proposed to have a role in the inactivation of synaptically released d-aspartate, as a peroxisome-targeting signal (PTS1) was investigated in vivo and in vitro. Bacterially expressed human d-aspartate oxidase was shown to interact with the human PTS1-binding protein, peroxin protein 5 (PEX5p). Binding was gradually abolished by carboxypeptidase treatment of the oxidase and competitively inhibited by a Ser-Lys-Leu (SKL)-containing peptide. After transfection of mouse fibroblasts with a plasmid encoding green fluorescent protein (GFP) extended by PKSNL (the C-terminal pentapeptide of the oxidase), a punctate fluorescent pattern was evident. The modified GFP co-localized with peroxisomal thiolase as shown by indirect immunofluorescence. On transfection in fibroblasts lacking PEX5p receptor, GFP-PKSNL staining was cytosolic. Peroxisomal import of GFP extended by PGSNL (replacement of the positively charged fourth-last amino acid by glycine) seemed to be slower than that of GFP-PKSNL, whereas extension by PKSNG abolished the import of the modified GFP. Taken together, these results indicate that SNL, a tripeptide not fitting the PTS1 consensus currently defined in mammalian systems, acts as a functional PTS1 in mammalian systems, and that the consensus sequence, based on this work and that of other groups, has to be broadened to (S/A/C/K/N)-(K/R/H/Q/N/S)-L.

Structural and mechanistic studies on D-amino acid oxidase x substrate complex: implications of the crystal structure of enzyme x substrate analog complex

As an extension of our recent X-ray crystallographic determination of the tertiary structure of D-amino acid oxidase (DAO) [Mizutani, H. et al. (1996) J. Biochem. 120, 14-17], we solved the crystal structure of the complex of DAO with a substrate analog, o-aminobenzoate (OAB). The alignment between flavin and OAB in the crystal structure of the complex is consistent with charge-transfer interaction through the overlap between the highest occupied molecular orbital of OAB and the lowest unoccupied molecular orbital of flavin. Starting with the atomic coordinates of this complex as the initial model, we carried out molecular mechanics simulation for the DAO-D-leucine complex and thus obtained a model for the enzyme-substrate complex. According to the enzyme-substrate complex model, the alpha-proton is pointed toward N(5) of flavin while the lone-pair of the substrate amino group can approach C(4a) of flavin within an interacting distance. This model as well as DAO-OAB complex enables the evaluation of the substrate-flavin interaction prior to electron transfer from the substrate to flavin and provides two possible mechanisms for the reductive-half reaction of DAO, i.e., the electron-proton-electron transfer mechanism and the ionic mechanism.

Spectroscopic studies of rat liver acyl-CoA oxidase with reference to recognition and activation of substrate

Two forms of rat peroxisomal acyl-CoA oxidase (ACO-I and -II) interact with the substrate analogs, 3-ketoacyl-CoAs, forming a complex characterized by the so-called charge-transfer (CT) band around 575 nm in the absorption spectra. The CT band of ACO-I exhibited a broad dependency on the acyl chain-length from C4 to C16, whereas that of ACO-II showed increased intensity with a longer acyl chain to reach a maximum with a chain-length of C12. These chain-length dependencies of the CT bands were compared with those of the enzymatic activities reported previously [Setoyama et al. (1995) Biochem. Biophys. Res. Commun. 217, 482-487]. The differences in spectroscopic and enzymatic properties between ACO-I and -II suggest that the amino acid stretch corresponding to the third exon in the ACO sequence affects the binding of the ligand and substrate, since the difference in the primary structure between ACO-I and -II lies in the short amino acid stretch corresponding to the third of the total of 14 exons. On the other hand, resonance Raman spectra of the complexes of ACO-I and -II with 3-ketoacyl-CoAs excited in the CT band showed similar features. The two prominent FAD bands II and III, associated with the C(4a)=N(5) moiety of FAD, were observed at 1,577 and 1,545 cm(-1), respectively. In contrast, the bands at 1,615 and 1,493 cm(-1) in the ACO-I x 3-keto-C8-CoA complex were assigned to the stretching modes of C=O at positions 3 and 1 of the ligand, respectively, by using the isotopically labeled ligands. Both C=O stretching bands were shifted to lower wave numbers upon complex formation with ACO-I, implying that the C=O bond involves the single bond (C-O-) character in the active site cavity. The downshift of the C(1)=O stretching band was larger than that of the C(3)=O stretching band. Therefore, the ligand lies in the active site as the anionic form with a major contribution from C(1)-O-. These observations demonstrate that the CT band around 575 nm arises from the charge-transfer interaction between the oxidized FAD and the enolate transformed after the elimination of the a-proton. The band II of FAD in the complexes reveals a significant decrease in the frequency in comparison with the complexes of medium-chain acyl-CoA dehydrogenase (MCAD) with 3-ketoacyl-CoA. This observation suggests a difference between ACO and MCAD in the hydrogen-bonding network associated with enzyme-bound FAD.

Structural and functional characterization of the human brain D-aspartate oxidase

D-Aspartate oxidase (DDO) cDNAs were isolated from the human brain RNA using the RT-PCR method. Two forms (DDO-1 and DDO-2) of DDO mRNA were detected. Structural analysis of the DDO cDNAs and genomic DNA showed that DDO-1 and DDO-2 are produced by alternative splicing from a single gene. A protein encoded by the DDO-1 cDNA consists of 341 amino acids, and the amino acid sequence of DDO-2 was identical to that of DDO-1 except for the absence of 59 amino acids covering residues 95-153 of DDO-1. A homogenous preparation of DDO-1 was obtained using an expression system in Escherichia coli. DDO-1 selectively catalyzed the oxidative deamination of D-aspartate and its N-methylated derivative, N-methyl D-aspartate; the values of K(m) and k(cat) for D-aspartate were 2.7 mM and 52.5 mol D-aspartate oxidized x s(-1) x mol(-1) and those for N-methyl D-aspartate were 6.8 mM and 37.7 mol N-methyl D-aspartate oxidized x s(-1) x mol(-1), respectively.

Three-dimensional structure of porcine kidney D-amino acid oxidase at 3.0 A resolution

The X-ray crystallographic structure of porcine kidney D-amino acid oxidase, which had been expressed in Escherichia coli transformed with a vector containing DAO cDNA, was determined by the isomorphous replacement method for the complex form with benzoate. The known amino acid sequence, FAD and benzoate were fitted to an electron density map of 3.0 A resolution with an R-factor of 21.0%. The overall dimeric structure exhibits an elongated ellipsoidal framework. The prosthetic group, FAD, was found to be in an extended conformation, the isoalloxazine ring being buried in the protein core. The ADP moiety of FAD was located in the typical beta alpha beta dinucleotide binding motif, with the alpha-helix dipole stabilizing the pyrophosphate negative charge. The substrate analog, benzoate, is located on the re-face of the isoalloxazine ring, while the si-face is blocked by hydrophobic residues. The carboxylate group of benzoate is ion-paired with the Arg283 side chain and is within interacting distance with the hydroxy moiety of Tyr228. The phenol ring of Tyr224 is located just above the benzene ring of benzoate, implying the importance of this residue for catalysis. There is no positive charge or alpha-helix dipole near N(1) of flavin. Hydrogen bonds were observed at C(2) = O, N(3)-H, C(4) = O, and N(5) of the flavin ring.

Crystallization of expressed porcine kidney D-amino acid oxidase and preliminary X-ray crystallographic characterization

The cDNA for porcine kidney D-amino acid oxidase (DAO) was cloned by means of the reverse transcription-polymerase chain reaction system from porcine kidney RNA and over-expressed in Escherichia coli which had been transformed with a vector containing the DAO cDNA. The expressed DAO was purified to homogeneity by a three-step procedure, i.e., heat-treatment, DEAE Sepharose column chromatography, and hydroxyapatite column chromatography. The purified DAO preparation, rDAO (recombinant DAO), showed an identical UV-visible absorption spectrum and catalytic activity with those of the wild-type enzyme purified from porcine kidney. Crystallization of rDAO was performed by the hanging-drop method and crystals of suitable quality for X-ray crystallography were obtained. The crystals so obtained diffracted to 2.5 A with a conventional X-ray source, and to 2.0 A with synchrotron radiation. The crystals belong to the orthorhombic space group P2(1)2(1)2(1) with unit cell dimensions of a = 110.3, b = 92.9, c = 71.6 A. A Vm value of 2.35 A3/Da indicates that there are two subunits related by a twofold non-crystallographic axis in the asymmetric unit. Two heavy atom derivatives have been identified.

Overexpression of Ca2+/calmodulin-dependent protein kinase II inhibits neurite outgrowth of PC12 cells

To investigate the physiological role of Ca2+/calmodulin-dependent protein kinase II (CaM kinase II) in neuronal differentiation, we transfected the cDNA of the alpha subunit of mouse CaM kinase II (CaM kinase II alpha) into PC12 cells and established clonal cell lines that constitutively express the transfected CaM kinase II alpha gene. The expression of CaM kinase II alpha was confirmed by northern blot and immunoblot analyses. Northern blot analysis showed that the gamma and delta subunits of CaM kinase II are mainly expressed in PC12 cells. Treatment of the cells with ionomycin activated CaM kinase II alpha through autophosphorylation and generation of the Ca2+/calmodulin-dependent form. It is interesting that the neurite outgrowth induced by dibutyryl cyclic AMP was inhibited in these cell lines in accordance with the activities of overexpressed CaM kinase II alpha. The activity of cyclic AMP-dependent protein kinase showed similar levels among these cell lines. These results suggest that CaM kinase II is involved in the modulation of the neurite outgrowth induced by activation of the cyclic AMP system.

Functional expression of two forms of rat acyl-CoA oxidase and their substrate specificities

Using the reverse transcription of RNA followed by the polymerase chain reaction, we cloned the cDNAs for the rat acyl-CoA oxidases I and II, which are produced by alternative splicing from a single gene, and developed a system for their expression in Escherichia coli. The homogeneous preparations of these enzymes, without proteolytic procession, showed oxidase activity with acyl-CoAs having various acyl-chain lengths. The two types of the enzyme exhibited different substrate specificities with respect to the acyl-chain length, acyl-CoA oxidase I showing the optimum activity at shorter chain-length relative to acyl-CoA oxidase II.

[Molecular mechanisms of the expression of cytosolic and mitochondrial isozyme genes]

We isolated the mouse cytosolic and mitochondrial malate dehydrogenase (cMDH and mMDH) and the mouse cytosolic and mitochondrial aminotransferase (cAspAT and mAspAT) genes functioning in the malate-aspartate shuttle, and localized the DNA regions required for the promoter activity of these isozyme genes. We also characterized nuclear proteins binding to the promoter regions, and found that a transcription factor, CTF/NFI may contribute to the regulation of cMDH, mMDH and cAspAT levels, and that another transcription factor, Sp1 is probably linked to the regulation of mAspAT level. Comparison of the amino acid sequences among the mammalian and bacterial MDHs revealed that the homology between the mouse cMDH and thermophilic bacterial MDH, as well as the homology between the mouse mMDH and E. coli MDH, markedly exceeds the intraspecies sequence homology between cMDH and mMDH from mice. Moreover, structural organizations of the two-pairs of isozyme genes indicated that introns antedate the divergence of these cytosolic and mitochondrial isozyme genes.

A novel nuclear protein with zinc fingers down-regulated during early mammalian cell differentiation

We introduced a promoter trap vector carrying a neo gene as a selectable marker into F9 cells and established several cell lines in which the expression of neo gene is under the control of an endogenous host gene that is active only in the undifferentiated F9 cells. Using one of these cell lines, G19, we isolated the integrated neo construct and its flanking host sequences by the plasmid rescue method, identified the host gene which contributes to the expression of neo gene, and named it the Zfp-57 gene. Two different Zfp-57 transcripts (1.8 and 3.2 kilobases) were identified in the undifferentiated F9 cells, and the levels of these transcripts were decreased significantly within a short time after induction of differentiation. We examined mouse organs for the presence of the Zfp-57 RNAs and found that the 1.8-kilobase RNA was detected only in the testis. The Zfp-57 cDNAs corresponding to the two different RNAs were isolated, and a comparison of the nucleotide sequences revealed that their coding regions were completely identical, but they differed both in length and in sequence of the 3'-untranslated region. The Zfp-57 cDNA encoded a protein consisting of 421 amino acids with an extremely high content of basic amino acid residues and multiple zinc finger motifs. Immunocytochemical analysis revealed that this protein is localized in the nucleus. These findings suggest that the Zfp-57 protein is a DNA-binding protein.

Expression of four mutant human ornithine transcarbamylase genes in cultured Cos 1 cells relates to clinical phenotypes

Ornithine transcarbamylase (OTC) deficiency is an X-linked disease with a heterogeneous phenotype, even in affected males. To detect mutations in the OTC gene using genomic DNA, we have developed a method in which all exons and adjacent introns are amplified and sequenced. Although this approach detected mutations in many cases, the relationship between a mutation and the OTC phenotype was not firmly established. Therefore, we investigated the issue by expression analysis of mutant OTC cDNA in cultured cells. Four mutant OTC cDNAs were constructed, based on the reported cases, using our newly developed method. The normal (wild-type) human OTC cDNA was reproducibly expressed at high levels in these Cos 1 cells. Predicted OTC activities of mutant OTC cDNAs ranged from 0% to 8.9% of the normal level together with variable amounts of the enzyme protein. The predicted enzyme activities account for the clinical phenotype of the disease. Our observations confirm that these mutations are responsible for OTC deficiency in these patients.

Two regulatory elements in the 5' region of the mouse mitochondrial malate dehydrogenase gene

We previously reported that the promoter region of the mouse mitochondrial malate dehydrogenase gene is located within the 160 base-pairs (bp) region upstream from the initiation codon, named P1, and that the -160/-131 bp region contains sequence(s) essential for the promoter activity of mitochondrial malate dehydrogenase gene. To define more precisely the regulatory mechanism of this gene, a 3' deletion analysis was performed using constructs with a constant 3' boundary at -130 bp. We obtained evidence of an additional positive regulatory element located between -393/-249 bp, named P2, the function of which can be separated from that of the P1. DNase I footprinting and gel-sift mobility experiments showed that nuclear protein binding to the P2 was not inhibited in the presence of the P1 sequences.

Four novel gene mutations in five Japanese male patients with neonatal or late onset OTC deficiency: application of PCR-single-strand conformation polymorphisms for all exons and adjacent introns [corrected]

Ornithine transcarbamylase deficiency (OTC), the most common inborn error of the urea cycle, shows an X-linked inheritance with frequent new mutations. Southern blots reveal only a small percent of the mutation, but amplification of cDNA or genomic DNA using the polymerase chain reaction (PCR) followed by DNA sequencing, has contributed greatly to overcoming this difficulty. Problems remaining are the limited availability of fresh liver samples for preparation of intact mRNA in the former case, and there are primer sequences for PCR for only some exons in the latter case. Here, we report the structures of intron sequences which are long enough to analyze all exons and adjacent introns of the OTC gene using PCR and PCR single-strand conformation polymorphisms (PCR-SSCP). We carried out a DNA analysis of findings in five Japanese male patients with neonatal or late onset form. Five patients had mutations in the protein coding region. C to G (S192R), A to T (D196V), A to G (T264A), T to C (M268T), and C to T (R277W) substitutions. The first four of these were novel missense mutations and the presence of the mutation was confirmed in the corresponding families.

A novel missense mutation in exon 8 of the ornithine transcarbamylase gene in two unrelated male patients with mild ornithine transcarbamylase deficiency

We studied two unrelated male probands with mild ornithine transcarbamylase (OTC) (E.C.2.1.3.3) deficiency presenting a similar clinical course. Previous analyses of their liver OTCs also revealed similar properties. To identify the underlying molecular defects, we first cloned the entire coding region of the OTC gene from one proband and found a single base-substitution (C to T) leading to the substitution of tryptophan for arginine at amino acid position 277. Using a genomic amplification technique followed by allele specific oligonucleotide hybridization, we identified the same point mutation in the OTC gene of the other proband. We observed the presence of the mutation among family members in at least three generations, and in one asymptomatic hemizygous sibling in each family.

Molecular cloning and sequence analysis of the human cytosolic aspartate aminotransferase gene

Structural organization of the human cytosolic aspartate aminotransferase gene was determined by analyzing the phage clones obtained from two kinds of genomic DNA libraries, using mouse cytosolic aspartate aminotransferase cDNA as a probe. The gene is more than 32 kb long and is split into 9 exons by 8 introns of various sizes. The 5' and 3'-flanking regions and the exact sizes and boundaries of the exon blocks were determined. The 5' end of the gene lacks the TATA and CAAT boxes, but contains G+C rich sequences and one potential binding site for the transcription factor, Sp1. Comparison of the nucleotide sequence of 250 bp upstream from the translation-initiation site revealed that the sequences of binding sites for the nuclear proteins, previously identified in the mouse, are highly conserved between human and mouse cytosolic aspartate aminotransferase genes.

Regulatory regions of the mitochondrial and cytosolic isoenzyme genes participating in the malate-aspartate shuttle

The malate-aspartate shuttle, consisting of mitochondrial and cytosolic aspartate aminotransferase and mitochondrial and cytosolic malate dehydrogenase, is a major pathway for the transport of reducing equivalents from cytosol to mitochondria in mammals. To elucidate molecular mechanisms regulating metabolic coordination between the mitochondria and the cytosol, we analyzed the 5'-flanking regulatory regions of the complete set of mouse isoenzyme genes playing a pivotal role in the shuttle. Deletion analysis and an in vivo transfection assay, using NIH3T3 cells, revealed that all the promoter regions are located within the 300-base pair regions upstream from the initiation codon. Subsequently, DNase I footprinting analyses using NIH3T3 cell nuclear extracts led to identification of several protein binding sites within these promoter regions. A synthetic oligomer containing the consensus binding site sequence for CTF/NFI, a transcription factor for RNA polymerase II, competed for the binding of proteins to the promoter regions of cytosolic aspartate aminotransferase and mitochondrial and cytosolic malate dehydrogenase genes, but not for that of the mitochondrial aspartate amino-transferase gene. On the other hand, a synthetic oligomer containing the consensus binding site sequence for Sp1, which activates transcription from promoters containing properly positioned GC boxes, competed for protein(s) binding to the promoter region of the mitochondrial aspartate aminotransferase gene.

Ornithine transcarbamylase deficiency resulting from a C-to-T substitution in exon 5 of the ornithine transcarbamylase gene

To define the molecular basis for the TaqI site alteration in the ornithine transcarbamylase (OTC) (E.C.2.1.3.3) gene of a female patient with mild OTC deficiency, we used a combination of genomic amplification followed by direct sequencing and oligodeoxyribonucleotide hybridization. We obtained evidence for a C-to-T substitution in exon 5 (codon 141) of this gene. This mutation generates a stop codon, in place of Arg, at amino acid 109 of the mature OTC protein. The mutation arose, de novo, in a germ cell of one of the parents.

Messenger RNA expressed in mouse teratocarcinoma stem cells and down-regulated by a tumor-promoting phorbol ester codes for a novel transmembrane protein

Cloning and sequence analysis of a DNA complementary to the mRNA expressed in undifferentiated mouse F9 teratocarcinoma stem cells but disappearing rapidly after treatment with a tumor-promoting phorbol ester revealed it to be a 1.9 kilobase pairs-long cDNA encoding a protein of 323 amino acid residues. Computer-assisted analyses of the deduced amino acid sequence indicated that this protein contains a typical hydrophobic signal peptide consisting of 33 amino acid residues and six putative membrane-spanning segments. The deduced amino acid sequence, as a whole, bears no significant sequence homology to any previously described protein.

Structural organization of the mouse cytosolic malate dehydrogenase gene: comparison with that of the mouse mitochondrial malate dehydrogenase gene

We cloned and characterized a mouse cytosolic malate dehydrogenase (cMDHase) (EC 1.1.1.37) gene, which is about 14 x 10(3) base-pairs long and is interrupted by eight introns. The 5' and 3' flanking regions and the exact sizes and boundaries of the exon blocks, including the transcription-initiation sites, were determined. The 5' end of the gene lacks the TATA and CAAT boxes characteristic of eukaryotic promoters, but contains G + C-rich sequences, one putative binding site for a cellular transcription factor, Sp1, and at least two major transcription-initiation sites. The sequences around the transcription-initiation sites are compatible with the formation of a number of potentially stable stem-loop structures. We compared structural organization of the mouse cMDHase gene with that of the previously characterized mouse mitochondrial MDHase (mMDHase) gene, and found that the conservation of intron positions spreads across much of the two genes. This result suggests that a common ancestral gene for the cytosolic MDHase and the mitochondrial MDHase was broken up by introns, before the divergence. We also compared the nucleotide sequence of the promoter region of the mouse cytosolic MDHase gene with that of the other three mouse genes coding for isoenzymes participating in the malate-aspartate shuttle, i.e. mitochondrial MDHase, cytosolic and mitochondrial aspartate aminotransferases (cAspATase and mAspATase). We found that highly conserved regions are present in the promoter region of the cAspATase gene.

Structural organization of the mouse aspartate aminotransferase isoenzyme genes. Introns antedate the divergence of cytosolic and mitochondrial isoenzyme genes

We have cloned and characterized a mouse cytosolic aspartate aminotransferase (AspAT) (EC 2.6.1.1) gene, which is about 32,000 base-pairs long and is interrupted by eight introns. The 5' and 3'-flanking regions, and the exact sizes and boundaries of the exon blocks, including the transcription-initiation sites, were determined. The 5' end of the gene lacks the TATA and CAAT boxes characteristic of eukaryotic promoters, but contains G + C-rich sequences, three putative binding sites for a cellular transcription factor, Sp1, and multiple transcription-initiation sites. The sequences around the transcription-initiation sites are compatible with the formation of a number of potentially stable stem-loop structures. We compared the structural organization of the mouse cytosolic AspAT gene with that of the mouse mitochondrial AspAT gene, which has nine introns. We found that the promoter regions share a high level of homology and five of the introns are at identical places. This close matching leads to the tentative conclusion that the introns were in place before the divergence of cytosolic and mitochondrial isoenzyme genes.

Structural organization of the mouse mitochondrial aspartate aminotransferase gene

Structural organization of the entire mouse mitochondrial aspartate aminotransferase (EC 2.6.1.1) gene was determined by analyzing the overlapping genomic clones obtained from a Charon 4A DNA library. The gene is 25 X 10(3) base-pairs long and contains ten exons interrupted by nine introns of various sizes. The 5' and 3'-flanking regions, the exact sizes and boundaries of the exon blocks including the transcription-initiation sites were determined. The 5' end of the gene lacks the prototypical 5' transcriptional regulatory sequence elements, such as TATA and CAAT boxes, but contains G + C-rich sequences, two putative binding sites for a cellular transcription factor, Sp1, and multiple transcription-initiation sites. Moreover, the sequences around the transcription-initiation sites are compatible with the formation of a number of potentially stable stem-loop structures. The leader sequence, which is essential for the transport of the protein into the mitochondria, is coded by the first exon and is separated from the mature protein by the first intron. The pyridoxal 5'-phosphate-binding domain, consisting of seven alternating beta-sheets and alpha-helical polypeptide strands, is separated by four introns present at the ends of alpha-helices. These genomic DNA structures suggest that the introns were not inserted into a previously uninterrupted coding sequence, but rather are products of evolution of the ancestral gene. However, a further correlation between the positions of introns relative to the well-defined structural domains of the mature protein was not obvious.

Cloning and sequence analysis of cDNAs encoding mammalian cytosolic malate dehydrogenase. Comparison of the amino acid sequences of mammalian and bacterial malate dehydrogenase

A cDNA clone, named ppcMDH-1 and covering a part of the coding region for the porcine cytosolic malate dehydrogenase (cMDH) mRNA, was isolated from a porcine liver cDNA library. Subsequently, mouse cMDH cDNA clones were isolated from mouse liver and heart cDNA libraries, using the ppcMDH-1 cDNA as a probe. The longest clone, named pmcMDH-5, was sequenced and the primary structure of the mouse cMDH deduced from its cDNA sequence showed that the mouse cMDH consists of the 334-amino acid residues. When the amino acid sequence of the mouse cMDH was compared with that of the porcine cMDH, they shared a 93% homology. On the other hand, the amino acid sequences of mouse cMDH and mitochondrial MDH (mMDH) showed about 23% overall homology. Surprisingly, comparison of the amino acid sequences among the mammalian and bacterial MDHs revealed that the homology between the mouse cMDH and thermophilic bacterial MDH, as well as the homology between the mouse mMDH and Escherichia coli MDH, markedly exceeds the intraspecies sequence homology between mMDH and cMDH from mice.

Isolation of complementary DNA clones for genes exhibiting reduced expression after treatment of mouse teratocarcinoma stem cells with a tumor-promoting phorbol ester

For the study of the effects of the phorbol ester 12-O-tetradecanoylphorbol-13-acetate (TPA) on early mammalian cell differentiation, a complementary DNA (cDNA) library was constructed on the poly(A)+RNAs extracted from undifferentiated F9 cells derived from a 129/Sv mouse teratocarcinoma OTT6050, and screening was done for the cNDA sequences corresponding to the mRNAs, the levels of which decreased significantly in the F9 cells after the TPA treatment. From about 80,000 clones screened, 3 different cDNA clones, pFT27, pFT43, and pFT60, were isolated and characterized. Levels of the RNAs hybridizable to these clones were decreased by fourfold to more than fiftyfold within 1-10 hours in the presence of TPA. Northern blotting experiments identified transcripts corresponding to these clones: pFT27 hybridized to 3.0 kb RNA, pFT43 hybridized to 1.5 kb RNA, and pFT60 hybridized to 1.0 kb RNA. The levels of these 3 transcripts were also decreased after treatment of the undifferentiated F9 cells with retinoic acid (RA) and dibutyryl cyclic AMP (cAMP). The TPA-induced as well as the RA- and cAMP-induced decreases in the RNAs hybridizable to pFT27 were regulated at the transcriptional level, whereas similar decreases in the RNAs hybridizable to pFT43 and pFT60 were regulated at the post-transcriptional level. These findings show that TPA treatment shares common effects with RA and cAMP on the undifferentiated F9 cells.

Decrease in the c-myb gene transcript during differentiation of mouse teratocarcinoma stem cells

Transcript of the c-myb gene, one of the proto-oncogenes, was clearly detected in undifferentiated mouse F9 teratocarcinoma stem cells, but not in terminally differentiated mouse parietal endoderm PYS-2 cells. As F9 cells can be induced to differentiate into parietal endoderm-like cells by the addition of retinoic acid and dibutyryl cAMP, we examined levels of the c-myb transcript under this experimental condition and found that the c-myb transcript was decreased significantly. Thus, a decrease in the c-myb transcript is probably related to early differentiation of mammalian cells.

Isolation and characterization of the cDNAs corresponding to mRNAs abundant in undifferentiated mouse embryonal teratocarcinoma stem cells, but not in differentiated mouse parietal endoderm cells

As retinoic acid (RA) and dibutyryl cAMP (cAMP) treatment induces differentiation of mouse teratocarcinoma F9 cells into parietal endoderm cells in vitro, we initiated studies on the molecular mechanisms underlying early mammalian cell differentiation in this system. We constructed cDNA libraries on the poly(A)+RNAs extracted from the undifferentiated F9 cells, and screened for cDNA sequences expressed abundantly in F9 cells, but not in terminally differentiated mouse parietal endoderm PYS-2 cells. Six different cDNA clones were isolated and characterized. The levels of RNAs hybridizable to these clones were at most 5 to 24% in the PYS-2 cells when compared with those in the undifferentiated F9 cells. The six clones were classified into two groups on the basis of their responses to the RA and cAMP treatment. In F9 cells, the levels of RNAs hybridizable to the first group, which contained four clones, were decreased within 72 h after the addition of RA and cAMP, while those of the second group, which contained the remaining two clones, did not decrease significantly. One of the first group clones, named pF9-1, corresponded to the mouse "early transposon-like elements" and another, named pF9-4, hybridized to multi-size RNAs extracted from the undifferentiated F9 cells. The mouse genomic DNA sequences hybridizable to pF9-4 were repeated approximately 5,000 times, and comprise a new gene family, the expression of which is developmentally regulated in mouse F9 cells.

Restriction enzyme digestions identify discrete domains in the chromatin around the promoter of the mouse alpha 2(I) collagen gene

We have examined the chromatin structure around the +1 transcriptional start site of the mouse alpha 2(I) collagen gene by studying the accessibility of DNA to several restriction enzymes as well as to DNase I. In NIH 3T3 cells, which express high levels of alpha 2(I) collagen mRNA, we detect a DNase I-hypersensitive site from -240 to +110 relative to the start site of transcription at +1. By digesting chromatin with restriction enzymes, which cleave naked DNA at multiple sites within the -2000 to +1000 region, a considerably more complex picture was revealed. DNA sequences upstream of around -550 and downstream of +150 are much less accessible to restriction enzymes than the region between these sites and are, therefore, probably packaged in a more compact conformation. The region from around -550 to -240 although not within the DNase I-hypersensitive domain is nevertheless accessible to restriction enzymes and, therefore, presumably in a relatively "open" conformation. In addition, beginning 5' to -100 there is a gradual decrease in restriction enzyme accessibility as one approaches +150. Of particular interest is the finding that although sites at +65 and +126 are relatively accessible, a HinfI site at +113 is resistant in chromatin. In v-mos transformed NIH 3T3 cells which express alpha 2(I) collagen at much lower levels than untransformed NIH 3T3 cells, the DNase I-hypersensitive site as well as the majority of the chromatin restriction enzyme accessibility patterns are similar to those found in untransformed NIH 3T3 cells. However, a SphI site at +58 appears less accessible in the transformed cells. We also examined the chromatin of a myeloma cell line which does not synthesize alpha 2(I) collagen at detectable levels. In the nuclei of these cells the DNA of the alpha 2(I) collagen promoter is inaccessible to DNase I and to all restriction enzymes.

V-fos stimulates expression of the alpha 1(III) collagen gene in NIH 3T3 cells

NIH 3T3 cells that are transformed by the v-fos containing FBR proviral DNA show a selective increase in alpha 1 (III) collagen synthesis, increased levels of alpha 1(III) collagen RNA and an increased synthesis of this RNA.

Transcriptional activation encoded by the v-fos gene

We present evidence that the fos oncogene encodes a transcriptional trans-activation function. trans-activation was assayed by cotransfection into NIH 3T3 mouse fibroblasts of v-fos DNA containing plasmids together with a plasmid containing a test promoter. Three v-fos DNAs were used: (i) pFBR-1, a plasmid containing the FBR proviral sequences; (ii) pFBJ-2, a plasmid harboring the FBJ proviral sequences; (iii) pMF-J, a plasmid containing the FBJ fos sequences linked to a mouse metallothionein promoter. Each of the three v-fos DNA plasmids stimulated the expression of a cotransfected chimeric gene consisting of a promoter segment of the mouse alpha 1(III) collagen gene linked to the gene for chloramphenicol transacetylase. In similar experiments the v-fos gene also stimulated the long terminal repeat promoter of Rous sarcoma virus (RSV) but neither the early promoter of simian virus 40 nor the beta-actin promoter. Evidence that the trans-activation function is specified by the v-fos coding sequences comes from the fact that a frameshift mutation in the v-fos coding sequence inhibits the trans-activation. Two mutations that map around nucleotide -100 in the RSV promoter do not respond to cotransfection with v-fos, whereas other mutations respond like the wild-type RSV promoter. These experiments suggest that the v-fos gene either encodes or induces an activator of transcription that recognizes specific sequences in promoters.

Pleiotropic mutants of NIH 3T3 cells with altered regulation in the expression of both type I collagen and fibronectin

Transformation of NIH 3T3 fibroblasts by v-mos causes a decrease in the levels of type I collagen RNA. In NIH 3T3 cells that have been made resistant to G418 by transfection with a plasmid in which the mouse alpha 2(I) collagen promoter is linked to the neo gene, subsequent v-mos transformation causes a loss of G418 resistance. After mutagenesis of these v-mos-transformed cells, G418-resistant colonies were selected. Two of these G418-resistant mutants showed an increased expression of the neo gene and of the endogenous type I collagen and fibronectin genes, without changes in their levels of v-mos RNA or in their ability to induce tumors. The mutations might alter cellular trans-acting factors that either directly or indirectly control the expression of the type I collagen and fibronectin genes in transformed cells.

Regulation of a collagen gene promoter by the product of viral mos oncogene

Oncogenic transformation of cells produces important changes in the biosynthetic pattern of certain cellular proteins. For example, the synthesis of type I collagen in transformed fibroblasts is severely reduced as a result of changes in transcription. Here we report the results of DNA-mediated transfection experiments using recombinant plasmids in which the promoter region of the alpha 2(I) collagen gene is fused to an easily recognizable marker gene, and cell lines expressing the marker gene are isolated. Our data show that the expression of the marker gene fused to the cloned alpha 2(I) collagen promoter is strongly inhibited by v-mos transformation, suggesting that a common mechanism inhibits both the transfected and endogeneous alpha 2(I) collagen promoters.

Presence of mitochondrial-DNA-like sequences in the human nuclear DNA

Two lambda phage clones carrying contiguous human nuclear DNA sequences with extensive homology to non-contiguous human mitochondrial 16S ribosomal RNA sequences were isolated from a human gene library. The one clone carried mitochondrial-DNA(mtDNA)-like sequences flanked with two kinds of repetitive nuclear DNA sequences and the other carried mtDNA-like sequences, between unique nuclear DNA sequences and repetitive DNA sequences of Alu-family. These results demonstrate that mtDNA-like sequences are present in human nuclear DNA.

The majority of cDNA clones with strong positive signals for the interferon-induction-specific sequences resemble mitochondrial ribosomal RNA genes

A complementary DNA library prepared from the 12S polyadenylated RNAs extracted from interferon-induced KG-1 cells, a human myeloblast cell line, was screened for the presence of induction-specific sequences. Clones that exhibited strong positive signals were separated by hybridization criteria into nine classes. Clones from classes I through IV consisted of about 78% of the total and unexpectedly were found to resemble human mitochondrial ribosomal RNA genes.