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The naturally transformable bacterium Haemophilus influenzae Rd contains 1471 copies of the DNA uptake signal sequence (USS) 5'-AAGTGCGGT in its genome. Neisseria meningitidis contains 1891 copies of the USS sequence 5'-GCCGTCTGAA. The USSs are often found in the base paired stem of transcription terminators.
Integrin alpha11beta1 is a collagen receptor which is expressed in a subset of mesenchymally-derived tissues during embryogenesis. Based on available human chromosome 15-derived sequences and genomic PCR, the complete exon structure of ITGA11, including the proximal promoter, was assembled into 30 exons. The inserted region (encoding amino acids 804-826) distinguishing alpha11 from other integrin alpha chains, was placed in the very beginning of exon 20. PCR data failed to show alternative splicing of RNA transcribed from this region. Using the oligo-capping technique a major transcription start site was mapped 30 nucleotides upstream of the translation start and identified as an abbreviated initiator sequence. Promoter sequence analysis in silico suggested the presence of multiple binding sites for transcription factors in the region upstream of the transcription start. 3 kb of the 5' flanking sequence was isolated and used to generate luciferase promoter constructs. In the fibrosarcoma cell line HT1080 a core promoter [nt (-)127-(+)25], a potential silencer region [nt (-)400-(-)127] and a potential enhancer region [nt (-)1519-(-)400], were identified as being important for alpha11 transcription in mesenchymal cells. Furthermore, studies of the promoter region will provide valuable information regarding the molecular mechanisms underlying the cell- and tissue- specific expression pattern of ITGA11.
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Both a 25-hydroxylation and a 1alpha-hydroxylation are necessary for the conversion of vitamin D(3) into the calcium-regulating hormone 1alpha,25-dihydroxyvitamin D(3). According to current knowledge, the hepatic mitochondrial cytochrome P450 (CYP) 27A and microsomal CYP2D25 are able to catalyze the former bioactivation step. Substantial 25-hydroxylase activity has also been demonstrated in kidney. This paper describes the molecular cloning and characterization of a microsomal vitamin D(3) 25- and 1alpha-hydroxylase in kidney. The enzyme purified from pig kidney and the recombinant enzyme expressed in COS cells catalyzed 25-hydroxylation of vitamin D(3) and 1alpha-hydroxyvitamin D(3) and, in addition, 1alpha-hydroxylation of 25-hydroxyvitamin D(3). The cDNA encodes a protein of 500 amino acids. Both the DNA sequence and the deduced peptide sequence of the renal enzyme are homologous with those of the hepatic vitamin D(3) 25-hydroxylase CYP2D25. Genomic Southern blot analysis suggested the presence of a single gene for CYP2D25 in the pig. Immunohistochemistry experiments indicated that CYP2D25 is expressed almost exclusively in the cells of cortical proximal tubules. The expression of CYP2D25 in kidney, but not in liver, was much higher in the adult pig than in the newborn. These findings indicate a tissue-specific developmental regulation of CYP2D25. The results from the current and previous studies on renal vitamin D hydroxylations imply that CYP2D25 has a biological role in kidney.
An oligonucleotide mixture based on the 21 base pair repeat sequence of Plasmodium falciparum was covalently coupled to biotin and used as a probe to detect P. falciparum DNA. The limit of detection was 10 ng. This method was further developed as a fingerprint assay for parasite strain typing. After restriction enzyme digestion, blotting and hybridization, distinct banding patterns were obtained for the strains tested and these were reproducible. In addition, discrete differences were found between PLF-3 S+/S-strains which may implicate genetic reorganization in the switching mechanism which occurs when parasites are passed from an intact to a splenectomized animal.
A simple and reproducible typing system based on restriction fragment size of chromosomal DNA was developed to compare isolates of Streptococcus uberis obtained from the bovine mammary gland. The endonuclease giving the most useful restriction patterns was Hind III. Although seven other endonucleases (Bgl 1, Eco R1, Not 1, Pst 1, Sfi 1, Sma 1, Xba 1) were also tested in the system. An image analyser was used to obtain a densitometric scan and a graphic display of the restriction patterns. Such a system will allow large scale data storage for future computer-aided comparison.
In the rat, gamma-glutamyltranspeptidase (gamma GT) is transcribed into four unique mRNAs from a single gene by use of at least three different promoters and alternative splicing. For the first time, two distinct full-length cDNAs encoding the protein for rat renal gamma-glutamyltranspeptidase have now been isolated. Characterization by restriction enzyme mapping and nucleotide sequencing indicates that the two cDNAs, corresponding to transcripts I and II, differ only in the 5' noncoding region. However, transcription from promoter I, most proximal to the coding sequence, apparently began 20 bases upstream from the major transcription start previously reported. Since in vitro transcription and translation of these two new gamma GT cDNAs were found to produce a full-length peptide (M(r) approximately 62,000), both cDNAs were used to transfect LLC-PK1 (porcine) cells, a polarized cell line most representative of the renal proximal tubule. Rat gamma GT was expressed in transfected cells as judged by immunofluorescence analysis, direct immunoprecipitation after metabolic labeling with [35S]methionine, and an increase in gamma GT specific enzymatic activity (up to 5-fold). When clonal cell lines (I or II) were grown on Falcon filter inserts, the increased gamma GT activity was found only at the apical surface, consistent with polarized expression of the rat gamma GT. In contrast, transfection of the same cells with cDNA of human growth hormone resulted in both apical (70%) and basal lateral (30%) secretion of the expressed hormone.(ABSTRACT TRUNCATED AT 250 WORDS)
We report site-specific binding constants for the intercalating anticancer drug actinomycin D (Act-D), binding to a 139-base-pair restriction fragment from pBR 322 DNA. The binding constants are derived from analysis of footprinting experiments, in which the radiolabeled 139-mer is cleaved using DNase I, the cleavage products undergo gel electrophoresis, and, from the gel autoradiogram, spot intensities, proportional to amounts of cleaved fragments, are measured. A bound drug prevents DNase I from cleaving at approximately 7 bonds, leading to decreased amounts of corresponding fragments. With the radiolabel on the 3' end of the noncoding strand (A-label), we measured relative amounts of 54 cleavage products at 25 Act-D concentrations. For cleavage of the 139-mer with the label on the 3' end of the coding strand (G-label), relative amounts of 43 cleavage products at 11 Act-D concentrations were measured. These measurements give information about approximately 120 base pairs of the restriction fragment (approximately 12 turns of the DNA helix); in this region, 14 strong and weak Act-D binding sites were identified. The model used to interpret the footprinting plots is derived in detail. Binding constants for 14 sites on the fragment are obtained simultaneously. It is important to take into account the effect of drug binding at its various sites on the local concentration of probe elsewhere. It is also necessary to include in the model weak as well as strong Act-D sites on the carrier DNA which is present, since the carrier DNA controls the free-drug concentration. As expected, the strongest sites are those with the sequence (all sequences are 5'----3') GC, with TGCT having the highest binding constant, 6.4 x 10(6) M-1. Sites having the sequence GC preceded by G are weak binding sites, having binding constants approximately 1 order of magnitude lower than those of the strong sites. Also, the non-GC-containing sequences CCG and CCC bind Act-D with a binding constant comparable to those of the weak GGC sites. The analysis may reveal drug-induced structural changes on the DNA, which are discussed in terms of the mechanism of Act-D binding.
In footprinting experiments, an increase in DNA cleavage with addition of ligand to a system may be due to a ligand-induced structural change. Ligand binding also enhances cleavage by displacing the cleavage agent from ligand-binding sites, thus increasing its concentration elsewhere. The theory and characteristics of this mass-action enhancement are given, and it is shown how it may be recognized. Results of DNase I footprinting of small oligomers, with actinomycin D as ligand, are analyzed to reveal which enhancements are due to mass action, and which can reasonably be ascribed to structural changes. Patterns in the footprinting plots from our experiments on actinomycin D binding to a 139-base-pair DNA fragment (with DNase I as a probe) are studied in the same way. The likely origins of these patterns are discussed, as are enhancements occurring with other probes commonly used in footprinting experiments.
L-Lactate dehydrogenase from Bacillus stearothermophilus was rebuilt by using site-directed mutagenesis to produce an enzymically active, tryptophan-less enzyme by replacing all the wild-type tryptophans (80, 150, and 203) by tyrosines. Nine single tryptophan-containing active enzymes were constructed from this enzyme by genetically replacing one of the tyrosines 36, 85, 147, 190, 203, 237, 248, 279, or 285 by tryptophan. The equilibrium and the time-resolved tryptophan fluorescence intensity and anisotropy were used to report unfolding events in guanidine hydrochloride (GHCl) monitored from these nine defined positions. Three structural transitions, half complete at 0.55, 1.7, and 2.8 M GHCl, were identified and defined four folding intermediates, I (native), II (expanded monomer 1), III (expanded monomer 2), and IV (random coil), stable at 0, 1, 2.2, and 4 M GHCl, respectively. Intermediate II is a globular monomer. All the probed alpha-helices and most of the beta-structure was intact. There was an increase in the rate but not the extent of the mobilities of six of the probed tryptophan side chains, indicating loss of tertiary structure. Circular dichroism (CD) showed all the secondary structure to be intact. Intermediate III is monomeric and still globular, but the tryptophan anisotropy indicated an increase mobility at positions 36, 85, 190, 203, 279, and 285. Helix alpha-B is further disrupted but helices alpha-1F, alpha-2G, and alpha 3G were still rigid. CD showed half the secondary structure to be still intact. Intermediate IV is a random coil in which all tryptophans have complete rotational freedom and the helix CD signal is lost.(ABSTRACT TRUNCATED AT 250 WORDS)
Regions of An.Tn, (GA)n.(TC)n, and (GT)n.(AC)n have been cloned into the SmaI (CCC/GGG) site of plasmid pUC19. HindIII-EcoRI restriction fragments containing these inserts have been used as substrates for footprinting experiments using DNase I, DNase II, and micrococcal nuclease as probes. These present good mithramycin binding sites (GGG) flanking repetitive regions to which the drug does not bind. In each case, mithramycin footprints are observed at the CCC/GGG sites, which are not affected by the nature of the surrounding sequences. Some weaker binding is detected at TCGA and ACCA sites and at regions of alternating GA. No binding is found to regions of alternating GT. An.Tn inserts (n = 23 or 69) are normally resistant to cleavage by all these probes; in the presence of mithramycin, a dramatic increase in DNase I cleavage is observed throughout the entire insert and is indicative of an alteration in DNA structure. Similar changes are seen with DNase II and micrococcal nuclease. These changes cannot be explained by invoking changes in the ratio of free substrate to cleavage agent. In contrast, cleavage of (GA)n.(CT)n and (GT)n.(AC)n inserts is not affected by drug binding. The results are consistent with a model in which mithramycin causes dramatic changes in the width of the DNA minor groove, generating a structure which has some properties of A-DNA, and suggest that this can be propagated into surrounding DNA regions in a sequence-dependent manner. The structural alterations with An.Tn are highly cooperative and can be transmitted over at least three turns of the DNA helix.
Fusion of a prokaryotic promoter to a yeast tRNA gene provides a means for uncoupling analyses of mutations affecting splicing from requirements for transcription and other processing steps. For this purpose, a phage lambda promoter was fused to the Saccharomyces cerevisiae tRNATyr(SUP3a) coding sequence. This fusion allows the synthesis of an end-mature precursor by in vitro transcription with Escherichia coli RNA polymerase. This precursor was accurately spliced by purified yeast endonuclease and ligase fractions. However, both the initial rate and the extent of the endonuclease cleavage reaction were reduced in comparison to those for substrates produced by yeast RNA polymerase III. Efficient splicing could be restored in a magnesium- and temperature-dependent renaturation step, suggesting a conformational transition was required. Enzymatic solution structure probing of transcripts from wild-type and intron-variant templates revealed that the essential conformational transition involved a segment of the tRNA-like portion of the precursor. These results (1) suggest that the primary sequence of the precursor alone may not be sufficient to ensure formation of the active conformer during synthesis, (2) provide direct evidence that endonuclease recognizes mature tRNA-like structure in the precursor, and (3) suggest a general caution for the use of semisynthetic transcripts in RNA processing reactions. Potentially, transcription and processing of tRNATyr in yeast may provide a useful paradigm for examining active control of conformation in RNA biosynthesis.
The interactions of T7 RNA polymerase with T7 late promoters were studied by using quantitative footprinting with methidiumpropyl-EDTA X Fe(II) [MPE-Fe(II)] as the DNA cleaving agent. Class II and class III T7 promoters have a highly conserved 23 base pair sequence from -17 to +6. Among class III promoters the -22 to -18 region is also highly conserved. For a class II promoter, T7 RNA polymerase protects the -17 to -4 region from MPE-Fe(II) cleavage; when GTP is present, protection extends from -17 to +5 (noncoding strand). For a class III promoter, protection extends from -20 to -4 and in the presence of GTP from -20 to +5 (noncoding strand). The protected regions for the coding strands of both promoters were nearly identical with that seen for the noncoding strands. The binding constant for the class III promoter is (4 +/- 1.5) X 10(7) M-1 and in the presence of GTP increases to (10 +/- 1.7) X 10(7) M-1. These binding constants are about 1000 and 200 times greater, respectively, than values reported previously [Ikeda, R. A., & Richardson, C. C. (1986) Proc. Natl. Acad. Sci. U.S.A. 83, 3614-3618]. The differences in binding constants are probably due to tRNA and high salt used in those earlier experiments. Both tRNA and high salt (greater than 50 mM NaCl and greater than 10 mM MgCl2) inhibit the binding of the polymerase to the promoter. Optimal binding conditions occur at 2-5 mM MgCl2 and 0-10 mM NaCl.(ABSTRACT TRUNCATED AT 250 WORDS)
Organic synthesis and recombinant DNA techniques have been used to situate a single 1,N6-ethenoadenine (epsilon Ade) DNA adduct at an amber codon in the genome of an M13mp19 phage derivative. The deoxyhexanucleotide d[GCT(epsilon A)GC] was chemically synthesized by the phosphotriester method. Mild nonaqueous conditions were employed for deprotection because of the unstable nature of the epsilon Ade adduct in aqueous basic milieu. Physical studies involving fluorescence, circular dichroism, and 1H NMR indicated epsilon Ade to be very efficiently stacked in the hexamer, especially with the 5'-thymine. Melting profile and circular dichroism studies provided evidence of the loss of base-pairing capabilities attendant with formation of the etheno ring. The modified hexanucleotide was incorporated into a six-base gap formed in the genome of an M13mp19 insertion mutant; the latter was constructed by blunt-end ligation of d(GCTAGC) in the center of the unique SmaI site of M13mp19. Phage of the insertion mutant, M13mp19-NheI, produced light blue plaques on SupE strains because of the introduced amber codon. Formation of a hybrid between the single-strand DNA (plus strand) of M13mp19-NheI with SmaI-linearized M13mp19 replicative form produced a heteroduplex with a six-base gap in the minus strand. The modified hexamer [5'-32P]d-[GCT(epsilon A)GC], after 5'-phosphorylation, was ligated into this gap by using bacteriophage T4 DNA ligase to generate a singly adducted genome with epsilon Ade at minus strand position 6274. Introduction of the radiolabel provided a useful marker for characterization of the singly adducted genome, and indeed the label appeared in the anticipated fragments when digested by several restriction endonucleases. Evidence that ligation occurred on both 5' and 3' sides of the oligonucleotide also was obtained. The adduct was introduced into a unique NheI site, and it was observed that this restriction endonuclease was able to cleave the adducted genome, albeit at a lower rate compared to unmodified DNA. The M13mp19-NheI genome containing epsilon Ade will be used as a probe for studying mutagenesis and repair of this DNA adduct in Escherichia coli.
We have used enzymic and chemical probes to search for altered DNA conformations in the 5' flanking region of the gene for a high mobility group protein (HMG-T) from trout. This search was conducted in order to identify potential genetic elements that might be involved in the transcriptional control of the HMG-T gene. We identified, in supercoiled plasmid DNA molecules containing a 900 base pair insert of the 5' region of the gene, an S1-sensitive site situated within an (AT)12 sequence approximately 120 base pairs upstream from the start of the HMG-T gene. Chemical modification of supercoiled DNA with the single-strand-selective reagent bromoacetaldehyde was limited to a region coincident with the S1 nuclease site. T7 endonuclease I, a probe highly specific for four-way helical junctions, cleaved predominantly at the boundaries of the (AT)12 stretch. These data are most consistent with the interpretation that the (AT)12 sequence adopts a cruciform structure when torsionally stressed by negative supercoiling. DNase I footprinting analyses demonstrated that HMG-T protects two regions almost equidistant from the center of the (AT)12 sequence, indicating that HMG-T is a sequence-specific DNA binding protein.
A gene coding for D-alanine:D-alanine (D-Ala-D-Ala) ligase (ADP forming) (EC 6.3.2.4) activity has been isolated from a lambda library of Salmonella typhimurium DNA. Insertion mutations in the gene indicate that the gene is not essential for growth of the bacterium. The encoded enzyme was purified from an overproducing strain of S. typhimurium. D-Ala-D-Ala ligase is a protein of 39,271 molecular weight and has a kcat of 644 min-1 at pH 7.2. A 2.4-kilobase SalI-SphI fragment containing the gene was sequenced, and the ddlA gene consists of 1092 nucleotides. The gene sequence was compared to the sequence of the ddl gene of Escherichia coli [Robinson, A. C., Kenan, D. J., Sweeney, J., & Donachie, W. D. (1986) J. Bacteriol. 167, 809-817]. Because of differences between the S. typhimurium gene and the E. coli ddl gene, the S. typhimurium gene has been named ddlA.
We have used deoxyribonuclease I (DNase I) and methidium-propyl-EDTA.Fe(II) digestion to characterize the chromosomal structure of the single-copy autonomously replicating sequence ARS1. The major feature of this chromatin is a region of strong hypersensitivity to both cleavage agents. The hypersensitive region contains most of the DNA sequences which have been suggested by in vitro mutagenesis studies [Celniker, S., Sweder, K., Srienc, F., Bailey, J., & Campbell, J. (1984) Mol. Cell. Biol. 4, 2455-2466] to be important in ARS function. It lies at the downstream end of the TRP1 gene. A chromosomal DNase I footprinting analysis was carried out on the hypersensitive region. These data give direct evidence for several localized DNA/protein contacts within the hypersensitive region. The most prominent of these chromatin-dependent contacts is located on the functionally most important 11 base pairs of ARS DNA. On the TRP1 side of the hypersensitive region, there are positioned nucleosomes. On the other side of the hypersensitive region, there is a complex (and possibly heterogeneous) structure.
Regions attached to the nuclear scaffold have been traced after transfecting a 36-kilobase (kb) piece of DNA, surrounding the human interferon-beta gene, into mouse L-cells. An extended attached region starts 1.7 kb upstream from the gene and a moderate binding site immediately downstream. These findings could be confirmed by reconstitution experiments in vitro which predict another scaffold-attached region (SAR) starting 12 kb downstream from the gene. Since no other transcripts originate from DNA between the major SARs, these elements could be involved in interferon gene regulation.