Homologous nucleotide sequences at the 5' termini of messenger RNAs synthesized from the yeast enolase and glyceraldehyde-3-phosphate dehydrogenase gene families. The primary structure of a third yeast glyceraldehyde-3-phosphate dehydrogenase gene

Genomic DNA containing a third yeast glyceraldehyde-3-phosphate dehydrogenase structural gene has been isolated on a bacterial plasmid designated pgap11. The complete nucleotide sequence of this structural gene was determined. The gene contains no intervening sequences, codon usage is highly biased, and the nucleotide sequence of the coding portion of this gene is 90% homologous to the other two glyceraldehyde-3-phosphate dehydrogenase genes (Holland, J. P., and Holland, M. J. (1980) J. Biol. Chem. 255, 2596-2605). Based on the extent of nucleotide sequence divergence among the three glyceraldehyde-3-phosphate dehydrogenase genes, it is likely that they arose as a consequence of two duplication events and the gene contained on the hybrid plasmid designated pgap11 is a product of the first duplication event. All three structural genes share extensive nucleotide sequence homology in the 5'-noncoding regions adjacent to the three respective translational initiation codons. The gene contained on pgap11 is not homologous to the others downstream from the respective translational termination codon, however. The 5' termini of messenger RNAs synthesized from the three glyceraldehyde-3-phosphate dehydrogenase and two yeast enolase genes have been mapped to sites ranging from 36 to 82 nucleotides upstream from the respective translational initiation codons. In each case the 5' terminus of the mRNA maps to a region of strong nucleotide sequence homology which is shared by all five structural genes. These latter data confirm that all five structural genes are expressed during vegetative cell growth and further support the hypothesis that a portion of the 5'-noncoding flanking region of the yeast glyceraldehyde-3-phosphate dehydrogenase and enolase genes evolved from a common precursor sequence.

RNA polymerase I-dependent selective transcription of yeast ribosomal DNA. Identification of a new cellular ribosomal RNA precursor

Selective transcription of hybrid plasmids containing yeast rDNA was achieved with a template-dependent S100 fraction from whole cell extracts of Saccharomyces cerevisiae. A small region of the yeast rDNA which directs selective initiation in vitro was identified by subcloning. An initiation site was mapped within this region on the basis of the molecular weights of transcripts synthesized in vitro from templates which were cleaved with restriction endonucleases at a series of sites downstream from the site of initiation. The initiation site maps to a position 3.0 kilobase pairs upstream from the sequences which encode the 5' terminus of 18 S rRNA. In vitro initiation from this site is not inhibited by 50 micrograms/ml of alpha-amanitin and is completely abolished when the reactions contain 0.2 M (NH4)2SO4. Based on these data, selective transcription of yeast rDNA in vitro is RNA polymerase I-dependent. Several S1 nuclease-resistant hybrids are formed between DNA probes labeled at restriction endonuclease sites downstream from the in vitro initiation site and high molecular weight cellular RNA. The 5' terminus of the most abundant rRNA precursor maps approximately 0.7 kilobase pair upstream from sequences which encode the 5' terminus of 18 S rRNA. This corresponds to the 5' terminus of the 35 S rRNA precursor reported by others. The 5' terminus of the largest detectable precursor synthesized in vivo corresponds closely with the initiation site identified in vitro. Based on the data presented here, RNA polymerase I traverses the interspersed 5 S rRNA gene. Since these two ribosomal genes are transcribed in opposite directions, this arrangement of the RNA polymerase I and III promoters may ensure that equivalent amounts of the two gene products are synthesized in vivo.

Purification of yeast RNA polymerases using heparin agarose affinity chromatography. Transcriptional properties of the purified enzymes on defined templates

A rapid procedure for the simultaneous purification of yeast RNA polymerases I, II, and III is described. The procedure involves direct fractionation of a yeast cell extract by heparin agarose affinity chromatography, followed by glycerol gradient centrifugation and DEAE-Sephadex chromatography. The purification can be completed in 3-4 days using 20-200 g of yeast cells. Two forms each of RNA polymerases I, II, and III are resolved after DEAE-Sephadex chromatography. In the cases of RNA polymerases I and II, these forms differ in subunit structure. The transcriptional properties of the isolated enzymes were determined using hybrid plasmid DNA templates containing yeast ribosomal and glycolytic structural genes. Both forms of RNA polymerases I and II transcribe plasmid DNA templates with low efficiency and no evidence for selective initiation of transcription was found for these enzymes using a wide variety of templates. Both forms of RNA polymerase III transcribe plasmid DNA templates with high efficiency and direct the synthesis of discrete transcripts. Sites for initiation and termination of transcription by RNA polymerase III within defined plasmid DNA templates were determined. The data show that RNA polymerase III-dependent synthesis of discrete transcripts from restriction endonuclease-digested plasmid DNA templates is initiated from selected ends of the templates and terminates at discrete sites downstream from the site of initiation. RNA polymerase III initiates synthesis at many sites within supercoiled plasmid DNA templates.

Targeted deletion of a yeast enolase structural gene. Identification and isolation of yeast enolase isozymes

Yeast contain two nontandemly repeated enolase structural genes which have been isolated on bacterial plasmids designated peno46 and peno8 (Holland, M. J., Holland, J. P., Thill, G. P., and Jackson, K. A. (1981) J. Biol. Chem. 256, 1385-1395). In order to study the expression of the enolase genes in vivo, the resident enolase gene in a wild type yeast strain corresponding to the gene isolated on peno46 was replaced with a deletion, constructed in vitro, which lacks 90% of the enolase coding sequences. Three catalytically active enolases are resolved differ DEAE-Sephadex chromatography of wild type cellular extracts. As expected, a single form of enolase was resolved from extracts of the mutant cell. Immunological and electrophoretic analyses of the multiple forms of enolase confirm that two enolase genes are expressed in wild type cells and that isozymes are formed in the cell by random assortment of the two polypeptides into three active enolase dimers. The yeast enolase loci have been designated ENO1 and ENO2. The deletion mutant lacks the enolase 1 polypeptide confirming that this polypeptide is encoded by the gene isolated on peno46. The intracellular steady state concentrations of the two polypeptides are dependent on the carbon source used to propagate the cells. Log phase cells grown on glucose contain 20-fold more enolase 2 polypeptide than enolase 1 polypeptide, whereas cells grown on ethanol or glycerol plus lactate contain similar amounts of the two polypeptides. The 20-fold higher than in cells grown on the nonfermentable carbon sources. In vitro translation of total cellular RNA suggests that the steady state concentrations of the two enolase mRNAs in cells grown on different carbon sources are proportional to the steady state concentrations of the respective enolase polypeptides.

The primary structures of two yeast enolase genes. Homology between the 5' noncoding flanking regions of yeast enolase and glyceraldehyde-3-phosphate dehydrogenase genes

Segments of yeast genomic DNA containing two enolase structural genes have been isolated by subculture cloning procedures using a cDNA hybridization probe synthesized from purified yeast enolase mRNA. Based on restriction endonuclease and transcriptional maps of these two segments of yeast DNA, each hybrid plasmid contains a region of extensive nucleotide sequence homology which forms hybrids with the cDNA probe. The DNA sequences which flank this homologous region in the two hybrid plasmids are nonhomologous indicating that these sequences are nontandemly repeated in the yeast genome. The complete nucleotide sequence of the coding as well as the flanking noncoding regions of these genes has been determined. The amino acid sequence predicted from one reading frame of both structural genes is extremely similar to that determined for yeast enolase (Chin, C. C. Q., Brewer, J. M., Eckard, E., and Wold, F. (1981) J. Biol. Chem. 256, 1370-1376), confirming that these isolated structural genes encode yeast enolase. The nucleotide sequences of the coding regions of the genes are approximately 95% homologous, and neither gene contains an intervening sequence. Codon utilization in the enolase genes follows the same biased pattern previously described for two yeast glyceraldehyde-3-phosphate dehydrogenase structural genes (Holland, J. P., and Holland, M. J. (1980) J. Biol. Chem. 255, 2596-2605). DNA blotting analysis confirmed that the isolated segments of yeast DNA are colinear with yeast genomic DNA and that there are two nontandemly repeated enolase genes per haploid yeast genome. The noncoding portions of the two enolase genes adjacent to the initiation and termination codons are approximately 70% homologous and contain sequences thought to be involved in the synthesis and processing messenger RNA. Finally there are regions of extensive homology between the two enolase structural genes and two yeast glyceraldehyde-3-phosphate dehydrogenase structural genes within the 5- noncoding portions of these glycolytic genes.

Characterization of phospholipase A inhibition of stereospecific opiate binding and its reversal by bovine serum albumin

Opiate receptor binding is inhibited by phospholipase A from some sources, whereas the enzyme from other sources is inactive even at much higher concentrations. Evidence is presented that an active enzymatic site is required for inhibition and that the degree of inhibition seems to correlate with the extent of phospholipolysis. The inhibition is reversed almost completely by treatment with 0.5 to 1% bovine serum albumin, even up to 90% inhibition by phospholipase. As more enzyme is added or incubation time is increased, the extent of reversal diminishes. Based on our evidence, the most likely explanation of these results is that the inhibition of opiate binding activity by phospholipase A is due to the toxicity of the products of phospholipolysis and that bovine serum albumin reverses the inhibition by removing these products from the membranes, thereby restoring the active conformation of the receptors.

Structural comparison of two nontandemly repeated yeast glyceraldehyde-3-phosphate dehydrogenase genes

A hybrid plasmid (pgap63) was isolated which contains a second yeast glyceraldehyde-3-phosphate dehydrogenase structural gene. The complete nucleotide sequence of this gene was determined and compared with the primary structure of a yeast glyceraldehyde-3-phosphate dehydrogenase gene (pgap49) which was reported previously (Holland, J.P., and Holland, M.J. (1979) J. Biol. Chem. 254, 9839-9845). Based on the restriction endonuclease cleavage maps of the isolated segments of yeast DNA which contain these genes, the two genes are nontandemly duplicated. Greater than 94% of the nucleotides within the coding regions of these genes are homologous and the polypeptides encoded by the two structural genes differ by only 15 amino acid residues. Both genes have the same, highly biased, codon usage pattern and neither contains intervening sequences. Approximately 100 nucleotides adjacent to the ATG initiation codons and 130 nucleotides beyond the TAA termination codons are greater than 70% homologous. Structures within the flanking sequences of the genes which are potentially relevant to transcriptional and translational control are described. Several sequences (8 to 15 nucleotides in length) are repeated in both the 5' and 3' flanking sequences of the genes in a noninverted fashion. Finally, a rapid procedure for the isolation of spontaneous deletions within hybrid plasmid DNAs is described, as is the isolation of a structural gene deletion in pgap49.

The primary structure of a glyceraldehyde-3-phosphate dehydrogenase gene from Saccharomyces cerevisiae

The complete nucleotide sequence of the coding, as well as the flanking noncoding regions, of a yeast glyceraldehyde-3-phosphate dehydrogenase gene was determined. Both the 5' and 3' noncoding sequences are extremely AT-rich and regions of partial dyad symmetry are present immediately adjacent to the 5' and 3' ends of the translated portion of the gene. The sequence AAUAAA is present in the 3' noncoding region of this gene and is a part of an extensive region of dyad symmetry which is structurally related to the 3'-terminal portion of both procaryotic mRNAs, as well as some eukaryotic mRNAs. The coding region of this gene does not contain intervening sequences. Establishment of the primary structure of this glyceraldehyde-3-phosphate dehydrogenase gene provides a basis for further studies involving in vitro mutation of the gene and subsequent analysis of gene expression in vivo.

Isolation and characterization of a gene coding for glyceraldehyde-3-phosphate dehydrogenase from Saccharomyces cerevisiae

A yeast glyceraldehyde-3-phosphate dehydrogenase gene has been isolated from a collection of Escherichia coli transformants containing randomly sheared segments of yeast genomic DNA. Complementary DNA, synthesized from partially purified glyceraldehyde-3-phosphate dehydrogenase messenger RNA, was used as a hybridization probe for cloning this gene. The isolated hybrid plasmid DNA has been mapped with restriction endonucleases and the location of the glyceraldehyde-3-phosphate dehydrogenase gene within the cloned segment of yeast DNA has been established. There are approximately 4.5 kilobase pairs of DNA sequence flanking either side of the glyceraldehyde-3-phosphate dehydrogenase gene in the cloned segment of yeast DNA. The isolated hybrid plasmid DNA has been used to selectively hybridize glyceraldehyde-3-phosphate dehydrogenase messenger RNA from unfractionated yeast poly(adenylic acid)-containing messenger RNA. The nucleotide sequence of a portion of the isolated hybrid plasmid DNA has been determined. This nucleotide sequence encodes 29 amino acids which are at the COOH terminus of the known amino acid sequence of yeast glyceraldehyde-3-phosphate dehydrogenase.

Isolation and identification of yeast messenger ribonucleic acids coding for enolase, glyceraldehyde-3-phosphate dehydrogenase, and phosphoglycerate kinase

Yeast poly(adenylic acid)-containing messenger ribonucleic acid isolated from two strains of Saccharomyces cerevisiae was fractionated by preparative polyacrylamide gel electrophoresis in the presence of formamide. Three messenger ribonucleic acids, present at high intracellular concentration, were electrophoretically eluted from the polyacrylamide gels and translated in a wheat germ cell-free extract. The in vitro synthesized polypeptides were identified by tryptic peptide analysis. Messenger ribonucleic acids coding for enolase and glyceraldehyde-3-phosphate dehydrogenase were isolated from commercially grown baker's yeast (strain F1), and messenger ribonucleic acid coding for phosphoglycerate kinase was isolated from Saccharomyces cerevisiae (ATCC 24657). Significant differences in the spectrum of abundant messenger ribonucleic acids isolated from commercially grown baker's yeast (strain F1) and strain 24657 were observed. When both strains were grown under identical conditions, however, the spectrum of messenger ribonucleic acid isolated from the cells is indistinguishable.

Effect of morphine analogues on chemotaxis in Escherichia coli

Pretreatment of Escherichia coli w3110 with levorphanol, a morphine analogue, reduced chemotaxis to serine, aspartic acid and galactose. This decreased chemotaxis was not due to decreased viability or motility. Pretreatment with 1.1 mM-levorphanol for 1 h, followed by washing to remove the drug prior to determination of chemotaxis, inhibited chemotaxis to each of the attractants by at least 80%. Pretreatment with dextrorphan, the enantiomorph of levorphanol, or levallorphan, the N-allyl analogue of levorphanol, resulted in a similar inhibition of chemotaxis. Reversal of the inhibition produced by pretreatment with levorphanol required a period of growth of at least one generation time.

Characterization of purified poly(adenylic acid)-containing messenger ribonucleic acid from Saccharomyces cerevisiae

Yeast poly(adenylic acid)-containing messenger RNA was isolated from total cellular RNA by affinity chromatography on poly(uridylic acid)-cellulose. The relative complexity of the isolated yeast mRNA was assessed by hybridization analysis with complementary DNA synthesized from the isolated messenger RNA (mRNA) with viral reverse transcriptase. Approximately 25% of the mRNA hybridized at an apparent Crt1/2 of 5 X 10(-3) mol sl.(-1), while the remainder hybridized at an average Crt1/2 of 10(-1) mol sl.-1. Poly(adenylic acid)-containing yeast mRNA was translated in vitro in a wheat germ cell-free extract, and the major polypeptides synthesized have the same molecular weight as the major proteins present in the cell. Four of these proteins were identified by coelectrophoresis and immune precipitation to be pyruvate kinase, enolase, aldolase, and glyceraldehyde-3-phosphate dehydrogenase. These data demonstrate in agreement with the hybridization results that yeast contains major mRNA species and that some of the glycolytic enzyme mRNAs make up part of the major fraction. A procedure is outlined for the preparation of yeast mRNA which is essentially free of ribosomal RNA contamination and is further enriched in the major mRNAs present in the cell.

Isolation of ribonucleic acid polymerases I, II, and III from Saccharomyces cerevisiae

A procedure for the simultaneous purification of RNA polymerases I, II, and III from Saccharomyces cerevisiae is described. High yields of each enzyme activity are obtained, allowing the preparation of approximately 10 mg of polymerase I, 25 mg of polymerase II, and 12 mg of polymerase III from 1.2 kg of cells (wet weight). Polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate indicates RNA polymerase I contains polypeptides with molecular weights 185 000, 137 000, 41 000, 35 000, 28 000, 24 000, 20 000, 16 000, 14 500, and 12 300; RNA polymerase II contains subunits with molecular weights 170 000, 145 000, 41 000, 33 500, 28 000, 24 000, 18 000, 14 500, and 12 500; and RNA polymerase III contains polypeptides with molecular weights 160 000, 128 000, 82 000, 53 000, 41 000, 37 000, 34 000, 28 000, 24 000, 20 000, 14 500, and 10 700.

Transcription of yeast DNA by homologous RNA polymerases I and II: selective transcription of ribosomal genes by RNA polymerase I

Purified yeast DNA was transcribed by homologous RNA polymerases I and II and Escherichia coli RNA polymerase. Transcripts synthesized in vitro were analyzed by molecular hybridization with complementary DNA (cDNA) synthesized from yeast poly(A)-containing mRNA with viral reverse transcriptase and ribosomal DNA labeled in vitro by nick translation with E. coli DNA polymerase I. RNA synthesized by polymerase I and II in the presence of Mn2+ contained sequences complementary to cDNA and rDNA at a frequency consistent with random transcription of the template. Similarly, E. coli RNA polymerase synthesized an apparently random transcript in the presence of either Mn2+ or Mg2+. In contrast to these results, RNA polymerase I but not polymerase II transcripts were markedly enriched in sequences complementary to rDNA when transcription was carried out in the presence of Mg2+. The observed enrichment was 15-30-fold higher than observed for polymerase II or E. coli polymerase transcripts and is consistent with the transcript being comprised of 6-10% ribosomal sequences. These data strongly suggest that RNA polymerase I plays a critical role in selective transcription of ribosomal cistrons.

Purine excretion by cultured skin fibroblasts from patients with abnormal purine metabolism

Cultured fibroblasts from patients with partial or complete deficiencies of enzymes involved in purine metabolism provide a model for investigating the biosynthesis, interconversion, and excretion of purine metabolites at the cellular level. Skin fibroblast cultures were derived from five patients with hypoxanthineguanine phosphoribosyltransferase deficiency, from five subjects with idiopathic overproduction gout, from one patient with adenosine deaminase deficiency, and from four control subjects. Purine excretion was measured by recovering labeled purines from the incubation medium of cells grown in the presence of 14C-formate. In general the patterns of purine excretion by these cultured cells resembled the urinary excretion patterns of the patients from whom they were derived.

Hypoxanthine phosphoribosyltransferase activity in intact fibroblasts from patients with X-linked hyperuricemia

Discordance between clinical phenotype and the level of a mutant enzyme activity may reflect differences between enzyme function in vivo and that measured by the customary enzyme assays on cell extracts. In the present study, the conversion of hypoxanthine to phosphorylated products was measured in intact skin fibroblasts and in cell extracts from seven patients with mutant hypoxanthine-guanine phosphoribosyltransferase (HPRT) and six control subjects. The patient's phenotypes ranged from asymptomatic hyperuricemia to the Lesch-Nyhan syndrome. Although there was a general correlation between the HPRT activity in cell extracts assayed by the usual methods and the function of the purine salvage pathway in patients, as reflected by urinary oxypurine excretion, there were notable exceptions. A more accurate appraisal of the functioning of the pathway at the cellular level is achieved by measuring the conversion of substrate to product in the intact cell at physiological concentrations of substrates, activators, and product and metabolite inhibitors, and in a physiological ionic environment. In one of the seven patients, the standard enzyme assay indicated normal function, whereas measurements in the intact cell exposed severe dysfunction of the salvage system. In another, the standard assay suggested a severe deficiency not evident in the intact cell or in the patient.

Denaturation mapping of R factor deoxyribonucleic acid

The R factor NR1 consists of two components: a resistance transfer factor which harbors the tetracycline resistance genes (RTF-TC) and the r-determinants component which harbors the other drug resistance genes. Using partial denaturation mapping it is possible to distinguish the RTF-TC region from the r-determinants region of the composite R factor NR1 DNA which has a contour length of 37 mum and a density of 1.712 g/ml. The r-determinants region was a relatively undenatured 8.5-mum segment of the molecule when the deoxyribonucleic acid was partially denatured at pH 10.7. An RTF-TC genetic segregant of NR1 which had lost the r-determinants component had a contour length of 28.7 mum and a density of 1.710 g/ml. Characterization of an RTF-TC using partial denaturation mapping at pH 10.7 confirmed that the relatively undenatured 8.5-mum r-determinants segment of the composite R factor had been deleted. Circular, transitioned NR1 DNA molecules (1.716 to 1.718 g/ml), whose contour lengths were consistent with an RTF-TC plus an integral number of tandem copies of r-determinants, were also characterized by denaturation mapping. The relatively undenatured region in these molecules had a length equal to an integral number of copies of r-determinants and was located at the same site in the partially denatured RTF-TC as the single copy of r-determinants in the 37-mum composite NR1. This indicates that there is a unique integration site for r-determinants in the RTF-TC component. The R factor UCR122, a TC deletion mutant of NR1, was also characterized by denaturation mapping. The translocation of the TC resistance gene(s) on the denaturation map permitted the alignment of the denaturation map with the heteroduplex map of Sharp et al. (u073). Linear and circular monomeric and presumed multimeric r-determinants DNA molecules (p = 1.718 g/ml) were partially denatured at a higher pH (11.10). The r-determinants multimers showed a repeating 8.3-mum (monomeric) partial denaturation pattern indicating a head-to-tail arrangement of monomers in these poly-r-determinant molecules.