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J D Friesen

Publications and source records attributed to J D Friesen.

At least 55 records · Page 3Linked to original sources
PubMed1990

The PRP4 (RNA4) protein of Saccharomyces cerevisiae is associated with the 5' portion of the U4 small nuclear RNA.

We have combined oligonucleotide-directed RNase H degradation and immunoprecipitation in a study of the association of the Saccharomyces cerevisiae PRP4 protein with the U4-U6 complex. We have found that three oligonucleotides were able to direct nearly to completion the RNase H-specific cleavage of the target RNA molecules as they exist in splicing extracts. Immunoprecipitation of the degradation products with PRP4 antibody showed that the 5' portion of U4 small nuclear RNA (snRNA) and the 3' portion of U6 snRNA coimmunoprecipitated with the PRP4 protein. Micrococcal nuclease protection experiments confirmed further that the 5' portion and 3' end of U4 snRNA were very resistant to nuclease digestion, whereas the 3' portion of U6 snRNA was protected to only a very small extent. We conclude that the PRP4 protein of S. cerevisiae is associated primarily with the 5' portion of U4 snRNA in the U4-U6 small nuclear ribonucleoprotein (snRNP).

Base Sequence↗
PubMed1989

Primary structure of the S. cerevisiae gene encoding uridine monophosphokinase.

In the yeast Saccharomyces cerevisiae, the biosynthesis of both pyrimidine nucleoside triphosphates UTP and CTP is dependent on the activity of the uridine monophosphokinase step. We have determined the sequence of the uridine monophosphokinase gene. The coding region is 615 base pairs long and encodes 205 amino acids (22,500 daltons). The 5' terminus is comprised of a 17 amino acid-long hydrophobic leader sequence which is not present in genes encoding adenylate kinases. The coding region shows a strong degree of homology with the cytosolic adenylate kinases of vertebrates, and a lesser degree of homology with yeast and E. coli adenylate kinases.

Adenylate Kinase↗
PubMed1989

On the effects of replacing the carboxylate-binding arginine-171 by hydrophobic tyrosine or tryptophan residues in the L-lactate dehydrogenase from Bacillus stearothermophilus.

For L-lactate dehydrogenases (LDH's), the interaction of the guanidinium group of their Arg 171 residue with the carboxylate group of an alpha-keto acid is of primary importance in orienting the substrate productively at the active site. LDH's such as that of Bacillus stearothermophilus (BSLDH) are of practical importance for the preparation of chiral 2-hydroxy acids used as synthons in asymmetric synthesis but would even be more valuable in this regard if their specificities were broader. With a view to tailoring the specificity of BSLDH toward carbonyl substrates that lack an alpha-carboxyl group such as ketones, site-directed mutagenesis has been applied to replace Arg 171 by the approximately isosteric, but hydrophobic, amino acids Tyr and Trp. The mutant enzymes exhibit remarkably good catalytic activities toward representative alpha-keto acids RCOCOOH, where R = Me, Et, n-Pr, n-Bu, and CH2OH, although for the mutant enzymes the kcat/KM's are lower by approximately 10(3)-10(4)-fold than those for native BSLDH. Surprisingly, the 171----Tyr/Trp enzymes are significantly more active than 171----Lys (Hart et al., 1987a), for which an interaction of a positively charged side chain with substrate COO- is retained. Preparative-scale 171----Trp catalyzed reduction of pyruvate gave optically pure L-lactate, showing that L stereospecificity of such LDH enzymes was unaffected by the loss of Arg 171. The retention of L stereospecificity is attributed to secondary polar or hydrogen-bonding associations of Arg 109 and Thr246, respectively, with the substrate COO-function that are of sufficient magnitude to maintain "normal" substrate orientation.(ABSTRACT TRUNCATED AT 250 WORDS)

Arginine↗
PubMed1989

On the effect on specificity of Thr246----Gly mutation in L-lactate dehydrogenase of Bacillus sterothermophilus.

The function of the amino acid Thr246 in L-lactate dehydrogenase from Bacillus stearothermophilus has been investigated by site-directed replacement with glycine. Kinetic experiments with a number of 2-oxo acids showed strongly reduced activity for the mutated enzyme. However, the mutant enzyme shows a relative preference for the large hydrophobic sidechains of alpha-keto acids and an even higher specific activity than the wild-type lactate dehydrogenase for the polar oxaloacetate substrate. Graphic analyses indicate that the loss of one hydrogen bond, or intrusion of water into the active site, might be responsible for the reduced activity. The kinetic results suggest that the binding modes of bulky hydrophobic or polar substrates compensate to some degree for the partially disrupted active site.

Amino Acid Sequence↗
PubMed1989

PRP4 (RNA4) from Saccharomyces cerevisiae: its gene product is associated with the U4/U6 small nuclear ribonucleoprotein particle.

The PRP4 (RNA4) gene product is involved in nuclear mRNA processing in yeast cells; we have previously cloned the gene by complementation of a temperature-sensitive mutation. Sequence and transcript analyses of the cloned gene predicted the gene product to be a 52-kilodalton protein, which was confirmed with antibodies raised against the PRP4 gene product. These antibodies inhibited precursor mRNA splicing in vitro, demonstrating a direct role of PRP4 in splicing. Immunoprecipitations with the antibodies indicated that the PRP4 protein is associated with the U4/U6 small nuclear ribonucleoprotein particle.

Amino Acid Sequence↗
PubMed1988

The nucleotide sequence of the Escherichia coli rts gene.

The nucleotide sequence of rts, an essential Escherichia coli gene, has been determined. Transformation of an rts mutant with the plasmid, pJAF1, containing the rts gene resulted in rescue of the defect. The transformation experiments indicate that the rts gene is distinct from the flanking birA, tRNA and tufB genes.

Amino Acid Sequence↗
PubMed1988

The nucleotide sequence and characterization of the relA gene of Escherichia coli.

The relA gene product of Escherichia coli is known to be responsible for the synthesis of guanosine 3',5'-bispyrophosphate (ppGpp) during the stringent response to amino acid starvation. This report presents the sequence of the relA gene region and assignment of its 743-codon open reading frame by the following criteria: 1) genetic complementation of ppGpp synthesis in a relaxed (relA1) mutant during the stringent response; 2) changes in 3-aminotriazole resistance during growth to mimic a relA+ phenotype; 3) verification of the presence of an amber codon at the normal carboxyl terminus of the relA gene; and 4) immunological assays of expression of the RelA protein. The apparent molecular mass of the cloned relA gene product is calculated to be 83,856 daltons and as visualized by immunoblotting is identical to that of the previously characterized protein. A promoter has been identified that directs relA gene transcription towards the pyrG gene, in a counterclockwise direction on the E. coli chromosome. Genomic Southern blot analyses verify that the relA regions cloned and subjected to nucleotide sequence analysis correspond to homologous regions on the E. coli chromosome.

Bacterial Proteins↗
PubMed1988

In vivo and in vitro structural analysis of the rplJ mRNA leader of Escherichia coli. Protection by bound L10-L7/L12.

The rplJL-rpoBC operon of Escherichia coli is regulated in part at the level of translation by an autogenous mechanism (feedback regulation) that involves ribosomal protein L10-L7/L12. Feedback regulation occurs as the result of L10-L7/L12 binding to a site on the untranslated leader region of the rplJ mRNA that is located more than 100 nucleotides upstream from the translation start site. Previous studies have indicated that the secondary structure of the rplJ leader region is important for efficient translation and feedback regulation. We have done chemical modification experiments to examine the secondary structure of approximately 200 nucleotides of the rplJ leader region, and we propose a secondary structure that is consistent with the experimental data. RNA structure was probed in vitro by treating samples of total cellular RNA with diethyl pyrocarbonate and in vivo by treating log-phase cultures with dimethyl sulfate. Modified bases were detected by primer extension using three different oligonucleotide primers. The proposed structure includes five double-stranded regions designated I to V, separated by single-stranded segments numbered 1 to 5. We have also identified specific nucleotides in the rplJ mRNA leader that are protected by purified L10-L7/L12 from methylation by dimethyl sulfate in vitro. The protected bases are located within a bulge-loop of region IV, a portion of the mRNA that has been shown genetically to be necessary for feedback regulation.

Base Sequence↗
PubMed1988

Eco-systemic analysis of anorexia nervosa.

Aspects of the eco-systemic approach were used to provide a framework for the understanding of anorexia nervosa and were empirically tested by comparing 30 anorexics and their parents to 34 matched control subjects and their parents. The theoretical model employed was an adaptation of Conger's Ecological-Systems approach which was based on the principles of Bronfenbrenner's theory of human development. The subjects were compared on selected variables arising from the individual, parent, family, and community systems using (a) the California Psychological Inventory (CPI), (b) the Structural Analysis of Social Behavior (SASB), (c) the Family Environment Scale (FES), and (d) the Pattison Psychological Inventory (PPI). Discriminant analysis revealed that the Affiliation score (SASB) for the anorexic and the control subjects and the Psychopathic Deviancy score (CPI-Clinical) of the mothers of the anorexics and the controls were the variables which contributed most to the discrimination between the groups. With the Affiliation and the Psychopathic Deviancy scores alone, it was possible to correctly classify 87.5 per cent of the research subjects. Analyses also showed statistically significant results at the individual, parent, and family levels. Interactions within the family, as perceived by the anorexics, were characterized by overprotection and control by the mothers, while the anorexics themselves responded with significantly less affiliation to both their mothers and their fathers. The mothers of the anorexics also viewed their daughters as being less friendly in the relationship. The families of the anorexics were less supportive, helpful, and committed to each other than were the families of the control subjects as measured by the FES.

Adolescent↗
PubMed1988

The accumulation of three yeast ribosomal proteins under conditions of excess mRNA is determined primarily by fast protein decay.

The suggestion that compensation for overabundant mRNA of the genes for Saccharomyces cerevisiae ribosomal protein (r-protein) L3, L29, or rp59 occurs by translation repression has been reinvestigated. First, analysis of the distribution of these three mRNAs in polysome profiles revealed no differences between normal and mRNA-overproducing strains, indicating that initiation of r-protein translation is not repressed under conditions of mRNA overaccumulation. Second, experiments involving radioactive pulse-labeling of proteins were done by using a modified method of data collection and analysis that allows quantitation and correction for fast decay during the pulse. These measurements revealed that the synthesis rate of the three r-proteins is increased when their mRNA levels are elevated and that their decay rate is also high, with half-lives ranging from a fraction of a minute to more than 10 min. We conclude that accumulation of excess r-protein mRNA has no effect on translation rate; rapid decay of protein during the course of the labeling period can account for the apparent discrepancy between mRNA levels and protein synthesis rates. Yeast r-proteins, when produced in excess, are among the most rapidly degraded proteins so far described.

Gene Expression Regulation↗
PubMed1987

Feedback regulation of the rplJL-rpoBC ribosomal protein operon of Escherichia coli requires a region of mRNA secondary structure.

The rplJ-rpoBC (L10) operon of Escherichia coli is regulated in part through translational repression (feedback regulation) by ribosomal protein L10 or a complex of ribosomal proteins L10 and L7/L12 (L10-L7/L12). We have constructed mutants in the untranslated leader region of a rplJ-lacZ fusion by oligonucleotide-directed mutagenesis. The mutations include several deletions and a number of single base changes, all of which fail to exhibit normal feedback regulation. Chemical probing of part of the rplJ mRNA leader in the mutagenized region confirms that all of the mutations lie in a stem structure located 140 nucleotides upstream from the translation start-site. The structure includes a 12 base-pair stem, a four base stem-loop, and a six base bulge-loop. Point mutations that abolish feedback regulation are presumed to disrupt this stem structure. Pseudorevertants of selected point mutations were constructed by combining pairs of single base mutations. In these cases, both the secondary structure of the RNA and feedback regulation were restored. The results allow us to define a region of secondary structure in the rplJ mRNA leader that is necessary for feedback regulation.

Base Sequence↗
PubMed1987

Effects on mRNA splicing of mutations in the 3' region of the Saccharomyces cerevisiae actin intron.

Point mutations, deletions, and a sequence context change were introduced at positions 3' to the internal conserved TACTAAC sequence of the Saccharomyces cerevisiae actin intron. In vivo analysis of yeast mRNA splicing suggests that, in contrast to the importance of the polypyrimidine tract in metazoan introns, specific sequences in this region are not required for efficient excision of a yeast intron. However, a double point mutation near the 3' junction (GG/AC) does severely inhibit splicing. Although this mutagenesis of the 3' junction, as well as deletion of most nucleotides between the TACTAAC and the 3' junction, caused only a slight accumulation of primary transcript, the observed accumulation of lariat intermediate by these mutants demonstrates the significance of this region for a step(s) in the splicing process after lariat formation.

Actins↗
PubMed1987

Isolation and characterization of temperature-sensitive RNA polymerase II mutants of Saccharomyces cerevisiae.

Three independent, recessive, temperature-sensitive (Ts-) conditional lethal mutations in the largest subunit of Saccharomyces cerevisiae RNA polymerase II (RNAP II) have been isolated after replacement of a portion of the wild-type gene (RPO21) by a mutagenized fragment of the cloned gene. Measurements of cell growth, viability, and total RNA and protein synthesis showed that rpo21-1, rpo21-2, and rpo21-3 mutations caused a slow shutoff of RNAP II activity in cells shifted to the nonpermissive temperature (39 degrees C). Each mutant displayed a distinct phenotype, and one of the mutant enzymes (rpo21-1) was completely deficient in RNAP II activity in vitro. RNAP I and RNAP III in vitro activities were not affected. These results were consistent with the notion that the genetic lesions affect RNAP II assembly or holoenzyme stability. DNA sequencing revealed that in each case the mutations involved nonconservative amino acid substitutions, resulting in charge changes. The lesions harbored by all three rpo21 Ts- alleles lie in DNA sequence domains that are highly conserved among genes that encode the largest subunits of RNAP from a variety of eucaryotes; one mutation lies in a possible Zn2+ binding domain.

Amino Acid Sequence↗
PubMed1986

Mutations in a yeast intron demonstrate the importance of specific conserved nucleotides for the two stages of nuclear mRNA splicing.

Mutations were introduced at all positions of the internal conserved sequence (ICS) and at three positions in the 5' junction sequence of a Saccharomyces cerevisiae actin intron contained within an actin-thymidine kinase fusion gene. Stage I of splicing is reduced by changes at all these positions. C or A replacement at the fifth nucleotide of the 5' sequence reduces the fidelity of RNA cleavage at the 5' exon-intron junction and results in an accumulation of aberrant lariat intermediate. Stage II of splicing is affected by changes in the first and second residues of the 5' sequence and in the penultimate position of the ICS. An A to G transition at the branch point of the ICS causes a major accumulation of lariat intermediate.

Actins↗
PubMed1985

Isolation of the fructose-1,6-bisphosphatase gene of the yeast Schizosaccharomyces pombe. Evidence for transcriptional regulation.

The fructose-1,6-bisphosphatase structural gene (FBP+) of Schizosaccharomyces pombe has been isolated by genetic complementation of a deficient mutant, which is characterized by the inability to grow on a nonfermentable carbon source such as glycerol. Growth on glycerol-containing medium was restored in a S. pombe fructose-1,6-bisphosphatase-deficient mutant (fbp-16) when it was transformed with a plasmid (pAVO4) carrying FBP+. The transformant displayed a 5-fold increase in enzymatic activity when compared to the parental S. pombe strain. Subcloning of DNA fragments from the 8.5-kilobase (kb) insert of pAVO4 defined a 4-kb DNA fragment which contained the functional FBP+ gene and its regulatory region. When this gene was placed under the control of the lac promoter-operator, functional expression in Escherichia coli was obtained, as deduced by complementation of bacterial fructose-1,6-bisphosphatase mutants. The FBP+ gene encodes a 1.9-kb glucose-repressible transcript whose appearance in S. pombe is correlated with fructose-1,6-bisphosphatase derepression in glycerol-containing medium. We suggest that the regulation of the S. pombe FBP+ gene is exerted at the transcriptional level. The S. pombe FBP+ gene gave rise to a 1.9-kb transcript in Saccharomyces cerevisiae, but not to measurable enzymatic activity.

Ascomycota↗
PubMed1985

Efficient expression of the Escherichia coli leuB gene in yeast.

Efficient expression of the Escherichia coli leuB (beta-isopropylmalate dehydrogenase) gene occurred in yeast after in vitro DNase digestion and religation of plasmid bound leuB and the yeast HIS3 DNA which placed the 5' end of the yeast HIS3 gene immediately adjacent to the coding region of the E. coli leuB gene. Two structurally distinct classes of gene fusions were constructed, each involved portions of the yeast HIS3 gene which contributed DNA sequences responsible for leuB expression in yeast. The first class involved fusion of the HIS3 coding region to bacterial DNA resulting in the production of a fusion protein with beta-isopropylmalate dehydrogenase activity. The second class consisted of bacterial DNA, including the leuB coding region, fused to the HIS3 promotor region with the absence of any portion of the HIS3 coding region. In both constructions the HIS3 promotor region is required for transcription, however, translation of the class two fusion is initiated at a bacterial DNA coded AUG, and the 5' end of the mRNA coded by the leuB gene mapped predominantly at bacterial DNA sequences. The DNA sequence responsible for the 5' end of the HIS3 mRNAs remain in the class two gene fusions but this did not preclude the initiation of transcription at bacterial DNA sequences. The pattern of mRNA initiation at bacterial DNA suggests that DNA sequences at, or adjacent to, the site of transcription initiation are involved in the determination of the sites of initiation, and perhaps the frequency at which initiation occurs.

3-Isopropylmalate Dehydrogenase↗
PubMed1985

Isolation of the SUP45 omnipotent suppressor gene of Saccharomyces cerevisiae and characterization of its gene product.

The Saccharomyces cerevisiae SUP45+ gene has been isolated from a genomic clone library by genetic complementation of paromomycin sensitivity, which is a property of a mutant strain carrying the sup45-2 allele. This plasmid complements all phenotypes associated with the sup45-2 mutation, including nonsense suppression, temperature sensitivity, osmotic sensitivity, and paromomycin sensitivity. Genetic mapping with a URA3+-marked derivative of the complementing plasmid that was integrated into the chromosome by homologous recombination demonstrated that the complementing fragment contained the SUP45+ gene and not an unlinked suppressor. The SUP45+ gene is present as a single copy in the haploid genome and is essential for viability. In vitro translation of the hybrid-selected SUP45+ transcript yielded a protein of Mr = 54,000, which is larger than any known ribosomal protein. RNA blot hybridization analysis showed that the steady-state level of the SUP45+ transcript is less than 10% of that for ribosomal protein L3 or rp59 transcripts. When yeast cells are subjected to a mild heat shock, the synthesis rate of the SUP45+ transcript was transiently reduced, approximately in parallel with ribosomal protein transcripts. Our data suggest that the SUP45+ gene does not encode a ribosomal protein. We speculate that it codes for a translation-related function whose precise nature is not yet known.

Actins↗