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2.
FEBS Lett ; 472(1): 1-4, 2000 Apr 21.
Article in English | MEDLINE | ID: mdl-10781793

ABSTRACT

An increasing body of evidence has demonstrated that NADPH oxidase plays a critical role in several early steps leading toward the development of atherosclerosis. These effects appear to be carried out by both the ability of O2- to act as a small second messenger molecule, and potentially the oxidation of low density lipoprotein by O2-. We describe a model for the initiation and development of atherosclerosis that suggests targeted inhibition of NADPH oxidase as a powerful site for prevention and treatment of this disease.


Subject(s)
Arteriosclerosis/enzymology , NADPH Oxidases/metabolism , Endothelium, Vascular/enzymology , Humans , Lipoproteins, LDL/metabolism , NADPH Oxidases/antagonists & inhibitors , Oxidation-Reduction , Superoxides/metabolism
3.
Gene ; 245(1): 175-84, 2000 Mar 07.
Article in English | MEDLINE | ID: mdl-10713458

ABSTRACT

The 340-nucleotide RNA component of Saccharomyces cerevisiae RNase MRP is encoded by the single-copy essential gene, NME1. To gain additional insight into the proposed structure and functions of this endoribonuclease, we have extensively mutagenized the NME1 gene and characterized yeast strains expressing mutated forms of the RNA using a gene shuffle technique. Strains expressing each of 26 independent mutations in the RNase MRP RNA gene were characterized for their ability to grow at various temperatures and on various carbon sources, stability of the RNase MRP RNA and processing of the 5.8S rRNA (a nuclear function of RNase MRP). 11 of the mutations resulted in a lethal phenotype, six displayed temperature-conditional lethality, and several preferred a non-fermentable carbon source for growth. In those mutants that exhibited altered growth phenotypes, the severity of the growth defect was directly proportional to the severity of the 5.8S rRNA processing defect in the nucleus. Together this analysis has defined essential regions of the RNase MRP RNA and provides evidence that is consistent with the proposed function of the RNase MRP enzyme.


Subject(s)
Cell Nucleus/metabolism , Endoribonucleases/genetics , RNA, Fungal/genetics , Saccharomyces cerevisiae/genetics , Base Sequence , Cell Division/drug effects , Cell Division/genetics , Cell Nucleus/genetics , Endoribonucleases/metabolism , Glycerol/pharmacology , Molecular Sequence Data , Mutagenesis , Mutation , Phenotype , RNA Stability/genetics , RNA, Ribosomal, 5.8S/metabolism , Saccharomyces cerevisiae/drug effects , Saccharomyces cerevisiae/growth & development , Temperature
4.
Endothelium ; 7(1): 11-22, 1999.
Article in English | MEDLINE | ID: mdl-10599557

ABSTRACT

Cultured human endothelial cells (EC) exposed to atherogenic low-density lipoprotein levels have increased reactive oxygen species (ROS) generation. The enzyme responsible for this ROS production elevation is unknown. We have examined for the presence of a functional leukocyte-type NADPH oxidase in EC to elucidate whether this enzyme could be the ROS source. The plasma membrane fraction of disrupted EC showed a reduced-minus-oxidized difference spectra with absorption peaks identical to those observed in the spectra of the leukocyte NADPH oxidase component, cytochrome b558. Western-blot analysis, using anti-gp91 -phox. anti -p22-phox. anti -p47-phox. and anti -p67-phox antibodies, demonstrated the protein expression of NADPH oxidase subunits in EC. Reverse transcriptase-polymerase chain reaction (RT-PCR) showed the mRNA expression of gp91-phox, p22-phox, p47-phox, and p67-phox in EC. Sonicates from unstimulated EC produced no measurable superoxide; whereas, exogenously applied arachidonic acid activated superoxide generation in a manner that was dependent upon the presence of NADPH and both membrane and cytosolic fractions combined. Apocynin, a specific leukocyte NADPH oxidase inhibitor, was shown by Western-blot analysis of membrane and cytoplasmic fractions to inhibit the translocation of p47-phox to the membrane of stimulated EC. These findings support the presence of a functionally active leukocyte-type NADPH oxidase in EC. NADPH oxidase could be the major cellular ROS source in EC perturbation, which has been hypothesized to be a major contributing factor in the pathogenesis of atherosclerosis.


Subject(s)
Endothelium, Vascular/cytology , Endothelium, Vascular/enzymology , Membrane Transport Proteins , NADPH Oxidases/analysis , Acetophenones/pharmacology , Antioxidants/pharmacology , Arteriosclerosis/enzymology , Biological Transport , Cell Membrane/chemistry , Cell-Free System/enzymology , Cells, Cultured , Cytochrome b Group/analysis , Enzyme Inhibitors/pharmacology , Humans , Leukocytes/enzymology , Membrane Glycoproteins/genetics , NADPH Dehydrogenase/genetics , NADPH Oxidase 2 , NADPH Oxidases/antagonists & inhibitors , NADPH Oxidases/genetics , Phosphoproteins/genetics , RNA, Messenger/metabolism , Reactive Oxygen Species , Superoxides/metabolism , Time Factors , Translocation, Genetic/drug effects , Umbilical Veins/cytology , Umbilical Veins/enzymology
5.
Mol Cell Biol ; 19(11): 7857-69, 1999 Nov.
Article in English | MEDLINE | ID: mdl-10523674

ABSTRACT

RNase MRP is a ribonucleoprotein endoribonuclease that has been shown to have roles in both mitochondrial DNA replication and nuclear 5.8S rRNA processing. SNM1 encodes an essential 22.5-kDa protein that is a component of yeast RNase MRP. It is an RNA binding protein that binds the MRP RNA specifically. This 198-amino-acid protein can be divided into three structural regions: a potential leucine zipper near the amino terminus, a binuclear zinc cluster in the middle region, and a serine- and lysine-rich region near the carboxy terminus. We have performed PCR mutagenesis of the SNM1 gene to produce 17 mutants that have a conditional phenotype for growth at different temperatures. Yeast strains carrying any of these mutations as the only copy of snm1 display an rRNA processing defect identical to that in MRP RNA mutants. We have characterized these mutant proteins for RNase MRP function by examining 5.8S rRNA processing, MRP RNA binding in vivo, and the stability of the RNase MRP RNA. The results indicate two separate functional domains of the protein, one responsible for binding the MRP RNA and a second that promotes substrate cleavage. The Snm1 protein appears not to be required for the stability of the MRP RNA, but very low levels of the protein are required for processing of the 5.8S rRNA. Surprisingly, a large number of conditional mutations that resulted from nonsense and frameshift mutations throughout the coding regions were identified. The most severe of these was a frameshift at amino acid 7. These mutations were found to be undergoing translational suppression, resulting in a small amount of full-length Snm1 protein. This small amount of Snm1 protein was sufficient to maintain enough RNase MRP activity to support viability. Translational suppression was accomplished in two ways. First, CEN plasmid missegregation leads to plasmid amplification, which in turn leads to SNM1 mRNA overexpression. Translational suppression of a small amount of the superabundant SNM1 mRNA results in sufficient Snm1 protein to support viability. CEN plasmid missegregation is believed to be the result of a prolonged telophase arrest that has been recently identified in RNase MRP mutants. Either the SNM1 gene is inherently susceptible to translational suppression or extremely small amounts of Snm1 protein are sufficient to maintain essential levels of MRP activity.


Subject(s)
Chromosomes, Fungal/genetics , DNA-Binding Proteins/genetics , Endoribonucleases/genetics , Fungal Proteins/genetics , Nuclear Proteins , Plasmids/genetics , Ribonucleoproteins/genetics , Saccharomyces cerevisiae Proteins , Saccharomyces cerevisiae/genetics , DNA-Binding Proteins/metabolism , Endodeoxyribonucleases , Endoribonucleases/metabolism , Fungal Proteins/metabolism , Genes, Essential , Genes, Fungal , Mutagenesis , Protein Binding , Protein Biosynthesis , Protein Structure, Secondary , RNA Processing, Post-Transcriptional , RNA Stability , RNA, Fungal/metabolism , RNA, Ribosomal, 5.8S/metabolism , Ribonucleoproteins/metabolism , Saccharomyces cerevisiae/enzymology , Spindle Apparatus/ultrastructure , Suppression, Genetic
6.
J Mol Biol ; 292(4): 827-36, 1999 Oct 01.
Article in English | MEDLINE | ID: mdl-10525408

ABSTRACT

RNase mitochondrial RNA processing (MRP) is a ribonucleoprotein endoribonuclease that is involved in RNA processing events in both the nucleus and the mitochondria. The MRP RNA is both structurally and evolutionarily related to RNase P, the ribonucleoprotein endoribonuclease that processes the 5'-end of tRNAs. Previous analysis of the RNase MRP RNA by phylogenetic analysis and chemical modification has revealed strikingly conserved secondary structural elements in all characterized RNase MRP RNAs. Utilizing successive constraint modeling and energy minimization I derived a three-dimensional model of the yeast RNase MRP RNA. The final model predicts several notable features. First, the enzyme appears to contain two separate structural domains, one that is highly conserved among all MRP and P RNAs and a second that is only conserved in MRP RNAs. Second, nearly all of the highly conserved nucleotides cluster in the first domain around a long-range interaction (LRI-I). This LRI-I is characterized by a ubiquitous uridine base, which points into a cleft between these two structural domains generating a potential active site for RNA cleavage. Third, helices III and IV (the yeast equivalent of the To-binding site) model as a long extended helix. This region is believed to be the binding site of shared proteins between RNase P and RNase MRP and would provide a necessary platform for binding these seven proteins. Indeed, several residues conserved between the yeast MRP and P RNAs cluster in the central region of these helixes. Lastly, characterized mutations in the MRP RNA localize in the model based on their severity. Those mutations with little or no effect on the activity of the enzyme localize to the periphery of the model, while the most severe mutations localize to the central portion of the molecule where they would be predicted to cause large structural defects. Press.


Subject(s)
Endoribonucleases/chemistry , Models, Molecular , Nucleic Acid Conformation , RNA, Fungal/chemistry , Saccharomyces cerevisiae/enzymology , Bacillus subtilis/enzymology , Bacillus subtilis/genetics , Base Pairing , Binding Sites , Computer Simulation , Conserved Sequence/genetics , Endoribonucleases/genetics , Mutation , RNA, Catalytic/chemistry , RNA, Catalytic/genetics , RNA, Fungal/genetics , Reproducibility of Results , Ribonuclease P , Ribonucleoproteins/chemistry , Ribonucleoproteins/genetics , Saccharomyces cerevisiae/genetics , Thermodynamics
7.
Endothelium ; 5(3): 191-207, 1997.
Article in English | MEDLINE | ID: mdl-9272382

ABSTRACT

The effects of arachidonic acid metabolism and NADPH oxidase inhibitor on the hydrogen peroxide (H2O2) generation and endocytotic activity of cultured human endothelial cells (EC) exposed to atherogenic low-density lipoprotein (LDL) levels have been investigated. EC were incubated with 240 mg/dl LDL cholesterol and cellular H2O2 production and endocytotic activity measured in the presence and absence of the arachidonic acid metabolism inhibitors, indomethacin, nordihydroguaiaretic acid, and SKF525A, and NADPH oxidase inhibitor, apocynin. All inhibitors, with the exception of indomethacin, markedly reduced high LDL-induced increases in EC H2O2 generation and endocytotic activity. EC exposed to exogenously applied arachidonic acid had cellular functional changes similar to those induced by high LDL concentrations. EC incubated with 1-25 uM arachidonic acid had increased H2O2 production and heightened endocytotic activity. Likewise, EC pre-loaded with [3H]arachidonic acid when exposed to increasing LDL levels (90-330 mg/dl cholesterol) had a dose-dependent rise in cytosolic [3H]arachidonic acid. The phospholipase A2 inhibitors, 4-bromophenacyl bromide and 7,7-dimethyleicosadienoic acid, markedly inhibited H2O2 production in EC exposed to 240 mg/dl LDL cholesterol. These findings suggest that arachidonic acid contributes mechanistically to high LDL-perturbed EC H2O2 generation and heightened endocytosis. Such cellular functional changes add to our understanding of endothelial perturbation, which has been hypothesized to be a major contributing factor in the pathogenesis of atherosclerosis.


Subject(s)
Arachidonic Acid/metabolism , Cholesterol, LDL/pharmacology , Cyclooxygenase Inhibitors/pharmacology , Endocytosis/drug effects , Endothelium, Vascular/drug effects , Enzyme Inhibitors/pharmacology , Hydrogen Peroxide/metabolism , NADPH Oxidases/antagonists & inhibitors , Acetophenones/pharmacology , Cells, Cultured , Endothelium, Vascular/metabolism , Fatty Acids, Unsaturated/pharmacology , Humans , Indomethacin/pharmacology , Masoprocol/pharmacology , Methoxsalen/pharmacology , Phospholipases A/antagonists & inhibitors , Phospholipases A2 , Proadifen/pharmacology , Reactive Oxygen Species/metabolism , Second Messenger Systems , Stimulation, Chemical
8.
J Nematol ; 28(4S): 624-8, 1996 Dec.
Article in English | MEDLINE | ID: mdl-19277185

ABSTRACT

Granular (Rugby 10G) and liquid (Rugby 100 ME) formulations of cadusafos were evaluated for the control of Tylenchulus semipenetrans on mature lemon trees in a commercial citrus orchard at Yuma, Arizona. Three applications of cadusafos, with 2 months between applications, at the rate of 2 g a.i./m(2) reduced nematode populations to undetectable levels and increased the yield and rate of fruit maturity of 'Rosenberger' lemons. Yields were increased 12,587 kg/ha with Rugby 100ME and 8,392 kg/ha with Rugby 10G. Nematode populations were suppressed for at least 12 months after the last application.

9.
J Biol Chem ; 270(17): 9961-70, 1995 Apr 28.
Article in English | MEDLINE | ID: mdl-7730379

ABSTRACT

Subunit 6 of the mitochondrial cytochrome bc1 complex regulates the activity of the bc1 complex in Saccharomyces cerevisiae but is not essential for respiration. To test whether QCR6, the nuclear gene which encodes subunit 6, might be functionally redundant with any other gene(s), we screened for mutations in yeast genes which are essential when the otherwise non-essential QCR6 is deleted from the yeast chromosome. We obtained such quinolcytochrome c reductase subunit-requiring mutants in two complementation groups, which we named qsr1 and qsr2. The qsr mutants require QCR6 for viability on fermentable and non-fermentable carbon sources, indicating that QCR6 is covering lethal mutations in qsr1 and qsr2, even when the yeast do not require respiration. QSR1 was cloned by rescuing the synthetic lethality of a qsr1-1 mutant. QSR1 encodes a 25.4-kDa protein which is 65% identical to a protein encoded by QM, a highly conserved human gene which has been implicated in tumorigenesis. In mammals QM is down-regulated during adipocyte, kidney, and heart differentiation, and in Nicotiana the homolog of QM is also down-regulated during differentiation. When one chromosomal copy of QSR1 was deleted in a diploid yeast strain, haploid spores derived therefrom and carrying the deletion were unable to grow on fermentable or non-fermentable carbon sources. Although QCR6 allows the qsr1-1 mutant to grow, it will not substitute for QSR1, since the deletion of QSR1 is lethal even if QCR6 is present. These results indicate a novel genetic relationship between a subunit of the mitochondrial respiratory chain and an essential gene in yeast which is homologous to a gene implicated in differentiation in other eukaryotes.


Subject(s)
Electron Transport Complex III/genetics , Fungal Proteins/genetics , Mitochondria/enzymology , Ribosomal Proteins , Saccharomyces cerevisiae Proteins , Saccharomyces cerevisiae/genetics , Alleles , Amino Acid Sequence , Base Sequence , Cell Differentiation/genetics , Cloning, Molecular , Cytoplasm/metabolism , DNA, Recombinant , Fungal Proteins/metabolism , Genes, Fungal , Genetic Complementation Test , Humans , Molecular Sequence Data , Mutation , Sequence Homology, Amino Acid , Transcription, Genetic
10.
Mol Biol Rep ; 22(2-3): 87-93, 1995.
Article in English | MEDLINE | ID: mdl-8901493

ABSTRACT

Ribonuclease P (RNase P) is a ribonucleoprotein responsible for the endonucleolytic cleavage of the 5'-termini of tRNAs. Ribonuclease MRP (RNase MRP) is a ribonucleoprotein that has the ability to cleave both mitochondrial RNA primers presumed to be involved in mitochondrial DNA replication and rRNA precursors for the production of mature rRNAs. Several lines of evidence suggest that these two ribonucleoproteins are related to each other, both functionally and evolutionarily. Both of these enzymes have activity in the nucleus and mitochondria. Each cleave their RNA substrates in a divalent cation dependent manner to generate 5'-phosphate and 3'-OH termini. In addition, the RNA subunits of both complexes can be folded into a similar secondary structure. Each can be immunoprecipitated from mammalian cells with Th antibodies. In yeast, both have been found to share at least one common protein. This review will discuss some of the recent advances in our understanding of the structure, function and evolutionary relationship of these two enzymes in the yeast, Saccharomyces cerevisiae.


Subject(s)
Endoribonucleases/chemistry , Endoribonucleases/metabolism , RNA, Catalytic/chemistry , RNA, Catalytic/metabolism , Saccharomyces cerevisiae/metabolism , Amino Acid Sequence , Animals , Base Sequence , Conserved Sequence , DNA Replication , DNA, Fungal/biosynthesis , DNA, Mitochondrial/biosynthesis , Evolution, Molecular , Mammals , Molecular Sequence Data , Nucleic Acid Conformation , Protein Structure, Secondary , Ribonuclease P , Ribonucleoproteins/chemistry , Ribonucleoproteins/metabolism , Saccharomyces cerevisiae/genetics , Sequence Homology, Amino Acid
11.
Genes Dev ; 8(21): 2617-28, 1994 Nov 01.
Article in English | MEDLINE | ID: mdl-7958920

ABSTRACT

RNase MRP is a ribonucleoprotein endoribonuclease that has been shown to cleave mitochondrial primer RNA sequences from a variety of sources. Most of the RNase MRP activity is found in the nucleus where it plays a role in the processing of 5.8S rRNA. A temperature-conditional point mutation in the yeast RNA component of the enzyme has been identified. This mutation results in a loss of normal rRNA processing at the nonpermissive temperature while cellular levels of the RNA component of RNase MRP remain stable. High-copy suppressor analysis of this point mutation was employed to identify interacting proteins. A unique suppressor, termed SNM1 (suppressor of nuclear mitochondrial endoribonuclease 1), was identified repeatedly. The SNM1 gene was localized to the right arm of chromosome IV, directly adjacent to the SNF1 gene, and it contains an open reading frame encoding a protein of 198 amino acids. The protein contains a leucine zipper motif, a zinc-cluster motif, and a serine/lysine-rich tail. The gene was found to be essential for viability in a yeast cell, consistent with it being a protein component of the RNase MRP ribonucleoprotein complex. Recombinant SNM1 protein binds RNA in both gel retardation and Northwestern assays. Antibodies raised against bacterially expressed proteins identified four separate species in yeast whole cell extracts. Antibodies directed against the SNM1 protein immunoprecipitated RNase MRP RNA from whole-cell extracts without precipitating the structurally and functionally related RNase P RNA. We propose that the SNM1 protein is an essential and specific component of the RNase MRP ribonucleoprotein complex, the first unique protein of this complex to be identified.


Subject(s)
Endoribonucleases/metabolism , Nuclear Proteins , Ribonucleoproteins/metabolism , Saccharomyces cerevisiae Proteins , Saccharomyces cerevisiae/metabolism , Amino Acid Sequence , Base Sequence , Cell Nucleus/metabolism , Chromosome Mapping , Chromosomes, Fungal , DNA Primers , DNA-Binding Proteins/biosynthesis , DNA-Binding Proteins/metabolism , Endodeoxyribonucleases , Endoribonucleases/biosynthesis , Endoribonucleases/isolation & purification , Fungal Proteins/biosynthesis , Fungal Proteins/metabolism , Genes, Fungal , Genes, Suppressor , Immunoblotting , Leucine Zippers , Mitochondria/metabolism , Molecular Sequence Data , Mutagenesis, Site-Directed , Open Reading Frames , Point Mutation , Polymerase Chain Reaction , Restriction Mapping , Saccharomyces cerevisiae/genetics , Suppression, Genetic , Zinc Fingers
12.
Mol Cell Biol ; 13(12): 7935-41, 1993 Dec.
Article in English | MEDLINE | ID: mdl-8247008

ABSTRACT

RNase MRP is a site-specific ribonucleoprotein endoribonuclease that cleaves RNA from the mitochondrial origin of replication in a manner consistent with a role in priming leading-strand DNA synthesis. Despite the fact that the only known RNA substrate for this enzyme is complementary to mitochondrial DNA, the majority of the RNase MRP activity in a cell is found in the nucleus. The recent characterization of this activity in Saccharomyces cerevisiae and subsequent cloning of the gene coding for the RNA subunit of the yeast enzyme have enabled a genetic approach to the identification of a nuclear role for this ribonuclease. Since the gene for the RNA component of RNase MRP, NME1, is essential in yeast cells and RNase MRP in mammalian cells appears to be localized to nucleoli within the nucleus, we utilized both regulated expression and temperature-conditional mutations of NME1 to assay for a possible effect on rRNA processing. Depletion of the RNA component of the enzyme was accomplished by using the glucose-repressed GAL1 promoter. Shortly after the shift to glucose, the RNA component of the enzyme was found to be depleted severely, and rRNA processing was found to be normal at all sites except the B1 processing site. The B1 site, at the 5' end of the mature 5.8S rRNA, is actually composed of two cleavage sites 7 nucleotides apart. This cleavage normally generates two species of 5.8S rRNA at a ratio of 10:1 (small to large) in most eukaryotes. After RNase MRP depletion, yeast cells were found to have almost exclusively the larger species of 5.8S rRNA. In addition, an aberrant 309-nucleotide precursor that stretched from the A2 to E processing sites of rRNA accumulated in these cells. Temperature-conditional mutations in the RNase MRP RNA gene gave an identical phenotype. Translation in yeast cells depleted of the smaller 5.8S rRNA was found to remain robust, suggesting a possible function for two 5.8S rRNAs in the regulated translation of select messages. These results are consistent with RNase MRP playing a role in a late step of rRNA processing. The data also indicate a requirement for having the smaller form of 5.8S rRNA, and they argue for processing at the B1 position being composed of two separate cleavage events catalyzed by two different activities.


Subject(s)
Endoribonucleases/metabolism , RNA Precursors/metabolism , RNA Processing, Post-Transcriptional , RNA, Fungal/metabolism , Saccharomyces cerevisiae/metabolism , Base Sequence , DNA, Fungal/genetics , Gene Expression , Molecular Sequence Data , Mutation , Protein Biosynthesis , Saccharomyces cerevisiae/genetics , Temperature
13.
Curr Opin Genet Dev ; 3(5): 769-74, 1993 Oct.
Article in English | MEDLINE | ID: mdl-8274861

ABSTRACT

Mammalian mitochondrial DNA replication is initiated by the processing of RNA transcripts derived from an upstream promoter to create RNA primers for DNA replication. In the yeast Saccharomyces cerevisiae, mitochondrial ori/rep sequences contain a transcription promoter upstream of the site of transition from RNA to DNA synthesis, suggesting a common mode of replication initiation. Recent research has identified features in the mode and machinery of DNA replication conserved from yeast to mammals.


Subject(s)
DNA Replication , DNA, Mitochondrial/biosynthesis , Saccharomyces cerevisiae/genetics , Animals , Biological Evolution , DNA, Fungal/biosynthesis , Humans , Mammals/genetics , Saccharomyces cerevisiae/ultrastructure
14.
FASEB J ; 7(1): 208-13, 1993 Jan.
Article in English | MEDLINE | ID: mdl-7678563

ABSTRACT

RNase MRP is a ribonucleoprotein endoribonuclease that has been shown to cleave mitochondrial primer RNA sequences from a variety of sources. The bulk of RNase MRP activity is found in the nucleus where its function remains unknown. Two different approaches have resulted in predictions of distinct secondary structures for RNase MRP RNA. In order to analyze more definitively the higher-order structure of RNase MRP RNA, we have conducted a phylogenetic comparison of the available RNase MRP RNA sequences from human, mouse, rat, cow, toad, and yeast. The resulting secondary structure shares features in common with previously described structures for prokaryotic and eukaryotic RNase P RNAs (1) and RNase MRP RNAs (2, 3). In addition, the phylogenetic structure is consistent with available chemical modification data on RNase MRP RNA and with the detailed analysis of the To antigen binding domain located near the 5' end of the RNase MRP RNA. The structure is not limited to RNase MRP RNAs, but can be expanded to cover both eukaryotic RNase P RNAs and RNase P/MRP RNAs from plants.


Subject(s)
Endoribonucleases/chemistry , Mitochondria/chemistry , Nucleic Acid Conformation , Animals , Base Sequence , Binding Sites , Endoribonucleases/genetics , Humans , Molecular Sequence Data , Phylogeny , RNA, Bacterial/chemistry , RNA, Catalytic/chemistry , Ribonuclease P , Sequence Alignment , Sequence Homology, Nucleic Acid
15.
Genes Dev ; 6(10): 1975-85, 1992 Oct.
Article in English | MEDLINE | ID: mdl-1398074

ABSTRACT

RNase MRP is a site-specific ribonucleoprotein endoribonuclease that cleaves RNA sequence complementary to mammalian mitochondrial origins of replication in a manner consistent with a role in primer RNA metabolism. The same activity in the yeast Saccharomyces cerevisiae has recently been identified; it cleaves an RNA substrate complementary to a yeast mitochondrial origin of replication at an exact site of linkage of RNA to DNA. We have purified this yeast enzyme further and detect a single, novel RNA of 340 nucleotides associated with the enzymatic activity. The single-copy nuclear gene for this RNA was sequenced and mapped to the right arm of chromosome XIV. The identity of the clone, as encoding the RNA copurifying with enzymatic activity, was confirmed by a match to the directly determined sequence of the RNA. The gene sequence also identified a 340-nucleotide RNA in total yeast RNA and in purified RNase MRP enzyme preparations. Inspection of the sequence of the yeast RNA revealed homologies to the RNA component of mouse RNase MRP, 49% overall with specific regions of much greater similarity. The flanking regions of the gene showed characteristics of an RNA polymerase II transcription unit, including a TATAAA box and a 7/8 match to the yeast cell cycle box UAS. The RNase MRP RNA gene was deleted by insertional replacement and found to be essential for cellular viability, indicating a critical nuclear role for RNase MRP.


Subject(s)
Endoribonucleases/genetics , RNA, Fungal/genetics , Saccharomyces cerevisiae/enzymology , Animals , Base Sequence , Cloning, Molecular , DNA, Fungal , Endoribonucleases/metabolism , Genes, Fungal , Mammals , Mitochondria/metabolism , Molecular Sequence Data , Oligonucleotides/metabolism , Plasmids , RNA Polymerase II/metabolism , RNA Processing, Post-Transcriptional , RNA, Fungal/metabolism , Saccharomyces cerevisiae/genetics , Sequence Homology, Amino Acid
16.
J Biol Chem ; 266(23): 14958-63, 1991 Aug 15.
Article in English | MEDLINE | ID: mdl-1651316

ABSTRACT

Disruption of the gene for subunit 6 of the yeast cytochrome bc1 complex (QCR6) causes a temperature-sensitive petite phenotype in contrast to deletion of the coding region of QCR6, which shows no growth defect. Mitochondria from the petite strain carrying the disruption allele were devoid of ubiquinol-cytochrome c oxidoreductase activity but retained cytochrome c oxidase and oligomycin-sensitive ATPase activities. Optical spectra of cytochromes in mitochondrial membranes from the petite strain lacked a cytochrome b absorption band and had a reduced amount of cytochrome c1. Analysis of mitochondrial translation products showed normal synthesis of cytochrome b. Western analysis of mitochondrial membranes from this disruption strain indicates core protein 1 of the cytochrome bc1 complex is present in normal amounts, while cytochrome c1, the Rieske iron-sulfur protein, subunit 6, and subunit 7 were absent or present in very low amounts. Taken together, these findings indicate a loss of assembly of the cytochrome bc1 complex. High copy suppressors of the disruption strain were selected. Two separate families of suppressors were found. The first contained QCR6. The second family consisted of overlapping clones of a second gene distinct from QCR6. These plasmids contained QCR9, the gene which codes for subunit 9 of the yeast cytochrome bc1 complex. Suppression of the QCR6 disruption strain by overexpression of QCR9 indicates a critical interaction between these two proteins in the assembly of the cytochrome bc1 complex.


Subject(s)
Electron Transport Complex III/metabolism , Mutation , Alleles , Blotting, Western , Electron Transport Complex III/genetics , Escherichia coli/genetics , Genes, Bacterial , Mitochondria/enzymology , Phenotype , Plasmids , Restriction Mapping , Saccharomyces cerevisiae/enzymology , Spectrum Analysis , Suppression, Genetic , Temperature
17.
J Biol Chem ; 265(34): 20813-21, 1990 Dec 05.
Article in English | MEDLINE | ID: mdl-2174427

ABSTRACT

A nuclear gene (QCR9) encoding the 7.3-kDa subunit 9 of the mitochondrial cytochrome bc1 complex from Saccharomyces cerevisiae has been isolated from a yeast genomic library by hybridization with a degenerate oligonucleotide corresponding to nine amino acids proximal to the N terminus of purified subunit 9. QCR9 includes a 195-base pair open reading frame capable of encoding a protein of 66 amino acids and having a predicted molecular weight of 7471. The N-terminal methionine of subunit 9 is removed posttranslationally because the N-terminal sequence of the purified protein begins with serine 2. The ATG triplet corresponding to the N-terminal methionine is separated from the open reading frame by an intron. The intron is 213 base pairs long and contains previously reported 5' donor, 3' acceptor, and TACTAAC sequences necessary for splicing. The splice junctions, as well as the 5' end of the message, were confirmed by isolation and sequencing of a cDNA copy of QCR9. In addition, the intron contains a nucleotide sequence in which 15 out of 18 nucleotides are identical with a sequence in the intron of COX4, the nuclear gene encoding cytochrome c oxidase subunit 4. The deduced amino acid sequence of the yeast subunit 9 is 39% identical with that of a protein of similar molecular weight from beef heart cytochrome bc1 complex. If conservative substitutions are allowed for, the two proteins are 56% similar. The predicted secondary structure of the 7.3-kDa protein revealed a single possible transmembrane helix, in which the amino acids conserved between beef heart and yeast are asymmetrically arranged along one face of the helix, implying that this domain of the protein is involved in a conserved interaction with another hydrophobic protein of the cytochrome bc1 complex. Two yeast strains, JDP1 and JDP2, were constructed in which QCR9 was deleted. Both strains grew very poorly, or not at all, on nonfermentable carbon sources and exhibited, at most, only 5% of wild-type ubiquinol-cytochrome c oxidoreductase activity. Optical spectra of mitochondrial membranes from the deletion strains revealed slightly reduced levels of cytochrome b. When JDP1 and JDP2 were complemented with a plasmid carrying QCR9, the resulting yeast grew normally on ethanol/glycerol and exhibited normal cytochrome c reductase activities and optical spectra. These results indicate that QCR9 encodes a 7.3-kDa subunit of the bc1 complex that is required for formation of a fully functional complex.(ABSTRACT TRUNCATED AT 400 WORDS)


Subject(s)
Cell Nucleus/metabolism , Electron Transport Complex III/genetics , Electron Transport Complex IV/genetics , Genes, Fungal , Introns , Saccharomyces cerevisiae/genetics , Amino Acid Sequence , Base Sequence , Chromosome Deletion , Cloning, Molecular , Genomic Library , Macromolecular Substances , Models, Molecular , Molecular Sequence Data , Protein Conformation , Restriction Mapping , Saccharomyces cerevisiae/enzymology , Saccharomyces cerevisiae/growth & development
18.
J Biol Chem ; 265(28): 17005-11, 1990 Oct 05.
Article in English | MEDLINE | ID: mdl-2170363

ABSTRACT

We have characterized the activities of the cytochrome bc1 complex in mitochondrial membranes from a yeast strain in which we deleted the nuclear gene (QCR6, COR3) which codes for the highly acidic subunit 6 of the bc1 complex. The chromosomal copy of QCR6 was replaced with a plasmid derived copy of QCR6, in which the entire coding region of QCR6 was replaced with the yeast LEU2 gene. The resulting deletion strain, MES8, contained no detectable mRNA for QCR6, and the cytochrome bc1 complex purified from the deletion strain lacked subunit 6. The deletion strain respired and grew on nonfermentable carbon sources such as ethanol and glycerol. Ubiquinol-cytochrome c reductase activity of mitochondria from the deletion strain was decreased 50% under conditions where the activity is zero order with respect to cytochrome c, and there was a similar decrease in the first-order rate constant for cytochrome c reduction. The loss of bc1 complex activities, observed at physiological ionic strengths, was reversible. Both the zero order rate and the first-order rate constant for cytochrome c reduction could be recovered to those of the parental strain by measuring these activities in mitochondrial membranes under conditions of low ionic strength. The zero order rate and first-order rate constant for cytochrome c reduction in membranes from the parent, wild-type yeast showed essentially no change coincident with this change in ionic strength. The 50% drop in both turnover number and first-order rate constant of ubiquinol-cytochrome c reductase activity indicates that half of the cytochrome bc1 complexes are inactive in the deletion strain at physiological ionic strengths. Inhibition by myxothiazol of cytochrome c reductase activity of mitochondrial membranes from the deletion strain showed an ionic strength-dependent lag in the titration curve that extended to the point where half of the inhibitor sites are filled. This lag was not observed with membranes from the wild-type, parent strain. This response to the inhibitor is consistent with half of the cytochrome bc1 complexes being inactive in mitochondria from the deletion strain at physiological ionic strength, but with both active and inactive complexes still able to bind inhibitor. The reversible, half-of-the-sites reactivity indicates that the bc1 complex must be dimeric in situ, in agreement with previous findings that the complexes isolated from fungal (Leonard, K., Wingfield, P., Arad, T., and Weiss, H. (1981) J. Mol. Biol. 149, 259-274) and mammalian (Nalecz, M. J., Bolli, R., and Azzi, A. (1985) Arch. Biochem. Biophys. 236, 619-628) mitochondria are structural dimers.(ABSTRACT TRUNCATED AT 400 WORDS)


Subject(s)
Electron Transport Complex III/metabolism , Saccharomyces cerevisiae/enzymology , Chromosome Deletion , Cytochrome c Group/metabolism , Electron Transport Complex III/genetics , Genes, Fungal , Intracellular Membranes/enzymology , Kinetics , Macromolecular Substances , Models, Structural , Molecular Weight , Plasmids , RNA, Fungal/genetics , RNA, Fungal/isolation & purification , Restriction Mapping , Saccharomyces cerevisiae/growth & development , Submitochondrial Particles/enzymology
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