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2.
Genetics ; 157(3): 1141-58, 2001 Mar.
Article in English | MEDLINE | ID: mdl-11238400

ABSTRACT

The SUF13 and SUF14 genes were identified among extragenic suppressors of +1 frameshift mutations. SUF13 is synonymous with MBF1, a single-copy nonessential gene coding for a POLII transcription factor. The suf13-1 mutation is a two-nucleotide deletion in the SUF13/MBF1 coding region. A suf13::TRP1 null mutant suppresses +1 frameshift mutations, indicating that suppression is caused by loss of SUF13 function. The suf13-1 suppressor alters sensitivity to aminoglycoside antibiotics and reduces the accumulation of his4-713 mRNA, suggesting that suppression is mediated at the translational level. The SUF14 gene is synonymous with RPS3, a single-copy essential gene that codes for the ribosomal protein S3. The suf14-1 mutation is a missense substitution in the coding region. Increased expression of S3 limits the accumulation of SUF14 mRNA, suggesting that expression is autoregulated. A frameshift mutation in SUF14 that prevents full-length translation eliminated regulation, indicating that S3 is required for regulation. Using CUP1-SUF14 and SUF14-lacZ fusions, run-on transcription assays, and estimates of mRNA half-life, our results show that transcription plays a minor role if any in regulation and that the 5'-UTR is necessary but not sufficient for regulation. A change in mRNA decay rate may be the primary mechanism for regulation.


Subject(s)
Frameshift Mutation , Genes, Fungal , Ribosomal Proteins/biosynthesis , Ribosomal Proteins/genetics , Saccharomyces cerevisiae Proteins , Suppression, Genetic , Trans-Activators/genetics , 5' Untranslated Regions , Alleles , Copper/pharmacology , Databases, Factual , Dose-Response Relationship, Drug , Gene Dosage , Models, Genetic , Mutation , Phenotype , Plasmids/genetics , Plasmids/metabolism , Promoter Regions, Genetic , RNA, Messenger/metabolism , Time Factors , Transcription Factors , Transcription, Genetic , Transformation, Genetic
3.
Mol Cell Biol ; 19(10): 6710-9, 1999 Oct.
Article in English | MEDLINE | ID: mdl-10490610

ABSTRACT

mRNAs are monitored for errors in gene expression by RNA surveillance, in which mRNAs that cannot be fully translated are degraded by the nonsense-mediated mRNA decay pathway (NMD). RNA surveillance ensures that potentially deleterious truncated proteins are seldom made. NMD pathways that promote surveillance have been found in a wide range of eukaryotes. In Saccharomyces cerevisiae, the proteins encoded by the UPF1, UPF2, and UPF3 genes catalyze steps in NMD and are required for RNA surveillance. In this report, we show that the Upf proteins are also required to control the total accumulation of a large number of mRNAs in addition to their role in RNA surveillance. High-density oligonucleotide arrays were used to monitor global changes in the yeast transcriptome caused by loss of UPF gene function. Null mutations in the UPF genes caused altered accumulation of hundreds of mRNAs. The majority were increased in abundance, but some were decreased. The same mRNAs were affected regardless of which of the three UPF gene was inactivated. The proteins encoded by UPF-dependent mRNAs were broadly distributed by function but were underrepresented in two MIPS (Munich Information Center for Protein Sequences) categories: protein synthesis and protein destination. In a UPF(+) strain, the average level of expression of UPF-dependent mRNAs was threefold lower than the average level of expression of all mRNAs in the transcriptome, suggesting that highly abundant mRNAs were underrepresented. We suggest a model for how the abundance of hundreds of mRNAs might be controlled by the Upf proteins.


Subject(s)
Fungal Proteins/metabolism , Gene Expression Regulation, Fungal , RNA Helicases/metabolism , RNA, Messenger/biosynthesis , RNA-Binding Proteins , Saccharomyces cerevisiae Proteins , Saccharomyces cerevisiae/genetics , Trans-Activators/metabolism , Adaptor Proteins, Signal Transducing , Gene Expression Profiling , Oligonucleotide Array Sequence Analysis , RNA Processing, Post-Transcriptional , RNA Stability , RNA, Messenger/classification , Transcription, Genetic
4.
Trends Genet ; 15(2): 74-80, 1999 Feb.
Article in English | MEDLINE | ID: mdl-10098411

ABSTRACT

Messenger RNAs are monitored for errors that arise during gene expression by a mechanism called RNA surveillance, with the result that most mRNAs that cannot be translated along their full length are rapidly degraded. This ensures that truncated proteins are seldom made, reducing the accumulation of rogue proteins that might be deleterious. The pathway leading to accelerated mRNA decay is referred to as nonsense-mediated mRNA decay (NMD). The proteins that catalyze steps in NMD in yeast serve two roles, one to monitor errors in gene expression and the other to control the abundance of endogenous wild-type mRNAs as part of the normal repertoire of gene expression. The NMD pathway has a direct impact on hundreds of genetic disorders in the human population, where about a quarter of all known mutations are predicted to trigger NMD.


Subject(s)
Gene Expression Regulation/physiology , Genetic Diseases, Inborn/genetics , Neoplasms/genetics , Peptide Chain Termination, Translational/physiology , RNA Processing, Post-Transcriptional , RNA, Messenger/metabolism , RNA-Binding Proteins , Saccharomyces cerevisiae Proteins , Animals , Base Sequence , Codon , Fungal Proteins/physiology , Helminth Proteins/physiology , Humans , Mice , Molecular Sequence Data , Mutation, Missense , Nucleic Acid Conformation , Peptide Termination Factors/physiology , RNA Helicases/physiology , RNA, Fungal/genetics , RNA, Fungal/metabolism , RNA, Messenger/genetics , Saccharomyces cerevisiae/genetics , Trans-Activators
5.
Genetics ; 150(3): 1019-35, 1998 Nov.
Article in English | MEDLINE | ID: mdl-9799255

ABSTRACT

The CTF13 gene codes for a subunit of the kinetochore in Saccharomyces cerevisiae. The temperature-sensitive mutation ctf13-30, which confers reduced fidelity of chromosome transmission, is a G --> A transition causing an amino acid substitution of Lys for Glu146. Strains carrying one chromosomal copy of ctf13-30 fail to grow at the restrictive temperature, whereas a haploid strain carrying two copies of ctf13-30 can grow. Four genes, UPF1, UPF2, UPF3, and ICK1, were represented among extragenic suppressors of ctf13-30. The UPF genes encode proteins that promote rapid decay of pre-mRNAs and mRNAs containing a premature stop codon. Suppressor mutations in these genes restore kinetochore function by causing increased accumulation of ctf13-30 mRNA. They also cause increased accumulation of CYH2 pre-mRNA, which is a natural target of UPF-mediated decay. Mutations in ICK1 restore kinetochore function but have no effect on ctf13-30 mRNA or CYH2 pre-mRNA accumulation. Most importantly, loss of UPF1 function causes increased accumulation of wild-type CTF13 mRNA but has no effect on the mRNA half-life. We propose that UPF-mediated decay modulates the mRNA level of one or more factors involved in CTF13 mRNA expression.


Subject(s)
Fungal Proteins/genetics , Gene Expression Regulation, Fungal , Genes, Fungal , Nuclear Proteins/genetics , RNA, Messenger/genetics , Saccharomyces cerevisiae Proteins , Saccharomyces cerevisiae/genetics , Kinetochores , RNA, Messenger/biosynthesis
6.
Mol Cell Biol ; 18(12): 6885-96, 1998 Dec.
Article in English | MEDLINE | ID: mdl-9819377

ABSTRACT

Sen1p from Saccharomyces cerevisiae is a nucleic acid helicase related to DEAD box RNA helicases and type I DNA helicases. The temperature-sensitive sen1-1 mutation located in the helicase motif alters the accumulation of pre-tRNAs, pre-rRNAs, and some small nuclear RNAs. In this report, we show that cells carrying sen1-1 exhibit altered accumulation of several small nucleolar RNAs (snoRNAs) immediately upon temperature shift. Using Northern blotting, RNase H cleavage, primer extension, and base compositional analysis, we detected three forms of the snoRNA snR13 in wild-type cells: an abundant TMG-capped 124-nucleotide (nt) mature form (snR13F) and two less abundant RNAs, including a heterogeneous population of approximately 1,400-nt 3'-extended forms (snR13R) and a 108-nt 5'-truncated form (snR13T) that is missing 16 nt at the 5' end. A subpopulation of snR13R contains the same 5' truncation. Newly synthesized snR13R RNA accumulates with time at the expense of snR13F following temperature shift of sen1-1 cells, suggesting a possible precursor-product relationship. snR13R and snR13T both increase in abundance at the restrictive temperature, indicating that Sen1p stabilizes the 5' end and promotes maturation of the 3' end. snR13F contains canonical C and D boxes common to many snoRNAs. The 5' end of snR13T and the 3' end of snR13F reside within C2U4 sequences that immediately flank the C and D boxes. A mutation in the 5' C2U4 repeat causes underaccumulation of snR13F, whereas mutations in the 3' C2U4 repeat cause the accumulation of two novel RNAs that migrate in the 500-nt range. At the restrictive temperature, double mutants carrying sen1-1 and mutations in the 3' C2U4 repeat show reduced accumulation of the novel RNAs and increased accumulation of snR13R RNA, indicating that Sen1p and the 3' C2U4 sequence act in a common pathway to facilitate 3' end formation. Based on these findings, we propose that Sen1p and the C2U4 repeats that flank the C and D boxes promote maturation of the 3' terminus and stability of the 5' terminus and are required for maximal rates of synthesis and levels of accumulation of mature snR13F.


Subject(s)
Fungal Proteins/genetics , RNA, Small Nuclear/biosynthesis , Saccharomyces cerevisiae/enzymology , Base Sequence , Chromosomes/genetics , DNA Helicases , Guanosine/analogs & derivatives , Molecular Sequence Data , Mutation/genetics , Nucleic Acid Conformation , RNA Caps/genetics , RNA Helicases , RNA Processing, Post-Transcriptional/genetics , RNA, Fungal/genetics , RNA, Small Nuclear/genetics , Ribonuclease H/genetics , Ribonucleoproteins, Small Nuclear/genetics , Saccharomyces cerevisiae Proteins
7.
J Cell Sci ; 111 ( Pt 21): 3129-43, 1998 Nov.
Article in English | MEDLINE | ID: mdl-9763508

ABSTRACT

In Saccharomyces cerevisiae, Upf3p is required for nonsense-mediated mRNA decay (NMD). Although localized primarily in the cytoplasm, Upf3p contains three sequence elements that resemble nuclear localization signals (NLSs) and two sequence elements that resemble nuclear export signals (NESs). We found that a cytoplasmic reporter protein localized to the nucleus when fused to any one of the three NLS-like sequences of Upf3p. A nuclear reporter protein localized to the cytoplasm when fused to one of the NES-like sequences (NES-A). We present evidence that NES-A functions to signal the export of Upf3p from the nucleus. Combined alanine substitutions in the NES-A element caused a re-distribution of Upf3p to a subnuclear location identified as the nucleolus and conferred an Nmd- phenotype. Single mutations in NES-A failed to affect the distribution of Upf3p and were Nmd+. When an NES element from HIV-1 Rev was inserted near the C terminus of a mutant Upf3p containing multiple mutations in NES-A, the cytoplasmic distribution typical of wild-type Upf3p was restored but the cells remained phenotypically Nmd-. These results suggest that NES-A is a functional nuclear export signal. Combined mutations in NES-A may cause multiple defects in protein function leading to an Nmd- phenotype even when export is restored.


Subject(s)
Cell Nucleus/metabolism , Cytoplasm/metabolism , Fungal Proteins/metabolism , Protein Sorting Signals/physiology , RNA Processing, Post-Transcriptional , RNA, Fungal/metabolism , RNA, Messenger/metabolism , RNA-Binding Proteins , Saccharomyces cerevisiae Proteins , Saccharomyces cerevisiae/metabolism , Amino Acid Substitution , Biological Transport , Fungal Proteins/genetics , Gene Dosage , Genes, Reporter , Genes, rev , HIV-1/genetics , Point Mutation , Protein Sorting Signals/genetics , Recombinant Fusion Proteins/metabolism , Regulatory Sequences, Nucleic Acid , Saccharomyces cerevisiae/cytology , Saccharomyces cerevisiae/genetics
8.
J Biol Chem ; 272(35): 22163-72, 1997 Aug 29.
Article in English | MEDLINE | ID: mdl-9268361

ABSTRACT

In yeast, the accelerated rate of decay of nonsense mutant mRNAs, called nonsense-mediated mRNA decay, requires three proteins, Upf1p, Upf2p, and Upf3p. Single, double, and triple disruptions of the UPF genes had nearly identical effects on nonsense mRNA accumulation, suggesting that the encoded proteins function in a common pathway. We examined the distribution of epitope-tagged versions of Upf proteins by sucrose density gradient fractionation of soluble lysates and found that all three proteins co-distributed with 80 S ribosomal particles and polyribosomes. Treatment of lysates with RNase A caused a coincident collapse of polyribosomes and each Upf protein into fractions containing 80 S ribosomal particles, as expected for proteins that are associated with polyribosomes. Mutations in the cysteine-rich (zinc finger) and RNA helicase domains of Upf1p caused loss of function, but the mutant proteins remained polyribosome-associated. Density gradient profiles for Upf1p were unchanged in the absence of Upf3p, and although similar, were modestly shifted to fractions lighter than those containing polyribosomes in the absence of Upf2p. Upf2p shifted toward heavier polyribosome fractions in the absence of Upf1p and into fractions containing 80 S particles and lighter fractions in the absence of Upf3p. Our results suggest that the association of Upf2p with polyribosomes typically found in a wild-type strain depends on the presence and opposing effects of Upf1p and Upf3p.


Subject(s)
Codon, Nonsense/metabolism , Fungal Proteins/metabolism , Polyribosomes/metabolism , RNA Helicases , RNA, Messenger/metabolism , RNA-Binding Proteins , Saccharomyces cerevisiae Proteins , Saccharomyces cerevisiae/genetics , Trans-Activators/metabolism , Adaptor Proteins, Signal Transducing , Cysteine/metabolism , Fungal Proteins/genetics , Mutagenesis, Site-Directed , Solubility , Trans-Activators/genetics
9.
Nucleic Acids Res ; 25(23): 4778-85, 1997 Dec 01.
Article in English | MEDLINE | ID: mdl-9365256

ABSTRACT

A single base change in the helicase superfamily 1 domain of the yeast Saccharomyces cerevisiae SEN1 gene results in a heat-sensitive mutation that alters the cellular abundance of many RNA species. We compared the relative amounts of RNAs between cells that are wild-type and mutant after temperature-shift. In the mutant several RNAs were found to either decrease or increase in abundance. The affected RNAs include tRNAs, rRNAs and small nuclear and nucleolar RNAs. Many of the affected RNAs have been positively identified and include end-matured precursor tRNAs and the small nuclear and nucleolar RNAs U5 and snR40 and snR45. Several small nucleolar RNAs co-immunoprecipitate with Sen1 but differentially associate with the wild-type and mutant protein. Its inactivation also impairs precursor rRNA maturation, resulting in increased accumulation of 35S and 6S precursor rRNAs and reduced levels of 20S, 23S and 27S rRNA processing intermediates. Thus, Sen1 is required for the biosynthesis of various functionally distinct classes of nuclear RNAs. We propose that Sen1 is an RNA helicase acting on a wide range of RNA classes. Its effects on the targeted RNAs in turn enable ribonuclease activity.


Subject(s)
Fungal Proteins/genetics , RNA Processing, Post-Transcriptional , RNA, Fungal/metabolism , RNA, Small Nuclear/metabolism , Saccharomyces cerevisiae/genetics , Antibodies/immunology , DNA Helicases , Fungal Proteins/immunology , Fungal Proteins/metabolism , Mutagenesis , RNA Helicases , RNA Precursors/metabolism , RNA Splicing , RNA, Messenger/metabolism , RNA, Ribosomal/metabolism , Saccharomyces cerevisiae Proteins
10.
Gene ; 182(1-2): 89-96, 1996 Dec 05.
Article in English | MEDLINE | ID: mdl-8982072

ABSTRACT

Immuno-detection by 'Midwestern' blotting provides a simple way to identify trimethylguanosine (TMG) capped RNAs. With this technique, over 20 bands are observed when total cellular RNA from Saccharomyces cerevisiae is transferred to a nylon membrane and probed with anti-TMG antibodies. Most, if not all, species known to contain a TMG cap are detected by this method. Only TMG-capped RNAs are detected on Midwestern blots unlike anti-TMG immunoprecipitates. Midwestern blotting is a useful alternative to immunoprecipitation and Northern analysis and may prove to be a better method for determining the relative abundance of capped RNAs. The blots can be reprobed multiple times with labeled antisense oligonucleotides to determine the identity of any TMG-capped species for which the primary sequence or a clone is available. This dual detection capability provides a powerful tool for the analysis of TMG-capped snRNAs and snoRNAs.


Subject(s)
Guanosine/analogs & derivatives , RNA Caps/analysis , Saccharomyces cerevisiae/chemistry , Antibodies/immunology , Antibodies/metabolism , Blotting, Northern , DNA Probes/chemistry , DNA Probes/genetics , DNA, Antisense/genetics , Electrophoresis, Polyacrylamide Gel , Immunoblotting , RNA, Fungal/analysis , RNA, Small Nuclear/analysis
11.
Mol Gen Genet ; 249(6): 571-84, 1995 Dec 20.
Article in English | MEDLINE | ID: mdl-8544822

ABSTRACT

A mutation in the Saccharomyces cerevisiae SEN1 gene causes accumulation of end-matured, intron-containing pre-tRNAs. Cells containing the thermosensitive sen1-1 mutation exhibit reduced tRNA splicing endonuclease activity. However, Sen1p is not the catalytic subunit of this enzyme. We have used Sen1p-specific antibodies for cell fractionation studies and immunofluorescent microscopy and determined that Sen1p is a low abundance protein of about 239 kDa. It localizes to the nucleus with a granular distribution. We verified that a region in SEN1 containing a putative nuclear localization signal sequence (NLS) is necessary for nuclear targeting. Furthermore, we found that inactivation of Sen1p by temperature shift of a strain carrying sen1-1 leads to mislocalization of two nucleolar proteins, Nop1 and Ssb1. Possible mechanisms are discussed for several related nuclear functions of Sen1p, including tRNA splicing and the maintenance of a normal crescent-shaped nucleolus.


Subject(s)
Cell Compartmentation , Cell Nucleolus/metabolism , Fungal Proteins/metabolism , Ribonucleoproteins, Small Nucleolar , Saccharomyces cerevisiae Proteins , Saccharomyces cerevisiae/metabolism , Amino Acid Sequence , Biological Transport , Cell Nucleus/metabolism , DNA Helicases , Fluorescent Antibody Technique, Indirect , Fungal Proteins/genetics , Genes, Fungal , HSP70 Heat-Shock Proteins , Molecular Sequence Data , Mutation , Nuclear Proteins/metabolism , RNA Helicases , RNA Ligase (ATP)/deficiency , RNA Precursors/metabolism , RNA Splicing , RNA, Transfer/metabolism , Saccharomyces cerevisiae/genetics , Sequence Deletion , Structure-Activity Relationship
12.
Mol Cell Biol ; 15(11): 6311-21, 1995 Nov.
Article in English | MEDLINE | ID: mdl-7565784

ABSTRACT

The yeast Sen1 protein was discovered by virtue of its role in tRNA splicing in vitro. To help determine the role of Sen1 in vivo, we attempted to overexpress the protein in yeast cells. However, cells with a high-copy SEN1-bearing plasmid, although expressing elevated amounts of SEN1 mRNA, show little increase in the level of the encoded protein, indicating that a posttranscriptional mechanism limits SEN1 expression. This control depends on an amino-terminal element of Sen1. Using a genetic selection for mutants with increased expression of Sen1-derived fusion proteins, we identified mutations in a novel gene, designated SEN3. SEN3 is essential and encodes a 945-residue protein with sequence similarity to a subunit of an activator of the 20S proteasome from bovine erythrocytes, called PA700. Earlier work indicated that the 20S proteasome associates with a multisubunit regulatory factor, resulting in a 26S proteasome complex that degrades substrates of the ubiquitin system. Mutant sen3-1 cells have severe defects in the degradation of such substrates and accumulate ubiquitin-protein conjugates. Most importantly, we show biochemically that Sen3 is a subunit of the 26S proteasome. These data provide evidence for the involvement of the 26S proteasome in the degradation of ubiquitinated proteins in vivo and for a close relationship between PA700 and the regulatory complexes within the 26S proteasome, and they directly demonstrate that Sen3 is a component of the yeast 26S proteasome.


Subject(s)
Cysteine Endopeptidases/chemistry , Fungal Proteins/metabolism , Genes, Fungal , Multienzyme Complexes/chemistry , Saccharomyces cerevisiae Proteins , Saccharomyces cerevisiae/enzymology , Amino Acid Sequence , DNA Helicases , Fungal Proteins/genetics , Genetic Complementation Test , Molecular Sequence Data , Proteasome Endopeptidase Complex , Proteins/metabolism , RNA Helicases , Saccharomyces cerevisiae/genetics , Ubiquitins/metabolism
13.
Proc Natl Acad Sci U S A ; 92(22): 10354-8, 1995 Oct 24.
Article in English | MEDLINE | ID: mdl-7479783

ABSTRACT

Loss of function of any one of three UPF genes prevents the accelerated decay of nonsense mRNAs in Saccharomyces cerevisiae. We report the identification and DNA sequence of UPF3, which is present in one nonessential copy on chromosome VII. Upf3 contains three putative nuclear localization signal sequences, suggesting that it may be located in a different compartment than the cytoplasmic Upf1 protein. Epitope-tagged Upf3 (FLAG-Upf3) does not cofractionate with polyribosomes or 80S ribosomal particles. Double disruptions of UPF1 and UPF3 affect nonsense mRNA decay in a manner indistinguishable from single disruptions. These results suggest that the Upf proteins perform related functions in a common pathway.


Subject(s)
Fungal Proteins/genetics , Genes, Fungal , RNA, Messenger/metabolism , RNA-Binding Proteins , Saccharomyces cerevisiae Proteins , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Amino Acid Sequence , Base Sequence , Chromosome Mapping , Chromosomes, Fungal , Fungal Proteins/biosynthesis , Kinetics , Molecular Sequence Data , Plasmids , RNA, Fungal/metabolism , Recombinant Fusion Proteins/biosynthesis , Species Specificity , Transcription, Genetic
14.
J Biol Chem ; 270(21): 12717-24, 1995 May 26.
Article in English | MEDLINE | ID: mdl-7759525

ABSTRACT

Casein kinase I, one of the first protein kinases identified biochemically, is known to exist in multiple isoforms in mammals. Using a partial cDNA fragment corresponding to an isoform termed CK1 gamma, three full-length rat testis cDNAs were cloned that defined three separate members of this subfamily. The isoforms, designated CK1 gamma 1, CK1 gamma 2, and CK1 gamma 3, have predicted molecular masses of 43,000, 45,500, and 49,700. CK1 gamma 3 may also exist in an alternatively spliced form. The proteins are more than 90% identical to each other within the protein kinase domain but only 51-59% identical to other casein kinase I isoforms within this region. Messages for CK1 gamma 1 (2 kilobases (kb)), CK1 gamma 2 (1.5 and 2.4 kb), and CK1 gamma 3 (2.8 kb) were detected by Northern hybridization of testis RNA. Message for CK1 gamma 3 was also observed in brain, heart, kidney, lung, liver, and muscle whereas CK1 gamma 1 and CK1 gamma 2 messages were restricted to testis. All three CK1 gamma isoforms were expressed as active enzymes in Escherichia coli and partially purified. The enzymes phosphorylated typical in vitro casein kinase I substrates such as casein, phosvitin, and a synthetic peptide, D4. Phosphorylation of the D4 peptide was activated by heparin whereas phosphorylation of the protein substrates was inhibited. The known casein kinase I inhibitor CK1-7 also inhibited the CK1 gamma s although less effectively than the CK1 alpha or CK1 delta isoforms. All three CK1 gamma s underwent autophosphorylation when incubated with ATP and Mg2+. The YCK1 and YCK2 genes in Saccharomyces cerevisiae encode casein kinase I homologs, defects in which lead to aberrant morphology and growth arrest. Expression of mammalian CK1 gamma 1 or CK1 gamma 3 restored growth and normal morphology to a yeast mutant carrying a disruption of YCK1 and a temperature-sensitive allele of YCK2, suggesting overlap of function between the yeast Yck proteins and these CK1 isoforms.


Subject(s)
Casein Kinase I , Isoenzymes/genetics , Multigene Family/genetics , Protein Kinases/genetics , Saccharomyces cerevisiae Proteins , Amino Acid Sequence , Animals , Base Sequence , Casein Kinases , Cloning, Molecular , Genes, Fungal/genetics , Genetic Complementation Test , Heparin/pharmacology , Isoenzymes/classification , Male , Molecular Sequence Data , Phosphorylation , Protein Kinases/classification , Protein Kinases/drug effects , RNA, Messenger/analysis , Rats , Restriction Mapping , Saccharomyces cerevisiae/enzymology , Saccharomyces cerevisiae/genetics , Sequence Homology, Amino Acid , Testis/enzymology , Tissue Distribution
15.
Mol Biol Cell ; 6(5): 611-25, 1995 May.
Article in English | MEDLINE | ID: mdl-7545033

ABSTRACT

In Saccharomyces cerevisiae the UPF1 protein is required for nonsense-mediated mRNA decay, the accelerated turnover of mRNAs containing a nonsense mutation. Several lines of evidence suggest that translation plays an important role in the mechanism of nonsense mRNA decay, including a previous report that nonsense mRNAs assemble in polyribosomes. In this study we show that UPF1 and ribosomal protein L1 co-localize in the cytoplasm and that UPF1 co-sediments with polyribosomes. To detect UPF1, three copies of the influenza hemagglutinin epitope were placed at the C-terminus. The tagged protein, UPF1-3EP, retains 86% (+/- 5%) of function. Using immunological detection, we found that UPF1-3EP is primarily cytoplasmic and was not detected either in the nucleus or in the mitochondrion. UPF1-3EP and L1 co-distributed with polyribosomes fractionated in a 7-47% sucrose gradient. The sucrose sedimentation profiles for UPF1-3EP and L1 exhibited similar changes using three different sets of conditions that altered the polyribosome profile. When polyribosomes were disaggregated, UPF1-3EP and L1 accumulated in fractions coincident with 80S ribosomal particles. These results suggest that UPF1-3EP associates with polyribosomes. L3 and S3 mRNAs, which code for ribosomal proteins of the 60S and 40S ribosomal subunits, respectively, were on average about 100-fold more abundant than UPF1 mRNA. Assuming that translation rates for L3, S3, and UPF1 mRNA are similar, this result suggests that there are far fewer UPF1 molecules than ribosomes per cell. Constraints imposed by the low UPF1 abundance on the functional relationships between UPF1, polyribosomes, and nonsense mRNA turnover are discussed.


Subject(s)
Fungal Proteins/analysis , Polyribosomes/chemistry , RNA Helicases , RNA, Fungal/metabolism , RNA, Messenger/metabolism , Saccharomyces cerevisiae/metabolism , Base Sequence , Cell Fractionation , Cytoplasm/chemistry , Epitopes/analysis , Fungal Proteins/genetics , Genetic Complementation Test , Hemagglutinins, Viral/genetics , Hemagglutinins, Viral/immunology , Molecular Sequence Data , Recombinant Fusion Proteins/analysis , Recombinant Fusion Proteins/biosynthesis , Ribosomal Proteins/analysis , Ribosomal Proteins/genetics , Ribosomes/chemistry , Saccharomyces cerevisiae Proteins
16.
Mol Biol Cell ; 5(10): 1065-80, 1994 Oct.
Article in English | MEDLINE | ID: mdl-7865875

ABSTRACT

Previously, we showed that the yeast Saccharomyces cerevisiae cold-sensitive mutation tcp1-1 confers growth arrest concomitant with cytoskeletal disorganization and disruption of microtubule-mediated processes. We have identified two new recessive mutations, tcp1-2 and tcp1-3, that confer heat- and cold-sensitive growth. Cells carrying tcp1 alleles were analyzed after exposure to the appropriate restrictive temperatures by cell viability tests, differential contrast microscopy, fluorescent, and immunofluorescent microscopy of DNA, tubulin, and actin and by determining the DNA content per cell. All three mutations conferred unique phenotypes indicative of cytoskeletal dysfunction. A causal relationship between loss of Tcp1p function and the development of cytoskeletal abnormalities was established by double mutant analyses. Novel phenotypes indicative of allele-specific genetic interactions were observed when tcp1-1 was combined in the same strain with tub1-1, tub2-402, act1-1, and act1-4, but not with other tubulin or actin mutations or with mutations in other genes affecting the cytoskeleton. Also, overproduction of wild-type Tcp1p partially suppressed growth defects conferred by act1-1 and act1-4. Furthermore, Tcp1p was localized to the cytoplasm and the cell cortex. Based on our results, we propose that Tcp1p is required for normal development and function of actin and microtubules either through direct or indirect interaction with the major cytoskeletal components.


Subject(s)
Actins/metabolism , Chaperonins , Fungal Proteins/metabolism , Microtubules/metabolism , Molecular Chaperones/metabolism , Alleles , Amino Acid Sequence , Animals , Cell Cycle/genetics , Cell Nucleus/metabolism , Chaperonin Containing TCP-1 , Cytoplasm/metabolism , Fungal Proteins/genetics , Genes, Fungal , Genes, Recessive , Mice , Molecular Chaperones/genetics , Molecular Sequence Data , Mutation , Phenotype , Saccharomyces cerevisiae/cytology , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Sequence Homology, Amino Acid , Temperature , Tubulin/genetics , Tubulin/metabolism
17.
Mol Gen Genet ; 244(3): 303-11, 1994 Aug 02.
Article in English | MEDLINE | ID: mdl-8058041

ABSTRACT

The COT1 and ZRC1 genes of Saccharomyces cerevisiae are structurally related dosage-dependent suppressors of metal toxicity. COT1 confers increased tolerance to high levels of cobalt; ZRC1 confers increased tolerance to high levels of zinc. The two genes are not linked and have been mapped; COT1 to chromosome XV and ZRC1 to chromosome XIII. Phenotypes related to metal homeostasis have been examined in strains with varied COT1 and ZRC1 gene doses. Overexpression of COT1 confers tolerance to moderately toxic levels of zinc and ZRC1 confers tolerance to moderately toxic levels of cobalt. Strains that carry null alleles at both loci are viable. The metal-hypersensitive phenotypes of mutations in either gene are largely unaffected by changes in dosage of the other. COT1 and ZRC1 function independently in conferring tolerance to their respective metals, yet the uptake of cobalt ions by yeast cells is dependent on the gene dosage of ZRC1 as well as of COT1. Strains that overexpress ZRC1 have increased uptake of cobalt ions, while ZRC1 null mutants exhibit decreased cobalt uptake. The defects in cobalt uptake due to mutations at COT1 and ZRC1 are additive, suggesting that the two genes are responsible for the majority of cobalt and zinc uptake in yeast cells. The function of either gene product seems to be more important in metal homeostasis than is the GRR1 gene product, which is also involved in metal metabolism. Mutations in the GRR1 gene have no effect on the cobalt-related phenotypes of strains that have altered gene dosage of either COT1 or ZRC1.


Subject(s)
Carrier Proteins , Cation Transport Proteins , Cations, Divalent/pharmacology , Fungal Proteins/metabolism , Saccharomyces cerevisiae Proteins , Saccharomyces cerevisiae/physiology , Ubiquitin-Protein Ligases , Base Sequence , Biological Transport , Cations, Divalent/metabolism , Cobalt/metabolism , Drug Resistance, Microbial , F-Box Proteins , Fungal Proteins/genetics , Genes, Fungal/genetics , Genes, Suppressor/genetics , Homeostasis , Membrane Transport Proteins , Models, Biological , Molecular Sequence Data , Mutation , Saccharomyces cerevisiae/drug effects , Zinc/metabolism
18.
J Biol Chem ; 269(34): 21670-5, 1994 Aug 26.
Article in English | MEDLINE | ID: mdl-8063810

ABSTRACT

Hyperlipidemia arises from a disturbance in the balance between production and degradation of lipoprotein particles. Variation in the secretion of human apolipoprotein B (apoB), the major protein component of triglyceride-rich lipoproteins, directly affects this homeostasis. Naturally occurring apoB signal peptide variants (associated with hypertriglyceridemia, altered postprandial lipid metabolism, or atherosclerosis) were investigated for their ability to direct transit through the secretion pathway. Three apoB signal peptide isoforms were fused to the secretory protein, invertase, and expressed in yeast. A deletion or insertion in the hydrophobic core of the signal peptide mediated inefficient translocation into the endoplasmic reticulum and was secretion-defective, relative to the common 27-residue isoform. Additionally, the insertion apoB isoform was observed in yeast to confer a defect in export from the endoplasmic reticulum. Secretion of the apoB signal peptide-invertase fusions responded positively to an inhibitor of calpain type I proteases. These observations suggest that the apoB signal peptide plays a role in determining the levels of apoB degradation and secretion and, thus, hyperlipidemia.


Subject(s)
Apolipoproteins B/metabolism , Genetic Variation , Protein Sorting Signals/genetics , Saccharomyces cerevisiae/genetics , Amino Acid Sequence , Apolipoproteins B/genetics , Base Sequence , Biological Transport, Active , Cell Compartmentation , Glycoside Hydrolases/genetics , Glycoside Hydrolases/metabolism , Humans , Molecular Sequence Data , Phenotype , Protein Sorting Signals/metabolism , Recombinant Fusion Proteins/metabolism , Recombinant Proteins/metabolism , beta-Fructofuranosidase
19.
FEMS Microbiol Lett ; 119(1-2): 221-7, 1994 Jun 01.
Article in English | MEDLINE | ID: mdl-8039662

ABSTRACT

Mutations at three loci in Saccharomyces cerevisiae have been shown to confer increased sensitivity to the antimalarial and antiarrhythmic alkaloid, quinidine. Two of these groups are composed of strains carrying recessive mutations, the other group contains two dominant alleles. The largest complementation group has been designated QDS1, for increased quinidine-sensitivity. Exposure of qds1 cells to lethal concentrations of quinidine results in a novel small-budded terminal morphology in about 70% of the cells in the culture. Strains which carry qds1 alleles share other pleiotropic phenotypes. qds1 mutants are incapable of mating as alpha but not a cells, due to a defect in alpha-factor production. Homozygous diploid qds1 strains cannot sporulate. Genetic evidence indicates that QDS1 is allelic to KEX2, a precursor processing protease. Loss of QDS1/KEX2 function results in quinidine sensitivity.


Subject(s)
Proprotein Convertases , Quinidine/pharmacology , Saccharomyces cerevisiae Proteins , Saccharomyces cerevisiae/drug effects , Alleles , Drug Resistance , Mutation , Saccharomyces cerevisiae/genetics , Subtilisins/physiology
20.
Radiat Res ; 137(3): 361-70, 1994 Mar.
Article in English | MEDLINE | ID: mdl-8146280

ABSTRACT

A total of 155 primary bone sarcomas were found in 131 of the 246 beagles injected with 226Ra and 5 primary bone sarcomas were found in 4 of the 158 unexposed controls. Of these 155 bone sarcomas, 146 (94%) were osteosarcomas and 9 were non-osteosarcomas. An additional 31 primary bone sarcomas (28 osteosarcomas) developed in 44 dogs terminated from the main study because of limb amputation for bone sarcoma. Non-osteosarcomas predominated in both the controls and the second lowest of six logarithmically increasing dose levels (there were no bone sarcomas in the lowest dose group). Osteosarcomas predominated at the higher dose levels, and incidence tended to increase as dose increased. The 146 osteosarcomas were distributed quite evenly between males and females (72:74). Of the 9 non-osteosarcomas, 6 occurred in males and 3 in females. The ratio of bone sarcomas of the appendicular skeleton to those in the axial skeleton was 110:45, with osteosarcomas occurring more often in the appendicular skeleton (108:38). Cases of multiple primary bone sarcomas in dogs injected with 226Ra were found only in the four highest dose groups. Amputations were performed on 44 of the 96 dogs (94 injected and 2 unexposed) that developed appendicular bone sarcomas. A statistical study of the distribution of bone sarcomas among 16 separate bone groups showed a statistically significant correlation to cancellous skeletal surface, but the variability among bone groups was too large for this relationship to be of real predictive value. It is postulated that the distribution of bone sarcomas reflects primarily the relative cell division rates in the bone groups and secondarily the radiation dose distribution, with the highest occurrence of bone sarcoma in the humeri, pelvis, femora and tibiae/fibular tarsal, and no occurrence in the coccygeal vertebrae, sternum, forepaws or hindpaws.


Subject(s)
Bone Neoplasms/etiology , Neoplasms, Radiation-Induced , Osteosarcoma/etiology , Radium/toxicity , Animals , Bone Neoplasms/mortality , Bone Neoplasms/secondary , Cohort Studies , Dogs , Dose-Response Relationship, Radiation , Female , Incidence , Male , Neoplasms, Multiple Primary/epidemiology , Neoplasms, Multiple Primary/etiology , Neoplasms, Radiation-Induced/metabolism , Neoplasms, Radiation-Induced/mortality , Neoplasms, Radiation-Induced/pathology , Osteosarcoma/mortality , Osteosarcoma/secondary
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