The genes for fifteen ribosomal proteins of Saccharomyces cerevisiae

Proteome studies of Saccharomyces cerevisiae: identification and characterization of abundant proteins

Two-dimensional (2-D) gel electrophoresis can now be coupled with protein identification techniques and genome sequence information for direct detection, identification, and characterization of large numbers of proteins from microbial organisms. 2-D electrophoresis, and new protein identification techniques such as amino acid composition, are proteome research techniques in that they allow direct characterization of many proteins at the same time. Another new tool important for yeast proteome research is the Yeast Protein Database (YPD), which provides the sequence-derived protein properties needed for spot identification and tabulations of the currently known properties of the yeast proteins. Studies presented here extend the yeast 2-D protein map to 169 identified spots based upon the recent completion of the yeast genome sequence, and they show that methods of spot identification based on predicted isoelectric point, predicted molecular mass, and determination of partial amino acid composition from radiolabeled gels are powerful enough for the identification of at least 80% of the spots representing abundant proteins. Comparison of proteins predicted by YPD to be detectable on 2-D gels based on calculated molecular mass, isoelectric point and codon bias (a predictor of abundance) with proteins identified in this study suggests that many glycoproteins and integral membrane proteins are missing from the 2-D gel patterns. Using the 2-D gel map and the information available in YDP, 2-D gel experiments were analyzed to characterize the yeast proteins associated with: (i) an environmental change (heat shock), (ii) a temperature-sensitive mutation (the prp2 mRNA splicing mutant), (iii) a mutation affecting post-translational modification (N-terminal acetylation), and (iv) a purified subcellular fraction (the ribosomal proteins). The methods used here should allow future extension of these studies to many more proteins of the yeast proteome.

Cloning, nucleotide sequence, and expression of tef-1, the gene encoding translation elongation factor 1 alpha (EF-1 alpha) of Neurospora crassa

The tef-1 gene encoding translation elongation factor 1 alpha was cloned from the ascomycete fungus Neurospora crassa. The sequences of genomic DNA and cDNA clones showed that the tef-1 gene contained one ORF of 1380 bp length that is interrupted by three short introns. The deduced polypeptide contained 460 amino acid residues, and the sequence had a high similarity with those of EF-1 alpha polypeptides from other species. The level of tef-1 mRNA was low in conidia but high in growing cells. When mycelia were transferred to poor nutrient media, the level of tef-1 gene mRNA decreased remarkably. The pattern of tef-1 expression was similar to the expression of genes for ribosomal proteins. The tef-1 gene was mapped between arg-3 and leu-4 loci on linkage group I by restriction fragment length polymorphism mapping. Southern blot analysis showed that Neurospora genomic DNA contained only one copy of the tef-1 gene in a genome.

S6 phosphorylation and the p70s6k/p85s6k

Activation of cell growth leads to the multiple phosphorylation of 40S ribosomal protein S6. The kinase responsible for controling this event is termed p70s6k/p85s6k. Both isoforms of the kinase are derived from a common gene activated by a complex set of phosphorylation events; each resides in a unique cellular compartment: the p70s6k in the cytoplasm and the p85s6k in the nucleus. Although p70s6k/p85s6k represent the first mitogen-activated serine/threonine kinase described, the signaling pathway leading to activation of both isoforms remains obscure. Recent studies have shown that this pathway is distinct from that of p21ras and the p42mapk/p44mapk, and that bifurcation of these pathways takes place at the level of the receptor. Experiments with point mutants of the PDGF receptor and inhibitors of phosphatidyl-inositol-3-OH kinase have implicated the latter molecule in this signaling event, but more recent findings suggest an alternative route may be employed. The p70s6k signaling pathway can also be ablated by the immunosuppressant rapamycin, which blocks p70s6k activation and S6 phosphorylation without affecting the other kinases whose activation is triggered by mitogen treatment. In parallel, rapamycin suppresses the translation of a family of mRNAs that contain a polypyrimidine tract at their 5' transcriptional start site. The implication is that this event is mediated by the phosphorylated form of S6 that may either (1) directly interact with the polypyrimidine tract or (2) alter the affinity of the 40S ribosome mRNA binding site for polypyrimidine tract mRNAs, or (3) recognize proteins that directly bind to the polypyrimidine tract.

Yeast single copy gene URP1 is a homolog of rat ribosomal protein gene L21

This communication reports on a single-copy gene of Saccharomyces cerevisiae which is homologous to the rat ribosomal protein gene L21. The yeast and the rat genes show 59% identity in DNA sequences and in the predicted protein sequences. This yeast gene is, therefore, assumed to code for an as yet unassigned ribosomal protein (URP1). The URP1 open reading frame is 480 nucleotides long and can encode a protein of about M(r) 18,200. Like most of the other known ribosomal protein genes, URP1 is interrupted by an intron in its 5' terminal part and it is preceded by upstream sequence elements which usually regulate transcription of these genes. Northern blot analysis reveals that the URP1 gene is actually expressed in vivo.

Efficient secretion in yeast based on fragments from K1 killer preprotoxin

The alpha and beta components of the secreted K1 killer toxin of Saccharomyces cerevisiae are derived from residues 45-147 and 234-316, respectively, of the 316 residue preprotoxin (ppTox). The beta N-terminus is produced by Kex2 cleavage after Lys Arg233; when beta la (the mature sequence of beta-lactamase) is fused at this site and the fusion is expressed from the PGK promoter in pDT17, a multicopy plasmid, unexpectedly modest levels of beta la secretion resulted. Over-expression of Kex2 failed to increase beta la secretion while a kex2-null mutation reduced secretion by 98%. beta la secretion in a Kex+ strain was not enhanced by inactivation of the alpha toxin component or by deletion of most of its central hydrophobic segments. However SP-beta la, produced by deletion of ppTox residues 35-176, expressed 10-fold higher beta la activity and the precursor was now secreted with similar efficiency in a kex2-null strain. Fusions of beta la to ppTox at Ala34 or Ala46 also led to efficient secretion in both KEX2 and kex2-null strains. Since these beta la fusions differ only in segments well downstream of the signal peptide and all had similar transcript levels, the efficiency of beta la secretion is apparently determined by the efficiency with which these fusions are translocated to the Golgi compartment where Kex2 is active. Efficiency is high for the shorter fusions, but is 10% or less for the longer fusions; even this fraction is apparently diverted to the vacuole if not cleaved by Kex2. SP-beta la was the most efficient construct tested; secreted beta la reached 4% of total cell protein, modestly exceeding levels produced by fusion to the MF alpha 1-encoded prepro alpha-factor, suggesting potential for the production of foreign proteins in yeast.

Both genes for EF-1 alpha in Candida albicans are translated

In previous work, we showed that Candida albicans has two genes, TEF-1 and TEF-2, which encode identical polypeptides for the highly conserved, essential, protein synthesis factor EF-1 alpha (Breviario et al., 1988). This result prompted questions as to whether C. albicans preferentially uses one of the genes over the other and whether both genes are actually translated into protein. Gene-specific sequence differences in the untranslated portion of each gene made it possible to prepare gene-specific oligonucleotide hybridization probes. Results with the probes showed that the relative steady-state mRNA levels of the two genes were equivalent and that the mRNA for each gene was present in active translation complexes.

The organization and expression of the Saccharomyces cerevisiae L4 ribosomal protein genes and their identification as the homologues of the mammalian ribosomal protein gene L7a

A cDNA for the mouse ribosomal protein (rp) L7a, formerly called Surf-3, was used as a probe to isolate two homologous genes from Saccharomyces cerevisiae. The two yeast genes (L4-1 and L4-2) were identified as encoding S. cerevisiae L4 by 2D gel analysis of the product of the in vitro translation of hybrid-selected mRNA and additionally by direct amino acid sequencing. The DNA sequences of the two yeast genes were highly homologous (95%) over the 771 bp that encode the 256 amino acids of the coding regions but showed little homology outside the coding region. L4-1 differed from L4-2 by 7 out of the 256 amino acids in the coding region, which is the greatest divergence between the products of any two duplicated yeast ribosomal protein genes so far reported. There is strong homology between the mouse rpL7a/Surf-3 and the yeast L4 genes -57% at the nucleic acid level and also 57% at the amino acid level (though some regions reach as much as 80-90% homology). While most yeast ribosomal protein genes contain an intron in their 5' region both L4-1 and L4-2 are intronless. The mRNAs derived from each yeast gene contained heterogenous 5' and 3' ends but in each case the untranslated leaders were short. The L4-1 mRNA was found to be much more abundant than the L4-2 mRNA as assessed by cDNA and transcription analyses. Yeast cells containing a disruption of the L4-1 gene formed much smaller colonies than either wild-type or disrupted L4-2 strains. Disruption of both L4 genes is a lethal event, probably due to an inability to produce functional ribosomes.

Some cis- and trans-acting mutants for splicing target pre-mRNA to the cytoplasm

We designed a strategy to identify splicing factors that act by preventing pre-mRNA transport into the cytoplasm. A yeast synthetic intron was inserted into a lacZ gene so that only the pre-mRNA could be translated to produce beta-galactosidase activity. Deletion of either of the 5' splice junction sequence GUAUGU and the branchpoint sequence UACUAAC resulted in a dramatic increase in pre-mRNA translation, indicating its cytoplasmic localization. In rna6 and rna9 mutant strains assayed at the nonpermissive temperature, splicing inhibition occurred simultaneously with a large increase in pre-mRNA translation. Similarly, a point mutation in U1 snRNA decreased splicing efficiency and increased pre-mRNA translation. From these results, we conclude that early acting factors, probably including U1 snRNA, and the RNA6 and RNA9 gene products, interact in vivo with the 5' splice junction and the branchpoint sequence to commit the pre-mRNA to the splicing pathway, thereby preventing its transport to the cytoplasm.

Sequence analysis of a processed gene coding for mouse ribosomal protein L32

The nucleotide sequence of a mouse ribosomal protein gene, identified by hybridization with the gene encoding the Drosophila ribosomal (r-) protein 49, was determined by cloning in the phage M13 and dideoxy sequencing. The mouse gene, L32', is a member of the multigene family encoding mammalian r-protein L32. L32' is a processed gene that could encode a 135 amino acid protein similar to that of mouse L32 and Drosophila r-protein 49.

Genomic organization of tRNA and aminoacyl-tRNA synthetase genes for two amino acids in Saccharomyces cerevisiae

The genomic organization in Saccharomyces cerevisiae of the tRNA and aminoacyl-tRNA synthetase genes for two amino acids was investigated. Aspartic acid and serine were chosen for the study because of the number and diversity of their tRNA gene sequences and the availability of cloned tRNA and aminoacyl-tRNA synthetase genes. Chromosome assignments were determined by hybridization to DNA gel blots of chromosomal DNA resolved by contour-clamped homogeneous electric field gel electrophoresis. Our results show that the tRNA and the cognate synthetase genes in such a family are dispersed and, therefore, cannot be regulated via a mechanism dependent on close proximity of genes. In general, the genome of S. cerevisiae contains randomly dispersed tRNA genes that are transcribed individually. We have supported and expanded this view by applying the facile method of contour-clamped homogeneous electric field gel electrophoresis to the investigation of these small multigene families.

Complete nucleotide sequence of the ribosomal 'A' protein operon from the archaebacterium, Halobacterium halobium

DNA fragments cloned from the halophilic archaebacterium Halobacterium halobium including the gene for ribosomal 'A' protein (HhaL20) were sequenced. Sequence and transcript analyzes indicated that the 'A' protein message (ORFC) was co-transcribed with two neighbouring open reading frames (ORFA and B) as a single unit. Comparison of the amino acid sequences deduced from ORFA and B with those from other organisms demonstrated that ORFA encoded the protein homologous to the ribosomal protein L8 of Halobacterium cutirubrum (HcuL8) and L1 of Escherichia coli (EL1), while ORFB encoded the protein homologous with the human ribosomal protein P0. The sequences which were able to facilitate mRNA.16S-rRNA hybridization were found about 10-20 nucleotides upstream of the initiation codon ATG of each of the three ORFs. The 5'- and 3'-ends of the operon were mapped with nuclease S1. A putative promoter (A+T-rich) and termination signal (T-rich) were found to be present within the 5'- and 3'-flanking sequence.

Expression of ribosomal protein genes during Xenopus development

The Xenopus ribosomal protein genes provide an excellent system to elucidate the complex regulation encompassing 60 functionally related proteins present in equimolar amounts in ribosomal subunits. Oogenesis and embryogenesis provide unique opportunities to investigate ribosome biosynthesis in situations wherein gene activation of individual components is uncoupled from assembly of the ribosomal subunits. This chapter has focused on the basic parameters that control ribosomal protein gene expression during development. Translational control is clearly a major level for coordinating the regulation of these genes during development, as is posttranslational stability of the ribosomal proteins and RNA splicing of the L1 gene. In addition to these levels of control under active investigation, a number of intriguing problems remain to be addressed in any detail. For example, the mechanisms that balance ribosomal protein production with subunit assembly in oocytes remain to be determined. Resolution of these events must also define the processes by which ribosomal proteins, upon synthesis in the cytoplasm, are first translocated to the nucleus and subsequently to the nucleolus for subunit assembly. Functional approaches in which these genes are assayed for accurate developmental control in microinjected oocytes and fertilized eggs will undoubtedly provide information on the synthesis of this eukaryotic organelle and the signals responsible for altering these processes at different developmental stages.

A novel role for the 3' region of introns in pre-mRNA splicing of Saccharomyces cerevisiae

To investigate the importance of sequences between the yeast (Saccharomyces cerevisiae) branch point (TACTAAC box) and 3' splice site (AG), we generated a series of pre-mRNA substrates that differed in the length of RNA retained on the 3' side of the TACTAAC box. These pre-mRNAs were compared as substrates for the first step of in vitro splicing (5' cleavage and lariat formation) and in vitro spliceosome assembly (complex formation) in a whole-cell yeast extract. The results indicate that for rp51A pre-mRNA at least 29 nucleotides of RNA on the 3' side of the TACTAAC box are required for 5' cleavage and lariat formation, as smaller substrates fail to manifest any detectable cleavage or ligation events. Analysis of splicing complex assembly indicates that these smaller substrates undergo efficient yet incomplete complex formation; they are blocked at a late stage of spliceosome assembly, the complex I to complex II transition (Pikielny et al. 1986), a result which suggests that the failure to form lariats is due to a specific assembly defect. The lariat formation block (and assembly defect) can be relieved by the addition of ribohomopolymer "tails" to the 3' end of the shortened rp51A pre-mRNAs, and similar results were obtained with shortened actin pre-mRNAs. The results of this study indicate that this region of the pre-mRNA serves a specific function late in in vitro spliceosome assembly.

Splicing of yeast nuclear pre-mRNA in vitro requires a functional 40S spliceosome and several extrinsic factors

We have previously shown that extracts prepared from most of the yeast temperature-sensitive rna mutants are heat sensitive for pre-mRNA splicing in vitro, and that the products of the corresponding RNA genes are essential for the early stages of the splicing region. In this report, we demonstrate that most heat-inactivated mutant extracts do not form the spliceosome, suggesting that their gene products are likely to be involved in spliceosome formation. Heat-inactivated rna2 extracts, on the other hand, do form a splicing-dependent 40S complex containing uncleaved pre-mRNA exclusively. The pre-mRNA in the 40S complex can be converted to the splicing products in the presence of ATP and complementing extracts. These results demonstrate that: (1) the 40S complex formed in heat-inactivated rna2 extracts is a spliceosome (termed the rna2 delta spliceosome), (2) the spliceosome is a functional intermediate in the splicing pathway, and (3) the splicing process can be dissected into two steps, spliceosome formation and cleavage-ligation reactions. Additional results indicate that at least two extrinsic factors, as well as the RNA2 gene product, are required for complementation of the rna2 delta spliceosome. A three-step mechanism for nuclear pre-mRNA splicing in yeast is proposed.

The role of small nuclear ribonucleoprotein particles in pre-mRNA splicing

A small set of distinctive short RNA molecules are found in the nuclei of all higher eukaryotic cells and yeast, in protein complexes known as 'small nuclear ribonucleoprotein particles', or snRNPs. Recent work has confirmed early suggestions that these particles form part of the machinery by which primary RNA transcripts are processed to their mature, functional form. In particular, snRNPs have been shown to be an integral part of the 'spliceosome', a multi-component complex involved in the removal of intron sequences from the coding regions of messenger RNA precursors.

Molecular evolution of the Saccharomyces cerevisiae histone gene loci

The core histone genes of Saccharomyces cerevisiae are arranged as duplicate nonallelic sets of specifically paired genes. The identity of structural organization between the duplicated gene pairs would have its simplest evolutionary origin in the duplication of a complete locus in a single event. In such a case, the time since the duplication of one of the genes should be identical to that since duplication of the gene adjacent to it on the chromosome. A calculation of the evolutionary distances between the coding DNA sequences of the histone genes leads to a duplication paradox: The extents of sequence divergence in the silent component of third-base positions for adjacent pairs of genes are not identical. Estimates of the evolutionary distance between the two H3-H4 noncoding intergene DNA sequences are large; the divergence between the two separate sequences is indistinguishable from the divergence between either of the regions and a randomly generated permutation of itself. These results suggest that the duplication event may have occurred much earlier than previously estimated. The potential age of the duplication, and the attractive simplicity of the duplication of both the H3-H4 and the H2A-H2B gene pairs having taken place in a single event, leads to the hypothesis that modern haploid S. cerevisiae may have evolved by diploidization or fusion of two ancient fungi.

The yeast RNA gene products are essential for mRNA splicing in vitro

The yeast rna mutations (rna2-rna11) are a set of temperature-sensitive mutations that result in the accumulation of intron-containing mRNA precursors at the restrictive temperature. We have used the yeast in vitro splicing system to investigate the role of products of the RNA genes in mRNA splicing. We have tested the heat lability of the in vitro mRNA splicing reaction in extracts isolated from mutant and wild-type cells. Extracts isolated from seven of the nine rna mutants demonstrated heat lability in this assay, while most wild-type extracts were stable under the conditions utilized. We have also demonstrated that heat inactivation usually results in the specific loss of an exchangeable component by showing that most combinations of heat-inactivated extracts from different mutants complement one another. In three cases (rna2, rna5, and rna11), the linkage of the in vitro defect to the rna mutations was ascertained by a combination of reversion, tetrad, and in vitro complementation analyses. Furthermore, each heat-inactivated extract was capable of complementation by at least one fraction of the wild-type splicing system. Thus many of the RNA genes are likely to code for products directly involved in and essential for mRNA splicing.

Identification of the RNA2 protein of Saccharomyces cerevisiae

The rna2-1 mutant of Saccharomyces cerevisiae has a conditional lethal phenotype, accumulating high molecular weight RNAs of intron-containing nuclear genes at 36 degrees C. The cloned RNA2 gene suppresses this phenotype and the RNA2 gene product has been implicated in RNA splicing. Rabbit antisera have been raised against an N-terminal synthetic peptide taken from the RNA2 gene DNA sequence data, and against a beta-galactosidase/RNA2 gene fusion protein. Both antisera identify the same 97-105 kd protein from S. cerevisiae cell extracts which is consistent with the predicted size of the RNA2 protein (from the 2800 nucleotide transcript size and DNA sequence data).

An altered ribosomal protein in an edeine-resistant mutant of Saccharomyces cerevisiae

The r-proteins of an edeine-resistant mutant of Saccharomyces cerevisiae were compared to those of the wild-type strain by using two different two-dimensional electrophoretic techniques: (1) the Kaltschmidt-Wittmann method and, (2) the Kaltschmidt-Wittmann system, in the first dimension and the Na Dodecyl-SO4 system in the second. With the first technique, the results indicate that the patterns of basic ribosomal proteins are similar in the two strains. However, the pattern of acidic ribosomal proteins of the mutant revealed an additional protein band with respect to the normal one. Using the other technique, the patterns of basic and acidic ribosomal proteins of the mutant demonstrated a similarity to the corresponding pattern of the wild-type strain. The data disclose that an acidic ribosomal protein of the mutant may have two forms with different electrophoretic mobilities and similar molecular weights.

Ribosomal proteins are encoded by single copy genes in Dictyostelium discoideum

Five recombinant plasmids which encode ribosomal proteins (r-proteins) from Dictyostelium discoideum have been isolated. Poly(A) + RNA was size-fractionated by preparative agarose gel electrophoresis and a fraction encoding proteins of less than 35 kDa was used to construct a cDNA library in the plasmid vector pBR322. Individual clones from the library were screened by hybrid-selected translation and those encoding r-proteins were identified by co-migration of the translation products in two-dimensional gel electrophoresis with marker proteins purified from Dictyostelium ribosomes. Initial characterization using the five cDNA plasmids indicates that these r-proteins are encoded by single copy genes and that they are not tightly clustered in the genome.

Molecular cloning of a ribosomal protein gene from the fission yeast Schizosaccharomyces pombe

Using the structural gene for the ribosomal protein L3 from Saccharomyces cerevisiae as a probe, we isolated a homologous fragment from genomic DNA of Schizosaccharomyces pombe. Analysis of the plasmid carrying this fragment by hybridization selection and 2D-electrophoresis revealed a 31 kDa ribosomal protein. Transformation of the vector pDB248x containing this fragment into Schizosaccharomyces pombe leads to an increased level of mRNA suggesting that we have cloned the entire and actively transcribed gene.

Molecular cloning and genetic mapping of the DNA topoisomerase II gene of Saccharomyces cerevisiae

The structural gene for DNA topoisomerase II from the yeast Saccharomyces cerevisiae has been cloned. The clones were selected from a YEp13 plasmid bank of yeast DNA by complementing a temperature-sensitive mutation (top2-1) in the topoisomerase II gene, TOP2. Chromosomal integrants of the clone were derived by homologous recombination in strains lacking the 2 mu circle plasmid. Genetic analysis of these integrants indicates that we have cloned the TOP2 gene and not an extragenic suppressor. A YEp13-TOP2 hybrid plasmid integrant was used to localize the TOP2 gene to the left arm of chromosome XIV by the 2 mu circle-directed marker loss method. Results from standard meiotic mapping experiments indicate that TOP2 is about 16 centi-Morgans to the centromere proximal side of MET4. Northern blot analysis of TOP2 RNA isolated from a wild-type strain and from an rna2 mutant shows the RNA to be 4.5 kb long in both cases, thus indicating that the TOP2 gene has no large introns.

Isolation of yeast ribosomal proteins L3 and L2 for immunological studies

We report on a rapid method for the isolation and purification of the yeast ribosomal proteins L3 and L2 using a simple instrumentation. Preparative dodecyl sulfate polyacrylamide gel electrophoresis was applied to the separation of cytoplasmatic ribosomal proteins of the large subunit from the yeast Saccharomyces cerevisiae. The polypeptides were removed from gel slices by electrophoretic elution. Subsequent analytical electrophoresis showed groups of proteins in all but two fractions. The latter were further analysed by a two-dimensional gel electrophoresis system which disclosed the purity of two polypeptides. They were identified as L3 and L2. Their molecular masses were 51.5 and 44 kDa as estimated from the gels. A possible application to the isolation of other yeast ribosomal proteins is discussed. An antiserum against the polypeptide L3 was raised in a rabbit. Applying an enzyme-linked immunosorbent assay (ELISA) we were able to determine the relative antibody concentration. Its specificity was demonstrated by immunoblotting.

Isolation of a mouse DNA fragment with homology to a Drosophila ribosomal protein gene

A mouse genomic library in lambda Charon 4A was screened for putative ribosomal protein genes using a fragment of the gene encoding Drosophila ribosomal protein 49 as a hybridization probe under nonstringent hybridization conditions. A recombinant phage was selected and its restriction enzyme map determined. The major species of mouse poly(A)+ mRNA homologous to the putative gene is about 740 nucleotides long.

The major promoter element of rRNA transcription in yeast lies 2 kb upstream

Conventional genetic analysis of the transcription of rDNA in yeast is precluded because the genes are highly reiterated. As an alternative strategy to determine which sequences modulate transcription of pre-rRNA, a series of artificial rRNA genes containing a fragment of DNA from E. coli bacteriophage T7 were introduced into the yeast Saccharomyces cerevisiae. Correct transcription of the artificial genes was observed. Three regions of ribosomal spacer are found to affect transcription of rRNA. Sequences within 210 bp of the 5' terminus of 35S rRNA support low levels of transcription, but at multiple initiation points. Sequences from -210 to -2230 direct correct initiation and increase somewhat the efficiency of transcription. Most striking is that sequences from -2230 to -2420 stimulate transcription 15-fold. The function of this major promoter element is absolutely orientation-dependent but relatively independent of position. Its activity is blocked when an rRNA transcription termination sequence is placed between it and the site of initiation.

Isolation and characterization of the RNA2+, RNA4+, and RNA11+ genes of Saccharomyces cerevisiae

We used genetic complementation to isolate DNA fragments that encode the Saccharomyces cerevisiae genes RNA2+, RNA4+, and RNA11+ and to localize the genes on the cloned DNA fragments. RNA blot-hybridization analyses coupled with genetic analyses indicated the RNA2+ is coded by a 3.0-kilobase (kb) transcript, RNA4+ is coded by a 1.6-kb transcript, and RNA11+ is coded by a 1.3-kb or a 1.7-kb transcript or both; none of the cloned genes contains detectable introns. All three genes were transcribed into messages of very low abundance (approximately 20 times lower than a ribosomal protein message). DNA blot-hybridization revealed that all cloned genes are represented only once in the yeast chromosome. mRNA for RNA2+ and RNA4+ is produced in approximate proportion to gene dosage, whereas RNA11+ transcription appears to be not nearly so dependent on gene dosage. On a medium-copy plasmid (5 to 10 copies per cell), each cloned gene complemented mutations only in its own gene, indicating that each gene encodes a unique function. Genetic analysis by integrative transformation indicated that we cloned the RNA2+, RNA4+, and RNA11+ structural genes and not second-site suppressors.

Stepwise dissociation of yeast 60S ribosomal subunits by LiCl and identification of L25 as a primary 26S rRNA binding protein

Treatment of yeast 60S ribosomal subunits with 0.5 M LiCl was found to remove all but six of the ribosomal proteins. The proteins remaining associated with the (26S + 5.8S) rRNA complex were identified as L4, L8, L10, L12, L16 and L25. These core proteins were split off sequentially in the order (L16 + L12), L10, (L4 + L8), L25 by further increasing the LiCl concentration. At 1.0 M LiCl only ribosomal protein L25 remains bound to the rRNA. Upon lowering the LiCl concentration the core proteins reassociate with the rRNA in the reverse order of their removal. The susceptibility of the ribosomal proteins to removal by LiCl corresponds quite well with their order of assembly into the 60S subunit in vivo as determined earlier [Kruiswijk et al. (1978) Biochim. Biophys. Acta 517, 378-389]. Binding studies in vitro using partially purified L25 showed that this protein binds specifically to 26S rRNA. Therefore our experiments for the first time directly identify a eukaryotic ribosomal protein capable of binding to high-molecular-mass rRNA. Binding studies in vitro using a blot technique demonstrated that core proteins L8 and L16 as well as protein L21, though not present in any of the core particles, are also capable of binding to 26S rRNA to approximately the same extent as L25. About nine additional 60S proteins appeared to interact with the 26S rRNA, though to a lesser extent.

Requirement of either of a pair of ras-related genes of Saccharomyces cerevisiae for spore viability

Cells of the yeast, Saccharomyces cerevisiae, containing disruptions of either of two genes that are members of the ras oncogene family are viable, but haploid yeast spores carrying disruptions of both genes fail to grow.