DRS1 to DRS7, novel genes required for ribosome assembly and function in Saccharomyces cerevisiae

NCL1, a novel gene for a non-essential nuclear protein in Saccharomyces cerevisiae

The nucleolar protein Nop2p is an essential gene product that is required for pre-rRNA processing and ribosome biogenesis in Saccharomyces cerevisiae (Hong, B. et al., 1997, Mol. Cell. Biol., 17, 378-388). A search for proteins similar to Nop2p identified a novel yeast gene product that also shares significant homology with the human proliferation associated nucleolar protein p120. The gene encoding this 78kDa protein was termed NCL1 (for nuclear protein 1; corresponding to YBL024w). Ncl1p and Nop2p contain an evolutionarily conserved motif that has been termed the 'NOL1/NOP2/fmu family signature' (NOL1 encodes p120). Epitope tagged Ncl1p was found to be localized to the nucleus, including the nucleolus, and was concentrated at the nuclear periphery. NCL1 is not essential. Strains containing a disruption of NCL1, or strains overexpressing NCL1, grow essentially identically to wildtype NCL1 strains on a number of different media and at different temperatures. Disruption of NCL1 does not affect steady-state levels of large and small ribosome subunits, monoribosomes, and polyribosomes. However, disruption of NCL1 leads to increased sensitivity to the antibiotic paromomycin.

The role of the Schizosaccharomyces pombe gar2 protein in nucleolar structure and function depends on the concerted action of its highly charged N terminus and its RNA-binding domains

Nonribosomal nucleolar protein gar2 is required for 18S rRNA and 40S ribosomal subunit production in Schizosaccharomyces pombe. We have investigated the consequences of the absence of each structural domain of gar2 on cell growth, 18S rRNA production, and nucleolar structure. Deletion of gar2 RNA-binding domains (RBDs) causes stronger inhibition of growth and 18S rRNA accumulation than the absence of the whole protein, suggesting that other factors may be titrated by its remaining N-terminal basic/acidic serine-rich domain. These drastic functional defects correlate with striking nucleolar hypertrophy. Point mutations in the conserved RNP1 motifs of gar2 RBDs supposed to inhibit RNA-protein interactions are sufficient to induce severe nucleolar modifications but only in the presence of the N-terminal domain of the protein. Gar2 and its mutants also distribute differently in glycerol gradients: gar2 lacking its RBDs is found either free or assembled into significantly larger complexes than the wild-type protein. We propose that gar2 helps the assembly on rRNA of factors necessary for 40S subunit synthesis by providing a physical link between them. These factors may be recruited by the N-terminal domain of gar2 and may not be released if interaction of gar2 with rRNA is impaired.

Yeast dom34 mutants are defective in multiple developmental pathways and exhibit decreased levels of polyribosomes

The DOM34 gene of Saccharomyces cerevisiae is similar to genes found in diverse eukaryotes and archaebacteria. Analysis of dom34 strains shows that progression through the G1 phase of the cell cycle is delayed, mutant cells enter meiosis aberrantly, and their ability to form pseudohyphae is significantly diminisehd. RPS30A, which encodes ribosomal protein S30, was identified in a screen for high-copy suppressors of the dom34delta growth defect. dom34delta mutants display an altered polyribosome profile that is rescued by expression of RPS30A. Taken together, these data indicate that Dom34p functions in protein translation to promote G1 progression and differentiation. A Drosophila homolog of Dom34p, pelota, is required for the proper coordination of meiosis and spermatogenesis. Heterologous expression of pelota in dom34delata mutants restores wild-type growth and differentiation, suggesting conservation of function between the eukaryotic members of the gene family.

Multiple members of a third subfamily of P-type ATPases identified by genomic sequences and ESTs

The Saccharomyces cerevisiae genome contains five P-type ATPases divergent from both of the well-known subfamilies of these membrane ion transporters. This newly recognized third subfamily can be further divided into four classes of genes with nearly equal relatedness to each other. Genes of this new subfamily are also present and expressed in multicellular organisms such as Caenorhabditis elegans and mammals; some, but not all, can be assigned to the classes identified in yeast. Different classes of genes and different genes within a class are expressed differentially in tissues of the mouse. The recently cloned gene for the mammalian aminophospholipid translocase belongs to this new subfamily, suggesting that other subfamily members may transport other lipids or lipid-like molecules from one leaflet of the membrane bilayer to the other.

The complete inventory of the yeast Saccharomyces cerevisiae P-type transport ATPases

A total of sixteen open reading frames encoding for P-type ATPases have been identified in the complete genome sequence of Saccharomyces cerevisiae. Phylogenetic analysis distinguishes 6 distinct families. Topology predictions, identification of aminoacid sequence motifs and phenotype analysis of the available mutants suggest that these families correspond to ATPases transporting either H+ (2 members), Ca2+ (2 members), Na+ (3 members), heavy metals (2 members), possibly aminophospholipids (5 members including 4 new ones) or unknown substrates (2 new members). It is proposed that the latter family which has homologs in Tetrahymena thermophila, Plasmodium falciparum and Caenorhabditis elegans constitutes a new group called P4-ATPases with characteristic topology and aminoacid signatures.

Functional analysis of human RPS14 null alleles

Previously we described a large collection of cloned human DNAs that encode chemically defined missense mutations within the ribosomal protein S14 sequence. We determined that biologically inactive (i.e. null) alleles resulted primarily from point mutations targeted to two internal segments of the S14-coding sequence and designated these functionally critical regions as domains B and D. Further, we inferred that structural determinants within domains B and D are required for proper incorporation of the S14 protein into nascent 40 S ribosomal particles and/or for the normal function of mature cytoplasmic ribosomes. In this study we have used immunofluorescence to monitor the intracellular trafficking of epitopically labeled human S14 protein isoforms transiently expressed by cultured Chinese hamster cells. Data obtained distinguish null alleles of RPS14 which encode proteins that are not incorporated into pre-ribosomal subunit particles from null alleles whose products are compatible with normal ribosome assembly processes but result in functionally inactive cytoplasmic 40 S ribosomal subunits. Mutations assigned to the first allele class involve amino acid replacements located within S14 domains B and D; whereas mutations assigned to the second class are distributed throughout the S14 protein-coding sequence.

Analysis of a 103 kbp cluster homology region from the left end of Saccharomyces cerevisiae chromosome I

The DNA sequence and preliminary functional analysis of a 103-kbp section of the left arm of yeast chromosome I is presented. This region, from the left telomere to the LTE1 gene, can be divided into two distinct portions. One portion, the telomeric 29 kbp, has a very low gene density (only five potential genes and 21 kbp of noncoding sequence), does not encode any "functionally important" genes, and is rich in sequences repeated several times within the yeast genome. The other portion, with 37 genes and only 14.5 kbp of noncoding sequence, is gene rich and codes for at least 16 "functionally important" genes. The entire gene-rich portion is apparently duplicated on chromosome XV as an extensive region of partial gene synteney called a cluster homology region. A function can be assigned with varying degrees of precision to 23 of the 42 potential genes in this region; however, the precise function is know for only eight genes. Nineteen genes encode products presently novel to yeast, although five of these have homologs elsewhere in the yeast genome.

The plant translational apparatus

Protein synthesis in both eukaryotic and prokaryotic cells is a complex process requiring a large number of macromolecules: initiation factors, elongation factors, termination factors, ribosomes, mRNA, amino-acylsynthetases and tRNAs. This review focuses on our current knowledge of protein synthesis in higher plants.

Identification and phylogenetic classification of eleven putative P-type calcium transport ATPase genes in the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe

Calcium is an essential second messenger in yeast metabolism and physiology. So far, only four genes coding for calcium translocating ATPases had been discovered in yeast. The recent completion of the yeast Saccharomyces cerevisiae genome allowed us to identify six new putative Ca(++)-ATPases encoding genes. Protein sequence homology analysis and phylogenetic classification of all putative Ca(++)-ATPase gene products from the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe reveal three clusters of homologous proteins. Two of them comprises seven proteins which might belong to a new class of P-type ATPases of unknown subcellular location and of unknown physiological function.

Multiple regions of yeast ribosomal protein L1 are important for its interaction with 5 S rRNA and assembly into ribosomes

Yeast ribosomal protein L1 binds to 5 S rRNA and can be released from 60 S ribosomal subunits as an intact ribonucleoprotein particle. To identify residues important for binding of Saccharomyces cerevisiae rpL1 to 5 S rRNA and assembly into functional ribosomes, we have isolated mutant alleles of the yeast RPL1 gene by site-directed and random mutagenesis. The rpl1 mutants were assayed for association of rpL1 with 5 S rRNA in vivo and in vitro and assembly of rpL1 into functional 60 S ribosomal subunits. Consistent with previous data implicating the importance of the carboxyl-terminal 47 amino acids of rpL1 for binding to 5 S rRNA in vitro, we find that deletion of the carboxyl-terminal 8, 25, or 44 amino acids of rpL1 confers lethality in vivo. Missense mutations elsewhere in rpL1 also affect its function, indicating that multiple regions of rpL1 are important for its association with 5 S rRNA and assembly into ribosomes.

An overview of membrane transport proteins in Saccharomyces cerevisiae

All eukaryotic cells contain a wide variety of proteins embedded in the plasma and internal membranes, which ensure transmembrane solute transport. It is now established that a large proportion of these transport proteins can be grouped into families apparently conserved throughout organisms. This article presents the data of an in silicio analysis aimed at establishing a preliminary classification of membrane transport proteins in Saccharomyces cerevisiae. This analysis was conducted at a time when about 65% of all yeast genes were available in public databases. In addition to approximately 60 transport proteins whose function was at least partially known, approximately 100 deduced protein sequences of unknown function display significant sequence similarity to membrane transport proteins characterized in yeast and/or other organisms. While some protein families have been well characterized by classical genetic experimental approaches, others have largely if not totally escaped characterization. The proteins revealed by this in silicio analysis also include a putative K+ channel, proteins similar to aquaporins of plant and animal origin, proteins similar to Na+-solute symporters, a protein very similar to electroneural cation-chloride cotransporters, and a putative Na+-H+ antiporter. A new research area is anticipated: the functional analysis of many transport proteins whose existence was revealed by genome sequencing.

Processing of pre-ribosomal RNA in Saccharomyces cerevisiae

Post-transcriptional processing of precursor-ribosomal RNA comprises a complex pathway of endonucleolytic cleavages, exonucleolytic digestion and covalent modifications. The general order of the various processing steps is well conserved in eukaryotic cells, but the underlying mechanisms are largely unknown. Recent analysis of pre-rRNA processing, mainly in the yeast Saccharomyces cerevisiae, has significantly improved our understanding of this important cellular activity. Here we will review the data that have led to our current picture of yeast pre-rRNA processing.

Trans-acting factors in yeast pre-rRNA and pre-snoRNA processing

The major intermediates in the pathway of pre-rRNA processing in yeast and other eukaryotes were originally identified by biochemical analyses. However, as a result of the analysis of the effects of mutations in trans-acting factors, the yeast pre-rRNA processing pathway is now characterized in far more detail than that of other eukaryotes. These analyses have led to the identification of processing sites and intermediates that were either too close in size or too short lived to detected by biochemical analyses alone. In addition, it was generally unclear whether pre-rRNA processing steps were endonucleolytic or exonucleolytic; analyses of trans-acting factors is now revealing a complex mixture of endonucleolytic and exonucleolytic processing steps. Many of the small nucleolar RNAs (snoRNAs) are excised from larger precursors. Analyses of trans-acting factors are also revealing details of pre-snoRNA processing in yeast. Interestingly, factors involved in pre-snoRNA processing turn out to be components that also function in pre-rRNA processing, suggesting a potential mechanism for the coregulation of rRNA and snoRNA synthesis. In general, very little is known about the regulation of pre-rRNA processing steps. The best candidate for a system regulating specific pre-rRNA processing reactions has recently been revealed by the analysis of a yeast pre-RNA methylase. Here we will review recent data on the trans-acting factors involved in yeast ribosome synthesis and discuss how these analyses have contributed to our current view of this complex process.

Molecular cloning and sequence of two novel P-type adenosinetriphosphatases from Plasmodium falciparum

We have identified two novel P-type ATPase genes from Plasmodium falciparum and report the full-length nucleotide and derived amino acid sequence of the ATPase2 gene from P. falciparum (PfATPase2). PfATPase2 is phylogenetically remote from the different members of prokaryotic and mammalian P-type ATPases but shares features with a putative membrane-spanning Ca2+ ATPase involved in ribosome function in yeast. PfATPase2 is expressed during the intraerythrocytic life cycle of the parasite and appears to be required in the late stages of its asexual development. We also present the partial sequence of another malarial gene displaying sequence similarity with the family of P-type transporting ATPases (PfATPase4). We have analysed the organisation of the genes encoding the P-type ATPases of P. falciparum and show that they are a highly dispersed gene family.