Characterization of the ORF YBR264c in Saccharomyces cerevisiae, which encodes a new yeast Ypt that is degraded by a proteasome-dependent mechanism

We identified the ORF YBR264c during the systematic sequencing of the Saccharomyces cerevisiae genome. It encodes a putative protein of 218 amino acids. We demonstrate here that the gene is indeed expressed and encodes a new Ypt in yeast. This protein specifically binds guanine nucleotides and interacts via its C-terminal end with the unique Rab GDP Dissociation Inhibitor (RabGDI). In accordance with a recent proposal, the gene is now designated YPT10. No mutant phenotype could be associated with inactivation of the gene. However, overexpression of YPT10 resulted in defects in growth; microscopic examination of such cells revealed an overabundance of vesicular and tubular structures, suggesting some alteration in the function of the Golgi apparatus. In addition, degradation of the Ypt10 protein, which possesses a PEST sequence, is shown to be dependent on proteasome activity.     

The Saccharomyces cerevisiae YBR159w gene encodes the 3-ketoreductase of the microsomal fatty acid elongase

The YBR159w gene encodes the major 3-ketoreductase activity of the elongase system of enzymes required for very long-chain fatty acid (VLCFA) synthesis. Mutants lacking the YBR159w gene display many of the phenotypes that have previously been described for mutants with defects in fatty acid elongation. These phenotypes include reduced VLCFA synthesis, accumulation of high levels of dihydrosphingosine and phytosphingosine, and accumulation of medium-chain ceramides. In vitro elongation assays confirm that the ybr159Delta mutant is deficient in the reduction of the 3-ketoacyl intermediates of fatty acid elongation. The ybr159Delta mutant also displays reduced dehydration of the 3-OH acyl intermediates of fatty acid elongation, suggesting that Ybr159p is required for the stability or function of the dehydratase activity of the elongase system. Green fluorescent protein-tagged Ybr159p co-localizes and co-immunoprecipitates with other elongating enzymes, Elo3p and Tsc13p. Whereas VLCFA synthesis is essential for viability, the ybr159Delta mutant cells are viable (albeit very slowly growing) and do synthesize some VLCFA. This suggested that a functional ortholog of Ybr159p exists that is responsible for the residual 3-ketoreductase activity. By disrupting the orthologs of Ybr159w in the ybr159Delta mutant we found that the ybr159Deltaayr1Delta double mutant was inviable, suggesting that Ayr1p is responsible for the residual 3-ketoreductase activity.     

Expression of the homeobox gene,Hox 2.1, during mouse embryogenesis

This article reviews recent studies on the expression of the homeobox gene, Hox 2.1, during mouse embryogenesis, using the technique of in situ hybridization. Differential hybridization of radiolabelled antisense versus sense strand RNA is first clearly detected in sections of 8.5 day post coitum (p.c.) early somite embryos. At 12.5 days p.c., higher levels of Hox 2.1 expression are seen in the spinal cord, extending into the base of the hind brain. Hybridization of antisense Hox 2.1 RNA is also seen in the spinal ganglia, in the nodose ganglia of the Xth cranial nerve (which contains derivatives of the neural crest arising from the posterior hind brain), and in the myenteric plexus. Mesodermal cells of certain visceral organs also express Hox 2.1 RNA, in particular the mesoderm of the lung, stomach and meso- and meta-nephric kidney. Comparison of the spatial domains of expression of mouse homeobox genes reveals a pattern consistent with the idea that they play a role in anteroposterior positional specification during embryogenesis.     

Identification of a novel methyltransferase,Bmt2, responsible for the N-1-methyl-adenosine base modification of 25S rRNA in Saccharomyces cerevisiae

The 25S rRNA of yeast contains several base modifications in the functionally important regions. The enzymes responsible for most of these base modifications remained unknown. Recently, we identified Rrp8 as a methyltransferase involved in m¹A645 modification of 25S rRNA. Here, we discovered a previously uncharacterized gene YBR141C to be responsible for second m¹A2142 modification of helix 65 of 25S rRNA. The gene was identified by reversed phase–HPLC screening of all deletion mutants of putative RNA methyltransferase and was confirmed by gene complementation and phenotypic characterization. Because of the function of its encoded protein, YBR141C was named BMT2 (base methyltransferase of 25S RNA). Helix 65 belongs to domain IV, which accounts for most of the intersubunit surface of the large subunit. The 3D structure prediction of Bmt2 supported it to be an Ado Met methyltransferase belonging to Rossmann fold superfamily. In addition, we demonstrated that the substitution of G180R in the S-adenosyl-l-methionine–binding motif drastically reduces the catalytic function of the protein in vivo. Furthermore, we analysed the significance of m¹A2142 modification in ribosome synthesis and translation. Intriguingly, the loss of m¹A2142 modification confers anisomycin and peroxide sensitivity to the cells. Our results underline the importance of RNA modifications in cellular physiology.     

Vhc1, a novel transporter belonging to the family of electroneutral cation–Cl− cotransporters,participates in the regulation of cation content and morphology of Saccharomyces cerevisiae vacuoles

Cation–Cl^? cotransporters (CCCs) are integral membrane proteins which catalyze the coordinated symport of Cl^? with Na⁺ and/or K⁺ ions in plant and mammalian cells. Here we describe the first Saccharomyces cerevisiae CCC protein, encoded by the YBR235w open reading frame. Subcellular localization studies showed that this yeast CCC is targeted to the vacuolar membrane. Deletion of the YBR235w gene in a salt-sensitive strain (lacking the plasma-membrane cation exporters) resulted in an increased sensitivity to high KCl, altered vacuolar morphology control and decreased survival upon hyperosmotic shock. In addition, deletion of the YBR235w gene in a mutant strain deficient in K⁺ uptake produced a significant growth advantage over the parental strain under K⁺-limiting conditions, and a hypersensitivity to the exogenous K⁺/H⁺ exchanger nigericin. These results strongly suggest that we have identified a novel yeast vacuolar ion transporter mediating a K⁺–Cl^? cotransport and playing a role in vacuolar osmoregulation. Considering its identified function, we propose to refer to the yeast YBR235w gene as VHC1 (vacuolar protein homologous to CCC family 1).     

In vitro selection supports the view of a kinetic control of antisense RNA-mediated inhibition of gene expression in mammalian cells

In principle, the steady-state concentrations of biomolecules in complex systems can be far from the thermodynamic equilibrium concentrations of individual processes. This means that, in addition to thermodynamics, reaction kinetics may play an important role. This view is not fully reflected in combinatorial studies in biochemistry that focus on the selection of stably interacting molecules reflected by high equilibrium constants. For kinetically controlled processes in vivo, forward or backward reaction rates are critical but not necessarily an equilibrium state. Here we have studied the control of antisense RNA-mediated gene suppression in human cells on a general basis and in a way that excludes individual structure-specific influences. The complete antisense sequence space against the chloramphenicol acetyltransferase gene (cat) was generated and a kinetic selection technique was established to enrich for fast annealing antisense species. Selected sub-populations showed successively faster annealing which was related to increased inhibition of cat gene expression in HeLa cells, providing strong evidence for the view that the suppression of gene expression by antisense RNA is controlled kinetically regardless of specific RNA structures.     

The sgp gene modulates stress responses of Streptococcus mutans: utilization of an antisense RNA strategy to investigate essential gene functions

The sgp gene from Streptococcus mutans has been previously isolated, characterized, and demonstrated to encode a G-protein. In order to investigate the function of this gene, a novel antisense RNA strategy was developed. Expression of sgp antisense RNA in Escherichia coli led to transient inhibition of growth. In addition, sgp antisense RNA expression in S. mutans resulted in decreased growth under environmental stress conditions (44°C, acidic pH, and high osmolarity). Therefore, these results suggest that the sgp gene plays a role in modulating the stress responses of S. mutans. This approach could be applicable for investigating the function of essential genes in other organisms for which mutants are not available.     

Masked antisense: a molecular configuration for discriminating similar RNA targets

Antisense technology has great potential for the control of RNA expression, but there remain few successful applications of the technology. Expressed antisense RNA can effectively down-regulate expression of a gene over long periods, but cannot differentiate partly identical sequences, such as the mRNA of fusion genes or those with point mutants. We have designed a structured form of expressed antisense, which can discriminate between highly similar mRNA molecules. These ‘masked’ antisense RNAs have most of the antisense sequence sequestered within duplex elements, leaving a short single-stranded region to initiate binding to target RNA. After contacting the correct target, the structured RNA can unravel, releasing the masked antisense region to form a stable duplex with the mRNA. We demonstrate that suitable masked antisense RNA can discriminate between the two forms of BCR–ABL mRNA that result from the Philadelphia chromosomal translocations, as well as discriminating the normal BCR and ABL mRNA.     

Two Distinct Pancreatic Amylase Genes Are Active in Ybr Mice

The genetic determinants of pancreatic amylase expression in YBR mice differ in two respects from those of other inbred strains. First, there are two nonallelic amylase isozymes present in YBR pancreas, while most mouse strains express a single pancreatic amylase protein. In addition, the in vivo rate of total pancreatic amylase synthesis is 50% of that in other strains. Both these traits are determined by genetic sites in the region of the Amy-2 locus on mouse chromosome 3. To determine the molecular basis for the presence of two isozymes in this strain, we have compared portions of their amino acid sequences. Two differences between isozymes A₁ and B₁ were identified among the 77 residues compared. This result demonstrates that two distinct amylase genes are expressed in YBR pancreas.     

Characterization of the ORF YBR264c in Saccharomyces cerevisiae, which encodes a new yeast Ypt that is degraded by a proteasome-dependent mechanism.

We identified the ORF YBR264c during the systematic sequencing of the Saccharomyces cerevisiae genome. It encodes a putative protein of 218 amino acids. We demonstrate here that the gene is indeed expressed and encodes a new Ypt in yeast. This protein specifically binds guanine nucleotides and interacts via its C-terminal end with the unique Rab GDP Dissociation Inhibitor (RabGDI). In accordance with a recent proposal, the gene is now designated YPT10. No mutant phenotype could be associated with inactivation of the gene. However, overexpression of YPT10 resulted in defects in growth; microscopic examination of such cells revealed an overabundance of vesicular and tubular structures, suggesting some alteration in the function of the Golgi apparatus. In addition, degradation of the Ypt10 protein, which possesses a PEST sequence, is shown to be dependent on proteasome activity. Received: 29 October 1998 / Accepted: 25 January 1999