Regulation of ribosome synthesis in yeast.
Explore the source record for details and available documents.
Fungal Proteins↗
Biomedical subjects
R J Planta
Publications and source records attributed to R J Planta.
Variable region V1 of Saccharomyces cerevisiae 18S rRNA participates in biogenesis and function of the small ribosomal subunit.
The role of helix 6, which forms the major portion of the most 5'-located expansion segment of Saccharomyces cerevisiae 18S rRNA, was studied by in vivo mutational analysis. Mutations that increased the size of the helical part and/or the loop, even to a relatively small extent, abolished 18S rRNA formation almost completely. Concomitantly, 35S pre-rRNA and an abnormal 23S precursor species accumulated. rDNA units containing these mutations did not support cell growth. A deletion removing helix 6 almost completely, on the other hand, had a much less severe effect on the formation of 18S rRNA, and cells expressing only the mutant rRNA remained able to grow, albeit at a much reduced rate. Disruption of the apical A.U base pair by a single point mutation did not cause a noticeable reduction in the level of 18S rRNA but did result in a twofold lower growth rate of the cells. This effect could not be reversed by introduction of a second point mutation that restores base pairing. We conclude that both the primary and the secondary structure of helix 6 play an important role in the formation and the biological function of the 40S subunit.
Base Sequence↗
Signalling pathways leading to transcriptional regulation of genes involved in the activation of glycolysis in yeast.
Addition of glucose to yeast cells growing on less preferred carbon sources triggers profound changes in the expression levels of several genes. This paper focuses on the signal transduction pathways leading to transcriptional activation of the glycolysis in Saccharomyces cerevisiae during the transition from respiratory to fermentative growth conditions. To this end, we studied the transcriptional regulation of glycolytic genes (PFK1, PYK1 and PDC), one gluconeogenic gene (FBP1) and the two genes encoding the 6-phosphofructo-2-kinase isoenzymes (PFK26 and PFK27) during this transition. The results of experiments using glycolysis mutants, different fermentable carbon sources and 2-deoxyglucose indicate that proper transcriptional regulation of these genes is dependent on the ability to form glucose 6-phosphate by any one of the three hexose kinases. In addition, we conclude that signalling via the Ras-adenylate cyclase pathway is not necessary for the proper transcriptional response of glycolytic and gluconeogenic genes to glucose, because the transcription of these genes is not significantly affected in mutants having either high or low activities of this pathway. In contrast, the transcriptional regulation of the PFK26 and PFK27 genes is significantly altered in several of the Ras-adenylate cyclase pathway mutants studied, indicating that protein kinase A plays an important role in the transcriptional regulation of these genes.
Adenylyl Cyclases↗
Molecular cloning and pharmacological characterization of a molluscan octopamine receptor.
We describe the cloning and functional expression of a cDNA encoding a novel G protein-coupled receptor, which was isolated from the central nervous system of the pond snail Lymnaea stagnalis. The amino acid sequence predicted by this cDNA shows highest similarity with the sequence of the Locusta tyramine receptor, the Drosophila tyramine/octopamine receptor, and the mammalian alpha-adrenergic receptors. On expression in mammalian cells, [3H]rauwolscine, an alpha2-adrenergic receptor antagonist, binds with high affinity (K(D) = 2.9 x 10(-9) M) to the receptor. Of several tested neurotransmitters, octopamine (which is considered to be the invertebrate counterpart of norepinephrine) showed the highest affinity (1.9 x 10(-6) M) for the receptor. Therefore, we consider this receptor to be the first true octopamine receptor to be cloned. The ligand binding properties of the novel receptor, designated Lym oa1, seem to be distinct from any of the binding profiles described for octopamine receptors in tissue preparations. Although the pharmacological profile of Lym oa1 shows some similarity with that of Tyr/Oct-Dro and Tyr-Loc, there are also clear differences. In particular, phentolamine, chlorpromazine, and mianserine display markedly higher affinities for Lym oa1 than for the insect receptors. As far as the vertebrate adrenergic receptors are concerned, the ligand binding properties of Lym oa1 resemble alpha2-adrenergic receptors more than they do alpha- or beta-adrenergic receptors. Octopaminergic stimulation of Lym oa1 induces an increase in both inositol phosphates and cAMP (EC50 = 9.1 x 10(-7) M and 5.1 x 10(-6) M, respectively). This is in contrast to the signal transduction pathways described for the related tyramine- and alpha2-adrenergic receptors, which couple in an inhibitory way to adenylyl cyclase.
Amino Acid Sequence↗
Functional characterisation of a 5-HT2 receptor cDNA cloned from Lymnaea stagnalis.
A G-protein-coupled receptor (5-HT2Lym) resembling members of the 5-HT2 receptor subfamily was cloned from the mollusc Lymnaea stagnalis. Serotonin induces a concentration-dependent increase in intracellular inositol phospates in HEK293 cells expressing this receptor (EC50 = 114 nM). 5-HT2Lym differs from mammalian 5-HT2 receptors by the presence of a large amino-terminal region. This large domain appears to preclude an adequate level of expression of 5-HT2Lym in HEK293. Therefore, we constructed a cDNA encoding an amino-terminally truncated receptor (delta N-5-HT2Lym) that appeared to be much better expressed in HEK293 cells. delta N-5-HT2Lym-expressing cells exhibit a serotonin-induced stimulation of phosphatidylinositol bisphosphate hydrolysis (EC50 = 11.4 nM) and a high-affinity binding of the 5-HT2-selective antagonist [3H]mesulergine (Kd = 4 nM). Inhibition of this binding by several 5-HT2 antagonists and agonists revealed a pharmacological profile most closely resembling those of 5HT2Dro, 5-HT2B and 5-HT2C.
Amino Acid Sequence↗
Factors affecting the mitotic stability of high-copy-number integration into the ribosomal DNA of Saccharomyces cerevisiae.
Yeast vectors suitable for high-level expression of heterologous proteins should combine a high copy number with high mitotic stability. The pMIRY integrative vector system, based upon targeted integration into the yeast rDNA locus, developed in our laboratory satisfies these criteria. However, insertion of a (foreign) gene drastically reduced its mitotic stability of the resulting vector in comparison to its parent. In this paper we have investigated a number of possible reasons for this reduction in stability. The results demonstrate that plasmid size is an important, but not the only, determinant of mitotic stability. Stable maintenance is only observed when the complete plasmid has a size no larger than that of the rDNA unit (9.1 kb). In addition stability depends upon the nature of the rDNA fragment present in the plasmid, required for targeting its integration. On the other hand, it turned out to be irrelevant for mitotic stability whether the heterologous gene was expressed or not. These findings will be important in the design of a pMIRY vector suitable for industrial production of heterologous proteins.
DNA, Fungal↗
C-terminal domains of general regulatory factors Abf1p and Rap1p in Saccharomyces cerevisiae display functional similarity.
Abf1p and Rap1p are global regulatory factors which play an essential role in the transcription activation of yeast ribosomal protein genes. This functional link prompted us to investigate whether these factors may be functionally interchangeable. We focused on the indispensable C-terminal portions of both factors and performed mutual domain swaps. The functional capacity of the resulting hybrid proteins was subsequently examined using yeast strains conditionally expressing either the ABF1 or the RAP1 gene. Both the Abf1p-Rap1p and the Rap1p-Abf1p fusion proteins were found to be able to complement the growth defect of the respective strains. Furthermore, Abf1p and Rap1p are both able to promote transcription of a reporter gene through a combination of the respective binding site and a T-rich promoter element. These data strongly suggest that the C-terminal domains of Abf1p and Rap1p have, at least partially, identical functions. Finally, a deletion analysis of the so far largely uncharacterized C-terminal domain of Abf1p was performed, which revealed that two regions of 50 amino acids can perform all essential Abf1p functions.
Amino Acid Sequence↗
Ribosomal protein gene transcription in Saccharomyces cerevisiae shows a biphasic response to nutritional changes.
Nutrients are major determinants of ribosomal protein (rp-) gene transcription in Saccharomyces cerevisiae. In order to investigate the molecular mechanisms underlying this nutritional control, yeast mutants that display defects in the glucose up-shift response of rp-gene transcription were isolated. Interestingly, although growth of these mutants on glucose-containing medium was severely affected an initial increase in rp-gene transcription by nutritional up-shift was still observed. However, at later time points, rp-mRNA levels decreased strongly. Various other types of severe growth limitation also did not prevent the initial up-shift in transcription. The results suggest that the glucose up-shift response of rp-gene transcription comprises two phases: an initial, transient response independent of the actual growth potential, and a sustained response which is dependent on growth and requires both glucose and adequate nitrogen sources. Previously, it was found that protein kinase A (Pka) mediates the initial up-shift response, without the need for regulation of Pka activity by cAMP. The present data substantiate that, besides the RAS/adenylate cyclase pathway, an alternative pathway through Pka regulates rp-gene transcription. In addition, evidence is presented that the sustained response does not require Pka activity. Based on these results, taken together, a model is proposed in which rp-gene transcription is dynamically regulated by multiple signal transduction pathways.
Blotting, Northern↗
Characterization of a putative molluscan insulin-related peptide receptor.
In the pond snail Lymnaea stagnalis (Ls), growth and associated processes are likely to be controlled by a family of molluscan insulin-related peptides (MIP). Here we report on the cloning of a cDNA encoding a putative receptor for these MIP. This cDNA was isolated from Ls via PCR with degenerate oligodeoxynucleotides corresponding to conserved parts of the tyrosine kinase domain of the human insulin receptor and its Drosophila homologue. Many of the typical insulin-receptor features, including a cysteine-rich domain, a single transmembrane domain and a tyrosine-kinase domain are conserved in the predicted, 1607-amino acid (aa) protein. Comparison of the aa sequence of the molluscan receptor to other insulin-receptor sequences revealed strong variations in the percentage of sequence identity for the different domains, ranging from 70% sequence identity in the tyrosine-kinase domain to virtually no sequence identity in the C-terminal sequence. Striking differences are the absence of a clear tetrabasic cleavage site, and the extremely long C-terminus of 308 aa that contains seven Tyr residues. Southern blot analyses at varying stringencies, extensive screening of cDNA- and genomic libraries, and PCR experiments indicate the presence of a single putative MIP receptor. This suggests that the four different MIP may exert their functional role in Ls by binding to the same receptor.
Amino Acid Sequence↗
A novel G protein alpha subunit containing atypical guanine nucleotide-binding domains is differentially expressed in a molluscan nervous system.
We described the characterization of a novel G protein alpha subunit, G alpha a. cDNA encoding this subunit was cloned from the central nervous system of the mollusc Lymnaea stagnalis. The deduced protein contains all characteristic guanine nucleotide-binding domains of G alpha subunits but shares only a limited degree of overall sequence identity with known subtypes (approximately 30%). Moreover, two of the nucleotide-binding domains exhibit salient deviations from corresponding sequences in other G protein alpha subunits. The A domain, determining kinetic features of the GTPase cycle, contains a markedly unique amino acid sequence (ILIIGGPGAGK). In addition, the C domain is also clearly distinct (DVAGQRSL). The presence of a leucine in this motif, instead of glutamic acid, has important implications for hypotheses concerning the GTPase mechanism. In contrast to other G alpha subtypes, G alpha a has no appropriate N-terminal residues that could be acylated. It does contain the strictly conserved arginine residue that serves as a cholera toxin substrate in G alpha s and G alpha t but lacks a site for ADP-ribosylation by pertussis toxin. In situ hybridization experiments indicate that G alpha a-encoding mRNA is expressed in a limited subpopulation of neurons within the Lymnaea brain. These data suggest that G alpha a defines a separate class of G proteins with cell type-specific functions.
Amino Acid Sequence↗
Evolutionarily conserved structural elements are critical for processing of Internal Transcribed Spacer 2 from Saccharomyces cerevisiae precursor ribosomal RNA.
Structural features of Internal Transcribed Spacer 2 (ITS2) important for the correct and efficient removal of this spacer from Saccharomyces cerevisiae pre-rRNA were identified by in vivo mutational analysis based upon phylogenetic comparison with its counterparts from four different yeast species. Compatibility between ITS2 structure and the S. cerevisiae processing machinery was found to have been maintained over only a short evolutionary distance, in contrast to the situation for ITS1. Nevertheless, cis-acting elements required for correct and efficient processing are confined predominantly to those regions of the spacer that show the highest degree of evolutionary conservation. Mutation or deletion of each of these regions severely reduced production of mature 26 S, but not 17 S rRNA, mainly by impeding processing of the 29 SB precursor. In some cases, however, conversion of 29SA into 29 SB pre-rRNA also appeared to be affected. Deletion of non-conserved segments, on the other hand, caused little or no disturbance in processing. Surprisingly, some combinations of such individually neutral deletions had a severe negative effect on the removal of ITS2, suggesting a requirement for a higher-order structure of ITS2. Finally, even structural alterations of ITS2 that did not noticeably affect processing, significantly reduced the growth rate of cells that exclusively express the mutant rDNA units. We take this as further evidence for a direct role of ITS2 in the formation of fully functional 60 S ribosomal subunits.
Base Sequence↗
Cloning of a molluscan G protein alpha subunit of the Gq class which is expressed differentially in identified neurons.
Through molecular cloning we have identified a molluscan G protein alpha subunit which belongs to the G alpha q family and is expressed in the central nervous system (CNS) of the pond snail, Lymnaea stagnalis. The deduced protein product shares a very high degree of amino sequence identity with vertebrate and invertebrate G alpha q/G alpha 11 subunits (80-82% and 76-77%, respectively). Large parts of the protein have been completely conserved, among which are residues 25-58, including the nucleotide-binding A domain. Especially the C-terminal half (amino acids 195-353), implicated in receptor and effector interactions, is highly conserved (94% sequence identity with murine sequences). This region includes the nucleotide-binding C, G, and I domains, which are identical to cognate motifs of vertebrate G alpha q/11. Like the latter proteins, the Lymnaea G alpha q C-terminus lacks a cysteine that could serve as a substrate for pertussis toxin. In situ hybridization reveals G alpha q-encoding mRNA(s) to be present throughout the CNS. Interestingly, however, close inspection of two identified cell types in the cerebral ganglia, the light-green cells, involved in the regulation of growth and metabolism and the anterior lobe cells which are involved in the control of male aspects of reproduction, indicates that they express the mRNA(s) at significantly different levels. Even within the heterologous cluster of light-green cells there appears to be differential expression of the pertinent mRNA. Such observations have hitherto not been reported for specific cell types occurring in vivo.
Amino Acid Sequence↗
Transcription activation of yeast ribosomal protein genes requires additional elements apart from binding sites for Abf1p or Rap1p.
All ribosomal protein (rp) gene promoters from Saccharomyces cerevisiae studied so far contain either (usually two) binding sites for the global gene regulator Rap1p or one binding site for another global factor, Abf1p. Previous analysis of the rpS33 and rpL45 gene promoters suggested that apart from the Abf1 binding site, additional cis-acting elements play a part in transcription activation of these genes. We designed a promoter reconstruction system based on the beta-glucuronidase reporter gene to examine the role of the Abf1 binding site and other putative cis-acting elements in promoting transcription. An isolated Abf1 binding site turned out to be a weak activating element. A T-rich sequence derived from the rpS33 proximal promoter was found to be stronger, but full transcription activation was only achieved by a combination of these elements. Both in the natural rpL45 promoter and in the reconstituted promoter, a Rap1 binding site could functionally replace the Abf1 binding site. Characteristic rp gene nutritional control of transcription, evoked by a carbon source upshift or by nitrogen re-feeding to nitrogen starved cells, could only be mediated by the combined Abf1 (or Rap1) binding site and T-rich element and not by the individual elements. These results demonstrate that Abf1p and Rap1p do not activate rp genes in a prototypical fashion, but rather may serve to potentiate transcription activation through the T-rich element.
Base Sequence↗
Sequence analysis of a 30 kb DNA segment from yeast chromosome XIV carrying a ribosomal protein gene cluster, the genes encoding a plasma membrane protein and a subunit of replication factor C, and a novel putative serine/threonine protein kinase gene.
We have determined the nucleotide sequence of a 30 kb fragment of chromosome XIV of Saccharomyces cerevisiae. The sequence revealed the presence of 19 open reading frames (ORFs) longer than 300 bp. NO422 and NO425 correspond to the split ribosomal protein genes encoding S16A and rp28, respectively, NO450 displays a striking similarity with serine/threonine protein kinase genes, in particular with STE20, and therefore may encode a novel member of this protein family. NO453 is the longest ORF in this DNA segment, having a size of 4908 bp, but its function is not yet known. NO530 encodes the plasma membrane protein Mid1p and NO533 corresponds to the gene coding for a 40 kDa subunit of replication factor C. The remaining ORFs show weak or no homology with proteins in the data bases.
Amino Acid Sequence↗
The Saccharomyces cerevisiae HSP12 gene is activated by the high-osmolarity glycerol pathway and negatively regulated by protein kinase A.
The HSP12 gene encodes one of the two major small heat shock proteins of Saccharomyces cerevisiae. Hsp12 accumulates massively in yeast cells exposed to heat shock, osmostress, oxidative stress, and high concentrations of alcohol as well as in early-stationary-phase cells. We have cloned an extended 5'-flanking region of the HSP12 gene in order to identify cis-acting elements involved in regulation of this highly expressed stress gene. A detailed analysis of the HSP12 promoter region revealed that five repeats of the stress-responsive CCCCT motif (stress-responsive element [STRE]) are essential to confer wild-type induced levels on a reporter gene upon osmostress, heat shock, and entry into stationary phase. Disruption of the HOG1 and PBS2 genes leads to a dramatic decrease of the HSP12 inducibility in osmostressed cells, whereas overproduction of Hog1 produces a fivefold increase in wild-type induced levels upon a shift to a high salt concentration. On the other hand, mutations resulting in high protein kinase A (PKA) activity reduce or abolish the accumulation of the HSP12 mRNA in stressed cells. Conversely, mutants containing defective PKA catalytic subunits exhibit high basal levels of HSP12 mRNA. Taken together, these results suggest that HSP12 is a target of the high-osmolarity glycerol (HOG) response pathway under negative control of the Ras-PKA pathway. Furthermore, they confirm earlier observations that STRE-like sequences are responsive to a broad range of stresses and that the HOG and Ras-PKA pathways have antagonistic effects upon CCCCT-driven transcription.
Consensus Sequence↗
The pathway to maturity: processing of ribosomal RNA in Saccharomyces cerevisiae.
The 17-18S, 5.8S, and 25-28S rRNA species of eukaryotic cells are transcribed by RNA polymerase I into a single precursor molecule, from which external and internal spacer sequences are subsequently removed in an order series of nucleolytic reactions. Whereas the order of the cleavage reactions has long been established, only recently has significant progress been made in detailing the cis-acting elements and the trans-acting factors involved in this process. The use of recently developed systems for in vivo mutational analysis of yeast rDNA has greatly enhanced our knowledge of cis-acting structural features within the pre-rRNA, which are critical for correct and efficient removal of the spacer sequences. The same systems also allow a link to be forged between trans-acting processing factors and these cis-acting elements. In this review the newly obtained information will be summarized, focused predominantly on pre-rRNA processing in the yeast Saccharomyces cerevisiae.
Fungal Proteins↗
Nutritional upshift response of ribosomal protein gene transcription in Saccharomyces cerevisiae.
Switching Saccharomyces cerevisiae from non-fermentative to fermentative growth by adding glucose to a medium with glycerol as the sole carbon source, leads to a sudden increase in the rate of ribosomal protein gene transcription. By analyzing the nutritional shift response in a variety of yeast mutants and in the presence of different drugs, evidence was obtained that: (i) no de novo protein synthesis is required for this response; (ii) protein kinase A is essential, though independent of intracellular levels of cAMP, whereas protein kinase C is not involved; (iii) proper regulation of sugar phosphorylation is essential; (iv) glycolysis is required for the long term effect of the nutritional upshift; and (v) pathways leading to glucose-induced activation differ from those leading to gene repression, probably already at the level of glucose transport.
Cyclic AMP↗
Complete DNA sequence of yeast chromosome XI.
The complete DNA sequence of the yeast Saccharomyces cerevisiae chromosome XI has been determined. In addition to a compact arrangement of potential protein coding sequences, the 666,448-base-pair sequence has revealed general chromosome patterns; in particular, alternating regional variations in average base composition correlate with variations in local gene density along the chromosome. Significant discrepancies with the previously published genetic map demonstrate the need for using independent physical mapping criteria.
Base Sequence↗