EBP2 Is a Member of the Yeast RRB Regulon, a Transcriptionally Coregulated Set of Genes That Are Required for Ribosome and rRNA Biosynthesis

Abstract

In an effort to identify sets of yeast genes that are coregulated across various cellular transitions, gene expression data sets derived from yeast cells progressing through the cell cycle, sporulation, and diauxic shift were analyzed. A partitioning algorithm was used to divide each data set into 24 clusters of similar expression profiles, and the membership of the clusters was compared across the three experiments. A single cluster of 189 genes from the cell cycle experiment was found to share 65 genes with a cluster of 159 genes from the sporulation data set. Many of these genes were found to be clustered in the diauxic-shift experiment as well. The overlapping set was enriched for genes required for rRNA biosynthesis and included genes encoding RNA helicases, subunits of RNA polymerases I and III, and rRNA processing factors. A subset of the 65 genes was tested for expression by a quantitative-relative reverse transcriptase PCR technique, and they were found to be coregulated after release from alpha factor arrest, heat shock, and tunicamycin treatment. Promoter scanning analysis revealed that the 65 genes within this ribosome and rRNA biosynthesis (RRB) regulon were enriched for two motifs: the 13-base GCGATGAGATGAG and the 11-base TGAAAAATTTT consensus sequences. Both motifs were found to be important for promoting gene expression after release from alpha factor arrest in a test rRNA processing gene (EBP2), which suggests that these consensus sequences may function broadly in the regulation of a set of genes required for ribosome and rRNA biosynthesis.Ribosome biosynthesis is a complex and demanding process that depends directly upon multiple metabolic pathways, including the activities of three different RNA polymerases (reviewed in references 21 and 27). In Saccharomyces cerevisiae there are 137 ribosomal protein genes (RP genes), and they are transcribed by RNA polymerase II to yield 78 ribosomal proteins. Because the RP genes are transcribed at such a high level, together they account for nearly 50% of the total RNA polymerase II-mediated transcription initiation events (18). The 25S, 18S, and 5.8S rRNAs are synthesized by RNA polymerase I, first as a large 35S transcript that subsequently gets processed into the three smaller, mature species. Synthesis of the 5S rRNA is distinct from the other rRNAs and is carried out by RNA polymerase III. In order to achieve the high levels of rRNA production that are required during rapid cell division, yeast cells contain roughly 150 repeats of the rRNA genes in a tandem array on chromosome XII. Together, these repeats represent 10% of the genome, and rRNA production alone accounts for some 60% of the total cellular transcription.Ribosome biogenesis also depends upon the activities of a large number of protein and RNA molecules that are not themselves components of the final ribosome. The complex processing pathway that converts the 35S precursor rRNA into the mature 25S, 18S, and 5.8S rRNA species requires a multitude of factors, including RNA endonucleases, exon...

Revisiting the role of yeast Sfp1 in ribosome biogenesis and cell size control: a chemostat study

“…Downregulation of the RP genes observed in sfp1D mutants during growth in shake flasks might be a secondary effect due to growth rate defects. Finally, several expression profiles published elsewhere (Saldanha et al, 2004;Wade et al, 2001) together with the observed differences in the promoter regions lend further support to our hypothesis on the differential regulation of RiBi and RP gene clusters.…”

“…The promoters of the 155 genes that were downregulated during glucose-limited growth were specially enriched for the presence of RRPE and PAC elements [RRPE5GAAAAWWTT, PAC5GMRATGARNT (Hughes et al, 2000); see Methods]. It has been previously shown that these elements are typical of the gene clusters involved in ribosome biogenesis, while they are not present in RP gene promoters (Hughes et al, 2000;Wade et al, 2001;Wang et al, 2004). We found that among the 155 analysed promoters, 106 and 55 contained RRPE and PAC, respectively, suggesting the existence of a functional link between Sfp1 activity and the genes containing these promoter elements.…”

Rrs1 Is Involved in Endoplasmic Reticulum Stress Response in Huntington Disease

“…This subnucleolar compartment contains actively transcribing rDNA along with nascent rRNA, and it is the site of maturation of pre-rRNA transcripts. These data are in full agreement with Rrs1 expression and function in yeast, where it was found to be a component of the yeast ribosome and rRNA biosynthesis regulon, a co-regulated cluster of genes that function in various aspects of ribosome biosynthesis (31).…”

Is Ribosome Synthesis Controlled by Pol I Transcription?

“…Although spread throughout the yeast genome, these genes are arguably the most coordinately regulated cluster of genes and are thus considered as a regulon (i.e., the RP regulon). 2,16,35 Remarkably, however, regulation of another regulon, the Ribi regulon (for ribosome biogenesis), which shows nearly identical transcriptional responses as RP genes to environmental or genetic perturbations, 16,[36][37][38][39] is similar in CARA and wild-type cells upon rapamycin treatment (Fig. 1).…”

“…The two spots, corresponding to RRN3 and RPA43 mRNAs (indicated by an arrow), which belongs to the Ribi regulon, are overexpressed in CARA cells because the Rrn3-A43 fusion is expressed from a multicopy plasmid. assemble and modify rRNA and RPs [36][37][38]40 as well as additional functional categories including subunits of Pol I and Pol III, enzymes involved in ribonucleotide metabolism, tRNA synthetases, and translation factors. 16,37,38 The Ribi regulon thus consists of non-RP genes that enhance translational capacity.…”