Comparative Research: Regulatory Mechanisms of Ribosomal Gene Transcription in Saccharomyces cerevisiae and Schizosaccharomyces pombe

Abstract

Restricting ribosome biosynthesis and assembly in response to nutrient starvation is a universal phenomenon that enables cells to survive with limited intracellular resources. When cells experience starvation, nutrient signaling pathways, such as the target of rapamycin (TOR) and protein kinase A (PKA), become quiescent, leading to several transcription factors and histone modification enzymes cooperatively and rapidly repressing ribosomal genes. Fission yeast has factors for heterochromatin formation similar to mammalian cells, such as H3K9 methyltransferase and HP1 protein, which are absent in budding yeast. However, limited studies on heterochromatinization in ribosomal genes have been conducted on fission yeast. Herein, we shed light on and compare the regulatory mechanisms of ribosomal gene transcription in two species with the latest insights.

Keywords: TOR pathway; TORC1; budding yeast; epigenetics; fission yeast; gene regulation; heterochromatin; ribosome.

Figure 1

The structure of rDNA in S. pombe. rDNA regions exist on both ends of chromosome III in S. pombe. A single repeat of rDNA is shown in the dotted black box. 18S, 5.8S, and 28S rRNAs are transcribed by RNA polymerase I as the precursor rRNA from 5′ETS (external transcribed spacer) to 3′ETS. Four transcribed spacers (white boxes), including ITS (internal transcribed spacer) 1 and ITS 2, are removed by endonuclease and exonuclease processing.

Figure 2

Regulatory mechanism of ribosomal genes by TOR and PKA pathways. Of the two TOR complexes, TORC1, composed of Tor1, Kog1, Lst8, and Tco89, primarily regulates the transcription of ribosomal genes. Nutrient limitation or rapamycin treatments causes the inactivation of TORC1, leading to the downregulation of ribosomal gene expressions. The PKA pathway also contributes to the expression of ribosomal genes. In the presence of glucose, Cyr1, activated by Ras1/2 and Gpa2, converts ATP to cAMP. As a result of cAMP inhibiting Bcy1, free Tpk activates the transcription of ribosomal genes.

Figure 3

Regulatory mechanisms of rRNA expression in S. cerevisiae. A graphical view of how rDNA genes are transcriptionally regulated before and after starvation. In S. cerevisiae, half of the 150 copies of rDNA genes are active (the pink area). In contrast, nutrient starvation inactivates many repeats by the degradation of Rrn3, dissociation of Hmo1, and loss of H2AQ105 methylation (the blue area). Upon starvation, TORC1 deprivation leads to the accumulation of repressor Crf1 at the HMO1 promoter, resulting in the downregulation of HMO1 expression (in black square boxes). The deacetylase Rpd3 maintains a closed-chromatin formation, and H3K4 methyltransferase Set1 represses rRNA transcription in inactive rDNA repeats.

Figure 4

Regulatory mechanisms of RP gene expression in S. cerevisiae. In nutrient-rich environments (the pink area on the left), histone acetyltransferase Esa1 is recruited to the promoter of RP genes via interaction with Rap1. Ifh1 and Sfp1, which are recruited via the Fhl1 scaffold, also contribute to the expression of RP genes. In addition, the repressor Stb3 is phosphorylated by Sch9, which acts downstream of TORC1 (Tor1), preventing its accumulation at RP gene promoters. In nutrient-poor environments (the blue area on the right), Gcn4, interacting with Rap1, prevents the recruitment of Esa1 to RP genes. Moreover, Ifh1 and Sfp1 are dissociated from Fhl1, and the repressors Crf1 and Stb3 are recruited instead, leading to the accumulation of Rpd3.

Figure 5

Regulatory mechanisms of Ribi gene expression in S. cerevisiae. In nutrient-rich conditions (the pink area on the left), Sfp1 resides at Ribi gene promoters without Ifh1. Sfp1 might recruit Esa1 and upregulate the transcription of Ribi genes. Stb3, Dot6, and Tod6 phosphorylated by Sch9 and PKA are in the cytoplasm. During nutrient starvation (the blue area on the right), Stb3 binds to the RRPE motif (AAAAATTT) of Ribi genes, and Dot6/Tod6 accumulates at the PAC motif (CTCATCG). As a result of the recruitment of Rpd3 by these factors, Ribi gene expression is repressed.

Figure 6

Regulatory mechanisms of rDNA gene expression in S. pombe. In nutrient-rich conditions (the pink area on the left), transcription factor Atf1 prevents the accumulation of histone chaperone FACT. Gcn5 HAT competes with histone deacetylase and methyltransferase to inhibit hypermethylation of H3K9. Without FACT, histone turnover is facilitated so that H3K9 methylation is quickly removed. TRAMP/exosome prevents the deposition of RNAi-related proteins in rDNA, preventing H3K9 methylation and heterochromatinization. Disruption of RNAi-related genes or deacetylase genes causes an enhancement in rRNA expression, suggesting that an RNAi-dependent pathway accelerates heterochromatin formation in dormant rDNA repeats. In nutrient starvation (the blue area on the right), Atf1 and Gcn5 dissociate from rDNA, leading to the recruitment of FACT. Methylated histones are maintained by FACT, which prevents histone turnover. Removal of TRAMP/exosome from rDNA accelerates Ago1-dependent sRNA generation, resulting in the heterochromatin formation by RNAi-dependent pathway.