Mechanisms Coordinating Ribosomal Protein Gene Transcription in Response to Stress

Abstract

While expression of ribosomal protein genes (RPGs) in the budding yeast Saccharomyces cerevisiae has been extensively studied, a longstanding enigma persists regarding their co-regulation under fluctuating nutrient and stress conditions. Most (<90%) of RPG promoters display one of two distinct arrangements of a core set of transcription factors (TFs; Rap1, Fhl1 and Ifh1) and are further differentiated by the presence or absence of the HMGB box protein Hmo1. However, a third group of promoters appears not to bind any of these proteins, raising the question of how the whole suite of genes is co-regulated. We demonstrate that all RPGs are regulated by two distinct, but complementary mechanisms driven by the TFs Ifh1 and Sfp1, both of which are required for maximal expression in optimal conditions and coordinated down-regulation upon stress. At the majority of RPG promoters Ifh1-dependent regulation predominates, whereas Sfp1 plays the major role at all other genes. We also uncovered an unexpected, protein homeostasis-dependent binding property of Hmo1 at a large subset of RPG promoters. Finally, we show that the Ifh1 paralog Crf1, previously described as a transcriptional repressor, can act as a constitutive RPG activator in the W303 strain background when overexpressed. Our study thus provides a more complete picture of RPG regulation and may serve as a paradigm for unravelling RPG regulation in multicellular eukaryotes.Ribosome biogenesis, one of the most energy consuming process in all organisms, is a major driver of rapid cell growth (Lempiainen and Shore, 2009;Warner, 1999). Ribosome production rates are estimated to be about 2-4,000 per minute in actively dividing Saccharomyces cerevisiae (hereafter yeast) and human cells, respectively. This intensive and complex production process involves several hundred Ribosome Biogenesis (RiBi) factors that direct the hierarchical assembly on to rRNA of the Ribosomal Proteins (RPs), which themselves constitute ~50% of total protein copy number and ~30% of protein mass in yeast.

Sen1 is a key regulator of transcription-driven conflicts

“…These alterations in the transcription scenery have a large potential for increased interference with concurrent processes, together with global alterations in gene expression homeostasis and cellular physiology. Indeed, we also describe changes in the gene expression program, which, at least to some extent, parallel the ribosome assembly stress described recently by the Shore and Churchman laboratories (Tye et al, 2019;Zencir et al, 2020). These phenotypes are possibly triggered by defective production of snoRNAs, which are major NNS targets and contribute to rRNA maturation, or by defects in transcription termination of rRNA genes, a process in which Sen1 has been implicated (Kawauchi et al, 2008).…”

ReporterSeq reveals genome-wide determinants of proteasome expression

“…The primary function of TORC1 in yeast is activation of ribosome biogenesis at the transcriptional level (Powers and Walter 1999; Crespo and Hall 2002; Martin, Soulard, and Hall 2004). Thus, rapamycin specifically results in the downregulation of ribosomal protein genes and other ribosome biogenesis factors while initially having few effects on the remaining transcriptome or translation (Reiter et al 2011; Zencir et al 2020). To assess the role of ribosome biogenesis in PSR activation, we treated wild type cells expressing the PSR reporter with bortezomib in the presence and absence of rapamycin and performed a time course to examine both the immediate and sustained effects of rapamycin.…”

Global and Gene-specific Transcriptional Responses to Acute Stress

“…Our data show a very clear relationship between transcription and nucleosome dynamics both for genes whose expression increases and those whose expression decreases. Due to many techniques lacking temporal resolution or relating nucleosomes to transcript levels, these relationships have not been observed at a genome-wide scale before although are widely predicted to be a key component of gene regulation (9). These shifts are relatively small, and highly dynamic, showing maximal movement with the point at which transcription, assessed by Pol2 occupancy, is maximally induced or repressed.…”

“…The transcription start site (TSS) occurs at the 5' boundary of the +1 nucleosome in yeast, but it is not clear whether or when the +1 nucleosome is displaced to facilitate transcription initiation or whether the position of the +1 nucleosome reflects increases or decreases in transcription. As many of the experimental approaches lack the necessary temporal and spatial resolution, it remains to be established whether this is a general mechanism of regulation or restricted to specific gene types in specific conditions (7,9) . For example, instead of being correlated with transcription, nucleosome occupancy or position is often related to transcript levels (10), which may be temporally separated from the events that lead to the activation or repression of transcription, as well as being confounded by post-transcriptional regulation.…”