Johnny Roosen

TOR and PKA Signaling Pathways Converge on the Protein Kinase Rim15 to Control Entry into G0

The highly conserved Tor kinases (TOR) and the protein kinase A (PKA) pathway regulate cell proliferation in response to growth factors and/or nutrients. In Saccharomyces cerevisiae, loss of either TOR or PKA causes cells to arrest growth early in G(1) and to enter G(0) by mechanisms that are poorly understood. Here we demonstrate that the protein kinase Rim15 is required for entry into G(0) following inactivation of TOR and/or PKA. Induction of Rim15-dependent G(0) traits requires two discrete processes, i.e., nuclear accumulation of Rim15, which is negatively regulated both by a Sit4-independent TOR effector branch and the protein kinase B (PKB/Akt) homolog Sch9, and release from PKA-mediated inhibition of its protein kinase activity. Thus, Rim15 integrates signals from at least three nutrient-sensory kinases (TOR, PKA, and Sch9) to properly control entry into G(0), a key developmental process in eukaryotic cells.

PKA and Sch9 control a molecular switch important for the proper adaptation to nutrient availability

In the yeast Saccharomyces cerevisiae, PKA and Sch9 exert similar physiological roles in response to nutrient availability. However, their functional redundancy complicates to distinguish properly the target genes for both kinases. In this article, we analysed different phenotypic read‐outs. The data unequivocally showed that both kinases act through separate signalling cascades. In addition, genome‐wide expression analysis under conditions and with strains in which either PKA and/or Sch9 signalling was specifically affected, demonstrated that both kinases synergistically or oppositely regulate given gene targets. Unlike PKA, which negatively regulates stress‐responsive element (STRE)‐ and post‐diauxic shift (PDS)‐driven gene expression, Sch9 appears to exert additional positive control on the Rim15‐effector Gis1 to regulate PDS‐driven gene expression. The data presented are consistent with a cyclic AMP (cAMP)‐gating phenomenon recognized in higher eukaryotes consisting of a main gatekeeper, the protein kinase PKA, switching on or off the activities and signals transmitted through primary pathways such as, in case of yeast, the Sch9‐controlled signalling route. This mechanism allows fine‐tuning various nutritional responses in yeast cells, allowing them to adapt metabolism and growth appropriately.

The Novel Yeast PAS Kinase Rim15 Orchestrates G 0 -Associated Antioxidant Defense Mechanisms

The highly conserved PKA and TOR proteins define key signaling pathways that control cell proliferation in response to growth factors and/or nutrients. In yeast, inactivation of PKA and/or TOR causes cells to arrest growth in early G1 and induces a program that is characteristic of G0 cells. We have recently shown that the protein kinase Rim15 integrates both PKA- and TOR-mediated signals. In this work, we demonstrate that the Rim15-activated genomic expression program following glucose limitation at the diauxic shift is mediated by the three transcription factors Gis1, Msn2, and Msn4. The Rim15 regulon comprises several gene clusters implicated in the adaptation to respiratory growth, including classical oxidative stress genes such as SOD1 and SOD2, suggesting that the reduced life span of rim15? cells may be due to their deficiency in oxidative damage prevention. Interestingly, we found that the primary amino acid sequence of Rim15 includes in its amino-terminal part a conserved PAS domain, known to act as a sensor for a variety of stimuli. We propose that Rim15 has evolved to integrate nutrient signals (transduced via TOR and PKA) and redox and/or oxidative stress signals to appropriately induce a transcriptional program that ensures survival in G0.

Rim15 and the crossroads of nutrient signalling pathways in Saccharomyces cerevisiae

In recent years, the general understanding of nutrient sensing and signalling, as well as the knowledge about responses triggered by altered nutrient availability have greatly advanced. While initial studies were directed to top-down elucidation of single nutrient-induced pathways, recent investigations place the individual signalling pathways into signalling networks and pursue the identification of converging effector branches that orchestrate the dynamical responses to nutritional cues. In this review, we focus on Rim15, a protein kinase required in yeast for the proper entry into stationary phase (G0). Recent studies revealed that the activity of Rim15 is regulated by the interplay of at least four intercepting nutrient-responsive pathways.

The Ccr4-Not Complex Independently Controls both Msn2-Dependent Transcriptional Activation—via a Newly Identified Glc7/Bud14 Type I Protein Phosphatase Module—and TFIID Promoter Distribution

ABSTRACT The Ccr4-Not complex is a conserved global regulator of gene expression, which serves as a regulatory platform that senses and/or transmits nutrient and stress signals to various downstream effectors. Presumed effectors of this complex in yeast are TFIID, a general transcription factor that associates with the core promoter, and Msn2, a key transcription factor that regulates expression of stress-responsive element (STRE)-controlled genes. Here we show that the constitutively high level of STRE-driven expression in ccr4-not mutants results from two independent effects. Accordingly, loss of Ccr4-Not function causes a dramatic Msn2-independent redistribution of TFIID on promoters with a particular bias for STRE-controlled over ribosomal protein gene promoters. In parallel, loss of Ccr4-Not complex function results in an alteration of the posttranslational modification status of Msn2, which depends on the type 1 protein phosphatase Glc7 and its newly identified subunit Bud14. Tests of epistasis as well as transcriptional analyses of Bud14-dependent transcription support a model in which the Ccr4-Not complex prevents activation of Msn2 via inhibition of the Bud14/Glc7 module in exponentially growing cells. Thus, increased activity of STRE genes in ccr4-not mutants may result from both altered general distribution of TFIID and unscheduled activation of Msn2.

SKN1, a novel plant defensin-sensitivity gene in Saccharomyces cerevisiae, is implicated in sphingolipid biosynthesis.

The antifungal plant defensin DmAMP1 interacts with the fungal sphingolipid mannosyl diinositolphosphoryl ceramide (M(IP)2C) and induces fungal growth inhibition. We have identified SKN1, besides the M(IP)2C‐biosynthesis gene IPT1, as a novel DmAMP1‐sensitivity gene in Saccharomyces cerevisiae. SKN1 was previously shown to be a KRE6 homologue, which is involved in β‐1,6‐glucan biosynthesis. We demonstrate that a Δskn1 mutant lacks M(IP)2C. Interestingly, overexpression of either IPT1 or SKN1 complemented the skn1 mutation, conferred sensitivity to DmAMP1, and resulted in M(IP)2C levels comparable to the wild type. These results show that SKN1, together with IPT1, is involved in sphingolipid biosynthesis in S. cerevisiae.

11 Integration of nutrient signalling pathways in the yeast Saccharomyces cerevisiae

The ability to sense and to respond to changes in the nutrient availability is an essential feature for the survival of every organism. Saccharomyces cerevisiae has several signal transduction cascades to optimally adapt its metabolism to the availability of nutrients in the environment. In this chapter, we focus on the convergence of signal transduction pathways for nutrient sensing in budding yeast. In the first part, we will give an overview of the glucose-induced signal transduction pathways, focusing in particular on the Ras/cAMP pathway and its pleiotropic characteristics. Secondly, the current knowledge of the protein kinases Sch9 and Pho85 in nutrient-induced signal transduction is reviewed. Finally, the interconnectivity between these multiple pathways in glycogen biosynthesis, control of Msn2 activity and pseudohyphal growth will be discussed. We conclude that complex networks are involved in the integration of nutrient signals, regulating the complete transcriptome and metabolome in an intriguingly dynamical manner.