The AMP-activated protein kinase (AMPK) is a major stress sensor of mammalian cells. AMPK's homolog in the yeast Saccharomyces cerevisiae, the SNF1 protein kinase, is a central regulator of carbon metabolism that inhibits the Snf3/Rgt2-Rgt1 glucose sensing pathway and activates genes involved in respiration. We present evidence that glucose induces modification of the Snf1 catalytic subunt of SNF1 with the small ubiquitin-like modifier protein SUMO, catalyzed by the SUMO (E3) ligase Mms21. Our results suggest that SUMOylation of Snf1 inhibits its function in two ways: by interaction of SUMO attached to lysine 549 with a SUMO-interacting sequence motif located near the active site of Snf1, and by targeting Snf1 for destruction via the Slx5-Slx8 (SUMO-directed) ubiquitin ligase. These findings reveal another way SNF1 function is regulated in response to carbon source.protein kinase regulation | protein modification | signal transduction G lucose is the preferred carbon source of most cells, including Saccharomyces cerevisiae, which ferments it to ethanol and CO 2 , producing only two ATPs, even when oxygen is available to drive production of much more ATP. This preference for fermentation (which cancer cells share), is known as the Crabtree or Warburg effect (1, 2). Because of the energetic inefficiency of fermentation, yeast cells must be adroit in sensing glucose. S. cerevisiae has three well-known glucose sensing pathways: (i) the Gpa1/2-Ras2-PKA pathway that regulates stress response (through Msn2/4) and other things; (ii) the SNF1 pathway, which regulates respiratory metabolism and other processes; and (iii) the Snf3/Rgt2-Rgt1 (SRR) pathway that regulates expression of genes encoding hexose transporters (3).The SRR (sensor/receptor-repressor) pathway begins at the cell surface with high-affinity (Snf3) (4) and low-affinity (Rgt2) glucose sensors (5) that are coupled to the casein kinases Yck1 and Yck2, which catalyze phosphorylation of the corepressor proteins Mth1 and Std1 (6), leading to their ubiquitinylation by SCF Grr1 (7,8). The subsequent destruction of Mth1 and Std1 inactivates the Rgt1 transcriptional repressor, resulting in derepression of HXT genes encoding hexose transporters (7, 9). In response to glucose, Yck1/2 also mediates inactivation and degradation of transporters of alternative carbon sources, such as maltose (Mal61) (10) and lactate/pyruvate/acetate (Jen1) (11). Achieving this glucose-induced switching of transporters seems to be the main purpose of the SRR pathway (12).The SNF1 protein kinase-the ortholog of the AMP-activated protein kinase (AMPK), a major stress-activated protein kinase in mammalian cells (13,14)-is a central regulator of carbon metabolism (15,16). This kinase is an activator of Adr1 and Cat8, which activate expression of genes involved in the diauxic shift, ethanol, and lactate uptake and catabolism, gluconeogenesis, and respiration (17-21), and is an inhibitor of the Mig1 repressor of glucose-repressed genes (22). SNF1 is a heterotrimer of the Snf1 catalytic subunit,...

Ubiquitylation controls protein function and degradation. Therefore, ubiquitin ligases need to be tightly controlled. We discovered an evolutionarily conserved allosteric restraint mechanism for Nedd4 ligases and demonstrated its function with diverse substrates: the yeast soluble proteins Rpn10 and Rvs167, and the human receptor tyrosine kinase FGFR1 and cardiac I potassium channel. We found that a potential trimerization interface is structurally blocked by the HECT domain α1-helix, which further undergoes ubiquitylation on a conserved lysine residue. Genetic, bioinformatics, biochemical and biophysical data show that attraction between this α1-conjugated ubiquitin and the HECT ubiquitin-binding patch pulls the α1-helix out of the interface, thereby promoting trimerization. Strikingly, trimerization renders the ligase inactive. Arginine substitution of the ubiquitylated lysine impairs this inactivation mechanism and results in unrestrained FGFR1 ubiquitylation in cells. Similarly, electrophysiological data and TIRF microscopy show that NEDD4 unrestrained mutant constitutively downregulates the I channel, thus confirming the functional importance of E3-ligase autoinhibition.

Yeast cells with DNA damage avoid respiration, presumably because products of oxidative metabolism can be harmful to DNA. We show that DNA damage inhibits the activity of the Snf1 (AMP-activated) protein kinase (AMPK), which activates expression of genes required for respiration. Glucose and DNA damage upregulate SUMOylation of Snf1, catalyzed by the SUMO E3-ligase Mms21, which inhibits SNF1 activity. The DNA damage checkpoint kinases Mec1/ATR and Tel1/ATM, as well as the nutrient sensing protein kinase A (PKA), regulate Mms21 activity towards Snf1. Mec1 and Tel1 are required for two SNF1-regulated processes—glucose sensing and ADH2 gene expression—even without exogenous genotoxic stress. Our results imply that inhibition of Snf1 by SUMOylation is a mechanism by which cells lower their respiration in response to DNA damage. This raises the possibility that activation of DNA damage checkpoint mechanisms could contribute to aerobic fermentation (Warburg effect), a hallmark of cancer cells.

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The ability to respond to available nutrients is critical for all living cells. The AMP-activated protein kinase (SNF1 in yeast) is a central regulator of metabolism that is activated when energy is depleted. We found that SNF1 activity in the nucleus is regulated by controlled relocalization of the SNF1 activator Std1 into puncta. This process is regulated by glucose through the activity of the previously uncharacterized protein kinase Vhs1 and its substrate Sip5, a protein of hitherto unknown function. Phosphorylation of Sip5 prevents its association with Std1 and triggers Std1 accretion. Reversible Std1 puncta formation occurs under non-stressful, ambient conditions, creating non-amyloid inclusion bodies at the nuclear-vacuolar junction, and it utilizes cellular chaperones similarly to the aggregation of toxic or misfolded proteins such as those associated with Parkinson's, Alzheimer's, and CJD diseases. Our results reveal a controlled, non-pathological, physiological role of protein aggregation in the regulation of a major metabolic cellular pathway.

Cells adapt their gene expression and their metabolism in response to a changing environment. Glucose represses expression of genes involved in the catabolism of other carbon sources in a process known as (carbon) catabolite repression. However, the relationships between “poor” carbon sources is less characterized. Here we show that in addition to the well-characterized glucose (and galactose) repression of ADH2 (alcohol dehydrogenase 2, required for efficient utilization of ethanol as a carbon source), ADH2 expression is also inhibited by acetate which is produced during ethanol catabolism. Thus, repressive regulation of gene expression occurs also between “poor” carbon sources. Acetate repression of ADH2 expression is via Haa1, independently from the well-characterized mechanism of AMPK (Snf1) activation of Adr1. The response to extracellular acetate is attenuated when all three acetate transporters (Ady2, Fps1 and Jen1) are deleted, but these deletions do not affect the acetate response resulting from growth with glucose or ethanol as the carbon source. Furthermore, genetic manipulation of the ethanol catabolic pathway affects this response. Together, our results show that acetate is sensed intracellularly and that a hierarchical control of carbon sources exists even for “poor” carbon sources.

Ndd1 activates the Mcm1-Fkh2 transcription factor to transcribe mitotic regulators. The anaphase-promoting complex/cyclosome activated by Cdh1 (APC/C Cdh1 ) mediates the degradation of proteins throughout G1. Here we show that the APC/C Cdh1 ubiquitinates Ndd1 and mediates its degradation, and that APC/C Cdh1 activity suppresses accumulation of Ndd1 targets. We confirm putative Ndd1 targets and identify novel ones, many of them APC/C Cdh1 substrates. The APC/C Cdh1 thus regulates these proteins in a dual manner-both pretranscriptionally and post-translationally, forming a multi-layered feedforward loop (FFL). We predict by mathematical modelling and verify experimentally that this FFL introduces a lag between APC/C Cdh1 inactivation at the end of G1 and accumulation of genes transcribed by Ndd1 in G2. This regulation generates two classes of APC/C Cdh1 substrates, early ones that accumulate in S and late ones that accumulate in G2. Our results show how the dual state APC/C Cdh1 activity is converted into multiple outputs by interactions between its substrates.