Acetyl-CoA induces transcription of the key G1 cyclin CLN3 to promote entry into the cell division cycle in Saccharomyces cerevisiae

Abstract

In budding yeast cells, nutrient repletion induces rapid exit from quiescence and entry into a round of growth and division. The G1 cyclin CLN3 is one of the earliest genes activated in response to nutrient repletion. Subsequent to its activation, hundreds of cellcycle genes can then be expressed, including the cyclins CLN1/2 and CLB5/6. Although much is known regarding how CLN3 functions to activate downstream targets, the mechanism through which nutrients activate CLN3 transcription in the first place remains poorly understood. Here we show that a central metabolite of glucose catabolism, acetyl-CoA, induces CLN3 transcription by promoting the acetylation of histones present in its regulatory region. Increased rates of acetyl-CoA synthesis enable the Gcn5p-containing Spt-AdaGcn5-acetyltransferase transcriptional coactivator complex to catalyze histone acetylation at the CLN3 locus alongside ribosomal and other growth genes to promote entry into the cell division cycle.growth control | metabolism | epigenetics T he most basic building blocks of biological organisms are smallmolecule metabolites. In recent years, there has been renewed interest in understanding how the fundamental processes of cell growth and proliferation are coordinated with cellular metabolism. Nutrient-starved yeast cells arrest in a quiescent, or G0, phase of the cell division cycle. Addition of nutrients stimulates exit from the G0 and transition into the G1 phase, and then ∼800 genes are periodically transcribed as a function of the cell cycle (1, 2). CLN3 is observed to be one of the earliest genes transcribed within this set (1-3). Cln3p regulates G1 length by coordinating growth and division and may influence cell size when passing Start, the point at which cells commit to division (4-7). In cln3Δ mutants, cells become larger and stay in the G1 phase longer, resulting in decreased growth and budding rates compared with WT (8, 9) (Fig. S1). Following CLN3 activation, the G1 transcription complexes Swi4p-Swi6p (SBF) and Mbp1-Swi6p (MBF) can be activated by CLN3/CDC28-catalyzed phosphorylation of the SBF inhibitor Whi5p (10-12), and other unknown mechanisms, to enable transcription of over 200 downstream cell-cycle genes (13), including CLN1/2 and CLB5/6. Cln1p and Cln2p can then further enhance SBF-and MBF-dependent G1 transcription through positive feedback mechanisms (14)(15)(16)(17)(18)(19)(20).Although many studies have focused on the mechanisms by which Cln3p regulates G1 transcription, the mechanisms that lead to transcriptional activation of CLN3 itself still remain unresolved. Since the discovery of CLN3 more than 20 y ago (6, 7), the gene and its encoded protein have been reported to be regulated at multiple levels. At the transcriptional level, CLN3 is activated by glucose (21, 22), which is reportedly mediated by Azf1p, a zinc-finger transcription factor (23). Following transcription, CLN3 mRNA availability is regulated by a RNAbinding protein, Whi3p (24). At the translational level, CLN3 is regulated by TOR (target of rapamyc...

The Yeast AMPK Homolog SNF1 Regulates Acetyl Coenzyme A Homeostasis and Histone Acetylation

“…10E). These results suggest that the increased level of acetyl-CoA is responsible for the increased expression of the ribo- somal protein genes in wild-type cells and are consistent with the notion that the increased cellular level of acetyl-CoA promotes the acetylation of histones at growth genes (31,70).…”

Protein Acetylation and Acetyl Coenzyme A Metabolism in Budding Yeast

“…The recruitment of SAGA to the CLN3 promoter depends on the autoacetylation of SAGA subunits. Other KATs, including NuA4, SAS2, and SAS3, cannot substitute for SAGA for induction of CLN3 transcription (142). These results suggest a model in which acetyl-CoA levels affect two events that regulate START, and it is possible that intracellular levels of acetyl-CoA are one of the key factors which determine whether a cell commits to cell division.…”

“…Another interesting area is the role of protein acetylation in the regulation of cell cycle progression and aging. Two events that regulate cell cycle progression from G 1 to S phase depend on protein acetylation: the assembly of the SBF complex requires Swi4p acetylation (6), and the transcription of CLN3 is induced by the acetylation of promoter histones (142). Combined with strong evidence implicating that the intracellular level of acetyl-CoA is a gauge of the metabolic state of the cell (146), these results suggest that acetyl-CoA may be one of the factors connecting metabolism with the cell cycle.…”

“…Cln3p is a rate-limiting activator of START (141). The transcriptional induction of CLN3 is triggered by SAGA-mediated acetylation of histones in the promoter region of CLN3 (142). The recruitment of SAGA to the CLN3 promoter depends on the autoacetylation of SAGA subunits.…”

Yeast Saccharomyces cerevisiae adiponectin receptor homolog Izh2 is involved in the regulation of zinc, phospholipid and pH homeostasis

“…We also specifically looked at genes involved in lipid metabolism and found several with decreased expression in izh2Δ cells: INO1, CHO1, TSC10 (encoding 3-ketosphinganine reductase, an essential enzyme in phytosphingosine synthesis), ERG28 (encoding an ER membrane protein involved in ergosterol biosynthesis), APQ12 (a gene with synthetic lethal genetic interactions with genes involved in lipid metabolism, encoding for a protein required for nuclear envelope morphology), and, again, MCD4. Among the genes with decreased expression in izh2Δ cells was also CLN3, encoding a G1 cyclin which, unlike other cyclins, is not regulated by the cell cycle, but is instead under the control of nutrient repletion by acetyl-CoA-mediated chromatin modification 64 . One of the few genes with decreased expression in izh2Δ cells under normal zinc conditions only was ZRT1.…”