Single-cell study links metabolism with nutrient signaling and reveals sources of variability

Abstract

BackgroundThe yeast AMPK/SNF1 pathway is best known for its role in glucose de/repression. When glucose becomes limited, the Snf1 kinase is activated and phosphorylates the transcriptional repressor Mig1, which is then exported from the nucleus. The exact mechanism how the Snf1-Mig1 pathway is regulated is not entirely elucidated.ResultsGlucose uptake through the low affinity transporter Hxt1 results in nuclear accumulation of Mig1 in response to all glucose concentrations upshift, however with increasing glucose concentration the nuclear localization of Mig1 is more intense. Strains expressing Hxt7 display a constant response to all glucose concentration upshifts. We show that differences in amount of hexose transporter molecules in the cell could cause cell-to-cell variability in the Mig1-Snf1 system. We further apply mathematical modelling to our data, both general deterministic and a nonlinear mixed effect model. Our model suggests a presently unrecognized regulatory step of the Snf1-Mig1 pathway at the level of Mig1 dephosphorylation. Model predictions point to parameters involved in the transport of Mig1 in and out of the nucleus as a majorsource of cell to cell variability.ConclusionsWith this modelling approach we have been able to suggest steps that contribute to the cell-to-cell variability. Our data indicate a close link between the glucose uptake rate, which determines the glycolytic rate, and the activity of the Snf1/Mig1 system. This study hence establishes a close relation between metabolism and signalling.Electronic supplementary materialThe online version of this article (doi:10.1186/s12918-017-0435-z) contains supplementary material, which is available to authorized users.

Carbon Catabolite Repression in Filamentous Fungi

“…CCR provides clues on how filamentous fungi cope with different nutrient situations. The genome machinery of CCR may involve various factors such as CreA , CreB , CreC , CreD , HulA , ApyA , RcoA , SsnF , SchA and Glc7-Reg1 [ 8 , 40 , 73 ]. CreA activity is regulated via ubiquitination and deubiquitination [ 5 ].…”

“…Glucose-regulated subcellular localization of Mig1 is very important for its proper function in repression. Mig1 quickly moves to the nucleus in repressing glucose levels, and binds to the promoters of glucose repressible genes [ 22 , 40 ]. However, under glucose starvation, Mig1 is mobilized back to the cytoplasm due to phosphorylation by Snf1 [ 40 ].…”

“…Moreover, it impacts the remodeling and restructuring of chromatins and adaptation of cells to stress [ 41 ]. Snf1 kinase activity is activated at low glucose levels and inhibited in the presence of high glucose levels [ 40 ]. Snf1 causes phosphorylation of Mig1, and moves it to the cytoplasm during glucose starvation [ 34 , 40 ].…”

“…Snf1 kinase activity is activated at low glucose levels and inhibited in the presence of high glucose levels [ 40 ]. Snf1 causes phosphorylation of Mig1, and moves it to the cytoplasm during glucose starvation [ 34 , 40 ]. The role of Glc7 in CCR is antagonistic to that of Snf1 [ 39 , 42 ] ( Figure 2 ).…”

“…They can play a major role in many processes such as functional regulation, metabolism, cell fate and secretion [ 71 ]. The protein kinase Snf1 stands for “Sucrose Non Fermenting”, which was named after a mutant unable to ferment sucrose but still can ferment glucose [ 40 , 149 ]. The gene Snf1 was first studied in S. cerevisiae , which is a homologue of the mammalian cyclic Adenosine Mono Phosphate (cAMP)-dependent Protein Kinase AMPK [ 150 ].…”