Fig. 2: Vacuolar pH dynamics are sensitive to extracellular amino acids and alanine, branched-chain and aromatic amino acids are sufficient to induce oscillations.
From: Cell cycle-linked vacuolar pH dynamics regulate amino acid homeostasis and cell growth
a, A schematic of the PSD pipeline to transform v-SEP intensity time-series data from cells grown in SDC (top) or YNBD (bottom) to amplitude versus frequency plots. Dominant amplitude is proportional to the magnitude of oscillatory pH changes over the imaging period (oscillatory vacuolar pH amplitude). b, Oscillatory vacuolar pH amplitude was obtained using the PSD pipeline for 339 cells grown in SDC (+amino acids (AA) +glucose), 133 cells grown in SCEG (+AA, +ethanol/glycerol) and 321 cells grown in YNBD (−AA, +glucose). Median vacuolar pH amplitude is displayed as box-and-whisker plots with whiskers calculated as 1.5 × the interquartile ranges, median values indicated by the horizontal red bar and P values are calculated by a two-sided Dunn’s test with Holm adjustment. Numbers inset below bar graphs are the median period of vacuolar pH oscillations. c, Cells grown in YNBD imaged every 2 min for 1,000 min in microfluidics chambers (CellASIC). v-SEP intensity over time is shown for two representative cells. Vertical dashed lines indicate the timing of bud emergence. d, Oscillatory vacuolar pH amplitude from cells grown in the presence of individual amino acid addbacks. Median vacuolar pH amplitude is displayed as box-and-whisker plots with whiskers calculated as 1.5 × the interquartile ranges, median values indicated by the horizontal black bar. Note, the y axis is fixed at 30,000 AU. Cell number used in the analysis and periodicity of vacuolar pH oscillations in minutes for each condition: Lys (n = 255, 111 ± 3 min), His (n = 132, 110 ± 5 min), Gly (n = 92, 104 ± 10 min), Pro (n = 26, 82 ± 18 min), Gln (n = 64, 96 ± 11 min), Ser (n = 60, 95 ± 8 min), Glu (n = 90, 87 ± 10 min), Thr (n = 54, 91 ± 13 min), Arg (n = 280, 110 ± 3 min), Val (n = 56, 106 ± 10 min), Asn (n = 163, 105 ± 3 min), Asp (n = 102, 100 ± 10 min), Ile (n = 420, 98 ± 2 min), Trp (n = 121, 112 ± 4 min), Leu (n = 356, 104 ± 2 min), Ala (n = 157, 97 ± 3 min), Phe (n = 429, 90 ± 2 min) and Tyr (n = 334, 101 ± 2 min). e, Cells grown in SCEG imaged every 2 min for 1,000 min in microfluidics chambers (CellASIC). v-SEP intensity over time is shown for two representative cells. Dashed lines indicate the timing of bud emergence. See Source Data for additional curves.
