Genome-wide analysis of intracellular pH reveals quantitative control of cell division rate by pHc in Saccharomyces cerevisiae

Abstract

BackgroundBecause protonation affects the properties of almost all molecules in cells, cytosolic pH (pHc) is usually assumed to be constant. In the model organism yeast, however, pHc changes in response to the presence of nutrients and varies during growth. Since small changes in pHc can lead to major changes in metabolism, signal transduction, and phenotype, we decided to analyze pHc control.ResultsIntroducing a pH-sensitive reporter protein into the yeast deletion collection allowed quantitative genome-wide analysis of pHc in live, growing yeast cultures. pHc is robust towards gene deletion; no single gene mutation led to a pHc of more than 0.3 units lower than that of wild type. Correct pHc control required not only vacuolar proton pumps, but also strongly relied on mitochondrial function. Additionally, we identified a striking relationship between pHc and growth rate. Careful dissection of cause and consequence revealed that pHc quantitatively controls growth rate. Detailed analysis of the genetic basis of this control revealed that the adequate signaling of pHc depended on inositol polyphosphates, a set of relatively unknown signaling molecules with exquisitely pH sensitive properties.ConclusionsWhile pHc is a very dynamic parameter in the normal life of yeast, genetically it is a tightly controlled cellular parameter. The coupling of pHc to growth rate is even more robust to genetic alteration. Changes in pHc control cell division rate in yeast, possibly as a signal. Such a signaling role of pHc is probable, and may be central in development and tumorigenesis.

Quantitative Analysis of the Modes of Growth Inhibition by Weak Organic Acids in Saccharomyces cerevisiae

“…Our first approach was to determine whether the intracellular acidification caused by the four weak acids could be considered the main mechanism of growth inhibition, as the pH i was shown to be in control of growth rate in nonstressed cells (34). Addition of weak acids to growing cells instantly acidified the cells, after which the pH i recovered to various extents.…”

“…At the near-to-neutral cytosolic pH during exponential growth on glucose (33), the acid dissociates to generate protons and anions, which are charged and therefore cannot simply diffuse back out. This causes intracellular acidification and anion accumulation, both of which impede metabolic function (23,34,35). Indirect consequences of weak acid stress are oxidative damage (41) and an inferred perturbation of the plasma membrane (47,50).…”

Noninvasive High-Throughput Single-Cell Analysis of the Intracellular pH of Saccharomyces cerevisiae by Ratiometric Flow Cytometry

“…For example, cells accumulate storage carbohydrates trehalose and glycogen (41). Medium composition also strongly affects pH i (42). Conversely, cells that are transferred from an exponential culture to a fresh medium without glucose are confronted with a different environment (i.e., different pH ex and nutrient availability).…”

Eukaryotic Phosphate Homeostasis: The Inositol Pyrophosphate Perspective

“…Mitochondria, by being able to pump protons, are an important component of the emerging "metabolic" signal mediated by cytosolic pH. A genome-wide screening of S. cerevisiae knockout mutants revealed that kcs1 has one of the lowest cytosolic pH and its metabolic rate is virtually unaffected by lowering medium pH [63]. With this in mind, the altered mitochondria functionality of ip6k1 -/-mice might explain the inability of these mice to become obese [64].…”