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

Introducing 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.While 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.Cytosolic pH (pHc) determines the relative protonation state of all weak acid compounds of the cytosol and affects many, if not all, processes in the cell. It is known to affect redox equilibria [1], metabolic rates and energy storing or generating gradients [2,3], protein interactions [4-7], as well as signal transduction [8-10], and it is an important thermodynamic constraint on metabolic reactions [11]. Furthermore, pHc homeostasis is intricately connected with that of other cations, with membrane potentials, and therefore with cellular energy homeostasis [12,13].Only relatively recently, with the development of green fluorescent protein (GFP)-based pH sensors, has it become possible to study pH in live, unperturbed cells, in an organelle specific fashion [14-18]. The use of this technology is generating inc