Aims: This work aimed to identify the molecular mechanism that allows yeast cells to survive at low pH environments such as those of bioethanol fermentation. Methods and Results: The industrial strain JP1 cells grown at pH 2 was evaluated by microarray analysis showing that most of the genes induced at low pH were part of the general stress response (GSR). Further, an acid-tolerant yeast mutant was isolated by adaptive selection that was prone to grow at low pH in inorganic but weak organic acid. It showed higher viability under acid-temperature synergistic treatment. However, it was deficient in some physiological aspects that are associated with defects in protein kinase A (PKA) pathway. Microarray analysis showed the induction of genes involved in inhibition of RNA and protein synthesis. Conclusions: The results point out that low pH activates GSR, mainly heat shock response, that is important for long-term cell survival and suggest that a fine regulatory PKA-dependent mechanism that might affect cell cycle in order to acquire tolerance to acid environment. Significance and Impact of the Study: These findings might guide the construction of a high-fermentative stress-tolerant industrial yeast strain that can be used in complex industrial fermentation processes.