Evolutionary engineering reveals divergent paths when yeast is adapted to different acidic environments

Area of Science:

• Microbiology
• Biotechnology
• Evolutionary Biology

Background:

• Yeast acid tolerance is crucial for industrial applications like organic acid production.
• Long-term adaptation mechanisms to acidic environments remain poorly understood.
• It is unknown if adaptation strategies differ between inorganic and organic acids.

Purpose of the Study:

• To investigate the molecular basis of long-term yeast adaptation to inorganic (HCl) and organic (L-lactic acid) acid stress.
• To identify distinct evolutionary pathways and genetic alterations conferring acid tolerance.
• To determine the influence of acid type and carbon source on adaptation strategies.

Main Methods:

• Evolutionary experiments with Saccharomyces cerevisiae under HCl and L-lactic acid stress at pH 2.8.
• Isolation and characterization of low pH tolerant strains.
• Whole genome sequencing and RNA-sequencing (RNA-seq) to identify genetic and transcriptional changes.

Main Results:

• Distinct genome alterations were observed for HCl and L-lactic acid tolerance.
• HCl tolerance involved altered sterol composition and impaired iron uptake.
• L-lactic acid tolerance was linked to multicellular morphology and lactate degradation.
• Carbon source (raffinose vs. glucose) influenced mutation patterns during lactic acid adaptation.

Conclusions:

• Yeast employs divergent evolutionary strategies for adapting to inorganic and organic acids.
• Acid type and carbon source significantly direct the evolutionary trajectory towards acid tolerance.
• Rational strain design for low pH tolerance necessitates tailored approaches based on the specific acid and industrial context.