Transcriptomics of cryophilic Saccharomyces kudriavzevii reveals the key role of gene translation efficiency in cold stress adaptations

Abstract

Background: Comparative transcriptomics and functional studies of different Saccharomyces species have opened up the possibility of studying and understanding new yeast abilities. This is the case of yeast adaptation to stress, in particular the cold stress response, which is especially relevant for the food industry. Since the species Saccharomyces kudriavzevii is adapted to grow at low temperatures, it has been suggested that it contains physiological adaptations that allow it to rapidly and efficiently acclimatise after cold shock.

Results: In this work, we aimed to provide new insights into the molecular basis determining this better cold adaptation of S. kudriavzevii strains. To this end, we have compared S. cerevisiae and S. kudriavzevii transcriptome after yeast adapted to cold shock. The results showed that both yeast mainly activated the genes related to translation machinery by comparing 12°C with 28°C, but the S. kudriavzevii response was stronger, showing an increased expression of dozens of genes involved in protein synthesis. This suggested enhanced translation efficiency at low temperatures, which was confirmed when we observed increased resistance to translation inhibitor paromomycin. Finally, 35S-methionine incorporation assays confirmed the increased S. kudriavzevii translation rate after cold shock.

Conclusions: This work confirms that S. kudriavzevii is able to grow at low temperatures, an interesting ability for different industrial applications. We propose that this adaptation is based on its enhanced ability to initiate a quick, efficient translation of crucial genes in cold adaptation among others, a mechanism that has been suggested for other microorganisms.

Figure 1

S . kudriavzevii has increased grow abilities at low temperature. A drop test assay was performed in rich media GPY with S. cerevisiae strain T73 and S. kudriavzevii strain IFO1802 and plates were incubated at different temperatures (12 or 28°C).

Figure 2

S. kudriavzevii has increased expression of the cold stress gene marker NSR1 at low temperature. Gene expression measured by qPCR technique after S. cerevisiae (T73) or S. kudriavzevii (IFO1802) cells were transferred to 12 (light grey) or 28°C (dark grey) synthetic grape must. Samples were taken 2 hours after the inoculation (A), when the OD₆₀₀ reached the double of the initial OD₆₀₀ (B), in the middle of exponential phase (C), and at the start (D) and at the end (E) of the stationary phase (sugar exhaustion). Average of biological triplicates was calculated and standard deviations were lower than 20%. Gene expression levels are shown as the changes in the concentration of the studied gene compare to the control sample and normalized with the concentration of the housekeeping ACT1 gene. Gene expression differences between 12 a 28°C were statistically significant, except in the case of time point A for S. kudriavzevii.

Figure 3

S. kudriavzevii presents increased translation efficiency at low temperatures. In panel A, the inhibitory effect of the translation inhibitor paromomycin was evaluated by measuring the halo diameter generated in S. cerevisiae (T73) or S. kudriavzevii (CR85) lawns growing in GPY plates at 28 or 12°C. In panel B, the translation efficiency was evaluated by measuring ³⁵S-Methionine incorporation 16 h after transfer S. cerevisiae (Q23) or S. kudriavzevii (CR85) cells to cold (12°C) rich media. Cpm values were normalized with OD₆₀₀, relativized to maximum value and represented against the time. Average of biological triplicates and standard deviations are shown.