The dominant role of post-transcriptional regulation in Yarrowia lipolytica to repeated O2 limitations

Rational scale-up strategies to accelerate bioprocess development, require sound knowledge of cellular behaviour under industrial conditions. In this study, the strictly aerobic yeast Yarrowia lipolytica is exposed to repeated oxygen limitations, approximated from a large-scale cultivation. A data-driven multi-omics strategy is deployed to elucidate its transcriptomic, proteomic, and metabolic response. Throughout a single perturbation, metabolite and protein levels showed dynamic profiles while they returned to steady state values when aerobic conditions were restored. After repeated oscillations, significant cellular rearrangements were found, with a special focus on central carbon metabolism, oxidative phosphorylation, lipid, and amino acid biosynthesis. Most notably, metabolite levels as well as the catabolic reduction charge are maintained at higher concentrations. Moreover, proteins involved in NADPH-consuming anabolic pathways showed an increased abundance, which is suggested to be compensated for through an increased pentose-phosphate pathway activity. Although dynamics were found on all three omics levels, the proteomic and metabolic changes were in most instances not supported by strong transcriptional changes. Thus, this work suggests that the response of Y. lipolytica to (repeated) oxygen oscillations is strongly regulated by post-transcriptional mechanisms. These findings provide novel insights into potential cellular regulation on an industrial scale, thereby facilitating a more efficient bioprocess development through mitigating any undesired behaviour. Key points- Dynamic response of Yarrowia lipolytica to industrial oxygen profiles. - New metabolic steady states are found after exposure to repeated oxygen oscillations. - A multi-omics strategy elucidates the importance of post-transcriptional mechanisms.