Transcriptome-guided identification of YALI0_F02013g and YALI0_A19910g as candidate NADPH-dependent oxidoreductases associated with enhanced erythritol production in Yarrowia lipolytica

Abstract

NADPH competition by non-erythrose-reductase oxidoreductases limits erythritol yields in Yarrowia lipolytica , yet the specific contributors remain poorly defined. This study characterised two candidate genes, YALI0_F02013g (putative pyridoxine 4-dehydrogenase) and YALI0_A19910g (putative glycerol 2-dehydrogenase), using time-resolved transcriptomics, molecular docking and metabolic modelling. RNA-seq analysis across 96 h of fermentation revealed distinct temporal profiles: YALI0_F02013g was progressively induced 3.4-fold (peak 5040 FPKM at 72 h), while YALI0_A19910g was repressed 920-fold by 96 h (Table 2). Expression trends were validated by qRT-PCR (Pearson r > 0.94; Table 3). YALI0_A19910g expression correlated strongly negatively with erythritol titre (Pearson r = − 0.858), whereas YALI0_F02013g showed a weak positive correlation. Molecular docking predicted high NADPH binding affinities for both enzymes (− 9.8 and − 8.6 kcal mol⁻ 1 , respectively; Fig. 2) and identified conserved catalytic triads. An integrated prioritisation model ranked YALI0_F02013g as the higher-priority target (5.6/10 vs 5.0/10; Table 7). In silico flux estimates suggest that repressing YALI0_F02013g could conserve approximately 67% of the competing NADPH demand, potentially increasing erythritol yield by ~14%; these projections require experimental validation (Table 8). These findings identify YALI0_F02013g as a candidate metabolic bottleneck in the strain background examined, offering a specific target for engineering improved cofactor efficiency in industrial Yarrowia lipolytica strains.