Molecular background of HAC1-driven improvement in the secretion of recombinant protein in Yarrowia lipolytica based on comparative transcriptomics

•HAC1 overexpression decreases intracellular r-Prot retention and enhances secretion.•HAC1 unconventional splicing rate was counted based on transcripts sequencing.•Implication of transcription factor Xbp1 and ligase Trl1 in Yarrowia UPR is proposed. While the unfolded protein response (UPR) and its major regulator – transcription factor Hac1 are well-conserved across Eukarya, species-specific variations are repeatedly reported. Here we investigated molecular mechanisms by which co-over-expression of HAC1 improves secretion of a recombinant protein (r-Prot) in Yarrowia lipolytica, using comparative transcriptomics. Co-over-expression of HAC1 caused an >2-fold increase in secreted r-Prot, but its intracellular levels were decreased. The unconventional splicing rate of the HAC1 mRNA was counted through transcript sequencing. Multiple biological processes were affected in the HAC1-and-r-Prot co-over-expressing strain, including ribosome biogenesis, nuclear and mitochondrial events, cell cycle arrest, attenuation of gene expression by RNA polymerase III and II, as well as modulation of proteolysis and RNA metabolism; but whether the HAC1 co-over-expression/induction was the actual causative agent for these changes, was not always clear. We settled that the expression of the “conventional” HAC1 targets (KAR2 and PDI1) is not affected by its over-expression. [Display omitted]