Transcriptional reprogramming of the stress response and translational-secretory machinery enhances recombinant secreted protein production in Yarrowia lipolytica.
TL;DR
The results of contrasting the Azf1- and Dep1-driven regulomes suggest that for efficient rProt secretion, upregulation in the vesicle-mediated transportation must co-occur, as in the case of Azf1-KO.
Abstract
Protein synthesis and secretion processes are non-pathway traits. The genetic complexity makes them very challenging to engineer and genetically optimize. Therefore, we exploit transcriptional reprogramming to create a favorable cellular environment for a trait of interest. In this study, we investigate the effects of transcription factor (TF) engineering on secretory recombinant protein (rProt) production in Y. lipolytica. High-throughput genome-wide pre-screening guided the TFs selection. Here, we run high-throughput functional studies, followed by transcriptome analysis for selected TF-modified strains from semi-steady state. We contrasted the overexpression (OE) vs. deletion (KO) genotypes for their capacity to produce two reporter proteins (fluorescent model and glucoamylase). Despite a wide set of TF-modified strains analyzed here, only several displayed consistent, unbiased phenotypes. Collected data indicated that the known general stress response TFs, Msn4 and Hsf1, elicit their highly beneficial rProt-promoting function specifically towards a "challenging" rProt, while the levels of "simple" rProt remain unaffected. Deletion of the previously identified strong repressor of intracellular rProt synthesis, Azf1, significantly enhanced production of secretory rProt. At the transcriptomic level, deletion of Azf1 was associated with massive upregulation of ribosome biogenesis and cytoplasmic translation, which underwent alternative splicing (global differential exon usage analysis). The results of contrasting the Azf1- and Dep1-driven regulomes (the latter identified as a strong repressor of intracellular rProt synthesis, with no positive effect on the secretory rProt production) suggest that for efficient rProt secretion, upregulation in the vesicle-mediated transportation must co-occur, as in the case of Azf1-KO. In our experimental setting, OE of the general stress response TFs was beneficial for the production of "problematic", UPR-awakening rProt, and deletion of Azf1 for tuning a molecular background beneficial for secretory rProt.