Hybrid-architectured double-promoter expression systems enhance and upregulate-deregulated gene expressions in Pichia pastoris in methanol-free media

Demir, Irem
Çalık, Pınar
Double-promoter expression system (DPES) design as de novo metabolic engineering strategy enables fine-tuned and enhanced gene expression. We constructed a collection of monodirectional hybrid-architectured DPESs with engineered promoter variants P(ADH2-Cat8-L2)and P(mAOX1)and with the naturally occurring promoter P(GAP)to enhance and upregulate-deregulated gene expressions inPichia pastorisin methanol-free media. Reporter red fluorescent protein (mApple) and enhanced green fluorescent protein (eGFP) were expressed under P(ADH2-Cat8-L2)and P(mAOX1)or P-GAP, respectively, enabling the determination of the transcription period and strength of each constituent in the DPESs. We determined fluorescent protein expressions in batch cultivations on 2% (v/v) ethanol, excess glucose, and excess glycerol, and compared them with single-promoter expression systems constructed with PADH2-Cat8-L2, P-mAOX1, and P-GAP. The transcription- and expression-upregulation power of bifunctional DPESs was higher than that of twin DPESs (two-copy expression systems). Our findings answer long-standing questions regarding the high- (or multi-) copy clone results in the literature. Our first conclusion is that increasing identical components in the DPES architectures linearly increases the concentrations ofcis-acting DNA sites and increases the demand for key transcription factors (TFs) that perturb their good coupling of supply and demand. The next is that the synthesis of some amino acids may create bottleneck(s) as rate-limiting amino acid(s) in recombinant protein synthesis. With bifunctional DPESs, each constituent upregulated the transcription and increased the expression and reduced the demand for the same TF(s) in the generation of novel regulatory circuits, due to the increased number of nonidenticalcis-acting DNA sites. We tested superior DPES performances in extracellular human growth hormone (rhGH) production. Thereby, the indications related to the rate-limiting amino acids were verified. Compared with its constituents P(ADH2-Cat8-L2)and P-mAOX1, the bifunctional DPES(4)enhanced rhGH production by 1.44- and 2.02-fold, respectively. The DPES design method, with its constraint and parameters, enables the generation of promising r-protein production platforms with high impact on industrial-scale production processes and opens up new avenues for research in yeasts.


Engineered Deregulation of Expression in Yeast with Designed Hybrid-Promoter Architectures in Coordination with Discovered Master Regulator Transcription Factor
Ergun, Burcu Gunduz; Demir, Irem; Ozdamar, Tuncer H.; Gasser, Brigitte; Mattanovich, Diethard; Çalık, Pınar (2020-04-01)
Engineered promoters are key components in the cell-factory design, allowing precise and enhanced expression of genes. Promoters having exceptional strength are attractive candidates for designing metabolic engineering strategies for tailoring de novo production strategies that require directed evolution methods by engineering with de novo synthetic biology tools. Here, the custom-designed AOX1 hybrid-promoter architectures in coordination with targeted transcription factors are shown, transcriptionally rew...
Engineering of alcohol dehydrogenase 2 hybrid-promoter architectures in Pichia pastoris to enhance recombinant protein expression on ethanol
Ergun, Burcu Gunduz; Gasser, Brigitte; Mattanovich, Diethard; Çalık, Pınar (2019-07-09)
The aim of this work is to increase recombinant protein expression in Pichia pastoris over the ethanol utilization pathway under novel-engineered promoter variants (NEPVs) of alcohol dehydrogenase 2 promoter (P-ADH2) through the generation of novel regulatory circuits. The NEPVs were designed by engineering of transcription factor binding sites (TFBSs) determined by in silico analyses and manual curation systematically, by (a) single-handedly replacement of specified TFBSs with synthetic motifs for Mxr1, Ca...
Design and construction of double promoter systems and their use in pharmaceutical protein production in P. Pastoris
Demir, İrem; Çalık, Pınar; Department of Chemical Engineering (2019)
Intracellular phenomena such as promoter strength, mRNA secondary structure, translation efficiency and codon preference, 5′-untranslated region processing, and protein turnover, have impacts directly on the expression of heterologous genes. Design of multi-promoter expression systems with constituent strong promoters and engineered promoter variants is a novel metabolic engineering strategy for increasing the promoter strength further, and tuning the expression for recombinant protein (r-protein) productio...
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Massahi, Aslan; Çalık, Pınar (2016-11-07)
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Bioactive Surface Design Based on Functional Composite Electrospun Nanofibers for Biomolecule Immobilization and Biosensor Applications
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The combination of nanomaterials and conducting polymers attracted remarkable attention for development of new immobilization matrices for enzymes. Hereby, an efficient surface design was investigated by modifying the graphite rod electrode surfaces with one-step electrospun nylon 6,6 nanofibers or 4% (w/w) multiwalled carbon nanotubes (MWCNTs) incorporating nylon 6,6 nanofibers (nylon 6,6/4MWCNT). High-resolution transmission electron microscopy study confirmed the successful incorporation of the MWCNTs in...
Citation Formats
I. Demir and P. Çalık, “Hybrid-architectured double-promoter expression systems enhance and upregulate-deregulated gene expressions in Pichia pastoris in methanol-free media,” APPLIED MICROBIOLOGY AND BIOTECHNOLOGY, pp. 8381–8397, 2020, Accessed: 00, 2020. [Online]. Available: https://hdl.handle.net/11511/42582.