Hybrid-architectured promoter design to deregulate expression in yeast

Date

2021-01-01

Author

Ergun, Burcu Gunduz
Çalık, Pınar

Metadata

Show full item record

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Item Usage Stats

170
views

0
downloads

Hybrid-architectured promoter design to deregulate expression in yeast under modulating power of carbon sources involves replacing native cis-acting DNA sequence(s) with de novo synthetic tools in coordination with master regulator transcription factor (TF) to alter crosstalk between signaling pathways, and consequently, transcriptionally rewire the expression. Hybrid-promoter architectures can be designed to mimic native promoter architectures in yeast's preferred carbon source utilization pathway. The method aims to generate engineered promoter variants (EPVs) that combine the advantages of being an exceptionally stronger EPV(s) than the naturally occurring promoters and permit "green-and-clean" production on a non-toxic carbon source. To implement the method, a predetermined essential part of the general transcription machinery is targeted. This targeting involves cis-acting DNA sequences to be replaced with synthetic cis-acting DNA sites in coordination with the targeted TF that must bind for transcription machinery activation. The method needs genomic and functional information that can lead to the discovery of the master TF(s) and synthetic cis-acting DNA elements, which enable the engineering of binding of master regulator TF(s). By introducing our recent work on the engineering of Pichia pastoris (syn. Komagataella phaffii) alcohol oxidase 1 (AOX1) hybrid-promoter architectures, we provide the method and protocol for the hybrid-architectured EPV design to deregulate expression in yeast. The method can be adapted to other promoters in different substrate utilization pathways in P. pastoris, as well as in other yeasts.

URI

https://hdl.handle.net/11511/96649

Journal

RECOMBINANT PROTEIN EXPRESSION: EUKARYOTIC HOSTS

DOI

https://doi.org/10.1016/bs.mie.2021.05.014

Collections

Department of Chemical Engineering, Article

Suggestions

OpenMETU
Core

Impact modified epoxy/montmorillonite nanocomposites: synthesis and characterization Isik, I; Yılmazer, Ülkü; Bayram, Göknur (2003-09-01) Diglycidyl ether of bisphenol A type epoxy resin-polyether polyol-organically treated montmorillonite ternary nanocomposites were synthesized in this study. The effects of addition of polyether polyol as an impact modifier on morphological, thermal and mechanical properties of nanocomposites were investigated by X-ray diffraction, scanning electron microscopy (SENI), differential scanning calorimetry, impact and tensile testing. The results showed that organically treated montmorillonite is intercalated by ...
Active carbon/graphene hydrogel nanocomposites as a symmetric device for supercapacitors ATEŞ, MURAT; Cinar, Damla; Caliskan, Sinan; GEÇGEL, ÜNAL; ÜNER, OSMAN; BAYRAK, YÜKSEL; Candan, Idris (Informa UK Limited, 2016-01-01) Activated carbons (ACs) are successfully synthesized from Elaeagnus grain by a simple chemical synthesis methodology and demonstrated as novel, suitable supercapacitor electrode materials for graphene hydrogel (GH)/AC nanocomposites. GH/AC nanocomposites are synthesized via hydrothermal process at temperature of 180 degrees C. The low-temperature thermal exfoliation approach is convenient for mass production of graphene hydrogel (GH) at low cost and it can be used as electrode material for energy storage ap...
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...
Phase transition of chemically synthesized FePt nanoparticles under high pressure ŞİMŞEK, TELEM; Karci, Ozgur; ÖZCAN, ŞADAN (The Scientific and Technological Research Council of Turkey, 2018-01-01) We present the results of a study related to phase transformation of chemically synthesized FePt nanoparticles under high pressure from face-centered cubic into face-centered tetragonal structure. As-synthesized nanoparticles are around 4.5 nm and show superparamagnetic behavior at 300 K. After annealing under 60 bar pressure of hydrogen at 400 degrees C for 2 h, nanoparticles exhibit strong ferromagnetic behavior with 5391 Oe coercivity. Results show that high-pressure annealing lowers the decomposition te...
Covalent and noncovalent functionalization of pristine and defective graphene by cyclohexane and dehydrogenated derivatives Sayin, Ceren Sibel; Toffoli, Daniele; Toffoli, Hande (2015-10-01) The interaction of cyclohexane (C6H12), cyclohexyl (C6H11*) and cyclohexene (C6H10) with both pristine and defective graphene (single vacancy and a carbon adatom), is systematically investigated within the density functional theory framework. C6H12 physisorbs on both pristine and defective graphene while C6H10 chemisorbs on graphene in the presence of an adatom. The C6H11* radical binds covalently with the graphene substrate in all adsorption geometries considered.

Citation Formats

B. G. Ergun and P. Çalık, “Hybrid-architectured promoter design to deregulate expression in yeast,” RECOMBINANT PROTEIN EXPRESSION: EUKARYOTIC HOSTS, vol. 660, pp. 105–125, 2021, Accessed: 00, 2022. [Online]. Available: https://hdl.handle.net/11511/96649.