Engineering of the hypoxia-induced Pichia stipitis ADH2 promoter to construct a promoter library for Pichia pastoris

Abad, 2010, Real-time PCR-based determination of gene copy numbers in Pichia pastoris, Biotechnol. J., 5, 413, 10.1002/biot.200900233 Ata, 2017, Transcriptional engineering of the glyceraldehyde-3-phosphate dehydrogenase promoter for improved heterologous protein production in Pichia pastoris, Biotechnol. Bioeng., 114, 2319, 10.1002/bit.26363 Baumann, 2008, Hypoxic fed-batch cultivation of Pichia pastoris increases specific and volumetric productivity of recombinant proteins, Biotechnol. Bioeng., 100, 177, 10.1002/bit.21763 Baumann, 2010, A multi-level study of recombinant Pichia pastoris in different oxygen conditions, BMC Syst. Biol., 4 Bourot, 1995, Isolation and characterization of the Saccharomyces cerevisiae SUT1 gene involved in sterol uptake, Gene, 165, 97, 10.1016/0378-1119(95)00478-O Camattari, 2007, Induction by hypoxia of heterologous-protein production with the KlPDC1 promoter in yeasts, Appl. Environ. Microbiol., 73, 922, 10.1128/AEM.01764-06 Castro-Mondragon, 2022, JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles, Nucleic Acids Res, 50, D165, 10.1093/nar/gkab1113 Chen, 2021, Enhanced recombinant protein production under special environmental stress, Front. Microbiol., 12 Chien, 2005, Expression of bacterial hemoglobin in the yeast, Pichia pastoris, with a low O2-induced promoter, Biotechnol. Lett., 27, 1491, 10.1007/s10529-005-1324-x Cho, 1999, Transcriptional control of ADH genes in the xylose-fermenting yeast Pichia stipitis, Appl. Environ. Microbiol., 65, 2363, 10.1128/AEM.65.6.2363-2368.1999 Dikshit, 1988, Cloning, characterization and expression of the bacterial globin gene from Vitreoscilla in Escherichia coli, Gene, 70, 377, 10.1016/0378-1119(88)90209-0 Duan, 2019, Screening endogenous signal peptides and protein folding factors to promote the secretory expression of heterologous proteins in Pichia pastoris, J. Biotechnol., 306, 193, 10.1016/j.jbiotec.2019.06.297 Eggeling, 2018, Disentangling transcription factor binding site complexity, Nucleic Acids Res, 46 Erden-Karaoglan, 2022, Deletion analysis of Pichia pastoris alcohol dehydrogenase 2 (ADH2) promoter and development of synthetic promoters, Biotechnol. J., 17, 10.1002/biot.202100332 Ergün, 2021, Hybrid-architectured promoter design to deregulate expression in yeast, Methods Enzym., 660, 105, 10.1016/bs.mie.2021.05.014 Ergün, 2021, Hybrid-architectured promoter design to engineer expression in yeast, Methods Enzym., 660, 81, 10.1016/bs.mie.2021.05.009 Ergün, 2019, Engineering of alcohol dehydrogenase 2 hybrid-promoter architectures in Pichia pastoris to enhance recombinant protein expression on ethanol, Biotechnol. Bioeng., 116, 2674, 10.1002/bit.27095 Ergün, 2020, Engineered deregulation of expression in yeast with designed hybrid-promoter architectures in coordination with discovered master regulator transcription factor, Adv. Biosyst., 4, 10.1002/adbi.201900172 Grishin, 1998, Mot3, a Zn finger transcription factor that modulates gene expression and attenuates mating pheromone signaling in Saccharomyces cerevisiae, Genetics, 149, 879, 10.1093/genetics/149.2.879 Hartner, 2008, Promoter library designed for fine-tuned gene expression in Pichia pastoris, Nucleic Acids Res, 36, 10.1093/nar/gkn369 Hongay, 2002, Mot3 is a transcriptional repressor of ergosterol biosynthetic genes and is required for normal vacuolar function in Saccharomyces cerevisiae, EMBO J., 21, 4114, 10.1093/emboj/cdf415 Hustmyer, 2018, Promoter boundaries for the luxCDABE and betIBA-proXWV operons in Vibrio harveyi defined by the method rapid arbitrary PCR insertion libraries (RAIL), J. Bacteriol., 200, e00724, 10.1128/JB.00724-17 Juarez, 2017, Aerobic expression of Vitreoscilla hemoglobin improves the growth performance of CHO-K1 cells, Biotechnol. J., 12, 10.1002/biot.201600438 Karaoglan, 2016, Functional analysis of alcohol dehydrogenase (ADH) genes in Pichia pastoris, Biotechnol. Lett., 38, 463, 10.1007/s10529-015-1993-z Liu, 2022, Pathway engineering facilitates efficient protein expression in Pichia pastoris, Appl. Microbiol. Biotechnol., 106, 5893, 10.1007/s00253-022-12139-y Liu, 1974, Spectral characteristics and interconversions of the reduced oxidized, and oxygenated forms of purified cytochrome o, J. Biol. Chem., 249, 4261, 10.1016/S0021-9258(19)42511-8 Livak, 2001, Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method, Methods, 25, 402, 10.1006/meth.2001.1262 Ness, 2001, SUT1 is a putative Zn[II]2Cys6-transcription factor whose upregulation enhances both sterol uptake and synthesis in aerobically growing Saccharomyces cerevisiae cells, Eur. J. Biochem, 268, 1585, 10.1046/j.1432-1327.2001.02029.x Nevoigt, 2007, Engineering promoter regulation, Biotechnol. Bioeng., 96, 550, 10.1002/bit.21129 Passoth, 2000, Production of a heterologous endo-1,4-beta-xylanase in the yeast Pichia stipitis with an O2-regulated promoter, Enzym. Microb. Technol., 26, 781, 10.1016/S0141-0229(00)00171-X Passoth, 1998, Molecular cloning of alcohol dehydrogenase genes of the yeast Pichia stipitis and identification of the fermentative ADH, Yeast, 14, 1311, 10.1002/(SICI)1097-0061(1998100)14:14<1311::AID-YEA315>3.0.CO;2-T Passoth, 2003, Analysis of the hypoxia-induced ADH2 promoter of the respiratory yeast Pichia stipitis reveals a new mechanism for sensing of oxygen limitation in yeast, Yeast, 20, 39, 10.1002/yea.933 Qin, 2011, Reliable high-throughput approach for screening of engineered constitutive promoters in the yeast Pichia pastoris, Lett. Appl. Microbiol, 52, 634, 10.1111/j.1472-765X.2011.03051.x Qin, 2011, GAP promoter library for fine-tuning of gene expression in Pichia pastoris, Appl. Environ. Microbiol., 77, 3600, 10.1128/AEM.02843-10 Sengupta, 2020, A Library of tunable, portable, and inducer-free promoters derived from cyanobacteria, ACS Synth. Biol., 9, 1790, 10.1021/acssynbio.0c00152 Song, 2022, Determination of nucleotide sequences within promoter regions affecting promoter compatibility between zymomonas mobilis and Escherichia coli, ACS Synth. Biol., 11, 2811, 10.1021/acssynbio.2c00187 Waters, 2006, Data merging for integrated microarray and proteomic analysis, Brief. Funct. Genom. Proteom., 5, 261, 10.1093/bfgp/ell019 Wu, 2012, Intracellular co-expression of Vitreoscilla hemoglobin enhances cell performance and beta-galactosidase production in Pichia pastoris, J. Biosci. Bioeng., 113, 332, 10.1016/j.jbiosc.2011.10.014 Xiao, 2021, Exploration and characterization of hypoxia-inducible endogenous promoters in Aspergillus niger, Appl. Microbiol. Biotechnol., 105, 5529, 10.1007/s00253-021-11417-5 Zhao, 2022, Precise prediction of promoter strength based on a de novo synthetic promoter library coupled with machine learning, ACS Synth. Biol., 11, 92, 10.1021/acssynbio.1c00117 Zhu, 2019, Pichia pastoris as a versatile cell factory for the production of industrial enzymes and chemicals: current status and future perspectives, Biotechnol. J., 14