1. Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China 2. Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, China 3. Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China 4. School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
Conflict between cell growth and product accumulation is frequently encountered in the biosynthesis of secondary metabolites. To address the growth-production conflict in yeast strains harboring the isoprene synthetic pathway in the mitochondria, the dynamic control of isoprene biosynthesis was explored. A dual temperature regulation system was developed through engineering and expression regulation of the transcriptional activator Gal4p. A cold-sensitive mutant, Gal4ep19, was created by directed evolution of Gal4p based on an internally developed growth-based high-throughput screening method and expressed under the heat-shock promoter PSSA4 to control the expression of PGAL-driven pathway genes in the mitochondria. Compared to the control strain with constitutively expressed wild-type Gal4p, the dual temperature regulation strategy led to 34.5% and 72% improvements in cell growth and isoprene production, respectively. This study reports the creation of the first cold-sensitive variants of Gal4p by directed evolution and provides a dual temperature control system for yeast engineering that may also be conducive to the biosynthesis of other high-value natural products.
. [J]. Frontiers of Chemical Science and Engineering, 2022, 16(7): 1079-1089.
Jiaxi Lin, Zhen Yao, Xiaomei Lyu, Lidan Ye, Hongwei Yu. Development of a dual temperature control system for isoprene biosynthesis in Saccharomyces cerevisiae. Front. Chem. Sci. Eng., 2022, 16(7): 1079-1089.
C E Vickers, S Suriana. Isoprene. Advances in Biochemical Engineering/Biotechnology, 2015, 148(9): 289–317 https://doi.org/10.1007/10_2014_303
2
X M Lv, F Wang, P P Zhou, L D Ye, W P Xie, H M Xu, H W Yu. Dual regulation of cytoplasmic and mitochondrial acetyl-CoA utilization for improved isoprene production in Saccharomyces cerevisiae. Nature Communications, 2016, 7(1): 12851 https://doi.org/10.1038/ncomms12851
3
Z Yao, P P Zhou, B M Su, S S Su, L D Ye, H W Yu. Enhanced isoprene production by reconstruction of metabolic balance between strengthened precursor supply and improved isoprene synthase in Saccharomyces cerevisiae. ACS Synthetic Biology, 2018, 7(9): 2308–2316 https://doi.org/10.1021/acssynbio.8b00289
4
F Wang, X M Lv, W P Xie, P P Zhou, Y Q Zhu, Z Yao, C C Yang, X H Yang, L D Ye, H W Yu. Combining Gal4p-mediated expression enhancement and directed evolution of isoprene synthase to improve isoprene production in Saccharomyces cerevisiae. Metabolic Engineering, 2017, 39: 257–266 https://doi.org/10.1016/j.ymben.2016.12.011
5
X Cao, S Yang, C Cao, Y J Zhou. Harnessing sub-organelle metabolism for biosynthesis of isoprenoids in yeast. Synthetic and Systems Biotechnology, 2020, 5(3): 179–186 https://doi.org/10.1016/j.synbio.2020.06.005
N A Da Silva, S Srikrishnan. Introduction and expression of genes for metabolic engineering applications in Saccharomyces cerevisiae. FEMS Yeast Research, 2012, 12(2): 197–214 https://doi.org/10.1111/j.1567-1364.2011.00769.x
8
W P Xie, M Liu, X M Lv, W Q Lu, J L Gu, H W Yu. Construction of a controllable β-carotene biosynthetic pathway by decentralized assembly strategy in Saccharomyces cerevisiae. Biotechnology and Bioengineering, 2014, 111(1): 125–133 https://doi.org/10.1002/bit.25002
9
G H Tan, M Chen, C Foote, C Tan. Temperature-sensitive mutations made easy: generating conditional mutations by using temperature-sensitive inteins that function within different temperature ranges. Genetics, 2009, 183(1): 13–22 https://doi.org/10.1534/genetics.109.104794
10
M P Zeidler, C Tan, Y Bellaiche, S Cherry, S Häder, U Gayko, N Perrimon. Temperature-sensitive control of protein activity by conditionally splicing inteins. Nature Biotechnology, 2004, 22(7): 871–876 https://doi.org/10.1038/nbt979
11
G Chakshusmathi, K Mondal, G S Lakshmi, G Singh, A Roy, Ch R Babu, S Madhusudhanan, R Varadarajan. Design of temperature-sensitive mutants solely from amino acid sequence. Proceedings of the National Academy of Sciences of the United States of America, 2004, 101(21): 7925–7930 https://doi.org/10.1073/pnas.0402222101
12
K Mondal, A G Dastidar, G Singh, S Madhusudhanan, S L Gande, K VijayRaghavan, R Varadarajan. Design and isolation of temperature-sensitive mutants of Gal4 in yeast and Drosophila. Journal of Molecular Biology, 2007, 370(5): 939–950 https://doi.org/10.1016/j.jmb.2007.05.035
13
P P Zhou, W P Xie, Z Yao, Y Q Zhu, L D Ye, H W Yu. Development of a temperature-responsive yeast cell factory using engineered Gal4 as a protein switch. Biotechnology and Bioengineering, 2018, 115(5): 1321–1330 https://doi.org/10.1002/bit.26544
14
K Mondal, K VijayRaghavan, R Varadarajan. Design and utility of temperature-sensitive Gal4 mutants for conditional gene expression in Drosophila. Fly, 2007, 1(5): 282–286 https://doi.org/10.4161/fly.5251
15
J D Boeke, F LaCroute, G R Fink. A positive selection for mutants lacking orotidine-5′-phosphate decarboxylase activity in yeast 5-fluoro-orotic acid resistance. Molecular Genetics and Genomics, 1984, 197(2): 345–346 https://doi.org/10.1007/BF00330984
16
R Sikorski, J D Boeke. In vitro mutagenesis and plasmid shuffling: from cloned gene to mutant yeast. Methods in Enzymology, 1991, 194: 302–318 https://doi.org/10.1016/0076-6879(91)94023-6
17
X D Meng, R M Smith, A V Giesecke, J K Joung, S A Wolfe. Counter-selectable marker for bacterial-based interaction trap systems. BioTechniques, 2006, 40(2): 179–184 https://doi.org/10.2144/000112049
18
C Baliga, S Majhi, K Mondal, A Bhattacharjee, K VijayRaghavan, R Varadarajan. Rational elicitation of cold-sensitive phenotypes. Proceedings of the National Academy of Sciences of the United States of America, 2016, 113(18): E2506–E2515 https://doi.org/10.1073/pnas.1604190113
19
C B Brachmann, A Davies, G J Cost, E Caputo, J Li, P Hieter, J D Boeke. Designer deletion strains derived from Saccharomyces cerevisiae S288C: a useful set of strains and plasmids for PCR-mediated gene disruption and other applications. Yeast (Chichester, England), 1998, 14(2): 115–132 https://doi.org/10.1002/(SICI)1097-0061(19980130)14:2<115::AID-YEA204>3.0.CO;2-2
20
R D Gietz, R H Schiestl. High-efficiency yeast transformation using the LiAc/SS carrier DNA/PEG method. Nature Protocols, 2007, 2(1): 31–34 https://doi.org/10.1038/nprot.2007.13
21
K J Livak, T D Schmittgen. Analysis of relative gene expression data using real-time quantitative PCR and the 2-ΔΔCT Method. Methods (San Diego, Calif.), 2001, 25(4): 402–408 https://doi.org/10.1006/meth.2001.1262
X Meng, R M Smith, A V Giesecke, J Keith Joung, S A Wolfe. Counter-selectable marker for bacterial-based interaction trap systems. BioTechniques, 2006, 40(2): 179–184 https://doi.org/10.2144/000112049
24
M Q Hong, M X Fitzgerald, S Harper, C Luo, D W Speicher, R Marmorstein. Structural basis for dimerization in DNA recognition by Gal4. Structure (London, England), 2008, 16(7): 1019–1026 https://doi.org/10.1016/j.str.2008.03.015
25
P Schjerling, S Holmberg. Comparative amino acid sequence analysis of the C6 zinc cluster family of transcriptional regulators. Nucleic Acids Research, 1996, 24(23): 4599–4607 https://doi.org/10.1093/nar/24.23.4599
M Johnston, J Dover. Mutational analysis of the Gal4-encoded transcriptional activator protein of Saccharomyces cerevisiae. Genetics, 1988, 120(1): 63–74 https://doi.org/10.1093/genetics/120.1.63
28
P P Zhou, N N Xu, Z F Yang, Y Du, C L Yue, N Xu, L D Ye. Directed evolution of the transcription factor Gal4 for development of an improved transcriptional regulation system in Saccharomyces cerevisiae. Enzyme and Microbial Technology, 2020, 142: 109675 https://doi.org/10.1016/j.enzmictec.2020.109675
29
W R Boorstein, E A Craig. Structure and regulation of the SSA4 HSP70 gene of Saccharomyces cerevisiae. Journal of Biological Chemistry, 1990, 265(31): 18912–18921 https://doi.org/10.1016/S0021-9258(17)30603-8
30
Y Chen, L Daviet, M Schalk, V Siewers, J Nielsen. Establishing a platform cell factory through engineering of yeast acetyl-CoA metabolism. Metabolic Engineering, 2013, 15: 48–54 https://doi.org/10.1016/j.ymben.2012.11.002
31
G Gill, M Ptashne. Negative effect of the transcriptional activator GAL4. Nature, 1988, 334(6184): 721–724 https://doi.org/10.1038/334721a0