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Zhang W, Shao W, Zhang A. Isobutanol tolerance and production of Saccharomyces cerevisiae can be improved by engineering its TATA-binding protein Spt15. Lett Appl Microbiol 2021; 73:694-707. [PMID: 34418130 DOI: 10.1111/lam.13555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 08/10/2021] [Accepted: 08/12/2021] [Indexed: 11/26/2022]
Abstract
Low isobutanol tolerance of Saccharomyces cerevisiae limits its application in isobutanol fermentation. Here, we used global transcription machinery engineering to screen mutants with higher isobutanol tolerance and elevated isobutanol titres. TATA-binding protein Spt15 was used as the target of global transcription machinery engineering for improvement of such complex phenotypes. A random mutagenesis library of S. cerevisiae TATA-binding protein Spt15 was constructed and subjected to screening under isobutanol stress. A mutant strain (denoted as spt15-3) with improved isobutanol tolerance was identified. There were three mutations of Spt15 in strain spt15-3, including deletion of A at position -132 nt upstream of initiation codon, insertion of G at position -65 nt upstream of initiation codon and a synonymous mutation at position 315 nt (T → C) downstream of initiation codon. We then metabolically engineered isobutanol synthesis in strains harbouring plasmids YCplac22 containing these Spt15 mutations. Delta integration was used to overexpress ILV3 gene, and 2μ plasmids carrying PGK1p-ILV2 and PGK1p-ARO10 were used to overexpress ILV2 and ARO10 genes. After 24-h micro-aerobic fermentation, Engi-3 produced 0·556 g l-1 isobutanol, which was 404% and 25·3% greater than isobutanol produced by control Engi-1 and engineered Engi-2, respectively. After 28 h, Engi-4 produced 0·459 g l-1 isobutanol, which was 315% and 3·2% greater than isobutanol produced Engi-1 and Engi-2, respectively. RNA-Seq-based transcriptome analysis shows that mutations of Spt15 in strain spt15-3 increased the expression of SPT15. Meanwhile, compared with strain Engi-3, the spt15-3 mutation downregulated the expression of genes involved in the TCA cycle and glyoxylic acid cycle, but increased the expression of genes related to cell stability. This work demonstrates that isobutanol tolerance and production of S. cerevisiae can be improved by engineering its TATA-binding protein Spt15. This study clarified the molecular mechanisms regulating isobutanol production and tolerance in S. cerevisiae.
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Affiliation(s)
- W Zhang
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin, China
| | - W Shao
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin, China
| | - A Zhang
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin, China
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Du Q, Liu Y, Song Y, Qin Y. Creation of a Low-Alcohol-Production Yeast by a Mutated SPT15 Transcription Regulator Triggers Transcriptional and Metabolic Changes During Wine Fermentation. Front Microbiol 2021; 11:597828. [PMID: 33381093 PMCID: PMC7768003 DOI: 10.3389/fmicb.2020.597828] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 11/23/2020] [Indexed: 11/23/2022] Open
Abstract
There is significant interest in the wine industry to develop methods to reduce the ethanol content of wine. Here the global transcription machinery engineering (gTME) technology was used to engineer a yeast strain with decreased ethanol yield, based on the mutation of the SPT15 gene. We created a strain of Saccharomyces cerevisiae (YS59-409), which possessed ethanol yield reduced by 34.9%; this was accompanied by the increase in CO2, biomass, and glycerol formation. Five mutation sites were identified in the mutated SPT15 gene of YS59-409. RNA-Seq and metabolome analysis of YS59-409 were conducted compared with control strain, suggesting that ribosome biogenesis, nucleotide metabolism, glycolysis flux, Crabtree effect, NAD+/NADH homeostasis and energy metabolism might be regulated by the mutagenesis of SPT15 gene. Furthermore, two genes related to energy metabolism, RGI1 and RGI2, were found to be associated with the weakened ethanol production capacity, although the precise mechanisms involved need to be further elucidated. This study highlighted the importance of applying gTME technology when attempting to reduce ethanol production by yeast, possibly reprogramming yeast’s metabolism at the global level.
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Affiliation(s)
- Qing Du
- College of Enology, Northwest A&F University, Yangling, China.,Shaanxi Engineering Research Center for Viti-Viniculture, Yangling, China.,National Forestry and Grassland Administration Engineering Research Center for Viti-Viniculture, Yangling, China
| | - Yanlin Liu
- College of Enology, Northwest A&F University, Yangling, China.,Shaanxi Engineering Research Center for Viti-Viniculture, Yangling, China.,National Forestry and Grassland Administration Engineering Research Center for Viti-Viniculture, Yangling, China
| | - Yuyang Song
- College of Enology, Northwest A&F University, Yangling, China.,Shaanxi Engineering Research Center for Viti-Viniculture, Yangling, China.,National Forestry and Grassland Administration Engineering Research Center for Viti-Viniculture, Yangling, China
| | - Yi Qin
- College of Enology, Northwest A&F University, Yangling, China.,Shaanxi Engineering Research Center for Viti-Viniculture, Yangling, China.,National Forestry and Grassland Administration Engineering Research Center for Viti-Viniculture, Yangling, China
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Abstract
The yeast Saccharomyces cerevisiae is one of the preferred hosts for the production of terpenoids through metabolic engineering. A genetic screen to identify novel mutants that can increase the flux in the isoprenoid pathway has been lacking. We present here the method that has led to the development of a carotenoid based visual screen by exploiting the carotenogenic genes from the red yeast Rhodosporidium toruloides, an organism known to have high levels of carotenoids. We also discuss the methods to use this screen for the identification of mutants that can lead to higher isoprenoid flux. The carotenoid based screen was developed in S. cerevisiae using phytoene synthase RtPSY1 and a hyperactive mutant of the enzyme phytoene dehydrogenase, RtCRTI(A393T) from Rhodosporidium toruloides. As validation of the genetic screen is critical at all stages, we describe the method to validate the screen using a known flux increasing gene, a truncated HMG1 (tHMG1). To demonstrate how this screen can be exploited to isolate mutants, we described how targeted mutagenesis of candidate gene, SPT15 a TATA binding protein involved in the global transcription machinery can be carried out to yield novel mutants with increased metabolic flux. Since it is also important to ensure that the isolated mutants are enhancing general isoprenoid flux, we describe how this can be established using an alternate isoprenoid, α-farnesene.
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Wadhwa M, Srinivasan S, Bachhawat AK, Venkatesh KV. Role of phosphate limitation and pyruvate decarboxylase in rewiring of the metabolic network for increasing flux towards isoprenoid pathway in a TATA binding protein mutant of Saccharomyces cerevisiae. Microb Cell Fact 2018; 17:152. [PMID: 30241525 PMCID: PMC6149198 DOI: 10.1186/s12934-018-1000-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Accepted: 09/18/2018] [Indexed: 11/13/2022] Open
Abstract
Background Production of isoprenoids, a large and diverse class of commercially important chemicals, can be achieved through engineering metabolism in microorganisms. Several attempts have been made to reroute metabolic flux towards isoprenoid pathway in yeast. Most approaches have focused on the core isoprenoid pathway as well as on meeting the increased precursors and cofactor requirements. To identify unexplored genetic targets that positively influence the isoprenoid pathway activity, a carotenoid based genetic screen was previously developed and three novel mutants of a global TATA binding protein SPT15 was isolated for heightened isoprenoid flux in Saccharomyces cerevisiae. Results In this study, we investigated how one of the three spt15 mutants, spt15_Ala101Thr, was leading to enhanced isoprenoid pathway flux in S. cerevisiae. Metabolic flux analysis of the spt15_Ala101Thr mutant initially revealed a rerouting of the central carbon metabolism for the production of the precursor acetyl-CoA through activation of pyruvate-acetaldehyde-acetate cycle in the cytoplasm due to high flux in the reaction caused by pyruvate decarboxylase (PDC). This led to alternate routes of cytosolic NADPH generation, increased mitochondrial ATP production and phosphate demand in the mutant strain. Comparison of the transcriptomics of the spt15_Ala101Thr mutant cell with SPT15WT bearing cells shows upregulation of phosphate mobilization genes and pyruvate decarboxylase 6 (PDC6). Increasing the extracellular phosphate led to an increase in the growth rate and biomass but diverted flux away from the isoprenoid pathway. PDC6 is also shown to play a critical role in isoprenoid pathway flux under phosphate limitation conditions. Conclusion The study not only proposes a probable mechanism as to how a spt15_Ala101Thr mutant (a global TATA binding protein mutant) could increase flux towards the isoprenoid pathway, but also PDC as a new route of metabolic manipulation for increasing the isoprenoid flux in yeast. Electronic supplementary material The online version of this article (10.1186/s12934-018-1000-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Manisha Wadhwa
- Department of Biological Sciences, Indian Institute of Science Education and Research, Mohali, Mohali, India
| | - Sumana Srinivasan
- Department of Chemical Engineering, Indian Institute of Technology, Bombay, Mumbai, India
| | - Anand K Bachhawat
- Department of Biological Sciences, Indian Institute of Science Education and Research, Mohali, Mohali, India.
| | - K V Venkatesh
- Department of Chemical Engineering, Indian Institute of Technology, Bombay, Mumbai, India.
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El-Rotail AAMM, Zhang L, Li Y, Liu SP, Shi GY. A novel constructed SPT15 mutagenesis library of Saccharomyces cerevisiae by using gTME technique for enhanced ethanol production. AMB Express 2017; 7:111. [PMID: 28582970 PMCID: PMC5457369 DOI: 10.1186/s13568-017-0400-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 05/04/2017] [Indexed: 01/15/2023] Open
Abstract
During the last few years, the global transcription machinery engineering (gTME) technique has gained more attention as an effective approach for the construction of novel mutants. Genetic strategies (molecular biology methods) were utilized to get mutational for both genes (SPT15 and TAF23) basically existed in the Saccharomyces cerevisiae genome via screening the gTME approach in order to obtain a new mutant S. cerevisiae diploid strain. The vector pYX212 was utilized to transform these genes into the control diploid strain S. cerevisiae through the process of mating between haploids control strains S. cerevisiae (MAT-a [CICC 1374]) and (MAT-α [CICC 31144]), by using the oligonucleotide primers SPT15-EcoRI-FW/SPT15-SalI-RV and TAF23-SalI-FW/TAF23-NheI-RV, respectively. The resultant mutants were examined for a series of stability tests. This study showed how strong the effect of using strategic gTME with the importance of the modification we conducted in Error Prone PCR protocol by increasing MnCl2 concentration instead of MgCl2. More than ninety mutants we obtained in this study were distinguished by a high level production of bio-ethanol as compared to the diploid control strain.
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Affiliation(s)
- Ashraf A. M. M. El-Rotail
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, National Engineering Laboratory for Cereal Fermentation Technology, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122 Jiangsu China
- Faculty of Environmental Agricultural Science, El Arish University, El Arish, North Sinai 45526 Egypt
| | - Liang Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, National Engineering Laboratory for Cereal Fermentation Technology, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122 Jiangsu China
| | - Youran Li
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, National Engineering Laboratory for Cereal Fermentation Technology, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122 Jiangsu China
| | - Shuang Ping Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, National Engineering Laboratory for Cereal Fermentation Technology, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122 Jiangsu China
| | - Gui Yang Shi
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, National Engineering Laboratory for Cereal Fermentation Technology, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122 Jiangsu China
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Seong YJ, Park H, Yang J, Kim SJ, Choi W, Kim KH, Park YC. Expression of a mutated SPT15 gene in Saccharomyces cerevisiae enhances both cell growth and ethanol production in microaerobic batch, fed-batch, and simultaneous saccharification and fermentations. Appl Microbiol Biotechnol 2017; 101:3567-3575. [PMID: 28168313 DOI: 10.1007/s00253-017-8139-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 01/05/2017] [Accepted: 01/20/2017] [Indexed: 12/01/2022]
Abstract
The SPT15 gene encodes a Saccharomyces cerevisiae TATA-binding protein, which is able to globally control the transcription levels of various metabolic and regulatory genes. In this study, a SPT15 gene mutant (S42N, S78R, S163P, and I212N) was expressed in S. cerevisiae BY4741 (BSPT15-M3), of which effects on fermentative yeast properties were evaluated in a series of culture types. By applying different nitrogen sources and air supply conditions in batch culture, organic nitrogen sources and microaerobic condition were decided to be more favorable for both cell growth and ethanol production of the BSPT15-M3 strain than the control S. cerevisiae BY4741 strain expressing the SPT15 gene (BSPT15wt). Microaerobic fed-batch cultures of BSPT15-M3 with glucose shock in the presence of high ethanol content resulted in a 9.5-13.4% higher glucose consumption rate and ethanol productivity than those for the BSPT15wt strain. In addition, BSPT15-M3 showed 4.5 and 3.9% increases in ethanol productivity from cassava hydrolysates and corn starch in simultaneous saccharification and fermentation processes, respectively. It was concluded that overexpression of the mutated SPT15 gene would be a potent strategy to develop robust S. cerevisiae strains with enhanced cell growth and ethanol production abilities.
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Affiliation(s)
- Yeong-Je Seong
- Department of Bio and Fermentation Convergence Technology, and BK21 PLUS Program, Kookmin University, Seoul, 136-702, South Korea
| | - Haeseong Park
- Department of Bio and Fermentation Convergence Technology, and BK21 PLUS Program, Kookmin University, Seoul, 136-702, South Korea
| | - Jungwoo Yang
- Department of Biotechnology, Graduate School, Korea University, Seoul, 136-713, South Korea
| | - Soo-Jung Kim
- Center for Food and Bioconvergence, Seoul National University, Seoul, 151-742, South Korea
| | - Wonja Choi
- Department of Life Sciences, College of Natural Sciences, Ewha Womans University, Seoul, 120-750, South Korea
| | - Kyoung Heon Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, 136-713, South Korea
| | - Yong-Cheol Park
- Department of Bio and Fermentation Convergence Technology, and BK21 PLUS Program, Kookmin University, Seoul, 136-702, South Korea.
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Wadhwa M, Bachhawat A. A genetic screen for increasing metabolic flux in the isoprenoid pathway of Saccharomyces cerevisiae: Isolation of SPT15 mutants using the screen. Metab Eng Commun 2016; 3:164-172. [PMID: 29468122 PMCID: PMC5779727 DOI: 10.1016/j.meteno.2016.05.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Revised: 05/24/2016] [Accepted: 05/25/2016] [Indexed: 01/17/2023] Open
Abstract
A genetic screen to identify mutants that can increase flux in the isoprenoid pathway of yeast has been lacking. We describe a carotenoid-based visual screen built with the core carotenogenic enzymes from the red yeast Rhodosporidium toruloides. Enzymes from this yeast displayed the required, higher capacity in the carotenoid pathway. The development also included the identification of the metabolic bottlenecks, primarily phytoene dehydrogenase, that was subjected to a directed evolution strategy to yield more active mutants. To further limit phytoene pools, a less efficient version of GGPP synthase was employed. The screen was validated with a known flux increasing gene, tHMG1. New mutants in the TATA binding protein SPT15 were isolated using this screen that increased the yield of carotenoids, and an alternate isoprenoid, α-Farnesene confirming increase in overall flux. The findings indicate the presence of previously unknown links to the isoprenoid pathway that can be uncovered using this screen.
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