Adaptive laboratory evolution of native methanol assimilation in Saccharomyces cerevisiae

Espinosa, Monica I.; Gonzalez-Garcia, R. Axayacatl; Valgepea, Kaspar; Plan, Manuel R.; Scott, Colin; Pretorius, Isak S.; Marcellin, Esteban; Paulsen, Ian T.; Williams, Thomas

doi:10.1038/s41467-020-19390-9

Cited by 78 publications

(85 citation statements)

References 57 publications

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“…However, conventional adaptive evolution for microorganisms is typically time-consuming and laborintensive, for example, 420 days for improving the conversion rate of nonglucose sugars of G. oxydans (Jin et al, 2019), 150 days for improving the salinity resistance of Schizochytrium sp. (Sun et al, 2018), 200 days for co-utilization of glucose and xylose of Zymomonas mobilis (Sarkar et al, 2020), and 230 generations for enhanced native methanol assimilation in S. cerevisiae (Espinosa et al, 2020). Reports on enhanced heat resistance by adaptive evolution or other rational strategies are rare (Cox et al, 2010).…”

Section: Discussionmentioning

confidence: 99%

Rapid Enabling of Gluconobacter oxydans Resistance to High D-Sorbitol Concentration and High Temperature by Microdroplet-Aided Adaptive Evolution

Liu

Zeng

et al. 2021

Front. Bioeng. Biotechnol.

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Gluconobacter oxydans is important in the conversion of D-sorbitol into l-sorbose, which is an essential intermediate for industrial-scale production of vitamin C. In a previous study, the strain G. oxydans WSH-004 could directly produce 2-keto-l-gulonic acid (2-KLG). However, its D-sorbitol tolerance was poor compared with that of other common industrial G. oxydans strains, which grew well in the presence of more than 200 g/L of D-sorbitol. This study aimed to use the microbial microdroplet culture (MMC) system for the adaptive evolution of G. oxydans WSH-004 so as to improve its tolerance to high substrate concentration and high temperature. A series of adaptively evolved strains, G. oxydans MMC1-MMC10, were obtained within 90 days. The results showed that the best strain MMC10 grew in a 300 g/L of D-sorbitol medium at 40°C. The comparative genomic analysis revealed that genetic changes related to increased tolerance were mainly in protein translation genes. Compared with the traditional adaptive evolution method, the application of microdroplet-aided adaptive evolution could improve the efficiency in terms of reducing time and simplifying the procedure for strain evolution. This research indicated that the microdroplet-aided adaptive evolution was an effective tool for improving the phenotypes with undemonstrated genotypes in a short time.

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Section: Discussionmentioning

confidence: 99%

Rapid Enabling of Gluconobacter oxydans Resistance to High D-Sorbitol Concentration and High Temperature by Microdroplet-Aided Adaptive Evolution

Liu

Zeng

et al. 2021

Front. Bioeng. Biotechnol.

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“…Intracellular metabolites were analysed using liquid chromatography-tandem mass spectrometry (LC-MS/MS) [ [31] , [32] , [33] , [34] ]. Analyses were performed using a Dionex Ultimate 3000 HPLC system coupled to an AB Sciex 4000 QTRAP mass spectrometer.…”

Section: Methodsmentioning

confidence: 99%

An anaplerotic approach to correct the mitochondrial dysfunction in ataxia-telangiectasia (A-T)

Yeo

Subramanian

Chong

et al. 2021

Molecular Metabolism

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Background ATM, the protein defective in the human genetic disorder, ataxia-telangiectasia (A-T) plays a central role in response to DNA double-strand breaks (DSBs) and in protecting the cell against oxidative stress. We showed that A-T cells are hypersensitive to metabolic stress which can be accounted for by a failure to exhibit efficient endoplasmic reticulum (ER)-mitochondrial signalling and Ca2 + transfer in response to nutrient deprivation resulting in mitochondrial dysfunction. The objective of the current study is to use an anaplerotic approach using the fatty acid, heptanoate (C7), a metabolic product of the triglyceride, triheptanoin to correct the defect in ER-mitochondrial signalling and enhance cell survival of A-T cells in response to metabolic stress. Methods We treated control cells and A-T cells with the anaplerotic agent, heptanoate to determine their sensitivity to metabolic stress induced by inhibition of glycolysis with 2- deoxyglucose (2DG) using live-cell imaging to monitor cell survival for 72 h using the Incucyte system. We examined ER-mitochondrial signalling in A-T cells exposed to metabolic stress using a suite of techniques including immunofluorescence staining of Grp75, ER-mitochondrial Ca 2+ channel, the VAPB-PTPIP51 ER-mitochondrial tether complexes as well as proximity ligation assays between Grp75-IP3R1 and VAPB1-PTPIP51 to establish a functional interaction between ER and mitochondria. Finally, we also performed metabolomic analysis using LC-MS/MS assay to determine altered levels of TCA intermediates A-T cells compared to healthy control cells. Results We demonstrate that heptanoate corrects all aspects of the defective ER-mitochondrial signalling observed in A-T cells. Heptanoate enhances ER-mitochondrial contacts; increases the flow of calcium from the ER to the mitochondrion; restores normal mitochondrial function and mitophagy and increases the resistance of ATM-deficient cells and cells from A-T patients to metabolic stress-induced killing. The defect in mitochondrial function in ATM-deficient cells was accompanied by more reliance on aerobic glycolysis as shown by increased lactate dehydrogenase A (LDHA), accumulation of lactate, and reduced levels of both acetyl CoA and ATP which are all restored by heptanoate. Conclusions We conclude that heptanoate corrects metabolic stress in A-T cells by restoring ER-mitochondria signalling and mitochondrial function and suggest that the parent compound, triheptanoin, has immense potential as a novel therapeutic agent for patients with A-T.

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“…An extreme extension of sustainable alcoholic beverage production would therefore be to engineer strains of yeast that are capable of fermentation from more sustainable carbon sources, such as sugars or greenhouse gases, so that resource intensive grains or grapes are not required. Utilisation of greenhouse gas derivatives is within reach, as S. cerevisiae has recently been engineered to metabolise methanol and formate [44,45], and the methylotrophic yeast Pichia pastoris was recently engineered to grow on CO 2 as the sole carbon source [46]. Producing complex alcoholic beverages from simple industrial carbon sources would involve extensive metabolic engineering of yeast to recapitulate the flavour and mouth feel components that are normally derived from grapes or grains in the yeast metabolic network, while maintaining ethanol production.…”

Section: Synthetic Biology For Future Alcoholic Beveragesmentioning

confidence: 99%

Bioinformational trends in grape and wine biotechnology

Dixon

Williams

Pretorius

2022

Trends in Biotechnology

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The creative destruction caused by the coronavirus pandemic is yielding immense opportunity for collaborative innovation networks. The confluence of biosciences, information sciences, and the engineering of biology, is unveiling promising bioinformational futures for a vibrant and sustainable bioeconomy. Bioinformational engineering, underpinned by DNA reading, writing, and editing technologies, has become a beacon of opportunity in a world paralysed by uncertainty. This article draws on lessons from the current pandemic and previous agricultural blights, and explores bioinformational research directions aimed at future-proofing the grape and wine industry against biological shocks from global blights and climate change. The shock and awe of the pandemic's creative destructionThe years of global pandemic outbreaks, 1346, 1918, and 2020, loom large in history because these low-probability, high-impact disasters have devastating impacts on people's lives with tranquilising effects on society as a whole. In this regard, the 2020 coronavirus outbreak was no less damaging than previous once-in-a-century pandemics, global blights (see Glossary), and other catastrophes. This paper explores the future of grape and wine biotechnology with future global biological shocks in mind. These shocks include both the potential for global blights but also the disruptive potential of climate change. It is important to note that these two shocks combine in a layered manner; temperature change combined with existing land use patterns can contribute to the likelihood of a new global blight emerging. COVID-19 exemplifies the power of a global biological shock. The virus has infected millions of people and reset the trajectory of macro political, economic, sociological, technological, legal, and environmental (PESTLE) forces that shape the modern world. Such powerful forces are of course not solely the province of human biological shocks, and global blights harbour similar levels of disruptive potential. This paper explores the emerging science and technologies that might mitigate the risks of a global blight in the grape and wine sector. HighlightsUncertainty caused by pandemics, global blights, and climate change, tends to heighten the focus on how biotechnological advances can mitigate challenges to public safety, cyberbio resilience, environmental sustainability, and bioeconomic security.Convergence of cyberbio technologies and high-throughput automation in biofoundries offers future-shaping bioinformational engineering opportunities with transformational potential to the wine industry.Consumer preferences, biosecurity, and bioethical considerations, must guide research directions and adoption of new bioinformational engineering technologies at the levels of both problem selection and experimental design.

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Adaptive laboratory evolution of native methanol assimilation in Saccharomyces cerevisiae

Cited by 78 publications

References 57 publications

Rapid Enabling of Gluconobacter oxydans Resistance to High D-Sorbitol Concentration and High Temperature by Microdroplet-Aided Adaptive Evolution

Rapid Enabling of Gluconobacter oxydans Resistance to High D-Sorbitol Concentration and High Temperature by Microdroplet-Aided Adaptive Evolution

An anaplerotic approach to correct the mitochondrial dysfunction in ataxia-telangiectasia (A-T)

Bioinformational trends in grape and wine biotechnology

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