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Metabolic network remodelling enhances yeast’s fitness on xylose using aerobic glycolysis

Abstract

The reprogramming of metabolism in response to switching the carbon source from glucose to non-preferred carbon sources is well-studied for yeast. However, understanding how metabolic networks respond to utilize a non-natural carbon source such as xylose is limited due to the incomplete knowledge of cellular response mechanisms. Here we applied a combination of metabolic engineering, systems biology and adaptive laboratory evolution to gain insights into how yeast can perform a global rewiring of cellular processes to efficiently accompany metabolic transitions. Through metabolic engineering, we substantially enhanced the cell growth on xylose after the growth on glucose. Transcriptome analysis of the engineered strains demonstrated that multiple pathways were involved in the cellular reprogramming. Through genome resequencing of the evolved strains and reverse engineering, we further identified that SWI/SNF chromatin remodelling, osmotic response and aldehyde reductase were responsible for the improved growth. Combined, our analysis showed that glycerol-3-phosphate and xylitol serve as two key metabolites that affect cellular adaptation to growth on xylose.

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Fig. 1: XI-driven xylose assimilation in engineered yeast.
Fig. 2: Enhancing cell fitness on xylose through metabolic engineering.
Fig. 3: Global transcriptional analysis.
Fig. 4: The yeast native xylose responsive network can be globally rewired.
Fig. 5: TF analysis.
Fig. 6: ALE of two rationally designed engineered yeast strains.
Fig. 7: Mutations in the evolved strains highlights glycerol-3-P and xylitol as two critical metabolites.

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Data availability

The RNA-seq raw data are available at the Genome Expression Omnibus website (https://www.ncbi.nlm.nih.gov/geo/) using series number GSE151478. The genome sequence data of the evolved strains used in this article are available at the Sequence Read Archive website (https://www.ncbi.nlm.nih.gov/sra) with the accession number PRJNA636080. All other data that support the findings in this study are available upon reasonable request. All plasmids and strains used in this study can be obtained from the corresponding author under a material transfer agreement. Source data are provided with this paper.

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Acknowledgements

We thank C. Zhan, Z. Dai, H. Lu, T. Doughty, K. Campbell, R. Yu and L. F.-Y. Chao for helpful discussions. We thank J. Hellgren for the help with the RNA-seq data processing and analysis. We thank X. Chen, Z. Zhu and B. Ji for giving valuable advice on writing the manuscript. We thank X. Chen and L. F.-Y. Chao for help with the final polishing of the manuscript. This research was supported by The Novo Nordisk Foundation (NNF10CC1016517, J.N.), the Knut and Alice Wallenberg Foundation (J.N.), FORMAS (2015-01546, Y.C.), the Swedish Energy Agency (43548-1, J.N.), Carl Tryggers Stiftelse (Y.C.) and Ångpanneföreningens Forskningsstiftelse (Y.C.).

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J.N., Y.C. and X.L. conceived the study. X.L. performed most of the experiments. X.L., Y.C. and J.N. analysed all the experimental data. G.L. analysed the partial RNA-seq data. Y.W. and Q.L. assisted with the experimental performance. R.P. and X.L. analysed the genome sequence data. X.L., Y.C. and J.N. wrote the manuscript.

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Correspondence to Jens Nielsen.

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Li, X., Wang, Y., Li, G. et al. Metabolic network remodelling enhances yeast’s fitness on xylose using aerobic glycolysis. Nat Catal 4, 783–796 (2021). https://doi.org/10.1038/s41929-021-00670-6

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