Data for Controlling Circuitry Underlies the Growth Optimization of Saccharomyces cerevisiae

Nguyen, Viviana; Xue, Pu; Li, Yifei; Zhao, Huimin; Lu, Ting

doi:10.13012/B2IDB-8315352_V1

Title: Data for Controlling Circuitry Underlies the Growth Optimization of Saccharomyces cerevisiae

Dataset
Other Related Research

Abstract

Microbial growth emerges from coordinated synthesis of various cellular components from limited resources. In Saccharomyces cerevisiae, cyclic AMP (cAMP)-mediated signaling is shown to orchestrate cellular metabolism; however, it remains unclear quantitatively how the controlling circuit drives resource partition and subsequently shapes biomass growth. Here we combined experiment with mathematical modeling to dissect the signaling-mediated growth optimization of S. cerevisiae. We showed that, through cAMP-mediated control, the organism achieves maximal or nearly maximal steady-state growth during the utilization of multiple tested substrates as well as under perturbations impairing glucose uptake. However, the optimal cAMP concentration varies across cases, suggesting that different modes of resource allocation are adopted for varied conditions. Under settings with nutrient alterations, S. cerevisiae tunes its cAMP level to dynamically reprogram itself to realize rapid adaptation. Moreover, to achieve growth maximization, cells employ additional regulatory systems such as the GCN2-mediated amino acid control. This study establishes a systematic understanding of global resource allocation in S. cerevisiae, providing insights into quantitative yeast physiology as well as metabolic strain engineering for biotechnological applications.

Authors:

Nguyen, Viviana; Xue, Pu; Li, Yifei;

; Lu, Ting

Department of Physics, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA; Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), Urbana, IL (United States)
Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA; Carl R Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA; Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), Urbana, IL (United States)
Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA; Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), Urbana, IL (United States)
Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA; Carl R Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA; Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA; Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA; Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), Urbana, IL (United States)
Department of Physics, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA; Carl R Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA; Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA; National Center for Supercomputing Applications, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA; Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), Urbana, IL (United States)

Publication Date:: Wed Sep 20 20:00:00 EDT 2023

DOE Contract Number:: SC0018420

Research Org.:: Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), Urbana, IL (United States); University of Illinois Urbana-Champaign

Sponsoring Org.:: U.S. Department of Energy (DOE)

Subject:: Conversion; Metabolomics; Modeling

OSTI Identifier:: 3014557

DOI:: https://doi.org/10.13012/B2IDB-8315352_V1

Citation Formats


                    Nguyen, Viviana, Xue, Pu, Li, Yifei, Zhao, Huimin, and Lu, Ting. Data for Controlling Circuitry Underlies the Growth Optimization of Saccharomyces cerevisiae.  United States: N. p., 2023. 
        Web.  doi:10.13012/B2IDB-8315352_V1.

Copy to clipboard


                    Nguyen, Viviana, Xue, Pu, Li, Yifei, Zhao, Huimin, & Lu, Ting. Data for Controlling Circuitry Underlies the Growth Optimization of Saccharomyces cerevisiae.  United States.  doi:https://doi.org/10.13012/B2IDB-8315352_V1

Copy to clipboard


                    Nguyen, Viviana, Xue, Pu, Li, Yifei, Zhao, Huimin, and Lu, Ting. 2023.  
"Data for Controlling Circuitry Underlies the Growth Optimization of Saccharomyces cerevisiae".  United States.  doi:https://doi.org/10.13012/B2IDB-8315352_V1.  https://www.osti.gov/servlets/purl/3014557. Pub date:Wed Sep 20 20:00:00 EDT 2023

Copy to clipboard


                    
@article{osti_3014557,

  title        = {Data for Controlling Circuitry Underlies the Growth Optimization of Saccharomyces cerevisiae},

  author       = {Nguyen, Viviana and Xue, Pu and Li, Yifei and Zhao, Huimin and Lu, Ting},

  abstractNote = {Microbial growth emerges from coordinated synthesis of various cellular components from limited resources. In Saccharomyces cerevisiae, cyclic AMP (cAMP)-mediated signaling is shown to orchestrate cellular metabolism; however, it remains unclear quantitatively how the controlling circuit drives resource partition and subsequently shapes biomass growth. Here we combined experiment with mathematical modeling to dissect the signaling-mediated growth optimization of S. cerevisiae. We showed that, through cAMP-mediated control, the organism achieves maximal or nearly maximal steady-state growth during the utilization of multiple tested substrates as well as under perturbations impairing glucose uptake. However, the optimal cAMP concentration varies across cases, suggesting that different modes of resource allocation are adopted for varied conditions. Under settings with nutrient alterations, S. cerevisiae tunes its cAMP level to dynamically reprogram itself to realize rapid adaptation. Moreover, to achieve growth maximization, cells employ additional regulatory systems such as the GCN2-mediated amino acid control. This study establishes a systematic understanding of global resource allocation in S. cerevisiae, providing insights into quantitative yeast physiology as well as metabolic strain engineering for biotechnological applications.},

  doi          = {10.13012/B2IDB-8315352_V1},

  journal      = {},

  number       = ,

  volume       = ,

  place        = {United States},

  year         = {Wed Sep 20 20:00:00 EDT 2023},

  month        = {Wed Sep 20 20:00:00 EDT 2023}

}

Copy to clipboard

Dataset:

View Dataset

DOI: https://doi.org/10.13012/B2IDB-8315352_V1

Save / Share:

Export Metadata

Save to My Library

Similar records in DOE Data Explorer and OSTI.GOV collections:

Controlling circuitry underlies the growth optimization of Saccharomyces cerevisiae

Journal Article Nguyen, Viviana ; Xue, Pu ; Li, Yifei ; ... - Metabolic Engineering

Microbial growth emerges from coordinated synthesis of various cellular components from limited resources. In Saccharomyces cerevisiae, cyclic AMP (cAMP)-mediated signaling is shown to orchestrate cellular metabolism; however, it remains unclear quantitatively how the controlling circuit drives resource partition and subsequently shapes biomass growth. Here we combined experiment with mathematical modeling to dissect the signaling-mediated growth optimization of S. cerevisiae. We showed that, through cAMP-mediated control, the organism achieves maximal or nearly maximal steady-state growth during the utilization of multiple tested substrates as well as under perturbations impairing glucose uptake. However, the optimal cAMP concentration varies across cases, suggesting that differentmore »« less
Data for L-Malic Acid Production from Xylose by Engineered Saccharomyces cerevisiae

Dataset Kang, Nam Kyu ; Lee, Jaewon ; Ort, Donald ; ...

L-malic acid is widely used in the food, chemical, and pharmaceutical industries. Here, we report on production of malic acid from xylose, the second most abundant sugar in lignocellulosic hydrolysates, by engineered Saccharomyces cerevisiae. To enable malic acid production in a xylose-assimilating S. cerevisiae, we overexpressed PYC1 and PYC2, coding for pyruvate carboxylases, a truncated MDH3 coding for malate dehydrogenase, and SpMAE1, coding for a Schizosaccharomyces pombe malate transporter. Additionally, both the ethanol- and glycerol-producing pathways were blocked to enhance malic acid production. The resulting strain produced malic acid from both glucose and xylose, but it produced much higher titersmore »« less
Data for Cloning and Characterization of a Panel of Mitochondrial Targeting Sequences for Compartmentalization Engineering in Saccharomyces cerevisiae

Dataset Dong, Chang ; Shi, Zhuwei ; Huang, Lei ; ...

Mitochondrion is generally considered as the most promising subcellular organelle for compartmentalization engineering. Much progress has been made in reconstituting whole metabolic pathways in the mitochondria of yeast to harness the precursor pools (i.e., pyruvate and acetyl-CoA), bypass competing pathways, and minimize transportation limitations. However, only a few mitochondrial targeting sequences (MTSs) have been characterized (i.e., MTS of COX4), limiting the application of compartmentalization engineering for multigene biosynthetic pathways in the mitochondria of yeast. In the present study, based on the mitochondrial proteome, a total of 20 MTSs were cloned and the efficiency of these MTSs in targeting heterologous proteins,more »« less
Data from Enhanced 2′-Fucosyllactose Production by Engineered Saccharomyces cerevisiae using Xylose as a Co-Substrate

Dataset Lee, Jaewon ; Kwak, Suryang ; Liu, Jing-Jing ; ...

2′-Fucosyllactose (2′-FL), a human milk oligosaccharide with confirmed benefits for infant health, is a promising infant formula ingredient. Although Escherichia coli, Saccharomyces cerevisiae, Corynebacterium glutamicum, and Bacillus subtilis have been engineered to produce 2′-FL, their titers and productivities need be improved for economic production. Glucose along with lactose have been used as substrates for producing 2′-FL, but accumulation of by-products due to overflow metabolism of glucose hampered efficient production of 2′-FL regardless of a host strain. To circumvent this problem, we used xylose, which is the second most abundant sugar in plant cell wall hydrolysates and is metabolized through oxidativemore »« less
Data for Glucose Assimilation Rate Determines the Partition of Flux at Pyruvate Between Lactic Acid and Ethanol in Saccharomyces cerevisiae

Dataset Lane, Stephan ; Turner, Timothy L. ; Jin, Yong-Su

Engineered Saccharomyces cerevisiae expressing a lactic acid dehydrogenase can metabolize pyruvate into lactic acid. However, three pyruvate decarboxylase (PDC) isozymes drive most carbon flux toward ethanol rather than lactic acid. Deletion of endogenous PDCs will eliminate ethanol production, but the resulting strain suffers from C2 auxotrophy and struggles to complete a fermentation. Engineered yeast assimilating xylose or cellobiose produce lactic acid rather than ethanol as a major product without the deletion of any PDC genes. We report here that sugar flux, but not sensing, contributes to the partition of flux at the pyruvate branch point in S. cerevisiae expressing themore »« less

Similar Records