skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Flux-Enabled Exploration of the Role of Sip1 in Galactose Yeast Metabolism

Abstract

13C metabolic flux analysis (13C MFA) is an important systems biology technique that has been used to investigate microbial metabolism for decades. The heterotrimer Snf1 kinase complex plays a key role in the preference Saccharomyces cerevisiae exhibits for glucose over galactose, a phenomenon known as glucose repression or carbon catabolite repression. The SIP1 gene, encoding a part of this complex, has received little attention, presumably, because its knockout lacks a growth phenotype. We present a fluxomic investigation of the relative effects of the presence of galactose in classically glucose-repressing media and/or knockout of SIP1 using a multi-scale variant of 13C MFA known as 2-Scale 13C metabolic flux analysis (2S-13C MFA). In this study, all strains have the galactose metabolism deactivated (gal1Δ background) so as to be able to separate the metabolic effects purely related to glucose repression from those arising from galactose metabolism. The resulting flux profiles reveal that the presence of galactose in classically glucose-repressing conditions, for a CEN.PK113-7D gal1Δ background, results in a substantial decrease in pentose phosphate pathway (PPP) flux and increased flow from cytosolic pyruvate and malate through the mitochondria toward cytosolic branched-chain amino acid biosynthesis. These fluxomic redistributions are accompanied by a higher maximum specificmore » growth rate, both seemingly in violation of glucose repression. Deletion of SIP1 in the CEN.PK113-7D gal1Δ cells grown in mixed glucose/galactose medium results in a further increase. Knockout of this gene in cells grown in glucose-only medium results in no change in growth rate and a corresponding decrease in glucose and ethanol exchange fluxes and flux through pathways involved in aspartate/threonine biosynthesis. Glucose repression appears to be violated at a 1/10 ratio of galactose-to-glucose. Based on the scientific literature, we may have conducted our experiments near a critical sugar ratio that is known to allow galactose to enter the cell. Additionally, we report a number of fluxomic changes associated with these growth rate increases and unexpected flux profile redistributions resulting from deletion of SIP1 in glucose-only medium.« less

Authors:
 [1];  [2];  [2];  [2];  [2];  [2];  [3];  [4]
  1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Joint BioEnergy Institute, Emeryville, CA (United States); Univ. of California, Berkeley, CA (United States)
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Joint BioEnergy Institute, Emeryville, CA (United States)
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Joint BioEnergy Institute, Emeryville, CA (United States); DOE Agile Biofoundry, Emeryville, CA (United States); Basque Center for Applied Mathematics, Bilbao, Basque Country (Spain)
  4. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Joint BioEnergy Institute, Emeryville, CA (United States); Univ. of California, Berkeley, CA (United States); Technical Univ. of Denmark, Horsholm (Denmark)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1379658
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Frontiers in Bioengineering and Biotechnology
Additional Journal Information:
Journal Volume: 5; Journal ID: ISSN 2296-4185
Publisher:
Frontiers Research Foundation
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES

Citation Formats

Shymansky, Christopher M., Wang, George, Baidoo, Edward E. K., Gin, Jennifer, Apel, Amanda Reider, Mukhopadhyay, Aindrila, Martin, Hector Garcia, and Keasling, Jay D. Flux-Enabled Exploration of the Role of Sip1 in Galactose Yeast Metabolism. United States: N. p., 2017. Web. doi:10.3389/fbioe.2017.00031.
Shymansky, Christopher M., Wang, George, Baidoo, Edward E. K., Gin, Jennifer, Apel, Amanda Reider, Mukhopadhyay, Aindrila, Martin, Hector Garcia, & Keasling, Jay D. Flux-Enabled Exploration of the Role of Sip1 in Galactose Yeast Metabolism. United States. doi:10.3389/fbioe.2017.00031.
Shymansky, Christopher M., Wang, George, Baidoo, Edward E. K., Gin, Jennifer, Apel, Amanda Reider, Mukhopadhyay, Aindrila, Martin, Hector Garcia, and Keasling, Jay D. Wed . "Flux-Enabled Exploration of the Role of Sip1 in Galactose Yeast Metabolism". United States. doi:10.3389/fbioe.2017.00031. https://www.osti.gov/servlets/purl/1379658.
@article{osti_1379658,
title = {Flux-Enabled Exploration of the Role of Sip1 in Galactose Yeast Metabolism},
author = {Shymansky, Christopher M. and Wang, George and Baidoo, Edward E. K. and Gin, Jennifer and Apel, Amanda Reider and Mukhopadhyay, Aindrila and Martin, Hector Garcia and Keasling, Jay D.},
abstractNote = {13C metabolic flux analysis (13C MFA) is an important systems biology technique that has been used to investigate microbial metabolism for decades. The heterotrimer Snf1 kinase complex plays a key role in the preference Saccharomyces cerevisiae exhibits for glucose over galactose, a phenomenon known as glucose repression or carbon catabolite repression. The SIP1 gene, encoding a part of this complex, has received little attention, presumably, because its knockout lacks a growth phenotype. We present a fluxomic investigation of the relative effects of the presence of galactose in classically glucose-repressing media and/or knockout of SIP1 using a multi-scale variant of 13C MFA known as 2-Scale 13C metabolic flux analysis (2S-13C MFA). In this study, all strains have the galactose metabolism deactivated (gal1Δ background) so as to be able to separate the metabolic effects purely related to glucose repression from those arising from galactose metabolism. The resulting flux profiles reveal that the presence of galactose in classically glucose-repressing conditions, for a CEN.PK113-7D gal1Δ background, results in a substantial decrease in pentose phosphate pathway (PPP) flux and increased flow from cytosolic pyruvate and malate through the mitochondria toward cytosolic branched-chain amino acid biosynthesis. These fluxomic redistributions are accompanied by a higher maximum specific growth rate, both seemingly in violation of glucose repression. Deletion of SIP1 in the CEN.PK113-7D gal1Δ cells grown in mixed glucose/galactose medium results in a further increase. Knockout of this gene in cells grown in glucose-only medium results in no change in growth rate and a corresponding decrease in glucose and ethanol exchange fluxes and flux through pathways involved in aspartate/threonine biosynthesis. Glucose repression appears to be violated at a 1/10 ratio of galactose-to-glucose. Based on the scientific literature, we may have conducted our experiments near a critical sugar ratio that is known to allow galactose to enter the cell. Additionally, we report a number of fluxomic changes associated with these growth rate increases and unexpected flux profile redistributions resulting from deletion of SIP1 in glucose-only medium.},
doi = {10.3389/fbioe.2017.00031},
journal = {Frontiers in Bioengineering and Biotechnology},
number = ,
volume = 5,
place = {United States},
year = {2017},
month = {5}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Save / Share:

Works referenced in this record:

Central carbon metabolism of Saccharomyces cerevisiae explored by biosynthetic fractional 13 C labeling of common amino acids : Central carbon metabolism of
journal, April 2001


Determination of confidence intervals of metabolic fluxes estimated from stable isotope measurements
journal, July 2006

  • Antoniewicz, Maciek R.; Kelleher, Joanne K.; Stephanopoulos, Gregory
  • Metabolic Engineering, Vol. 8, Issue 4
  • DOI: 10.1016/j.ymben.2006.01.004

Evolved hexose transporter enhances xylose uptake and glucose/xylose co-utilization in Saccharomyces cerevisiae
journal, January 2016

  • Reider Apel, Amanda; Ouellet, Mario; Szmidt-Middleton, Heather
  • Scientific Reports, Vol. 6, Issue 1
  • DOI: 10.1038/srep19512

Network Identification and Flux Quantification in the Central Metabolism of Saccharomyces cerevisiae under Different Conditions of Glucose Repression
journal, February 2001


A new efficient gene disruption cassette for repeated use in budding yeast
journal, July 1996


Population Diversification in a Yeast Metabolic Program Promotes Anticipation of Environmental Shifts
journal, January 2015


Natural Variation in Preparation for Nutrient Depletion Reveals a Cost–Benefit Tradeoff
journal, January 2015


13C Metabolic Flux Analysis for Systematic Metabolic Engineering of S. cerevisiae for Overproduction of Fatty Acids
journal, October 2016

  • Ghosh, Amit; Ando, David; Gin, Jennifer
  • Frontiers in Bioengineering and Biotechnology, Vol. 4
  • DOI: 10.3389/fbioe.2016.00076

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models
journal, October 2015

  • King, Zachary A.; Lu, Justin; Dräger, Andreas
  • Nucleic Acids Research, Vol. 44, Issue D1
  • DOI: 10.1093/nar/gkv1049

Connecting extracellular metabolomic measurements to intracellular flux states in yeast
journal, January 2009

  • Mo, Monica L.; Palsson, Bernhard Ø; Herrgård, Markus J.
  • BMC Systems Biology, Vol. 3, Issue 1
  • DOI: 10.1186/1752-0509-3-37

Transformation of Saccharomyces cerevisiae by the lithium acetate/single-stranded carrier DNA/polyethylene glycol protocol
journal, January 1998


De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology
journal, January 2012

  • Nijkamp, Jurgen F.; van den Broek, Marcel; Datema, Erwin
  • Microbial Cell Factories, Vol. 11, Issue 1
  • DOI: 10.1186/1475-2859-11-36

HipA-Triggered Growth Arrest and β-Lactam Tolerance in Escherichia coli Are Mediated by RelA-Dependent ppGpp Synthesis
journal, May 2013

  • Bokinsky, G.; Baidoo, E. E. K.; Akella, S.
  • Journal of Bacteriology, Vol. 195, Issue 14, p. 3173-3182
  • DOI: 10.1128/JB.02210-12

13C metabolic flux analysis in complex systems
journal, February 2011


Glucose repression in Saccharomyces cerevisiae
journal, July 2015


A kinetic-based approach to understanding heterologous mevalonate pathway function in E. coli : A Kinetic-Based Approach to Understanding Heterologous
journal, August 2014

  • Weaver, Lane J.; Sousa, Mirta M. L.; Wang, George
  • Biotechnology and Bioengineering, Vol. 112, Issue 1
  • DOI: 10.1002/bit.25323

Metabolic networks in motion: 13 C‐based flux analysis
journal, January 2006


Metabolic engineering of yeast for production of fuels and chemicals
journal, June 2013

  • Nielsen, Jens; Larsson, Christer; van Maris, Antonius
  • Current Opinion in Biotechnology, Vol. 24, Issue 3
  • DOI: 10.1016/j.copbio.2013.03.023

Galactose metabolic genes in yeast respond to a ratio of galactose and glucose
journal, January 2015

  • Escalante-Chong, Renan; Savir, Yonatan; Carroll, Sean M.
  • Proceedings of the National Academy of Sciences, Vol. 112, Issue 5
  • DOI: 10.1073/pnas.1418058112

How Saccharomyces Responds to Nutrients
journal, December 2008


Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p
journal, April 2009

  • Moxley, J. F.; Jewett, M. C.; Antoniewicz, M. R.
  • Proceedings of the National Academy of Sciences, Vol. 106, Issue 16
  • DOI: 10.1073/pnas.0811091106

Different Levels of Catabolite Repression Optimize Growth in Stable and Variable Environments
journal, January 2014


A Method to Constrain Genome-Scale Models with 13C Labeling Data
journal, September 2015

  • García Martín, Héctor; Kumar, Vinay Satish; Weaver, Daniel
  • PLOS Computational Biology, Vol. 11, Issue 9
  • DOI: 10.1371/journal.pcbi.1004363

Metabolic-Flux Profiling of the Yeasts Saccharomyces cerevisiae and Pichia stipitis
journal, February 2003


Achieving Metabolic Flux Analysis for S. cerevisiae at a Genome-Scale: Challenges, Requirements, and Considerations
journal, September 2015


A comprehensive strategy enabling high-resolution functional analysis of the yeast genome
journal, July 2008

  • Breslow, David K.; Cameron, Dale M.; Collins, Sean R.
  • Nature Methods, Vol. 5, Issue 8
  • DOI: 10.1038/nmeth.1234

Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools
journal, June 2012

  • Ham, T. S.; Dmytriv, Z.; Plahar, H.
  • Nucleic Acids Research, Vol. 40, Issue 18
  • DOI: 10.1093/nar/gks531

Metabolic flux analysis inEscherichia coli by integrating isotopic dynamic and isotopic stationary13C labeling data
journal, January 2008

  • Schaub, Jochen; Mauch, Klaus; Reuss, Matthias
  • Biotechnology and Bioengineering, Vol. 99, Issue 5
  • DOI: 10.1002/bit.21675

13C Metabolic Flux Analysis
journal, July 2001


Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods
journal, February 2012

  • Lewis, Nathan E.; Nagarajan, Harish; Palsson, Bernhard O.
  • Nature Reviews Microbiology, Vol. 10, Issue 4
  • DOI: 10.1038/nrmicro2737

    Works referencing / citing this record:

    Book Review: Recent Advances in Yeast Metabolic Engineering
    journal, November 2017

    • Gohil, Nisarg; Panchasara, Happy; Patel, Shreya
    • Frontiers in Bioengineering and Biotechnology, Vol. 5
    • DOI: 10.3389/fbioe.2017.00071