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 »
- Authors:
-
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Joint BioEnergy Institute, Emeryville, CA (United States); Univ. of California, Berkeley, CA (United States)
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Joint BioEnergy Institute, Emeryville, CA (United States)
- 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)
- 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 Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- 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. https://doi.org/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. https://doi.org/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 = {Wed May 24 00:00:00 EDT 2017},
month = {Wed May 24 00:00:00 EDT 2017}
}
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
- Maaheimo, Hannu; Fiaux, Jocelyne; Çakar, Z. Petek
- European Journal of Biochemistry, Vol. 268, Issue 8
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
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
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
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
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
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
A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae.
journal, May 1989
- Sikorski, R. S.; Hieter, P.
- Genetics, Vol. 122, Issue 1
SIP1 is a catabolite repression-specific negative regulator of GAL gene expression.
journal, July 1994
- Mylin, L. M.; Bushman, V. L.; Long, R. M.
- Genetics, Vol. 137, Issue 3
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
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
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
Different Levels of Catabolite Repression Optimize Growth in Stable and Variable Environments
journal, January 2014
- New, Aaron M.; Cerulus, Bram; Govers, Sander K.
- PLoS Biology, Vol. 12, Issue 1
Glucose repression in Saccharomyces cerevisiae
journal, July 2015
- Kayikci, Ömur; Nielsen, Jens
- FEMS Yeast Research, Vol. 15, Issue 6
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
Achieving Metabolic Flux Analysis for S. cerevisiae at a Genome-Scale: Challenges, Requirements, and Considerations
journal, September 2015
- Gopalakrishnan, Saratram; Maranas, Costas
- Metabolites, Vol. 5, Issue 3
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
How Saccharomyces Responds to Nutrients
journal, December 2008
- Zaman, Shadia; Lippman, Soyeon Im; Zhao, Xin
- Annual Review of Genetics, Vol. 42, Issue 1
Different Levels of Catabolite Repression Optimize Growth in Stable and Variable Environments
journal, January 2014
- New, Aaron M.; Cerulus, Bram; Govers, Sander K.
- PLoS Biology, Vol. 12, Issue 1
Metabolic networks in motion: 13 C‐based flux analysis
journal, January 2006
- Sauer, Uwe
- Molecular Systems Biology, Vol. 2, Issue 1
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
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
13C Metabolic Flux Analysis
journal, July 2001
- Wiechert, Wolfgang
- Metabolic Engineering, Vol. 3, Issue 3
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
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
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
A new efficient gene disruption cassette for repeated use in budding yeast
journal, July 1996
- Guldener, U.
- Nucleic Acids Research, Vol. 24, Issue 13
Population Diversification in a Yeast Metabolic Program Promotes Anticipation of Environmental Shifts
journal, January 2015
- Venturelli, Ophelia S.; Zuleta, Ignacio; Murray, Richard M.
- PLOS Biology, Vol. 13, Issue 1
Natural Variation in Preparation for Nutrient Depletion Reveals a Cost–Benefit Tradeoff
journal, January 2015
- Wang, Jue; Atolia, Esha; Hua, Bo
- PLOS Biology, Vol. 13, Issue 1
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
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
Integrated Genomic and Proteomic Analyses of a Systematically Perturbed Metabolic Network
journal, May 2001
- Ideker, T.
- Science, Vol. 292, Issue 5518
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
Population Diversification in a Yeast Metabolic Program Promotes Anticipation of Environmental Shifts
journal, January 2015
- Venturelli, Ophelia S.; Zuleta, Ignacio; Murray, Richard M.
- PLOS Biology, Vol. 13, Issue 1
Natural Variation in Preparation for Nutrient Depletion Reveals a Cost–Benefit Tradeoff
journal, January 2015
- Wang, Jue; Atolia, Esha; Hua, Bo
- PLOS Biology, Vol. 13, Issue 1
13C metabolic flux analysis in complex systems
journal, February 2011
- Zamboni, Nicola
- Current Opinion in Biotechnology, Vol. 22, Issue 1
Transformation of Saccharomyces cerevisiae by the lithium acetate/single-stranded carrier DNA/polyethylene glycol protocol
journal, January 1998
- Agatep, Ronald; Kirkpatrick, Robert D.; Parchaliuk, Debra L.
- Technical Tips Online, Vol. 3, Issue 1
A new efficient gene disruption cassette for repeated use in budding yeast
journal, July 1996
- Guldener, U.
- Nucleic Acids Research, Vol. 24, Issue 13
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
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
13C metabolic flux analysis in complex systems
journal, February 2011
- Zamboni, Nicola
- Current Opinion in Biotechnology, Vol. 22, Issue 1
TCA cycle activity in Saccharomyces cerevisiae is a function of the environmentally determined specific growth and glucose uptake rates
journal, April 2004
- Blank, L. M.
- Microbiology, Vol. 150, Issue 4
Metabolic flux analysis in a nonstationary system: Fed-batch fermentation of a high yielding strain of E. coli producing 1,3-propanediol
journal, May 2007
- Antoniewicz, M.; Kraynie, D.; Laffend, L.
- Metabolic Engineering, Vol. 9, Issue 3
Metabolic networks in motion: 13 C‐based flux analysis
journal, January 2006
- Sauer, Uwe
- Molecular Systems Biology, Vol. 2, Issue 1
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
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
TCA cycle activity in Saccharomyces cerevisiae is a function of the environmentally determined specific growth and glucose uptake rates
journal, April 2004
- Blank, L. M.
- Microbiology, Vol. 150, Issue 4
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
13C Metabolic Flux Analysis
journal, July 2001
- Wiechert, Wolfgang
- Metabolic Engineering, Vol. 3, Issue 3
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
Achieving Metabolic Flux Analysis for S. cerevisiae at a Genome-Scale: Challenges, Requirements, and Considerations
journal, September 2015
- Gopalakrishnan, Saratram; Maranas, Costas
- Metabolites, Vol. 5, Issue 3
AMP-activated protein kinase, a metabolic master switch: possible roles in Type 2 diabetes
journal, July 1999
- Winder, W. W.; Hardie, D. G.
- American Journal of Physiology-Endocrinology and Metabolism, Vol. 277, Issue 1
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
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
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
The β-subunits of the Snf1 kinase in Saccharomyces cerevisiae, Gal83 and Sip2, but not Sip1, are redundant in glucose derepression and regulation of sterol biosynthesis: Snf1 kinase in glucose derepression
journal, June 2010
- Zhang, Jie; Olsson, Lisbeth; Nielsen, Jens
- Molecular Microbiology, Vol. 77, Issue 2
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
GENE DUPLICATION IN SACCHAROMYCES CEREVISIAE
journal, April 1978
- Hansche, P. E.; Beres, V.; Lange, P.
- Genetics, Vol. 88, Issue 4
How Saccharomyces Responds to Nutrients
journal, December 2008
- Zaman, Shadia; Lippman, Soyeon Im; Zhao, Xin
- Annual Review of Genetics, Vol. 42, Issue 1
Metabolic flux analysis in a nonstationary system: Fed-batch fermentation of a high yielding strain of E. coli producing 1,3-propanediol
journal, May 2007
- Antoniewicz, M.; Kraynie, D.; Laffend, L.
- Metabolic Engineering, Vol. 9, Issue 3
Glucose repression in Saccharomyces cerevisiae
journal, July 2015
- Kayikci, Ömur; Nielsen, Jens
- FEMS Yeast Research, Vol. 15, Issue 6
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
GENE DUPLICATION IN SACCHAROMYCES CEREVISIAE
journal, April 1978
- Hansche, P. E.; Beres, V.; Lange, P.
- Genetics, Vol. 88, Issue 4
A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae.
journal, May 1989
- Sikorski, R. S.; Hieter, P.
- Genetics, Vol. 122, Issue 1
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