Growth Landscape Formed by Perception and Import of Glucose in Yeast

An important challenge in systems biology is to quantitatively describe microbial growth using a few measurable parameters that capture the essence of this complex phenomenon. Two key events at the cell membrane—extracellular glucose sensing and uptake—initiate the budding yeast’s growth on glucose. However, conventional growth models focus almost exclusively on glucose uptake. Here we present results from growth-rate experiments that cannot be explained by focusing on glucose uptake alone. By imposing a glucose uptake rate independent of the sensed extracellular glucose level, we show that despite increasing both the sensed glucose concentration and uptake rate, the cell’s growth rate can decrease or even approach zero. We resolve this puzzle by showing that the interaction between glucose perception and import, not their individual actions, determines the central features of growth, and characterize this interaction using a quantitative model. Disrupting this interaction by knocking out two key glucose sensors significantly changes the cell’s growth rate, yet uptake rates are unchanged. This is due to a decrease in burden that glucose perception places on the cells. Our work shows that glucose perception and import are separate and pivotal modules of yeast growth, the interaction of which can be precisely tuned and measured.

[1]  Sven Bergmann,et al.  Rewiring of the Yeast Transcriptional Network Through the Evolution of Motif Usage , 2005, Science.

[2]  U. Alon,et al.  Just-in-time transcription program in metabolic pathways , 2004, Nature Genetics.

[3]  I. Paulsen,et al.  Major Facilitator Superfamily , 1998, Microbiology and Molecular Biology Reviews.

[4]  E. Boles,et al.  Kinetic characterization of individual hexose transporters of Saccharomyces cerevisiae and their relation to the triggering mechanisms of glucose repression. , 1997, European journal of biochemistry.

[5]  D. Kell Metabolomics and systems biology: making sense of the soup. , 2004, Current opinion in microbiology.

[6]  J. Gancedo,et al.  The early steps of glucose signalling in yeast. , 2008, FEMS microbiology reviews.

[7]  David Botstein,et al.  Influence of genotype and nutrition on survival and metabolism of starving yeast , 2008, Proceedings of the National Academy of Sciences.

[8]  M. Savageau Biochemical Systems Analysis: A Study of Function and Design in Molecular Biology , 1976 .

[9]  M. Schweizer,et al.  The metabolism and molecular physiology of Saccharomyces cerevisiae , 1998 .

[10]  C. Hollenberg,et al.  Catabolite inactivation of the high‐affinity hexose transporters Hxt6 and Hxt7 of Saccharomyces cerevisiae occurs in the vacuole after internalization by endocytosis 1 , 1998, FEBS letters.

[11]  E. Boles,et al.  Characterisation of glucose transport in Saccharomyces cerevisiae with plasma membrane vesicles (countertransport) and intact cells (initial uptake) with single Hxt1, Hxt2, Hxt3, Hxt4, Hxt6, Hxt7 or Gal2 transporters. , 2002, FEMS yeast research.

[12]  J. Broach,et al.  Efficient transition to growth on fermentable carbon sources in Saccharomyces cerevisiae requires signaling through the Ras pathway , 1998, The EMBO journal.

[13]  T. Hwa,et al.  Growth-rate-dependent partitioning of RNA polymerases in bacteria , 2008, Proceedings of the National Academy of Sciences.

[14]  P. Mayinger Faculty Opinions recommendation of Growth control of the eukaryote cell: a systems biology study in yeast. , 2007 .

[15]  A. Kruckeberg,et al.  Yeast sugar transporters. , 1993, Critical reviews in biochemistry and molecular biology.

[16]  J. Nielsen,et al.  Metabolic Engineering of Saccharomyces cerevisiae , 2000, Microbiology and Molecular Biology Reviews.

[17]  Mark Johnston,et al.  Specificity and Regulation of DNA Binding by the Yeast Glucose Transporter Gene Repressor Rgt1 , 2003, Molecular and Cellular Biology.

[18]  Jeremy Gunawardena,et al.  Programming with models: modularity and abstraction provide powerful capabilities for systems biology , 2009, Journal of The Royal Society Interface.

[19]  Edoardo M. Airoldi,et al.  Predicting Cellular Growth from Gene Expression Signatures , 2009, PLoS Comput. Biol..

[20]  M. Johnston,et al.  Two Glucose-sensing Pathways Converge on Rgt1 to Regulate Expression of Glucose Transporter Genes in Saccharomyces cerevisiae* , 2006, Journal of Biological Chemistry.

[21]  Mark Johnston,et al.  Regulatory Network Connecting Two Glucose Signal Transduction Pathways in Saccharomyces cerevisiae , 2004, Eukaryotic Cell.

[22]  J. Collins,et al.  A network biology approach to aging in yeast , 2009, Proceedings of the National Academy of Sciences.

[23]  J. Nielsen,et al.  Bioreaction Engineering Principles , 1994, Springer US.

[24]  D. Hoyle,et al.  Growth control of the eukaryote cell: a systems biology study in yeast , 2007, Journal of biology.

[25]  M. Ciriacy,et al.  Identification of novel HXT genes in Saccharomyces cerevisiae reveals the impact of individual hexose transporters on qlycolytic flux , 1995, Molecular microbiology.

[26]  C. Hollenberg,et al.  The molecular genetics of hexose transport in yeasts. , 1997, FEMS microbiology reviews.

[27]  M. Walsh,et al.  Glucose sensing and signalling properties in Saccharomyces cerevisiae require the presence of at least two members of the glucose transporter family , 1996, Journal of bacteriology.

[28]  Uri Alon,et al.  Simplicity in biology , 2007, Nature.

[29]  Bernhard Ø Palsson,et al.  Integrated analysis of metabolic phenotypes in Saccharomyces cerevisiae , 2004, BMC Genomics.

[30]  C. Hollenberg,et al.  Concurrent knock‐out of at least 20 transporter genes is required to block uptake of hexoses in Saccharomyces cerevisiae , 1999, FEBS letters.

[31]  M. Schweizer,et al.  Metabolism and Molecular Physiology of Saccharomyces Cerevisiae, 2nd Edition , 2004 .

[32]  Michael A Savageau,et al.  Phenotypes and tolerances in the design space of biochemical systems , 2009, Proceedings of the National Academy of Sciences.

[33]  H. Westerhoff,et al.  Control of glycolytic dynamics by hexose transport in Saccharomyces cerevisiae. , 2001, Biophysical journal.

[34]  G. Stephanopoulos Challenges in Engineering Microbes for Biofuels Production , 2007, Science.

[35]  Mark Johnston,et al.  Function and Regulation of Yeast Hexose Transporters , 1999, Microbiology and Molecular Biology Reviews.

[36]  Z Yin,et al.  Differential post‐transcriptional regulation of yeast mRNAs in response to high and low glucose concentrations , 2000, Molecular microbiology.

[37]  J. Pronk,et al.  Effect of Specific Growth Rate on Fermentative Capacity of Baker’s Yeast , 1998, Applied and Environmental Microbiology.

[38]  K. Thorn,et al.  Optimized cassettes for fluorescent protein tagging in Saccharomyces cerevisiae , 2004, Yeast.

[39]  Eytan Ruppin,et al.  Conservation of Expression and Sequence of Metabolic Genes Is Reflected by Activity Across Metabolic States , 2006, PLoS Comput. Biol..

[40]  Zhikang Yin,et al.  Glucose triggers different global responses in yeast, depending on the strength of the signal, and transiently stabilizes ribosomal protein mRNAs , 2003, Molecular microbiology.

[41]  J. Stelling Mathematical models in microbial systems biology. , 2004, Current opinion in microbiology.

[42]  D. Fell Understanding the Control of Metabolism , 1996 .

[43]  J. Monod,et al.  Recherches sur la croissance des cultures bactériennes , 1942 .

[44]  U. Alon,et al.  Optimality and evolutionary tuning of the expression level of a protein , 2005, Nature.

[45]  Kim Sneppen,et al.  Combinatorics of feedback in cellular uptake and metabolism of small molecules , 2007, Proceedings of the National Academy of Sciences.

[46]  B. Palsson,et al.  Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[47]  M. Bennett,et al.  Metabolic gene regulation in a dynamically changing environment , 2008, Nature.

[48]  G. Santangelo,et al.  Glucose Signaling in Saccharomyces cerevisiae , 2006, Microbiology and Molecular Biology Reviews.

[49]  Jan Ihmels,et al.  Principles of transcriptional control in the metabolic network of Saccharomyces cerevisiae , 2004, Nature Biotechnology.

[50]  Naama Barkai,et al.  Strategy of Transcription Regulation in the Budding Yeast , 2007, PloS one.

[51]  Ned S. Wingreen,et al.  Growth-induced instability in metabolic networks. , 2007, Physical review letters.

[52]  M. Johnston,et al.  Three different regulatory mechanisms enable yeast hexose transporter (HXT) genes to be induced by different levels of glucose , 1995, Molecular and cellular biology.

[53]  E. Boles,et al.  Characterisation of glucose transport in with plasma membrane vesicles (countertransport) and intact cells (initial uptake) with single Hxt1, Hxt2, Hxt3, Hxt4, Hxt6, Hxt7 or Gal2 transporters , 2002 .

[54]  T. Hwa,et al.  Stochastic fluctuations in metabolic pathways , 2007, Proceedings of the National Academy of Sciences.

[55]  Barbara M. Bakker,et al.  The fluxes through glycolytic enzymes in Saccharomyces cerevisiae are predominantly regulated at posttranscriptional levels , 2007, Proceedings of the National Academy of Sciences.

[56]  Mark Johnston,et al.  Glucose sensing and signaling in Saccharomyces cerevisiae through the Rgt2 glucose sensor and casein kinase I. , 2004, Proceedings of the National Academy of Sciences of the United States of America.