Carbohydrate-active enzymes exemplify entropic principles in metabolism

Glycans comprise ubiquitous and essential biopolymers, which usually occur as highly diverse mixtures. The myriad different structures are generated by a limited number of carbohydrate‐active enzymes (CAZymes), which are unusual in that they catalyze multiple reactions by being relatively unspecific with respect to substrate size. Existing experimental and theoretical descriptions of CAZyme‐mediated reaction systems neither comprehensively explain observed action patterns nor suggest biological functions of polydisperse pools in metabolism. Here, we overcome these limitations with a novel theoretical description of this important class of biological systems in which the mixing entropy of polydisperse pools emerges as an important system variable. In vitro assays of three CAZymes essential for central carbon metabolism confirm the power of our approach to predict equilibrium distributions and non‐equilibrium dynamics. A computational study of the turnover of the soluble heteroglycan pool exemplifies how entropy‐driven reactions establish a metabolic buffer in vivo that attenuates fluctuations in carbohydrate availability. We argue that this interplay between energy‐ and entropy‐driven processes represents an important regulatory design principle of metabolic systems.

[1]  Brandi L. Cantarel,et al.  The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics , 2008, Nucleic Acids Res..

[2]  R. Goldberg,et al.  Thermodynamics of the hydrolysis and cyclization reactions of α-, β-, and γ-cyclodextrin , 1997 .

[3]  Vincent Danos,et al.  Internal coarse-graining of molecular systems , 2009, Proceedings of the National Academy of Sciences.

[4]  S. H. Duke,et al.  Characterization of Pea Chloroplast D-Enzyme (4-α-d-Glucanotransferase) , 1989 .

[5]  Alison M. Smith,et al.  Starch: its metabolism, evolution, and biotechnological modification in plants. , 2010, Annual review of plant biology.

[6]  S. Ball,et al.  Biochemical characterization of the chlamydomonas reinhardtii alpha-1,4 glucanotransferase supports a direct function in amylopectin biosynthesis , 1999, Plant physiology.

[7]  A. Tobolsky.  Equilibrium Distribution in Sizes for Linear Polymer Molecules , 1944 .

[8]  M. Steup,et al.  Eukaryotic starch degradation: integration of plastidial and cytosolic pathways. , 2009, Journal of experimental botany.

[9]  Alison M. Smith,et al.  A Previously Unknown Maltose Transporter Essential for Starch Degradation in Leaves , 2004, Science.

[10]  M. Galbe,et al.  Biomass Recalcitrance: Engineering Plants and Enzymes for Biofuels Production , 2007 .

[11]  Alison M. Smith,et al.  Starch degradation. , 2005, Annual Review of Plant Biology.

[12]  C. Mathews.  Thermodynamics of biochemical reactions , 2004 .

[13]  T. Sharkey,et al.  The role of amylomaltase in maltose metabolism in the cytosol of photosynthetic cells , 2004, Planta.

[14]  J. François,et al.  Reserve carbohydrates metabolism in the yeast Saccharomyces cerevisiae. , 2001, FEMS microbiology reviews.

[15]  T. Kuroiwa,et al.  Chloroplasts Divide by Contraction of a Bundle of Nanofilaments Consisting of Polyglucan , 2010, Science.

[16]  Shiro Kobayashi,et al.  Enzymatic polymerization to polysaccharides , 2006 .

[17]  R. Goldberg,et al.  Thermodynamics of hydrolysis of oligosaccharides. , 1991, Biophysical chemistry.

[18]  P. Lerouge,et al.  Production and glycosylation of plant-made pharmaceuticals: the antibodies as a challenge. , 2004, Plant biotechnology journal.

[19]  T. Takaha,et al.  The functions of 4-alpha-glucanotransferases and their use for the production of cyclic glucans. , 1999, Biotechnology & genetic engineering reviews.

[20]  J. Preiss,et al.  Characterization of d-Enzyme (4-α-Glucanotransferase) in Arabidopsis Leaf , 1988 .

[21]  S. H. Lillie,et al.  Reserve carbohydrate metabolism in Saccharomyces cerevisiae: responses to nutrient limitation , 1980, Journal of bacteriology.

[22]  R. Alberty.  Thermodynamics of Biochemical Reactions: Alberty/Thermodynamics , 2005 .

[23]  D. Botstein,et al.  The transcriptional program of sporulation in budding yeast. , 1998, Science.

[24]  W. Whelan,et al.  The action pattern of d-enzyme, a transmaltodextrinylase from potato , 1969 .

[25]  T. Suganuma,et al.  Analysis of the characteristic action of D-enzyme from sweet potato in terms of subsite theory , 1991 .

[26]  Synthesis of Amylose by Potato D-Enzyme , 1959, Nature.

[27]  H. Uyama,et al.  Enzymatic polymerization. , 2001, Chemical Reviews.

[28]  J. Thoma,et al.  Subsite Mapping of Enzymes , 2005 .

[29]  H. Nakatani.  Monte Carlo simulation of 4-alpha-glucanotransferase reaction. , 1999, Biopolymers.

[30]  D. Cosgrove.  Growth of the plant cell wall , 2005, Nature Reviews Molecular Cell Biology.

[31]  Alison M. Smith,et al.  A transglucosidase necessary for starch degradation and maltose metabolism in leaves at night acts on cytosolic heteroglycans (SHG). , 2006, The Plant journal : for cell and molecular biology.

[32]  T. Sharkey,et al.  Engineering plants for elevated CO(2): a relationship between starch degradation and sugar sensing. , 2004, Plant biology.

[33]  P. Seeberger.  Exploring life's sweet spot , 2005, Nature.

[34]  B. Henrissat,et al.  Structural enzymology of carbohydrate-active enzymes: implications for the post-genomic era. , 2001, Biochemical Society transactions.

[35]  Alison M. Smith,et al.  Starch and the clock: the dark side of plant productivity. , 2011, Trends in plant science.

[36]  B. Usadel,et al.  Arabidopsis and primary photosynthetic metabolism - more than the icing on the cake. , 2010, The Plant journal : for cell and molecular biology.

[37]  M. Steup,et al.  Glucose-1-Phosphate Transport into Protoplasts and Chloroplasts from Leaves of Arabidopsis1 , 2010, Plant Physiology.

[38]  L. Dijkhuizen,et al.  Three-way Stabilization of the Covalent Intermediate in Amylomaltase, an α-Amylase-like Transglycosylase* , 2007, Journal of Biological Chemistry.

[39]  W. Jencks,et al.  From chemistry to biochemistry to catalysis to movement. , 1997, Annual review of biochemistry.

[40]  D. Gillespie.  Exact Stochastic Simulation of Coupled Chemical Reactions , 1977 .

[41]  J. BeMiller.  Polysaccharides: Occurrence, Significance, and Properties , 2008 .

[42]  Bernard Henrissat,et al.  An evolving hierarchical family classification for glycosyltransferases. , 2003, Journal of molecular biology.

[43]  A. Warshel,et al.  Electrostatic basis for enzyme catalysis. , 2006, Chemical reviews.

[44]  S. Zeeman,et al.  A critical role for disproportionating enzyme in starch breakdown is revealed by a knock-out mutation in Arabidopsis. , 2001, The Plant journal : for cell and molecular biology.

[45]  N. Craig.  Entropy Analysis: An Introduction to Chemical Thermodynamics , 1992 .

[46]  J. Thoma,et al.  Subsite mapping of enzymes. Correlation of product patterns with Michaelis parameters and substrate-induced strain. , 1971, Journal of Biological Chemistry.

[47]  T. Sharkey,et al.  The Role of Cytosolic α-Glucan Phosphorylase in Maltose Metabolism and the Comparison of Amylomaltase in Arabidopsis and Escherichia coli1 , 2006, Plant Physiology.

[48]  J. François,et al.  Dynamic responses of reserve carbohydrate metabolism under carbon and nitrogen limitations in Saccharomyces cerevisiae , 1999, Yeast.

[49]  Rutherford Aris,et al.  Reactions in Continuous Mixtures , 1989 .

[50]  David K. Johnson,et al.  Biomass Recalcitrance: Engineering Plants and Enzymes for Biofuels Production , 2007, Science.

[51]  J. Thoma.  Models for depolymerizing enzymes. Application to α‐amylases , 1976 .

[52]  S. Ball,et al.  From bacterial glycogen to starch: understanding the biogenesis of the plant starch granule. , 2003, Annual review of plant biology.

[53]  M. Steup,et al.  Cytosolic heteroglycans in photoautotrophic and in heterotrophic plant cells. , 2009, Phytochemistry.

[54]  D. Thorneycroft,et al.  A cytosolic glucosyltransferase is required for conversion of starch to sucrose in Arabidopsis leaves at night. , 2004, The Plant journal : for cell and molecular biology.

[55]  P. Flory.  Thermodynamics of Heterogeneous Polymers and Their Solutions , 1944 .

[56]  J. Fisahn,et al.  Adjustment of diurnal starch turnover to short days: depletion of sugar during the night leads to a temporary inhibition of carbohydrate utilization, accumulation of sugars and post-translational activation of ADP-glucose pyrophosphorylase in the following light period. , 2004, The Plant journal : for cell and molecular biology.

[57]  T. Sharkey,et al.  Domain Characterization of a 4-α-Glucanotransferase Essential for Maltose Metabolism in Photosynthetic Leaves* , 2008, Journal of Biological Chemistry.