Metabolic Dissipative Structures - Systems Biology of Metabolic and Signaling Networks - page 183

8.2 Quantitative Analysis of the Effective Functional
Structure in Yeast Glycolysis

Yeast glycolysis is considered one of the prototypical biochemical oscillators, and
one of the most studied metabolic pathways. It was the first metabolic system in
which spontaneous oscillations were observed (Duysens and Amesz 1957 ; Chance
et al. 1964 ), and these studies led to the first models of this pathway based on
enzyme kinetics (Goldbeter and Lefever 1972 , Goldbeter 1973 ).
From a structural viewpoint, glycolytic enzymes can interact with structural
proteins and membranes generating metabolic microcompartments. For instance, it
has been observed that the entire glycolytic pathway is associated with the cytosolic
face of the outer mitochondrial membrane (Graham et al. 2007 ), or forms a
multienzyme complex on the inner surface of the plasma membrane (Campanella
et al. 2008 ). The interaction of glycolytic enzymes with cytoskeletal proteins has
also been suggested as another mechanism of compartmentation of this pathway
(Clarke and Masters 1975 ; Waingeh et al. 2006 ).
Reported evidence shows substrate channeling in glycolytic enzymes (Malaisse
et al. 2004 ; Shearer et al. 2005 ). For example, the three irreversible glycolytic
enzymes hexokinase (Malaisse et al. 2004 ; Zhang et al. 2005 ), phosphofructokinase
(Cascante et al. 2000 ; Commichau et al. 2009 ), and pyruvate kinase (Clarke and
Masters 1975 ; Commichau et al. 2009 ; Waingeh et al. 2006 ) show substrate
channeling or compartmentation. These experimental observations are consistent
with the existence of a glycolytic multienzymatic complex. Mowbray and Moses
( 1976 ) proposed the existence of such a complex from studies performed using cell-
free extracts (Mowbray and Moses 1976 ).
As in other dissipative structures, the metabolic dynamic patterns of yeast
glycolysis find their roots in the nonlinear regulatory processes, e.g., stoichiometric
autocatalysis, allosteric regulation and product activation (Cortassa et al. 1991 ;
Goldbeter 2002 , 2007 ), and other sources (Cortassa and Aon 1994 ; Olsen
et al. 2009 ).
In yeast glycolysis, it has been shown that an instability-generating mechanism
is given by the regulation of phosphofructokinase, specifically, the positive feed-
back exerted by the reaction products, ADP and fructose-1,6-bisphosphate (Boiteux
et al. 1975 ; Goldbeter and Lefever 1972 ; Goldbeter 2002 ). In yeast extracts,
traveling waves of NADH and protons were observed associated with glycolysis
(Mair et al. 2001 ). All this evidence shows that yeast glycolysis constitutes an
example of a dissipatively structured enzymatic association that can display
microcompartmentation, substrate channeling, and spatiotemporal dynamic

behavior.
Over the last 30 years a large number of studies have been focusing on the
molecular mechanisms underlying the emergence of self-organized glycolytic
patterns (Dano et al. 1999 ; De la Fuente et al. 1995 ; Madsen et al. 2005 ; Olsen
et al. 2009 ; Termonia and Ross 1981 ; Wolf et al. 2000 ). Nevertheless, and despite