Metabolic Dissipative Structures - Systems Biology of Metabolic and Signaling Networks - page 178

During the last four decades, extensive studies of biochemical dynamics in both
prokaryotic and eukaryotic cells have revealed that oscillations exist in most of the
fundamental metabolic processes. For instance, specific ultradian oscillations were
reported to occur in free fatty acids (Getty-Kaushik et al. 2005 ), NAD(P)H concen-
tration (Rosenspire et al. 2001 ), biosynthesis of phospholipids (Marquez
et al. 2004 ), cyclic AMP concentration (Holz et al. 2008 ), ATP (Ainscow
et al. 2002 ) and other adenine nucleotide levels (Zhaojun et al. 2004 ), intracellular
glutathione concentration (Lloyd and Murray 2005 ), actin polymerization (Rengan
and Omann 1999 ), ERK/MAPK metabolism (Shankaran et al. 2009 ), mRNA levels
(Zhaojun et al. 2004 ), intracellular free amino acid pools (Hans et al. 2003 ),
cytokinins (Hartig and Beck 2005 ), cyclins (Hungerbuehler et al. 2007 ), transcrip-
tion of cyclins (Shaul et al. 1996 ), gene expression (Chabot et al. 2007 ; Tian
et al. 2005 ; Tonozuka et al. 2001 ; Klevecz et al. 2004 ), microtubule polymerization
(Lange et al. 2004 ), membrane receptor activities (Placantonakis and Welsh 2001 ),
membrane potential (De Forest and Wheeler 1999 ), intracellular pH (S´nchez-
Arm´ss et al. 2006 ), respiratory metabolism (Lloyd et al. 2002 ), glycolysis (Dano
et al. 1999 ), intracellular calcium concentration (Ishii et al. 2006 ), metabolism of
carbohydrates (Jules et al. 2005 ), beta-oxidation of fatty acids (Getty et al. 2000 ),
metabolism of mRNA (Klevecz and Murray 2001 ), tRNA (Brodsky et al. 1992 ),
proteolysis (Kindzelskii et al. 1998 ), urea cycle (Fuentes et al. 1994 ), Krebs cycle
(Wittmann et al. 2005 ), mitochondrial metabolic processes (Aon et al. 2008 ),
nuclear translocation of the transcription factor (Garmendia-Torres et al. 2007 ),
amino acid transports (Barril and Potter 1968 ), peroxidase-oxidase reactions
(Møller et al. 1998 ), protein kinase activities (Chiam and Rajagopal 2007 ), and
photosynthetic reactions (Smrcinov ´ et al. 1998 ).
Experimental observations performed in S. cerevisiae during continuous culture
have shown that most of transcriptome and the metabolome exhibit oscillatory
dynamics (Klevecz et al. 2004 ; Murray et al. 2007 ). From transcriptome data, it has
been inferred that at least 60 % of all gene expression oscillates with an approxi-
mate period of 300 min (Tu et al. 2005 ). Moreover, the entire transcriptome exhibits
low-amplitude oscillatory behavior (Lloyd and Murray 2006 ) and this phenomenon
has been described as a genome-wide oscillation (Klevecz et al. 2004 ; Lloyd and
Murray 2005 , 2006 ; Murray et al. 2007 ; Oliva et al. 2005 ; Tu et al. 2005 ). Evidence
that cells exhibit multi-oscillatory metabolic processes with fractal properties has
also been reported. This dynamic behavior appears to be consistent with scale-free
dynamics spanning a wide range of frequencies of at least three orders of magnitude
(Aon et al. 2008 ).
The temporal organization of the metabolic processes in terms of rhythmic
phenomena spans periods ranging from milliseconds (Aon et al. 2006 ) to seconds
(Roussel et al. 2006 ), minutes (Berridge and Galione 1988 ; Chance et al. 1973 ), and
hours (Brodsky 2006 ). Transitions from simple periodic behavior to complex
oscillations, including bursting (oscillations with one large spike and series of
secondary oscillations) (Dekhuijzen and Bagust 1996 ) and chaotic phenomena
(Olsen and Degn 1985 ), have often been observed.