Temporal Partitioning of the Yeast Cellular Network - Systems Biology of Metabolic and Signaling Networks - page 319

between this and the maximum first derivative is defined as the oxidative phase
(where oxygen uptake and electron flux though the electron transport chain is at a
maximum; Fig. 7.1 a). The time between the maximum first derivative and the next
minimum first derivative is defined as the reductive phase (conversely oxygen
uptake rate is lowest).
Nicotinamide nucleotide (NAD(P)H) redox state (Fig. 12.1b ), the most useful
single indicator of intracellular redox state (Chance et al. 2005 ), was maximally
reduced just before dissolved O 2 reached maximal values as the culture entered the
reductive phase (Murray et al. 1999 ). Flavin fluorescence emission (oxidised FAD
and FMN; Fig. 12.1c ) indicates predominant coenzyme oxidation during the oxida-
tive phase (Sasidharan et al. 2012 ). Waveforms of these cofactors are more complex
than those for respiration, but show major phase relationships with dissolved O 2 on
a 40-min cycle. Maximum CO 2 production rates occurred at the end of the oxidative
phase (Fig. 12.1d ), whereas highest H 2 S production rates were seen as dissolved O 2
was attaining its maximum (Fig. 12.1e ). Major peaks and troughs of heat transfer
from the culture corresponded closely with maxima and minima in respiration
(Fig. 12.1f ) may indicate uncoupling of the electron transport chain from energy
production and accompanying thermogenesis (Lloyd 2003 ; Jarmuszkiewicz
et al. 2009 ; Murray et al. 2011 ). The two shoulders of heat production also separate
the three active periods of transcriptional activity previously described (Klevecz
et al. 2004 ; Li and Klevecz 2006 ) and thus may also correlate with chromosomal
rearrangements during the remodelling of the transcriptional landscape (Machn ´
and Murray 2012 ).
12.4 Carbon Metabolism
Glucose (Satroutdinov et al. 1992 ; Keulers et al. 1996a ), ethanol (Keulers
et al. 1996b ; Murray et al. 1999 ) or acetaldehyde (Keulers and Kuriyama 1998 )
have been used as major carbon sources. Glucose or ethanol gave respiratory
periods of about 40 min, and with 290 mM acetaldehyde as primary carbon source
it was approximately 80 min. Acetaldehyde, acetate, ethanol, dissolved O 2 and CO 2
production all showed high signal-to-noise ratio oscillation, with acetaldehyde
and acetate approximately in phase with O 2 uptake rate (i.e. these products were
elevated during the stages of enhanced respiration). Potentially, inhibitory levels of
acetaldehyde and acetate were never exceeded; ethanol production from acetalde-
hyde occurred periodically during the oscillation and was accompanied by
decreased acetaldehyde conversion to acetate and acetyl-CoA. Diminished rates
of acetaldehyde flux to the TCA cycle may indicate that the decreased respiratory
activity was due to some inhibitory effect on the mitochondrial respiratory chain.
The importance of acetaldehyde (rather than O 2 or ethanol) as a specific culture
synchronising agent was suggested (Keulers and Kuriyama 1998 ), as high aeration
rates leading to loss of CO 2 and the volatile aldehyde led to de-synchronisation.
Phase shift experiments (Murray et al. 2003 ) demonstrated that acetaldehyde was