Báo cáo khoa học: Collective behavior in gene regulation: Metabolic clocks and cross-talking doc

MINIREVIEW
Collective behavior in gene regulation: Metabolic clocks
and cross-talking
Michele M. Bianchi
Department of Cell and Developmental Biology, University of Rome ‘La Sapienza’, Italy
By cosmic rule, as day yields night, so winter sum-
mer, war peace, plenty famine. All things change…
the harmonious structure of the world depends
upon opposite tensions.
(Heraclitus, 500 bc)
In the modern age, life scientists subscribe to the ergo-
dic cell hypothesis (Fig. 1): they use homogenized
tissues or cultured cells, analyze extracts and draw
conclusions about a hypothetical representative cell on
the basis that all cells are ‘on average’ identical over
(short) time and space scales [1]. In this representation
(statistical mechanics, where it allowed a microscopic
basis to be given to thermodynamics), the average of a
process parameter for a single cell over time and the
average over the statistical ensemble of individuals at a
given time coincide.
In the ergodic hypothesis, genes are generally
divided into housekeeping genes, which are always
expressed, and regulated genes, which are expressed or
repressed under the effect of external signals. The
external signal might have various origins: an environ-
mental condition, a physiological signal from other
regions of a multicellular organism, the result of a
developmental programme, epigenetic control and so
on. In any case, these external signals occur inciden-
tally and ‘on average’ elicit the same response in all

cells; this means that they may have different effects
depending on the status of each cell but, given that the
population is very large and a point in time displays
the same distribution of states, the average result is the
same irrespective of time. If we want to study the
behavior of a single cell in a time-dependent manner,
by analysing a representative population of individuals,
we must artificially put all the cells into the same state
by synchronization, in order to collapse the ensemble
distribution into a single state. This collapse is usually
unstable and, after a relatively short time, the cell pop-
ulation reverts to the statistical distribution of states.
Keywords
circadian clock; cross-talk; cycles; ergodic
system; message; metabolism; redox;
synchronization; transcription dynamics;
ultradian clock
Correspondence
M. M. Bianchi, Department of Cell and
Developmental Biology, p.le Aldo Moro 5,
00185 Rome, Italy
Fax: +39 064 991 2351
Tel: +39 064 991 2215
E-mail:
(Received 10 December 2007, accepted 30
January 2008)
doi:10.1111/j.1742-4658.2008.06397.x
Biological functions governed by the circadian clock are the evident result
of the entrainment operated by the earth’s day and night cycle on living
organisms. However, the circadian clock is not unique, and cells and

organisms possess many other cyclic activities. These activities are difficult
to observe if carried out by single cells and the cells are not coordinated
but, if they can be detected, cell-to-cell cross-talk and synchronization
among cells must exist. Some of these cycles are metabolic and cell syn-
chronization is due to small molecules acting as metabolic messengers. We
propose a short survey of cellular cycles, paying special attention to meta-
bolic cycles and cellular cross-talking, particularly when the synchroniza-
tion of metabolism or, more generally, cellular functions are concerned.
Questions arising from the observation of phenomena based on cell com-
munication and from basic cellular cycles are also proposed.
Abbreviations
ROS, reactive oxygen species; YGO, yeast glycolytic oscillation; YMC, yeast metabolic cycle.
2356 FEBS Journal 275 (2008) 2356–2363 ª 2008 The Author Journal compilation ª 2008 FEBS
Clocks
Looking closer at the cell or organism and taking time
into account, in addition to space, chronobiologists have
shown that life actually has an intimate dual existence
between opposite states: day and night, wake and sleep,
oxidation and reduction. The organism moves cyclically
from one physiological state to the other during its life.
Besides the intuition of Heraclitus, it has been known
for a long time that animals and plants have light-
dependent physiological activities entrained to the
earth’s day–night cycle. Over the past few decades, the
molecular bases of these cyclic activities, governed by
the circadian clock, have been elucidated [2]. In mam-
mals, they are based on the autoregulation of transcrip-
tion factors and the translation feedback loops of
specific clock genes [3]. Circadian clocks are also present
in micro-organisms, such as cyanobacteria and fungi

[4,5], and involve similar transcription ⁄ translation
feedback oscillators [6]. By definition, clocks are self-
sustained and temperature compensated [7]. Clocks are
also cell-autonomous, i.e. they work even in isolated
cells, independent of the presence of other cells [8].
Although the clocks of different organisms share
many characteristics, it is becoming clear that the
underlying molecular mechanisms might involve differ-
ent and functionally unrelated actors, cyclic cellular
activity being the only common behavior of function-
ally convergent evolutionary pathways [9]. In theory,
cellular clocks are self-sustained and hence can work
in the absence of external input signals. Such signals
(light, temperature, metabolites, other environmental
inputs) do exist but their modes of action are not
always known. The outward effect of the clock is the
output signal, which modulates the activity ⁄ transcrip-
tion of target gene(s) and ⁄ or affects the functioning of
target cells and is fundamental for cellular cross-talk
and synchronization. Multicellular organisms are com-
posed of tissues and organs with highly specialized
physiological functions and which work in a coordi-
nated manner. With respect to this organization, cells
of mammalian peripheral tissues also possess internal
clocks, but they are hierarchically synchronized by the
pacemaker activity of the suprachiasmatic nucleus [10].
However, the autonomous timekeeping of peripheral
tissues remains an open question [11].
The circadian clock is intimately connected with
metabolism, in particular with the redox balance in the

cell [the NAD(P)H ⁄ NAD(P) ratio] and heme metabo-
lism [12,13] and with cyclic transcriptome profiling
[14,15]. Cyclically expressed genes allow the chronolog-
ical separation of antagonistic metabolic pathways and
confine them to the appropriate time of day [16].
t1
t2
t3
t4
abcd
Ergodic system: cells with
clocks not entrained
Ergodic system: cells
without a clock
t1
t2
t3
t4
a
bcd
Space
Space
TimeTime
Space
Time
Non-ergodic system: cells
with entrained clocks
t1
t2
t3

t4
abcd
Fig. 1. Application of the ergodic hypothesis to a cell population.
Expression of a representative gene in individual cells a, b, c and
d (space dimension) at different but close time points t1, t2, t3
and t4 (time dimension). The colour of the cell indicates the
gene-expression level: black, high expression; white, low expres-
sion; grey, average ⁄ physiological expression, for example, as
reported for the metabolic status in current transcription analysis.
(Upper) The ergodic hypothesis: all cells are similar in time and
space and the ‘average’ cell is truly representative of the cell
population. (Middle) Cells have clocks affecting gene expression
but these clocks are not synchronized. The ergodic cell is aver-
agely representative of the population in time and space, but not
of single cells. Only analysis on individuals can detect the actual
oscillatory situation. (Lower) The nonergodic model with synchro-
nized cellular clocks. Gene expression does not vary in space,
but changes cyclically over time. Expression waves are detect-
able in the population.
M. M. Bianchi Metabolic cycles
FEBS Journal 275 (2008) 2356–2363 ª 2008 The Author Journal compilation ª 2008 FEBS 2357
In addition to the circadian cycle, other cycles are
known. Infradian cycles, like the female oestrus cycle
or temperature cycles during hibernation [17], have
periods longer than 24 h. Ultradian cycles, like the
neuron electric firing, the heart beat, the basic rest–
activity cycle during sleep and the yeast metabolic
cycle (YMC) have periods shorter than 24 h [18,19]. In
yeast, an ultradian glycolytic cycle (yeast glycolytic
oscillation; YGO) has been known for 50 years [20].

All these cycles are composed of recurrent transitions
of the cell from one state to another, often with oppos-
ing characteristics. Some can be defined as clocks
because they are cell-autonomous, self-sustained and
temperature compensated, and for some, like the
YMC, important transcriptional effects have been
demonstrated at the genomic level [21].
Cross-talking
If one were able to look at the level of the individual
cell, in addition to constitutive and regulated gene
expression, gene transcription should also vary in a
way related to the clock activity. When cell popula-
tions are considered, the situation is more complex. In
the ergodic cell hypothesis, expression cycles are barely
observable because each cell goes its own way, thus
averaging out any population-level oscillation. How-
ever, if cells could talk to each other, synchronization
of cycles may happen. The molecular oscillators of
cells in tissues and organs might be entrained by an
external pacemaker (zeitgeber in the chronobiology
literature), such as occurs in mammals, where periph-
eral clocks are synchronized by signals from the
suprachiasmatic nucleus [10]. The logic underlying
temporal segregation of metabolic activities in the
single cell is then transferred to the entire tissue and to
the organism level. The biological significance of the
synchronization of cellular clocks is thus correlated
with the organ’s function and is obtained by a hier-
archical cascade of signals. Many different signal-
ing pathways might finally be involved in the

entrainment of the individual oscillator of peripheral
cells to the main circadian rhythm of the suprachias-
matic nucleus [22].
In comparison with a developed organism, cells cul-
tured in plates, flasks or bioreactors might be consid-
ered a physiologically homogeneous and isotropic
system in which, according to the ergodic hypothesis,
the cells live without any coordination among them,
each has its own clock working. What happens to the
cyclic activities in the case of cultured cells devoid of
any higher level of structuring like tissues and organs?
This question is of particular importance when single-
cell micro-organisms are considered but the results are
not concordant. In cyanobacteria, the circadian clock
is a self-sustained property of individual cells, not
influenced by cell duplication (i.e. transmitted in phase
to daughter cells) or by other cells (not entrained by
close cells with a different phase) [8]. In yeast, how-
ever, the ultradian YGO responsible for NADH oscil-
lations occurs in isolated cells, although only if the
molecular messenger is cyclically and externally
provided, and in dense cultures [23]. When a high cell
density is reached or during colony formation cross-
talk between cells becomes critically important. In
these cases, collective behaviors, which require cell-
to-cell communication and simultaneous responses,
can be easily detected. Growth inhibition by contact
and quorum sensing in micro-organisms are typical
examples of this kind of communication. Quorum-
sensing molecules are secreted continuously during

growth in amounts proportional to the cell density.
The accumulation of such chemical signals induces col-
lective and coordinated actions, like bioluminescence,
horizontal DNA transfer, biofilm formation, secondary
metabolite production [24] and morphological transi-
tion in yeasts [25,26]. Quorum-sensing molecules are
oligopeptides [27] and acyl-homoserine lactones [28] in
bacteria, and alcohols like farnesol or aromatic alco-
hols [29] in yeast, and their production is also affected
by environmental conditions.
Metabolic messages
Cyclic collective behaviors, by contrast to phenomena
induced by quorum-sensing molecules, are not epi-
sodic and require synchronization, entrained by a
signal transmitted via the medium, to be detectable
in cell populations. YGO is a regular alternation of
high and low NADH fluorescence [20] that can be
explained by regular variation in the glycolytic flux in
cells with synchronous metabolism. The physiological
status of the cells is critical to detect or induce detect-
able YGO [30]. Provided that a high density of sta-
tionary phase cells is attained, YGOs can be
synchronized or induced by the metabolic messengers
glucose or acetaldehyde [31–33]. Pulsed glucose feeds
also induce YGO and glucose transport seems to be
deeply involved in glycolytic oscillations [34]. Some
researchers have suggested that the appearance ⁄
disappearance of YGOs derive from an on ⁄ off set of
collective cyclic dynamics, rather than the synchroni-
zation ⁄ desynchronization of pre-existing ⁄ persisting

cycles [32,34].
Furthermore, continuously cultured yeast cells at
high density show a cyclic metabolism, YMC, that
Metabolic cycles M. M. Bianchi
2358 FEBS Journal 275 (2008) 2356–2363 ª 2008 The Author Journal compilation ª 2008 FEBS
alternates between high and low redox conditions [35].
YMC has the characteristics of an ultradian clock and
in continuous cultivations individual cellular oscillators
are entrained by the secretion of a signal molecule
from other cells and become synchronized. The imme-
diate macroscopic event is a cyclic variation in dis-
solved oxygen, as a result of the simultaneous
transition of a large number of cells between different
phases of respiratory metabolism. Many other intracel-
lular and extracellular metabolic parameters change
during YMC, e.g. carbon catabolite concentrations,
ATP, NAD(P)H and sulfur compounds [36]. Acetalde-
hyde and hydrogen sulfide are highly diffusible mole-
cules that entrain individual cellular oscillators and
synchronize the culture [37,38].
In addition to NAD(P)H, reduced glutathione seems
to play an important role in recycling damaged proteins
by the reactive oxygen species (ROS) produced by
defective electron transport to molecular oxygen. Pro-
tection against ROS damage during chromosomal
DNA replication might also be connected to the YMC
[39]. In fact, three distinct phases can be distinguished
within the YMC: an oxidative phase, when oxygen is
reduced in the cell by mitochondrial respiration and
ROS are produced; a reductive phase, when DNA is

synthesized; and a second reductive phase, when meta-
bolic reactions producing NAD(P)H occur (glycolysis,
fatty acid oxidation). Division of the YMC into distinct
metabolic phases, in addition to the physical compart-
mentalization ensured by the presence of specialized
organelles (mitochondria, peroxisomes, endoplasmic
reticulum), prevents dangerous, futile or antagonistic
reactions from taking place simultaneously [40].
A cell will pass through a certain number of meta-
bolic rounds before it duplicates, therefore, the YMC
has been proposed as a unit for measuring cell ageing
in pace with or in addition to the number of replica-
tive cell cycles [41]. What happens in the cell between
duplication events? How deeply are cellular activities
involved or entrained with metabolic changes? Tran-
scriptome analysis has revealed that gene expression
follows the metabolic rhythm [21,40]. Almost all genes
are cyclically transcribed and can be clustered in three
groups: 650 are expressed in the oxidative phase, and
2429 and 2250 are expressed in the first and second
reductive phase, respectively. Fewer than 200 are
expressed in each phase and can be considered ‘phase
independent’. Genes involved in specific cellular func-
tions are preferentially expressed in one phase. We can
thus deduce by functional clustering, that amino acid
synthesis, ribosome assembly, sulfur metabolism and
RNA metabolism occur in the oxidative phase; cell
division and mitochondrial biogenesis occur in the first
reductive phase and glycolysis and fatty acid oxidation
occur in the second reductive phase. As a conse-

quence, the metabolic composition of the cell varies
cyclically [42].
Different metabolism, different clock?
Animals, plants and light-sensitive bacteria have devel-
oped and adapted their physiology to the presence of
day–night cycles on earth, which is their natural envi-
ronment and the circadian clock is their natural
rhythm of life. However, it has been reported that the
circadian clock, although often predominant, is not the
only oscillator working in organisms or cells, and that
other cycles might emerge when the circadian clock is
impaired. The YMC has been characterized in yeast
cells cultured in a continuous manner, under very low
nutrient feed and at very high density. Whether these
can be considered ‘natural’ conditions for yeast is
dubious and poses many questions. First, yeast is one
of the oldest domestic organisms, selected over millen-
nia of food manufacturing but, in recent decades, also
selected in research laboratories where it is extensively
studied as model organism. Hence, its natural environ-
mental conditions must be searched for in the
pre-domestication era. Like the majority of living
organisms, its environment was probably characterized
by alternations between plenty and famine, the abun-
dance and scarcity of sugars, high and low growth
rates, fermentation and respiration. In this scenario,
the YMC might be a cycle within a cycle and not be
the unique yeast metabolic cycle.
Reiterated redox cycles are not exclusive to continu-
ous cultivation because they occur also in batch culti-

vations [43] (our unpublished results) at the end of cell
growth (stationary phase), although with different per-
iod length and regularity. Metabolic cycles are also
present in yeast species other than Saccharomyces cere-
visiae. The majority of yeasts are not physiologically
inclined to fermentative metabolism, as is S. cerevisiae,
and prefer to respire or ferment and respire. The exis-
tence of a fermentative mutant of the yeast Kluyver-
omyces lactis with an extremely long stationary phase
characterized by an active oxidative metabolism in
batch cultivation [44] (M. M. Bianchi, unpublished),
might allow us to study redox cycles in other related
yeast species.
Our preliminary data indicate that cycles, i.e. sus-
tained oscillations of pH in the medium, are also pres-
ent during the exponential growth phase, suggesting
the possibility of a metabolic cycle involving the entire
population, even at low cell density, and linked to
fermentative metabolism (Fig. 2). We have also dem-
M. M. Bianchi Metabolic cycles
FEBS Journal 275 (2008) 2356–2363 ª 2008 The Author Journal compilation ª 2008 FEBS 2359
onstrated the presence of collective and coordinated
transcriptional cycles in cultured yeast and mammal
cells [1]. The cyclically expressed genes were not func-
tionally correlated and yeast cells showing this behav-
ior were from standard batch cultivations. The period
of these transcription waves was shorter than the
YMC. Our data indicate that the genomic mRNA
pool varies continuously over time, with the concentra-
tion of the majority of mRNA species changing by

two- to fivefold during cycling [1]. This suggests that
regulation of gene expression in response to defined
stimuli might not be performed uniquely at the level of
mRNA synthesis, but should also involve coordinated
mechanisms acting at the level of mRNA degradation
or translation (Fig. 3). It is not known whether regula-
tory steps downstream of transcription can prevent
cyclic variation of the mRNA pool from being directly
transmitted at the level of protein abundance.
Cyclic variation in mRNA should also be taken into
account when planning time-course-based screening of
the global transcription response to external stimuli.
The currently preferred hypothesis, that the cell will
synthesize a protein only when transcription of the
corresponding gene is induced by a specific input,
should inevitably be challenged. The mechanistic
dogma ‘input fi transcription factor fi gene pro-
moter fi mRNA fi protein’ does not seem to be as
simple and true as assumed to date, especially in
humans, where the genome is pervasively transcribed
[45]: it would be of interest to experimentally investi-
gate a possible correlation between cyclic and perva-
sive transcription.
Other questions arising
YMC is typical of dense continuous cultures [23], but
continuous feeding of yeast per se is unlikely to be a
zeitgeber of YMC and the nature of the carbon source
does not seem to affect the onset of the cycle, provided
that respiration has occurred. In continuous yeast cul-
tivations, high cell density is inevitably associated with

a low growth rate, low nutrient feed and respiration.
The effect of each single parameter on YMC is hence
hardly determined. In the current literature, densities
Fig. 2. Growth of yeast cells (cell number · 10
5
) in a bioreactor (batch culture) is reported, together with changes in pH. The course of the
three major components of pH during the exponential growth phase (hours 2–14), are reported on the right. Factors 2 and 3 show a cyclic
behavior.
Metabolic cycles M. M. Bianchi
2360 FEBS Journal 275 (2008) 2356–2363 ª 2008 The Author Journal compilation ª 2008 FEBS
as high as 10
9
cellsÆmL
)1
are reported to detect YMC.
This means an average distance of 10 lm between cells
and extremely frequent (and cyclic) contact between
cells. Has this phenomenon any relevance for cell-to-
cell communication and the entrainment of the YCM,
besides the chemical signals acetaldehyde and hydro-
gen sulfide? We have mentioned that S. cerevisiae is a
domestic organism and that standard methods of labo-
ratory cultivation in flasks or a bioreactor are very far
removed from the natural environmental conditions
for yeast. Colony formation on agar plates is probably
closer to wild (nondomestic) growth. Interestingly,
yeast growing in a colony undergoes cyclic changes in
metabolism, from acidic to alkaline [46]. Furthermore,
alkali-producing colonies can entrain colonies in the
acidic phase and generate synchronous metabolism on

the plate, gaseous ammonia being the zeitgeber.
The alternation of conditions with opposing charac-
teristics, as suggested 25 centuries ago, is fundamental
to all phenomena involving oscillations and cycles,
which are diffused in all disciplines of natural (and
not only) sciences. In biological studies over recent
decades, it has become more and more clear that
clocks are deeply involved in governing many aspects
of life at different levels: are they tricks to resolve
specific problems or are they intimately linked to the
existence and propagation of living material? One
hypothesis about the evolution of the circadian clock
and YMC is that they allowed the segregation of
potential harmful reactions, UV mutagenesis and
ROS damage, and protect organisms. Is this final
statement true or are these side effects of the basi-
cally cyclic nature of life, even at the molecular level?
Is homeostasis an old idea that should be abandoned
and is homeodynamics the new key [47]? Continuous
and cyclic variation in cell composition, transcriptome,
proteome and metabolome, is certainly well suited to
the optimization of metabolic reactions, to the amelio-
ration of defence and to speeding up responses to envi-
ronmental stimuli, but is counterbalanced by the high
energetic demand of biosynthetic reactions at the gen-
ome size.
Acknowledgements
This work was supported by MIUR (2006051483);
Istituto Pasteur Fondazione Cenci-Bolognetti; Centro
di Eccellenza di Biologia e Medicina Molecolari, and

Universita
`
degli Studi di Roma ‘La Sapienza’.
References
1 Tsuchyia M, Wong ST, Yeo ZX, Colosimo A, Palumbo
MC, Farina L, Crescenzi M, Mazzola A, Negri R,
Bianchi MM et al. (2007) Gene expression waves – cell
cycle independent collective dynamics in cultured cells.
FEBS J 274, 2878–2886.
2 Reppert SM & Weaver DR (2001) Molecular analysis
of mammalian circadian rhythms. Annu Rev Physiol 63,
647–676.
3 Ko CH & Takahashi JS (2006) Molecular components
of the mammalian circadian clock. Hum Mol Genet 15,
271–277.
4 Iwasaki H & Kondo T (2004) Circadian timing mecha-
nisms in the prokaryotic clock system of cyanobacteria.
J Biol Rhythms 19, 436–444.
5 Dunlap JC & Loros JJ (2004) The neurospora circadian
system. J Biol Rhythms 19, 414–424.
6 Lakin-Thomas PL (2000) Circadian rhythms: new func-
tions for old clock genes. Trends Genet 16, 135–142.
7 Schibler U & Naef F (2005) Cellular oscillators: rhyth-
mic gene expression and metabolism. Curr Opin Cell
Biol 17, 223–229.
turnover
GENOME
cyclic
transcription
mRNA

degradation
additive
induction
translation
Metabolome
Proteome
state B state A
specific
INPUT
metabolic
OUTPUT
CLOCK
messenger
Transcriptome
Fig. 3. mRNA, proteomic and metabolite
composition of cells governed by clocks.
Cyclic variation in mRNA depends on cyclic
whole-genome transcription and mRNA
degradation. A cellular response to specific
environmental conditions contributes
additively to increase ⁄ decrease further the
mRNA levels. The cellular response at the
level of protein ⁄ enzyme composition might
also rely on selective translation of mRNAs
and ⁄ or turnover. Oscillation of proteome
composition determines the cyclic variation
of metabolism ⁄ metabolome between states
(A and B).
M. M. Bianchi Metabolic cycles
FEBS Journal 275 (2008) 2356–2363 ª 2008 The Author Journal compilation ª 2008 FEBS 2361

8 Mihalcescu I, Hsing W & Leibler S (2004) Resilient cir-
cadian oscillator revealed in individual cyanobacteria.
Nature 430, 81–85.
9 Lakin-Thomas PL (2006) New models for circadian sys-
tems in microorganisms. FEMS Microbiol Lett 259 , 1–6.
10 Yoo SH, Yamazaki S, Lowrey PL, Shimomura K,
Ko CH, Buhr ED, Siepka SM, Hong HK, Oh WJ, Yoo
OJ et al. (2004) PERIOD::2LUCIFERASE real-time
reporting of circadian dynamics reveals persistent circa-
dian oscillations in mouse peripheral tissues. Proc Natl
Acad Sci USA 101, 5339–5346.
11 Storch KF, Paz C, Signorovitch J, Raviola E, Pawlyk
B, Li T & Weitz CJ (2007) Intrinsic circadian clock of
the mammalian retina: importance for retinal processing
of visual information. Cell 130, 730–741.
12 Rutter J, Reick M, Wu LC & McKnight SL (2001)
Regulation of clock and NPAS2 DNA binding by the
redox state of NAD cofactor. Science 293, 510–514.
13 Kaasik K & Lee CC (2004) Reciprocal regulation of
haem biosynthesis and the circadian clock in mammals.
Nature 430, 467–471.
14 Panda S, Antoch MP, Miller BH, Su AI, Schook AB,
Straume M, Schultz PG, Kay SA, Takahashi JS &
Hogenesch JB (2002) Coordinated transcription of key
pathways in the mouse by the circadian clock. Cell 109,
307–320.
15 Storch KF, Lipan O, Leykin I, Viswanathan N, Davis
FC, Wong WH & Weitz CJ (2002) Extensive and diver-
gent circadian gene expression in liver and heart. Nature
417, 78–83.

16 Rudic RD, McNamara P, Curtis AM, Boston RC,
Panda S, Hogenesch JB & Fitzgerald GA (2004)
BMAL1 and CLOCK, two essential components of the
circadian clock, are involved in glucose homeostasis.
PLoS Biol 2, e377.
17 Carey HV, Andrews MT & Martin SL (2003) Mamma-
lian hibernation: cellular and molecular responses to
depressed metabolism and low temperature. Physiol Rev
83, 1153–1181.
18 Tu BP & McKnight SL (2006) Metabolic cycles as an
underlying basis of biological oscillations. Nat Rev Mol
Cell Biol 7, 696–701.
19 Lloyd D & Murray DB (2007) Redox rhythmicity: clocks
at the core of temporal coherence. BioEssays 29, 465–473.
20 Duysens LNM & Amesz J (1957) Fluorescence spectro-
photometry of reduced phosphopyridine nucleotide in
intact cells in the near-ultraviolet and visible region.
Biochim Biophys Acta 24, 19–26.
21 Klevecz RR, Bolen J, Forrest G & Murray DB (2004)
A genome-wide oscillation in transcription gates DNA
replication and cell cycle. Proc Natl Acad Sci USA 101,
1200–1205.
22 Schibler U, Rippenger J & Brown SA (2003) Peripheral
circadian oscillators in mammals: time and food. J Biol
Rhythms 18, 250–260.
23 Poulsen AK, Petersen MO & Olsen LF (2007) Single
cell studies and simulation of cell–cell interactions using
oscillating glycolysis in yeast cells. Biophys Chem 125,
275–280.
24 Whitehead NA, Barnard AM, Slater H, Simpson NJ &

Salmond GP (2001) Quorum-sensing in Gram negative
bacteria. FEMS Microbiol Rev 25, 365–404.
25 Hornby JM, Jensen EC, Lisec AD, Tatso JJ, Jahnke B,
Shoemaker R, Dussault P & Nickerson KW (2001)
Quorum sensing in the dimorphic fungus Candida albi-
cans is mediated by farnesol. Appl Environ Microbiol 67
,
2982–2992.
26 Chen H, Fujita M, Feng Q, Clardy J & Fink GR
(2004) Tyrosol is a quorum sensing molecule in Can-
dida albicans. Proc Natl Acad Sci USA 101, 5048–5052.
27 Dunny GM & Leonard BA (1997) Cell–cell communi-
cation in gram-positive bacteria. Annu Rev Microbiol
51, 527–564.
28 More
´
MI, Finger LD, Stryker JL, Fuqua C, Eberhard
A & Winans SC (1996) Enzymatic synthesis of a
quorum-sensing autoinducer through use of defined
substrates. Science 272, 1655–1658.
29 Chen H & Fink GR (2006) Feedback control of mor-
phogenesis in fungi by aromatic alcohols. Genes Dev 20,
1150–1161.
30 Alridge J & Pye EK (1976) Cell density dependence of
oscillatory metabolism. Nature 259, 670–671.
31 Richard P, Bakker BM, Teusink B, Van Dam K &
Westerhoff HV (1996) Acetaldehyde mediates the
synchronization of sustained glycolytic oscillations in
populations of yeast cells. Eur J Biochem 235, 238–241.
32 Dano S, Sorensen PG & Hynne F (1999) Sustained

oscillations in living cells. Nature 402, 320–322.
33 Reijenga KA, Snoep JL, Diderich JA, van Verseveld
HW, Westerhoff HV & Teusink B (2001) Control of
glycolytic dynamics in hexose transport in Saccharomy-
ces cerevisiae. Biophys J 80, 626–634.
34 Reijenga KA, Bakker BM, van der Weijden CC &
Westerhoff HV (2005) Training of yeast cell dynamics.
FEBS J 272, 1616–1624.
35 Satroutdinov AD, Kuriyama H & Kobayashi H
(1992) Oscillatory metabolism of Saccharomyces cerevi-
siae in continuous culture. FEMS Microbiol Lett 77,
261–267.
36 Murray DB, Engelen F, Lloyd D & Kuriyama H
(1999) Involvement of glutathione in the regulation of
respiratory oscillation during a continuous culture of
Saccharomyces cerevisiae. Microbiology 145, 2739–
2745.
37 Murray DB, Klevecz RR & Lloyd D (2003) Generation
and maintenance of synchrony in Saccharomyces cerevi-
siae continuous cultures. Exp Cell Res 287, 10–15.
38 Dano S, Madsen MF & Sorensen PG (2007) Quantita-
tive characterization of cell synchronization in yeast.
Proc Natl Acad Sci USA 104 , 12732–12736.
Metabolic cycles M. M. Bianchi
2362 FEBS Journal 275 (2008) 2356–2363 ª 2008 The Author Journal compilation ª 2008 FEBS
39 Chen Z, Odstrcil EA, Tu BP & McKnight SL (2007)
Restriction of DNA replication to the reductive phase
of the metabolic cycle protects genome integrity. Science
316, 1916–1919.
40 Tu BP, Kudlicki A, Rowicka M & McKnight SL (2005)

Logic of the yeast metabolic cycle: temporal compart-
mentalization of cellular processes. Science 310, 1152–
1158.
41 Lloyd D, Lemar KM, Eshantha L, Salgado J, Gould
TM & Murray DB (2003) Respiratory oscillations
in yeast: mitochondrial reactive oxygen species,
apoptosis and time; a hypothesis. FEMS Yeast Res 3,
333–339.
42 Murray DB, Beckmann M & Kitano H (2007) Regula-
tion of yeast oscillatory dynamics. Proc Natl Acad Sci
USA 104, 2241–2246.
43 Murray DB (2004) On the temporal self-organization of
Saccharomyces cerevisiae. Curr Genomics 5, 665–671.
44 Salani F & Bianchi MM (2006) Production of glucoam-
ylase in pyruvate decarboxylase deletion mutants of the
yeast Kluyveromyces lactis. Appl Microbiol Biotechnol
69, 564–572.
45 The ENCODE Project Consortium (2007) Identification
and analysis of functional elements in 1% of the human
genome by the ENCODE pilot project. Nature 447,
799–816.
46 Palkova Z & Vachova L (2006) Life within a commu-
nity: benefit to yeast long-term survival. FEMS Micro-
biol Rev 30, 806–824.
47 Lloyd D, Aon M & Cortassa S (2001) Why homeody-
namics, not homeostasis? ScientificWorldJournal 1,
133–145.
M. M. Bianchi Metabolic cycles
FEBS Journal 275 (2008) 2356–2363 ª 2008 The Author Journal compilation ª 2008 FEBS 2363