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
Trang 1Collective 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: michele.bianchi@uniroma1.it
(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 funcsynchroniza-tions 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.
Trang 2Clocks 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 translatranscrip-tion 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
a b c d
Ergodic system: cells with
clocks not entrained
Ergodic system: cells
without a clock
t1 t2 t3 t4
a b c d Space
Space
Space
Non-ergodic system: cells
with entrained clocks
t1 t2 t3 t4
a b c d
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.
Trang 3In 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
Trang 4alternates 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 extracelintracel-lular 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 exponpres-ential 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
Trang 5dem-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.
Trang 6as high as 109 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
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).
Trang 78 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
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
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
38 Dano S, Madsen MF & Sorensen PG (2007) Quantita-tive characterization of cell synchronization in yeast Proc Natl Acad Sci USA 104, 12732–12736
Trang 839 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 decarboxglucoam-ylase 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