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: 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 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 . MINIREVIEW Collective behavior in gene regulation: Metabolic clocks and cross-talking Michele M. Bianchi Department of Cell and Developmental Biology, University. 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,. (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