Modeling the molecular regulatory mechanism of circadian rhythms in Drosophila

Computational studies of gene regulatory networks: in numero molecular biology

Remarkable progress in genomic research is leading to a complete map of the building blocks of biology. Knowledge of this map is, in turn, setting the stage for a fundamental description of cellular function at the DNA level. Such a description will entail an understanding of gene regulation, in which proteins often regulate their own production or that of other proteins in a complex web of interactions. The implications of the underlying logic of genetic networks are difficult to deduce through experimental techniques alone, and successful approaches will probably involve the union of new experiments and computational modelling techniques.

Genetics of the mammalian circadian system: Photic entrainment, circadian pacemaker mechanisms, and posttranslational regulation

During the past four years, significant progress has been made in identifying the molecular components of the mammalian circadian clock system. An autoregulatory transcriptional feedback loop similar to that described in Drosophila appears to form the core circadian rhythm generating mechanism in mammals. Two basic helix-loop-helix (bHLH) PAS (PER-ARNT-SIM) transcription factors, CLOCK and BMAL1, form the positive elements of the system and drive transcription of three Period and two Cryptochrome genes. The protein products of these genes are components of a negative feedback complex that inhibits CLOCK and BMAL1 to close the circadian loop. In this review, we focus on three aspects of the circadian story in mammals: the genetics of the photic entrainment pathway; the molecular components of the circadian pacemaker in the hypothalamic suprachiasmatic nucleus; and the role of posttranslational regulation of circadian elements. A molecular description of the mammalian circadian system has revealed that circadian oscillations may be a fundamental property of many cells in the body and that a circadian hierarchy underlies the temporal organization of animals.

From simple to complex oscillatory behavior in metabolic and genetic control networks

We present an overview of mechanisms responsible for simple or complex oscillatory behavior in metabolic and genetic control networks. Besides simple periodic behavior corresponding to the evolution toward a limit cycle we consider complex modes of oscillatory behavior such as complex periodic oscillations of the bursting type and chaos. Multiple attractors are also discussed, e.g., the coexistence between a stable steady state and a stable limit cycle (hard excitation), or the coexistence between two simultaneously stable limit cycles (birhythmicity). We discuss mechanisms responsible for the transition from simple to complex oscillatory behavior by means of a number of models serving as selected examples. The models were originally proposed to account for simple periodic oscillations observed experimentally at the cellular level in a variety of biological systems. In a second stage, these models were modified to allow for complex oscillatory phenomena such as bursting, birhythmicity, or chaos. We consider successively (1) models based on enzyme regulation, proposed for glycolytic oscillations and for the control of successive phases of the cell cycle, respectively; (2) a model for intracellular Ca(2+) oscillations based on transport regulation; (3) a model for oscillations of cyclic AMP based on receptor desensitization in Dictyostelium cells; and (4) a model based on genetic regulation for circadian rhythms in Drosophila. Two main classes of mechanism leading from simple to complex oscillatory behavior are identified, namely (i) the interplay between two endogenous oscillatory mechanisms, which can take multiple forms, overt or more subtle, depending on whether the two oscillators each involve their own regulatory feedback loop or share a common feedback loop while differing by some related process, and (ii) self-modulation of the oscillator through feedback from the system's output on one of the parameters controlling oscillatory behavior. However, the latter mechanism may also be viewed as involving the interplay between two feedback processes, each of which might be capable of producing oscillations. Although our discussion primarily focuses on the case of autonomous oscillatory behavior, we also consider the case of nonautonomous complex oscillations in a model for circadian oscillations subjected to periodic forcing by a light-dark cycle and show that the occurrence of entrainment versus chaos in these conditions markedly depends on the wave form of periodic forcing. (c) 2001 American Institute of Physics.

Extracting information from cDNA arrays

High-density DNA arrays allow measurements of gene expression levels (messenger RNA abundance) for thousands of genes simultaneously. We analyze arrays with spotted cDNA used in monitoring of expression profiles. A dilution series of a mouse liver probe is deployed to quantify the reproducibility of expression measurements. Saturation effects limit the accessible signal range at high intensities. Additive noise and outshining from neighboring spots dominate at low intensities. For repeated measurements on the same filter and filter-to-filter comparisons correlation coefficients of 0.98 are found. Next we consider the clustering of gene expression time series from stimulated human fibroblasts which aims at finding co-regulated genes. We analyze how preprocessing, the distance measure, and the clustering algorithm affect the resulting clusters. Finally we discuss algorithms for the identification of transcription factor binding sites from clusters of co-regulated genes. (c) 2001 American Institute of Physics.

pH homeostasis of the circadian sporulation rhythm in clock mutants of Neurospora crassa

The influence of environmental (extracellular) pH on the sporulation rhythm in Neurospora crassa was investigated for wild-type (frq+) and the mutants chr, frq1, frq7, and frq8. In all mutants, including wild type, the growth rate was found to be influenced strongly by extracellular pH in the range 4-9. On the other hand, for the same pH range, the period length of the sporulation rhythm is little influenced in wild type, chr, and frq1. A loss of pH homeostasis of the period, however, was observed in the mutants frq7 and frq8, which also are known to have lost temperature compensation. Concerning the influence of extracellular pH on growth rates, a clear correspondence between growth rates and the concentration of available H2PO4- ion has been found, indicating that the uptake of H2PO4- may be a limiting factor for growth under our experimental conditions. The loss of pH compensation in the frq7 and frq8 mutants may be related to less easily degradable FRQ7,8 proteins when compared with wild-type FRQ. Results from recent model considerations and experimental results predict that, with increasing extra-and intracellular pH, the FRQ7 protein degradation increases and should lead to shorter period lengths.

Theoretical models for circadian rhythms in Neurospora and Drosophila

We examine theoretical models proposed for the molecular mechanism of circadian rhythms in Drosophila. The models are based on the negative feedback exerted by a complex between the PER and TIM proteins on the expression of the per and tim genes. We show that a similar model can account for circadian oscillations in Neurospora, where the protein FRQ negatively regulates the expression of the frq gene. The effect of light on the circadian rhythms is included by considering that it elicits a rise in the rate of TIM degradation in Drosophila, whereas in Neurospora it enhances the rate of frq transcription. The models account for the occurrence of sustained circadian oscillations in continuous darkness in Drosophila and Neurospora. Numerical simulations further indicate that the periodic forcing of circadian oscillations by light-dark cycles can result either in the entrainment to the external periodicity or in aperiodic oscillations (i.e. chaos), depending on the magnitude of the periodic changes in the light-controlled parameter.