Multiscale complexity in the mammalian circadian clock

The field of systems biology studies how the interactions among individual components (e.g. genes and proteins) yield interesting and complex behavior. The circadian (daily) timekeeping system in mammals is an ideal system to study complexity because of its many biological scales (from genes to animal behavior). A wealth of data at each of these scales has recently been discovered. Within each scale, modeling can advance our understanding of challenging problems that arise in studying mammalian timekeeping. However, future work must focus on bridging the multiple spatial and temporal scales in the modeling of SCN network. Here we review recent advances, and then delve into a few areas that are promising research directions. We also discuss the flavor of modeling needed (simple or detailed) as well as new techniques that are needed to meet the challenges in modeling data across scales.     

Initial processing of visual information within the retina and the LGN

The initial stage of information processing by the visual system reduces the information contained in the continuous image on the retina into a discrete set of responses which are carried from the lateral geniculate nucleus (LGN) to the visual cortex.-1. The optimal sampling of the light intensity distribution in the visual environment is achieved only if each channel in the visual pathways carries undistorted information corresponding to an image element. The visual system approaches as closely as possible the scheme of optimal spatial sampling, retaining the full information on the low spatial frequency content of the object light intensity. The ideal receptive field of a sustained LGN cell is then of the form J₁(Kr)/Kr.-2. The experimentally determined receptive fields of sustained LGN cells (and to some extent retinal ganglion cells as well) in cat closely resemble the functional form J₁(Kr)/Kr. The centre-surround organization of the receptive fields is therefore understood as a scheme which leads to a maximal information flow through the visual pathways.-3. The optimal sampling scheme cannot be realized by the retina alone, because of restrictions on the size of neural networks. It is therefore constructed in two stages, ending at the LGN level. A recombination of ganglion cell signals into optimal receptive fields is a major role of the LGN.     

Kinases and phosphatases in the mammalian circadian clock

Posttranslational modifications of circadian oscillator components are crucial for the generation of circadian rhythms. Among those phosphorylation plays key roles ranging from regulating degradation, complex formation, subcellular localization and activity. Although most of the known clock proteins are phosphoproteins in vivo, a comprehensive view about the regulation of clock protein phosphorylation is still missing. Here, we review our current knowledge about the role of clock protein phosphorylation and its regulation by kinases and phosphatases in eukaryotes with a major focus on the mammalian circadian clock.     

Parallel processing in the mammalian retina

Our eyes send different 'images' of the outside world to the brain - an image of contours (line drawing), a colour image (watercolour painting) or an image of moving objects (movie). This is commonly referred to as parallel processing, and starts as early as the first synapse of the retina, the cone pedicle. Here, the molecular composition of the transmitter receptors of the postsynaptic neurons defines which images are transferred to the inner retina. Within the second synaptic layer - the inner plexiform layer - circuits that involve complex inhibitory and excitatory interactions represent filters that select 'what the eye tells the brain'.     

JNK regulates the photic response of the mammalian circadian clock

The posttranslational regulation of mammalian clock proteins has been assigned a time-keeping function, but seems to have more essential roles. Here we show that c-Jun N-terminal kinase (JNK), identified by inhibitor screening of BMAL1 phosphorylation at Ser 520/Thr 527/Ser 592, confers dynamic regulation on the clock. Knockdown of JNK1 and JNK2 abrogates BMAL1 phosphorylation and lengthens circadian period in fibroblasts. Mice deficient for neuron-specific isoform JNK3 have altered behavioural rhythms, with longer free-running period and compromised phase shifts to light. The locomotor rhythms are insensitive to intensity variance of constant light, deviating from Aschoff's rule. Thus, JNK regulates a core characteristic of the circadian clock by controlling the oscillation speed and the phase in response to light.     

Signaling in the mammalian circadian clock: the NO/cGMP pathway

Mammalian circadian rhythms are generated by a hypothalamic suprachiasmatic nuclei (SCN) clock. Light pulses synchronize body rhythms by inducing phase delays during the early night and phase advances during the late night. Phosphorylation events are known to be involved in circadian phase shifting, both for delays and advances. Pharmacological inhibition of the cGMP-dependent kinase (cGK) or Ca2+/calmodulin-dependent kinase (CaMK), or of neuronal nitric oxide synthase (nNOS) blocks the circadian responses to light in vivo. Light pulses administered during the subjective night, but not during the day, induce rapid phosphorylation of both p-CAMKII and p-nNOS (specifically phosphorylated by CaMKII). CaMKII inhibitors block light-induced nNOS activity and phosphorylation, suggesting a direct pathway between both enzymes. Furthermore, SCN cGMP exhibits diurnal and circadian rhythms with maximal values during the day or subjective day. This variation of cGMP levels appears to be related to temporal changes in phosphodiesterase (PDE) activity and not to guanylyl cyclase (GC) activity. Light pulses increase SCN cGMP levels at circadian time (CT) 18 (when light causes phase advances of rhythms) but not at CT 14 (the time for light-induced phase delays). cGK II is expressed in the hamster SCN and also exhibits circadian changes in its levels, peaking during the day. Light pulses increase cGK activity at CT 18 but not at CT 14. In addition, cGK and GC inhibition by KT-5823 and ODQ significantly attenuated light-induced phase shifts at CT 18. This inhibition did not change c-Fos expression SCN but affected the expression of the clock gene per in the SCN. These results suggest a signal transduction pathway responsible for light-induced phase advances of the circadian clock which could be summarized as follows: Glu-Ca2+-CaMKII-nNOS-GC-cGMP-cGK-->-->clock genes. This pathway offers a signaling window that allows peering into the circadian clock machinery in order to decipher its temporal cogs and wheels.     

Phase resetting of the mammalian circadian clock by DNA damage

To anticipate the momentum of the day, most organisms have developed an internal clock that drives circadian rhythms in metabolism, physiology, and behavior [1]. Recent studies indicate that cell-cycle progression and DNA-damage-response pathways are under circadian control [2-4]. Because circadian output processes can feed back into the clock, we investigated whether DNA damage affects the mammalian circadian clock. By using Rat-1 fibroblasts expressing an mPer2 promoter-driven luciferase reporter, we show that ionizing radiation exclusively phase advances circadian rhythms in a dose- and time-dependent manner. Notably, this in vitro finding translates to the living animal, because ionizing radiation also phase advanced behavioral rhythms in mice. The underlying mechanism involves ATM-mediated damage signaling as radiation-induced phase shifting was suppressed in fibroblasts from cancer-predisposed ataxia telangiectasia and Nijmegen breakage syndrome patients. Ionizing radiation-induced phase shifting depends on neither upregulation or downregulation of clock gene expression nor on de novo protein synthesis and, thus, differs mechanistically from dexamethasone- and forskolin-provoked clock resetting [5]. Interestingly, ultraviolet light and tert-butyl hydroperoxide also elicited a phase-advancing effect. Taken together, our data provide evidence that the mammalian circadian clock, like that of the lower eukaryote Neurospora[6], responds to DNA damage and suggest that clock resetting is a universal property of DNA damage.