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Background Circadian clocks have evolved to provide an adaptive advantage to most organisms that live under alternating cycles of light and darkness [1-3]. The clock provides a mechanism whereby physiological and behavioral processes can be parsed out into the appropriate time of day or night. Furthermore, the evolution of a true oscillator, rather than just a light-responsive sand-timer, enables organisms to predict the alterations that occur in relative proportion to day and night throughout the year in most clines. In mammals, many aspects of behavior and physiology are regulated by endogenous circadian clocks and are subject to daily oscillations [4]. In higher plants, the circadian clock regulates many key physiological processes, ranging from flowering time [5, 6] and growth [7] to stomatal opening and CO2 assimilation [8]. Moreover, in Arabidopsis thaliana the expression of at least 6% of the transcriptome is regulated by the circadian clock [9-11], and recent findings show that the matching of internal and external cycles optimizes growth and survival [3]. Figure 1 Circadian systems can be thought of consisting of 3 parts (Figure 1). The imput pathways are involved in the entrainment or reprograming of the central oscillator which is the core of the circadian system. In turn this molecular self-sustained oscillator regulates the different physiological processes by regulating output pathways. Although circadian clocks in different species utilize distinct protein motifs for the positive and negative limbs of the clock, the same general pattern of regulation is maintained: transcriptional regulatory loops in combination with post-translational regulation. The first regulatory feedback loop described for Arabidopsis consisted of the repression by the morning expressed CCA1 (CIRCADIAN CLOCK ASSOCIATED 1) and LHY (LATE ELONGATED HYPOCOTYL) of the evening expressed TOC1 (TIMING OF CAB EXPRESSION). In turn, TOC1 has been shown to be necessary for CCA1 and LHY activation [12] (Figure 1). Genetic analysis has demonstrated that CCA1 and LHY have partial redundant functions [13-15] [16]. TOC1 was identified as a circadian mutant in Arabidopsis that exhibited a short period phenotype for multiple outputs [17]. TOC1 belongs to the multigene family of circadian regulated PSEUDO-RESPONSE REGULATORS (PRR), which, in Arabidopsis consists of four other members: PRR3, PRR5, PRR7, PRR9 [18]. In addition to TOC1, there are several other evening expressed genes that are necessary for the morning expression of CCA1 and LHY. These include the putative MYB transcription factor LUX (LUX ARRYTHMO)[19], as well as ELF3 and ELF4 (EARLY FLOWERING 3, 4) [20-22](Figure 2). Figure 2 Recent results have shown that post-translational regulation of protein levels plays a key role in the control of the plant circadian clock. The F-box protein ZEITLUPE (ZTL) is involved in the degradation of both TOC1 and PRR5 but not PRR9 and PRR7 [23-25] (Figure 1). LKP2 (LOV KELCH PROTEIN 2) is a homologue of ZTL whose arrhythmic overexpression phenotype indicates a key role in regulating circadian rhythms [26]. This ZTL family of F-box proteins that also includes FKF1 (FLAVIN BINDING, KELCH REPEAT, F-BOX 1), a protein involved in the regulation of flowering time [27-29], contain a LOV/PAS domain that mediates blue light dependent protein-protein interactions [30, 31] (Figure 2). Overexpression and mutant analyses indicate that all the circadian regulated PRRs play a role in the regulation of the circadian clock in Arabidopsis [32, 33]. Furthermore, experiments performed in rice, wheat and barley show that the PRRs also play a role in the regulation of the circadian rhythms and flowering time in these species [34-39]. The expression of all PRRs is clock regulated with each peaking at a different time of the day or night [18]. As indicated above, recent results also suggest that post-translational regulation plays a key role in the function of these proteins [23-25, 40]. Genetic analyses have shown that PRR7, PRR9 and PRR5 play partially redundant functions [41-44]. PRRs share two conserved protein domains. The pseudo-receiver domain (PR) shares homology with the receiver domains found in response regulators involved in the two-component signaling pathways found in bacteria and plants [45, 46]. However, it lacks the specific aspartate residue that becomes phosphorylated in canonical receiver domains and in vitro experiments suggest that unlike other plant response regulators it cannot be phosphorylated by sensor histidine kinases [47, 48]. The CCT domain (CONSTANS,CONSTANTS-LIKE, TOC1) contains a putative nuclear localization signal and shares some homology with the DNA binding domain of yeast HEME activator protein 2 (HAP2), which is a subunit of the HAP2/HAP3/HAP5 trimeric complex that binds to CCAAT boxes in eukaryotic promoters [49]. However, the DNA binding capacity of CCT domains has not been reported. Recent work indicates that PRR3 is involved in the regulation of TOC1 stability [50], which represents the first report of the biochemical function of a PRRs (Figure 2). The biochemical function of the other PRRs remains to be elucidated.