Circadian clocks: complex and highly conserved mechanisms for coordinating metabolism and physiology with the environment

has made it clear that whole genome duplication (polyploidization) has occurred frequently during angiosperm evolution. It is thought that the provision of duplicated genes permits evolution through functional specialization as well as the acquisition of innovative functions. ere are several examples in which multiple members of gene families contribute to the circadian clock mechanism, raising a number of questions. Practically, functional redundancy among family members limits the identification of clock components through forward genetics [1]. Of more general interest is the question of how these gene families have evolved among plants. In addition, there is considerable interest in determining the extent to which the clock model that has been developed for Arabidopsis will serve as a model for clock function among plants in general. A recent paper in BMC Evolutionary Biology describing the angiosperm PSEUDO-RESPONSE REGULATOR (PRR) gene family addresses each of these questions [2]. Circadian clocks: complex and highly conserved mechanisms for coordinating metabolism and physiology with the environment A circadian rhythm is an endogenously generated rhythm with a period of about 24 h, approximating the period of the rotation of the earth on its axis. ese rhythms provide temporal organization of biological processes from cyanobacteria to mammals [3]. In plants, circadian rhythmicity is widespread and pervasive [4,5]. Approximately one-third of the Arabidopsis transcriptome shows circadian oscillations in abundance in continuous conditions [6], but if one looks under a variety of light and temperature cycles that proportion grows to an astonishing ~90% [7], underlining the probable importance of circadian rhythm to overall fitness [4,5]. Circadian clocks of taxonomic groups as diverse as plants, fungi and animals are composed of multiple interlocked feedback loops with positive and negative components [3] and many of the components of these clocks are encoded by members of gene families. e Arabidopsis circadian clock, an example of this common design principle, is composed of at least four interlocked feedback loops (Figure 1). In the central loop (blue in Figure 1), TIMING OF CAB EXPRESSION 1 (TOC1), the founding member of a family of five PSEUDORESPONSE REGULATOR (PRR) genes, is a positive regulator of CIRCADIAN AND CLOCK ASSOCIATED 1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY). CCA1 and LHY are members of a small family of REVEILLE genes that encode single Myb domain transcription factors. Others members of this family have been shown to play roles in clock function as well as in regulation of clock output pathways [4,5]. To complete the first loop, CCA1 and LHY bind to the TOC1 promoter to inhibit its expression. In a second loop (green in Figure 1) within the central loop, CCA1 and LHY also repress expression of CCA1 HIKING EXPEDITION (CHE), which encodes a TCP transcription factor that binds to and represses expression from the CCA1 promoter [1]. In the third loop (yellow in Figure 1), Abstract