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Circadian clocks


Circadian clocks have evolved to provide an adaptive advantage to most organisms that live under alternating cycles of light and darkness (Dodd et al., 2005; Ouyang et al., 1998; Woelfle et al., 2004). The clock provides a mechanism whereby physiological and behavioral processes can be performed at the appropriate times 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 (Hastings et al., 2003). In higher plants, the circadian clock regulates many key physiological processes, ranging from flowering time (Imaizumi and Kay, 2006; Yanovsky and Kay, 2003) and growth (Dowson-Day and Millar, 1999; Farre, 2012) to stomatal opening and CO2 assimilation (Farre and Weise, 2012). Moreover, in Arabidopsis thaliana the expression of at least 6% of the transcriptome is regulated by the circadian clock (Harmer et al., 2000; Michael and McClung, 2003; Schaffer et al., 2001), and recent findings show that the matching of internal and external cycles optimizes growth and survival (Dodd et al., 2005).

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.


Arabidopsis thaliana

We focus our work on the role of the PSEUDO-RESPONSE REGULATORS (PRR)(Farre and Liu, 2013). These proteins are not only involved in the regulation of the Arabidopsis circadian oscillator (Figure 2) but are also involved in the direct regulation of physiological processes (Huang et al., 2012; Liu et al., 2013; Nakamichi et al., 2012).


Figure 2

Figure 2. Current status of the Arabidopsis circadian clock (2014)


Nannochloropsis oceanica

Nannochloropsis species are small unicellular alga with a diameter of about 2 μm. Marine Nannochloropsis species are used as a source of fish food and omega-3 fatty acids (Adarme-Vega et al., 2012). Due to their high lipid content, which is particularly elevated under nitrogen deprivation, these species have been considered as a potential source of biofuels (Hu and Gao, 2003; Rodolfi et al., 2009; Van Vooren et al., 2012; Xu et al., 2004). The genomes of two Nannochloropsis species have been recently sequenced (Jinkerson et al., 2012; Pan et al., 2011; Radakovits et al., 2012; Vieler et al., 2012). Both species have a small genome of ~30 Mb, containing ~9,000-12,000 genes, similar to the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana (Armbrust et al., 2004; Bowler et al., 2008). Current research suggests that Nannochloropsis species are haploid and homologous gene replacement has been recently reported (Kilian et al., 2011; Pan et al., 2011). Cell division and lipid content are strongly diurnally regulated in Nannochloropsis (Fábregas et al., 2002; Sukenik and Carmeli, 1990). We are currently characterizing diel and circadian gene expression in Nannochloropsis oceanica.



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