How the green alga Chlamydomonas reinhardtii keeps time

A potential EARLY FLOWERING 3 homolog in Chlamydomonas is involved in the red/violet and blue light signaling pathways for the degradation of RHYTHM OF CHLOROPLAST 15

Light plays a major role in resetting the circadian clock, allowing the organism to synchronize with the environmental day and night cycle. In Chlamydomonas the light-induced degradation of the circadian clock protein, RHYTHM OF CHLOROPLAST 15 (ROC15), is considered one of the key events in resetting the circadian clock. Red/violet and blue light signals have been shown to reach the clock via different molecular pathways; however, many of the participating components of these pathways are yet to be elucidated. Here, we used a forward genetics approach using a reporter strain that expresses a ROC15-luciferase fusion protein. We isolated a mutant that showed impaired ROC15 degradation in response to a wide range of visible wavelengths and impaired light-induced phosphorylation of ROC15. These results suggest that the effects of different wavelengths converge before acting on ROC15 or at ROC15 phosphorylation. Furthermore, the mutant showed a weakened phase resetting in response to light, but its circadian rhythmicity remained largely unaffected under constant light and constant dark conditions. Surprisingly, the gene disrupted in this mutant was found to encode a protein that possessed a very weak similarity to the Arabidopsis thaliana EARLY FLOWERING 3 (ELF3). Our results suggest that this protein is involved in the many different light signaling pathways to the Chlamydomonas circadian clock. However, it may not influence the transcriptional oscillator of Chlamydomonas to a great extent. This study provides an opportunity to further understand the mechanisms underlying light-induced clock resetting and explore the evolution of the circadian clock architecture in Viridiplantae.

Resetting of the circadian clock is crucial for an organism, as it allows the synchronization of its internal processes with the day/night cycle. Environmental signals—such as light and temperature—contribute to this event. In plants, the molecular mechanisms underlying the light-induced resetting of the circadian clock have been well-studied in the streptophyte, Arabidopsis thaliana, and has been explored in some chlorophyte algae such as Ostreococcus tauri and Chlamydomonas reinhardtii. Here, we used a forward genetics approach to examine the light signaling pathway of a process considered critical for the light resetting of the Chlamydomonas clock—light-induced degradation of the circadian clock protein ROC15. We explored various aspects of the isolated mutant, such as the degradation of ROC15 in response to a range of visible wavelengths, the circadian rhythm, and the phase resetting of the rhythm. We show that the effects of different wavelengths of light converge before acting on ROC15 or at ROC15 phosphorylation with the aid of a potential homolog of the Arabidopsis thaliana ELF3. Our findings contradict the existing view that there is no known homolog of ELF3 in chlorophyte algae. This study, therefore, sheds light on the evolutionary aspects of the Viridiplantae circadian clocks and their light resetting.

Comparative Phenotyping of Two Commonly Used Chlamydomonas reinhardtii Background Strains: CC-1690 (21gr) and CC-5325 (The CLiP Mutant Library Background)

The unicellular green alga Chlamydomonas reinhardtii is an excellent model organism to investigate many essential cellular processes in photosynthetic eukaryotes. Two commonly used background strains of Chlamydomonas are CC-1690 and CC-5325. CC-1690, also called 21gr, has been used for the Chlamydomonas genome project and several transcriptome analyses. CC-5325 is the background strain for the Chlamydomonas Library Project (CLiP). Photosynthetic performance in CC-5325 has not been evaluated in comparison with CC-1690. Additionally, CC-5325 is often considered to be cell-wall deficient, although detailed analysis is missing. The circadian rhythms in CC-5325 are also unclear. To fill these knowledge gaps and facilitate the use of the CLiP mutant library for various screens, we performed phenotypic comparisons between CC-1690 and CC-5325. Our results showed that CC-5325 grew faster heterotrophically in dark and equally well in mixotrophic liquid medium as compared to CC-1690. CC-5325 had lower photosynthetic efficiency and was more heat-sensitive than CC-1690. Furthermore, CC-5325 had an intact cell wall which had comparable integrity to that in CC-1690 but appeared to have reduced thickness. Additionally, CC-5325 could perform phototaxis, but could not maintain a sustained circadian rhythm of phototaxis as CC1690 did. Finally, in comparison to CC-1690, CC-5325 had longer cilia in the medium with acetate but slower swimming speed in the medium without nitrogen and acetate. Our results will be useful for researchers in the Chlamydomonas community to choose suitable background strains for mutant analysis and employ the CLiP mutant library for genome-wide mutant screens under appropriate conditions, especially in the areas of photosynthesis, thermotolerance, cell wall, and circadian rhythms.

Evolutionary conservations, changes of circadian rhythms and their effect on circadian disturbances and therapeutic approaches

The circadian rhythm is essential for the interaction of all living organisms with their environments. Several processes, such as thermoregulation, metabolism, cognition and memory, are regulated by the internal clock. Disturbances in the circadian rhythm have been shown to lead to the development of neuropsychiatric disorders, including attention-deficit hyperactivity disorder (ADHD). Interestingly, the mechanism of the circadian rhythms has been conserved in many different species, and misalignment between circadian rhythms and the environment results in evolutionary regression and lifespan reduction. This review summarises the conserved mechanism of the internal clock and its major interspecies differences. In addition, it focuses on effects the circadian rhythm disturbances, especially in cases of ADHD, and describes the possibility of recombinant proteins generated by eukaryotic expression systems as therapeutic agents as well as CRISPR/Cas9 technology as a potential tool for research and therapy. The aim is to give an overview about the evolutionary conserved mechanism as well as the changes of the circadian clock. Furthermore, current knowledge about circadian rhythm disturbances and therapeutic approaches is discussed.

The role of ROC75 as a daytime component of the circadian oscillator in Chlamydomonas reinhardtii

The circadian clocks in chlorophyte algae have been studied in two model organisms, Chlamydomonas reinhardtii and Ostreococcus tauri. These studies revealed that the chlorophyte clocks include some genes that are homologous to those of the angiosperm circadian clock. However, the genetic network architectures of the chlorophyte clocks are largely unknown, especially in C. reinhardtii. In this study, using C. reinhardtii as a model, we characterized RHYTHM OF CHLOROPLAST (ROC) 75, a clock gene encoding a putative GARP DNA-binding transcription factor similar to the clock proteins LUX ARRHYTHMO (LUX, also called PHYTOCLOCK 1 [PCL1]) and BROTHER OF LUX ARRHYTHMO (BOA, also called NOX) of the angiosperm Arabidopsis thaliana. We observed that ROC75 is a day/subjective day-phase-expressed nuclear-localized protein that associates with some night-phased clock genes and represses their expression. This repression may be essential for the gating of reaccumulation of the other clock-related GARP protein, ROC15, after its light-dependent degradation. The restoration of ROC75 function in an arrhythmic roc75 mutant under constant darkness leads to the resumption of circadian oscillation from the subjective dawn, suggesting that the ROC75 restoration acts as a morning cue for the C. reinhardtii clock. Our study reveals a part of the genetic network of C. reinhardtii clock that could be considerably different from that of A. thaliana.

Cryptochrome photoreceptors in green algae: Unexpected versatility of mechanisms and functions

Green algae have a highly complex and diverse set of cryptochrome photoreceptor candidates including members of the following subfamilies: plant, plant-like, animal-like, DASH and cryptochrome photolyase family 1 (CPF1). While some green algae encode most or all of them, others lack certain members. Here we present an overview about functional analyses of so far investigated cryptochrome photoreceptors from the green algae Chlamydomonas reinhardtii (plant and animal-like cryptochromes) and Ostreococcus tauri (CPF1) with regard to their biological significance and spectroscopic properties. Cryptochromes of both algae have been demonstrated recently to be involved to various extents in circadian clock regulation and in Chlamydomonas additionally in life cycle control. Moreover, CPF1 even performs light-driven DNA repair. The plant cryptochrome and CPF1 are UVA/blue light receptors, whereas the animal-like cryptochrome responds to almost the whole visible spectrum including red light. Accordingly, plant cryptochrome, animal-like cryptochrome and CPF1 differ fundamentally in their structural response to light as revealed by their visible and infrared spectroscopic signatures, and in the role of the flavin neutral radical acting as dark form or signaling state.

Regulation of ascorbate biosynthesis in green algae has evolved to enable rapid stress-induced response via the VTC2 gene encoding GDP-l-galactose phosphorylase

Ascorbate (vitamin C) plays essential roles in stress resistance, development, signaling, hormone biosynthesis and regulation of gene expression; however, little is known about its biosynthesis in algae. In order to provide experimental proof for the operation of the Smirnoff-Wheeler pathway described for higher plants and to gain more information on the regulation of ascorbate biosynthesis in Chlamydomonas reinhardtii, we targeted the VTC2 gene encoding GDP-l-galactose phosphorylase using artificial microRNAs. Ascorbate concentrations in VTC2 amiRNA lines were reduced to 10% showing that GDP-l-galactose phosphorylase plays a pivotal role in ascorbate biosynthesis. The VTC2 amiRNA lines also grow more slowly, have lower chlorophyll content, and are more susceptible to stress than the control strains. We also demonstrate that: expression of the VTC2 gene is rapidly induced by H₂ O₂ and ¹ O₂ resulting in a manifold increase in ascorbate content; in contrast to plants, there is no circadian regulation of ascorbate biosynthesis; photosynthesis is not required per se for ascorbate biosynthesis; and Chlamydomonas VTC2 lacks negative feedback regulation by ascorbate in the physiological concentration range. Our work demonstrates that ascorbate biosynthesis is also highly regulated in Chlamydomonas albeit via mechanisms distinct from those previously described in land plants.

CSL encodes a leucine-rich-repeat protein implicated in red/violet light signaling to the circadian clock in Chlamydomonas

The green alga Chlamydomonas reinhardtii shows various light responses in behavior and physiology. One such photoresponse is the circadian clock, which can be reset by external light signals to entrain its oscillation to daily environmental cycles. In a previous report, we suggested that a light-induced degradation of the clock protein ROC15 is a trigger to reset the circadian clock in Chlamydomonas. However, light signaling pathways of this process remained unclear. Here, we screened for mutants that show abnormal ROC15 diurnal rhythms, including the light-induced protein degradation at dawn, using a luciferase fusion reporter. In one mutant, ROC15 degradation and phase resetting of the circadian clock by light were impaired. Interestingly, the impairments were observed in response to red and violet light, but not to blue light. We revealed that an uncharacterized gene encoding a protein similar to RAS-signaling-related leucine-rich repeat (LRR) proteins is responsible for the mutant phenotypes. Our results indicate that a previously uncharacterized red/violet light signaling pathway is involved in the phase resetting of circadian clock in Chlamydomonas.

The unicellular green alga Chlamydomonas reinhardtii is used as a model system in many biological researches. Although blue light responses of this alga (e.g., phototaxis) are well known and well characterized, far less is understood about responses to other wavelengths. One such photoresponse is the circadian clock, which can be reset by various wavelengths of light, ranging from violet to red, to entrain its oscillation to daily environmental cycles. In this study, we identified a gene responsible for red and violet light responses of the circadian clock by a forward genetic screen. Our results shed light on a previously unrecognized red/violet light signaling pathway in green algae.

Genetic basis of allochronic differentiation in the fall armyworm

BACKGROUND

Very little is known on how changes in circadian rhythms evolve. The noctuid moth Spodoptera frugiperda (Lepidoptera: Noctuidae) consists of two strains that exhibit allochronic differentiation in their mating time, which acts as a premating isolation barrier between the strains. We investigated the genetic basis of the strain-specific timing differences to identify the molecular mechanisms of differentiation in circadian rhythms.

RESULTS

Through QTL analyses we identified one major Quantitative trait chromosome (QTC) underlying differentiation in circadian timing of mating activity. Using RADtags, we identified this QTC to be homologous to Bombyx mori C27, on which the clock gene vrille is located, which thus became the major candidate gene. In S. frugiperda, vrille showed strain-specific polymorphisms. Also, vrille expression differed significantly between the strains, with the rice-strain showing higher expression levels than the corn-strain. In addition, RT-qPCR experiments with the other main clock genes showed that pdp1, antagonist of vrille in the modulatory feedback loop of the circadian clock, showed higher expression levels in the rice-strain than in the corn-strain.

CONCLUSIONS

Together, our results indicate that the allochronic differentiation in the two strains of S. frugiperda is associated with differential transcription of vrille or a cis-acting gene close to vrille, which contributes to the evolution of prezygotic isolation in S. frugiperda.

Genetic tools and techniques for Chlamydomonas reinhardtii

The development of tools has always been a major driving force for the advancement of science. Optical microscopes were the first instruments that allowed discovery and descriptive studies of the subcellular features of microorganisms. Although optical and electron microscopes remained at the forefront of microbiological research tools since their inventions, the advent of molecular genetics brought about questions which had to be addressed with new "genetic tools". The unicellular green microalgal genus Chlamydomonas, especially the most prominent species C. reinhardtii, has become a frequently used model organism for many diverse fields of research and molecular genetic analyses of C. reinhardtii, as well as the available genetic tools and techniques, have become increasingly sophisticated throughout the last decades. The aim of this review is to provide an overview of the molecular key features of C. reinhardtii and summarize the progress related to the development of tools and techniques for genetic engineering of this organism, from pioneering DNA transformation experiments to state-of-the-art techniques for targeted nuclear genome editing and high-throughput screening approaches.

Challenges and opportunities for microalgae-mediated CO2 capture and biorefinery

Aquacultures of microalgae are frontrunners for photosynthetic capture of CO2 from flue gases. Expedient implementation mandates coupling of microalgal CO2 capture with synthesis of fuels and organic products, so as to derive value from biomass. An integrated biorefinery complex houses a biomass growth and harvesting area and a refining zone for conversion to product(s) and separation to desired purity levels. As growth and downstream options require energy and incur loss of carbon, put together, the loop must be energy positive, carbon negative, or add substantial value. Feasibility studies can, thus, aid the choice from among the rapidly evolving technological options, many of which are still in the early phases of development. We summarize basic engineering calculations for the key steps of a biorefining loop where flue gases from a thermal power station are captured using microalgal biomass along with subsequent options for conversion to fuel or value added products. An assimilation of findings from recent laboratory and pilot-scale experiments and life cycle analysis (LCA) studies is presented as carbon and energy yields for growth and harvesting of microalgal biomass and downstream options. Of the biorefining options, conversion to the widely studied biofuel, ethanol, and manufacture of the platform chemical, succinic acid are presented. Both processes yield specific products and do not demand high-energy input but entail 60-70% carbon loss through fermentative respiration. Thermochemical conversions, on the other hand, have smaller carbon and energy losses but yield a mixture of products.

The Chlamydomonas cell cycle

The position of Chlamydomonas within the eukaryotic phylogeny makes it a unique model in at least two important ways: as a representative of the critically important, early-diverging lineage leading to plants; and as a microbe retaining important features of the last eukaryotic common ancestor (LECA) that has been lost in the highly studied yeast lineages. Its cell biology has been studied for many decades and it has well-developed experimental genetic tools, both classical (Mendelian) and molecular. Unlike land plants, it is a haploid with very few gene duplicates, making it ideal for loss-of-function genetic studies. The Chlamydomonas cell cycle has a striking temporal and functional separation between cell growth and rapid cell division, probably connected to the interplay between diurnal cycles that drive photosynthetic cell growth and the cell division cycle; it also exhibits a highly choreographed interaction between the cell cycle and its centriole-basal body-flagellar cycle. Here, we review the current status of studies of the Chlamydomonas cell cycle. We begin with an overview of cell-cycle control in the well-studied yeast and animal systems, which has yielded a canonical, well-supported model. We discuss briefly what is known about similarities and differences in plant cell-cycle control, compared with this model. We next review the cytology and cell biology of the multiple-fission cell cycle of Chlamydomonas. Lastly, we review recent genetic approaches and insights into Chlamydomonas cell-cycle regulation that have been enabled by a new generation of genomics-based tools.

Dealing with light: the widespread and multitasking cryptochrome/photolyase family in photosynthetic organisms

Light is essential for the life of photosynthetic organisms as it is a source of energy and information from the environment. Light excess or limitation can be a cause of stress however. Photosynthetic organisms exhibit sophisticated mechanisms to adjust their physiology and growth to the local environmental light conditions. The cryptochrome/photolyase family (CPF) is composed of flavoproteins with similar structures that display a variety of light-dependent functions. This family encompasses photolyases, blue-light activated enzymes that repair ultraviolet-light induced DNA damage, and cryptochromes, known for their photoreceptor functions in terrestrial plants. For this review, we searched extensively for CPFs in the available genome databases to trace the distribution and evolution of this protein family in photosynthetic organisms. By merging molecular data with current knowledge from the functional characterization of CPFs from terrestrial and aquatic organisms, we discuss their roles in (i) photoperception, (ii) biological rhythm regulation and (iii) light-induced stress responses. We also explore their possible implication in light-related physiological acclimation and their distribution in phototrophs living in different environments. The outcome of this structure-function analysis reconstructs the complex scenarios in which CPFs have evolved, as highlighted by the novel functions and biochemical properties of the most recently described family members in algae.

Chlamydomonas reinhardtii strain CC-124 is highly sensitive to blue light in addition to green and red light in resetting its circadian clock, with the blue-light photoreceptor plant cryptochrome likely acting as negative modulator

The unicellular green alga Chlamydomonas reinhardtii has long served as model organism for studies on the circadian clock. This clock is present in all eukaryotes and some prokaryotes allowing them to anticipate and take advantage of the daily oscillations in the environment. Although much is known about the circadian clock in C. reinhardtii, the photoreceptors mediating entrainment of the clock to the daily changes of light remain obscure. Based on its circadian rhythm of phototaxis as a reporter of the clock's phase, we show here that C. reinhardtii strain CC-124 is highly sensitive to blue light of 440 nm when resetting its circadian clock upon light pulses. Thus, CC-124 differs in this respect from what was previously reported for a cell wall-deficient strain. An action spectrum analysis revealed that CC-124 also responds with high sensitivity to green (540 nm), red (640-660 nm), and possibly UV-A (≤400 nm) light, and therefore shows similarities as well to what has been reported for the cell wall-deficient strain. We also investigated two RNA interference strains with reductions in the level of the blue light photoreceptor plant cryptochrome (CPH1). One of them, the strain with the greater reduction, surprisingly showed an increased sensitivity in clock resetting upon blue light pulses of 440 nm. This increase in sensitivity reverted to wild-type levels when the RNA interference strain reverted to wild-type protein levels. It suggests that plant cryptochrome in C. reinhardtii could function as negative rather than positive modulator of circadian clock resetting.

Comparative phosphoproteomics to identify targets of the clock-relevant casein kinase 1 in C. reinhardtii Flagella

In the green biflagellate alga Chlamydomonas reinhardtii different clock-relevant components have been identified that are involved in maintaining phase, period, and amplitude of circadian rhythms. It became evident that several of them are interconnected to flagellar function such as CASEIN KINASE1 (CK1). CK1 is involved in keeping the period. But it is also relevant for the formation of flagella, where it is physically located, and it controls the swimming velocity. In this chapter, we describe (1) how the flagellar sub-proteome is purified, (2) how phosphopeptides from this organelle are enriched, (3) how in vivo phosphorylation sites are determined, and (4) how direct and indirect flagellar targets of CK1 can be found using a specific inhibitor. Such a procedure can also be employed with other clock-relevant kinases if specific inhibitors or mutants are available.

Protein disulfide isomerase 2 of Chlamydomonas reinhardtii is involved in circadian rhythm regulation

Protein disulfide isomerases (PDIs) are known to play important roles in the folding of nascent proteins and in the formation of disulfide bonds. Recently, we identified a PDI from Chlamydomonas reinhardtii (CrPDI2) by a mass spectrometry approach that is specifically enriched by heparin affinity chromatography in samples taken during the night phase. Here, we show that the recombinant CrPDI2 is a redox-active protein. It is reduced by thioredoxin reductase and catalyzes itself the reduction of insulin chains and the oxidative refolding of scrambled RNase A. By immunoblots, we confirm a high-amplitude change in abundance of the heparin-bound CrPDI2 during subjective night. Interestingly, we find that CrPDI2 is present in protein complexes of different sizes at both day and night. Among three identified interaction partners, one (a 2-cys peroxiredoxin) is present only during the night phase. To study a potential function of CrPDI2 within the circadian system, we have overexpressed its gene. Two transgenic lines were used to measure the rhythm of phototaxis. In the transgenic strains, a change in the acrophase was observed. This indicates that CrPDI2 is involved in the circadian signaling pathway and, together with the night phase-specific interaction of CrPDI2 and a peroxiredoxin, these findings suggest a close coupling of redox processes and the circadian clock in C. reinhardtii.

Phase-resetting mechanism of the circadian clock in Chlamydomonas reinhardtii

Although the circadian clock is a self-sustaining oscillator having a periodicity of nearly 1 d, its period length is not necessarily 24 h. Therefore, daily adjustment of the clock (i.e., resetting) is an essential mechanism for the circadian clock to adapt to daily environmental changes. One of the major cues for this resetting mechanism is light. In the unicellular green alga Chlamydomonas reinhardtii, the circadian clock is reset by blue/green and red light. However, the underlying molecular mechanisms remain largely unknown. In this study, using clock protein-luciferase fusion reporters, we found that the level of RHYTHM OF CHLOROPLAST 15 (ROC15), a clock component in C. reinhardtii, decreased rapidly after light exposure in a circadian-phase-independent manner. Blue, green, and red light were able to induce this process, with red light being the most effective among them. Expression analyses and inhibitor experiments suggested that this process was regulated mainly by a proteasome-dependent protein degradation pathway. In addition, we found that the other clock gene, ROC114, encoding an F-box protein, was involved in this process. Furthermore, we demonstrated that a roc15 mutant showed defects in the phase-resetting of the circadian clock by light. Taken together, these data strongly suggest that the light-induced degradation of ROC15 protein is one of the triggers for resetting the circadian clock in C. reinhardtii. Our data provide not only a basis for understanding the molecular mechanisms of light-induced phase-resetting in C. reinhardtii, but also insights into the phase-resetting mechanisms of circadian clocks in plants.

The heme-binding protein SOUL3 of Chlamydomonas reinhardtii influences size and position of the eyespot

The flagellated green alga Chlamydomonas reinhardtii has a primitive visual system, the eyespot. It is situated at the cells equator and allows the cell to phototax. In a previous proteomic analysis of the eyespot, the SOUL3 protein was identified among 202 proteins. Here, we investigate the properties and functions of SOUL3. Heterologously expressed SOUL3 is able to bind specifically to hemin. In C. reinhardtii, SOUL3 is expressed at a constant level over the diurnal cycle, but forms protein complexes that differ in size during day and night phases. SOUL3 is primarily localized in the eyespot and it is situated in the pigment globule layer thereof. This is in contrast to the channelrhodopsin photoreceptors, which are localized in the plasma membrane region of the eyespot. Knockdown lines with a significantly reduced SOUL3 level are characterized by mislocalized eyespots, a decreased eyespot size, and alterations in phototactic behavior. Mislocalizations were either anterior or posterior and did not affect association with acetylated microtubules of the daughter four-membered rootlet. Our data suggest that SOUL3 is involved in the organization and placement of the eyespot within the cell.

Beyond Arabidopsis: the circadian clock in non-model plant species

Circadian clocks allow plants to temporally coordinate many aspects of their biology with the diurnal cycle derived from the rotation of Earth on its axis. Although there is a rich history of the study of clocks in many plant species, in recent years much progress in elucidating the architecture and function of the plant clock has emerged from studies of the model plant, Arabidopsis thaliana. There is considerable interest in extending this knowledge of the circadian clock into diverse plant species in order to address its role in topics as varied as agricultural productivity and the responses of individual species and plant communities to global climate change and environmental degradation. The analysis of circadian clocks in the green lineage provides insight into evolutionary processes in plants and throughout the eukaryotes.

Gene regulation of carbon fixation, storage, and utilization in the diatom Phaeodactylum tricornutum acclimated to light/dark cycles

The regulation of carbon metabolism in the diatom Phaeodactylum tricornutum at the cell, metabolite, and gene expression levels in exponential fed-batch cultures is reported. Transcriptional profiles and cell chemistry sampled simultaneously at all time points provide a comprehensive data set on carbon incorporation, fate, and regulation. An increase in Nile Red fluorescence (a proxy for cellular neutral lipids) was observed throughout the light period, and water-soluble glucans increased rapidly in the light period. A near-linear decline in both glucans and lipids was observed during the dark period, and transcription profile data indicated that this decline was associated with the onset of mitosis. More than 4,500 transcripts that were differentially regulated during the light/dark cycle are identified, many of which were associated with carbohydrate and lipid metabolism. Genes not previously described in algae and their regulation in response to light were integrated in this analysis together with proposed roles in metabolic processes. Some very fast light-responding genes in, for example, fatty acid biosynthesis were identified and allocated to biosynthetic processes. Transcripts and cell chemistry data reflect the link between light energy availability and light energy-consuming metabolic processes. Our data confirm the spatial localization of processes in carbon metabolism to either plastids or mitochondria or to glycolysis/gluconeogenesis, which are localized to the cytosol, chloroplast, and mitochondria. Localization and diel expression pattern may be of help to determine the roles of different isoenzymes and the mining of genes involved in light responses and circadian rhythms.

News about cryptochrome photoreceptors in algae

Cryptochromes (CRYs) are flavoproteins that are known as blue light photoreceptors in many organisms. Recently, genome sequences from a variety of algae became available. Functional characterizations of animal-like CRYs from Oestreococcus tauri, Chlamydomonas reinhardtii and Phaeodactylum tricornutum highlighted novel functions and properties. As arising from studies in fungi, certain algal CRYs of the "cryptochrome photolyase family" (PtCPF1, OtCPF1) have dual or even triple functions. They are involved in blue light perception and/or in the circadian clock and are able to repair DNA damages. On the other hand, the animal-like aCRY from C. reinhardtii is not only acting as sensory blue light- but also as sensory red light receptor thus expanding our current view of flavoproteins in general and CRYs in particular. The observed broad spectral response points to the neutral radical state of flavin, which is assumed to be the dark form in aCRY in contrast to the plant CRYs.

Novel interaction of two clock-relevant RNA-binding proteins C3 and XRN1 in Chlamydomonas reinhardtii

The RNA-binding protein CHLAMY1 of the green alga Chlamydomonas reinhardtii consists of two subunits, named C1 and C3 that maintain the period and phase of the circadian clock. Here, we investigated if any of its subunits interact with other clock components involved in RNA metabolism. We found that C3, but not C1 strongly interacts with exoribonuclease XRN1 whose knockout results in low amplitude rhythms. XRN1 is subject to degradation by the proteasome pathway. Its level increases in cells grown at lower ambient temperature simulating night, which was also observed for C3. Our data indicate a network of clock-relevant RNA-binding proteins.

N-terminal acetyltransferase 3 gene is essential for robust circadian rhythm of bioluminescence reporter in Chlamydomonas reinhardtii

Chlamydomonas reinhardtii is a model species of algae for studies on the circadian clock. Previously, we isolated a series of mutants showing defects in the circadian rhythm of a luciferase reporter introduced into the chloroplast genome, and identified the genes responsible for the defective circadian rhythm. However, we were unable to identify the gene responsible for the defective circadian rhythm of the rhythm of chloroplast 97 (roc97) mutant because of a large genomic deletion. Here, we identified the gene responsible for the roc97 mutation through a genetic complementation study. This gene encodes a protein that is homologous to the subunit of N-terminal acetyltransferase (NAT) which catalyzes N-terminal acetylation of proteins. Our results provide the first example of involvement of the protein N-terminal acetyltransferase in the circadian rhythm.

CONSTANS and the evolutionary origin of photoperiodic timing of flowering

A network of promoting and inhibiting pathways that respond to environmental and internal signals controls the flowering transition. The outcome of this regulatory network establishes, for any particular plant, the correct time of the year to flower. The photoperiod pathway channels inputs from light, day length, and the circadian clock to promote the floral transition. CONSTANS (CO) is a central regulator of this pathway, triggering the production of the mobile florigen hormone FT (FLOWERING LOCUS T) that induces flower differentiation. Because plant reproductive fitness is directly related to its capacity to flower at a precise time, the photoperiod pathway is present in all known plant species. Recent findings have stretched the evolutionary span of this photophase signal to unicellular algae, which show unexpected conserved characteristics with modern plant photoperiodic responses. In this review, a comparative description of the photoperiodic systems in algae and plants will be presented and a general role for the CO family of transcriptional activators proposed.

Multiple light inputs to a simple clock circuit allow complex biological rhythms

Circadian clocks are biological timekeepers that allow living cells to time their activity in anticipation of predictable environmental changes. Detailed understanding of the circadian network of higher plants, such as Arabidopsis thaliana, is hampered by the high number of partially redundant genes. However, the picoeukaryotic alga Ostreococcus tauri, which was recently shown to possess a small number of non-redundant clock genes, presents an attractive alternative target for detailed modelling of circadian clocks in the green lineage. Based on extensive time-series data from in vivo reporter gene assays, we developed a model of the Ostreococcus clock as a feedback loop between the genes TOC1 and CCA1. The model reproduces the dynamics of the transcriptional and translational reporters over a range of photoperiods. Surprisingly, the model is also able to predict the transient behaviour of the clock when the light conditions are altered. Despite the apparent simplicity of the clock circuit, it displays considerable complexity in its response to changing light conditions. Systematic screening of the effects of altered day length revealed a complex relationship between phase and photoperiod, which is also captured by the model. The complex light response is shown to stem from circadian gating of light-dependent mechanisms. This study provides insights into the contributions of light inputs to the Ostreococcus clock. The model suggests that a high number of light-dependent reactions are important for flexible timing in a circadian clock with only one feedback loop.

Spotlight on post-transcriptional control in the circadian system

An endogenous timing mechanism, the circadian clock, causes rhythmic expression of a considerable fraction of the genome of most organisms to optimally align physiology and behavior with their environment. Circadian clocks are self-sustained oscillators primarily based on transcriptional feedback loops and post-translational modification of clock proteins. It is increasingly becoming clear that regulation at the RNA level strongly impacts the cellular circadian transcriptome and proteome as well as the oscillator mechanism itself. This review focuses on posttranscriptional events, discussing RNA-binding proteins that, by influencing the timing of pre-mRNA splicing, polyadenylation and RNA decay, shape rhythmic expression profiles. Furthermore, recent findings on the contribution of microRNAs to orchestrating circadian rhythms are summarized.