Circadian expression of the luciferin-binding protein correlates with the binding of a protein to the 3' untranslated region of its mRNA

Rhythms and Clocks in Marine Organisms

The regular movements of waves and tides are obvious representations of the oceans' rhythmicity. But the rhythms of marine life span across ecological niches and timescales, including short (in the range of hours) and long (in the range of days and months) periods. These rhythms regulate the physiology and behavior of individuals, as well as their interactions with each other and with the environment. This review highlights examples of rhythmicity in marine animals and algae that represent important groups of marine life across different habitats. The examples cover ecologically highly relevant species and a growing number of laboratory model systems that are used to disentangle key mechanistic principles. The review introduces fundamental concepts of chronobiology, such as the distinction between rhythmic and endogenous oscillator-driven processes. It also addresses the relevance of studying diverse rhythms and oscillators, as well as their interconnection, for making better predictions of how species will respond to environmental perturbations, including climate change. As the review aims to address scientists from the diverse fields of marine biology, ecology, and molecular chronobiology, all of which have their own scientific terms, we provide definitions of key terms throughout the article.

From the sxtA4 Gene to Saxitoxin Production: What Controls the Variability Among Alexandrium minutum and Alexandrium pacificum Strains?

Paralytic shellfish poisoning (PSP) is a human foodborne syndrome caused by the consumption of shellfish that accumulate paralytic shellfish toxins (PSTs, saxitoxin group). In PST-producing dinoflagellates such as Alexandrium spp., toxin synthesis is encoded in the nuclear genome via a gene cluster (sxt). Toxin production is supposedly associated with the presence of a 4th domain in the sxtA gene (sxtA4), one of the core genes of the PST gene cluster. It is postulated that gene expression in dinoflagellates is partially constitutive, with both transcriptional and post-transcriptional processes potentially co-occurring. Therefore, gene structure and expression mode are two important features to explore in order to fully understand toxin production processes in dinoflagellates. In this study, we determined the intracellular toxin contents of twenty European Alexandrium minutum and Alexandrium pacificum strains that we compared with their genome size and sxtA4 gene copy numbers. We observed a significant correlation between the sxtA4 gene copy number and toxin content, as well as a moderate positive correlation between the sxtA4 gene copy number and genome size. The 18 toxic strains had several sxtA4 gene copies (9-187), whereas only one copy was found in the two observed non-toxin producing strains. Exploration of allelic frequencies and expression of sxtA4 mRNA in 11 A. minutum strains showed both a differential expression and specific allelic forms in the non-toxic strains compared with the toxic ones. Also, the toxic strains exhibited a polymorphic sxtA4 mRNA sequence between strains and between gene copies within strains. Finally, our study supported the hypothesis of a genetic determinism of toxin synthesis (i.e., the existence of several genetic isoforms of the sxtA4 gene and their copy numbers), and was also consistent with the hypothesis that constitutive gene expression and moderation by transcriptional and post-transcriptional regulation mechanisms are the cause of the observed variability in the production of toxins by A. minutum.

Emerging Roles of Translational Control in Circadian Timekeeping

A large part of mammalian physiology and behaviour shows regular daily variations. This temporal organisation is driven by the activity of an endogenous circadian clock, whose molecular basis consists of diurnal waves in gene expression. Circadian transcription is the major driver of these rhythms, yet post-transcriptional mechanisms, some of which occur in response to systemic cues and in a tissue-specific fashion, have central roles in ultimately establishing the oscillatory gene expression programme as well. Regulatory control that occurs at the level of translation is emerging as an important player in the generation and modulation of protein accumulation rhythms. As a mechanism, translation lies at a privileged position to integrate genetically encoded rhythmic signals with other, external and internal stimuli, including nutrient-derived cues. In this review, we summarise our current knowledge of how diurnal control of translation affects both bulk protein levels and gene-specific protein biosynthesis. We discuss mechanisms of regulation, in particular with regard to the complex interplay between circadian cycles and feeding/fasting cycles, as well as emerging roles for upstream open reading frames in clock control.

Human Periapical Cyst-Derived Stem Cells Can Be A Smart "Lab-on-A-Cell" to Investigate Neurodegenerative Diseases and the Related Alteration of the Exosomes' Content

Promising researches have demonstrated that the alteration of biological rhythms may be consistently linked to neurodegenerative pathologies. Parkinson's disease (PD) has a multifactorial pathogenesis, involving both genetic and environmental and/or molecular co-factors. Generally, heterogeneous alterations in circadian rhythm (CR) are a typical finding in degenerative processes, such as cell aging and death. Although numerous genetic phenotypes have been discovered in the most common forms of PD, it seems that severe deficiencies in synaptic transmission and high vesicular recycling are frequently found in PD patients. Neuron-to-neuron interactions are often ensured by exosomes, a specific type of extracellular vesicle (EV). Neuron-derived exosomes may carry several active compounds, including miRNAs: Several studies have found that circulating miRNAs are closely associated with an atypical oscillation of circadian rhythm genes, and they are also involved in the regulation of clock genes, in animal models. In this context, a careful analysis of neural-differentiated Mesenchymal Stem Cells (MSCs) and the molecular and genetic characterization of their exosome content, both in healthy cells and in PD-induced cells, could be a strategic field of investigation for early diagnosis and better treatment of PD and similar neurodegenerative pathologies. A novel MSC population, called human periapical cyst-mesenchymal stem cells (hPCy-MSCs), has demonstrated that it naively expresswa the main neuronal markers, and may differentiate towards functional neurons. Therefore, hPCy-MSCs can be considered of particular interest for testing of in vitro strategies to treat neurological diseases. On the other hand, the limitations of using stem cells is an issue that leads researchers to perform experimental studies on the exosomes released by MCSs. Human periapical cyst-derived mesenkymal stem cells can be a smart "lab-on-a-cell" to investigate neurodegenerative diseases and the related exosomes' content alteration.

Translation and Translational Control in Dinoflagellates

Dinoflagellates are unicellular protists that feature a multitude of unusual nuclear features, including large genomes, packaging of DNA without histones, and multiple gene copies organized as tandem gene arrays. Furthermore, all dinoflagellate mRNAs experience trans-splicing with a common 22-nucleotide splice leader (SL) sequence. These features challenge some of the concepts and assumptions about the regulation of gene expression derived from work on model eukaryotes such as yeasts and mammals. Translational control in the dinoflagellates, based on extensive study of circadian bioluminescence and by more recent microarray and transcriptome analyses, is now understood to be a crucial element in regulating gene expression. A picture of the translation machinery of dinoflagellates is emerging from the recent availability of transcriptomes of multiple dinoflagellate species and the first complete genome sequences. The components comprising the translational control toolkit of dinoflagellates are beginning to take shape and are outlined here.

miRNAs Do Not Regulate Circadian Protein Synthesis in the Dinoflagellate Lingulodinium polyedrum

Dinoflagellates have been shown to express miRNA by bioinformatics and RNA blot (Northern) analyses. However, it is not yet known if miRNAs are able to alter gene expression in this class of organisms. We have assessed the possibility that miRNA may mediate circadian regulation of gene expression in the dinoflagellate Lingulodinium polyedrum using the Luciferin Binding Protein (LBP) as a specific example. LBP is a good candidate for regulation by miRNA since mRNA levels are constant over the daily cycle while protein synthesis is restricted by the circadian clock to a period of several hours at the start of the night phase. The transcriptome contains a potential DICER and an ARGONAUTE, suggesting the machinery for generating miRNAs is present. Furthermore, a probe directed against an abundant Symbiodinium miRNA cross reacts on Northern blots. However, L. polyedrum has no small RNAs detectable by ethidium bromide staining, even though higher plant miRNAs run in parallel are readily observed. Illumina sequencing of small RNAs showed that the majority of reads did not have a match in the L. polyedrum transcriptome, and those that did were almost all sense strand mRNA fragments. A direct search for 18-26 nucleotide long RNAs capable of forming duplexes with a 2 base 3' overhang detected 53 different potential miRNAs, none of which was able to target any of the known circadian regulated genes. Lastly, a microscopy-based test to assess synthesis of the naturally fluorescent LBP in single cells showed that neither double-stranded nor antisense lbp RNA introduced into cells by microparticle bombardment prior to the time of LBP synthesis were able to reduce the amount of LBP produced. Taken together, our results indicate that circadian control of protein synthesis in L. polyedrum is not mediated by miRNAs.

Regulation of Mammalian Physiology by Interconnected Circadian and Feeding Rhythms

Circadian clocks are endogenous timekeeping systems that adapt in an anticipatory fashion the physiology and behavior of most living organisms. In mammals, the master pacemaker resides in the suprachiasmatic nucleus and entrains peripheral clocks using a wide range of signals that differentially schedule physiology and gene expression in a tissue-specific manner. The peripheral clocks, such as those found in the liver, are particularly sensitive to rhythmic external cues like feeding behavior, which modulate the phase and amplitude of rhythmic gene expression. Consequently, the liver clock temporally tunes the expression of many genes involved in metabolism and physiology. However, the circadian modulation of cellular functions also relies on multiple layers of posttranscriptional and posttranslational regulation. Strikingly, these additional regulatory events may happen independently of any transcriptional oscillations, showing that complex regulatory networks ultimately drive circadian output functions. These rhythmic events also integrate feeding-related cues and adapt various metabolic processes to food availability schedules. The importance of such temporal regulation of metabolism is illustrated by metabolic dysfunctions and diseases resulting from circadian clock disruption or inappropriate feeding patterns. Therefore, the study of circadian clocks and rhythmic feeding behavior should be of interest to further advance our understanding of the prevention and therapy of metabolic diseases.

The Circadian Clock Modulates Global Daily Cycles of mRNA Ribosome Loading

Circadian control of gene expression is well characterized at the transcriptional level, but little is known about diel or circadian control of translation. Genome-wide translation state profiling of mRNAs in Arabidopsis thaliana seedlings grown in long day was performed to estimate ribosome loading per mRNA. The experiments revealed extensive translational regulation of key biological processes. Notably, translation of mRNAs for ribosomal proteins and mitochondrial respiration peaked at night. Central clock mRNAs are among those subject to fluctuations in ribosome loading. There was no consistent phase relationship between peak translation states and peak transcript levels. The overlay of distinct transcriptional and translational cycles can be expected to alter the waveform of the protein synthesis rate. Plants that constitutively overexpress the clock gene CCA1 showed phase shifts in peak translation, with a 6-h delay from midnight to dawn or from noon to evening being particularly common. Moreover, cycles of ribosome loading that were detected under continuous light in the wild type collapsed in the CCA1 overexpressor. Finally, at the transcript level, the CCA1-ox strain adopted a global pattern of transcript abundance that was broadly correlated with the light-dark environment. Altogether, these data demonstrate that gene-specific diel cycles of ribosome loading are controlled in part by the circadian clock.

Age-related expression analysis of mouse liver nuclear protein binding to 3'-untranslated region of Period2 gene

In mammals, both circadian rhythm and aging play important roles in regulating time-dependent homeostasis. We previously discovered an age-related increase element binding protein, hnRNP A3, which binds to the 3'-untranslated region (UTR) of blood coagulation factor IX (FIX). Here, we describe other members of this protein family, hnRNP C and hnRNP H, which bind to the 3'-UTR of the mouse circadian clock gene Period 2 (mPer2). RNA electrophoretic mobility shift assays using a (32)P-labeled Per2 RNA probe coupled with two-dimensional gel electrophoresis followed by MALDI-TOF/MS peptide mass fingerprint analysis was used to analyze these proteins. Western blotting suggested that the total expression of these proteins in mouse liver cell nuclei does not increase with age. Two-dimensional gel electrophoresis analysis of age-related protein expression showed that many isoforms of these proteins exist in the liver and that each protein exhibits a complex age-related expression pattern. These results suggest that many isoforms of proteins are regulated by different aging systems and that many age regulation systems function in the liver.

Clocks in algae

As major contributors to global oxygen levels and producers of fatty acids, carotenoids, sterols, and phycocolloids, algae have significant ecological and commercial roles. Early algal models have contributed much to our understanding of circadian clocks at physiological and biochemical levels. The genetic and molecular approaches that identified clock components in other taxa have not been as widely applied to algae. We review results from seven species: the chlorophytes Chlamydomonas reinhardtii, Ostreococcus tauri, and Acetabularia spp.; the dinoflagellates Lingulodinium polyedrum and Symbiodinium spp.; the euglenozoa Euglena gracilis; and the red alga Cyanidioschyzon merolae. The relative simplicity, experimental tractability, and ecological and evolutionary diversity of algal systems may now make them particularly useful in integrating quantitative data from "omic" technologies (e.g., genomics, transcriptomics, metabolomics, and proteomics) with computational and mathematical methods.

Metabolic and nontranscriptional circadian clocks: eukaryotes

Circadian clocks are cellular timekeeping mechanisms that coordinate behavior and physiology around the 24-h day in most living organisms. Misalignment of an organism's clock with its environment is associated with long-term adverse fitness consequences, as exemplified by the link between circadian disruption and various age-related diseases in humans. Current eukaryotic models of the circadian oscillator rely on transcription/translation feedback loop mechanisms, supplemented with accessory cytosolic loops that connect them to cellular physiology. However, mounting evidence is questioning the absolute necessity of transcription-based oscillators for circadian rhythmicity, supported by the recent discovery of oxidation-reduction cycles of peroxiredoxin proteins, which persist even in the absence of transcription. A more fundamental mechanism based on metabolic cycles could thus underlie circadian transcriptional and cytosolic rhythms, thereby promoting circadian oscillations to integral properties of cellular metabolism.

Understanding Bioluminescence in Dinoflagellates-How Far Have We Come?

Some dinoflagellates possess the remarkable genetic, biochemical, and cellular machinery to produce bioluminescence. Bioluminescent species appear to be ubiquitous in surface waters globally and include numerous cosmopolitan and harmful taxa. Nevertheless, bioluminescence remains an enigmatic topic in biology, particularly with regard to the organisms' lifestyle. In this paper, we review the literature on the cellular mechanisms, molecular evolution, diversity, and ecology of bioluminescence in dinoflagellates, highlighting significant discoveries of the last quarter of a century. We identify significant gaps in our knowledge and conflicting information and propose some important research questions that need to be addressed to advance this research field.

Ribonucleoprotein complexes that control circadian clocks

Circadian clocks are internal molecular time-keeping mechanisms that enable organisms to adjust their physiology and behavior to the daily surroundings. Misalignment of circadian clocks leads to both physiological and health impairment. Post-transcriptional regulation and translational regulation of circadian clocks have been extensively investigated. In addition, accumulating evidence has shed new light on the involvement of ribonucleoprotein complexes (RNPs) in the post-transcriptional regulation of circadian clocks. Numerous RNA-binding proteins (RBPs) and RNPs have been implicated in the post-transcriptional modification of circadian clock proteins in different model organisms. Herein, we summarize the advances in the current knowledge on the role of RNP complexes in circadian clock regulation.

Diversity of Eukaryotic Translational Initiation Factor eIF4E in Protists

The greatest diversity of eukaryotic species is within the microbial eukaryotes, the protists, with plants and fungi/metazoa representing just two of the estimated seventy five lineages of eukaryotes. Protists are a diverse group characterized by unusual genome features and a wide range of genome sizes from 8.2 Mb in the apicomplexan parasite Babesia bovis to 112,000-220,050 Mb in the dinoflagellate Prorocentrum micans. Protists possess numerous cellular, molecular and biochemical traits not observed in “text-book” model organisms. These features challenge some of the concepts and assumptions about the regulation of gene expression in eukaryotes. Like multicellular eukaryotes, many protists encode multiple eIF4Es, but few functional studies have been undertaken except in parasitic species. An earlier phylogenetic analysis of protist eIF4Es indicated that they cannot be grouped within the three classes that describe eIF4E family members from multicellular organisms. Many more protist sequences are now available from which three clades can be recognized that are distinct from the plant/fungi/metazoan classes. Understanding of the protist eIF4Es will be facilitated as more sequences become available particularly for the under-represented opisthokonts and amoebozoa. Similarly, a better understanding of eIF4Es within each clade will develop as more functional studies of protist eIF4Es are completed.

Post-transcriptional control of circadian rhythms

Circadian rhythms exist in most living organisms. The general molecular mechanisms that are used to generate 24-hour rhythms are conserved among organisms, although the details vary. These core clocks consist of multiple regulatory feedback loops, and must be coordinated and orchestrated appropriately for the fine-tuning of the 24-hour period. Many levels of regulation are important for the proper functioning of the circadian clock, including transcriptional, post-transcriptional and post-translational mechanisms. In recent years, new information about post-transcriptional regulation in the circadian system has been discovered. Such regulation has been shown to alter the phase and amplitude of rhythmic mRNA and protein expression in many organisms. Therefore, this Commentary will provide an overview of current knowledge of post-transcriptional regulation of the clock genes and clock-controlled genes in dinoflagellates, plants, fungi and animals. This article will also highlight how circadian gene expression is modulated by post-transcriptional mechanisms and how this is crucial for robust circadian rhythmicity.

Transcriptomic response of the red tide dinoflagellate, Karenia brevis, to nitrogen and phosphorus depletion and addition

BACKGROUND

The role of coastal nutrient sources in the persistence of Karenia brevis red tides in coastal waters of Florida is a contentious issue that warrants investigation into the regulation of nutrient responses in this dinoflagellate. In other phytoplankton studied, nutrient status is reflected by the expression levels of N- and P-responsive gene transcripts. In dinoflagellates, however, many processes are regulated post-transcriptionally. All nuclear encoded gene transcripts studied to date possess a 5' trans-spliced leader (SL) sequence suggestive, based on the trypanosome model, of post-transcriptional regulation. The current study therefore sought to determine if the transcriptome of K. brevis is responsive to nitrogen and phosphorus and is informative of nutrient status.

RESULTS

Microarray analysis of N-depleted K. brevis cultures revealed an increase in the expression of transcripts involved in N-assimilation (nitrate and ammonium transporters, glutamine synthetases) relative to nutrient replete cells. In contrast, a transcriptional signal of P-starvation was not apparent despite evidence of P-starvation based on their rapid growth response to P-addition. To study transcriptome responses to nutrient addition, the limiting nutrient was added to depleted cells and changes in global gene expression were assessed over the first 48 hours following nutrient addition. Both N- and P-addition resulted in significant changes in approximately 4% of genes on the microarray, using a significance cutoff of 1.7-fold and p ≤ 10-4. By far, the earliest responding genes were dominated in both nutrient treatments by pentatricopeptide repeat (PPR) proteins, which increased in expression up to 3-fold by 1 h following nutrient addition. PPR proteins are nuclear encoded proteins involved in chloroplast and mitochondria RNA processing. Correspondingly, other functions enriched in response to both nutrients were photosystem and ribosomal genes.

CONCLUSIONS

Microarray analysis provided transcriptomic evidence for N- but not P-limitation in K. brevis. Transcriptomic responses to the addition of either N or P suggest a concerted program leading to the reactivation of chloroplast functions. Even the earliest responding PPR protein transcripts possess a 5' SL sequence that suggests post-transcriptional control. Given the current state of knowledge of dinoflagellate gene regulation, it is currently unclear how these rapid changes in such transcript levels are achieved.

Posttranscriptional mechanisms in controlling eukaryotic circadian rhythms

The circadian clock is essential in almost all living organisms to synchronise biochemical, metabolic, physiological and behavioural cycles to daily changing environmental factors. In a highly conserved fashion, the circadian clock is primarily controlled by multiple positive and negative molecular circuitries that control gene expression. More recently, research in Neurospora and other eukaryotes has uncovered the involvement of additional regulatory components that operate at the posttranslational level to fine tune the circadian system. Though it remains poorly understood, a growing body of evidence has shown that posttranscriptional regulation controls the expression of both circadian oscillator and output gene transcripts at a number of different steps. This regulation is crucial for driving and maintaining robust circadian rhythms. Here we review recent advances in circadian rhythm research at the RNA level.

Post-transcriptional controls - adding a new layer of regulation to clock gene expression

Living organisms undergo biochemical, physiological and behavioral cycles with periods ranging from seconds to years. Cycles with intermediate periods are governed by endogenous clocks that depend on oscillating gene expression. Here we illustrate the modalities and specific functions of post-transcriptional control of gene expression (exerted on pre-mRNAs and mRNAs) in biological clocks through two examples: the circadian clock and the vertebrate somite segmentation clock, an embryonic clock with a period far below a day. We conclude that both constitutive and cyclic post-transcriptional controls underpin clock function.

Lifetimes of mRNAs for Clock‐Regulated Proteins in a Dinoflagellate

Both pulsed and continuous applications of the RNA polymerase II inhibitor thiolutin cause a dramatic but reversible loss of bioluminescence and its overt rhythmicity in cells of the dinoflagellate Lingulodinium polyedrum (formerly Gonyaulax polyedra). Such cells remain alive, and the rhythm resumes after an interval, the length of which depends on the concentration of thiolutin used. The period and phase of the resumed rhythm were not systematically altered following such treatments, and the effects were not different at different circadian phases. For three different genes, luciferin binding protein (lbp), luciferase (lcf), and glyceraldehyde-3-phosphate dehydrogenase (gapdh), which are circadian-regulated at the level of translation, the amounts of their mRNAs were determined by Northern blots for times up to 12.5 h following the addition of 1.5 microM thiolutin. Consistent with previous reports that their abundances do not change with circadian time, their levels remained high for several hours after thiolutin addition, but then did diminish.

At least four distinct circadian regulatory mechanisms are required for all phases of rhythms in mRNA amount

Since the advent of techniques to investigate gene expression on a large scale, numerous circadian rhythms in mRNA amount have been reported. These rhythms generally differ in amplitude and phase. The authors investigated how far a parameter not regulated by the circadian clock can influence the phase of a rhythm in RNA amount arising from a circadian rhythm of transcription. Using a discrete-time approach, they modeled a sinusoidal rhythm in transcription with various constant exponential RNA decay rates. They found that the slower the RNA degradation, the later the phase of the RNA amount rhythm compared with the phase of the transcriptional rhythm. However, they also found that the phase of the RNA amount rhythm is limited to a timeframe spanning the first quarter of the period following the phase of the transcriptional rhythm. This finding is independent of the amplitude and vertical shift of the transcriptional rhythm or even of the way constant RNA degradation is modeled. The authors confirmed their results with a continuous-time model, which allowed them to derive a simple formula relating the phase of the RNA amount rhythm solely to the phase and period of its sinusoidal transcriptional rhythm and its constant RNA half-life. This simple formula even holds true for the best sinusoidal approximations of a nonsinusoidal rhythm of transcription and RNA amount. When expanding the model to include additional events with constant exponential kinetics, such as RNA processing, they found that each event expands the phase limit by another quarter of the period when it occurs in sequence but not when it occurs as a competing process. However, the limit expansion comes at the price of minuscule amplitudes. When using a discrete-time approach to model constant rates of transcription with a sinusoidal RNA half-life, the authors found that the phase of the RNA amount rhythm is unaffected by changes in the constant rate of transcription. In summary, their data show that at least 4 distinct circadian regulatory mechanisms are required to allow for all phases in rhythms of RNA amount, one for each quarter of the period.

The Gonyaulax clock at 50: translational control of circadian expression

The unicellular circadian clock of Gonyaulax polyedra (now renamed Lingulodinium polyedrum) has provided important insights concerning circadian rhythmicity. Many, perhaps most, of its key systems are circadian-controlled, ranging from bioluminescence and photosynthesis to motility, cell division, and the synthesis of many proteins, favoring the "master clock" concept. But different rhythms may have different free-running periods and different phase angles under different T cycles, observations not easily accommodated in a single oscillator model. Gonyaulax has a feature significantly different from that of other known systems, namely, that clock control of protein synthesis occurs at the translational level. With one mRNA, this involves a protein binding to a 22-nucleotide region in the 3'-untranslated region (3'UTR), but no similar regions have been found in other mRNAs. Pulses of protein synthesis inhibitors cause phase shifts, whereas inhibitors of protein phosphorylation administered chronically cause period changes. In Gonyaulax and other systems, low temperature results in arrhythmicity. A return to a permissive temperature results in a reinitiation of the rhythm, with the phase established by the time of increase, similar to the effect of bright light. Evidence for cellular communication via substance(s) in the medium has been obtained.

Phytophthora infestans-triggered response of growth- and defense-related genes in potato cultivars with different levels of resistance under the influence of nitrogen availability

The effects of high and low N concentrations on the Solanum tuberosum-Phytophthora infestans interaction were studied in the potato cultivars Bettina, New York 121, Indira and Arkula, which exhibited different levels of resistance. Aboveground biomass and Chl and N content were significantly higher in all cultivars grown in higher N environments, while C:N ratios were lower, confirming successful application of N. High availability of N significantly increased susceptibility of three of the four potato cultivars, and amounts of pathogen within the infected leaflets determined in a quantitative real-time reverse transcriptase-polymerase chain reaction reflected this. Differential gene expression of P. infestans-induced and -repressed genes derived from three subtracted cDNA libraries at 0, 24, 48 and 72 h post-inoculation was studied in parallel. P. infestans attack led to an induction of defense-related and at the same time repression of growth-related potato genes mainly encoding photosynthetic genes. High N supply led to higher transcript abundance of photosynthetic genes such as Chl a/b-binding protein and ribulose bisphosphate carboxylase. N-dependent suppression of defense-related compounds in absence of the pathogen was not observed. Better N nutrition appeared to allow the plants to invest more resources in defense reactions.

Reassessing the role of a 3′-UTR-binding translational inhibitor in regulation of circadian bioluminescence rhythm in the dinoflagellate Gonyaulax

The nightly bioluminescence of the dinoflagellateGonyaulaxis a circadian rhythm caused by the presence in cells of specialized bioluminescent organelles, termed scintillons, containing the reaction catalyst luciferase, the substrate luciferin and a luciferin-binding protein (LBP). LBP levels increase at the start of the night phase because of increased protein synthesis ratesin vivo, and this regulation has been ascribed to circadian binding of an inhibitory protein factor binding to the 3′ untranslated region (UTR) oflbpmRNA at times when LBP is not normally synthesized. To purify and characterize the binding factor, the electrophoretic mobility shift assays and UV crosslinking experiments used to first characterize the factor were repeated. However, neither these protocols nor binding to biotinylated RNA probes confirmed the presence of a specific circadian RNA-binding protein. Furthermore, neither RNA probe screening of a cDNA library expressed in bacteria nor three-hybrid assays in yeast were successful in isolating a cDNA encoding a protein able to bind specifically to thelbp3′UTR. Taken together, these results suggest that alternative mechanisms for regulatinglbptranslation should now be examined.

Interplay of circadian clocks and metabolic rhythms

This review examines the connections between circadian and metabolic rhythms. Examples from a wide variety of well-studied organisms are used to illustrate some of the genetic and molecular pathways linking circadian timekeeping to metabolism. The principles underlying biological timekeeping by intrinsic circadian clocks are discussed briefly. Genetic and molecular studies have unambiguously identified the importance of gene expression feedback circuits to the generation of overt circadian rhythms. This is illustrated particularly well by the results of genome-wide expression studies, which have uncovered hundreds of clock-controlled genes in cyanobacteria, fungi, plants, and animals. The potential connections between circadian oscillations in gene expression and circadian oscillations in metabolic activity are a major focus of this review.

LARK activates posttranscriptional expression of an essential mammalian clock protein, PERIOD1

The mammalian molecular clock is composed of feedback loops to keep circadian 24-h rhythms. Although much focus has been on transcriptional regulation, it is clear that posttranscriptional controls also play important roles in molecular circadian clocks. In this study, we found that mouse LARK (mLARK), an RNA binding protein, activates the posttranscriptional expression of the mouse Period1 (mPer1) mRNA. A strong circadian cycling of the mLARK protein is observed in the suprachiasmatic nuclei with a phase similar to that of mPER1, although the level of the Lark transcripts are not rhythmic. We demonstrate that LARK causes increased mPER1 protein levels, most likely through translational regulation and that the LARK1 protein binds directly to a cis element in the 3' UTR of the mPer1 mRNA. Alterations of mLark expression in cycling cells caused significant changes in circadian period, with mLark knockdown by siRNA resulting in a shorter circadian period, and the overexpression of mLARK1 resulting in a lengthened period. These data indicate that mLARKs are novel posttranscriptional regulators of mammalian circadian clocks.

Posttranscriptional regulation of mammalian circadian clock output

Circadian clocks are present in many different cell types/tissues and control many aspects of physiology. This broad control is exerted, at least in part, by the circadian regulation of many genes, resulting in rhythmic expression patterns of 5-10% of the mRNAs in a given tissue. Although transcriptional regulation is certainly involved in this process, it is becoming clear that posttranscriptional mechanisms also have important roles in producing the appropriate rhythmic expression profiles. In this chapter, we review the available data about posttranscriptional regulation of circadian gene expression and highlight the potential role of Nocturnin (Noc) in such processes. NOC is a deadenylase-a ribonuclease that specifically removes poly(A) tails from mRNAs-that is expressed widely in the mouse with high-amplitude rhythmicity. Deadenylation affects the stability and translational properties of mRNAs. Mice lacking the Noc gene have metabolic defects including a resistance to diet-induced obesity, decreased fat storage, changes in lipid-related gene expression profiles in the liver, and altered glucose and insulin sensitivities. These findings suggest that NOC has a pivotal role downstream from the circadian clockwork in the post-transcriptional regulation genes involved in the circadian control of metabolism.

A heteromeric RNA-binding protein is involved in maintaining acrophase and period of the circadian clock

The RNA-binding protein CHLAMY1 from the green alga Chlamydomonas reinhardtii consists of two subunits. One (named C1) contains three lysine homology motifs and the other (named C3) has three RNA recognition motifs. CHLAMY1 binds specifically to uridine-guanine-repeat sequences and its circadian-binding activity is controlled at the posttranslational level, presumably by time-dependent formation of protein complexes consisting of C1 and C3 or C1 alone. Here we have characterized the role of the two subunits within the circadian system by measurements of a circadian rhythm of phototaxis in strains where C1 or C3 are either up- or down-regulated. Further, we have measured the rhythm of nitrite reductase activity in strains with reduced levels of C1 or C3. In case of changes in the C3 level (both increases and decreases), the acrophase of the phototaxis rhythm and of the nitrite reductase rhythm (C3 decrease) was shifted by several hours from subjective day (maximum in wild-type cells) back towards the night. In contrast, both silencing and overexpression of C1 resulted in disturbed circadian rhythms and arrhythmicity. Interestingly, the expression of C1 is interconnected with that of C3. Our data suggest that CHLAMY1 is involved in the control of the phase angle and period of the circadian clock in C. reinhardtii.

Circadian Orchestration of the Hepatic Proteome

Circadian rhythms are essential to health. Their disruption is associated with metabolic diseases in experimental animals and man. Local metabolic rhythms represent an output of tissue-based circadian clocks. Attempts to define how local metabolism is temporally coordinated have focused on gene expression by defining extensive and divergent "circadian transcriptomes" involving 5%-10% of genes assayed. These analyses are inevitably incomplete, not least because metabolic coordination depends ultimately upon temporal regulation of proteins. We therefore conducted a systematic analysis of a mammalian "circadian proteome." Our analysis revealed that up to 20% of soluble proteins assayed in mouse liver are subject to circadian control. Many of these circadian proteins are novel and cluster into discrete phase groups so that the liver's enzymatic profile contrasts dramatically between day and night. Unexpectedly, almost half of the cycling proteins lack a corresponding cycling transcript, as determined by quantitative PCR, microarray, or both and revealing for the first time the extent of posttranscriptional mechanisms as circadian control points. The circadian proteome includes rate-limiting factors in vital pathways, including urea formation and sugar metabolism. These findings provide a new perspective on the extensive contribution of circadian programming to hepatic physiology.

Circadian rhythm of a TCA cycle enzyme is apparently regulated at the translational level in the dinoflagellate Lingulodinium polyedrum

Previously, the authors have reported that intracellular amounts of several metabolic-related enzymes from the photosynthetic dinoflagellate Lingulodinium polyedrum(formerly Gonyaulax polyedra) showed a daily rhythm under a 12:12 h LD cycle. This led the authors to hypothesize that a circadian clock controls metabolism, including the tricarboxylic acid (TCA) cycle. In this study, the authors investigated daily changes in the levels of mRNA, protein, and enzyme activity of several metabolic enzymes during 12:12 h LD, 8:16 h LD, and constant light conditions. The NADP-dependent isocitrate dehydrogenase (NADPICDH) in the TCA cycle exhibited circadian changes of protein abundance and enzyme activity under all conditions, whereas its mRNA level remained constant throughout the cycle. These results indicate that the rhythm of NADPICDH is regulated by a circadian control of protein synthesis or modification rather than by message levels and suggest that the TCA cycle may be controlled by the circadian clock system.

The circadian RNA-binding protein CHLAMY 1 represents a novel type heteromer of RNA recognition motif and lysine homology domain-containing subunits

The RNA-binding protein CHLAMY 1 from Chlamydomonas reinhardtii binds specifically to UG> or =7 repeat sequences situated in the 3' untranslated regions of several mRNAs. Its binding activity is controlled by the circadian clock. The biochemical purification and characterization of CHLAMY 1 revealed a novel type of RNA-binding protein. It includes two different subunits (named C1 and C3), whose interaction appears necessary for RNA binding. One of them (C3) belongs to the proteins of the CELF (CUG-BP-ETR-3-like factors) family and thus bears three RNA recognition motif domains. The other is composed of three lysine homology domains and a protein-protein interaction domain (WW). The subunits C1 and C3 have theoretical molecular masses of 45 and 52 kDa, respectively, and are present in nearly equal amounts during the circadian cycle. At the beginning of the subjective night, both can be found in protein complexes of 100 to 160 kDa. However, during subjective day when binding activity of CHLAMY 1 is low, the C1 subunit in addition is present in a high-molecular-mass protein complex of more than 680 kDa. These data indicate posttranslational control of the circadian binding activity of CHLAMY 1. Notably, the C3 subunit shows significant homology to the rat CUG-binding protein 2. Anti-C3 antibodies can recognize the rat homologue, which can also be found in a protein complex in this vertebrate.

Comparative analysis of Phytophthora infestans induced gene expression in potato cultivars with different levels of resistance

Differential gene expression was analyzed after infection with Phytophthora infestans in six potato cultivars with different levels of resistance to late blight. To verify the infection of the potato leaflets, the amount of phytopathogen mRNA within the plant material was quantified by real-time quantitative PCR. The expression of 182 genes selected from two subtracted cDNA libraries was studied with cDNA array hybridization using RNA from non-infected and infected potato leaflets. Gene up- and down-regulation were clearly detectable in all cultivars 72 h post inoculation. Gene expression patterns in susceptible cultivars differed from those in potato varieties with a higher level of resistance. In general, a stronger gene induction was observed in the susceptible cultivars compared to the moderately to highly resistant potato varieties. Five genes with the highest homology to stress and/or defence-related genes were induced specifically in the susceptible cultivars. Four genes responded to pathogen attack independently of the level of resistance of the cultivar used, and three genes were repressed in infected tissue of most cultivars. Even in the absence of P. infestans infection, six genes showed higher expression levels in the somewhat resistant cultivars Bettina and Matilda. Possible reasons for the different levels of gene expression are discussed.

Circadian control of messenger RNA stability. Association with a sequence-specific messenger RNA decay pathway

Transcriptional and posttranscriptional regulation are well-established mechanisms for circadian gene expression. Among the latter, differential messenger RNA (mRNA) stability has been hypothesized to control gene expression in response to the clock. However, direct proof that the rate of mRNA turnover can be regulated by the clock is lacking. Previous microarray expression data for unstable mRNAs in Arabidopsis (Arabidopsis thaliana) revealed that mRNA instability is associated with a group of genes controlled by the circadian clock. Here, we show that CCR-LIKE (CCL) and SENESCENCE ASSOCIATED GENE 1 transcripts are differentially regulated at the level of mRNA stability at different times of day. In addition, the changes in CCL mRNA stability continue under free-running conditions, indicating that it is controlled by the Arabidopsis circadian clock. Furthermore, we show that these mRNAs are targets of the mRNA degradation pathway mediated by the downstream (DST) instability determinant. Disruption of the DST-mediated decay pathway in the dst1 mutant leads to aberrant circadian mRNA oscillations that correlate with alterations of the half-life of CCL mRNA relative to parental plants in the morning and afternoon. That this is due to an effect on the circadian control is evidenced by mRNA decay experiments carried out in continuous light. Finally, we show that the defects exhibited by dst mutants are reflected by an impact on circadian regulation at the whole plant level. Together, these results demonstrate that regulation of mRNA stability is important for clock-controlled expression of specific genes in Arabidopsis. Moreover, these data uncover a connection between circadian rhythms and a sequence-specific mRNA decay pathway.

Brefeldin A Inhibits Circadian Remodeling of Chloroplast Structure in the Dinoflagellate Gonyaulax

Circadian increases in the rate of carbon fixation in the dinoflagellate Gonyaulax are correlated with extensive plastid remodeling. One marker for this remodeling is mobilization of ribulose bisphosphate carboxylase/oxygenase (Rubisco) from the plastid periphery to plastid regions nearer the cell center called pyrenoids. Nuclear-encoded proteins such as Rubisco transit through the Golgi in dinoflagellates; hence, we blocked protein import into the plastids using Brefeldin A (BFA) to explore the mechanism for plastid remodeling. We find that pyrenoid formation normally occurs concurrently with increased Rubisco synthesis rates in vivo, and when BFA is given prior to the onset of Rubisco synthesis, pyrenoid formation is partially or completely inhibited by 0.1 or 0.3 microg/mL BFA, respectively. Rubisco synthesis itself is not affected, and BFA-treated cells accumulate Rubisco in novel structures we term BFA bodies. Interestingly, when given just after the onset of Rubisco synthesis, BFA delays but does not block Rubisco mobilization, suggesting that a timing signal for plastid remodeling is delivered to the organelles at the same time as newly synthesized Rubisco. BFA also inhibits the circadian increases in carbon fixation rates, supporting the hypothesis that the biochemical basis for this circadian rhythm may be Rubisco distribution within the plastid.

Identification of novel clock-controlled genes by cDNA macroarray analysis in Chlamydomonas reinhardtii

Circadian rhythms are self-sustaining oscillations whose period length under constant conditions is about 24 h. Circadian rhythms are widespread and involve functions as diverse as human sleep-wake cycles and cyanobacterial nitrogen fixation. In spite of a long research history, knowledge about clock-controlled genes is limited in Chlamydomonas reinhardtii. Using a cDNA macroarray containing 10 368 nuclear-encoded genes, we examined global circadian regulation of transcription in Chlamydomonas. We identified 269 candidates for circadianly expressed gene. Northern blot analysis confirmed reproducible and sustainable rhythmicity for 12 genes. Most genes exhibited peak expression at the transition point between day and night. One hundred and eighteen genes were assigned predicted annotations. The functions of the cycling genes were diverse and included photosynthesis, respiration, cellular structure, and various metabolic pathways. Surprisingly, 18 genes encoding chloroplast ribosomal proteins showed a coordinated circadian pattern of expression and peaked just at the beginning of subjective day. The co-regulation of genes bearing a similar function was also observed in genes involved in cellular structure. They peaked at the end of the subjective night, which is when the regeneration of cell walls and flagella in daughter cells occurs. Expression of the chlamyopsin gene, which encodes an opsin-type photoreceptor, also exhibited circadian rhythm.

Analysis of differentially expressed genes in a susceptible and moderately resistant potato cultivar upon Phytophthora infestans infection

SUMMARY To gain deeper understanding of the host-pathogen interaction in the system potato-Phytophthora infestans, subtractive hybridization in combination with cDNA array hybridization was used. Leaflets of a moderately resistant and a susceptible potato cultivar were inoculated with P. infestans. The infection of the potato leaves was quantified by real-time quantitative PCR. Using infected and control tissue, two cDNA libraries highly enriched for P. infestans-induced genes were prepared. Within 531 clones randomly picked and sequenced from the libraries, 285 unigenes were found, from which 182 clones were selected for further analysis by cDNA array hybridization. Sixteen hours post inoculation genes were not induced significantly, whereas 72 h post inoculation induction of gene expression was clearly detectable. In both cultivars, 143 genes were induced moderately (>/= two-fold), and 35 of the selected genes appeared to be strongly induced (>/= seven-fold). Among these clones were mainly genes associated with stress and/or defence mechanisms. The strongest gene induction was found in 4-week-old susceptible plants. In the moderately resistant cultivar, transcripts of a number of genes accumulate with plant age; as a result, induction of gene expression upon infection was less pronounced. Down-regulation of three genes was observed in both cultivars, upon infection. Transcript levels of these three genes increased in uninfected plants within 4 weeks of growth. Other differences in defence responses of the two cultivars could be determined and their effects are discussed.

The function of circadian RNA-binding proteins and their cis-acting elements in microalgae

An endogenous clock regulates the temporal expression of genes/mRNAs that are involved in the circadian output pathway. In the bioluminescent dinoflagellate Gonyaulax polyedra circadian expression of the luciferin-binding protein (LBP) is controlled at the translational level. Thereby, a clock-controlled RNA-binding protein, called circadian controlled translational regulator (CCTR), interacts specifically with an UG-repeat, which is situated in the lbp 3' UTR. Its binding activity correlates negatively with the amount of LBP during a circadian cycle. In the green alga Chlamydomonas reinhardtii, a clock-controlled RNA-binding protein (CHLAMY 1) was identified, which represents an analog of the CCTR from the phylogenetically diverse alga G. polyedra. CHLAMY 1 binds specifically to the 3' UTRs of several mRNAs and recognizes them all via a common cis-acting element, composed of at least seven UG-repeats. The binding strength of CHLAMY 1 is strongest to mRNAs, whose products are key components of nitrogen metabolism resulting in arginine biosynthesis as well as of CO2 metabolism. Since temporal activities of processes involved in nitrogen metabolism have an opposite phase than CHLAMY 1 binding activity, the protein might repress the translation of the cognate mRNAs.

The circadian clock of the unicellular eukaryotic model organism Chlamydomonas reinhardtii

The green unicellular alga Chlamydomonas reinhardtii, also called 'green yeast', emerged in the past years as a model organism for specific scientific questions such as chloroplast biogenesis and function, the composition of the flagella including its basal apparatus, or the mechanism of the circadian clock. Sequencing of its chloroplast and mitochondrial genomes have already been completed and a first draft of its nuclear genome has also been released recently. In C. reinhardtii several circadian rhythms are physiologically well characterized, and one of them has even been shown to operate in outer space. Circadian expression patterns of nuclear and plastid genes have been studied. The mode of regulation of these genes occurs at the transcriptional level, although there is also evidence for posttranscriptional control. A clock-controlled, phylogenetically conserved RNA-binding protein was characterized in this alga, which interacts with several mRNAs that all contain a common cis-acting motif. Its function within the circadian system is currently under investigation. This review summarizes the current state of the knowledge about the circadian system in C. reinhardtii and points out its potential for future studies.

Light-regulated translation mediates gated induction of the Arabidopsis clock protein LHY

The transcription factor LHY and the related protein CCA1 perform overlapping functions in a regulatory feedback loop that is closely associated with the circadian oscillator of Arabidopsis: Overexpression of LHY abolished function of the circadian clock in constant light, but rhythmic expression of several circadian clock-regulated transcripts was observed under light- dark cycles. These oscillations correlated with high amplitude changes in LHY protein levels, caused by light-induced translation of the LHY transcript. Increases in LHY protein levels were also observed in light-grown wild-type plants, when light signals coincided with the circadian-regulated peak of LHY transcription at dawn. Unexpectedly, translational induction coincided with acute downregulation of LHY transcript levels. We suggest that the simultaneous translational induction and transcriptional repression of LHY expression play a role to narrow the peak of LHY protein synthesis at dawn and increase the robustness and accuracy of circadian oscillations. Strong phase shifting responses to light signals were observed in plants lacking function of LHY, CCA1 or both, suggesting that light-regulated expression of these proteins does not mediate entrainment of the clock to light-dark cycles.

Structural and functional analysis of 3' untranslated region of mouse Period1 mRNA

In order to investigate the post-transcriptional regulation of Period1 (Per1), the 3(')-untranslated region (3(')UTR) of mouse Per1 (mPer1) mRNA was characterized. In addition to high similarity between human and mouse Per1 3(')UTRs, AU-rich element and differentiation control element were found in both species. Transient transfection assays using LUC::mPer1 3(')UTR fusion genes revealed that the mPer1 3(')UTR repressed its own expression in a post-transcriptional manner. The region critical for this translational down-regulation was confined to nucleotide positions 322-517. These results suggest that the mPer1 3(')UTR could be involved in the generation of time lag between the transcriptional and translational products of mPer1 in the suprachiasmatic nucleus.

The circadian clock regulated RNA-binding protein AtGRP7 autoregulates its expression by influencing alternative splicing of its own pre-mRNA

The clock-regulated RNA-binding protein AtGRP7 is part of a negative feedback circuit through which the protein influences circadian oscillations of its own transcript. Constitutive overexpression of AtGRP7 in transgenic plants leads to the appearance of a low amount of an alternatively spliced Atgrp7 transcript with a premature stop codon. It is generated by the use of a 5' cryptic splice site in the middle of the intron at the expense of the fully spliced mRNA, indicating a role for AtGRP7 in splice site selection. Accelerated decay of this transcript accounts for its low steady state abundance. This implicates a mechanism for the AtGRP7 feedback loop: Atgrp7 expression is downregulated, as AtGRP7 protein accumulates over the circadian cycle, partly by the generation of an alternate transcript that due to its instability does not accumulate to high levels and does not produce a functional protein. Recombinant AtGRP7 protein specifically interacts with the 3' untranslated region and the intron of its transcript, suggesting that the shift in splice site selection and downregulation involves binding of AtGRP7 to its pre-mRNA. AtGRP7 also influences the choice of splice sites in the Atgrp8 transcript encoding a related RNA-binding protein, favoring the production of an alternatively spliced, unstable Atgrp8 transcript. This conservation points to the importance of this regulatory mechanism to control the level of the clock-regulated glycine-rich RNA-binding proteins and shows how AtGRP7 can control abundance of target transcripts.

Transcript levels of the eukaryotic translation initiation factor 5A gene peak at early G(1) phase of the cell cycle in the dinoflagellate Crypthecodinium cohnii

A cDNA encoding a eukaryotic translation initiation factor 5A (eIF-5A) homolog in heterotrophic dinoflagellate Crypthecodinium cohnii (CceIF-5A) was isolated through random sequencing of a cDNA library. The predicted amino acid sequence possesses the 12 strictly conserved amino acids around lysine 52 (equivalent to lysine 50 or 51 in other eukaryotes). A single 1.2-kb band was detected in Northern blot analysis. In synchronized C. cohnii cells, the transcript level peaked at early G(1) and decreased dramatically on the entry to S phase. Although this has not been previously reported, studies of budding yeast (Saccharomyces cerevisiae) and certain mammalian cell types suggest a role for eIF-5A in the G(1)/S transition of the eukaryotic cell cycle. Phylogenetic trees constructed with 26 other published eIF-5A sequences suggest that CceIF-5A, while falling within the eukaryotic branches, forms a lineage separate from those of the plants, animals, and archaebacteria. The posttranslational modification of eIF-5A by a transfer of a 4-aminobutyl moiety from spermidine to conserved lysine 50 or 51, forming amino acid hypusine, is the only demonstrated specific function of polyamines in cell proliferation. It has been suggested that polyamines stimulate population growth of bloom-forming dinoflagellates in the sea. We demonstrate here putrescine-stimulated cell proliferation. Furthermore, ornithine decarboxylase inhibitor D-difluoromethylornithine and the specific hypusination inhibitor N-guanyl-1,7-diaminoheptane exhibited inhibitory effects in two species of dinoflagellates. The possible links of polyamines and saxitoxin synthesis to the arginine cycle are also discussed.

Molecular bases of circadian rhythms

Circadian rhythms are found in most eukaryotes and some prokaryotes. The mechanism by which organisms maintain these roughly 24-h rhythms in the absence of environmental stimuli has long been a mystery and has recently been the subject of intense research. In the past few years, we have seen explosive progress in the understanding of the molecular basis of circadian rhythms in model systems ranging from cyanobacteria to mammals. This review attempts to outline these primarily genetic and biochemical findings and encompasses work done in cyanobacteria, Neurospora, higher plants, Drosophila, and rodents. Although actual clock components do not seem to be conserved between kingdoms, central clock mechanisms are conserved. Somewhat paradoxically, clock components that are conserved between species can be used in diverse ways. The different uses of common components may reflect the important role that the circadian clock plays in adaptation of species to particular environmental niches.

RNA-binding proteins and circadian rhythms in Arabidopsis thaliana

An Arabidopsis transcript preferentially expressed at the end of the daily light period codes for the RNA-binding protein AtGRP7. A reverse genetic approach in Arabidopsis thaliana has revealed its role in the generation of circadian rhythmicity: AtGRP7 is part of a negative feedback loop through which it influences the oscillations of its own transcript. Biochemical and genetic experiments indicate a mechanism for this autoregulatory circuit: Atgrp7 gene transcription is rhythmically activated by the circadian clock during the day. The AtGPR7 protein accumulates with a certain delay and represses further accumulation of its transcript, presumably at the post-transcriptional level. In this respect, the AtGRP7 feedback loop differs from known circadian oscillators in the fruitfly Drosophila and mammals based on oscillating clock proteins that repress transcription of their own genes with a 24 h rhythm. It is proposed that the AtGRP7 feedback loop may act within an output pathway from the Arabidopsis clock.