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

Regulation of circadian methyl benzoate emission in diurnally and nocturnally emitting plants

Emission of methyl benzoate, one of the most abundant scent compounds of bee-pollinated snapdragon flowers, occurs in a rhythmic manner, with maximum emission during the day, and coincides with the foraging activity of bumblebees. Rhythmic emission of methyl benzoate displays a "free-running" cycle in the absence of environmental cues (in continuous dark or continuous light), indicating the circadian nature of diurnal rhythmicity. Methyl benzoate is produced in upper and lower snapdragon petal lobes by enzymatic methylation of benzoic acid in the reaction catalyzed by S-adenosyl-L-methionine:benzoic acid carboxyl methyltransferase (BAMT). When a detailed time-course analysis of BAMT activity in upper and lower petal lobes during a 48-hr period was performed, high BAMT activity was found at night as well as in continuous darkness, indicating that the BAMT activity is not an oscillation-determining factor. Analysis of the level of benzoic acid during a 24-hr period revealed oscillations in the amount of benzoic acid during the daily light/dark cycle that were retained in continuous darkness. These data clearly show that the total amount of substrate (benzoic acid) in the cell is involved in the regulation of the rhythmic emission of methyl benzoate. Our results also suggest that similar molecular mechanisms are involved in the regulation of methyl benzoate production in diurnally (snapdragon) and nocturnally (tobacco and petunia) emitting plants.

Regulation of circadian methyl benzoate emission in diurnally and nocturnally emitting plants

Emission of methyl benzoate, one of the most abundant scent compounds of bee-pollinated snapdragon flowers, occurs in a rhythmic manner, with maximum emission during the day, and coincides with the foraging activity of bumblebees. Rhythmic emission of methyl benzoate displays a "free-running" cycle in the absence of environmental cues (in continuous dark or continuous light), indicating the circadian nature of diurnal rhythmicity. Methyl benzoate is produced in upper and lower snapdragon petal lobes by enzymatic methylation of benzoic acid in the reaction catalyzed by S-adenosyl-L-methionine:benzoic acid carboxyl methyltransferase (BAMT). When a detailed time-course analysis of BAMT activity in upper and lower petal lobes during a 48-hr period was performed, high BAMT activity was found at night as well as in continuous darkness, indicating that the BAMT activity is not an oscillation-determining factor. Analysis of the level of benzoic acid during a 24-hr period revealed oscillations in the amount of benzoic acid during the daily light/dark cycle that were retained in continuous darkness. These data clearly show that the total amount of substrate (benzoic acid) in the cell is involved in the regulation of the rhythmic emission of methyl benzoate. Our results also suggest that similar molecular mechanisms are involved in the regulation of methyl benzoate production in diurnally (snapdragon) and nocturnally (tobacco and petunia) emitting plants.

Endogenous timekeepers in photosynthetic organisms

Circadian and photoperiodic timing mechanisms were first described in photosynthetic organisms. These organisms depend upon sunlight for their energy, so adaptation to daily and seasonal fluctuations in light must have generated a strong selective pressure. Studies of the endogenous timekeepers of photosynthetic organisms provide evidence for both a fitness advantage and for selective pressures involved in early evolution of circadian clocks. Photoperiodic timing mechanisms in plants appear to use their circadian timers as the ruler by which the day/night length is measured. As in animals, the overall clock system in plants appears to be complex; the system includes multiple oscillators, several input pathways, and a myriad of outputs. Genes have now been isolated from plants that are likely to encode components of the central clockwork or at least that act very close to the central mechanism. Genetic and biochemical analyses of the central clockwork of a photosynthetic organism are most highly advanced in cyanobacteria, where a cluster of clock genes and interacting factors have been characterized.

Different regulatory mechanisms modulate the expression of a dinoflagellate iron-superoxide dismutase

Regulation of antioxidant enzymes is critical to control the levels of reactive oxygen species in cell compartments highly susceptible to oxidative stress. In this work, we studied the regulation of a chloroplastic iron superoxide dismutase (Fe-SOD) from Lingulodinium polyedrum (formerly Gonyaulax polyedra) under different physiological conditions. A cDNA-encoding Fe-SOD was isolated from this dinoflagellate, showing high sequence similarity to cyanobacterial, algal, and plant Fe-SODs. Under standard growth conditions, on a 12:12-h light-dark cycle, Lingulodinium polyedrum Fe-SOD exhibited a daily rhythm of activity and cellular abundance with the maximum occurring during the middle of the light phase. Northern analyses showed that this rhythmicity is not related to changes in Fe-SOD mRNA levels, indicative of translational regulation. By contrast, conditions of metal-induced oxidative stress resulted in higher levels of Fe-SOD transcripts, suggesting that transcriptional control is responsible for increased protein and activity levels. Daily (circadian) and metal-induced up-regulation of Fe-SOD expression in L. polyedrum are thus mediated by different regulatory pathways, allowing biochemically distinct changes appropriate to oxidative challenges.

Identification and characterization of three differentially expressed genes, encoding S-adenosylhomocysteine hydrolase, methionine aminopeptidase, and a histone-like protein, in the toxic dinoflagellate Alexandrium fundyense

Genes showing differential expression related to the early G(1) phase of the cell cycle during synchronized circadian growth of the toxic dinoflagellate Alexandrium fundyense were identified and characterized by differential display (DD). The determination in our previous work that toxin production in Alexandrium is relegated to a narrow time frame in early G(1) led to the hypothesis that transcriptionally up- or downregulated genes during this subphase of the cell cycle might be related to toxin biosynthesis. Three genes, encoding S-adenosylhomocysteine hydrolase (Sahh), methionine aminopeptidase (Map), and a histone-like protein (HAf), were isolated. Sahh was downregulated, while Map and HAf were upregulated, during the early G(1) phase of the cell cycle. Sahh and Map encoded amino acid sequences with about 90 and 70% similarity to those encoded by several eukaryotic and prokaryotic Sahh and Map genes, respectively. The partial Map sequence also contained three cobalt binding motifs characteristic of all Map genes. HAf encoded an amino acid sequence with 60% similarity to those of two histone-like proteins from the dinoflagellate Crypthecodinium cohnii Biecheler. This study documents the potential of applying DD to the identification of genes that are related to physiological processes or cell cycle events in phytoplankton under conditions where small sample volumes represent an experimental constraint. The identification of an additional 21 genes with various cell cycle-related DD patterns also provides evidence for the importance of pretranslational or transcriptional regulation in dinoflagellates, contrary to previous reports suggesting the possibility that translational mechanisms are the primary means of circadian regulation in this group of organisms.

Role of posttranscriptional regulation in circadian clocks: lessons from Drosophila

Incredible progress has been made in the last few years in our understanding of the molecular mechanisms underlying circadian clocks. Many of the recent insights have been gained by the isolation and characterization of novel clock mutants and their associated gene products. As might be expected based on theoretical considerations and earlier studies that indicated the importance of temporally regulated macromolecular synthesis for the manifestation of overt rhythms, daily oscillations in the levels of "clock" RNAs and proteins are a pervasive feature of these timekeeping devices. How are these molecular rhythms generated and synchronized? Recent evidence accumulated from a wide variety of model organisms, ranging from bacteria to mammals, points toward an emerging trend; at the "heart" of circadian oscillators lies a cell autonomous transcriptional feedback loop that is composed of alternatively functioning positive and negative elements. Nonetheless, it is also clear that to bring this transcriptional feedback loop to "life" requires important contributions from posttranscriptional regulatory schemes. For one thing, there must be times in the day when the activities of negative-feedback regulators are separated from the activities of the positive regulators they act on, or else the oscillatory potential of the system will be dissipated, resulting in a collection of molecules at steady state. This review mainly summarizes the role of posttranscriptional regulation in the Drosophila melanogaster time-keeping mechanism. Accumulating evidence from Drosophila and other systems suggests that posttranscriptional regulatory mechanisms increase the dynamic range of circadian transcriptional feedback loops, overlaying them with appropriately timed biochemical constraints that not only engender these loops with precise daily periods of about 24 h, but also with the ability to integrate and respond rapidly to multiple environmental cues such that their phases are aligned optimally to the prevailing external conditions.

Diurnal regulation of a DNA binding protein to the period repeat sequence in the SCN nuclear extract of rat brain

We previously reported the mammalian period repeat mRNA fluctuates during circadian time in the rat suprachiasmatic nucleus (SCN) which is considered to be a clock pacemaker in mammalian brain. Presently we discovered a period repeat sequence (PR) DNA-binding protein in the rat SCN nuclear extract. In the SCN, the binding activity of PR DNA-binding protein to (ACAGGC)3 was most highest during the late day and most lowest during the late night by electro-mobility shift assay (EMSA). In the cortex nuclear extract, the binding of PR DNA-binding protein did not show a significant variation during a day. This is the first report to show the existence of diurnal regulated PR DNA-binding protein in the SCN.

Bioluminescence

Bioluminescence has evolved independently many times; thus the responsible genes are unrelated in bacteria, unicellular algae, coelenterates, beetles, fishes, and others. Chemically, all involve exergonic reactions of molecular oxygen with different substrates (luciferins) and enzymes (luciferases), resulting in photons of visible light (approximately 50 kcal). In addition to the structure of luciferan, several factors determine the color of the emissions, such as the amino acid sequence of the luciferase (as in beetles, for example) or the presence of accessory proteins, notably GFP, discovered in coelenterates and now used as a reporter of gene expression and a cellular marker. The mechanisms used to control the intensity and kinetics of luminescence, often emitted as flashes, also vary. Bioluminescence is credited with the discovery of how some bacteria, luminous or not, sense their density and regulate specific genes by chemical communication, as in the fascinating example of symbiosis between luminous bacteria and squid.

Time at the end of the millennium: the Neurospora clock

In the past two years we have entered the log phase for unraveling the molecular clockworks. Rapid progress in understanding the Neurospora clock has been complemented by a flood of information from diverse systems including cyanobacteria, insects and mice. There are broadly conserved features in transcription/translation based feedback loops. Conservation is also found at the sequence level, from fungi to mammals, in the PAS domains of the heterodimeric partners of the transcription factors that act as the positive components of the feedback cycle. Pivotal PAS proteins from Neurospora, the WCs, provide an evolutionary link connecting the clock in insects and mammals to the fungi and to light-harvesting proteins from bacteria.

The structure and organization of the luciferase gene in the photosynthetic dinoflagellate Gonyaulax polyedra

The structural features of dinoflagellate nuclei are distinct from those of other eukaryotes in several respects, and the mechanisms of DNA replication and transcription are almost completely unknown. In this study we investigated the structure and organization of the gene coding for luciferase (LCF), the enzyme catalyzing the bioluminescent reaction in the dinoflagellate Gonyaulax polyedra. The genomic lcf sequence, including its flanking regions, were completely determined. The transcription initiation site was identified using primer extension and RNase protection assays. Sequence analysis shows that, like the luciferin-binding protein gene (lbp) from G. polyedra, lcf does not contain introns. Analysis of results from genomic Southern blots, inverse PCR, and sequencing revealed that the lcf gene is organized as tandem repeats in the genome. The spacer region between the lcf genes, which very likely contains the promoter elements necessary for transcription initiation, has no TATA box or other known promoter elements or consensus sequences. However, a conserved sequence motif was identified by comparing the two intergene spacer regions of lcf and the peridinin chlorophyll protein gene, pcp; a novel 13 nt sequence, CGTGAACGCAGTG, which might be a dinoflagellate promoter, was found to be present in both.

The mRNA level of the circadian regulated Gonyaulax luciferase remains constant over the cycle

The expression of luciferin-binding protein (LBP) and luciferase (LCF), two proteins that are involved in bioluminescence in Gonyaulax polyedra, is controlled by a cellular circadian clock. In the case of LBP, its temporal expression is reported to be regulated at the translational level, involving both 5' and 3' untranslated regions (UTRs) of lbp mRNA. Here, we show that the amounts of lcf mRNA are constant throughout the day-night cycle, indicating that the circadian expression of LCF is also regulated at the translational level.

Post-transcriptional regulation contributes to Drosophila clock gene mRNA cycling

The period (per) and timeless (tim) genes are intimately involved in the generation and maintenance of Drosophila circadian rhythms. Both genes are expressed in a circadian manner, and the two proteins (PER and TIM) participate in feedback regulation which contributes to the mRNA oscillations. Previous studies indicate that the circadian regulation is in part transcriptional. To investigate quantitative features of per and tim transcription, we analyzed the in vivo transcription rate in fly-head nuclei with a nuclear run-on assay. The results show a robust transcriptional regulation, which is similar but not identical for the two genes. In addition, per mRNA levels are regulated at a post-transcriptional level. This regulatory mode makes a major contribution to the per mRNA oscillations from a previously described per transgenic strain as well as to the mRNA oscillations of a recently identified Drosophila circadianly regulated gene (Crg-1). The data show that circadian mRNA oscillations can take place without evident transcriptional regulation.

Circadian and ultradian clock-controlled rhythms in unicellular microorganisms

The time structure of a biological system is at least as intricate as its spatial structure. Whereas we have detailed information about the latter, our understanding of the former is still rudimentary. As techniques for monitoring intracellular processes continuously in single cells become more refined, it becomes increasingly evident that periodic behaviour abounds in all time domains. Circadian timekeeping dominates in natural environments. Here the free-running period is about 24 h. Circadian rhythms in eukaryotes and prokaryotes allow predictive matching of intracellular states with environmental changes during the daily cycles. Unicellular organisms provide excellent systems for the study of these phenomena, which pervade all higher life forms. Intracellular timekeeping is essential. The presence of a temperature-compensated oscillator provides such a timer. The coupled outputs (epigenetic oscillations) of this ultradian clock constitute a special class of ultradian rhythm. These are undamped and endogenously driven by a device which shows biochemical properties characteristic of transcriptional and translational elements. Energy-yielding processes, protein turnover, motility and the timing of the cell-division cycle processes are all controlled by the ultradian clock. Different periods characterize different species, and this indicates a genetic determinant. Periods range from 30 min to 4 h. Mechanisms of clock control are being elucidated; it is becoming evident that many different control circuits can provide these functions.

Differential translational initiation of lbp mRNA is caused by a 5' upstream open reading frame

Expression of the luciferin-binding protein (LBP) from Gonyaulax polyedra is regulated by the circadian clock at the translational level. Here we report that in vitro translation of lbp mRNA results in the synthesis of two LBP variants of different sizes, which is shown to be due to translational initiation at different in-frame AUG codons on lbp mRNA. Differential initiation is caused by a small open reading frame (ORF, situated in the 5' untranslated region of lbp mRNA), which gives rise to a leaky scanning mechanism. In Gonyaulax, only one of these variants, which is produced by initiation from the first AUG of the lbp ORF, exhibits a circadian rhythm and is far more abundant during night phase.

Conserved circadian elements in phylogenetically diverse algae

Circadian expression of the luciferin-binding protein (LBP) from the dinoflagellate Gonyaulax polyedra is regulated at the translational level. A small interval in the lbp 3'-untranslated region, which contains seven UG-repeats, serves as a cis-acting element to which a trans-acting factor (CCTR) binds in a circadian manner. Its binding activity correlates negatively with the circadian expression of LBP. Here I report the identification of a protein in the green alga Chlamydomonas reinhardtii that represents a CCTR analog. It binds both specifically and under control of the circadian clock to the UG-repeat region. The data show for the first time that circadian cis-elements implicated in translational regulation have been conserved during evolution.

Circadian clock-controlled genes isolated from Neurospora crassa are late night- to early morning-specific

An endogenous circadian biological clock controls the temporal aspects of life in most organisms, including rhythmic control of genes involved in clock output pathways. In the fungus Neurospora crassa, one pathway known to be under control of the clock is asexual spore (conidia) development. To understand more fully the processes that are regulated by the N. crassa circadian clock, systematic screens were carried out for genes that oscillate at the transcriptional level. Time-of-day-specific cDNA libraries were generated and used in differential screens to identify six new clock-controlled genes (ccgs). Transcripts specific for each of the ccgs preferentially accumulate during the late night to early morning, although they vary with respect to steady-state mRNA levels and amplitude of the rhythm. Sequencing of the ends of the new ccg cDNAs revealed that ccg-12 is identical to N. crassa cmt encoding copper metallothionein, providing the suggestion that not all clock-regulated genes in N. crassa are specifically involved in the development of conidia. This was supported by finding that half of the new ccgs, including cmt(ccg-12), are not transcriptionally induced by developmental or light signals. These data suggest a major role for the clock in the regulation of biological processes distinct from development.

Regulation of a specific circadian clock output pathway by lark, a putative RNA-binding protein with repressor activity

An endogenous clock within the Drosophila brain regulates circadian rhythms in adult eclosion and locomotor activity. Although molecular elements of the Drosophila circadian clock have been well characterized, little is known about the clock output pathways that mediate the control of rhythmic events. Previous genetic analysis indicates that a gene known as lark encodes an element of the clock output pathway regulating adult eclosion. We now present evidence that lark encodes a novel member of the RNA recognition motif (RRM) class of RNA-binding proteins. Similar to other members of this protein superfamily, lark contains two copies of a bipartite consensus RNA-binding motif. Unlike any other RRM family member, however, lark protein also contains a distinct class of nucleic acid binding motif, a retroviral-type zinc finger, that is present in the nucleocapsid protein of retroviruses and in several eukaryotic proteins. In contrast to identified clock elements, lark mRNA does not exhibit diurnal fluctuations in abundance in late pupae or in adult heads. Thus rhythmic transcription of the gene does not contribute to the temporal regulation of eclosion by lark protein. Gene dosage experiments show that decreased or increased lark product, respectively, leads to an early or late eclosion phenotype, indicating that the protein negatively regulates the eclosion process. It is postulated that lark is required for the posttranscriptional repression of genes encoding other elements of this clock output pathway.

Distinct cis-acting elements mediate clock, light, and developmental regulation of the Neurospora crassa eas (ccg-2) gene

The Neurospora crassa eas (ccg-2) gene, which encodes a fungal hydrophobin, is transcriptionally regulated by the circadian clock. In addition, eas (ccg-2) is positively regulated by light and transcripts accumulate during asexual development. To sort out the basis of this complex regulation, deletion analyses of the eas (ccg-2) promoter were carried out to localize the cis-acting elements mediating clock, light, and developmental control. The primary sequence determinants of a positive activating clock element (ACE) were found to reside in a 45-bp region, just upstream from the TATA box. Using a novel unregulated promoter/reporter system developed for this study, we show that a 68-bp sequence encompassing the ACE is sufficient to confer clock regulation on the eas (ccg-2) gene. Electrophoretic mobility shift assays using the ACE reveal factors present in N. crassa protein extracts that recognize and bind specifically to DNA containing this element. Separate regions of the eas (ccg-2) promoter involved in light induction and developmental control are identified and shown not to be required for clock-regulated expression of eas (ccg-2). The distinct nature of the ACE validates its use as a tool for the identification of upstream regulatory factors involved in clock control of gene expression.

Diversity of cytoplasmic functions for the 3' untranslated region of eukaryotic transcripts

The 3' untranslated region (3' UTR) can control gene expression by affecting the localization, stability and translation of mRNAs. The recent finding that 3' UTRs can control the decapping rate of mRNAs, in combination with their ability to influence the initiation of translation, suggests that 3' UTRs act through a direct or indirect interaction between the 3' and 5' ends of mRNAs.

Translational control. Awakening dormant mRNAs

The translational control of many maternal mRNAs in oocytes and early embryos relies on changes in poly(A) tail length; the factors controlling poly(A) tail length are being identified in a range of species.