Cell cycle oscillators. Temperature compensation of the circadian rhythm of cell division in Euglena

Circadian oscillations in Trichoderma atroviride and the role of core clock components in secondary metabolism, development, and mycoparasitism against the phytopathogen Botrytis cinerea

Circadian clocks are important for an individual’s fitness, and recent studies have underlined their role in the outcome of biological interactions. However, the relevance of circadian clocks in fungal–fungal interactions remains largely unexplored. We sought to characterize a functional clock in the biocontrol agent Trichoderma atroviride to assess its importance in the mycoparasitic interaction against the phytopathogen Botrytis cinerea. Thus, we confirmed the existence of circadian rhythms in T. atroviride, which are temperature-compensated and modulated by environmental cues such as light and temperature. Nevertheless, the presence of such molecular rhythms appears to be highly dependent on the nutritional composition of the media. Complementation of a clock null (Δfrq) Neurospora crassa strain with the T. atroviride-negative clock component (tafrq) restored core clock function, with the same period observed in the latter fungus, confirming the role of tafrq as a bona fide core clock component. Confrontation assays between wild-type and clock mutant strains of T. atroviride and B. cinerea, in constant light or darkness, revealed an inhibitory effect of light on T. atroviride’s mycoparasitic capabilities. Interestingly, when confrontation assays were performed under light/dark cycles, T. atroviride’s overgrowth capacity was enhanced when inoculations were at dawn compared to dusk. Deleting the core clock-negative element FRQ in B. cinerea, but not in T. atroviride, was vital for the daily differential phenotype, suggesting that the B. cinerea clock has a more significant influence on the result of this interaction. Additionally, we observed that T. atroviride clock components largely modulate development and secondary metabolism in this fungus, including the rhythmic production of distinct volatile organic compounds (VOCs). Thus, this study provides evidence on how clock components impact diverse aspects of T. atroviride lifestyle and how daily changes modulate fungal interactions and dynamics.

Systematic Studies of the Circadian Clock Genes Impact on Temperature Compensation and Cell Proliferation Using CRISPR Tools

Simple Summary

One of the major characteristics of the circadian clock is temperature compensation, and previous studies suggested a single clock gene may determine the temperature compensation. In this study, we report the first full collection of clock gene knockout cell lines using CRISPR/Cas9 tools. Our full collections indicate that the temperature compensation is a complex gene regulation system instead of being regulated by any single gene. Besides, we systematically compared the proliferation rates and circadian periods using our full collections, and we found that the cell growth rate is not dependent on the circadian period. Therefore, complex interaction between clock genes and their protein products may underlie the mechanism of temperature compensation, which needs further investigations.

Abstract

Mammalian circadian genes are capable of producing a self-sustained, autonomous oscillation whose period is around 24 h. One of the major characteristics of the circadian clock is temperature compensation. However, the mechanism underlying temperature compensation remains elusive. Previous studies indicate that a single clock gene may determine the temperature compensation in several model organisms. In order to understand the influence of each individual clock gene on the temperature compensation, twenty-three well-known mammalian clock genes plus Timeless and Myc genes were knocked out individually, using a powerful gene-editing tool, CRISPR/Cas9. First, Bmal1, Cry1, and Cry2 were knocked out as examples to verify that deleting genes by CRISPR is effective and precise. Cell lines targeting twenty-two genes were successfully edited in mouse fibroblast NIH3T3 cells, and off-target analysis indicated these genes were correctly knocked out. Through measuring the luciferase reporters, the circadian periods of each cell line were recorded under two different temperatures, 32.5 °C and 37 °C. The temperature compensation coefficient Q₁₀ was subsequently calculated for each cell line. Estimations of the Q₁₀ of these cell lines showed that none of the individual cell lines can adversely affect the temperature compensation. Cells with a longer period at lower temperature tend to have a shorter period at higher temperature, while cells with a shorter period at lower temperature tend to be longer at higher temperature. Thus, the temperature compensation is a fundamental property to keep cellular homeostasis. We further conclude that the temperature compensation is a complex gene regulation system instead of being regulated by any single gene. We also estimated the proliferation rates of these cell lines. After systematically comparing the proliferation rates and circadian periods, we found that the cell growth rate is not dependent on the circadian period.

Nontransgenic Marker-Free Gene Disruption by an Episomal CRISPR System in the Oleaginous Microalga, Nannochloropsis oceanica CCMP1779

Utilization of microalgae has been hampered by limited tools for creating loss-of-function mutants. Furthermore, modified strains for deployment into the field must be free of antibiotic resistance genes and face fewer regulatory hurdles if they are transgene free. The oleaginous microalga, Nannochloropsis oceanica CCMP1779, is an emerging model for microalgal lipid metabolism. We present a one-vector episomal CRISPR/Cas9 system for N. oceanica that enables the generation of marker-free mutant lines. The CEN/ARS6 region from Saccharomyces cerevisiae was included in the vector to facilitate its maintenance as circular extrachromosal DNA. The vector utilizes a bidirectional promoter to produce both Cas9 and a ribozyme flanked sgRNA. This system efficiently generates targeted mutations, and allows the loss of episomal DNA after the removal of selection pressure, resulting in marker-free nontransgenic engineered lines. To test this system, we disrupted the nitrate reductase gene ( NR) and subsequently removed the CRISPR episome to generate nontransgenic marker-free nitrate reductase knockout lines (NR-KO).

Influence of different light-dark cycles on motility and photosynthesis of Euglena gracilis in closed bioreactors

Abstract The unicellular photosynthetic freshwater flagellate Euglena gracilis is a promising candidate as an oxygen producer in biological life-support systems. In this study, the capacity of Euglena gracilis to cope with different light regimes was determined. Cultures of Euglena gracilis in closed bioreactors were exposed to different dark-light cycles (40 W/m(2) light intensity on the surface of the 20 L reactor; cool white fluorescent lamps in combination with a 100 W filament bulb): 1 h-1 h, 2 h-2 h, 4 h-4 h, 6 h-6 h, and 8 h-16 h, respectively. Motility and oxygen development in the reactors were measured constantly. It was found that, during exposure to light-dark cycles of 1 h-1 h, 2 h-2 h, 4 h-4 h, and 6 h-6 h, precision of gravitaxis as well as the number of motile cells increased during the dark phase, while velocity increased in the light phase. Oxygen concentration did not yet reach a plateau phase. During dark-light cycles of 8 h-16 h, fast changes of movement behavior in the cells were detected. The cells showed an initial decrease of graviorientation after onset of light and an increase after the start of the dark period. In the course of the light phase, graviorientation increased, while motility and velocity decreased after some hours of illumination. In all light profiles, Euglena gracilis was able to produce sufficient oxygen in the light phase to maintain the oxygen concentration above zero in the subsequent dark phase.

Circadian-independent cell mitosis in immortalized fibroblasts

Two prominent timekeeping systems, the cell cycle, which controls cell division, and the circadian system, which controls 24-h rhythms of physiology and behavior, are found in nearly all living organisms. A distinct feature of circadian rhythms is that they are temperature-compensated such that the period of the rhythm remains constant (approximately 24 h) at different ambient temperatures. Even though the speed of cell division, or growth rate, is highly temperature-dependent, the cell-mitosis rhythm is temperature-compensated. Twenty-four-hour fluctuations in cell division have also been observed in numerous species, suggesting that the circadian system is regulating the timing of cell division. We tested whether the cell-cycle rhythm was coupled to the circadian system in immortalized rat-1 fibroblasts by monitoring cell-cycle gene promoter-driven luciferase activity. We found that there was no consistent phase relationship between the circadian and cell cycles, and that the cell-cycle rhythm was not temperature-compensated in rat-1 fibroblasts. These data suggest that the circadian system does not regulate the cell-mitosis rhythm in rat-1 fibroblasts. These findings are inconsistent with numerous studies that suggest that cell mitosis is regulated by the circadian system in mammalian tissues in vivo. To account for this discrepancy, we propose two possibilities: (i) There is no direct coupling between the circadian rhythm and cell cycle but the timing of cell mitosis is synchronized with the rhythmic host environment, or (ii) coupling between the circadian rhythm and cell cycle exists in normal cells but it is disconnected in immortalized cells.

Temperature-compensated chemical reactions

Circadian rhythms are daily oscillations in behaviors that persist in constant light/dark conditions with periods close to 24 h. A striking feature of these rhythms is that their periods remain fairly constant over a wide range of physiological temperatures, a feature called temperature compensation. Although circadian rhythms have been associated with periodic oscillations in mRNA and protein levels, the question of how to construct a network of chemical reactions that is temperature compensated remains unanswered. We discuss a general framework for building such a network.

Light Regulates the Cell Cycle in Zebrafish

The timing of cell proliferation is a key factor contributing to the regulation of normal growth. Daily rhythms of cell cycle progression have been documented in a wide range of organisms. However, little is known about how environmental, humoral, and cell-autonomous factors contribute to these rhythms. Here, we demonstrate that light plays a key role in cell cycle regulation in the zebrafish. Exposure of larvae to light-dark (LD) cycles causes a range of different cell types to enter S phase predominantly at the end of the day. When larvae are raised in constant darkness (DD), a low level of arrhythmic S phase is observed. In addition, light-entrained cell cycle rhythms persist for several days after transfer to DD, both observations pointing to the involvement of the circadian clock. We show that the number of LD cycles experienced is essential for establishing this rhythm during larval development. Furthermore, we reveal that the same phenomenon exists in a zebrafish cell line. This represents the first example of a vertebrate cell culture system where circadian rhythms of the cell cycle are observed. Thus, we implicate the cell-autonomous circadian clock in the regulation of the vertebrate cell cycle by light.

Automated biomonitoring using real time movement analysis of Euglena gracilis

An automated biomonitoring system for early warning of pollutants in aquatic environments is described and characterized. The system uses sublethal changes in the movement behavior of the flagellate Euglena gracilis as biological endpoints. The movement is determined by real time image analysis. All parameters describing motility, velocity, orientation, and form of the cells are calculated during measurement, and changes of these parameters are interpreted as effect. By automatic dilution of the water sample, dose-effect relationships can be recorded automatically. A total measurement procedure, including control and sample measurement and filling and rinsing of the system, typically requires 8 min. Measurements with different organic and inorganic toxic compounds were performed and the calculated EC(50) values compared with literature data for the bioluminescence test with Vibrio fischeri. Also, measurements with waste water samples from different industrial plants were performed. The fast response time, the small size, the reliable image analysis system, the calculation of several endpoints, and the automatic measuring procedure are major advantages compared to other biological test systems.

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.

Temperature compensation of the circadian period length--a special case among general homeostatic mechanisms of gene expression?

In Neurospora crassa, as well as in other organisms, the expression of housekeeping genes is transiently suppressed after exposure to higher temperatures (30-45 degrees C); expression is then reactivated and adapts after a few-hours to values closer to the initial rates. Adaptive mechanisms apparently exist in the processes of transcription, RNA processing, and translation and render protein synthesis rates temperature compensated. Heat shock proteins (HSPs) play an important role within these mechanisms ("acquired thermotolerance of protein synthesis"), but their function is as yet not exactly known. Adaptive mechanisms seem also to involve intracellular ion changes after exposure to moderate temperature elevation. The expression of heat shock genes is transiently enhanced after exposure to higher temperatures and also adapts after a few hours. The adaptation mechanism includes inactivation of the heat shock transcription factor (HSF) by means of phosphorylation changes and possibly by binding of a gene product (HSP70)-a mechanism representing a negative feedback control. These examples demonstrate the existence of general adaptive mechanisms at different levels of gene expression that may also be at work in the temperature compensation of clock gene expression. Apart from such adaptation processes, antagonistic reactions within the processes of gene expression and protein modification might be equally enhanced or suppressed by temperature changes, leaving the equilibrium unaffected or balanced (antagonistic balance, see Ruoff et al., this issue of Chronobiology International). This principle is shown to apply to the effect of temperature elevation on total protein synthesis and degradation. It may also apply to other antagonistic processes such as phosphorylation-dephosphorylation or monomer-dimer formation. The circadian clock mechanism is assumed to consist of several processes that can either adapt or produce a balance. Single amino acid changes in a clock protein are assumed to partially upset this adaptation or balance.

Is the cell division cycle gated by a circadian clock? The case of Chlamydomonas reinhardtii

Circadian oscillators are known to regulate the timing of cell division in many organisms. In the case of Chlamydomonas reinhardtii, however, this conclusion has been challenged by several investigators. We have reexamined this issue and find that the division behavior of Chlamydomonas meets all the criteria for circadian rhythmicity: persistence of a cell division rhythm (a) with a period of approximately 24 h under free-running conditions, (b) that is temperature compensated, and (c) which can entrain to light/dark signals. In addition, a mutation that lengthens the circadian period of the phototactic rhythm similarly affects the cell division rhythm. We conclude that a circadian mechanism determines the timing of cell division in Chlamydomonas reinhardtii.

The GTS1 gene, which contains a Gly-Thr repeat, affects the timing of budding and cell size of the yeast Saccharomyces cerevisiae

A gene with an open reading frame encoding a protein of 417 amino acid residues with a Gly-Thr repeat was isolated from the yeast Saccharomyces cerevisiae by using synthetic oligonucleotides encoding three Gly-Thr dimers as probes. The deduced amino acid sequence showed partial homology to the clock-affecting gene, per, of Drosophila melanogaster in the regions including the GT repeat. The function of the gene, named GTS1, was examined by characterizing the phenotypes of transformants with different copy numbers of the GTS1 gene produced either by inactivating the GTS1 gene by gene disruption (TM delta gts1) or by transformation with multicopy plasmid pPER119 (TMpGTS1). They grew at similar rates during the exponential growth phase, but the lag phases were shorter for TM delta gts1 and longer for TMpGTS1 cells than that for the wild type. Analyses of their cell cycle parameters using synchronized cells revealed that the unbudding period changed as a function of gene dosage; that is, the periods of TM delta gts1 and TMpGTS1 were about 20% shorter and longer, respectively, than that of the wild-type. Another significant change in the transformants was detected in the distribution of the cell size. The mean cell volume of the TM delta gts1 cells in the unbudded period (single cells) was 27% smaller than that of single wild-type cells, whereas that of single TMpGTS1 cells was 48% larger. Furthermore, in the temperature-sensitive cdc4 mutant, the GTS1 gene affected the timing of budding at the restrictive temperature. Thus, the GTS1 gene product appears to modulate the timing of budding to obtain an appropriate cell size independent of the DNA replication cycle.

The GTS1 gene, which contains a Gly-Thr repeat, affects the timing of budding and cell size of the yeast Saccharomyces cerevisiae

A gene with an open reading frame encoding a protein of 417 amino acid residues with a Gly-Thr repeat was isolated from the yeast Saccharomyces cerevisiae by using synthetic oligonucleotides encoding three Gly-Thr dimers as probes. The deduced amino acid sequence showed partial homology to the clock-affecting gene, per, of Drosophila melanogaster in the regions including the GT repeat. The function of the gene, named GTS1, was examined by characterizing the phenotypes of transformants with different copy numbers of the GTS1 gene produced either by inactivating the GTS1 gene by gene disruption (TM delta gts1) or by transformation with multicopy plasmid pPER119 (TMpGTS1). They grew at similar rates during the exponential growth phase, but the lag phases were shorter for TM delta gts1 and longer for TMpGTS1 cells than that for the wild type. Analyses of their cell cycle parameters using synchronized cells revealed that the unbudding period changed as a function of gene dosage; that is, the periods of TM delta gts1 and TMpGTS1 were about 20% shorter and longer, respectively, than that of the wild-type. Another significant change in the transformants was detected in the distribution of the cell size. The mean cell volume of the TM delta gts1 cells in the unbudded period (single cells) was 27% smaller than that of single wild-type cells, whereas that of single TMpGTS1 cells was 48% larger. Furthermore, in the temperature-sensitive cdc4 mutant, the GTS1 gene affected the timing of budding at the restrictive temperature. Thus, the GTS1 gene product appears to modulate the timing of budding to obtain an appropriate cell size independent of the DNA replication cycle.

On the molecular mechanism of the circadian clock. The 41,000 M(r) clock protein of Chlorella was identified as 3-phosphoglycerate kinase

A 41,000 M(r) polypeptide of Chlorella exhibits a circadian rhythm in its synthesis and possesses characteristic features of a putative essential clock protein as was proposed by the coupled translation-membrane model. Purification of this polypeptide and a microsequencing analysis yielded a N-terminal sequence of 35 amino acids that showed no homology to known sequences that were thought to be involved in circadian rhythm such as the per gene of Drosophila and the frq gene of Neurospora. However, strong homology was observed to 3-phosphoglycerate kinase (PGK) of different organisms. The highest homology (83%) of this Chlorella sequence was found with the PGK of wheat chloroplast. PGK activity and the 41,000 M(r) polypeptide co-purified through differential centrifugation and gel filtration. These data, and comparison with the physical properties of other known PGK molecules, support the conclusion that the 41,000 M(r) polypeptide of Chlorella, a candidate for a putative essential clock protein, is 3-phosphoglycerate kinase.