The nitrate reductase circadian system. The central clock dogma contra multiple oscillatory feedback loops

Far-Red Light Coordinates the Diurnal Changes in the Transcripts Related to Nitrate Reduction, Glutathione Metabolism and Antioxidant Enzymes in Barley

Spectral quality, intensity and period of light modify many regulatory and stress signaling pathways in plants. Both nitrate and sulfate assimilations must be synchronized with photosynthesis, which ensures energy and reductants for these pathways. However, photosynthesis is also a source of reactive oxygen species, whose levels are controlled by glutathione and other antioxidants. In this study, we investigated the effect of supplemental far-red (735 nm) and blue (450 nm) lights on the diurnal expression of the genes related to photoreceptors, the circadian clock, nitrate reduction, glutathione metabolism and various antioxidants in barley. The maximum expression of the investigated four photoreceptor and three clock-associated genes during the light period was followed by the peaking of the transcripts of the three redox-responsive transcription factors during the dark phase, while most of the nitrate and sulfate reduction, glutathione metabolism and antioxidant-enzyme-related genes exhibited high expression during light exposure in plants grown in light/dark cycles for two days. These oscillations changed or disappeared in constant white light during the subsequent two days. Supplemental far-red light induced the activation of most of the studied genes, while supplemental blue light did not affect or inhibited them during light/dark cycles. However, in constant light, several genes exhibited greater expression in blue light than in white and far-red lights. Based on a correlation analysis of the gene expression data, we propose a major role of far-red light in the coordinated transcriptional adjustment of nitrate reduction, glutathione metabolism and antioxidant enzymes to changes of the light spectrum.

Are cyclic plant and animal behaviours driven by gravimetric mechanical forces?

The celestial mechanics of the Sun, Moon, and Earth dominate the variations in gravitational force that all matter, live or inert, experiences on Earth. Expressed as gravimetric tides, these variations are pervasive and have forever been part of the physical ecology with which organisms evolved. Here, we first offer a brief review of previously proposed explanations that gravimetric tides constitute a tangible and potent force shaping the rhythmic activities of organisms. Through meta-analysis, we then interrogate data from three study cases and show the close association between the omnipresent gravimetric tides and cyclic activity. As exemplified by free-running cyclic locomotor activity in isopods, reproductive effort in coral, and modulation of growth in seedlings, biological rhythms coincide with temporal patterns of the local gravimetric tide. These data reveal that, in the presumed absence of rhythmic cues such as light and temperature, local gravimetric tide is sufficient to entrain cyclic behaviour. The present evidence thus questions the phenomenological significance of so-called free-run experiments.

The light and dark sides of nitric oxide: multifaceted roles of nitric oxide in plant responses to light

Light drives photosynthesis and informs plants about their surroundings. Regarded as a multifunctional signaling molecule in plants, nitric oxide (NO) has been repeatedly demonstrated to interact with light signaling cascades to control plant growth, development and metabolism. During early plant development, light-triggered NO accumulation counteracts negative regulators of photomorphogenesis and modulates the abundance of, and sensitivity to, plant hormones to promote seed germination and de-etiolation. In photosynthetically active tissues, NO is generated at distinct rates under light or dark conditions and acts at multiple target sites within chloroplasts to regulate photosynthetic reactions. Moreover, changes in NO concentrations in response to light stress promote plant defenses against oxidative stress under high light or ultraviolet-B radiation. Here we review the literature on the interaction of NO with the complicated light and hormonal signaling cascades controlling plant photomorphogenesis and light stress responses, focusing on the recently identified molecular partners and action mechanisms of NO in these events. We also discuss the versatile role of NO in regulating both photosynthesis and light-dependent stomatal movements, two key determinants of plant carbon gain. The regulation of nitrate reductase (NR) by light is highlighted as vital to adjust NO production in plants living under natural light conditions.

The nodulation and nyctinastic leaf movement is orchestrated by clock gene LHY in Medicago truncatula

As sessile organisms, plants perceive, respond, and adapt to the environmental changes for optimal growth and survival. The plant growth and fitness are enhanced by circadian clocks through coordination of numerous biological events. In legume species, nitrogen-fixing root nodules were developed as the plant organs specialized for symbiotic transfer of nitrogen between microsymbiont and host. Here, we report that the endogenous circadian rhythm in nodules is regulated by MtLHY in legume species Medicago truncatula. Loss of function of MtLHY leads to a reduction in the number of nodules formed, resulting in a diminished ability to assimilate nitrogen. The operation of the 24-h rhythm in shoot is further influenced by the availability of nitrogen produced by the nodules, leading to the irregulated nyctinastic leaf movement and reduced biomass in mtlhy mutants. These data shed new light on the roles of MtLHY in the orchestration of circadian oscillator in nodules and shoots, which provides a mechanistic link between nodulation, nitrogen assimilation, and clock function.

Responses of Manila Grass (Zoysia matrella) to chilling stress: From transcriptomics to physiology

Manila grass (Zoysia matrella), a warm-season turfgrass, usually wilts and browns by late autumn because of low temperature. To elucidate the molecular mechanisms regarding Manila grass responses to cold stress, we performed transcriptome sequencing of leaves exposed to 4°C for 0 (CK), 2h (2h_CT) and 72h (72h_CT) by Illumina technology. Approximately 250 million paired-end reads were obtained and de novo assembled into 82,605 unigenes. A total of 34,879 unigenes were annotated by comparing their sequence to public protein databases. At the 2h- and 72h-cold time points, 324 and 5,851 differentially expressed genes (DEGs) were identified, respectively. Gene ontology (GO) and metabolism pathway (KEGG) enrichment analyses of DEGs indicated that auxin, gibberellins, ethylene and calcium took part in the cold signal transduction in the early period. And in the late cold period, electron transport activities, photosynthetic machinery and activity, carbohydrate and nitrogen metabolism, redox equilibrium and hormone metabolism were disturbed. Low temperature stress triggered high light, drought and oxidative stress. At the physiological level, cold stress induced a decrease in water content, an increase in levels of total soluble sugar, free proline and MDA, and changes in bioactive gibberellins levels, which supported the changes in gene expression. The results provided a large set of sequence data of Manila grass as well as molecular mechanisms of the grass in response to cold stress. This information will be helpful for future study of molecular breeding and turf management.

Multiple circadian clock outputs regulate diel turnover of carbon and nitrogen reserves

Plants accumulate reserves in the daytime to support growth at night. Circadian regulation of diel reserve turnover was investigated by profiling starch, sugars, glucose 6-phosphate, organic acids, and amino acids during a light-dark cycle and after transfer to continuous light in Arabidopsis wild types and in mutants lacking dawn (lhy cca1), morning (prr7 prr9), dusk (toc1, gi), or evening (elf3) clock components. The metabolite time series were integrated with published time series for circadian clock transcripts to identify circadian outputs that regulate central metabolism. (a) Starch accumulation was slower in elf3 and prr7 prr9. It is proposed that ELF3 positively regulates starch accumulation. (b) Reducing sugars were high early in the T-cycle in elf3, revealing that ELF3 negatively regulates sucrose recycling. (c) The pattern of starch mobilization was modified in all five mutants. A model is proposed in which dawn and dusk/evening components interact to pace degradation to anticipated dawn. (d) An endogenous oscillation of glucose 6-phosphate revealed that the clock buffers metabolism against the large influx of carbon from photosynthesis. (e) Low levels of organic and amino acids in lhy cca1 and high levels in prr7 prr9 provide evidence that the dawn components positively regulate the accumulation of amino acid reserves.

Exogenously applied hydrogen peroxide modifies the course of the Chlamydomonas reinhardtii cell cycle

The interaction of NO and H₂O₂ in the regulation of plant development is well documented. We have recently shown that the content of NO and H₂O₂ changes in a characteristic way during the cell cycle of Chlamydomonas reinhardtii (Pokora et al., 2017), which implies participation of these molecules in the regulation of Chlamydomonas development. To verify this assumption, H₂O₂ was supplied at a concentration about 1.5 times higher than that determined in the control cells. Cells were synchronized by alternating the light/dark (10/14 h) regimen. H₂O₂ was added to zoospore suspensions, previously held in the dark, and cells growing for 3, 6, and 9 h in the light. The data indicate that, depending on the phase of the Chlamydomonas cell cycle, H₂O₂, via mild modification of redox homeostasis, may: a) accelerate or delay the duration of the cell cycle; b) increase the number of replication rounds occurring in one cell cycle; c) modify the biomass and cell volume of progeny cells and d) accelerate the liberation of daughter cells. This provides a tool to control the development of Chlamydomonas cell and thus offers the opportunity to obtain a population of cells with characteristics desired in biotechnology.

Expression of novel nitrate reductase genes in the harmful alga, Chattonella subsalsa

Eukaryotic nitrate reductase (NR) catalyzes the first step in nitrate assimilation and is regulated transcriptionally in response to external cues and intracellular metabolic status. NRs are also regulated post-translationally in plants by phosphorylation and binding of 14-3-3 proteins at conserved serine residues. 14-3-3 binding motifs have not previously been identified in algal NRs. A novel NR (NR2-2/2HbN) with a 2/2 hemoglobin domain was recently described in the alga Chattonella subsalsa. Here, a second NR (NR3) in C. subsalsa is described with a 14-3-3 binding motif but lacking the Heme-Fe domain found in other NRs. Transcriptional regulation of both NRs was examined in C. subsalsa, revealing differential gene expression over a diel light cycle, but not under constant light. NR2 transcripts increased with a decrease in temperature, while NR3 remained unchanged. NR2 and NR3 transcript levels were not inhibited by growth on ammonium, suggesting constitutive expression of these genes. Results indicate that Chattonella responds to environmental conditions and intracellular metabolic status by differentially regulating NR transcription, with potential for post-translational regulation of NR3. A survey of algal NRs also revealed the presence of 14-3-3 binding motifs in other algal species, indicating the need for future research on regulation of algal NRs.

The nitrogen-potassium intersection: membranes, metabolism, and mechanism

Nitrogen (N) and potassium (K) are the two most abundantly acquired mineral elements by plants, and their acquisition pathways interact in complex ways. Here, we review pivotal interactions with respect to root acquisition, storage, translocation and metabolism, between the K⁺ ion and the two major N sources, ammonium (NH₄⁺ ) and nitrate (NO₃^- ). The intersections between N and K physiology are explored at a number of organizational levels, from molecular-genetic processes, to compartmentation, to whole plant physiology, and discussed in the context of both N-K cooperation and antagonism. Nutritional regulation and optimization of plant growth, yield, metabolism and water-use efficiency are also discussed.

Biological Timekeeping: The Business of a Blind Watchmaker

Fundamental understanding of life depends on both structural and functional details at the molecular level. Continually improving means of measurement of spatial and dynamic properties of biochemical constituents and cellular components complement studies of whole organisms. Integration of the interaction of components to provide coherent behaviour depends on highly elaborate orchestration in space and time. Whereas spatial information on a nanometre resolution is available, and fast dynamic analyses provide biochemical reaction rates measured in nanoseconds, functional coordination of the system requires integrated time dependence. While we are well aware of the special complexity of living organisms, appreciation of temporal scales and their organisation in time is still fragmentary. This article summarises current developments in research on biological time on scales from nanoseconds to years, the networks that connect different time domains and the oscillations, rhythms and biological clocks that coordinate and synchronise the complexity of the living state.

“It is the pattern maintained by this homeostasis, which is the touchstone of our personal identity. Our tissues change as we live: the food we eat and the air we breathe become flesh of our flesh, and bone of our bone, and the momentary elements of our flesh and bone pass out of our body every day with our excreta. We are but whirlpools in a river of ever-flowing water. We are not the stuff that abides, but patterns that perpetuate themselves”60.

Wiener, 1954

“What are called structures are slow processes of long duration, functions are quick processes of short duration”61.

Von Bertalanffy, 1952

The interactions between the circadian clock and primary metabolism

Primary metabolism in plants is tightly regulated by environmental factors such as light and nutrient availability at multiple levels. The circadian clock is a self-sustained endogenous oscillator that enables organisms to predict daily and seasonal changes. The regulation of primary metabolism by the circadian clock has been proposed to explain the importance of circadian rhythms in plant growth and survival. Recent transcriptomic and metabolomic analyses indicate a wide spread circadian regulation of different metabolic processes. We review evidence of circadian regulation of pathways in primary metabolism, discuss the challenges faced for discerning the mechanisms regulating circadian metabolic oscillations and present recent evidence of regulation of the circadian clock by metabolites.

GNC and CGA1 modulate chlorophyll biosynthesis and glutamate synthase (GLU1/Fd-GOGAT) expression in Arabidopsis

Chloroplast development is an important determinant of plant productivity and is controlled by environmental factors including amounts of light and nitrogen as well as internal phytohormones including cytokinins and gibberellins (GA). The paralog GATA transcription factors GNC and CGA1/GNL up-regulated by light, nitrogen and cytokinin while also being repressed by GA signaling. Modifying the expression of these genes has previously been shown to influence chlorophyll content in Arabidopsis while also altering aspects of germination, elongation growth and flowering time. In this work, we also use transgenic lines to demonstrate that GNC and CGA1 exhibit a partially redundant control over chlorophyll biosynthesis. We provide novel evidence that GNC and CGA1 influence both chloroplast number and leaf starch in proportion to their transcript level. GNC and CGA1 were found to modify the expression of chloroplast localized GLUTAMATE SYNTHASE (GLU1/Fd-GOGAT), which is the primary factor controlling nitrogen assimilation in green tissue. Altering GNC and CGA1 expression was also found to modulate the expression of important chlorophyll biosynthesis genes (GUN4, HEMA1, PORB, and PORC). As previously demonstrated, the CGA1 transgenic plants demonstrated significantly altered timing to a number of developmental events including germination, leaf production, flowering time and senescence. In contrast, the GNC transgenic lines we analyzed maintain relatively normal growth phenotypes outside of differences in chloroplast development. Despite some evidence for partial divergence, results indicate that regulation of both GNC and CGA1 by light, nitrogen, cytokinin, and GA acts to modulate nitrogen assimilation, chloroplast development and starch production. Understanding the mechanisms controlling these processes is important for agricultural biotechnology.

In folio isotopic tracing demonstrates that nitrogen assimilation into glutamate is mostly independent from current CO2 assimilation in illuminated leaves of Brassica napus

*Nitrogen assimilation in leaves requires primary NH(2) acceptors that, in turn, originate from primary carbon metabolism. Respiratory metabolism is believed to provide such acceptors (such as 2-oxoglutarate), so that day respiration is commonly seen as a cornerstone for nitrogen assimilation into glutamate in illuminated leaves. However, both glycolysis and day respiratory CO(2) evolution are known to be inhibited by light, thereby compromising the input of recent photosynthetic carbon for glutamate production. *In this study, we carried out isotopic labelling experiments with (13)CO(2) and (15)N-ammonium nitrate on detached leaves of rapeseed (Brassica napus), and performed (13)C- and (15)N-nuclear magnetic resonance analyses. *Our results indicated that the production of (13)C-glutamate and (13)C-glutamine under a (13)CO(2) atmosphere was very weak, whereas (13)C-glutamate and (13)C-glutamine appeared in both the subsequent dark period and the next light period under a (12)CO(2) atmosphere. Consistently, the analysis of heteronuclear ((13)C-(15)N) interactions within molecules indicated that most (15)N-glutamate and (15)N-glutamine molecules were not (13)C labelled after (13)C/(15)N double labelling. That is, recent carbon atoms (i.e. (13)C) were hardly incorporated into glutamate, but new glutamate molecules were synthesized, as evidenced by (15)N incorporation. *We conclude that the remobilization of night-stored molecules plays a significant role in providing 2-oxoglutarate for glutamate synthesis in illuminated rapeseed leaves, and therefore the natural day : night cycle seems critical for nitrogen assimilation.

The bZIP transcription factors HY5 and HYH are positive regulators of the main nitrate reductase gene in Arabidopsis leaves, NIA2, but negative regulators of the nitrate uptake gene NRT1.1

Previously we have shown that nitrate reductase (NR) activity was impaired in Arabidopsis seedlings and rosette stage leaves when the basic leucine zipper transcription factors HY5 and HYH were absent. In the present work, we investigated the influence of hy5 and hyh null mutations on the expression of the NR encoding genes NIA1 and NIA2, as well as genes involved in nitrate uptake and further assimilation of nitrite. Only NIA2, and not NIA1, transcript levels were positively influenced by the presence of HY5 and HYH. In the hy5 hyh mutant, enhancement of NIA2 expression by light was impaired in both seedlings and rosette stage plants. Induction of NIA2 transcription by nitrate was not influenced by HY5 or HYH. Although the peak NIA2 transcript level was much higher in wild type in comparison with the hy5 hyh mutant plant, diurnal variations of NIA2 expression were also observed in the mutant. A dual affinity nitrate transporter gene, NRT1.1, was expressed at a higher level in hy5 hyh than in the wild type, indicating that HY5 and HYH are repressors of NRT1.1. In conclusion, HY5 and HYH were activators of NIA2, but inhibitors of NRT1.1 when tested across various light treatments and tissue types.

UNRAVELING THE REGULATION OF NITROGEN ASSIMILATION IN THE MARINE DIATOM THALASSIOSIRA PSEUDONANA (BACILLARIOPHYCEAE): DIURNAL VARIATIONS IN TRANSCRIPT LEVELS FOR FIVE GENES INVOLVED IN NITROGEN ASSIMILATION(1)

We examined the diurnal expression of five genes encoding nitrogen-assimilating enzymes in the marine diatom Thalassiosira pseudonana (Hust.) Hasle et Heimdal following a transition from NH4 (+) - to NO3 (-) -supplemented media. The accumulation of nia transcripts (encoding nitrate reductase, NR) following the transition to NO3 (-) -supplemented media was similar to previously reported changes in NR abundance and activity. Nia mRNA levels varied diurnally, and the diurnal oscillations were abolished when cells were transferred to continuous light. Genes encoding chloroplastic (niiA) and cytosolic (nirB) nitrite reductases were identified in the genome of T. pseudonana. NiiA and nirB transcript levels increased within 2 h following the addition of NO3 (-) and varied diurnally. Patterns of diurnal variation in nia, niiA, and glnII (encoding the chloroplast-localized glutamine synthetase) mRNA abundances were similar. NirB and glnN (encoding the cytosolic-localized glutamine synthetase) mRNA levels also oscillated diurnally; however, the oscillation was out of phase with nia, niiA, and glnII. We propose that NO3 (-) is assimilated into organic molecules in both the chloroplast and cytosol of diatoms and that enzymes encoded by nirB and glnN contribute to the ecologically important dark assimilation of NO3 (-) observed in marine diatoms. As with nia, the diurnal variations in niiA, nirB, glnII, and glnN were abolished when cells were transferred to continuous light. Our results demonstrate that transcript accumulation is not circadian controlled, but, rather, changes in metabolic pools triggered by light:dark (L:D) transitions may be important in regulating the cellular mRNA levels encoding these key nitrogen assimilating enzymes.

Signalling cascades integrating light-enhanced nitrate metabolism

In higher plants, light is crucial for regulation of nitrate uptake, translocation and assimilation into organic compounds. Part of this metabolism is tightly coupled to photosynthesis because the enzymes involved, nitrite reductase and glutamate synthase, are localized to the chloroplasts and receive reducing power from photosynthetic electron transport. However, important enzymes in nitrate acquisition and reduction are localized to cellular compartments other than chloroplasts and are also up-regulated by light, i.e. transporters in cell and organellar membranes and nitrate reductase in the cytosol. This review describes the different light-dependent signalling cascades regulating nitrate metabolism at the transcriptional as well as post-transcriptional level, and how reactions in different compartments of the cell are co-ordinated. Essential players in this network are phytochrome and HY5 (long hypocotyls 5)/HYH (HY5 homologue)-dependent signalling pathways, the energy-related AMPK (AMP-activated protein kinase) protein kinase homologue SNRK1 (sucrose non-fermenting kinase 1-related kinase), chloroplastic thioredoxins and the prokaryotically originated PII protein. A complex light-dependent network of regulation emerges, which appears to be necessary for optimal nitrogen assimilation and for avoiding the accumulation of toxic intermediates and side products, such as nitrite and reactive oxygen compounds.

Mutation of the Arabidopsis NRT1.5 nitrate transporter causes defective root-to-shoot nitrate transport

Little is known about the molecular and regulatory mechanisms of long-distance nitrate transport in higher plants. NRT1.5 is one of the 53 Arabidopsis thaliana nitrate transporter NRT1 (Peptide Transporter PTR) genes, of which two members, NRT1.1 (CHL1 for Chlorate resistant 1) and NRT1.2, have been shown to be involved in nitrate uptake. Functional analysis of cRNA-injected Xenopus laevis oocytes showed that NRT1.5 is a low-affinity, pH-dependent bidirectional nitrate transporter. Subcellular localization in plant protoplasts and in planta promoter-beta-glucuronidase analysis, as well as in situ hybridization, showed that NRT1.5 is located in the plasma membrane and is expressed in root pericycle cells close to the xylem. Knockdown or knockout mutations of NRT1.5 reduced the amount of nitrate transported from the root to the shoot, suggesting that NRT1.5 participates in root xylem loading of nitrate. However, root-to-shoot nitrate transport was not completely eliminated in the NRT1.5 knockout mutant, and reduction of NRT1.5 in the nrt1.1 background did not affect root-to-shoot nitrate transport. These data suggest that, in addition to that involving NRT1.5, another mechanism is responsible for xylem loading of nitrate. Further analyses of the nrt1.5 mutants revealed a regulatory loop between nitrate and potassium at the xylem transport step.

Circadian output, input, and intracellular oscillators: insights into the circadian systems of single cells

Circadian output comprises the business end of circadian systems in terms of adaptive significance. Work on Neurospora pioneered the molecular analysis of circadian output mechanisms, and insights from this model system continue to illuminate the pathways through which clocks control metabolism and overt rhythms. In Neurospora, virtually every strain examined in the context of rhythms bears the band allele that helps to clarify the overt rhythm in asexual development. Recent cloning of band showed it to be an allele of ras-1 and to affect a wide variety of signaling pathways yielding enhanced light responses and asexual development. These can be largely phenocopied by treatments that increase levels of intracellular reactive oxygen species. Although output is often unidirectional, analysis of the prd-4 gene provided an alternative paradigm in which output feeds back to affect input. prd-4 is an allele of checkpoint kinase-2 that bypasses the requirement for DNA damage to activate this kinase; FRQ is normally a substrate of activated Chk2, so in Chk2(PRD-4), FRQ is precociously phosphorylated and the clock cycles more quickly. Finally, recent adaptation of luciferase to fully function in Neurospora now allows the core FRQ/WCC feedback loop to be followed in real time under conditions where it no longer controls the overt rhythm in development. This ability can be used to describe the hierarchical relationships among FRQ-Less Oscillators (FLOs) and to see which are connected to the circadian system. The nitrate reductase oscillator appears to be connected, but the oscillator controlling the long-period rhythm elicited upon choline starvation appears completely disconnected from the circadian system; it can be seen to run with a very long noncompensated 60-120-hour period length under conditions where the circadian FRQ/WCC oscillator continues to cycle with a fully compensated circadian 22-hour period.

How plants tell the time

Plants, like all eukaryotes and most prokaryotes, have evolved sophisticated mechanisms for anticipating predictable environmental changes that arise due to the rotation of the Earth on its axis. These mechanisms are collectively termed the circadian clock. Many aspects of plant physiology, metabolism and development are under circadian control and a large proportion of the transcriptome exhibits circadian regulation. In the present review, we describe the advances in determining the molecular nature of the circadian oscillator and propose an architecture of several interlocking negative-feedback loops. The adaptive advantages of circadian control, with particular reference to the regulation of metabolism, are also considered. We review the evidence for the presence of multiple circadian oscillator types located in within individual cells and in different tissues.

Posttranslational regulation of nitrate reductase strongly affects the levels of free amino acids and nitrate, whereas transcriptional regulation has only minor influence

Diurnal variations in nitrate reductase (NR) activity and nitrogen metabolites were examined in wild-type Nicotiana plumbaginifolia and transformants with various degrees of NR deregulation. In the C1 line, NR was only deregulated at the transcriptional level by placing the NR gene under the control of the cauliflower mosaic virus 35S RNA promoter. In the Del8 and S521D lines, NR was additionally deregulated at the posttranslational level either by a deletion mutation in the N-terminal domain or by a mutation of the regulatory phosphorylation site (serine-521). Posttranslational regulation was essential for pronounced diurnal variations in NR activity. Low nitrate content was related to deregulation of NR, whereas the level of total free amino acids was much higher in plants with fully deregulated NR. Abolishing transcriptional and posttranslational regulation (S521D plants) resulted in an increase of glutamine and asparagine by a factor of 9 and 14, respectively, compared with wild type, whereas abolishing transcriptional regulation (C1 plants) only resulted in increases of glutamine and asparagine by factors <2. Among the minor amino acids, isoleucine and threonine, in particular, showed enhanced levels in S521D. Nitrate uptake rates were the same in S521D and wild type as determined with (15)N feeding. Deregulation of NR appears to set the level of certain amino acids, whereas diurnal variations were still determined by light/dark. Generally, deregulation of NR at the transcriptional level did not have much influence on metabolite levels, but additional deregulation at the posttranslational level resulted in profound changes of nitrogen metabolite levels.

A model for the circadian oscillations in expression and activity of nitrate reductase in higher plants

BACKGROUND AND AIMS

Nitrate is the major nitrogen source for many plants. The first step of the nitrate assimilation pathway is the reduction of nitrate to nitrite, catalysed by nitrate reductase (NR). Circadian oscillations in expression and activity of NR have been demonstrated in many plant species. The pathway by which this circadian behaviour is regulated remains to be elucidated. In this study, based on recent experimental observations, a mathematical model is proposed to explain the origin of diurnal and circadian oscillations in NR gene expression and enzyme activity.

METHODS

The dynamic model is based on the feedback interconnections between NR and its substrate, nitrate. In the model, NR activity is regulated at the transcriptional level, in response to the balance between nitrate influx and reduction, and at the post-translational levels in response to signals from carbon assimilation. Conditions for the model system to generate self-sustained circadian oscillations are investigated by numerical simulations.

KEY RESULTS AND CONCLUSIONS

Under light/dark cycles, the simulation results are in agreement with the observed diurnal pattern of changes in leaf nitrate concentration, NR transcript level and NR activity. Within a range of kinetic parameter values, circadian oscillation behaviour persists even under constant light, with periods of approx. 24 h. These simulation results suggest that sustained circadian oscillations can originate from the feedback interactions between NR and its substrate, nitrate, without the need to postulate the existence of an endogenous 'circadian clock'.

The two nitrogen mobilisation- and senescence-associated GS1 and GDH genes are controlled by C and N metabolites

In tobacco, the two enzymes of nitrogen metabolism, cytosolic glutamine synthetase (GS1; E.C.6.3.1.2) and glutamate dehydrogenase (GDH; E.C.1.4.1.2), are induced during leaf senescence, whereas the chloroplastic glutamine synthetase (GS2; E.C.6.3.1.2) and nitrate reductase (NR; E.C.1.6.1.1) are repressed in the course of ageing. In this report, we showed in discs of fully expanded Nicotiana tabacum L. cv. Xanthi leaves that sucrose (Suc) and amino acids were involved in the regulation of the expression of GS1 and GDH genes. Suc induced the expression of GS1 and repressed that of GDH. Therefore, we concluded that in response to Suc, GS1 behaved as an "early" Senescence Associated Gene (SAG), whereas GDH behaved as a "late" SAG. Moreover, amino acids induced the expression of both genes. Among the amino acids tested as signal molecules, proline (Pro) and glutamate (Glu) were major inducers of GDH and GS1 expression, respectively. Interestingly, an opposite regulation of GS1 and GS2 by Pro and Glu was shown. The contrary effect of Suc on NIA (NR encoding gene) and GDH mRNA accumulation was also emphasized.

A nitrate-induced frq-less oscillator in Neurospora crassa

When nitrate is the only nitrogen source, Neurospora crassa's nitrate reductase (NR) shows endogenous oscillations in its nitrate reductase activity (NRA) on a circadian time scale. These NRA oscillations can be observed in darkness or continuous light conditions and also in a frq(9) mutant in which no functional FRQ protein is formed. Even in a white-collar-1 knockout mutant, NRA oscillations have been observed, although with a highly reduced amplitude. This indicates that the NRA oscillations are not a simple output rhythm of the white-collar-driven frq oscillator but may be generated by another oscillator that contains the nit-3 autoregulatory negative feedback loop as a part. In this negative feedback loop, a product in the reaction chain catalyzed by nitrate reductase, probably glutamine, induces repression of the nitrate reductase gene and thus downregulates its own production. This is the first example of an endogenous, nutritionally induced daily rhythm with known molecular components that is observed in the absence of an intact FRQ protein.

Mechanism and importance of post-translational regulation of nitrate reductase

In higher plants, nitrate reductase (NR) is inactivated by the phosphorylation of a conserved Ser residue and binding of 14-3-3 proteins in the presence of divalent cations or polyamines. A transgenic Nicotiana plumbaginifolia line (S521) has been constructed where the regulatory, conserved Ser 521 of tobacco NR (corresponding to Ser 534 in Arabidopsis) was mutated into Asp. This mutation resulted in the complete abolition of activation/inactivation in response to light/dark transitions or other treatments known to regulate the activation state of NR. Analysis of the transgenic plants showed that, under certain conditions, when whole plants or cut tissues are exposed to high nitrate supply, post-translational regulation is necessary to avoid nitrite accumulation. Abolition of the post-translational regulation of NR also results in an increased flux of nitric oxide from the leaves and roots. In view of the results obtained from examining the different transgenic N. plumbaginifolia lines, compartmentation of nitrate into an active metabolic pool and a large storage pool appears to be an important factor for regulating nitrate reduction. The complex regulation of nitrate reduction is likely to have evolved not only to optimize nitrogen assimilation, but also to prevent and control the formation of toxic, and possibly regulatory, products of NR activities. Phos phorylation of NR has previously been found to influence the degradation of NR in spinach leaves and Arabidopsis cell cultures. However, experiments with whole plants of N. plumbaginifolia, Arabidopsis, or squash are in favour of NR degradation being the same in light and darkness and independent of phosphorylation at the regulatory Ser.

Phosphorylation and 14-3-3 binding of Arabidopsis 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase

Fructose 2,6-bisphosphate (fru-2,6-P2) is a signalling metabolite that regulates photosynthetic carbon partitioning in plants. The content of fru-2,6-P2 in Arabidopsis leaves varied in response to photosynthetic activity with an abrupt decrease at the start of the photoperiod, gradual increase through the day, and modest decrease at the start of the dark period. In Arabidopsis suspension cells, fru-2,6-P2 content increased in response to an unknown signal upon transfer to fresh culture medium. This increase was blocked by either 2-deoxyglucose or the protein phosphatase inhibitor, calyculin A, and the effects of calyculin A were counteracted by the general protein kinase inhibitor K252a. The changes in fru-2,6-P2 at the start of dark period in leaves and in the cell experiments generally paralleled changes in nitrate reductase (NR) activity. NR is inhibited by protein phosphorylation and binding to 14-3-3 proteins, raising the question of whether fructose-6-phosphate,2-kinase/fructose-2,6-bisphosphatase protein from Arabidopsis thaliana (AtF2KP), which both generates and hydrolyses fru-2,6-P2, is also regulated by phosphorylation and 14-3-3s. Consistent with this hypothesis, AtF2KP and NR from Arabidopsis cell extracts bound to a 14-3-3 column, and were eluted specifically by a synthetic 14-3-3-binding phosphopeptide (ARAApSAPA). 14-3-3s co-precipitated with recombinant glutathione S-transferase (GST)-AtF2KP that had been incubated with Arabidopsis cell extracts in the presence of Mg-ATP. 14-3-3s bound directly to GST-AtF2KP that had been phosphorylated on Ser220 (SLSASGpSFR) and Ser303 (RLVKSLpSASSF) by recombinant Arabidopsis calcium-dependent protein kinase isoform 3 (CPK3), or on Ser303 by rat liver mammalian AMP-activated protein kinase (AMPK; homologue of plant SNF-1 related protein kinases (SnRKs)) or an Arabidopsis cell extract. We have failed to find any direct effect of 14-3-3s on the F2KP activity in vitro to date. Nevertheless, our findings indicate the possibility that 14-3-3 binding to SnRK1-phosphorylated sites on NR and F2KP may regulate both nitrate assimilation and sucrose/starch partitioning in leaves.

The physiology of circadian rhythms in plants

Circadian rhythms regulate many aspects of plant physiology including leaf, organ and stomatal movements, growth and signalling. The genetic identity of some of the components of the core circadian oscillator has recently become known. Similarly, the photoperception and phototransduction pathways that entrain the oscillator to the day and night cycle are being determined. Less clear are the pathways by which the circadian oscillator regulates cellular physiology. Circadian oscillations in cytosolic free calcium might act to transduce the temporal outputs of the circadian oscillator. This hypothesis requires rigorous testing using novel noninvasive technologies. Plants might gain advantage from the circadian clock by being able to predict changes in the environment and coordinate physiological processes, presumably increasing survival and hence, reproductive fitness. Technical advances coupled with cell-specific measurement techniques will allow the advantages of the circadian regulation of physiology to be quantified. Summary 281 I. Introduction 282 II. The circadian clock 283 III. The regulation of cellular physiology by circadian oscillations in cytosolic free Ca²⁺ 286 IV. The circadian regulation of physiology 292 V. The benefits of the circadian regulation of physiology 298 VI. Future prospects 299 VIII. Conclusions 300 Acknowledgements 300 References 300.

Identification of rhythmic subsystems in the circadian cycle of crassulacean acid metabolism under thermoperiodic perturbations

Leaves of the Crassulacean acid metabolism (CAM) plant Kalanchoë daigremontiana Hamet et Perrier de la Bâthie show overt circadian rhythms in net CO2 uptake, leaf conductance to water and intercellular CO2 concentration, which are entrained by periodic temperature cycles. To probe their sensitivity to thermoperiodic perturbations, intact leaves were exposed to continuous light intensity and temperature cycles with a period of 16 h, applying a set of different baseline temperatures and thermodriver amplitudes. All three overt rhythms were analyzed with respect to their frequency spectra and their phase relations with the thermodriver. For most stimulation protocols, stomatal conductance and net CO2 change were fully or partially entrained by the temperature pulses, while the internal CO2 concentration remained dominated by oscillations in the circadian range. Prolonged time series recorded for up to 22 d in continuous light underline the robustness of these circadian oscillations. This suggests that the overt circadian rhythm of net CO2 uptake in CAM results from the interaction of two coupled original systems: (i) an endogenous cycle of CO2 fixation in the mesophyll, showing very robust periodic activity, and (ii) stomatal movements that respond to environmental stimuli independently of rhythmic processes in the mesophyll, and thus modulate the gas exchange amplitude.

Oscillation of mRNA level and activity of granule-bound starch synthase I in Arabidopsis leaves during the day/night cycle

Granule-bound starch synthase (GBSSI) is one of the most extensively studied enzymes of the starch synthesis pathway and its role in the synthesis of amylose has been well established. However, few studies have been carried out to characterize the regulation of GBSSI gene. Regulation of starch synthesis genes is especially interesting in photosynthetic tissues, where starch is subjected to a periodical alternation of synthesis and degradation during the day/night cycle. In this report we show a circadian oscillation of GBSSI mRNA levels in leaves of Arabidopsis during the day/night cycle, and provide evidence that GBSSI expression is controlled by the transcription factors CCA1 and LHY. Over-expression of both CCA1 and LHY genes causes the elimination of GBSSI mRNA oscillation. Binding shift assays indicate that this control may be exerted through a direct interaction of those regulatory proteins with the GBSSI promoter. Oscillation is not observed on the GBSSI protein levels, which remains constant along the cycle. However, GBSSI activity shows a clear oscillation with a period of 24 h that is altered in transgenic plants over-expressing CCA1. Possible mechanisms controlling GBSSI activity during the day/night cycle are discussed.

Circadian period lengths of lipid synthesis mutants (cel, chol-1) of Neurospora show defective temperature, but intact pH-compensation

The influence of extracellular pH on the circadian sporulation rhythm of Neurospora crassa has been investigated for the mutants chol-1 and cel. Both mutants have a defect in the lipid synthesis pathway and require either choline or palmitate, respectively, as supplements for normal growth. The chol-1 and cel mutants also show an impaired temperature-compensation when growing on minimal medium. We investigated the possible correlation between loss of temperature- and pH-compensation in cel and chol-1 similar to the correlation found earlier for the frq7 mutant. Our results show that the cel and the chol-1 mutants, although defective in temperature-compensation have an intact pH-compensation of their circadian rhythms. At present, the products of the frq-locus are the only components of the clock that affect the sporulation rhythm of Neurospora both through pH- and temperature-compensation.

Low temperature induces expression of nitrate reductase in tomato that temporarily overrides circadian regulation of activity

Overnight low-temperature exposure inhibits photosynthesis in chilling-sensitive species, such as tomato and cucumber, by as much as 60%. Earlier work showed that low temperature stalled the endogenous rhythm controlling transcription of certain nuclear-encoded genes in chilling-sensitive plants causing the synthesis of the corresponding transcripts and proteins to be mistimed upon rewarming. The activity of nitrate reductase (NR), the first and rate-limiting step in the assimilation of nitrate into amino acids in leaves, is subjected to a varied range of regulatory influences including a robust circadian rhythm. We show here that although NR regulation is disrupted by low temperatures, the change is transient and does not alter the phase of the NR endogenous rhythm following the chill. There is a temporary induction of de novo transcription of NR causing an increase in both NR protein and activity. This occurs regardless of the time in the circadian cycle that the chilling episode is initiated thereby decoupling the normally closely coordinated processes of carbon and nitrogen assimilation. This decoupling would be expected to deplete cellular reductant and carbon skeleton reserves as well as allow accumulation of cytotoxic intermediates of nitrogen assimilation thereby contributing to the low temperature induced disruption of metabolism that takes place in photosynthetic cells of chilling sensitive plant species.

Biological timing and the clock metaphor: oscillatory and hourglass mechanisms

Living organisms have developed a multitude of timing mechanisms--"biological clocks." Their mechanisms are based on either oscillations (oscillatory clocks) or unidirectional processes (hourglass clocks). Oscillatory clocks comprise circatidal, circalunidian, circadian, circalunar, and circannual oscillations--which keep time with environmental periodicities--as well as ultradian oscillations, ovarian cycles, and oscillations in development and in the brain, which keep time with biological timescales. These clocks mainly determine time points at specific phases of their oscillations. Hourglass clocks are predominantly found in development and aging and also in the brain. They determine time intervals (duration). More complex timing systems combine oscillatory and hourglass mechanisms, such as the case for cell cycle, sleep initiation, or brain clocks, whereas others combine external and internal periodicities (photoperiodism, seasonal reproduction). A definition of a biological clock may be derived from its control of functions external to its own processes and its use in determining temporal order (sequences of events) or durations. Biological and chemical oscillators are characterized by positive and negative feedback (or feedforward) mechanisms. During evolution, living organisms made use of the many existing oscillations for signal transmission, movement, and pump mechanisms, as well as for clocks. Some clocks, such as the circadian clock, that time with environmental periodicities are usually compensated (stabilized) against temperature, whereas other clocks, such as the cell cycle, that keep time with an organismic timescale are not compensated. This difference may be related to the predominance of negative feedback in the first class of clocks and a predominance of positive feedback (autocatalytic amplification) in the second class. The present knowledge of a compensated clock (the circadian oscillator) and an uncompensated clock (the cell cycle), as well as relevant models, are briefly re viewed. Hourglass clocks are based on linear or exponential unidirectional processes that trigger events mainly in the course of development and aging. An important hourglass mechanism within the aging process is the limitation of cell division capacity by the length of telomeres. The mechanism of this clock is briefly reviewed. In all clock mechanisms, thresholds at which "dependent variables" are triggered play an important role.