Microbial circadian oscillatory systems in Neurospora and Synechococcus: models for cellular clocks

doi:10.1016/S1369-5274(00)00074-6

Current Opinion in Microbiology

Volume 3, Issue 2, 1 April 2000, Pages 189-196

https://doi.org/10.1016/S1369-5274(00)00074-6 Get rights and content

Abstract

Common regulatory patterns have emerged among the feedback loops lying within circadian systems. Significant progress in dissecting the mechanism of clock resetting by temperature and the role of the WC proteins in the Neurospora light response has accompanied documentation of the importance of nuclear localization and phosphorylation-induced turnover of FRQ to this circadian cycle. The long-awaited molecular description of a transcription/translation loop in the Synechococcus circadian system represents a quantal step forward, followed by the identification of additional important proteins and interactions. Finally, the adaptive significance of rhythms in Synechococcus and by extension in all clocks nicely ties up an extraordinary year.

Introduction

An extremely wide range of organisms living on the earth have developed the ability to measure time on a 24 hour basis and thus to adapt their lives to Earth’s dependable geophysical cycles of light/dark and warm/cold (reviewed in [1]). In all organisms studied, the cellular machinery underlying this temporal regulation, which is known as circadian rhythmicity, is based within cells and does not require intercellular communication to create the oscillation. In this way circadian rhythmicity is the essence of cellular regulation. At the same time, however, the study of rhythms drives an recurrent need to look back from the cell and into the environment in which the organism lives, because it is from this environment that the daily time cues arrive that the clock uses to reset its phase. This interplay connecting detailed analysis of a true cellular regulatory mechanism — the circadian oscillatory system — with a constant appreciation of the role of the environment in shaping the rhythm (through ‘input’ to the clock), the role of the rhythm in shaping the environment of the cell (through feedback of the clock on input and behavior), and the export of this time information (through ‘output’ from the clock) has kept the study of circadian rhythms a great research problem. Further, because all such clocks are cellular, microbial systems — and in particular the two genetically tractable systems on which we focus here, Neurospora and Synechococcus — have provided excellent models for predicting and understanding the paradigms and requirements for building circadian systems in living things.

All such rhythms share common features [2]: they have period lengths close to but rarely equal to 24 hours (‘circa dies’, about a day), and the oscillatory systems are compensated such that at different ambient temperatures or during growth with different nutritional supplementation the period length of the cycle is about the same (known as ‘temperature and nutritional compensation’). The rhythms operate only within defined ranges of temperature and adopt distinct phases with respect to environmental stimuli, including changes in light and temperature. By convention, rhythms that have period lengths far outside of the circadian range, that are not compensated, or that cannot be reset by light and temperature are not considered circadian. The intracellular molecular oscillatory system that generates the rhythm with circadian characteristics, whether a single oscillator or, as appears to be more likely the case, the coupled ensemble of oscillators, is considered the circadian clock 3, 4. Within the past few years, the molecular bases of many of these characteristics have come to be understood both in model systems and more recently by extension also in mammals. This review will provide focus on recent advances in our understanding of how cellular circadian systems can accurately keep time and be reset by environmental cues.

Section snippets

A model eukaryotic clock system

Neurospora has revealed a number of molecular characteristics now known to be common among the circadian systems found universally among the ‘Crown Eukaryotes’ [5] that emerged during the Cambrian explosion. Reviews in the Current Opinion series within the past year focused on the common conceptual and molecular threads that characterize these eukaryotic clocks 6, 7, 8. In general, a feedback loop central to these circadian oscillatory systems involves positive and negative elements and is

The Neurospora clock

The Neurospora circadian oscillator comprises an autoregulatory negative feedback cycle where the White Collar-1 (WC1) and White Collar-2 (WC2) proteins and both frq mRNA and FRQ protein serve as central components 9, 15, 24, 25. Mutations in frq or wc-2 can result in substantial period length defects (yielding periods from 16 to 34 hours), arrhythmia, and loss of temperature and nutritional compensation of the clock. The deletion of frq, wc-1, or wc-2 results in loss of normal circadian

Resetting the Neurospora clock with environmental cues

We are beginning to learn a great deal about how the Neurospora cycle is reset by the dominant environmental time cues of light and temperature. Light resets the Neurospora clock by acting rapidly through a complex of WC1 and WC2 proteins (which associate via PAS-like LOV domains, 39••, 40••). Light further influences the stability of the component proteins probably through protein kinase C (PKC)-driven phosphorylation which plays a role in light adaptation [41^•] and may influence protein

FRQ-less oscillator(s)

Although significant progress has been made in explaining many circadian characteristics in molecular terms, a few remain elusive, including temperature compensation and sustainability. Much effort has focused on the feedback loop involving FRQ and the WC proteins since frq is essential for establishing sustainability, a circadian period length, temperature and nutritional compensation, and the clock’s response to light — the rhythmic characteristics that render an oscillation circadian in

Cyanobacterial circadian rhythms

Cyanobacteria are the simplest organisms known to exhibit circadian rhythms. The cyanobacterial clock regulates many physiological processes, such as photosynthesis, nitrogenase activity, amino acid uptake, cell division, and carbohydrate synthesis [53]. Such rhythms can ‘free-run’ with a circadian period even in cells dividing faster than once every 24 hours 54, 55, 56•. Some diazotrophic (nitrogen-fixing) cyanobacteria exhibit robust circadian rhythms of oxygen-producing photosynthesis and

Components of the cyanobacterial circadian oscillator

What is the biochemical basis of the oscillator that Mother Nature has evolved for this circadian machinery? Now classic studies in which a bioluminescent reporter was driven by a clock-regulated photosynthetic gene identified the first cyanobacterial clock genes [59]. This was followed by molecular genetic studies showing that Synechococcus uses an essential clock gene cluster, kai, composed of three genes, kaiA, kaiB and kaiC for circadian timing [60^••]. These genes share no homology to known

Inputs and outputs of the cyanobacterial clock

Several lines of experiments in a diazotrophic Synechococcus sp. RF-1 suggested that a break of photosynthetic activity by darkness is partly responsible for photic-entraining mechanism [57]. However, additional photoreceptive mechanisms may be required for intact circadian photoreception. Interestingly, a Synechococcus sp. RF-1 rhythm mutant designated CR-1 [62] is not fully entrainable to light/dark cycles but is to temperature cycles [63^•]. Although CR-1 may be the first cyanobacterial

Conclusion — the evolution of circadian systems

Although kai-like genes have not been found in eukaryotes, the kai genes are of particular interest for considering the evolution of circadian systems. First, genes similar to kaiB and kaiC are found in genomes of some Archaea and thermophilic Eubacteria in which circadian rhythms have not been reported; could these be predictors of rhythmicity? Next, although plants may have developed circadian systems independently, the possibility exists that cyanobacterial circadian clocks may have a

Acknowledgements

H Iwasaki thanks T Kondo, M Ishiura, and S Golden for discussion and sharing unpublished results, and CH Johnson and members of the Kondo lab for helpful discussion. H Iwasaki is supported by Japan Society for Promotion of Science for young scientist (JSPS; 09001517). JC Dunlap gratefully acknowledges insightful discussion and feedback from members of the Dartmouth rhythms community, especially J Loros, and was supported by grants from the National Institutes of Health (GM 34985, MH01186 and

Note added in proof

The work by Nishiwaki et al. that appears in the text as unpublished data has been accepted for publication [78^••].

An additional paper has recently been published describing the effects of lipid starvation on the noncircadian long period rhythms of chol-1 mutants with and without mutations in the frq and wc genes [79].

References and recommended reading

Papers of particular interest, published within the annual period of review, have been highlighted as:

• of special interest
•• of outstanding interest

References (79)

J.C. Dunlap
Molecular bases for circadian clocks
Cell
(1999)
J.C. Dunlap
Common threads in eukaryotic circadian systems
Curr Opin Genet Dev
(1998)
J.J. Loros
Time at the end of the millennium: The Neurospora clock
Curr Opin Microbiol
(1998)
D. King et al.
Positional cloning of the mouse circadian CLOCK gene
Cell
(1997)
K. Kume et al.
mCRY1 and mCRY2 are essential components of the negative limb of the circadian clock feedback loop
Cell
(1999)
N. Garceau et al.
Alternative initiation of translation and time-specific phosphorylation yield multiple forms of the essential clock protein FREQUENCY
Cell
(1997)
S.C. Crosthwaite et al.
Light-induced resetting of a circadian clock is mediated by a rapid increase in frequency transcript
Cell
(1995)
P. Ruoff et al.
The Goodwin model: simulating the effect of cycloheximide and heat shock on the sporulation rhythm of Neurospora crassa
J Theor Biol
(1999)
Y. Liu et al.
Thermally regulated translational control mediates an aspect of temperature compensation in the Neurospora circadian clock
Cell
(1997)
J.L. Price et al.
double-time is a new Drosophila clock gene that regulates PERIOD protein accumulation
Cell
(1998)

C.S. Pittendrigh

Temporal organization: reflections of a Darwinian clock-watcher

Ann Rev Physiol

(1993)

C. Pittendrigh et al.

Daily rhythms as coupled oscillator systems and their relation to thermoperiodism and photoperiodism

J.C. Dunlap

An end in the beginning

Science

(1998)

M.L. Sogin

(1998)

J.J. Loros et al.

Loss of temperature compensation of circadian period length in the frq-9 mutant of Neurospora crassa

J Biol Rhythms

(1986)

J.C. Dunlap

Genetic and molecular dissection of the Neurospora circadian system

M. Merrow et al.

Assignment of circadian function for the Neurospora clock gene frequency

Nature

(1999)

C. Luo et al.

Nuclear localization is required for function of the essential clock protein FREQUENCY

EMBO J

(1998)

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Citation Excerpt :
A number of rhythmic phenomena with periods ranging from a few to over 100 h persist or emerge in the absence of the FRQ‐WCC oscillator (Aronson et al., 1994b; Christensen et al., 2004; Correa et al., 2003; Granshaw et al., 2003; He et al., 2005a; Lakin‐Thomas and Brody, 2000; Loros and Feldman, 1986; Merrow et al., 1999). Because such rhythms were first noticed in strains lacking a functional frq gene (Loros and Feldman, 1986), the oscillators that presumably control these rhythms were given the name FLOs (Iwasaki and Dunlap, 2000). Most of these rhythms are noncircadian, that have highly variable period length, cannot be entrained by light, and their periods are not temperature or nutritionally compensated.
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ReviewMicrobial circadian oscillatory systems in Neurospora and Synechococcus: models for cellular clocks

Abstract

Introduction

Section snippets

A model eukaryotic clock system

The Neurospora clock

Resetting the Neurospora clock with environmental cues

FRQ-less oscillator(s)

Cyanobacterial circadian rhythms

Components of the cyanobacterial circadian oscillator

Inputs and outputs of the cyanobacterial clock

Conclusion — the evolution of circadian systems

Acknowledgements

Note added in proof

References and recommended reading

Cell

Curr Opin Genet Dev

Curr Opin Microbiol

Cell

Cell

Cell

Cell

J Theor Biol

Cell

Cell

Cell

Cell

Neuron

Cell

Cell

Cell

Temporal organization: reflections of a Darwinian clock-watcher

Ann Rev Physiol

Daily rhythms as coupled oscillator systems and their relation to thermoperiodism and photoperiodism

An end in the beginning

Science

The origin of eukaryotes and evolution into major kingdoms

Clocks for the real world

Curr Biol

Neurospora wc-1 and wc-2: transcription, photoresponses, and the origins of circadian rhythmicity

Science

Closing the circadian loop: CLOCK-induced transcription of its own inhibitors per and tim

Science

A mutant Drosophila homolog of mammalian CLOCK disrupts circadian rhythms and transcription of period and timeless

Cell

CYCLE is a second bHLH-PAS clock protein essential for circadian rhythmicity and transcription of Drosophila period and timeless

Cell

Negative feedback defining a circadian clock: autoregulation in the clock gene frequency

Science

Feedback of the Drosophila period gene product on circadian cycling of its messenger RNA levels

Nature

Rhythmic expression of timeless: a basis for promoting circadian cycles in period gene autoregulation

Science

RIGUI, a putative mammalian ortholog of the Drosophila period gene

Cell

Circadian oscillation of a mammalian homologue of the Drosophila period gene

Nature

Temporal phosphorylation of the Drosophila period protein

Proc Natl Acad Sci USA

Light-induced degradation of TIMELESS and entrainment of the Drosophila circadian clock

Science

Post-translational regulation contributes to Drosophila clock gene mRNA cycling

EMBO J

The circadian clock locus frequency: a single ORF defines period length and temperature compensation

Proc Natl Acad Sci USA

Control of cell lineage-specific development and transcription by bHLH-PAS proteins

Genes Dev

Loss of temperature compensation of circadian period length in the frq-9 mutant of Neurospora crassa

J Biol Rhythms

Genetic and molecular dissection of the Neurospora circadian system

Assignment of circadian function for the Neurospora clock gene frequency

Nature

Nuclear localization is required for function of the essential clock protein FREQUENCY

EMBO J

Review
Microbial circadian oscillatory systems in Neurospora and Synechococcus: models for cellular clocks