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Chapter 29 : Circadian Rhythms

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Abstract:

There are three cardinal properties that define circadian rhythms. First, the period length of circadian rhythms is, by definition, close to 24 h. The second characteristic of circadian rhythms is that the rhythms are entrained to environmental signals such as light and temperature cycles. Thirdly, circadian rhythms are temperature compensated such that the period length of the rhythm is relatively constant at different physiologically relevant temperatures. In the FRQ/WCC molecular cycle, degradation and posttranslational modifications of FRQ play an essential role in period length determination and the overall function of the circadian negative-feedback loop. The study of mutations that altered the pattern of rhythmic development was critical for the initial identification of FRQ/WCC oscillator components in , and the identification of genes that are regulated by the circadian clock has supported the existence of FRQ-independent oscillators in the cell. Circadian rhythms have been observed in several different fungal species but are primarily limited to field documentation of rhythms in spore development and liberation. Solving the mechanisms of the circadian clock has become an important goal, mainly because of their ubiquity, their adaptive value, and their significance for health and disease in many organisms. The past several years have seen significant advances in one's understanding of the mechanisms of circadian rhythmicity, with the molecular genetic analysis of clocks in continuing to provide major insights into the molecular bases of circadian rhythmicity.

Citation: Vitalini M, Dunlap J, Heintzen C, Liu Y, Loros J, Bell-Pedersen D. 2010. Circadian Rhythms, p 442-466. In Borkovich K, Ebbole D (ed), Cellular and Molecular Biology of Filamentous Fungi. ASM Press, Washington, DC. doi: 10.1128/9781555816636.ch29

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Image of FIGURE 1
FIGURE 1

Circadian clock properties. Flow of information in the circadian system. See the text for details.

Citation: Vitalini M, Dunlap J, Heintzen C, Liu Y, Loros J, Bell-Pedersen D. 2010. Circadian Rhythms, p 442-466. In Borkovich K, Ebbole D (ed), Cellular and Molecular Biology of Filamentous Fungi. ASM Press, Washington, DC. doi: 10.1128/9781555816636.ch29
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Image of FIGURE 2
FIGURE 2

Properties of a circadian rhythm. From left to right, the rhythm is entrained to a 12-h LD cycle and then released into DD. In the entrained cycle, the dark boxes represent night, and the light boxes represent day. In the free-running rhythm, the hatched boxes represent subjective night. Period, phase, and amplitude are indicated and are described in the text.

Citation: Vitalini M, Dunlap J, Heintzen C, Liu Y, Loros J, Bell-Pedersen D. 2010. Circadian Rhythms, p 442-466. In Borkovich K, Ebbole D (ed), Cellular and Molecular Biology of Filamentous Fungi. ASM Press, Washington, DC. doi: 10.1128/9781555816636.ch29
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Image of FIGURE 3
FIGURE 3

Plot of a representative phase-response curve in to a light 30-min light pulse given at the indicated circa-dian time (CT) ( axis) ( ). The change in phase compared to cultures that were not given a light pulse is plotted. Positive numbers represent a phase advance, and negative numbers represent a phase delay in the developmental rhythm.

Citation: Vitalini M, Dunlap J, Heintzen C, Liu Y, Loros J, Bell-Pedersen D. 2010. Circadian Rhythms, p 442-466. In Borkovich K, Ebbole D (ed), Cellular and Molecular Biology of Filamentous Fungi. ASM Press, Washington, DC. doi: 10.1128/9781555816636.ch29
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Image of FIGURE 4
FIGURE 4

Assays used to examine rhythmicity in . (A) The race tube assay. In , the developmental rhythm is typically assayed in hollow glass tubes that are partially filled with a solid medium, although petri dishes or capped, horizontal 150-mm test tubes can also be used ( ). Cultures of mycelia or conidia are inoculated at one end of the tube and incubated in LL for about a day. The growth front is marked, and the culture is transferred to DD to monitor the free-running rhythm (A) or can be maintained in an environmental cycle, such as an LD cycle (B) to monitor an entrained rhythm. In constant conditions, the growth front is marked every 24 h, and in the 12-h LD cycle, the race tube is marked at lights on. Under constant conditions, the developmental switch for the production of conidiophores is activated in the late subjective night of the circadian cycle, resulting in the production of conidial spores (conidial band) for a defined part of the day. Once the asexual pathway is initiated, this developmental process proceeds at a rate dependent on factors that are independent of the clock, including culture and strain type. The signal for development is switched off some time later in the middle of the subjective circadian day, and undifferentiated filamentous mycelia again predominate. Note that in DD, the period of the rhythm is shorter than 24 h, but in the 12-h LD cycle, the period is exactly 24 h.

Citation: Vitalini M, Dunlap J, Heintzen C, Liu Y, Loros J, Bell-Pedersen D. 2010. Circadian Rhythms, p 442-466. In Borkovich K, Ebbole D (ed), Cellular and Molecular Biology of Filamentous Fungi. ASM Press, Washington, DC. doi: 10.1128/9781555816636.ch29
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Image of FIGURE 5
FIGURE 5

Graphic depiction of the locus and WC-1 and WC-2 proteins. See the text for details of the loci. The thin lines underneath the locus indicate alternative splicing events. Although not shown, transcription initiation of is initiated at several sites, and two forms of the protein are made by the use of alternative initiation sites ).

Citation: Vitalini M, Dunlap J, Heintzen C, Liu Y, Loros J, Bell-Pedersen D. 2010. Circadian Rhythms, p 442-466. In Borkovich K, Ebbole D (ed), Cellular and Molecular Biology of Filamentous Fungi. ASM Press, Washington, DC. doi: 10.1128/9781555816636.ch29
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Image of FIGURE 6
FIGURE 6

The current model of the FRQ/WCC oscillator. Both the positive loops (black arrows) and negative loops (white arrows) are shown. See the text for details of the model. P, phosphorylation.

Citation: Vitalini M, Dunlap J, Heintzen C, Liu Y, Loros J, Bell-Pedersen D. 2010. Circadian Rhythms, p 442-466. In Borkovich K, Ebbole D (ed), Cellular and Molecular Biology of Filamentous Fungi. ASM Press, Washington, DC. doi: 10.1128/9781555816636.ch29
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Image of FIGURE 7
FIGURE 7

How light (A) and temperature (B) reset the circadian clock. See the text for details of the models.

Citation: Vitalini M, Dunlap J, Heintzen C, Liu Y, Loros J, Bell-Pedersen D. 2010. Circadian Rhythms, p 442-466. In Borkovich K, Ebbole D (ed), Cellular and Molecular Biology of Filamentous Fungi. ASM Press, Washington, DC. doi: 10.1128/9781555816636.ch29
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Image of FIGURE 8
FIGURE 8

The role of CKIIβ in temperature compensation of the clock. Induced expression of (the β subunit of CKII) from a quinic acid-inducible promoter () affects temperature compensation of the clock. As the concentration of quinic acid (QA) decreases, the levels of CKII decrease. This results in changes in temperature compensation of the developmental rhythm from slightly undercompensated, similar to the wild type (WT; black line), to overcompensation. In contrast, as the levels of CK1a drop, the period changes, but temperature compensation is still slightly undercompensated at all levels of CK1a.

Citation: Vitalini M, Dunlap J, Heintzen C, Liu Y, Loros J, Bell-Pedersen D. 2010. Circadian Rhythms, p 442-466. In Borkovich K, Ebbole D (ed), Cellular and Molecular Biology of Filamentous Fungi. ASM Press, Washington, DC. doi: 10.1128/9781555816636.ch29
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Image of FIGURE 9
FIGURE 9

Rhythmic liquid culture assay. To isolate RNA or protein from cultures harvested at different times of day, liquid shaking cultures are routinely used ( ). Transfer of the cultures from LL to DD is staggered to allow harvesting at different circadian times but near the same developmental age. An example of a rhythmic Northern blot is shown for the morning peaking clock-controlled gene from a wild-type (wt) and long-period (29-h) mutant strain. Note that at DD32, mRNA cycles almost 180° out of phase in the mutant versus the wt strain, reflecting the long period of the allele.

Citation: Vitalini M, Dunlap J, Heintzen C, Liu Y, Loros J, Bell-Pedersen D. 2010. Circadian Rhythms, p 442-466. In Borkovich K, Ebbole D (ed), Cellular and Molecular Biology of Filamentous Fungi. ASM Press, Washington, DC. doi: 10.1128/9781555816636.ch29
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Image of FIGURE 10
FIGURE 10

Rhythmic luciferase assays. By using a codon-optimized firefly luciferase, rhythmicity can be monitored by generating promoter fusions to the modified luciferase open reading frame ( ). Luciferase activity is determined by the level of luminescence, as shown here for the promoter (p):luciferase fusion expressed in cells ( ).

Citation: Vitalini M, Dunlap J, Heintzen C, Liu Y, Loros J, Bell-Pedersen D. 2010. Circadian Rhythms, p 442-466. In Borkovich K, Ebbole D (ed), Cellular and Molecular Biology of Filamentous Fungi. ASM Press, Washington, DC. doi: 10.1128/9781555816636.ch29
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Image of FIGURE 11
FIGURE 11

Functional classification of ccgs. All of the known or predicted ccgs (182 ccgs) ( ) were classified according to their known or predicted functions from the Broad Institute Sequencing Project (http://www.genome.wi.mit.edu/annotation/fungi/neurospora/). The number of genes in each category is in parentheses.

Citation: Vitalini M, Dunlap J, Heintzen C, Liu Y, Loros J, Bell-Pedersen D. 2010. Circadian Rhythms, p 442-466. In Borkovich K, Ebbole D (ed), Cellular and Molecular Biology of Filamentous Fungi. ASM Press, Washington, DC. doi: 10.1128/9781555816636.ch29
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Image of FIGURE 12
FIGURE 12

Model for the regulation of circadian output pathways in . The WCC binds to the promoters of genes that lie within circadian output pathways, including , and possibly other genes, including transcription factors that would control rhythmic expression of downstream target genes ( ). In addition, the FRQ/WCC oscillator signals to the osmotic-stress-sensing phosphorelay (the OS pathway) to control rhythms in OS-2 MAPK phosphorylation. Rhythmic phospho-OS would control rhythmic activity of target effector molecules, including transcription factors and factors involved in translation, which would, in turn, regulate downstream ccgs ( ). Together, these and other possible mechanisms control circadian output pathways that regulate rhythms in ccg expression responsible for overt rhythmicity in the organism.

Citation: Vitalini M, Dunlap J, Heintzen C, Liu Y, Loros J, Bell-Pedersen D. 2010. Circadian Rhythms, p 442-466. In Borkovich K, Ebbole D (ed), Cellular and Molecular Biology of Filamentous Fungi. ASM Press, Washington, DC. doi: 10.1128/9781555816636.ch29
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Tables

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TABLE 1

Known components of the FRQ/WCC oscillator

Citation: Vitalini M, Dunlap J, Heintzen C, Liu Y, Loros J, Bell-Pedersen D. 2010. Circadian Rhythms, p 442-466. In Borkovich K, Ebbole D (ed), Cellular and Molecular Biology of Filamentous Fungi. ASM Press, Washington, DC. doi: 10.1128/9781555816636.ch29

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