4 From Genetics to Molecular Oscillations: The Circadian Clock in
Neurospora crassa
MEAGHAN S. JANKOWSKI
1
, ZACHARY A. CHASE
1
, JENNIFER M. HURLEY
1,2
CONTENTS
I. Introduction: Neurospora crassa is an
Important Model Organism for Research in
Circadian Rhythms . . . . . . . . . . . . . . . . . . . . . . . . . 77
II. Input: Various Inputs to the Core Clock Allow
Phase Entrainment to the External
Environment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
A. Neurospora crassa, the Circadian Clock, and
Photoreception . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
B. The Effect of Temperature on the Negative
Arm of the Clock . . . . . . . . . . . . . . . . . . . . . . . . . 82
C. The Impact of Nutrient Sensing on the
Circadian Clock . . . . . . . . . . . . . . . . . . . . . . . . . . 83
III. Core Oscillator: The N. crassa Core Circadian
Timekeeping Mechanism . . . . . . . . . . . . . . . . . . . 84
A. The Transcriptionally Active Positive Arm
of the Clock . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
B. The Negative Arm of the Clock . . . . . . . . . . . 85
C. The Negative Arm Represses the Positive
Arm to Close the TTFL . . . . . . . . . . . . . . . . . . . 88
D. Post-translational Modifications in Clock
Regulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
E. Ubiquitination and Degradation Contribute
to a Robust Circadian Clock . . . . . . . . . . . . . . 90
IV. Output: Clock Output Regulates Cellular
Physiology at the Transcriptional and Posttranscriptional Levels . . . . . . . . . . . . . . . . . . . . . . . 91
A. Transcriptional Regulation of Cellular
Output via the Circadian Clock . . . . . . . . . . 91
B. Post-transcriptional Regulation via the
Circadian Clock . . . . . . . . . . . . . . . . . . . . . . . . . . 92
C. Circadian Output Interfaces with Many
Cellular Systems . . . . . . . . . . . . . . . . . . . . . . . . . . 93
V. Methods for Detecting Circadian
Rhythms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
VI. Clock Conservation in Fungi . . . . . . . . . . . . . . . . 95
VII. Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
I. Introduction: Neurospora crassa is
an Important Model Organism for
Research in Circadian Rhythms
Many organisms have evolved an anticipatory
mechanism called the circadian clock to predict
the consistent and dramatic daily changes in the
levels of light, temperature, and UV radiation
imposed by the Earth’s rotation. Importantly,
there is a strong correlation between the maintenance of a molecular clock that generates circadian (around 24 h) oscillations in a variety of
behavioral and molecular processes and the
biological fitness of an organism. For example,
when different cyanobacteria strains are grown
together, the strain whose circadian period is
most closely aligned to an artificially generated
light-dark cycle will outcompete the other
strains to become the predominant organism in
the environment (Ouyang et al. 1998). In addition, squirrels and chipmunks with functioning
clocks have a higher survival rate against predators as compared to those with a dysfunctional
circadian clock (DeCoursey et al. 1997, 2000;
DeCoursey 2014). Proper circadian timing
also increases the virulence of some fungi during
plant infection (Hevia et al. 2015). Indeed, we
know that innumerable biological functions are
timed by the clock to occur at their optimal
phase of the day (e.g., Hurley et al. 2014, 2018;
Panda et al. 2002), and the benefits of these
circadian rhythms have led them to be conserved
in almost all branches of life (Dunlap 1999).
Authors “Meaghan S. Jankowski” and “Zachary A. Chase”
contributed equally.
1 Department of Biological Sciences, Rensselaer Polytechnic
Institute, Troy, NY, USA; e-mail: hurlej2@rpi.edu
2 Center
for
Biotechnology
and
Interdisciplinary
Sciences, Rensselaer Polytechnic Institute, Troy, NY, USA
Genetics and Biotechnology, 3 rd Edition
The Mycota II
J.P. Benz, K. Schipper (Eds.)
© Springer Nature Switzerland AG 2020
Neurospora crassa
MEAGHAN S. JANKOWSKI
1
, ZACHARY A. CHASE
1
, JENNIFER M. HURLEY
1,2
CONTENTS
I. Introduction: Neurospora crassa is an
Important Model Organism for Research in
Circadian Rhythms . . . . . . . . . . . . . . . . . . . . . . . . . 77
II. Input: Various Inputs to the Core Clock Allow
Phase Entrainment to the External
Environment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
A. Neurospora crassa, the Circadian Clock, and
Photoreception . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
B. The Effect of Temperature on the Negative
Arm of the Clock . . . . . . . . . . . . . . . . . . . . . . . . . 82
C. The Impact of Nutrient Sensing on the
Circadian Clock . . . . . . . . . . . . . . . . . . . . . . . . . . 83
III. Core Oscillator: The N. crassa Core Circadian
Timekeeping Mechanism . . . . . . . . . . . . . . . . . . . 84
A. The Transcriptionally Active Positive Arm
of the Clock . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
B. The Negative Arm of the Clock . . . . . . . . . . . 85
C. The Negative Arm Represses the Positive
Arm to Close the TTFL . . . . . . . . . . . . . . . . . . . 88
D. Post-translational Modifications in Clock
Regulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
E. Ubiquitination and Degradation Contribute
to a Robust Circadian Clock . . . . . . . . . . . . . . 90
IV. Output: Clock Output Regulates Cellular
Physiology at the Transcriptional and Posttranscriptional Levels . . . . . . . . . . . . . . . . . . . . . . . 91
A. Transcriptional Regulation of Cellular
Output via the Circadian Clock . . . . . . . . . . 91
B. Post-transcriptional Regulation via the
Circadian Clock . . . . . . . . . . . . . . . . . . . . . . . . . . 92
C. Circadian Output Interfaces with Many
Cellular Systems . . . . . . . . . . . . . . . . . . . . . . . . . . 93
V. Methods for Detecting Circadian
Rhythms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
VI. Clock Conservation in Fungi . . . . . . . . . . . . . . . . 95
VII. Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
I. Introduction: Neurospora crassa is
an Important Model Organism for
Research in Circadian Rhythms
Many organisms have evolved an anticipatory
mechanism called the circadian clock to predict
the consistent and dramatic daily changes in the
levels of light, temperature, and UV radiation
imposed by the Earth’s rotation. Importantly,
there is a strong correlation between the maintenance of a molecular clock that generates circadian (around 24 h) oscillations in a variety of
behavioral and molecular processes and the
biological fitness of an organism. For example,
when different cyanobacteria strains are grown
together, the strain whose circadian period is
most closely aligned to an artificially generated
light-dark cycle will outcompete the other
strains to become the predominant organism in
the environment (Ouyang et al. 1998). In addition, squirrels and chipmunks with functioning
clocks have a higher survival rate against predators as compared to those with a dysfunctional
circadian clock (DeCoursey et al. 1997, 2000;
DeCoursey 2014). Proper circadian timing
also increases the virulence of some fungi during
plant infection (Hevia et al. 2015). Indeed, we
know that innumerable biological functions are
timed by the clock to occur at their optimal
phase of the day (e.g., Hurley et al. 2014, 2018;
Panda et al. 2002), and the benefits of these
circadian rhythms have led them to be conserved
in almost all branches of life (Dunlap 1999).
Authors “Meaghan S. Jankowski” and “Zachary A. Chase”
contributed equally.
1 Department of Biological Sciences, Rensselaer Polytechnic
Institute, Troy, NY, USA; e-mail: hurlej2@rpi.edu
2 Center
for
Biotechnology
and
Interdisciplinary
Sciences, Rensselaer Polytechnic Institute, Troy, NY, USA
Genetics and Biotechnology, 3 rd Edition
The Mycota II
J.P. Benz, K. Schipper (Eds.)
© Springer Nature Switzerland AG 2020