VI. Clock Conservation in Fungi
Neurospora crassa is not only a model for
clocks in higher eukaryotes but is a model for
clocks in other fungi. An analysis of 64 fungal
genomes based on the N. crassa circadian genes
frq, wc-1, wc-2, frh, and fwd-1 (Salichos and
Rokas 2010) showed that FRH and FWD-1
were the earliest conserved clock proteins, not
surprising based on their other essential functions in the organism (Jonkers and Rep 2009;
Putnam and Jankowsky 2013). WC-1 and WC2 are further along the evolutionary tree and
FRQ is the most recently evolved protein, with
sequential homologs appearing in only three
classes within the Ascomycetes: Sordariomycetes, Leotiomycetes, and Dothideomycetes
(Salichos and Rokas 2010). However, as FRQ
is a known IDP, and it has been documented
that there is little conservation of sequence
among IDPs, it is likely that the functional
homologs of FRQ may not have sequence
homology and that other negative arm proteins
exist in the wider fungal families (Hurley et al.
2013). Though many species contain homologs
of clock proteins, and some even display oscillatory phenotypes (e.g., Podospora anserina),
so far only a few fungi that display measurable
phenotypic or molecular rhythms have been
shown to be truly circadian, such as the
rhythms in Ascomycetes Sordaria fimicola, Pyronema confluens, Botrytis cinerea, Aspergillus
flavus, and Cercospora kikuchii and the Basidiomycete Neonothopanus gardneri (Brandt
1953; Austin 1968; Lysek and Esser 1970;
Greene et al. 2003; Bluhm et al. 2010; Hevia
et al. 2015, 2016; Traeger and Nowrousian
2015).
B. cinerea has the best molecular and phenotypic evidence for a fungal circadian clock
outside of N. crassa (Montenegro-Montero et al.
2015). It has orthologues of frq, wc-1, and wc2 (bcfrq1, bcwcl1, and bcwcl2, respectively), and
the clock has been shown to maximize virulence through the control of its sexual and
asexual cycle (Schumacher and Tudzynski
2012; Canessa et al. 2013; Hevia et al. 2015). In
contrast, while the Aspergillus family does not
contain a recognized frq homolog, they do have
wc-1 and wc-2 homologs and evidence of circadian regulation. The level of the gpdA gene may
oscillate under free running conditions in A.
nidulans, and A. flavus has rhythms in sclerotia
formation (Greene et al. 2003). Cercospora
kikuchii, of the Dothideomycetes subclass, displays phenotypic rhythms through concentric
hyphal rings which persist on Petri dishes
under free-running conditions for several days
that are both temperature-compensated and
dependent on a white collar-like gene (Bluhm
et al. 2010). Through these examples it can be
seen that the clock of N. crassa can be used to
gain further insights into the clocks of other
fungi.
VII. Summary
Neurospora crassa is a key model organism for
research into the molecular mechanism of the
circadian clock. All of the above discussed elements of clock function were, at least in part,
discovered through the use of molecular and
genetic techniques in N. crassa. The more that
is understood about the clock in N. crassa,
including the similarity of its basic architecture
and circadian output to the clocks in higher
eukaryotes, the more we understand what this
organism has to contribute as a model system
to studies of clocks in other eukaryotes. It is
therefore likely that N. crassa will continue to
contribute as a model for circadian and fungal
research for years to come.
Acknowledgments This work was supported by a NIHNational Institute of General Medical Sciences T32
Training Grant GM067545 (M.S.J. and Z.A.C), a NIHNational Institute of Biomedical Imaging and Bioengineering Grant EB022546 (J.M.H.), a NIH-National Institute of General Medical Sciences Grant GM128687 (J.M.
H.), and Rensselaer Polytechnic Startup funds (J.M.H.).
References
Adhvaryu K, Firoozi G, Motavaze K, Lakin-Thomas P
(2016) PRD-1, a component of the circadian
system of Neurospora crassa, is a member of
the DEAD-box RNA helicase family. J Biol
Rhythm 31:258–271. https://doi.org/10.1177/
0748730416639717
4 From Genetics to Molecular Oscillations: The Circadian Clock in Neurospora crassa
95
Neurospora crassa is not only a model for
clocks in higher eukaryotes but is a model for
clocks in other fungi. An analysis of 64 fungal
genomes based on the N. crassa circadian genes
frq, wc-1, wc-2, frh, and fwd-1 (Salichos and
Rokas 2010) showed that FRH and FWD-1
were the earliest conserved clock proteins, not
surprising based on their other essential functions in the organism (Jonkers and Rep 2009;
Putnam and Jankowsky 2013). WC-1 and WC2 are further along the evolutionary tree and
FRQ is the most recently evolved protein, with
sequential homologs appearing in only three
classes within the Ascomycetes: Sordariomycetes, Leotiomycetes, and Dothideomycetes
(Salichos and Rokas 2010). However, as FRQ
is a known IDP, and it has been documented
that there is little conservation of sequence
among IDPs, it is likely that the functional
homologs of FRQ may not have sequence
homology and that other negative arm proteins
exist in the wider fungal families (Hurley et al.
2013). Though many species contain homologs
of clock proteins, and some even display oscillatory phenotypes (e.g., Podospora anserina),
so far only a few fungi that display measurable
phenotypic or molecular rhythms have been
shown to be truly circadian, such as the
rhythms in Ascomycetes Sordaria fimicola, Pyronema confluens, Botrytis cinerea, Aspergillus
flavus, and Cercospora kikuchii and the Basidiomycete Neonothopanus gardneri (Brandt
1953; Austin 1968; Lysek and Esser 1970;
Greene et al. 2003; Bluhm et al. 2010; Hevia
et al. 2015, 2016; Traeger and Nowrousian
2015).
B. cinerea has the best molecular and phenotypic evidence for a fungal circadian clock
outside of N. crassa (Montenegro-Montero et al.
2015). It has orthologues of frq, wc-1, and wc2 (bcfrq1, bcwcl1, and bcwcl2, respectively), and
the clock has been shown to maximize virulence through the control of its sexual and
asexual cycle (Schumacher and Tudzynski
2012; Canessa et al. 2013; Hevia et al. 2015). In
contrast, while the Aspergillus family does not
contain a recognized frq homolog, they do have
wc-1 and wc-2 homologs and evidence of circadian regulation. The level of the gpdA gene may
oscillate under free running conditions in A.
nidulans, and A. flavus has rhythms in sclerotia
formation (Greene et al. 2003). Cercospora
kikuchii, of the Dothideomycetes subclass, displays phenotypic rhythms through concentric
hyphal rings which persist on Petri dishes
under free-running conditions for several days
that are both temperature-compensated and
dependent on a white collar-like gene (Bluhm
et al. 2010). Through these examples it can be
seen that the clock of N. crassa can be used to
gain further insights into the clocks of other
fungi.
VII. Summary
Neurospora crassa is a key model organism for
research into the molecular mechanism of the
circadian clock. All of the above discussed elements of clock function were, at least in part,
discovered through the use of molecular and
genetic techniques in N. crassa. The more that
is understood about the clock in N. crassa,
including the similarity of its basic architecture
and circadian output to the clocks in higher
eukaryotes, the more we understand what this
organism has to contribute as a model system
to studies of clocks in other eukaryotes. It is
therefore likely that N. crassa will continue to
contribute as a model for circadian and fungal
research for years to come.
Acknowledgments This work was supported by a NIHNational Institute of General Medical Sciences T32
Training Grant GM067545 (M.S.J. and Z.A.C), a NIHNational Institute of Biomedical Imaging and Bioengineering Grant EB022546 (J.M.H.), a NIH-National Institute of General Medical Sciences Grant GM128687 (J.M.
H.), and Rensselaer Polytechnic Startup funds (J.M.H.).
References
Adhvaryu K, Firoozi G, Motavaze K, Lakin-Thomas P
(2016) PRD-1, a component of the circadian
system of Neurospora crassa, is a member of
the DEAD-box RNA helicase family. J Biol
Rhythm 31:258–271. https://doi.org/10.1177/
0748730416639717
4 From Genetics to Molecular Oscillations: The Circadian Clock in Neurospora crassa
95