morning-specific repression of CSP-1 target
genes (Sancar et al. 2011).
Carbon catabolite regulation-1 (CRE-1) is
also a WCC-regulated repressor that interacts
with RCO-1 and RCM-1 to inhibit the transcription of genes related to the use of alternative
carbon sources when glucose is present, otherwise known as carbon catabolite repression
(Bailey and Arst 1975; Hurley et al. 2014; Cupertino et al. 2015; Adnan et al. 2017). Among
other things, CRE-1 is an inhibitor of glycogen
synthesis and represses glycogenic genes, such
as gsn, gbn, and gnn (Cupertino et al. 2015).
Interestingly, the WCC and other WCC-target
transcription factors, such as Viability Of
Spores-1 (VOS-1) and CSP-1, also target these
glycogenic genes, highlighting the complexity
of clock regulation of ccgs (Smith et al. 2010;
Baek et al. 2019). An additional example, the
NOT1-CCR4 (negative on TATA 1-carbon
catabolite repression 4) complex regulates
WCC stability and is important for circadian
phase determination (Fig. 4.2a) (Huang et al.
2013). NOT1 acts directly on the WCC and its
mRNA displays circadian oscillations in a similar phase to frq (Huang et al. 2013). When
NOT1 or CCR4 levels are reduced, the clock’s
phase is delayed by 3–4 h (Huang et al. 2013).
These examples show that not all clock output
involves transcriptional activation but that
transcriptional repressors are also important
for the clock, including some clock-regulated
repressors that feedback onto the core clock
itself.
B. Post-transcriptional Regulation via the
Circadian Clock
While transcriptional regulation has long been
considered the primary output of the circadian
clock, recent research suggests that clock output is also regulated post-transcriptionally. The
initial evidence for this post-transcriptional
regulation is the mismatch between promoter
activation and steady state mRNA levels for a
given gene (Fig. 4.3a). There are many genes
whose promoters are rhythmically activated
but whose steady-state mRNA levels remain
constant and vice versa (Hurley et al. 2014).
This post-transcriptional regulation occurs at
the protein level as well, as approximately one
quarter of reliably detected proteins oscillate
with a circadian period but 40% of these arise
from transcripts that are not oscillating
(Fig. 4.3a) (Hurley et al. 2018). Moreover,
post-transcriptional regulation appears to be
circadianly directed. For example, differential
peak phase timing of enzymes that are rhythmic only at the protein level within central
metabolic pathways yields a coordination of
peak timing within pathways such as glycolysis
and the TCA cycle that peak anti-phase to the
alternate pentose-phosphate pathway (Hurley
et al. 2018). Many similar studies in higher
eukaryotes demonstrate that circadian posttranscriptional regulation is conserved (Beckwith and Yanovsky 2014; Koike et al. 2012;
Kojima et al. 2011).
There are several circadianly regulated
mechanisms that impart circadian posttranscriptional output, including mRNA degradation, translation rates, and protein degradation. The FFC interacts with components of the
exosome, which facilitate a circadian influence
over mRNA degradation (Guo et al. 2009). The
clock also regulates MAPK pathways that
impact the phosphorylation state of translation
factors, such as translation elongation factor
eEF-2 (Lamb et al. 2011, 2012; Bennett et al.
2013; Caster et al. 2016). eEF-2 has lower phosphorylation levels and therefore higher activity
near subjective dusk, a time when there seems
to be more energy available for translation, as
well as more translation initiation factors and
ribosomes (Fig. 4.3b) (Caster et al. 2016; Hurley
et al. 2018; Kafri et al. 2016). Finally, circadian
regulation of E3 ubiquitin ligases could yield
rhythms in protein degradation (Lu ¨ck et al.
2014; Hurley et al. 2018). As clock regulation
affects numerous additional cell regulatory systems, there may be many other avenues
through which the clock can direct posttranscriptional regulation (Hurley et al. 2014,
2018; Sancar et al. 2015).
92
M. S. Jankowski et al.
genes (Sancar et al. 2011).
Carbon catabolite regulation-1 (CRE-1) is
also a WCC-regulated repressor that interacts
with RCO-1 and RCM-1 to inhibit the transcription of genes related to the use of alternative
carbon sources when glucose is present, otherwise known as carbon catabolite repression
(Bailey and Arst 1975; Hurley et al. 2014; Cupertino et al. 2015; Adnan et al. 2017). Among
other things, CRE-1 is an inhibitor of glycogen
synthesis and represses glycogenic genes, such
as gsn, gbn, and gnn (Cupertino et al. 2015).
Interestingly, the WCC and other WCC-target
transcription factors, such as Viability Of
Spores-1 (VOS-1) and CSP-1, also target these
glycogenic genes, highlighting the complexity
of clock regulation of ccgs (Smith et al. 2010;
Baek et al. 2019). An additional example, the
NOT1-CCR4 (negative on TATA 1-carbon
catabolite repression 4) complex regulates
WCC stability and is important for circadian
phase determination (Fig. 4.2a) (Huang et al.
2013). NOT1 acts directly on the WCC and its
mRNA displays circadian oscillations in a similar phase to frq (Huang et al. 2013). When
NOT1 or CCR4 levels are reduced, the clock’s
phase is delayed by 3–4 h (Huang et al. 2013).
These examples show that not all clock output
involves transcriptional activation but that
transcriptional repressors are also important
for the clock, including some clock-regulated
repressors that feedback onto the core clock
itself.
B. Post-transcriptional Regulation via the
Circadian Clock
While transcriptional regulation has long been
considered the primary output of the circadian
clock, recent research suggests that clock output is also regulated post-transcriptionally. The
initial evidence for this post-transcriptional
regulation is the mismatch between promoter
activation and steady state mRNA levels for a
given gene (Fig. 4.3a). There are many genes
whose promoters are rhythmically activated
but whose steady-state mRNA levels remain
constant and vice versa (Hurley et al. 2014).
This post-transcriptional regulation occurs at
the protein level as well, as approximately one
quarter of reliably detected proteins oscillate
with a circadian period but 40% of these arise
from transcripts that are not oscillating
(Fig. 4.3a) (Hurley et al. 2018). Moreover,
post-transcriptional regulation appears to be
circadianly directed. For example, differential
peak phase timing of enzymes that are rhythmic only at the protein level within central
metabolic pathways yields a coordination of
peak timing within pathways such as glycolysis
and the TCA cycle that peak anti-phase to the
alternate pentose-phosphate pathway (Hurley
et al. 2018). Many similar studies in higher
eukaryotes demonstrate that circadian posttranscriptional regulation is conserved (Beckwith and Yanovsky 2014; Koike et al. 2012;
Kojima et al. 2011).
There are several circadianly regulated
mechanisms that impart circadian posttranscriptional output, including mRNA degradation, translation rates, and protein degradation. The FFC interacts with components of the
exosome, which facilitate a circadian influence
over mRNA degradation (Guo et al. 2009). The
clock also regulates MAPK pathways that
impact the phosphorylation state of translation
factors, such as translation elongation factor
eEF-2 (Lamb et al. 2011, 2012; Bennett et al.
2013; Caster et al. 2016). eEF-2 has lower phosphorylation levels and therefore higher activity
near subjective dusk, a time when there seems
to be more energy available for translation, as
well as more translation initiation factors and
ribosomes (Fig. 4.3b) (Caster et al. 2016; Hurley
et al. 2018; Kafri et al. 2016). Finally, circadian
regulation of E3 ubiquitin ligases could yield
rhythms in protein degradation (Lu ¨ck et al.
2014; Hurley et al. 2018). As clock regulation
affects numerous additional cell regulatory systems, there may be many other avenues
through which the clock can direct posttranscriptional regulation (Hurley et al. 2014,
2018; Sancar et al. 2015).
92
M. S. Jankowski et al.