Proteins associated with regulation of circadian system
Photoperiodic time measurement and seasonal responses involve the
circadian system. In mammals, the circadian basis of the seasonal
response, the circadian clock pacemaker, has been shown to communicate
with the GnRH1 neurons and the feeding center. In contrast, the avian
circadian clock consists of a multi-oscillatory system, and no firm
evidence has yet shown direct involvement of circadian clock molecules
in day length measurement and photoperiodic response (Singh et al.,
2015; Mishra et al., 2017). A few studies have shown expression of clock
gene(s), clock controlled genes, accessory clock genes, neuropeptides
and neuromodulators that transmit the photic information to a circadian
pacemaker located in the hypothalamus and further transduce these inputs
to brain areas involved in the regulation of GnRH secretory system, food
intake, locomotion, and energy homeostasis (Ward et al., 2009; Rastogi,
Kumari, Rani, & Kumar, 2013). Vasoactive intestinal peptide (VIP)
neuropeptide has been implicated in both synchronization of circadian
pacemaker cells in mammals (Vosko, Schroeder, Loh, Colwell, 2007) and
transduction of the photoperiodic response giving rise to reproduction
in birds (Macnamee, Sharp, Lea, Sterling, & Harvey, 1986; Teruyama &
Beck et al., 2001). Resident juncos showed higher abundance of VIP
protein, which may indicate that it has a role GnRH secretion and early
gonadal recrudescence. In migrants we found high abundance of
salt-inducible kinases 3 (SIK3) and TAR-binding protein 43 (TDP-43).
SIK3 is a protein involved in the stability of Period 2 (Per 2) and
cryptochromes 1, and 2 (Cry 1,2) respectively (Hirano et al., 2016;
Hayasaka et al., 2017). SIK3 and TDP-43 proteins have also been related
to energy homeostasis, glucose, cholesterol metabolism, and food intake
(Piguet et al., 2011; Hayasaka et al., 2017). These proteins could be
directly or indirectly involved in the preparation of pre-migratory
physiology.
While proteomics has emerged as a promising tool for clinical study in
humans and laboratory raised animals (Klose et al., 2002; Samara et al.,
2011), very few studies have addressed eco- physiological questions
relevant to seasonal timing and adaptation to changing environment. This
scant use of proteome experiments in non-model systems is probably due
to challenges in the proteome quantification methods, data analysis, and
statistical inference of the data (Kammers, Cole, Tiengwe , &
Ruczinski, 2015). Experimental design for quantitative proteomic studies
is not a trivial task, and key factors influencing successful
quantitative measurement of proteins includes number of biological
replicates, few replicates due to high reagent costs, limited time
availability of instruments, technical variation introduced during
preparation of samples, digestion, TMT labeling, fractionation, and MS
stages of LC-MS/MS analysis (Pascovici, Handler, Wu, & Haynes, 2016).
The TMT-labeling chemistry has the advantage of chemical labeling and
sample multiplexing to combine different samples into a single mixture
of peptide, which appears to be a suitable approach to overcome any
technical variation, batch effect, and increased quantitation of
peptides across different samples (O’Connell, Paulo, O’Brien, & Gygi,
2018).