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).