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Circadian rhythms and proteomics: It's all about posttranslational modifications!

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Abstract The circadian clock is a molecular endogenous timekeeping system and allows organisms to adjust their physiology and behavior to the geophysical time. Organized hierarchically, the master clock in the suprachiasmatic nuclei, coordinates peripheral clocks, via direct, or indirect signals. In peripheral organs, such as the liver, the circadian clock coordinates gene expression, notably metabolic gene expression, from transcriptional to posttranslational level. The metabolism in return feeds back on the molecular circadian clock via posttranslational‐based mechanisms. During the last two decades, circadian gene expression studies have mostly been relying primarily on genomics or transcriptomics approaches and transcriptome analyses of multiple organs/tissues have revealed that the majority of protein‐coding genes display circadian rhythms in a tissue specific manner. More recently, new advances in mass spectrometry offered circadian proteomics new perspectives, that is, the possibilities of performing large scale proteomic studies at cellular and subcellular levels, but also at the posttranslational modification level. With important implications in metabolic health, cell signaling has been shown to be highly relevant to circadian rhythms. Moreover, comprehensive characterization studies of posttranslational modifications are emerging and as a result, cell signaling processes are expected to be more deeply characterized and understood in the coming years with the use of proteomics. This review summarizes the work studying diurnally rhythmic or circadian gene expression performed at the protein level. Based on the knowledge brought by circadian proteomics studies, this review will also discuss the role of posttranslational modification events as an important link between the molecular circadian clock and metabolic regulation. This article is categorized under: Laboratory Methods and Technologies > Proteomics Methods Physiology > Mammalian Physiology in Health and Disease Biological Mechanisms > Cell Signaling
Hierarchical organization of the mammalian molecular circadian clock. BMAL1, brain and muscle Arnt‐like protein‐1; CCGs, clockcontrolled genes; CLOCK, circadian locomotor output cycles kaput; CRY, Cryptochromes (CRY1, CRY2); Dbp, D site of albumin promoter (albumin D‐box) binding protein; PER, Periods (PER1, PER2); REV‐ERB's, REV‐ERBA alpha (NR1D1: nuclear receptor subfamily 1, group D, member 1), REV‐ERBA beta (NR1D2: nuclear receptor subfamily 1, group D, member 2); ROR, Retinoid‐related orphan receptors; SCN, suprachiasmatic nuclei; ZT, zeitgeber time
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Quantitative mass spectrometry approaches used in circadian/diurnal studies: Red and gray boxes or tubes represent the different experimental conditions and the stars indicate the steps at which samples are labeled and combined allowing the quantification of relative protein abundance in the different experimental conditions. Earlier labeling and samples combination decreases the risk of quantification errors due to technical experimental variations. **In the case of label free, the combination is performed post data acquisition by computational treatment of the mass spectrometry data
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Experimental design of the SILAC diurnal proteomic experiment in mouse liver used in Mauvoisin et al. (). SILAC, stable‐isotope labeling by amino acids in cell culture
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Biological Mechanisms > Cell Signaling
Physiology > Mammalian Physiology in Health and Disease
Laboratory Methods and Technologies > Proteomics Methods

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