Multitissue Circadian Proteome Atlas of WT and Per1−/−/Per2−/− Mice

Abstract

•11,651 proteins are quantified in multitissue circadian proteome atlas.•Proteome rhythm reflects circadian anticipatory phenomena.•Tissue-specific protein cyclers in the WT mice are mainly PER-dependent.•Diminished oscillations in nucleotide excision repair in DKO mice. The molecular basis of circadian rhythm, driven by core clock genes such as Per1/2, has been investigated on the transcriptome level, but not comprehensively on the proteome level. Here we quantified over 11,000 proteins expressed in eight types of tissues over 46 h with an interval of 2 h, using WT and Per1/Per2 double knockout mouse models. The multitissue circadian proteome landscape of WT mice shows tissue-specific patterns and reflects circadian anticipatory phenomena, which are less obvious on the transcript level. In most peripheral tissues of double knockout mice, reduced protein cyclers are identified when compared with those in WT mice. In addition, PER1/2 contributes to controlling the anticipation of the circadian rhythm, modulating tissue-specific cyclers as well as key pathways including nucleotide excision repair. Severe intertissue temporal dissonance of circadian proteome has been observed in the absence of Per1 and Per2. The γ-aminobutyric acid might modulate some of these temporally correlated cyclers in WT mice. Our study deepens our understanding of rhythmic proteins across multiple tissues and provides valuable insights into chronochemotherapy. The data are accessible at https://prot-rhythm.prottalks.com/. The molecular basis of circadian rhythm, driven by core clock genes such as Per1/2, has been investigated on the transcriptome level, but not comprehensively on the proteome level. Here we quantified over 11,000 proteins expressed in eight types of tissues over 46 h with an interval of 2 h, using WT and Per1/Per2 double knockout mouse models. The multitissue circadian proteome landscape of WT mice shows tissue-specific patterns and reflects circadian anticipatory phenomena, which are less obvious on the transcript level. In most peripheral tissues of double knockout mice, reduced protein cyclers are identified when compared with those in WT mice. In addition, PER1/2 contributes to controlling the anticipation of the circadian rhythm, modulating tissue-specific cyclers as well as key pathways including nucleotide excision repair. Severe intertissue temporal dissonance of circadian proteome has been observed in the absence of Per1 and Per2. The γ-aminobutyric acid might modulate some of these temporally correlated cyclers in WT mice. Our study deepens our understanding of rhythmic proteins across multiple tissues and provides valuable insights into chronochemotherapy. The data are accessible at https://prot-rhythm.prottalks.com/. In mammals, physical, mental, and behavioral activities usually exhibit a 24-h oscillation pattern, which is called the circadian rhythm. The suprachiasmatic nuclei (SCN) in the brain not only maintains its own circadian rhythm but also functions as the master pacemaker to synchronize the rhythm of peripheral tissues in both day-night (i.e. light-dark, LD) and constant darkness (i.e. dark-dark, DD) conditions (1Welsh D.K. Takahashi J.S. Kay S.A. Suprachiasmatic nucleus: cell autonomy and network properties.Annu. Rev. Physiol. 2010; 72: 551-577Crossref PubMed Scopus (903) Google Scholar). The major molecular basis for circadian rhythm is an autoregulatory transcriptional-translational feedback loop (TTFL), which is expressed in almost every cell. In the TTFL, two transcriptional factors, namely CLOCK and BMAL1, form a heterodimer that can initiate transcription of multiple target genes containing a specific DNA sequence called E-box. Two major groups of these target genes are PERIOD (Per1, Per2, and Per3) and cryptochrome (Cry1 and Cry2) (2Lowrey P.L. Takahashi J.S. Mammalian circadian biology: elucidating genome-wide levels of temporal organization.Annu. Rev. Genomics Hum. Genet. 2004; 5: 407-441Crossref PubMed Scopus (787) Google Scholar). PERs and CRYs form a protein complex, which then translocates to the nucleus and represses the CLOCK-BMAL1 complex-induced transcription, thereby establishing the negative feedback loop (2Lowrey P.L. Takahashi J.S. Mammalian circadian biology: elucidating genome-wide levels of temporal organization.Annu. Rev. Genomics Hum. Genet. 2004; 5: 407-441Crossref PubMed Scopus (787) Google Scholar). In core clock gene KO models, such as Bmal1−/− mice, Per1−/−; Per2−/− mice, and Cry1−/−; Cry2−/− mice, locomotor rhythmicity has been reported to be abolished in DD (3Bunger M.K. Wilsbacher L.D. Moran S.M. Clendenin C. Radcliffe L.A. Hogenesch J.B. et al.Mop3 is an essential component of the master circadian pacemaker in mammals.Cell. 2000; 103: 1009-1017Abstract Full Text Full Text PDF PubMed Scopus (1241) Google Scholar, 4Zheng B. Albrecht U. Kaasik K. Sage M. Lu W. Vaishnav S. et al.Nonredundant roles of the mPer1 and mPer2 genes in the mammalian circadian clock.Cell. 2001; 105: 683-694Abstract Full Text Full Text PDF PubMed Scopus (739) Google Scholar, 5van der Horst G.T. Muijtjens M. Kobayashi K. Takano R. Kanno S. Takao M. et al.Mammalian Cry1 and Cry2 are essential for maintenance of circadian rhythms.Nature. 1999; 398: 627-630Crossref PubMed Scopus (1161) Google Scholar). However, retained oscillations in transcripts, proteins, and protein phosphorylation are still observed in ex vivo skin fibroblasts and liver slices from Bmal1−/− mice (6Ray S. Valekunja U.K. Stangherlin A. Howell S.A. Snijders A.P. Damodaran G. et al.Circadian rhythms in the absence of the clock gene Bmal1.Science. 2020; 367: 800-806Crossref PubMed Scopus (110) Google Scholar). This sustained rhythmicity in molecules may be mediated by E26 transformation-specific factors and redox oscillations (6Ray S. Valekunja U.K. Stangherlin A. Howell S.A. Snijders A.P. Damodaran G. et al.Circadian rhythms in the absence of the clock gene Bmal1.Science. 2020; 367: 800-806Crossref PubMed Scopus (110) Google Scholar). In addition, more rhythmic proteins with higher amplitude are identified in the ex vivo lung fibroblasts from Cry1−/−; Cry2−/− mice than that in the WT mice, probably due to CRYs’ function on protein homeostasis (7Wong D.C.S. Seinkmane E. Zeng A. Stangherlin A. Rzechorzek N.M. Beale A.D. et al.CRYPTOCHROMES promote daily protein homeostasis.EMBO J. 2022; 41e108883Crossref Google Scholar). In mouse liver, the daily oscillation in key mitochondrial enzymes and their substrates has been reported to be dependent on the PERIOD proteins (8Neufeld-Cohen A. Robles M.S. Aviram R. Manella G. Adamovich Y. Ladeuix B. et al.Circadian control of oscillations in mitochondrial rate-limiting enzymes and nutrient utilization by PERIOD proteins.Proc. Natl. Acad. Sci. U. S. A. 2016; 113: E1673-1682Crossref PubMed Scopus (164) Google Scholar). However, the role of PERIOD in the circadian proteome, especially in multiple organs and tissues in vivo, remains elusive. are and the can synchronize the peripheral the and of circadian cyclers are tissue-specific at the transcriptional level. et the circadian transcriptome of mouse organs and the of rhythmic from the to the R. Hogenesch J.B. circadian gene in for and Natl. Acad. Sci. U. S. A. PubMed Scopus Google in more than transcriptome study of tissues also observed tissue-specific rhythmic patterns G. et transcriptome of a across major and peripheral PubMed Scopus Google Scholar). the to the circadian molecular across the multiple The molecular basis of circadian rhythm driven by has been investigated on the transcriptome R. Hogenesch J.B. circadian gene in for and Natl. Acad. Sci. U. S. A. PubMed Scopus Google Scholar, G. et transcriptome of a across major and peripheral PubMed Scopus Google Scholar, A. M. The of the of PubMed Google Scholar, et al.Circadian of the mouse liver as by is driven by the suprachiasmatic Full Text Full Text PDF PubMed Scopus Google Scholar, S. C. et al.Circadian in by transcriptome and network PubMed Scopus Google Scholar, et of the circadian transcriptome in mouse PubMed Scopus Google Scholar, S. J. et al.Circadian and of the mouse transcriptome and cell Natl. Acad. Sci. U. S. A. PubMed Scopus Google Scholar). However, the not with its protein level. In the of proteins are by Y. A. R. the of protein levels on 2016; Full Text Full Text PDF PubMed Google Scholar). proteome reported that M.S. J. M. a key of to the circadian of liver Genet. PubMed Scopus Google to J. C. E. et al.Circadian and rhythmic functions in mouse Natl. Acad. Sci. U. S. A. PubMed Scopus Google of these proteins are by transcripts, to of rhythmic proteins are by genes J. E. et in mouse Full Text Full Text PDF PubMed Scopus Google Scholar). for the of the rhythmic genes at both protein and transcript more than has been identified in the protein cyclers than transcript The circadian proteome has been in such as the A. J. et landscape of the suprachiasmatic nucleus clock of key Genet. PubMed Scopus Google B. J. K. et circadian clock of in the PubMed Scopus Google circadian in temporally PubMed Google M. C. C. et al.Circadian daily in Full Text Full Text PDF PubMed Scopus Google and Y. C. S. G. et control of and by the circadian PubMed Scopus Google Scholar). However, the is to these the role of protein rhythms in circadian the and of R. M. of proteome and 2016; PubMed Scopus Google Scholar, et of into proteome PubMed Scopus Google Scholar, R. B. et landscape of Full Text Full Text PDF PubMed Scopus Google Scholar, B. Y. J. C. et and of 2020; Full Text Full Text PDF PubMed Scopus Google Scholar, J. Y. M. et and of in Scopus Google Scholar). However, is proteins to the multitissue circadian we a mouse circadian proteome from WT and Per1−/−; Per2−/− double knockout mice constant darkness and from eight tissues every 2 h over 2 and with over 11,000 proteins quantified in the eight we identified and proteins from the WT and DKO mice, This understanding of the molecular basis of circadian rhythm on protein and the molecular by the by the and of WT mice from with the Per1 and genes as B. Albrecht U. Kaasik K. Sage M. Lu W. 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In cyclers from the of the protein cyclers the of from the to that the protein rhythm in the in the anticipation of the of proteins in the DKO mice to that of the WT mice, we observed a In the DKO mice, the of tissues a and only a across tissues and the in the DKO mice of those protein cyclers that at and in the WT mice the PER1/2 may control the anticipation of the circadian rhythm. investigated the of cyclers in the WT mice. of the protein cyclers higher than the cyclers and that not by gene levels across the eight we also the tissue-specific cyclers on the genes quantified at both the transcriptome and the proteome levels with we still a higher of tissue-specific protein cyclers than cyclers in and This that the higher of tissue-specific protein rhythm is to be to the higher of tissue-specific proteins when the of cyclers to multiple we observed that but only protein cyclers tissues the to for and for protein cyclers when more than tissues of and in the tissue-specific the of in protein and the of we on cyclers with a D.C.S. Stangherlin Zeng A. Rzechorzek N.M. Beale A.D. J. et the circadian proteome and protein homeostasis.EMBO J. 2020; Scholar). the the of tissue-specific cyclers in both the WT and the DKO mice and the cyclers with and cyclers over cyclers of tissue-specific in the WT and the DKO mice, and the liver as an in the WT a of cyclers of which specific to the In the of the DKO of cyclers to be specific to liver In the WT mice, the tissue-specific cyclers with also in the of the such as the in and in and and we identified cyclers that in the WT mice and in protein and and and and and of proteins in these the protein and the protein of the and the factors proteins and and the protein the cyclers in the DKO mice with mitochondrial and and and the circadian of our two mice at been driven by these insights into the functions and of protein cyclers in the WT mice, we to pathways for cyclers with and temporal at a specific circadian R. 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PubMed Scopus Google Scholar). to be and at is which is mainly in is to into the is in and J. S. of a Full Text Full Text PDF PubMed Scopus Google Scholar). Our data in with at and and may the circadian rhythms of the and the protein cyclers in the of and including and protein and at two proteins in mitochondrial Y. protein roles and in namely protein and both in of the WT mice and at our data that most of the tissue-specific cyclers in pathways are mainly by and the we a of the cyclers in the WT and DKO mice using that the pathways with nucleotide excision repair and in the WT mice the most we a by and with the WT mice still more cyclers than the DKO and and of we observed that circadian and rhythmic as well as DNA only in the WT mice and the that circadian rhythm in the DKO mice M. A. oscillation of nucleotide excision repair in mammalian Natl. Acad. Sci. U. S. A. PubMed Scopus Google Scholar, L.A. A. control of and excision repair of by cryptochrome and Natl. Acad. Sci. U. S. A. 2010; PubMed Scopus Google Scholar). the pathways in the WT mice, in most of the brain

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