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Impact of Exposure to Chronic Light-Dark Phase Shifting Circadian Disruptions on Muscle Proteome in Periparturient Dairy Cows and Relationship of Proteome to Markers of Metabolic Status

ABSTRACT: Circadian rhythms are present in all tissues and cells to help animals anticipate the timing of daily events. Proteomic analysis of muscle tissue from dairy cattle exposed to a 6 hr forward phase shift during the late gestational period resulted in a greater abundance of proteins related to oxidative phosphorylation and stress at 21 d before expected calving.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Bos Taurus (ncbitaxon:9913)

SUBMITTER: Theresa M Casey

PROVIDER: MSV000087432 | MassIVE | Fri May 14 14:19:00 BST 2021

REPOSITORIES: MassIVE

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Project description:The circadian clock is an evolutionary system that allows organisms to anticipate and thus adapt to daily changes in the environment. In mammals, the circadian clock is found in virtually every tissue regulating rhythms of metabolism and physiology. While a lot of studies have focused in how circadian clocks regulate gene expression little is known about daily control of protein abundance. Here we applied state of the art mass spectrometry in combination with quantitative proteomics to investigate global circadian oscillations of the proteome in the mouse liver. We found that approximately 6% of the liver proteins are cycling daily and interestingly the majority of these oscillations diverge from the behavior of their transcripts. Our data indicates that post-transcriptional mechanisms play an essential role in shaping the phase of rhythmic proteins downstream of transcription regulation to ultimately drive rhythms of metabolism. Moreover, the contribution of post-transcriptional regulation seems to differ among distinct metabolic pathways. Overall we not only found circadian oscillations in the abundance of proteins involved in liver specific metabolic pathways but also in essential cellular processes. Data processing: Raw MS files were processed with MaxQuant (version. 1.1.1.9), a freely available software suite. Peak list files were searched by the ANDROMEDA a search engine, incorporated into the MaxQuant framework, against the IPI-mouse (version 3.68) containing both forward and reversed protein sequences. Initial maximum precursor and fragment mass deviations were set to 7 ppm and 0.5 Da, respectively, but MaxQuant achieved sub-ppm mass accuracy for the majority of peptide precursors. The search included variable modifications for oxidation of methionine, protein N-terminal acetylation and carbamidomethylation as fixed modification. Peptides with at least six amino acids were considered for identification specifying as enzyme LysC allowing N-terminal cleavage to proline. The false discovery rate, determined by searching a reverse database, was set at 0.01 for both peptides and proteins. Identification across different replicates and adjacent fractions was achieved by enabling matching between runs option in MaxQuant within a time window of 2 minutes. Quantification of SILAC pairs was performed by MaxQuant with standard settings using a minimum ratio count of 2.

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Impact of Exposure to Chronic Light-Dark Phase Shifting Circadian Disruptions on Muscle Proteome in Periparturient Dairy Cows and Relationship of Proteome to Markers of Metabolic Status

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