Alterations in the liver phosphoproteome of finishing cattle with divergent dry matter intake

Variation in voluntary dry matter intake (DMI) is an important component of feed efficiency in finishing cattle; however, the molecular processes associated with individual variation in DMI remain poorly understood. The liver contributes to DMI regulation through both cell signaling and vagal signaling. The objective of this study was to investigate alterations in the phosphoproteome of finishing beef steers with divergent DMI to identify hepatic molecular processes associated with variation in voluntary feed intake. Fifty-four Angus steers (initial body weight = 518 ± 27 kg) underwent a 63-day intake trial using the Insentec Roughage Intake Control System (Hokofarm Group, Emmeloord, The Netherlands). Liver biopsy samples were collected 2 days prior to trial initiation. Samples from steers with the highest and lowest DMI (n = 8 each) were used for phosphoproteomic analysis. Proteins were labeled with isobaric tandem mass tagging reagents, enriched for phosphopeptides, and analyzed by high-performance liquid chromatography tandem mass spectrometry, with spectral data searched and analyzed using MaxQuant (version 2.2.0.0; Max Planck Inst., Munich, Germany) and Perseus (version 2.0.10.0; Max Planck Inst.). Data are available via ProteomeXchange with identifier PXD083668. A total of 16,365 phosphopeptides and 13,808 phosphosites were identified. There were 310 differentially abundant phosphopeptides and 1,158 differentially abundant phosphosites (False Discovery Rate < 0.05). For functional enrichment analysis, 2,777 phosphopeptides meeting an unadjusted P < 0.05 were used as input, and Gene Ontology processes and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were evaluated. Phosphosite data were used for kinase-substrate enrichment analysis (KSEApp package in R). Three enriched Gene Ontology terms were identified: nucleosome, structural constituent of chromatin, and RNA binding. Enriched KEGG pathways included adipocytokine signaling, insulin signaling, and insulin resistance. There were 43 enriched kinases following multiple-testing correction within KSEApp. Collectively, these results demonstrate differences in the hepatic phosphoproteome of cattle with divergent DMI and identify hepatic signaling pathways associated with variation in voluntary feed intake. These pathway-level findings provide potential targets for further investigation but do not establish causal mechanisms regulating DMI.