Cell Cycle Profiling Reveals Protein Oscillation, Phosphorylation, and Localization Dynamics

Abstract

The cell cycle is a highly conserved process involving the coordinated separation of a single cell into two daughter cells. To relate transcriptional regulation across the cell cycle with oscillatory changes in protein abundance and activity, we carried out a proteome- and phospho-proteome-wide mass spectrometry profiling. We compared protein dynamics with gene transcription, revealing many transcriptionally regulated G2 mRNAs that only produce a protein shift after mitosis. Integration of CRISPR/Cas9 survivability studies further highlighted proteins essential for cell viability. Analyzing the dynamics of phosphorylation events and protein solubility dynamics over the cell cycle, we characterize predicted phospho-peptide motif distributions and predict cell cycle-dependent translocating proteins, as exemplified by the S-adenosylmethionine synthase MAT2A. Our study implicates this enzyme in translocating to the nucleus after the G1/S-checkpoint, which enables epigenetic histone methylation maintenance during DNA replication. Taken together, this data set provides a unique integrated resource with novel insights on cell cycle dynamics.

Low cell number proteomic analysis using in-cell protease digests reveals a robust signature for cell cycle state classification

“…The frequency of PsPs identified (1.7%, 119 / 6,899) compares well with a recent antibody-based screen for cell cycle regulated proteins (2.6%, 331 / 12,390) [48]. Included in 331 hits are proteins that vary in subcellular localization but not abundance across the cell cycle, consistent with other datasets using biochemical fractionation [49]. PsPs identified in this study will be limited to proteins that change in abundance.…”

Proteogenomic characterization of pancreatic ductal adenocarcinoma

“…Interestingly, mutations in TP53 were associated with an increase in phosphorylation of proteins involved in DNA damage repair pathways (e.g., MSH6, TP53, and TP53BP1), which suggests that these alterations play a role in maintaining genome integrity and preventing apoptosis (Figure 2C). In TP53 mutant tumors, we also observed higher phosphorylation of MKI67, a marker for cellular proliferation, which implies that these mutations may lead to increased cell growth rates (Herr et al, 2020). We further explored the effects of TP53 missense mutations compared to truncating mutations and observed a significantly greater cis-effect with higher TP53 protein expression and TP53-S315 phosphosite expression in the TP53 missense group compared to the wild-type group (Figure S2A), while there were no significant TP53 protein changes in cis-effects between the truncation and wild-type groups (Figure S2A).…”

MAT2A Localization and Its Independently Prognostic Relevance in Breast Cancer Patients

“…maintenance during DNA replication [31]. This study pointed out a significant role of MAT2A in cell cycle and possibly cell proliferation.…”

“…Proteome-wide mass spectrometry profiling revealed that MAT2A is among the cell cycle-dependent translocating proteins. Further analyses indicated that MAT2A may translocate to the nucleus after the G1/S-checkpoint, which enables epigenetic histone methylation maintenance during DNA replication [31]. This study pointed out a significant role of MAT2A in cell cycle and possibly cell proliferation.…”

“…Using the GEPIA, a poorer breast cancer survival was observed in patients with higher MAT2A mRNA level, suggesting a potential role of MAT2A in breast cancer development. Previous in vitro cell cycle profiling in Hela cells revealed that the translocation of MAT2A to the nucleus occurred after G1/S checkpoint, which enabled epigenetic histone methylation during DNA replication on cell cycle dynamics [31]. Despite the potential regulatory role of MAT2A translocation in tumor development, whether MAT2A distribution affect in breast cancer progression is unknown, thus we aimed to explore the relationship between MAT2A distribution and breast cancer clinical indicators.…”