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

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.

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Cell cycle-dependent phosphorylation and regulation of cellular differentiation

Biochemical Society Transactions ◽

10.1042/bst20180276 ◽

2018 ◽

Vol 46 (5) ◽

pp. 1083-1091 ◽

Cited By ~ 5

Author(s):

Laura J.A. Hardwick ◽

Roberta Azzarelli ◽

Anna Philpott

Keyword(s):

Cell Cycle ◽

Cell Proliferation ◽

Diverse Range ◽

Cyclin Dependent Kinases ◽

Cell Proliferation And Differentiation ◽

Proliferation And Differentiation ◽

Stem And Progenitor Cells ◽

Cycle Dependent ◽

Cell Cycle Dynamics ◽

Bidirectional Interactions

Embryogenesis requires an exquisite regulation of cell proliferation, cell cycle withdrawal and differentiation into a massively diverse range of cells at the correct time and place. Stem cells also remain to varying extents in different adult tissues, acting in tissue homeostasis and repair. Therefore, regulated proliferation and subsequent differentiation of stem and progenitor cells remains pivotal throughout life. Recent advances have characterised the cell cycle dynamics, epigenetics, transcriptome and proteome accompanying the transition from proliferation to differentiation, revealing multiple bidirectional interactions between the cell cycle machinery and factors driving differentiation. Here, we focus on a direct mechanistic link involving phosphorylation of differentiation-associated transcription factors by cell cycle-associated Cyclin-dependent kinases. We discuss examples from the three embryonic germ layers to illustrate this regulatory mechanism that co-ordinates the balance between cell proliferation and differentiation.

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Myosin-driven peroxisome partitioning in S. cerevisiae

The Journal of Cell Biology ◽

10.1083/jcb.200904050 ◽

2009 ◽

Vol 186 (4) ◽

pp. 541-554 ◽

Cited By ~ 57

Author(s):

Andrei Fagarasanu ◽

Fred D. Mast ◽

Barbara Knoblach ◽

Yui Jin ◽

Matthew J. Brunner ◽

...

Keyword(s):

Cell Cycle ◽

Molecular Motors ◽

Cell Cycle Progression ◽

Cycle Progression ◽

Class V ◽

Daughter Cells ◽

Mother And Daughter ◽

Specific Receptors ◽

Cycle Dependent ◽

Mother Cells

In Saccharomyces cerevisiae, the class V myosin motor Myo2p propels the movement of most organelles. We recently identified Inp2p as the peroxisome-specific receptor for Myo2p. In this study, we delineate the region of Myo2p devoted to binding peroxisomes. Using mutants of Myo2p specifically impaired in peroxisome binding, we dissect cell cycle–dependent and peroxisome partitioning–dependent mechanisms of Inp2p regulation. We find that although total Inp2p levels oscillate with the cell cycle, Inp2p levels on individual peroxisomes are controlled by peroxisome inheritance, as Inp2p aberrantly accumulates and decorates all peroxisomes in mother cells when peroxisome partitioning is abolished. We also find that Inp2p is a phosphoprotein whose level of phosphorylation is coupled to the cell cycle irrespective of peroxisome positioning in the cell. Our findings demonstrate that both organelle positioning and cell cycle progression control the levels of organelle-specific receptors for molecular motors to ultimately achieve an equidistribution of compartments between mother and daughter cells.

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Control of tissue development by cell cycle dependent transcriptional filtering

10.1101/2020.02.25.964650 ◽

2020 ◽

Author(s):

Maria Abou Chakra ◽

Ruth Isserlin ◽

Thinh Tran ◽

Gary D. Bader

Keyword(s):

Cell Cycle ◽

Cell Fate ◽

Control Cell ◽

Cell Types ◽

Cycle Duration ◽

Cell Diversity ◽

Cycle Dependent ◽

Cell Cycle Dynamics ◽

Different Cell Types ◽

Long Genes

AbstractCell cycle duration changes dramatically during development, starting out fast to generate cells quickly and slowing down over time as the organism matures. The cell cycle can also act as a transcriptional filter to control the expression of long genes which are partially transcribed in short cycles. Using mathematical simulations of cell proliferation, we identify an emergent property, that this filter can act as a tuning knob to control cell fate, cell diversity and the number and proportion of different cell types in a tissue. Our predictions are supported by comparison to single-cell RNA-seq data captured over embryonic development. Evolutionary genome analysis shows that fast developing organisms have a narrow genomic distribution of gene lengths while slower developers have an expanded number of long genes. Our results support the idea that cell cycle dynamics may be important across multicellular animals for controlling gene expression and cell fate.

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Cell cycle-dependent active stress drives epithelia remodeling

10.1101/804294 ◽

2019 ◽

Cited By ~ 1

Author(s):

John Devany ◽

Daniel M. Sussman ◽

M. Lisa Manning ◽

Margaret L. Gardel

Keyword(s):

Cell Cycle ◽

Cell Shape ◽

Shape Change ◽

Epithelial Tissue ◽

Experimental Conditions ◽

Active Stress ◽

Cell Shapes ◽

Cycle Dependent ◽

Cell Cycle Dynamics ◽

Dependent Processes

AbstractEpithelia have distinct cellular architectures, which are established in development, re-established after wounding, and maintained during tissue homeostasis despite cell turnover and mechanical perturbations. In turn, cell shape also controls tissue function as a regulator of cell differentiation, proliferation, and motility. Here we investigate cell shape changes in a model epithelial monolayer. After the onset of confluence, cells continue to proliferate and change shape over time, eventually leading to a final architecture characterized by arrested motion and more regular cell shapes. Such monolayer remodeling is robust, with qualitatively similar changes in cell shape and dynamics observed across disparate perturbations. Here we quantify differences in monolayer remodeling guided by the active vertex model to identify underlying order parameters controlling epithelial architecture. For instance, for monolayers formed atop extracellular matrix with varied stiffness, we find the cell density at which motion arrests varies significantly but the cell shape remains constant. In contrast, pharmacological perturbations can significantly alter the cell shape at which tissue dynamics is arrested. Remarkably, we find across all experimental conditions the final cell shape is well correlated to the cell proliferation rate. Furthermore, inhibition of the cell cycle immediately arrests both cell motility and shape change, demonstrating that active stress from cell cycle-dependent processes contributes significantly to monolayer remodeling. Thus, the architecture and mechanics of epithelial tissue can arise from an interplay between cell mechanics and stresses arising from cell cycle dynamics.

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Cell cycle–dependent active stress drives epithelia remodeling

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1917853118 ◽

2021 ◽

Vol 118 (10) ◽

pp. e1917853118

Author(s):

John Devany ◽

Daniel M. Sussman ◽

Takaki Yamamoto ◽

M. Lisa Manning ◽

Margaret L. Gardel

Keyword(s):

Cell Cycle ◽

Cell Shape ◽

Epithelial Tissue ◽

Experimental Conditions ◽

Active Stress ◽

Cell Cycle Inhibition ◽

Cell Shapes ◽

Cycle Dependent ◽

Cell Cycle Dynamics ◽

Shape Changes

Epithelia have distinct cellular architectures which are established in development, reestablished after wounding, and maintained during tissue homeostasis despite cell turnover and mechanical perturbations. In turn, cell shape also controls tissue function as a regulator of cell differentiation, proliferation, and motility. Here, we investigate cell shape changes in a model epithelial monolayer. After the onset of confluence, cells continue to proliferate and change shape over time, eventually leading to a final architecture characterized by arrested motion and more regular cell shapes. Such monolayer remodeling is robust, with qualitatively similar evolution in cell shape and dynamics observed across disparate perturbations. Here, we quantify differences in monolayer remodeling guided by the active vertex model to identify underlying order parameters controlling epithelial architecture. When monolayers are formed atop an extracellular matrix with varied stiffness, we find the cell density at which motion arrests varies significantly, but the cell shape remains constant, consistent with the onset of tissue rigidity. In contrast, pharmacological perturbations can significantly alter the cell shape at which tissue dynamics are arrested, consistent with varied amounts of active stress within the tissue. Across all experimental conditions, the final cell shape is well correlated to the cell proliferation rate, and cell cycle inhibition immediately arrests cell motility. Finally, we demonstrate cell cycle variation in junctional tension as a source of active stress within the monolayer. Thus, the architecture and mechanics of epithelial tissue can arise from an interplay between cell mechanics and stresses arising from cell cycle dynamics.

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Myt1 kinase promotes mitotic cell cycle exit in Drosophila intestinal progenitor cells

10.1101/785949 ◽

2019 ◽

Author(s):

Reegan J. Willms ◽

Jie Zeng ◽

Shelagh D. Campbell

Keyword(s):

Cell Cycle ◽

Progenitor Cells ◽

Cyclin A ◽

Mitotic Cell ◽

Cell Cycle Exit ◽

Developmental Context ◽

Daughter Cells ◽

Cycle Arrest ◽

Cell Cycle Dynamics ◽

Coupling Cell

SUMMARYInhibitory phosphorylation of Cdk1 is a well-established mechanism for gating mitotic entry during development. However, failure to inhibit Cdk1 in adult organs causes ectopic cell division and tissue dysplasia, indicating that Cdk1 inhibition is also required for cell cycle exit. Two types of progenitor cells populate the adult Drosophila midgut: intestinal stem cells (ISCs) and post-mitotic enteroblasts (EBs). ISCs are the only mitotic cells under homeostatic conditions, dividing asymmetrically to produce quiescent EB daughter cells. We show here that Myt1, the membrane associated Cdk1 inhibitory kinase, is required for EB quiescence and subsequent differentiation. Loss of Myt1 disrupts EB cell cycle dynamics, promoting Cyclin A-dependent mitosis and accumulation of smaller progenitor-like cells that fail to differentiate. Thus, Myt1 inhibition of Cyclin A/Cdk1 functions as a mechanism for coupling cell cycle arrest with terminal cell differentiation in this developmental context.

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