Dynamic cell cycle-dependent phosphorylation modulates CENP-L-CENP-N centromere recruitment

The kinetochore is a macromolecular structure that is required to ensure proper chromosome segregation during each cell division. The kinetochore is assembled upon a platform of the 16-subunit Constitutive Centromere Associated Network (CCAN), which is present at centromeres throughout the cell cycle. The nature and regulation of CCAN assembly, interactions, and dynamics required to facilitate changing centromere properties and requirements remain to be fully elucidated. The CENP-LN CCAN sub-complex displays a unique cell cycle-dependent localization behavior, peaking in S phase. Here, we demonstrate that phosphorylation of CENP-L and CENP-N controls CENP-LN complex formation and localization in a cell cycle-dependent manner. Mimicking constitutive phosphorylation of either CENP-L or CENP-N or simultaneously preventing phosphorylation of both proteins prevents CENP-LN localization and disrupts chromosome segregation. Together, our work suggests that cycles of phosphorylation and dephosphorylation are critical for CENP-LN complex recruitment and dynamics at centromeres to enable cell cycle-dependent CCAN reorganization.

Fragile X–Related Protein 1 Regulates Nucleoporin Localization in a Cell Cycle–Dependent Manner

Nuclear pore complexes (NPCs) are embedded in the nuclear envelope (NE) where they ensure the transport of macromolecules between the nucleus and the cytoplasm. NPCs are built from nucleoporins (Nups) through a sequential assembly order taking place at two different stages during the cell cycle of mammalian cells: at the end of mitosis and during interphase. In addition, fragile X–related proteins (FXRPs) can interact with several cytoplasmic Nups and facilitate their localization to the NE during interphase likely through a microtubule-dependent mechanism. In the absence of FXRPs or microtubule-based transport, Nups aberrantly localize to the cytoplasm forming the so-called cytoplasmic nucleoporin granules (CNGs), compromising NPCs’ function on protein export. However, it remains unknown if Nup synthesis or degradation mechanisms are linked to the FXRP–Nup pathway and if and how the action of FXRPs on Nups is coordinated with the cell cycle progression. Here, we show that Nup localization defects observed in the absence of FXR1 are independent of active protein translation. CNGs are cleared in an autophagy- and proteasome-independent manner, and their presence is restricted to the early G1 phase of the cell cycle. Our results thus suggest that a pool of cytoplasmic Nups exists that contributes to the NPC assembly specifically during early G1 to ensure NPC homeostasis at a short transition from mitosis to the onset of interphase.

Cell-Cycle—Dependent Chromatin Dynamics at Replication Origins

Origins of DNA replication are specified by the ordered recruitment of replication factors in a cell-cycle—dependent manner. The assembly of the pre-replicative complex in G1 and the pre-initiation complex prior to activation in S phase are well characterized; however, the interplay between the assembly of these complexes and the local chromatin environment is less well understood. To investigate the dynamic changes in chromatin organization at and surrounding replication origins, we used micrococcal nuclease (MNase) to generate genome-wide chromatin occupancy profiles of nucleosomes, transcription factors, and replication proteins through consecutive cell cycles in Saccharomyces cerevisiae. During each G1 phase of two consecutive cell cycles, we observed the downstream repositioning of the origin-proximal +1 nucleosome and an increase in protected DNA fragments spanning the ARS consensus sequence (ACS) indicative of pre-RC assembly. We also found that the strongest correlation between chromatin occupancy at the ACS and origin efficiency occurred in early S phase, consistent with the rate-limiting formation of the Cdc45–Mcm2-7–GINS (CMG) complex being a determinant of origin activity. Finally, we observed nucleosome disruption and disorganization emanating from replication origins and traveling with the elongating replication forks across the genome in S phase, likely reflecting the disassembly and assembly of chromatin ahead of and behind the replication fork, respectively. These results provide insights into cell-cycle–regulated chromatin dynamics and how they relate to the regulation of origin activity.

Synthetic Condensed-Phase Signaling Expands Kinase Specificity and Responds to Macromolecular Crowding

Liquid–liquid phase separation (LLPS) can concentrate biomolecules and accelerate reactions within membraneless organelles. For example, the nucleolus and PML-nuclear bodies are thought to create network hubs by bringing signaling molecules such as kinases and substrates together. However, the mechanisms and principles connecting mesoscale organization to signaling dynamics are difficult to dissect due to the pleiotropic effects associated with disrupting endogenous condensates. Here, we recruited multiple distinct kinases and substrates into synthetic LLPS systems to create new phosphorylation reactions within condensates, and generally found increased activity and broadened specificity. Dynamic phosphorylation within condensates could drive cell-cycle-dependent localization changes. Detailed comparison of phosphorylation of clients with varying recruitment valency and affinity into condensates comprised of either flexible or rigid scaffolds revealed unexpected principles. First, high client concentration within condensates is important, but is not the main factor for efficient multi-site phosphorylation. Rather, the availability of a large number of excess client binding sites, together with a flexible scaffold is crucial. Finally, phosphorylation within a suboptimal, flexible condensate was modulated by changes in macromolecular crowding. Thus, condensates readily generate new signaling connections and can create sensors that respond to perturbations to the biophysical properties of the cytoplasm.

Cell cycle-dependent recruitment of FtsN to the divisome in Escherichia coli

Cell division in Escherichia coli starts with the formation of an FtsZ protofilament network in the middle of the cell, the Z ring. However, only after a considerable lag period do the cells start to form a midcell constriction. The basis of this cell cycle checkpoint is yet unclear. The onset of constriction is dependent upon the arrival of so-called late divisome proteins, among which, FtsN is the last arriving essential one. The timing and dependency of FtsN arrival to the divisome, along with genetic evidence, suggests it triggers cell division. In this study, we used high throughput fluorescence microscopy to quantitatively determine the arrival of FtsN and the early divisome protein ZapA to midcell at a single-cell level during the cell cycle. Our data show that recruitment of FtsN coincides with the initiation of constriction within experimental uncertainties and that the relative fraction of ZapA/FtsZ reaches its highest value at this event. We also find that FtsN is recruited to midcell in two distinct temporal stages with septal peptidoglycan synthesis starting in the first stage and accelerating in the second stage, during which the amount of ZapA/FtsZ in the midcell decreases. In the presence of FtsA*, recruitment of FtsN becomes concurrent with the formation of the Z-ring, but constriction is still delayed indicating FtsN recruitment is not rate limiting, at least under these conditions. Finally, our data support the recently proposed idea that ZapA/FtsZ and FtsN are part of physically separate complexes in midcell throughout the whole septation process.

Field Data and Laboratory Study to Investigate Water and Gas Injectivity and Cyclic Hysteresis in Miscible WAG Injection in Carbonate Reservoir

The objective of this paper is to investigate the water and gas injectivity in water alternating gas (WAG) projects using laboratory and field scale data. It has been reported in the literature that both gas and water mobility has been significantly reduced in three-phase flow compared to two-phase flow. This behaviour has been attributed to a cycle dependent hysteresis effect which reduced both gas and water mobility in the different injection cycles. To address the gas and water injectivity and the cycle dependent hysteresis concept, the results of a detailed experimental program in addition to field injectivity data will be presented. The experimental program included three-phase experiments performed under reservoir conditions using live crude oil and carbonate reservoir core material. The core wettability was restored by ageing the core in crude oil for several weeks under reservoir conditions and CO2 was used as miscible injectant. The field injectivity data is obtained from two CO2 WAG pilots in a carbonate reservoir. The main conclusions of the study are: 1- Gas injectivity in the presence of mobile water is much lower than that in the absence of water, 2- Water injectivity in experiments starting with water cycle is better than that in experiments starting with gas cycle when compared at the same water saturation, 3- Cyclic hysteresis in gas relative permeability was observed when comparing the first and second gas cycle, however, no further hysteresis was observed in the subsequent gas injection cycles, 4- Cyclic hysteresis in water relative permeability was not observed, the injectivity was either the same or higher in the subsequent cycles. 5- The gas injectivity at similar gas saturation for experiments starting with gas is better than that for experiments starting with water, 6- Gas and water injectivity field data from ongoing CO2 WAG projects in carbonate reservoirs showed no cyclic hysteresis, the injectivity either the same or improved in the subsequent cycles, 7- The CO2 injectivity was lower than expected, in the same order as water injectivity, which could be due to injecting CO2 in high water saturation zone and 8) The low CO2 injectivity could have a positive impact on sweep efficiency and potential improvement of oil recovery. This paper presents the results of a well-designed experimental program and field data from two CO2 WAG pilots to systematically investigate water and gas injectivity in miscible WAG projects in carbonate reservoirs. The paper provides a rich and rarely available set of experimental and field data that can help improve and optimize gas and WAG injection projects in carbonate reservoirs. Detailed analysis of the field gas and water injectivity data will be presented and discussed in-light of the laboratory experimental data.

TargetGeneReg 2.0: a comprehensive web-atlas for p53, p63, and cell cycle-dependent gene regulation

In recent years, our web-atlas at www.TargetGeneReg.org has enabled many researchers to uncover new biological insights and to identify novel regulatory mechanisms that affect p53 and the cell cycle – signaling pathways that are frequently dysregulated in diseases like cancer. Here, we provide a substantial upgrade of the database that comprises an extension to include non-coding genes and the transcription factors ΔNp63 and RFX7. TargetGeneReg 2.0 combines gene expression profiling and transcription factor DNA binding data to determine, for each gene, the response to p53, ΔNp63, and cell cycle signaling. It can be used to dissect common, cell type, and treatment-specific effects, identify the most promising candidates, and validate findings. We demonstrate the increased power and more intuitive layout of the resource using realistic examples.

Ser68 phosphoregulation is essential for CENP-A deposition, centromere function and viability in mice

Centromere identity is defined by nucleosomes containing CENP-A, a histone H3 variant. The deposition of CENP-A at centromeres is tightly regulated in a cell-cycle-dependent manner. We previously reported that the spatiotemporal control of centromeric CENP-A incorporation is mediated by the phosphorylation of CENP-A Ser68. However, a recent report argued that Ser68 phosphoregulation is dispensable for accurate CENP-A loading. Here, we report that the substitution of Ser68 of endogenous CENP-A with either Gln68 or Glu68 severely impairs CENP-A deposition and cell viability. We also find that mice harboring the corresponding mutations are lethal. Together, these results indicate that the dynamic phosphorylation of Ser68 ensures cell-cycle-dependent CENP-A deposition and cell viability.

Cell cycle progression and transmitotic apoptosis resistance promote escape from extrinsic apoptosis

Extrinsic apoptosis relies on TNF-family receptor activation by immune cells or receptor-activating biologics. Here, we monitored cell cycle progression at minutes resolution to relate apoptosis kinetics and cell-to-cell heterogeneities in death decisions to cell cycle phases. Interestingly, we found that cells in S phase delay TRAIL receptor-induced death in favour for mitosis, thereby passing on an apoptosis-primed state to their offspring. This translates into two distinct fates, apoptosis execution post mitosis or cell survival from inefficient apoptosis. Transmitotic resistance is linked to Mcl-1 upregulation and increased accumulation at mitochondria from mid S phase onwards, which allows cells to pass through mitosis with activated caspase-8, and with cells escaping apoptosis after mitosis sustaining sublethal DNA damage. Antagonizing Mcl-1 suppresses cell cycle-dependent delays in apoptosis, prevents apoptosis-resistant progression through mitosis and averts unwanted survival from apoptosis induction. Cell cycle progression therefore modulates signal transduction during extrinsic apoptosis, with Mcl-1 governing decision making between death, proliferation and survival. Cell cycle progression thus is a crucial process from which cell-to-cell heterogeneities in fates and treatment outcomes emerge in isogenic cell populations during extrinsic apoptosis.