Biology subjects

Ouyang, Q.

Publications and source records attributed to Ouyang, Q..

4 recordsLinked to original sources

bioRxiv2018

Yeast replicative aging leads to permanent cell cycle arrest in G1 effectuated by the start repressor Whi5

Yeast replicative aging has been a canonical model for aging research. Since replicative aging eventually leads to permanent cell cycle arrest, a fundamental question is how cells sense the signals from aging and communicate that to the cell cycle control machineries. Using microfluidic devices to track individual mother cells labeled by two different cell cycle markers Whi5-tdTomato and Myo1-EGFP, we measured the length of different cell cycle phases as a function of age and the distribution of cell death in different cell cycle phases. We found that the majority of the cells died in the G1 phase, and their G1 cell cycle length increased drastically in the last few cell divisions. This increase of G1 length correlates with the increase of the nuclear concentration of Whi5, which is a major transcriptional suppressor of the cell cycle start check point. Interestingly, this correlation is apparent only above a threshold concentration of Whi5. We show that in response to external stress, Whi5 concentration increases and cell growth slows down in a Whi5 dependent manner, and that Whi5 deletion significantly extends the lifespan. Together these data suggest the existence of a programmed control to arrest cell cycle in G1 in response to stress signals due to aging, and that Whi5 is a major mediator of this process. Our findings may have important implications in understanding senescence and cancer in mammalian cells, which have a parallel G1/S control system with Rb (a well known tumor suppressor) as the analog of Whi5.\n\nSignificance statementIn this work, we used microfluidic devices to track individual mother cells labeled by two cell cycle markers Whi5-tdTomato and Myo1-EGFP. We found that aging leads to significant lengthening of G1 phase in old cells and the eventual permanent cell cycle arrest in G1, and Whi5 plays an important role in implementing such a program. We show that oxidative stress can lead to the increase of Whi5 expression and the slow-down of cell division. Furthermore, Whi5 deletion significantly extends the lifespan. The result suggest the existence of a programmed control to arrest cell cycle in G1 in response to stress signals due to aging, and that Whi5 is a major mediator of this process.

cell biology↗

bioRxiv2017

Nucleotide-Driven Triple-State Remodeling Of The AAA-ATPase Channel In The Activated Human 26S Proteasome

The proteasome is a sophisticated ATP-dependent molecular machine responsible for protein degradation in all eukaryotic cells. It remains elusive how conformational changes of the AAA-ATPase unfoldase in the regulatory particle (RP) control the gating of substrate-translocation channel to the proteolytic chamber of the core particle (CP). Here we report three alternative states of the ATP-{gamma}S-bound human proteasome, in which the CP gate is asymmetrically open, visualized by cryo-EM at near-atomic resolutions. Only four nucleotides are stably bound to the AAA-ATPase ring in the open-gate states. Concerted nucleotide exchange gives rise to a back-and-forth wobbling motion of the AAA-ATPase channel, coincident with remarkable transitions of their pore loops between the spiral staircase and saddle-shaped circle topologies. Gate opening in the CP is thus controlled with nucleotide-driven remodeling of the AAA-ATPase unfoldase. These findings demonstrate an elegant mechanism of allosteric coordination among sub-machines within the holoenzyme that is crucial for substrate translocation.

biochemistry↗

bioRxiv2016

Conformational landscape of the p28-bound human proteasome regulatory particle

The proteasome holoenzyme is activated by its regulatory particle (RP) consisting of two subcomplexes, the lid and the base. A key event in base assembly is the formation of a heterohexameric ring of AAA-ATPases, which is guided by at least four RP assembly chaperones in mammals: PAAF1, p28/gankyrin, p27/PSMD9 and S5b. We determined a cryo-EM structure of the human RP in complex with its assembly chaperone p28 at 4.5-[A] resolution. The Rpn1-p28-AAA subcomplex in the p28-bound RP is highly dynamic and was resolved to subnanometer resolution in seven states, which recapitulate the conformational landscape of the complex. Surprisingly, the p28-bound AAA ring does not form a channel in the free RP. Instead, it spontaneously samples multiple open and closed topologies. Our analysis suggests that p28 guides the proteolytic core particle to select certain conformation of the ATPase ring for RP engagement in the last step of the chaperone-mediated proteasome assembly.

biochemistry↗

bioRxiv2016

Phosphorylation energy and nonlinear kinetics as key determinants for G2/M transition in fission yeast cell cycle

The living cell is an open nonequilibrium biochemical system, where ATP hydrolysis serves as the energy source for a wide range of intracellular processes including the assurance for decision-making. In the fission yeast cell cycle, the transition from G2 phase to M phase is triggered by the activation of Cdc13/Cdc2 and Cdc25, and the deactivation of Wee1. Each of these three events involves a phosphorylation-dephosphorylation (PdP) cycle, and together they form a regulatory circuit with feedback loops. Almost all quantitative models for cellular networks in the past have invalid thermodynamics due to the assumption of irreversible enzyme kinetics. We constructed a thermodynamically realistic kinetic model of the G2/M circuit, and show that the phosphorylation energy ({Delta}G), which is determined by the cellular ATP/ADP ratio, critically controls the dynamics and the bistable nature of Cdc2 activation. Using fission yeast nucleoplasmic extract (YNPE), we are able to experimentally verify our model prediction that increased {Delta}G, being synergistic to the accumulation of Cdc13, drives the activation of Cdc2. Furthermore, Cdc2 activation exhibits bistability and hysteresis in response to changes in phosphorylation energy. These findings suggest that adequate maintenance of phosphorylation energy ensures the bistability and robustness of the activation of Cdc2 in the G2/M transition. Free energy might play a widespread role in biological decision-making processes, connecting thermodynamics with information processing in biology.

systems biology↗