北京大學定量生物學中心

學術報告 

題    目: Cytoplasmic density affects cell cycle and protein translation

報告人: Yuping Chen（陳于平）, Ph.D.

Postdoctoral Researcher，Department of Chemical and Systems Biology，Stanford University School of Medicine

時    間: 1月10日（周一）13:00-14:00

地    點: 呂志和樓B101報告廳

主持人: 林傑 研究員

摘 要:

The cytoplasm is dense, viscous, and crowded. A classic way to understand a biochemical reaction is through in vitro reconstitution. Recent studies have shown that the reconstituted systems do not reflect how biochemical reactions behave in the cytoplasm, as the physical nature of the environment is different. How do chemical reactions work in the cytoplasm? Do the cytoplasmic viscosity and crowding affect chemical reaction rates and balances? How is the density of the cytoplasm maintained? Due to limitations in experimental procedures to directly perturb the cytoplasmic density in a living cell, the progress of understanding these fundamental biochemical and cell biological questions was slow. In this talk, I will talk about the use of the Xenopus egg extract, an undiluted living cytoplasm to study how cell cycle behaviors and protein translation and degradation respond to direct physical perturbations. Diluting or condensing the cytoplasm as well as other physical perturbations of the cytoplasm affects molecular motions in the Xenopusegg extract. Combining measurements of the rate of protein translation in different conditions with a chemical reaction model, we found that protein translation is partially diffusion-limited. Moreover, we found that protein translation rate responds to cytoplasmic dilution in a biphasic manner, initially increasing then decreasing. These findings help to explain how cells maintain their cytoplasmic density and how cytoplasmic dilution causes senescence.

報告人簡介:

陳于平目前是斯坦福大學化學與系統生物學系James Ferrell教授實驗室的博士後研究員。2008年入學中國農業大學生命科學試驗班；2009年至2011年在陳忠周教授和王賓教授（現于複旦大學基礎醫學院）實驗室參與科學研究；2011年加入加州大學伯克利分校Jennifer Doudna教授實驗室，研究CRISPR系統中新間隔序列（spacer sequence）的插入問題；2012年至2018年在石溪大學 Bruce Futcher教授實驗室攻讀遺傳學博士學位，研究（1）主要的細胞周期調控蛋白細胞周期蛋白依賴激酶（CDK）對糖代謝的直接控制，以及（2）細胞尺寸控制（cell size control）的遺傳學和細胞學基礎；2019年至今在斯坦福大學Jim Ferrell教授實驗室當任博士後研究員。研究興趣包括了解細胞質物理特性如何影響生化反應速率、基因表達和其他生物學過程。主要研究成果有：發現細胞周期蛋白依賴激酶（CDK1）直接調控碳水化合物代謝（Zhao, Chen, et al, Molecular Cell, 2016）、細胞周期相關蛋白的差異表達決定細胞尺寸（Chen, et al, Molecular Cell, 2020; Chen and Futcher, Current Genetics, 2021）；生物個體密度影響群落形成（Chen and Ferrell, Nature Communications, 2021）。

代表論文

Zhao G*, Chen Y*, Carey L, Futcher B. Cyclin-dependent kinase co-ordinates carbohydrate metabolism and cell cycle in S. cerevisiae. Molecular Cell. 2016;62(4):546-557. doi:10.1016/j.molcel.2016.04.026. *Co-first author

Chen Y, Zhao G, Zahumensky J, Honey S, Futcher B. Differential scaling of transcripts with cell size may explain size control in yeast. Molecular Cell, 2020;78(2):359-370. doi:10.1016/j.molcel.2020.03.012

Chen Y, Futcher B, Scaling gene expression for cell size control and senescence in Saccharomyces cerevisiae. Current Genetics, 2020; 67:41-47. doi: 10.1007/s00294-020-01098-4

Chen Y, Ferrell JE Jr., C. elegans colony formation as a condensation phenomenon. Nature Communications, 2021; 12:4947. doi: 10.1038/s41467-021-25244-9