北京大学定量生物学中心

学术报告 

题    目: Cytoplasmic density affects cell cycle and protein translation

报告人: Yuping Chen（陈于平）, Ph.D.

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

时    间: 1月10日（周一）13:00-14:00

地    点: 吕志和楼B101报告厅

主持人: 林杰 研究员

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 Xenopus egg 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.

报告人简介:

陈于平目前是斯坦福大学化学与系统生物学系James Ferrell教授实验室的博士后研究员。2008年入学中国农业大学生命科学试验班；2009年至2011年在陈忠周教授和王宾教授（现于复旦大学基础医学院）实验室参与科学研究；2011年加入加州大学伯克利分校Jennifer Doudna教授实验室，研究CRISPR系统中新间隔序列（spacer sequence）的插入问题；2012年至2018年在石溪大学 Bruce Futcher教授实验室攻读遗传学博士学位，研究（1）主要的细胞周期调控蛋白细胞周期蛋白依赖激酶（CDK）对糖代谢的直接控制，以及（2）细胞尺寸控制（cell size control）的遗传学和细胞学基础；2019年至今在斯坦福大学Jim Ferrell教授实验室当任博士后研究员。研究兴趣包括了解细胞质物理特性如何影响生化反应速率、基因表达和其他生物学过程。主要研究成果有：发现细胞周期蛋白依赖激酶（CDK1）直接调控碳水化合物代谢（Zhao, Chen, et al, Molecular Cell, 2016）、细胞周期相关蛋白的差异表达决定细胞尺寸（Chen, et al, Molecular Cell, 2020; Chen and Futcher, Current Genetics, 2021）；生物个体密度影响群落形成（Chen and Ferrell, Nature Communications, 2021）。

代表论文

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