Tsuboi Lab @ Tsinghua-Shenzhen
清华大学深圳

* Recruiting Grad students and Postdocs! Please email me!
Please apply for the international Ph.D. courses during 10/15-2/28 (click),
Master Program: 制药工程, 精准医学与公共健康, 生物医学工程, 循证健康工程
Ph.D. Program: Chemical Engineering and Technology (化学工程与技术)

Decoding the Mechanistic Principles of Gene Regulation by Mitochondrial 3D Spatial Organization

Mitochondria are key organelles within the cell involved in the production of ATP, serve as a hub for biological reactions, and regulate many aspects of cellular activity such as cell senescence (aging), cancer, and stressful conditions. Mitochondria are also very dynamic structures with fluctuating morphologic transitions in response to cellular and environmental perturbations. While there have been many studies investigating the pathways and conditions that alter mitochondrial morphology, the connection between these morphological changes and gene expression regulation is still a poorly explored question. How does changing mitochondrial morphology during aging, cancer, and stress impact gene regulation? How do mitochondria regulate mRNA localization and control translation in response to the metabolic needs of the cell?

1. Decipher the mechanistic basis of enhanced protein synthesis on the mitochondria surface 

2. Investigate how fluctuating mitochondrial morphology during stress and disease affects gene expression of yeast and mammalian cells 

3. Pursue application method from the understanding of fluctuating mitochondrial morphology, such as screening of anti-aging drugs

As a model system, I will study mRNA localization and mitochondrial morphology in budding yeast and mammalian cells using an interdisciplinary approach combining quantitative microscopy, computational modeling, biochemistry, and molecular genetics. By focusing on a systems-level view of gene expression, I will advance our understanding of how organelle morphology impacts the physiology of the cell. My multi-pronged, quantitative approach toward mRNA and mitochondrial morphological measurements will also allow me to tackle questions about the spatial relationship between biomolecules and other organelles, such as the vacuole and endoplasmic reticulum.

Tatsuhisa Tsuboi Ph.D.

Assistant Professor (tenure-track)
Institute of Biopharmaceutical and Health Engineering 

I am exploring single cell and single-molecule analysis of mitochondrial mRNA localization during stress conditions in yeast with techniques of microscopic analysis, microfluidics, and biochemistry. I grew up in Tokyo, Japan, and obtained my Ph.D. from Tohoku University in 2014. During my Ph.D., I worked on mRNA quality control systems under the supervision of Dr. Toshifumi Inada. I spend my postdoc period with Dr. Susanne Rafelski at the University of California Irvine and Dr. Brian Zid at the University of California San Diego, where I worked on mitochondrial mRNA regulatory mechanisms. I love yeast in many ways ;)

TIM50 mRNA associates with mitochondria

Trajectories of ideal Brownian particles in in the space between the cell wall and mitochondria surface

Reconstruction of the spatial relationship between mRNAs and mitochondria

We measured the distances between mRNA foci and closest points on the mitochondrial surface.

Mitochondrial volume fraction and binding affinity regulates mRNA localization

Each mRNA species (colored lines) shows distinctive correlative patterns between localization and mitochondrial volume fraction upon respiratory condition change according to its unique binding affinity.

Publications

Khan AH, Gu X, Patel RJ, Chuphal P, Viana MP, Brown AI, Zid BM*, Tsuboi T*. (2024) Mitochondrial protein heterogeneity stems from the stochastic nature of co-translational protein targeting in cell senescence. Nature Communications 15, 8274. [*correspondence]

Ma J, Tsuboi T. (2024) Efficient Prediction Model of mRNA End-to-End Distance and Conformation: Three-Dimensional RNA Illustration Program (TRIP). Methods Mol Biol. 2024;2784:191-200.

Guo T, Modi O, Hirano J, Guzman H, Tsuboi T*. (2022) Single-chain models illustrate the 3D RNA folding shape during translation. Biophysical Reports, 100065.

Tsuboi T*, Leff J, Zid BM*. (2020) Post-transcriptional control of mitochondrial protein composition in changing environmental conditions. Biochem Soc Trans. BST20200250. [*co-correspondence authors] Review

Tsuboi T*, Viana MP, Xu F, Yu J, Chanchani R, Arceo XG, Tutucci E, Choi J, Chen YS, Singer RH, Rafelski SM*, Zid BM*. (2020) Mitochondrial volume fraction and translation duration impact mitochondrial mRNA localization and protein synthesis. Elife, 9, e57814. https://doi.org/10.7554/eLife.57814. [*co-correspondence authors]

Tsuboi T, Yamazaki R, Nobuta R, Ikeuchi K, Makino S, Ohtaki A, Suzuki Y, Yoshihisa T, Trotta C, Inada T.  (2015) The tRNA Splicing Endonuclease Complex Cleaves the Mitochondria-localized CBP1 mRNA. The Journal of Biological Chemistry, 290(26), 16021-16030.

Izawa T, Tsuboi T, Kuroha K, Inada T, Nishikawa S, Endo T. (2012) Roles of dom34:hbs1 in nonstop protein clearance from translocators for normal organelle protein influx. Cell Reports, 2(3), 447-453

Tsuboi T, Kuroha K, Kudo K, Makino S, Inoue E, Kashima I, Inada T. (2012) Dom34:hbs1 plays a general role in quality-control systems by dissociation of a stalled ribosome at the 3' end of aberrant mRNA. Molecular Cell, 46(4), 518-529.

Tsuboi T, Inada T. (2010) Tethering of poly(A)-binding protein interferes with non-translated mRNA decay from the 5' end in yeast. The Journal of Biological Chemistry, 285(44), 33589-33601.


CV

RESEARCH EXPERIENCE

January 2025 – Current
Associate Professor (tenure-track)

September 2021 – December 2025
Assistant Professor (tenure-track)
Tsinghua University Shenzhen International Graduate School
Institute of Biopharmaceutical and Health Engineering

December 2016 - July 2021                                        
Assistant Project Scientist and Postdoctoral Scholar with Prof. Brian M. Zid
University of California, San Diego: Department of Chemistry and Biochemistry
Interdisciplinary research on mRNA localization and translation in S. cerevisiae combining computation, image processing, genetics, cell biology, and biochemistry                                                                       

April 2014 - November 2016
Postdoctoral Scholar with Prof. Susanne M. Rafelski
University of California, Irvine: Department of Developmental & Cell Biology
Development of live cell imaging system for mRNA and mitochondria in S. cerevisiae combining computation, image processing, genetics, and cell biology                                               

EDUCATION                                      

Doctor of Philosophy (Ph.D.) in Pharmaceutical Sciences                      
Tohoku University, Japan: Graduate School of Pharmaceutical Sciences  
Thesis: “Analysis of molecular mechanism of No-Go Decay and Dom34:Hbs1 targeting mRNA”
Advisor: Prof. Toshifumi Inada 

Master of Science                                                
Nagoya University, Japan: Graduate School of Science
Thesis: “Analysis of translational regulator Pab1p on non-translating mRNA”       
Advisor: Prof. Toshifumi Inada 

Bachelor of Science                                             
Nagoya University, Japan: School of Science


Contact

Email:

ttsuboi@sz.tsinghua.edu.cn

Phone:

+86-15216795216
+1-949-295-5425

Tsinghua Shenzhen International Graduate School

International Building A 1708, University Town of Shenzhen, Nanshan District, Shenzhen 518055 P.R. China 

Phone：+86-15216795216

校区地址：广东省深圳市南山区西丽大学城清华大学深圳国际研究生院国际一期A座1708