Kotaro Fujii

Kotaro Fujii,

Assistant Professor

Department: Molecular Genetics & Microbiology
Business Phone: (352) 273-7279
Business Email: kotaro.fujii@ufl.edu

About Kotaro Fujii

Fun Fact: I used to play football (soccer). My research focuses on delineating new regulatory mechanisms of gene regulation at the step of mRNA translation by the ribosome. Our research will unravel new layers of spatiotemporal specificity and fidelity of protein synthesis to further understand the impact of translational regulation in development—and in diseases, particularly those caused by protein aggregation such as neurodegenerative disorders. Key questions we are seeking to understand are “What is the trigger of protein aggregation?” and “How does the regulation of protein synthesis contribute to disease onset?” We believe such knowledge will bring a novel strategy for treatment and prevention. We approach these questions using a variety of model systems such as mice, cultured cells, and yeast, and we apply cutting-edge biochemistry and genetics & genomics to dissect the impact of translation regulation in mammalian homeostasis and elucidate the molecular mechanism.

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Accomplishments

1st Grant: PRESTO
2020-2024 · JST
Starting Fujii laboratory
2020 · University of Florida
Poster Award 1st Place
2017 · The Bay Area RNA Club
Human Frontier Science Program (HFSP), Long Term Fellow
2013-2016 · Human Frontier Science Program (HFSP)
The Uehara Memorial Foundation, Postdoctoral fellowship
2012-2013 · The Uehara Memorial Foundation
Start postdoc at the Barna laboratory
2012 · Stanford (Start at UCSF them Barna lab move to Stanford)
Obtain Ph.D
2011 · Kyoto University
Japan Society for the Promotion of Science (JSPS), Research fellowship for young scientists
2010-2012 · Japan Society for the Promotion of Science (JSPS)
Return exemption of scholarship due to outstanding achievements
2010 · Japan Student Services Organization (JASSO)
Outstanding Young Scientist (2nd Place)
2009 · 16th East Asia Joint Conference on Biomedical Research

Teaching Profile

Courses Taught
2022-2025
GMS6920 Genetics Journal Colloquy
2023
GMS6001 Fundamentals of Biomedical Sciences I
2024-2025
BCH6415 Advanced Molecular and Cell Biology
2024
GMS6905 Independent Studies in Medical Sciences

Research Profile

Dr. Fujii’s research has been centered on delineating new regulatory mechanisms of gene regulation at the step of mRNA translation by the ribosome. Given that the building blocks of our bodies are proteins, maintaining homeostasis of the proteome is critical for our health. His work has elucidated the quality control mechanism of the functional protein synthesis (Fujii et al., 2009 and 2012) and the fidelity of protein production (Fujii et al., 2018). His research also revealed spatiotemporal regulation of mRNA translation in developing mouse embryos (Fujii et al., 2017) and translational regulation by the ribosome itself (Shi et al., 2017) as well as core translation initiation factor eIF3 complex (Fujii et al., 2021). Dr. Fujii’s research program will unravel new layers of spatiotemporal specificity and fidelity of protein synthesis, to further understand the impact of mRNA translation regulation in development and diseases, particularly those caused by protein aggregation such as neurodegenerative disorders.

Open Researcher and Contributor ID (ORCID)

0000-0002-6028-4776

Publications

2023
RAPIDASH: A tag-free enrichment of ribosome-associated proteins reveals compositional dynamics in embryonic tissues and stimulated macrophages.
bioRxiv : the preprint server for biology. [DOI] 10.1101/2023.12.07.570613. [PMID] 38106052.
2022
Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics
Nature Communications. 13(1) [DOI] 10.1038/s41467-022-28776-w.
2022
Silver nanoparticles enhance the efficacy of aminoglycosides against antibiotic-resistant bacteria.
Frontiers in microbiology. 13 [DOI] 10.3389/fmicb.2022.1064095. [PMID] 36798870.
2021
Controlling tissue patterning by translational regulation of signaling transcripts through the core translation factor eIF3c
Developmental Cell. 56(21):2928-2937.e9 [DOI] 10.1016/j.devcel.2021.10.009. [PMID] 34752747.
2021
VELCRO-IP RNA-seq reveals ribosome expansion segment function in translation genome-wide.
Cell reports. 34(3) [DOI] 10.1016/j.celrep.2020.108629. [PMID] 33472078.
2020
Gene- and Species-Specific Hox mRNA Translation by Ribosome Expansion Segments.
Molecular cell. 80(6):980-995.e13 [DOI] 10.1016/j.molcel.2020.10.023. [PMID] 33202249.
2018
Decoding the Function of Expansion Segments in Ribosomes
Molecular Cell. 72(6):1013-1020.e6 [DOI] 10.1016/j.molcel.2018.11.023. [PMID] 30576652.
2017
Heterogeneous Ribosomes Preferentially Translate Distinct Subpools of mRNAs Genome-wide
Molecular Cell. 67(1):71-83.e7 [DOI] 10.1016/j.molcel.2017.05.021. [PMID] 28625553.
2017
Pervasive translational regulation of the cell signalling circuitry underlies mammalian development
Nature Communications. 8(1) [DOI] 10.1038/ncomms14443. [PMID] 28195124.
2015
Crt10 directs the cullin-E3 ligase Rtt101 to nonfunctional 25S rRNA decay
Biochemical and Biophysical Research Communications. 457(1):90-94 [DOI] 10.1016/j.bbrc.2014.12.072.
2015
RNA regulons in Hox 5′ UTRs confer ribosome specificity to gene regulation
Nature. 517(7532):33-38 [DOI] 10.1038/nature14010. [PMID] 25409156.
2012
40S subunit dissociation and proteasome-dependent RNA degradation in nonfunctional 25S rRNA decay
The EMBO Journal. 31(11):2579-2589 [DOI] 10.1038/emboj.2012.85. [PMID] 22505030.
2009
[Quality control of ribosomal RNAs].
Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme. 54(16 Suppl):2195-200 [PMID] 21089640.
2009
A role for ubiquitin in the clearance of nonfunctional rRNAs
Genes & Development. 23(8):963-974 [DOI] 10.1101/gad.1775609. [PMID] 19390089.

Grants

Sep 2023 ACTIVE
Role of a viral long non-coding RNA in virus superinfection exclusion
Role: Other
Funding: NATL SCIENCE FOU
Apr 2021 – Mar 2024
The spatiotemporal landscape for the accuracy of protein synthesis in mammalian development and disease.
Role: Principal Investigator
Funding: JAPAN SCIENCE AND TECHNOLOGY AGENCY

Education

Postdoc in Developmental Biology and Genetics
2020 · Stanford University
PhD in Biochemistry
2008-2011 · Kyoto University (Japan)
MA in Biochemistry
2006-2008 · Kyoto University (Japan)
BA in Biology
2002-2006 · Tohoku University (Japan)

Contact Details

Phones:
Business:
(352) 273-7279
Emails:
Addresses:
Business Mailing:
PO Box 103610
GAINESVILLE FL 32611