Satoshi Kimura

About

Satoshi Kimura is a researcher whose work focuses extensively on RNA modifications, particularly in tRNA and ribosomal RNA, and their roles in translation and cellular function. His research includes the discovery and characterization of RNA modification enzymes using comparative genomics approaches, as well as the study of the biogenesis and functional implications of various RNA modifications such as methylations and hydroxylations. Kimura's work has elucidated mechanisms by which RNA modifications influence decoding capabilities, translation efficiency, and bacterial growth under different conditions, including hypoxia and intracellular environments. His studies also explore the evolutionary pathways of tRNA modifications and their regulation, contributing to a deeper understanding of RNA biology and its impact on microbial physiology and pathogenesis.

Research topics

• Biology
• Biochemistry
• Computational biology
• Genetics
• Chemistry
• Cell biology
• Anatomy

Selected publications

• A tRNA modification with aminovaleramide facilitates AUA decoding in protein synthesis

  Nature Chemical Biology · 2024-09-19 · 23 citations

  articleOpen access

  Abstract Modified tRNA anticodons are critical for proper mRNA translation during protein synthesis. It is generally thought that almost all bacterial tRNAs Ile use a modified cytidine—lysidine (L)—at the first position (34) of the anticodon to decipher the AUA codon as isoleucine (Ile). Here we report that tRNAs Ile from plant organelles and a subset of bacteria contain a new cytidine derivative, designated 2-aminovaleramididine (ava 2 C). Like L34, ava 2 C34 governs both Ile-charging ability a…

  PublisherOA PDFDOI

• Remodeling of tRNA modification in <i>Trypanosoma cruzi</i> life forms

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-06-08 · 1 citations

  preprintOpen accessSenior author

  Abstract Trypanosoma cruzi, the etiological agent of Chagas disease, infects millions of people in the Americas. This parasite undergoes drastic changes in its morphology and metabolism between infective and noninfective forms through global remodeling of its proteome. Chemical modification of tRNA (tRNA modification) contributes to the control of protein expression by modulating the codon decoding process. However, knowledge of tRNA modification profiles, the enzymes that create modifications a…

  PublisherOA PDFDOI

• Integrating tDNA Epigenomics and Expression with Codon Usage Unravel an Intricate Connection with Protein Expression Dynamics in <i>Trypanosoma cruzi</i>

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-07-06 · 1 citations

  preprintOpen access

  Abstract Codon usage bias impacts protein expression across all kingdoms of life, including trypanosomatids. These protozoa, such as the Trypanosoma cruzi , primarily regulate their protein-coding genes through posttranscriptional mechanisms. Here, we integrated analyses of codon usage with multiple high-throughput sequencing data to investigate whether codon usage bias is present into surface virulence factors (disruptive compartment), conserved housekeeping proteins (core compartment), and pro…

  PublisherOA PDFDOI

Frequent coauthors

• Matthew K. Waldor

  Howard Hughes Medical Institute

  114 shared

• Kaoru Shimada

  National Cancer Center Hospital East

  48 shared

• Tsuguyuki Saito

  The University of Tokyo

  45 shared

• Shinichi Oka

  National Center for Global Health and Medicine

  37 shared

• Takashi Kadowaki

  Niigata Institute of Technology

  34 shared

• Eric J. Rubin

  32 shared

• Akira Isogai

  32 shared

• Francesca G. Tomasi

  Harvard University

  32 shared

Labs

• Kimura LabPI

Education

• PhD, Department of Chemistry and Biotechnology

  University of Tokyo

  2012

• Master, Department of Chemistry and Biotechnology

  University of Tokyo

  2009

• Bachelor, Department of Chemistry and Biotechnology

  University of Tokyo

  2007

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