Kotaro Fujii, Ph.D.

Kotaro Fuji


Dr. Fujii is an Assistant Professor of Molecular Genetics & Microbiology and Center for NeuroGenetics at the University of Florida College of Medicine. He obtained Ph.D. degrees in RNA biochemistry and molecular biology. He came to the United States as a postdoctoral fellow at Stanford University and complemented his experience with developmental biology as well as state-of-the-art genome-wide sequence analyses by applying his biochemical techniques to the developing mammalian embryo. The research vision of Dr. Fujii is to molecularly understand mammalian development and homeostasis by utilizing a variety of interdisciplinary approaches from cutting edge biochemistry to in vivo animal models.


Translation fidelity regulation by ribosome
Kotaro Fujii

Gene expression must be precise and accurate; however, the mRNA translation step has the highest error rate across gene expression with an estimated 10-15% of nascent proteins having translational errors, which include amino acid (AA) misincorporation, ribosomal frameshift, and stop codon readthrough. These error-containing proteins are readily unfolded and aggregated, which are associated with neurodegeneration and aging. The mechanisms that govern translational errors and maintain translation fidelity remain a critical knowledge gap. Although translation fidelity is known to be higher in eukaryotes than in prokaryotes, it remains unknown how the ribosome itself has evolved to increase accuracy. Using yeast genetics, we identified an eukaryote-specific rRNA domain, called expansion segment 27L (ES27L), that plays an important role in translation fidelity. ES27L is one of the most dynamic ESs, which is not present in prokaryotic ribosomes and is dramatically extended from 159 nt in yeast to 714 nt in human. Using quantitative mass spectrometry, we further revealed that ES27L recruits an N-terminal processing factor, methionine aminopeptidases (MetAPs), to the ribosome. Indeed, the ES27L∆ yeast strain reduced MetAP activity and increased failure of initiator methionine (iMet) removal. This MetAP activity is critical to maintaining translation fidelity in Eukaryotes. However, how the failure of iMet processing reduces translation fidelity is still unknown. MetAPs remove iMet from 2/3 of nascent proteins including ribosomal proteins (RPs). We hypothesized that iMet retention on RPs affects translation fidelity. Indeed, when methionine (Met) was labeled with Met analog, ribosomes purified from ES27L∆ mutant increased Met signals, suggesting iMet retention on the ribosomes. In vitro translation assay further confirmed that purified ribosomes from yeast strain with reduced iMet removal had lower translation fidelity. We will further discuss how the retention of iMet on the ribosome induces translation errors