Takuma Okabe

This spotlight takes us to Japan to meet Takuma Okabe, a PhD. student in the Department of Life Science and Medical Bioscience at Waseda University in Tokyo. Takuma earned his Bachelor's degree in 2021, followed by a Master's degree in 2023, both from Waseda University. With a keen interest in the microbiome, Takuma joined Professor Tsuneda’s laboratory during his undergraduate studies to acquire expertise in microbiology and RNA biology.

Using structural analyses, he studied how RNA-cleaving enzymes bind RNA and characterized the functional importance of these interactions for the host microorganism. Now, as a Ph.D. candidate in the same lab, Takuma focuses on the mRNA interferase MazF, a sequence-specific endoribonuclease that is widely conserved among prokaryotes. In particular, he investigates the molecular bases that control the recognition of target sequences by MazF, with a particular focus on measuring its enzymatic activity using RNA/DNA chimeric fluorescent oligonucleotide probes. He highlights this method as a favorite method when presenting at conferences, noting that its smart and innovative approach consistently resonates with audiences.

Takuma’s PhD work has already led to a first manuscript published in the Journal of Biological chemistry earlier in 2024. He explains that the originality of this study lies in mutating a single residue (Arg73) of the protein to change the enzyme's specificity. “Previous studies had attempted to modify MazF function by replacing its RNA-binding domain, but in our study, we were able to do it by substituting a single residue.” Regarding the impact of his work, Takuma believes it not only contributes to deciphering the molecular and structural bases of MazF substrate recognition but also provides insights into the enzyme's evolution. He is convinced that in the future, using tools like AlphaFold3 will further enhance his understanding of MazF-RNA interactions and lead to the identification additional residues for modifying MazF function, which could lead to significant applications. “Many enzymes such as CRISPR and restriction enzymes have been discovered in bacteria and are now used in genetic engineering. We think MazF could be as useful as restriction enzymes in the future, and we are working hard for that.” Publishing his first article has undoubtedly been a milestone in Takuma’s career, yet it also stands as his most significant challenge to date. He shares “it took me two years to finish writing my first paper. I read articles closely related to my field, studied their language use, and considered how to make it understandable to people outside my field.”

“It makes me feel relaxed. I think having an activity outside the lab is important for health, and this is something I would definitely recommend to a younger student joining the lab.”

Regarding his professional future, Takuma thinks about joining a pharmaceutical or microbiology-related company. “I would like to use the experience I have acquired during my PhD to contribute to future company research.” For that, he is keen on moving abroad. “My father did so.” In fact, Takuma says that his father (also a scientist) has been his main source of inspiration and gave him the desire to become a scientist since he was a child.

Furthermore, one of Takuma’s dreams is to meet Professor Shinya Yamanaka, laureate of the Nobel Prize in Physiology or Medicine with Sir John B. Gurdon recognized for their groundbreaking discovery of induced Pluripotent Stem (iPS) cells.

When not in the lab, Takuma enjoys playing golf, tennis, and skiing. He also loves camping. “It makes me feel relaxed. I think having an activity outside the lab is important for health, and this is something I would definitely recommend to a younger student joining the lab.”

Takuma became a member of the RNA Society this year but has not yet had the opportunity to attend its annual meeting. He is enthusiastic about participating in a future edition. However, he attended the Microbe & RNA meeting in the USA last year and has participated in several microbiology conferences. “I am getting used to presenting in front of others. It is a valuable opportunity to discuss bacteriology and other topics with other scientists, and I keep working hard on my project to produce more data to present and initiate more discussions.” Perhaps at the 30^th meeting of the RNA Society in San Diego.

His favorite RNA journal article is a publication from Jörg Vogel’s lab in 2021, which shows that the ability of the RNA-binding protein ProQ to bind RNA determines its stability, suggesting a quality control mechanism where nonfunctional ProQ is rapidly degraded by the major ATP-dependent protease Lon.

You can contact Takuma by e-mail ([email protected]) and follow him on Instagram (@okabe_takuma).