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Biochemistry Lab
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The lab explores the mechanisms of defense and response in bacteria and archaea.
AboutAbout the lab
Decoding bacterial defense and response mechanisms at the molecular level
The Biochemistry Lab studies the molecular mechanisms of antiviral defense and stress response in bacteria and archaea.
Focusing on interactions between nucleic acids and proteins, the lab combines methods from biochemistry, molecular biology, and structural biology to elucidate how these systems work.
Building on its findings, the lab also pursues research on genome editing, cell manipulation, and the development of antibacterial agents.
The lab celebrated its 100th anniversary in 2021.
Key terms
- CRISPR-Cas system
- The adaptive immunity of prokaryotes. Cas proteins and crRNA cleave viral DNA to suppress viral replication
- Riboswitch
- An RNA region in bacterial mRNA that binds a specific substance and regulates the expression of downstream genes
- Metagenome
- A collection of DNA sequences analyzed together from environmental samples, without isolating individual microorganisms or viruses
ResearchResearch themes
The lab aims to clarify how bacteria and archaea carry out antiviral defense and stress response, through the functions and structures of proteins that act on nucleic acids. The findings are linked to research with medical and industrial applications in view.
*Illustrative imageBiology and applications of CRISPR-Cas systems
The lab discovers novel Cas proteins in CRISPR-Cas systems, the adaptive immunity of prokaryotes, and analyzes their functions and structures. Based on three-dimensional structures, it modifies their functions, aiming to create effectors useful for genome editing.
*Illustrative imageNon-coding RNAs that regulate gene expression
The lab studies how riboswitches in bacterial mRNAs bind specific substances and regulate the expression of downstream genes. It also aims to develop new antibiotics that target riboswitches.
*Illustrative imageFunctions of toxin-antitoxin systems
The lab studies how toxin-antitoxin (TA) systems, which are combinations of a toxin and an antitoxin, work when prokaryotes are under stress. It aims to elucidate their mechanisms of action and expression regulation, and to understand their relationship with other biological defense systems.
*Illustrative imageSearching environmental DNA for useful genes
The lab analyzes its own environmental DNA prepared from seawater, lake and marsh water, and hot spring water to search for novel useful genes. So far, it has identified many CRISPR-Cas system genes from its original metagenomes and analyzed their functions and structures.
MembersFaculty
The members of the Biochemistry Lab consist of faculty members, staff, academic researchers, doctoral, master's, and undergraduate students, and exchange students.As of 2026
- Associate ProfessorTomoyuki Numata
- Assistant ProfessorTakeshi Yamagami
- Assistant ProfessorTakashi Nakashima
- Assistant ProfessorShunsuke Matsumoto
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Report an errorAbout the images
The top and research theme images are illustrative and were not taken at the lab. They are cropped from Wikimedia Commons images. Cropped CC BY-SA images are provided under the same CC BY-SA license as the original (version shown on each line).
- Top image: “LambdaPlaques” No machine-readable author provided. Madboy assumed (based on copyright claims). / CC BY-SA 3.0 (cropped)
- Biology and applications of CRISPR-Cas systems: “CRISPR CAS9 technology” Elena I Leonova / CC BY 4.0 (cropped)
- Non-coding RNAs that regulate gene expression: “G riboswitch RNA ribbon” Jane & David Richardson / CC BY 3.0 (cropped)
- Functions of toxin-antitoxin systems: “E-coli (Escherichia coli)” Nurgul D / CC BY-SA 4.0 (cropped)
- Searching environmental DNA for useful genes: “EDNA Water Sampling ( )” Monica Blaser, photographer, U.S. Fish and Wildlife Service, Midwest Region. USFWSmidwest / Public domain (cropped)
- Related lab (Genome Chemistry and Engineering Lab): “Bryophyte Leaf Cells” KarlGaff / CC BY-SA 4.0 (cropped)
- Related lab (Gene Regulation Lab): “Genome Sequencer2” Database Center for Life Science (DBCLS) / CC BY 3.0 (cropped)
- Related lab (Biophysical Chemistry Lab): “Crystal structure ( )” Jun from Melbourne, Australia / CC BY-SA 2.0 (cropped)
- Related lab (Plant Nutrition Lab): “Plant Cells 03” Debojit37 / CC BY-SA 4.0 (cropped)
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