CSBL::Computational & Synthetic Biology Laboratory at
We Seek Answers for Big Questions by Reading Genome, Writing Genome and Editing Genome. From Molecules To Organisms, We See Everything in the Light of Evolution.
NGS - Reading Genomes
We understand living things by their genomes and transcriptomes
- Sequencing is a procedure collecting the genetic code of all living things. Decoding the code of life begins with sequencing and annotation. We have sequenced and annotated various genomes (DNAseq) and transcriptomes (RNAseq) of living organisms ranging from prokaryotes (bacteria) to eukaryotes (fungi).
- Since 2013, we have involved in the 1000 fungal genome project (1kFGP) geared by Joint Genome Institute (JGI), DOE USA. It is a data-driven approach to access all fungi on earth.
- We investigate Fungal Genome Universe by consolidating all known fungal genome information. We mainly focus on the biology of edible, medicinal and poisonous mushrooms. We attempt to parse new knowledge of fungal biology by various NGS techniques.
Structural genomics - A path to molecular function
What you see is what you understand
- We use X-ray crystallography as a magnifier to investigate bio-macromolecules at the molecular level
- The matters in the universe are composed of a limited number of elements (see, the periodic table). Likewise, the protein folds can be decomposed to the limited number of construction units (folding units). The question is, ‘are there Structural Foldons such as protein structure alphabets that recombine to provide molecular diversity of protein universe during evolution’?
- Are there DNA/RNA foldons, too? (Check out later!)
Genes and Proteins
- A vast number of genes and proteins exists in the protein universe. We explore the protein universe to see how protein structures are evolved? We mapped the protein space - Protein Structure Universe where the protein structures are born, developed and innovated.
- We examine the functionality of protein domains and families in the pan-genome space where genes/proteins are born, developed, innovated, horizontally transferred and eventually destroyed.
Biology is Technology
What I cannot create, I do not understand
Richard Feynman said, ‘What I cannot create, I do not understand’, which is followed by ‘Know how to solve every problem that has been solved’. This is the goal of synthetic biology as a technology tinkering living things.
- Construction by Design - We can construct syntheic metabolic pathway by design (e.g. iPNN - intelligent Pathway Network Navigator).
- Learning by Construction - We can learn how nature builds ‘things’ by synthesis (e.g. PKSDS - PolyKetide Synthetase Design Suite)
iGEM $ DIYBio
Synthetic biology is a hacking tool for biology. Amateur and citizen scientists applying synthetic biology approach are called as ‘biohackers’. CSBL supports biohackers.
We learn and discover nature’s design principles for engineering biology. For instance, deconstruction of Red Algal Biomass can be accelerated by a designed pathway.
- Agar, a recalcitrant polysaccharide, has a great potential as renewable biomass. We have recently elucidated the details of bacterial agarolytic pathways. We have sequenced genomes (DNAseq) and transcriptomes (RNAseq) of several agarolytic microorganisms using next-generation sequencing (NGS) techniques. We have identified key enzymes (e.g. beta-agarases, agarooligosaccharide beta-galactosidase - ABG, neoagarobiose hydrolase - NABH, anhydrogalactose dehydrogenase -AHGD and anhydrogalactonate cycloisomerase - ACI, etc.) in the agar metabolic pathway and determined atomic structures of key enzymes. The full understanding of molecular and cellular functions of these novel agarolytic enzymes will provide the design principle of synthetic agar degradation pathways and eventually guide the construction of synthetic microorganisms converting agar into valuable chemicals.