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
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
- 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
- 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 -
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.