[Genome programming] Year Started : 2019

Takashi Ito

Achieving constraint-free design and evolvability of synthetic genomes through new interpretations of DNA sequences

Research Director
Takashi Ito

Professor
Graduate School of Medical Sciences
Kyushu University

Collaborator
Yasukazu Daigaku Project Leader
The Cancer Institute
Japanese Foundation for Cancer Research
Outline

This project aims to develop novel techniques to duplicate any regions in the genome, apply selection pressure to any genomic sequences, and introduce mutations throughout the target regions, by fully exploiting CRISPR-Cas system, two-hybrid system, and base editing enzymes in the baker’s yeast as a model system. We will combine these techniques to take a constructive approach to deepen the understanding of adaptive evolution by gene duplication. These techniques will provide an important step toward constraint-free design of evolvable genomes.

Wataru Iwasaki

Bioinformatics for predicting new functions in DNA sequence space

Research Director
Wataru Iwasaki

Professor
Graduate School of Frontier Sciences
The University of Tokyo

Outline

In the era of genome synthesis, new bioinformatic technologies for predicting new functions in DNA sequence space are needed. The aim of this project to develop such bioinformatic technologies to take full advantage of ever-increasing sequence data. Development of new biotechnological tools for modifying and controlling genomes is also envisioned.

Takehiko Kobayashi

Construction of gene amplification system and chromosomal vector

Research Director
Takehiko Kobayashi

Professor
Institute for Quantitative Biosciences
The University of Tokyo

Collaborator
Hiro-oki Iwakawa Associate professor
College of Science
Rikkyo University
Outline

We develop a gene amplification system that increases any genes. Moreover, using the amplification system, we make a chromosomal vector that clones ~100 genes. This vector makes it possible to construct heterogeneous physiological systems and to face establishment of artificial cells in the future.

Hiroyuki Noji

Artificial cell reactor system for long-chain DNA synthesis and creation of autonomous artificial cells

Research Director
Hiroyuki Noji

Professor
Graduate School of Engineering
The University of Tokyo

Collaborator
Takahiro Muraoka Professor
Institute of Global Innovation Research
Tokyo University of Agriculture and Technology
Outline

This project pursues novel technology of autonomous artificial cell reactors. We develop chemical microreactor systems that are capable to actively condense and hold biological macromolecules such as DNA and proteins and also to undergo cell-like morphological changes as growth, fission and division. We also develop new chemical/biological tool boxes in order to newly confer and enhance the functionalities of artificial cell reactors. By implementing cell-free systems for gene-replication and gene–expression in artificial cell reactors, we aim to create artificial cells with the capability of autonomous self-replication.

Makoto Miyata

Construction of cell evolution model using synthetic bacterium JCVI syn3.0B and genome manipulation

Research Director
Makoto Miyata

Professor
Graduate school of Science
Osaka Metropolitan University

Collaborator
Daisuke Shiomi Professor
College of Science
Rikkyo University
Akihiro Narita Associate Professor
Graduate Schcol of Science
Nagoya University
Robert Robinson Specially Appointed Professor
Research Institute for Interdisciplinary Science (RIIS)
Okayama University
Outline

JCVI-syn3.0B is a synthetic bacterium established in 2016 on the basis of mycoplasma. Its genome consists only of genes essential for growth. In this study, we will transfer and express various genes into this synthetic bacterium, and experimentally reproduce events which happened in the evolution from primitive cells to eukaryotes, the acquisition of abilities such as motility, cell wall formation, DNA segregation, and membrane remodeling. Furthermore, new cell construction will be performed by free design of the cells.

Yoko Yamanishi

Delivery of long-chain DNA by the novel bubble injector and microstructures

Research Director
Yoko Yamanishi

Professor
Graduate School of Engineering
Kyusyu University

Collaborator
Shigeo S.Sugano Senior Researcher
Bioproduction Research Institute
National Institute of Advanced Industrial Science and Technology
Miho Tagawa Associate Professor
Institute of Materials and Systems for Sustainability
Nagoya University
Tomomi Tsubouchi Associate Professor
Laboratory of Stem Cell Biology
National Institutes of Natural Sciences National Institute for Basic Biology
Outline

For applications of long-chain DNA to cell biology, delivery methods to cells are limited since long-chain DNA has both a bulky 3D structure and a high fragility to the physical stimuli. In this study, we will combine the novel bubble injector and the micro-structure to develop the new long-chain DNA delivery system.

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