Hidehiro Ishizawa

Establishment of a new indicator to bridge the gap between the individual and the whole in microbial community engineering

Researcher

Hidehiro Ishizawa

Outline

Microbial communities are relevant to a variety of industries and environmental issues through their metabolic activities and influences on host plants and animals. To improve our ability to manipulate beneficial and detrimental functions of microbial communities, this study proposes a new analytical approach that focuses on the interactions between the functions of individual species in a diverse community. Specifically, this study aims to establish an experimental device and mathematical model that explain how each individual in a community contributes to the function of the whole.

Masao Inoue

A novel method for the prediction of environmental microbial selenoproteome

Researcher

Masao Inoue

Outline

The world of environmental microbiology has changed dramatically with the widespread use of next-generation sequencers, but are we truly deciphering the vast amount of genomic information? This project aims to develop a novel prediction method for selenoproteins, which have been difficult to predict genes because they contain selenocysteine, the 21st amino acid encoded by the termination codon UGA, and to discover functional genes that are cleverly hidden in the genomic information of environmental microorganisms and to elucidate diversity in translation mechanisms.

Atsushi Usami

Creation of biocatalysts for highly efficient production of functional nanocarbon materials

Researcher

Atsushi Usami

Outline

Nanocarbon materials are one of the fields in which Japan is at the top level in the world. However, the synthesis of many functional nanocarbon materials requires a great deal of energy and produces a large amount of waste. Therefore, there is an urgent need to develop low environmental impact and highly efficient production methods. The purpose of this research is to create biocatalysts for highly efficient production of functional nanocarbon materials, focusing on bioprocesses, which are attracting attention as a technology that contributes to the realization of a society capable of sustainable development.

Taisuke Ekino

Functional analysis of the characteristic sensory neurons of plant parasitic nematode

Researcher

Taisuke Ekino

Outline

Different animals perceive different worlds, namely, Umwelt. Understanding the Umwelt of pest species leads us to control them in an environmentally friendly way. The purpose of the present study is understanding the Umwelt of plant parasitic nematode, which is causing tremendous damage to crops and trees. I try to reveal the function of the sensory neuron that is observed only in plant parasitic nematode, which enable us to understand what kind world the plant parasitic nematode perceive.

Hiroki Onoda

Exploring biogasoline synthesis enzyme with structure prediction AI

Researcher

Hiroki Onoda

Outline

CYP152 family enzymes catalyze the fatty acid length controlling reactions and alkene production reactions. I plan to explore “biogasoline synthesis enzymes” from 4700 species of CYP152 family enzymes. Enzyme activities will be estimated by clustering amino acid sequence, predicting the protein structures, and simulating molecular dynamics. For the production of medium-chain bio-hydrocarbons, I am going to find an ideal enzyme, which selectively catalyze alkene production reaction of medium-chain fatty acid. Candidates of the ideal enzyme were evaluated on in vitro experiments. The last stop on my research plan is microbial production of biogasoline with the ideal enzyme.

Shunsuke Kato

Evolutionary engineering of biocatalysts for light-driven radical coupling reactions

Researcher

Shunsuke Kato

Outline

The main challenge associated with biocatalysis is to expand the repertoire of the enzymatic transformations to meet the industrial requirements of synthetic chemistry. To adress this challenge, this study aims to generate a new artificial enzyme which utilizes light energy to drive abiotic radical transformations. By genetically enigineering the artificial enzymes based on the directed evolution methodology, biocatalytic radical coupling reaction between α-keto acid and alkyl halides will be achieved with high efficiency and high selectivity.

Masahiro Kuramochi

Understanding the structure-specific function of freezing- and low- temperature working molecules and the development of preservation method for whole animal.

Researcher

Masahiro Kuramochi

Outline

Ice-binding proteins (IBPs) can inhibit the ice crystal growth. Recently, the ability of IBPs also gather attention to protect the cells from low temperature exposure. Here, I will perform three main works to understand the IBP molecular mechanisms for exhibiting biological effects. (1) Elucidating the specific structure mechanism to induce the ice-binding ability. (2) Evaluation in vivo of ice crystal growth by time-resolved X-ray measurements. (3) Understanding the mechanism of cellular protection from cold shock by fluorescence observation. Based on these basical scientific findings, I will establish the technology for the preservation of living organisms.

Yuhei Goto

Developing a platform for material production using optogenetic multistep switching

Researcher

Yuhei Goto

Outline

The material production using biotechnology reconstitutes the metabolic activities of cells and produces valuable compounds from inexpensive materials. Though optimization of the reconstituted system is necessary for efficient production, dynamic parameters of enzymes in cells have not yet been optimized. The aim of this project is to develop a fundamental platform that enables multistep optimization of dynamic parameters in intracellular material production. Optogenetics, which can manipulate intracellular functions with high time resolution, will be utilized to switching enzyme activities.

Mikiyasu Sakanaka

Elucidation of symbiotic mechanism between gut bacteria and host mediated by glycoprotein metabolism

Researcher

Mikiyasu Sakanaka

Outline

Gut bacteria have established a close symbiotic relationship with humans, but the mechanisms underlying the symbiosis remain largely unclear. In this project, I elucidate the mechanism by which gut bacteria metabolize the glycans attached to glycoproteins and clarify the physiological roles of glycan metabolism on the gut microbiota and humans. I thereby propose a new symbiotic strategy between gut bacteria and humans mediated by glycan metabolism.

Yuma Shisaka

Development of the CO2 fixation system using a biocatalyst

Researcher

Yuma Shisaka

Outline

Carbon dioxide (CO2) is a greenhouse gas emitted by human activities. Thus, removal of CO2 from the atmosphere is a powerful means to stem the progress of global warming. In this research, I will establish a biocatalytic system that directly fixes CO2 to organic molecules. This research will promote the development of innovative technologies to transform harmful CO2 into useful chemicals.

Mio Shibuta

Study of quick transcription regulated by RNA polymerase II

Researcher

Mio Shibuta

Outline

As sessile organisms, plants have to response to fluctuating environments through various transcription regulations. Quick transcription regulations play an important role in stress responses such as heat stress. Modifications of RNA polymerase II (PolII) are indicators of transcription, and control transcription at the downstream of transcription factors, providing rapid and efficient transcription changes. To elucidate the mechanism of PolII modification-mediated transcription control, I focus on PolII dynamics in heat stress responses in a model plant, Arabidopsis thaliana. I observe the PolII dynamics using a new PolII dynamics imaging system and conduct functional analysis of PolII modifications.

Rei Suo

Studies on tetrodotoxin origin in toxic flatworm: exploration of chemical cue for larval settlement and metamorphosis

Researcher

Rei Suo

Outline

Tetrodotoxin (TTX) has been detected in a wide range of marine organisms, but its origin remains a mystery. Marine polyclad toxic flatworms constantly contain high concentration of TTX, and act as one of the major TTX sources for TTX-bearing fish species in the nature. It is known that artificially reared pufferfish are TTX-free when fed a diet that does not contain TTX. However, rearing experiments of the toxic flatworm from the egg stage has not been conducted because the larvae do not settle and metamorphose in a laboratory aquarium. This project aims to identify chemical factors that may have effects on larval settlement and metamorphosis of the flatworm in order to establish the artificial rearing method for the flatworm larvae.

Kenshi Suzuki

Maintenance mechanisms of microbial diversity and functional stability in microbial communities

Researcher

Kenshi Suzuki

Outline

Microbial communities are capable of forming huge networks and exhibit functions such as those comprising carbon and nitrogen cycles. Therefore, it is necessary that understand how microbes form such networks and respond to environmental changes to maintain their functions. Although many researches using omics visualized microbial communities structure and predicted their network structure, these have not been experimentally proven yet. In this project, I focus on metabolite cross-feeding to elucidate a real microbial network and its stability. I will use laminar microfluidics with microscopic Raman spectrum analysis and FISH imaging to analyze correlations of microbes at the single-cell level. The results will contribute to a complete understanding of microbial communities in nature.

Yuki Soma

Synthetic microbial consortia for expansion of metabolic function

Researcher

Yuki Soma

Outline

By designing the mutual donation relationship of metabolites using metabolically modified microorganisms, it is possible to construct an artificial microbial consortium in which multiple strains grow codependently. In this synthetic microbial consortium, the co-growth rate of the entire consortium varies depending on the enzymatic reactions involved in metabolite cross-donation. By utilizing this property, it is possible to select highly active enzyme mutants using the ”co-growth rate” as an index. In this study, I will develop an innovative enzyme screening technology using artificially synthesized bacterial consortium as a selection field.

Eiichiro Takamura

Establishment of comprehensive enzyme design guideline decision method by multivariate analysis

Researcher

Eiichiro Takamura

Outline

Redox enzymes, which are excellent electrocatalysts, are needed in devices for bioelectronics.However, conventional enzyme activity screening is unsuitable for obtaining qualified information for modifying enzymes for devices using electroenzymatic reactions. In the present study, screening is performed based on electroenzymatic reactions, and the big data (ex. electrocatalytic activity, amino acid properties, etc.) is analyzed by multivariate analysis. By applying the results and findings to machine learning, a novel design method for high-performance enzyme variants for bioelectronic devices will be established.

Kenya Tanaka

Development of a comprehensive protein potential determination method to elucidate the adaptation mechanism of photosynthesis

Researcher

Kenya Tanaka

Outline

Intracellular redox variations caused by photosynthetic activity changes are reflected in redox states of proteins, which in turn lead to regulation of downstream enzymes and/or reductive detoxication of reactive oxygen species. Many redox-regulated proteins forms a complex regulatory network. This study aims to develop a novel method to comprehensively determine protein redox potentials and elucidate the mechanisms of metabolic regulation and adaptation in photosynthetic organisms.

Kotaro Nishiyama

Elucidation and regulation of flowering by integrating chemical biology and structural biology

Researcher

Kotaro Nishiyama

Outline

Flowering deeply concerns agriculture and selective breeding. Both the elucidation of flowering pathways and the artificial regulation of flowering time can allow us to securely produce crops and quickly construct novel cultivars. In this study, I will develop novel organic molecules, that act on flowering-related proteins, by integrating chemical biology and structural biology. The developed molecules will be used to elucidate molecular mechanism of flowering and to regulate timing of flowering.

Hiroyuki Hikida

Development of novel gene engineering technology utilizing giant viruses

Researcher

Hiroyuki Hikida

Outline

Ginat viruses have extraordinary large genome reaching 2 Mbp. Based on the idea that these viruses can be used as a novel vector to express exogenous biological functions, this project aims to deteremine the magnitude of coding capacity of theses viruses. Also, mobile genetic elements associated with these viruses will be focused and examined as the possible tools to modify giant viruses genome.

Manami Ishii-Hyakutake

Modification of bioplastic terminal structure for an effective production cost

Researcher

Manami Ishii-Hyakutake

Outline

Polyhydroxyalkanoate (PHA) is a bio-based polyester produced from a myriad array of microorganisms. It is an eco-friendly material thus can be used as an alternative to the existing commodity plastic material. However, the entry of PHA to the commercial world is hindered due to its poor physical properties and high production cost. Thus, it is necessary to improve the physical properties and reduce the production cost to expand the use of PHA in various fields. Therefore, the aim of this study is to synthesize low molecular weight of PHA with a specific terminal structure to improve the physical properties and for an effective cost reduction.

Satoshi Hiraoka

Exploring epigenomics in thermophilic microbial communities.

Researcher

Satoshi Hiraoka

Outline

DNA chemical modifications (epigenome) are widespread and play important roles in prokaryotes and viruses as well as eukaryotes. However, current knowledge of these modification systems is severely biased towards a limited number of culturable prokaryotes, despite the fact that a vast majority of microorganisms have not yet been cultured. This limited sample size skews our knowledge of microbial epigenomics, particularly in terms of diversity, distribution, and impact upon ecology and evolution. In this project, using single-molecule real-time sequencing, I will conduct culture-independent ‘metaepigenomic’ analyses (an integrated analysis of metagenomics and epigenomics) of thermophilic microbial communities for comprehensive understanding of microbial epigenomics.

Ryosuke Fujiwara

High-yield styrene production from CO2-derived carbons

Researcher

Ryosuke Fujiwara

Outline

Technologies of Carbon dioxide Capture, Utilization and Storage (CCUS) are indispensable for the realization of a decarbonized society. At the same time, to reduce the use of fossil resources and reduce CO2 emissions, it is essential to develop technology to produce valuable chemicals from renewable resources. In this project, I will develop technology for the high-yield production of styrene, an industrially important compound, by microbial fermentation using low-molecular compounds synthesized from CO2 as raw materials. I use two unique techniques to improve the production yield: dividing the metabolic system into two and modularizing the carbon fixation reaction. Through these unique strategies, I aim to produce styrene with an ultra-high yield, which was impossible with conventional approaches.

Kanako Bessho-Uehara

Identification of the factor derived from beetles to change plant morphogenesis

Researcher

Kanako Bessho-Uehara

Outline

In this study, I will narrow down the candidates of gall inducing factors derived from beetles by bioinformatics and evolutionary analysis. In addition, by using a plant tissue culture system called VISUAL (Vascular Cell Induction Culture System Using Arabidopsis Leaves), I will try to visualize the response of plant to the insect-derived factors at the cellular level and examine the gene expression change by treating the synthesized insect-derived factors. The goal of this study is to elucidate the molecular mechanism of plant tissue modification by the gall inducing factors.

Shigetaka Yasuda

Development of a basis for plant disease control under high humidity

Researcher

Shigetaka Yasuda

Outline

Atmospheric humidity greatly influences plant-microbe interactions, and high humidity often favors plant diseases. Bacterial pathogen develops a water-soaked leaf apoplast to promote the growth, thereby causes severe disease symptom under high humidity. Our recent findings imply that plants restrict bacterial water soaking by recognizing high humidity, however, the underlying mechanisms have remained elusive. In this study, I aim to elucidate the mechanisms by which plants perceive changes in high humidity and dissect the molecular basis of plant-bacterial pathogen interactions under high humidity. This study will provide insights into the development of plant disease control adapted to high humidity.

Aya Yoshimura

Studies on bacterial cell-to-cell communication through membrane vesicles and secondary metabolites

Researcher

Aya Yoshimura

Outline

Bacterial secondary metabolite biosynthesis is regulated by external stimuli in nature. Although the regulation indicates that secondary metabolites play indispensable roles to improve bacterial growth environments, the functions remain largely unknown. Herein, this study focuses on membrane vesicles (MVs), signaling mediators in bacterial cell-to-cell communication, to find secondary metabolites potentially work for bacterial communication. Moreover, this study uncovers the mechanism of bacterial communication through MVs and secondary metabolites. New insights from this study will contribute to launch new biotechnologies for controlling microbiota by utilizing MVs and secondary metabolites.