The database is available from the National Institute of Technology and Evaluation of Products (NITE) under its Data and Biological Resource Platform (DBRP) website https://www.nite.go.jp/nbrc/dbrp/taglist and currently (June 2021) contains the following projects:

Title Proteome analysis_Aspergillus oryzae : Proteome analysis of Aspergillus oryzae

[English] The proteome of Aspergillus oryzae RIB40 (= NBRC 100959) grown under liquid culture and membrane-transfer culture have been analyzed.

Project URL: https://www.nite.go.jp/nbrc/genome/project/proteome/rib40_p.html 

Title Proteome analysis_Brevibacillus brevis : Proteome analysis of Brevibacillus brevis

[English] The proteome of Brevibacillus brevis 47 (= NBRC 100599) grown under T2 medium and minimal medium have been analyzed.

Project URL: https://www.nite.go.jp/nbrc/genome/project/proteome/BB_p.html 

Title Proteome analysis_Aeropyrum pernix : Proteome analysis of Aeropyrum pernix

[English] The proteome of the aerobic hyper-thermophilic crenarchaeon, Aeropyrum pernix K1 (= NBRC 100138) grown at 90 ˚C has been analyzed.

Project URL: https://www.nite.go.jp/nbrc/genome/project/proteome/K1_p.html 

Title Proteome analysis of Methanococcus maripaludis : Proteome analysis of Methanococcus maripaludis

[English] The proteome of methanogenic archaea, Methanococcus maripaludis strain OS7 (= NBRC 103642) with the iron corrosive property and its corrosion-defective mutant OS7mut1 (= NBRC 105638) have been analyzed.

Project URL: https://www.nite.go.jp/nbrc/genome/project/proteome/mm2_p.html 

Title Proteome analysis of Escherichia coli : Proteome analysis of Escherichia coli

[English] The proteome of Escherichia coli K-12 W3110 grown under glucose minimal medium has been analyzed.

Project URL: https://www.nite.go.jp/nbrc/genome/project/proteome/index.html 

Title Proteome analysis of Rhodococcus opacus: Proteome analysis of Rhodococcus opacus

English] The proteome of Rhodococcus opacus B4 (= NBRC 108011) and its mutants have been analyzed.

Project URL: https://www.nite.go.jp/nbrc/genome/project/proteome/B4_p.html 

Title Proteome analysis of Kocuria rhizophila : Proteome analysis of Kocuria rhizophila

[English] The proteome of Kocuria rhizophila DC2201 (= NBRC 103217), which is the bacteria tolerant to organic solvents, grown under several conditions The proteome of Kocuria rhizophila DC2201 (= NBRC 103217), which is the bacterial tolerant to organic solvents, grown under several conditions

Project URL: https://www.nite.go.jp/nbrc/genome/project/proteome/KR_p.html 

Title Proteome analysis of Anaerolinea thermophila: Proteome analysis of Anaerolinea thermophila

[English] The proteome of Anaerolinea thermophila UNI-1 has been analyzed.

Project URL: https://www.nite.go.jp/nbrc/genome/project/proteome/at1_p.html 

Data Title Project (Proteome Analysis_Arthrospira platensis (Spirulina platensis))

[English] The proteome of Arthrospira platensis (Spirulina platensis) NIES-39 have been analyzed.

Project URL: https://www.nite.go.jp/nbrc/genome/project/proteome/apl_p.html 

Title Proteome analysis_Gemmatimonas aurantiaca: Proteome analysis of Gemmatimonas aurantiaca

English] The proteome of Gemmatimonas aurantiaca T-27 have been analyzed.

Project URL: https://www.nite.go.jp/nbrc/genome/project/proteome/ga1_p.html 

Title Proteome analysis of Sulfurisphaera tokodaii: Proteome analysis of Sulfurisphaera tokodaii

English] The proteome of Sulfurisphaera tokodaii strain 7 (Sulfolobus tokodaii strain 7) has been analyzed.

Project URL: https://www.nite.go.jp/nbrc/genome/project/proteome/st7_p.html 

Title Proteome analysis of Caldilinea aerophila: Proteome analysis of Caldilinea aerophila

English] The proteome of Caldilinea aerophila STL-6-O1 (NBRC 104270T) has been analyzed.

Project URL: https://www.nite.go.jp/nbrc/genome/project/proteome/ca1_p.html 

Title Proteome analysis of Tetragenococcus halophilus : Proteome analysis of Tetragenococcus halophilus

[English] We have analyzed the proteome of Tetragenococcus halophilus (= NBRC 12172) cultured with added salt concentration of 0% and 10%.

Project URL: https://www.nite.go.jp/nbrc/genome/project/proteome/th1_p.html 

Institution Name Strain Management Group, Planning and Management Department, Production Control Center, AminoScience Division, Ajinomoto Co.

Title Aquatic Imperfect Bacteria Screening Project

Abstract To create new medical and agricultural resources from aquatic imperfect bacteria known to have unique metabolites, a library of aquatic imperfect bacteria isolated as a screening source

Institution National Institute of Advanced Industrial Science and Technology (AIST)

Title Development of genome and transcriptome analysis technology suitable for information analysis

Abstract In order to realize reliable RNA-Seq analysis, the project aimed to expand the number of RNA reference materials for spike-ins and to apply them to industrial microorganisms, as well as to establish a method for obtaining gene expression information for RNA that is considered to be of low quality by general-purpose evaluation indices.

Project URL: https://www.jba.or.jp/nedo_smartcell/technology/14.php 

Institution Ajinomoto Co.

Title Development of a rapid search technology for DNA sequence factor combinations using the Combi-OGAB method and machine learning

Abstract By creating a microbial library using the Combi-OGAB method and analyzing the data using machine learning, we extracted the laws necessary for gene sequence design and high production of target substances. Specifically, by regulating the expression intensity of limonene biosynthetic enzymes in E. coli, we extracted the bottleneck enzymes and the rules for high production.

Institution Osaka University

Title Proteome analysis technology development

Abstract We constructed a multiple reaction monitoring (MRM) assay to measure the expression levels of E. coli central metabolic enzyme proteins. Specifically, we obtained proteome data by performing nano-LC-MS/MS analysis of tryptic digested samples of E. coli ASKA strain (one gene overexpression strain) and wild strain.

Project URL: https://www.jba.or.jp/nedo_smartcell/technology/16.php 

Institution Name Kobe University

Title Development of high-throughput microbial construction and evaluation technology

Abstract We developed a semi-automated transformation technology that can obtain several thousand transformants at once. Carotenoid pigment (lycopene or β-carotene) biosynthesis pathway plasmids were comprehensively introduced into gene-disrupted strains (approximately 4,000 strains of E. coli and 5,000 strains of budding yeast), and carotenoid productivity was comprehensively evaluated and data obtained by image analysis of bacterial coloration.

Project URL: https://www.jba.or.jp/nedo_smartcell/technology/07.php 

Institution Name Kobe University

Title Metabolome analysis technology development

Abstract Project Summary: In the course of developing analysis technology to obtain metabolome data that contributes to metabolic pathway design with high accuracy and high throughput, we established a metabolome measurement method using LC/MS/MS and developed an “automatic pretreatment system.

Project URL: https://www.jba.or.jp/nedo_smartcell/technology/15.php 

Institution Name University of Tsukuba, Nikon Instec Co.

Title Development of production technologies for high-functional products using plants and other organisms / Development of information analysis systems that contribute to the creation of highly productive microorganisms

Abstract We succeeded in predicting the amount of oil and fat produced by each cell by obtaining the single-cell autofluorescence profile of oil-producing yeast using the single-cell autofluorescence profile analysis platform.

Project URL: https://www.jba.or.jp/nedo_smartcell/technology/17.php 

Organization National Institute of Technology and Evaluation (NITE)

Title Development of design and optimization methods for novel metabolic pathways

Abstract Aiming to design new metabolic pathways for carotenoids and alkaloids using the metabolic pathway design platform tool we developed, we evaluated the carotenoid production culture of NBRC strains, obtained enzyme gene information that is expected to improve the productivity of these substances from genome information, literature and patent information, and verified the introduction effect. In addition, we obtained information on enzyme genes that are expected to improve the production of these substances from genome information, literature, and patent information, and verified the effects of their introduction.

Institution Asahi Kasei Pharma Co.

Title Efficacy verification by improving the productivity of cholesterol esterase

Abstract Cholesterol esterase is used for the diagnosis of blood cholesterol. In order to improve the productivity of cholesterol esterase producing strain Burkholderia stabilis, we conducted genome analysis of the producing bacteria. In addition, DNAseq and RNAseq analyses were conducted to search for genes that contribute to productivity.

Institution Nagaoka University of Technology

Title Validation of simultaneous control of production of useful proteins using filamentous fungi

Abstract T. reesei produces several extracellular enzymes, and omics analysis of the standard strain and the industrial production base strain was conducted in order to vary the production of each enzyme. Gene expression network analysis using the omics data was used to find the factors that change the enzyme components and to verify the disruptive effects.

Project URL: https://www.jba.or.jp/nedo_smartcell/proof/01.php 

Institution Kobe Natural Products Chemistry Ltd. and National Institute of Advanced Industrial Science and Technology

Title Verification of the effectiveness of enzyme design technology using monoterpenoid oxidase such as limonene ~Development of enzyme modification technology using MD simulation~.

Abstract Regioselectivity and productivity are sometimes issues when using enzymatic reactions. Therefore, in collaboration with the National Institute of Advanced Industrial Science and Technology (AIST), we have developed a method for predicting enzyme modification sites that improve reaction regioselectivity using molecular dynamics (MD) simulation. In addition, the oxidation of monoterpenoids such as limonene was used as a model case, and the function of the modified enzyme was evaluated using P450 in the Kobe Natural Products Chemistry cytochrome P450 library.

Project URL: https://www.kncweb.co.jp/technology/bioconversion.html 

Institution Name Mitsubishi Chemical Corporation

Title Validation of Metabolic Analysis Technology by Improving the Productivity of Useful Isoprenoids

Abstract In order to breed microbial strains that produce high levels of isoprenoid compounds, we analyzed the products of various breeding strains and their expression levels under a number of culture conditions, and used the results to extract candidate genes and reactions that contribute to solving bottlenecks.

Institution Name Research Institute of Innovative Technology for the Earth

Title Validation of Metabolic Analysis Technology by Improving the Productivity of Useful Aromatic Compounds Using Bacillus subtilis

Abstract A smart cell design system was verified through the improvement of catechol productivity. In the process, we conducted an omics analysis of catechol-producing strains and shikimic acid-producing strains under various conditions, contributing to the improvement of the accuracy of metabolic pathway design technology, expression control network construction technology, and transporter search technology.

Project URL: https://www.jba.or.jp/nedo_smartcell/proof/02.php 

Institution National Institute of Advanced Industrial Science and Technology

Title Efficacy Verification by Controlling Pigment Production Using Red Yeast Rice Mold

Abstract To improve the productivity of red yeast rice pigment, a natural food pigment produced by red yeast rice mold, we conducted comprehensive gene expression analysis of the reference strain, mutant strains, and validation strains under various culture conditions to verify the effectiveness of genetic modification using a new mathematical model based on expression control network model. In addition, we clarified the pigment synthesis gene cluster and citrinin synthesis gene cluster by draft genome analysis of the reference strain, and constructed a biosynthetic model.

Institution National Institute of Advanced Industrial Science and Technology

Title Validation of a new production method for paprika-derived carotenoids using microorganisms

Abstract Targeting two industrially useful carotenoids (β-cryptoxanthin and lutein) derived from paprika, we selected enzymes involved in the efficient biosynthesis of these carotenoids and verified their production in E. coli and yeast. As a result, we succeeded in producing these two carotenoids in E. coli and yeast.

Project URL: https://www.jba.or.jp/nedo_smartcell/proof/07.php 

Institution Niigata University of Pharmacy and Applied Life Sciences, Nagaoka University of Technology

Title Verification of the efficacy of oils and fats containing ω-3 polyunsaturated fatty acids by improving their productivity

Abstract We attempted to construct eicosapentaenoic acid C20:5 (EPA)-producing strains using two kinds of oil and fat yeasts (Lipomyces starkeyi and Rhodosporidium toruloides) and created EPA-producing L. starkeyi. In addition, we identified genes that improve oil and fat production by constructing an expression regulatory network model using transcriptome analysis data of oil and fat accumulation mutants, metabolome analysis, proteome analysis, and genome comparison analysis, and created a high-producing strain by utilizing these genes. 

Abstracts of related presentations at the Japan Society for Bioscience and Biotechnology 

Development of high oil and fat producing strains of the oil and fat yeast Lipomyces starkeyi (https://ci.nii.ac.jp/search?q=9000291273015) 

Expression analysis of genes related to fat and oil synthesis and degradation in a low-fat accumulation mutant strain of Lipomyces starkeyi (https://ci.nii.ac.jp/search?q=9000316621316) 

Acquisition of fat and oil hyperaccumulating mutant strains of Lipomyces starkeyi using density gradient centrifugation (https://ci.nii.ac.jp/search?q=9000316621322) 

Acquisition of fat and oil hyperaccumulating mutant strains of the industrial oil and fat yeast Lipomyces starkeyi (https://ci.nii.ac.jp/search?q=9000321425083) 

Expression analysis of genes involved in fat and oil accumulation in the oil and fat yeast Rhodosporidium toruloides (https://ci.nii.ac.jp/search?q=9000316621333) 

Improvement of oleaginous yeasts using informatics for the production of functional fats and oils (https://jsbba.bioweb.ne.jp/cgi-bin/jsbba_db/jsbba_summary.cgi?id=58970) 

Identification of genes responsible for low fat accumulation in the oleaginous yeast Lipomyces starkeyi by comparative genomic analysis (https://jsbba.bioweb.ne.jp/cgi-bin/jsbba_db/jsbba_summary.cgi?id=57534) 

Identification and functional analysis of novel regulators of lipid accumulation in the oleaginous yeast Lipomyces starkeyi by comparative genomic analysis (https://jsbba.bioweb.ne.jp/cgi-bin/jsbba_db/jsbba_summary.cgi?id=57532) 

Identification and analysis of the causative gene of lipid hypoaccumulation mutants in the oleaginous yeast Lipomyces starkeyi (https://jsbba.bioweb.ne.jp/cgi-bin/jsbba_db/jsbba_summary.cgi?id=56884)

Project URL: https://www.jba.or.jp/nedo_smartcell/proof/03.php 

Institution Name Ishikawa Prefectural University, Kobe University

Title Validation of a new production method for alkaloids and other compounds using microorganisms

Abstract Five new biosynthetic pathways from tyrosine to 3,4-DHPAA were established by information analysis. In addition, we searched for enzymes with similar functions to tyrosine hydroxylase and monoamine oxidase, which are the rate-limiting reactions in the reticulin biosynthetic pathway, and introduced plasmids. In addition, we constructed a genome-inserted reticulin-producing E. coli strain for practical use, and also produced a genome-inserted tyrosine and dopamine high-producing E. coli strain.

Project URL: https://www.jba.or.jp/nedo_smartcell/proof/04.php