「次世代治療・診断実現のための創薬基盤技術開発(国際基準に適合した次世代抗体医薬等の製造技術のうち高生産宿主構築の効率化基盤技術の開発に係るもの)」 日本医療研究開発機構 委託事業

1 Maruyama, s., Matsuyama, Y., Aburatani,S. (2015) Application of KL Divergence for Estimation of Each Metabolic Pathway Genes., International Journal of Medical, Health, Pharmaceutical and Biomedical Engineering, 9(3), 233-237
2 近藤昭彦植田充美合成生物工学の未来展望生物工学会誌, 93(9), 522-541 (2015)
3 柘植謙爾板谷光泰枯草菌による遺伝子集積法のOGAB法による長鎖DNA合成生物工学会誌, 93(9), 527–529 (2015)
4 Aburatani, S., Tashiro, K., Kuhara, S. (2015) Classification method for heterogeneity in monoclonal cell population., J. Phys.: Conf. Ser., 633, 012077, 1-4
5 Tominaga, D., Mori, K., Aburatani, S.  (2015)  Linear and Nonlinear Regression for Combinatorial Optimization Problem of Multiple Transgenesis., IPSJ Transactions on Bioinformatics., 9, 7-11.
6 Terai, G., Kamegai, S., Asai, K.  (2016) CDSfold: an algorithm for designing a protein-coding sequence with the most stable secondary structure., Bioinformatics (Oxford, England). 32(6), 828-834.
7 Kumagai T, Machida M. (2017) Practical data processing approach for RNA-sequencing of microorganisms, Transcriptome Analysis, P.D.R. Cirillo & E.C.C. Mateo eds., InTechOpen, DOI: 10.5772/intechopen.69157
8 Terai G, Kamegai S, Taneda A, Asai K. (2017) Evolutionary design of multiple genes encoding the same proteinBioinformatics., 33(11), 1613-1620
9 Sugiyama, A., Umetsu, M.,Nakazawa, H., Niide, T., Onodera, T., Hosokawa, K., Hattori, S., Asano. R. &Kumagai, I.  (2017) A semi high-throughput method for screening small bispecific antibodies with high cytotoxicity., Scientific Reports, 7:2862, 1-12
10 Nambu-Nishida, Y., Nishida, K., Hasunuma, T., Kondo, A. (2017) Development of a comprehensive set of tools for genome engineering in a cold- and thermo-tolerant Kluyveromyces marxianus yeast strain, Scientific Reports, 7(1): 8993
11 Nambu-Nishida, Y., Sakihama, Y., Ishii, J., Hasunuma, T., Kondo, A. (2017) Selection of yeast Saccharomyces cerevisiae promoters available for xylose cultivation and fermentation., Journal of Bioscience and Bioengineering, in press



「革新的バイオマテリアル実現のための高機能化ゲノムデザイン技術開発」経済産業省 委託事業

1 Wang, M., Hashimoto, M.,Hashidoko, Y. (2013) Carot-4-en-9,10-diol, a conidiation-inducing sesquiterpene diol produced by Trichoderma virens PS1-7 upon exposure to chemical stress from highly active iron chelators., Applied and Environmental Microbiology, 79(6), 1906-1914
2 M. Hibi, T. Kawashima, P.M. Sokolov, S.V. Smirnov, T. Kodera, M. Sugiyama, S. Shimizu, K. Yokozeki, J. Ogawa. (2013) l-Leucine 5-hydroxylase of Nostoc punctiforme is a novel type of Fe(II)/α-ketoglutarate-dependent dioxygenase that is useful as a biocatalyst., Appl. Microbiol. Biotechnol., 97 (6), 2467-2472
3 Nishida, N., Ozato, N, Matsui, K., Kuroda, K., Ueda, M . (2013) ABC transporters and cell wall proteins involved in organic solvent tolerance in Saccharomyces cerevisiae., Journal of Biotechnology, 165(2), 145-152
4 S. V. Smirnov, P.M. Sokolov, V.A. Kotlyarova, N.N. Samsonova, T. Kodera, M. Sugiyama, T. Torii, M. Hibi, S. Shimizu, K. Yokozeki, J. Ogawa. (2013) A novel l-isoleucine-4'-dioxygenase and L-isoleucine dihydroxylation cascade in Pantoea ananatis., MicrobiologyOpen, 2 (3), 471-481 
5 M. Hibi, T. Kawashima, H. Yajima, S.V. Smirnov, T. Kodera, M. Sugiyama, S. Shimizu, K. Yokozeki , J. Ogawa. (2013) Enzymatic synthesis of chiral amino acid sulfoxides by Fe(II)/α-ketoglutarate-dependent dioxygenase., Tetrahedron: Asymmetry, 24 (17), 990-994
6 石井純,蓮沼誠久,松田史生, 近藤昭彦, 革新的なものづくり実現のための「合成生物工学」,生物工学会誌,91(6), 314-318 (2013)
7 梅野太輔, 冨永将大, 古林真衣子, 池紘平, 代謝経路と制御ネットワークの組織的な進化工学技術, 生物工学会誌,91(6)26-29 (2013)
8 関根亮二, 木賀大介, 細胞内における人工遺伝子回路の構築  生物工学会誌, 91(6), 327-333 (2013)
9 古林真衣子, 梅野太輔人工代謝経路構築のための進化分子工学, 伏見譲(監修)進化分子工学~高速分子進化によるタンパク質・核酸の開発~, エヌ・ティー・エス (2013)
10 Umemura et al. (2013) MIDDAS-M: Motif-independent de novo detection of secondary metabolite gene clusters through the integration of genome sequencing and transcriptome data., Plos One , 8(12): e84028
11 Nakatsui, M., Araki, M., Kondo, A. (2013) An approach for dynamical network reconstruction of simple network motifs., BMC System Biology, 7(6), 54
12 関根亮二, 木賀大介, Waddington地形に沿った細胞種多様化のモデル実験, 生物物理学会誌, 53(6), 319-320 (2013) 
13 関根亮二, 木賀大介, ロバストな試験管内・細胞内分子ネットワークの構築, 細胞工学,  33(1), 26-30 (2014)
14 Ike, K., Umeno, D. (2014) Nucleotide kinase-based selection system for genetic switchesJosé-Luis Barredo (ed.), Artificial Riboswitches, Methods in Molecular Biology, 1111, 141-152
15 Ishii, J., Kondo, T., Makino, H., Ogura, A., Matsuda, F., Kondo, A. (2014) Three gene expression vector sets for concurrently expressing multiple genes in Saccharomyces cerevisiae., FEMS Yeast Research, 14(3), 399-411
16 関根亮二, 木賀大介, 「人工遺伝子回路」の構築とその制御, 生化学会誌, 86(2), 201-208 (2014) 
17 M. Furubayashi, M. Ikezumi, J. Kajiwara, M. Iwasaki, A. Fujii, L. Li, K. Saito, and D. Umeno  (2014) A high-throughput colorimetric screening assay for terpene synthase activity based on substrate consumption., PLOS One, 9(3): e93317
18 M. Furubayashi, K. Saito, D. Umeno (2013) Evolutionary analysis of the functional plasticity of Staphylococcus aureus C30 carotenoid synthases., J. Bioscience Bioengin., 79, 7298-7304 
19 M. Hibi, J. Ogawa. (2014) Characteristics and biotechnology applications of aliphatic amino acid hydroxylases belonging to the Fe(II)/α-ketoglutarate-dependent dioxygenase superfamily., Appl. Microbiol. Biotechnol., 98(9), 3869-3876
20 M. Furubayashi, L. Li, A. Katabami, K. Saito, D. Umeno (2014) Construction of carotenoid biosynthetic pathways using squalene synthase., FEBS Letters, 588, 436-442 
21 Umemura et al. (2014) Characterization of the biosynthetic gene cluster for the ribosomally synthesized cyclic peptide ustiloxin B in Aspergillus flavus., Fungal Genetics and Biology, 68 , 23-30
22 Tominaga, D. (2014) Statistical stage transition detection method for small sample gene expression time series data., Mathematical Biosciences, 254, 58-63 
23 Nao Nishida, Dongyu Jing, Kouichi Kuroda, Mitsuyoshi Ueda (2014) Activation of signaling pathways related to cell wall integrity and multidrug resistance by organic solvent in Saccharomyces cerevisiae., Current Genetics, 60(3), 149-162
24 Moriya, T., Yamamura, M., Kiga, D. (2014) Effects of downstream genes on synthetic genetic circuits., BMC systems biology, 8(4), 54
25 Ishimatsu, K., Hata, T., Mochizuki, A., Sekine, R., Yamamura, M., Kiga, D. (2014) General Applicability of Synthetic Gene-Overexpression for Cell-Type Ratio Control via Reprogramming.,  ACS Synth. Biol, 3 (9), 638–644
26 Furubayashi M, Li L, Katabami A, Saito K, Umeno D. (2014) Directed evolution of squalene synthase for dehydrosqualene biosynthesis., FEBS Lett., 588(18), 3375-81
27 A.M. Poole, N. Horinouchi, R.J. Catchpole, D. Si, M. Hibi, K. Tanaka, J. Ogawa. (2014) The Case for an Early Biological Origin of DNA., J. Mol. Evol., 79, 204-212
28 八反順一郎, 三沢典彦, 芳香植物のテルペン合成酵素遺伝子のカタログ化-ツバキの花を例に-, Aroma Research(Journal of Aroma Science Technology and Safety), 57 (15 (1)): 38-47. (2014)
29 Katabami, A, Li, L., Iwasaki, M., Furubayashi, M., Saito, K., Umeno, D. (2015) Production of squalene by squalene synthases and their truncated mutants in Escherichia coli., J. Bioscience Bioengin.,119, 165-171
30 Tominaga M, Kawai-Noma S, Kawagishi I, Sowa Y, Saito K, Umeno D. (2015) Liquid-based iterative recombineering method tolerant to negative selection escape., PLOS One, 10(3): e0119818
31 Tominaga, M., Ike, K., Kawai-Noma, S., Saito, K., Umeno, D. (2015)  Rapid and liquid-based selection of genetic switches using nucleoside kinase fused with aminoglycoside phosphotransferase., PLOS One, 10(3):e0120243
32 Tsukui, T., Nagano, N., Umemura, M., Kumagai, T., Terai, G., Machida, M., Asai, K. (2015) Ustiloxins, fungal cyclic peptides, are ribosomally synthesized in Ustilaginoidea virens., Bioinformatics, 31(7), 981-5
33 梅村舞子, 長野希美, 糸状菌におけるリボソームペプチド生合成経路の発見, 化学と生物, 53(5), 273-276 (2015)
34 Satomura A, Kuroda K, Ueda M. (2014) Environmental stress tolerance engineering by modification of cell surface and transcription factor in Saccharomyces cerevisiae., Current Environ. Eng., 1, 149-156 
35 Nagano, N,, Nakayama, N., Ikeda, K., Fukuie, M., Yokota, K., Doi, T., Kato, T., Tomii, K. (2015) EzCatDB: the enzyme reaction database, Nucleic Acids Res, 43, D453-D458.
36 M. Takeuchi, S. Kishino, A. Hirata, S.B. Park, N. Kitamura, J. Ogawa. (2015) Characterization of the linoleic acid Δ9 hydratase catalyzing the first step of polyunsaturated fatty acid saturation metabolism in Lactobacillus plantarum AKU 1009a., J. Biosci. Bioeng., 119, 636-641
37 Holliday GL, Bairoch A, Bagos PG, Chatonnet A, Craik DJ, Flinn RD, Henrissat B, Landsman D, Manning G, Nagano N, O'Donovan C, Pruitt KD, Rawlings ND, Saier M, Sowdhamini R, Spedding M, Srinivasan N, Vriend G, Patricia C. Babbitt PC, Alex Bateman A. (2015) Key challenges for the creation and maintenance of specialist protein resources., Proteins, 83(6) , 1005-1013
38 Takeuchi M, Kishino S, Park SB, Kitamura N, Ogawa J. (2015) Characterization of hydroxy fatty acid dehydrogenase involved in polyunsaturated fatty acid saturation metabolism in Lactobacillus plantarum AKU 1009a., J. Mol. Catal., B Enzym., 117, 7-12 
39 Furubayashi M, Ikezumi M, Takaichi S, Maoka T, Hemmi H, Ogawa T, Saito K, Tobias AV, Umeno D. (2015) A highly selective biosynthetic pathway to non-natural C50 carotenoids assembled from moderately selective enzymes., Nat Commun. 6:7534
40 Babbitt PC, Bagos PG, Bairoch A, Bateman A, Chatonnet A, Chen MJ, Craik DJ, Finn RD, Gloriam D, Haft DH, Henrissat B, Holliday GL, Isberg V, Kaas Q, Landsman D, Lenfant N, Manning G, Nagano N, Srinivasan N, O'Donovan C, Pruitt KD, Sowdhamini R, Rawlings ND, Saier MH, Sharman JL, Spedding M, Tsirigos KD, Vastermark A, Vriend G. (2015) Creating a Specialist Protein Resource Network: A meeting report for the Protein Bioinformatics and Community Resources Retreat., Database, bav063
41 Takeda I, Machida M, Aburatani S. (2015) Development of an Algorithm for Reconstructing a Comprehensive Pathway Model: Application to Saccharomyces cerevisiae., J Biomed Sci Eng., 8(8), 500-510
42 Matsui M, Yokoyama T, Kumagai T, Nemoto K, Terai G, Machida M, Shibata T, Aburatani S. (2016) Genomic Analysis of Fungal Species No.11243 Mutant Strains Provides Insights into the Relationship between Mutations and High Productivity., British Biotechnology Journal, 10(2), 1-13 
43 Ike K, Arasawa Y, Koizumi S, Mihashi S, Kawai-Noma S, Saito, K, Umeno D.(2015)  Evolutionary Design of Choline-Inducible and -Repressible T7-Based Induction Systems., ACS Synth., 4, 1352-1360
44 里村淳, 黒田浩一, 植田充美,  高効率物質生産に向けた転写因子デザインによるストレス耐性工学, 日本生物工学会誌, 93(9), 539-541 (2015)
45  木賀大介,『細胞を創る』研究とその展開, 生物工学会誌, 93(10), 2–22 (2015)
46 Relator R, Nagano N, Kato T. (2016) Using Bregmann Divergence Regularized Machine For Comparison of Molecular Local Structures., IEICE Transactions on Information and Systems, E99-D: 275-278
47 Nagano N, Umemura M, Izumikawa M, Kawano J, Ishii T, Kikuchi M, Tomii K, Kumagai T, Yoshimi A, Machida M, Abe K, Shin-Ya K, Asai K.  (2016) Class of cyclic ribosomal peptide synthetic genes in filamentous fungi., Fungal Genet Biol, 86, 58-70
48 原田尚志, 小島基, 鈴木宗典, 金本浩介, 組換え微生物によるカロテノイド生産, 日本生物工学会誌, 93(7), 397-402 (2015)
49 Satomura A, Miura N, Kuroda K, Ueda M. (2016) Reconstruction of thermotolerant yeast by one-point mutation identified through whole-genome analyses of adaptively-evolved strains., Sci. Rep., 6, 23157
50 Tominaga, D, Mori, K, Aburatani, S. (2016) Linear and Nonlinear Regression for Combinatorial Optimization Problem of Multiple Transgenesis. IPSJ Transactions on Bioinformatics, 9, 7-11
51 日比 , 小川 , アミノ酸水酸化酵素を例にした酵素触媒の多様化への試み, 科学と工業, 90(3), 68-75 (2016)
52 Saeki K, Tominaga M, Kawai-Noma S, Umeno, D.  (2016)  Rapid Diversification of BetI-Based Transcriptional Switches for the Control of Biosynthetic Pathways and Genetic Circuits., ACS Synth. Biol., 5 (11), 1201–1210
53 Hattan, J., Shindo, K., Ito, T., Shibuya, Y., Watanabe, A., Tagaki, C., Ohno, F., Sasaki, T., Ishii, J., Kondo, A., Misawa, N. (2016) Identification of a novel hedycaryol synthase gene isolated from Camellia brevistyla flowers andfloral scent of Camellia cultivars., Planta, 243(4), 959-972
54 Takeuchi M, Kishino S, Park SB, Hirata A, Kitamura N, Saika A, Ogawa J.(2016) Efficient enzymatic production of hydroxy fatty acids by linoleic acid Δ9 hydratase from Lactobacillus plantarum AKU 1009a., J. Appl. Microbiol., 120(5), 1282-1288 
55 Terai, G., Kamegai, S., Asai, K.(2016) CDSfold: an algorithm for designing a protein-coding sequence with the most stable secondary structure., Bioinformatics., 32 (6), 828-834
56 Kumagai T, Ishii T, Terai G, Umemura M, Machida M, Asai K. (2016) Genome sequence of Ustilaginoidea virens IPU010, a rice pathogenic fungus causing false smut. Genome Announc ,4(3):e00306-16
57 Wang M, Tachibana S, Murai Y, Li L, Lau SYL, Cao M, Zhu G, Hashimoto M, Hashidoko Y. (2016) Indole-3-Acetic Acid Produced by Burkholderia heleia Acts as a Phenylacetic Acid Antagonist to Disrupt Tropolone Biosynthesis in Burkholderia plantarii., Scientific reports, 6, 22596 
58 Tashiro M, Kiyota H, Kawai-Noma S, Saito K, Ikeuchi M, Iijima Y, Umeno D.  (2016) Bacterial production of pinene by laboratory-evolved pinene-synthase., ACS Synth. Biol., 5 (9), 1011-1020
59 Hibi M, Mori R, Miyake R, Kawabata H, Kozono S, Takahashi S, Ogawa J.  (2016) Novel enzyme family found in filamentous fungi catalyzing trans-4-hydroxylation of L-pipecolic acid.,  Appl. Environ. Microbiol., 82, 2070-2077
60 Takeuchi, M, Kishino S, Park SB, Kitamura N, Watanabe H, Saika A, Hibi M, Yokozeki K, Ogawa J. (2016) Production of dicarboxylic acids from novel unsaturated fatty acids by laccase-catalyzed oxidative cleavage.,  Biosci Biotechnol Biochem, 80(11), 2132-2137
61 Kaishima, M., Ishii, J., Matsuno, T., Fukuda, N., Kondo, A. (2016) Expression of varied GFPs in Saccharomyces cerevisiae: codon optimization yields stronger than expected expression and fluorescence intensity., Scientific Reports, 6, 35932
62 Saeki K, Tominaga M, Kawai-Noma S, Saito K, Umeno D.  (2016) Rapid diversification of BetI-based transcriptional switches for the control of biosynthetic pathways and genetic circuits., ACS Synth. Biol., 5 (11),1201-1210
63 Kimura Y, Tashiro Y, Saito K, Kawai-Noma S, Umeno D. (2016) Directed evolution of Vibrio fischeri LuxR signal sensitivity., J.Biosci. Bioeng., 122(5), 533-538
64 古林真衣子, 梅野太輔, 香料の合成生物学, 香料, 269, 21-29 (2016) 
65 Tashiro Y, Kimura Y, Saito K, Kawai-Noma S, Umeno D.  (2016) Directed evolution of the autoinducer selectivity of Vibrio fischeri LuxR., J. Gen. Appl. Microbiol., 62(5), 240-247
66 田代美希,梅野太輔,テルペノイド合成酵素の機能進化デザイン,化学と生物,54(8), 562-567 (2016)
67 日比 , 木村隆利, 小川 , 糸状菌に由来する新規ステロイド11β水酸化酵素の同定, バイオサイエンスとインダストリー, 74(3), 226-227 (2016)
68 里村淳, 黒田浩一, 植田充美, 酵母の熱適応進化戦略, バイオサイエンスとバイオインダストリー, 74(6), 505-507 (2016)
69 梅野太輔, 進化分子工学による実用的な遺伝子誘導系の開発, バイオサイエンスとインダストリー,75(3) (2016)
70 黒田浩一, 植田充美, セルファクトリーから真のスマートセル構築に向けて, 人工細胞の創製とその応用(シーエムシー出版), 207-215 (2017)
71 Matsui M, Yokoyama T, Nemoto K, Kumagai T, Terai G, Tamano K, Machida M, Shibata T. (2017) Identification of a putative FR901469 biosynthesis gene cluster in fungal sp. No. 11243 and enhancement of the productivity by overexpressing the transcription factor gene frbF., J. Biosci. Bioeng., 123 (2), 147-153 
72 Ryo, S., Ishii, J., Matsuno, T., Nakamura, Y., Matsubara, D., Tominaga, M., Kondo, A. (2017) Positive feedback genetic circuit incorporating a constitutively active mutant Gal3 into yeast GAL induction system., ACS Synthetic Biology6(6), 928-935
73 Itoh H, Matsui M, Kumagai T, Arita M, Machida M, Shibata T. (2017) Genome Sequence of Fungal sp. No.14919 Producing HMG-CoA Reductase Inhibitor FR901512., Genome Announc,  5(14), e00129-17
74 Shimatani, Z., Kashojiya, S., Takayama, M., Terada, R., Arazoe, T., Ishii, H., Teramura, H., Yamamoto, T., Komatsu, H., Miura, K., Ezura, H., Nishida, K., Ariizumi, T., Kondo, A. (2017) Targeted base editing in rice and tomato using a CRISPR-Cas9 cytidine deaminase fusion., Nature Biotechnology, 35(5), 441-443
75 Hibi, M., K. Takahashi, J. Kako, Y. Wakita, T. Kodera, S. Shimizu, K. Yokozeki, J. Ogawa. (2017) Attempt to simultaneous generation of three chiral centers in 4-hydroxyisoleucine with microbial carbonyl reductases. Bioorg. Med. Chem., doi: 10.1016/j.bmc.2017.06.044
76 Matsui M, Yokoyama T, Nemoto K, Kumagai T, Tamano K, Machida M, Shibata T. (2017) Further enhancement of FR901469 productivity by co-overexpression of cpcA, a cross-pathway control gene, and frbF in fungal sp. No. 11243. Journal of Bioscience and Bioengineering, 124(1), 8-14
77 Kozono, I., K. Mihara, K. Minagawa, M. Hibi, J. Ogawa. (2017) Engineering of the cytochrome P450 monooxygenase system for benzyl maltol hydroxylation., Appl. Microbiol. Biotechnol., 101(17), 6651-6658
78 Tashiro M, Fujii A, Kawai-Noma S, Saito K, Umeno D. (2017) Directed evolution and expression tuning of geraniol synthase for efficient geraniol production in Escherichia coli., J. Gen. Appl. Microbiol., doi 10.2323/jgam.2017.01.006
79 小島基, 鈴木宗典, 油性酵母による植物テルペノイド生産, アグリバイオ Vol.1 (12), 1256-1260 (2017)
80 Shindo, K., Hattan, J., Kato, M., Sato, M., Ito, T., Shibuya, Y., Watanabe, A., Sugiyama, M., Nakamura, Y., Misawa, N. (2017) Purification and structural analysis of volatile sesquiterpenes produced by Escherichia coli carrying unidentified terpene synthase genes from edible plants of the family Araliaceae. Biosci. Biotechnol. Biochem. e-pub
81 Itoh, H., Miura, A., Matsui, M., Arazoe, T., Nishida, K., Kumagai, T., Arita, M., Tamano, K., Machida, M., Shibata, T. Knockout of the SREBP system increases production of the polyketide FR901512 in filamentous fungal sp. No. 14919 and lovastatin in Aspergillus terreus ATCC20542, Applied Microbiology and Biotechnology, in press