Hokkaido University Laboratory of Microbial Physiology
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Tawthep S, Fukiya S, Lee JY, Hagio M, Ogura Y, Hayashi T, Yokota A. Isolation of six novel 7-oxo- or urso-type secondary bile acid-producing bacteria from rat cecal contents. Journal of Bioscience and Bioengineering in press (2017) doi: 10.1016/j.jbiosc.2017.06.002. >>pubmed

Watanabe M, Fukiya S, Yokota A. Comprehensive evaluation of the bactericidal activities of free bile acids in the large intestine of humans and rodents. Journal of LIPID RESEARCH. 58: 1143-1152(2017) doi: 10.1194/jlr.M075143 >>pubmed

Nagano S, Shibano K, Matsumoto Y, Yokota A, Wada M. Isolation and amino acid sequence of a dehydratase acting on D-erythro-3-hydroxyaspartate from Pseudomonas sp. N99, and its application in the production of optically active 3-hydroxyaspartate. Bioscience, Biotechnology, and Biochemistry. 81(6): 1156-1164 (2017) doi:10.1080/09168451.2017.1295804 >>Taylor Francis Online

Yokota A, Sawada K, Wada M. Boosting Anaplerotic Reactions by Pyruvate Kinase Gene Deletion and Phosphoenolpyruvate Carboxylase Desensitization for Glutamic Acid and Lysine Production in Corynebacterium glutamicum. Advances in Biochemical Engineering/Biotechnology. 159: 181-198 (2017) doi:10.1007/10_2016_31 >>pubmed


Maeda S, Shimizu K, Kihira C, Iwabu Y, Kato R, Sugimoto M, Fukiya S, Wada M, Yokota A. Pyruvate dehydrogenase complex regulator (PdhR) gene deletion boosts glucose metabolism in Escherichia coli under oxygen-limited culture conditions. Journal of Bioscience and Bioengineering. 123(4):437-443 (2016) doi:10.1016/j.jbiosc.2016.11.004 >>pubmed

Yanase M, Aikoh T, Sawada K, Ogura K, Hagiwara T, Imai K, Wada M, Yokota A. Pyruvate kinase deletion as an effective phenotype to enhance lysine production in Corynebacterium glutamicum ATCC13032: Redirecting the carbon flow to a precursor metabolite. Journal of Bioscience and Bioengineering. 122 (2):160-167 (2016) doi:10.1016/j.jbiosc.2015.12.023 >>ScienceDirect


Sawada K, Wada M, Hagiwara T, Zen-in S, Imai K, Yokota A. Effect of pyruvate kinase gene deletion on the physiology of Corynebacterium glutamicum ATCC13032 under biotin-sufficient non-glutamate-producing conditions: Enhanced biomass production.
Metabolic Engineering Communications.2:67-75.(2015) doi:10.1016/j.meteno.2015.07.001>>ScienceDirect

Wada M, Sawada K, Ogura K, Shimono Y, Hagiwara T, Sugimoto M, Onuki A, Yokota A. Effects of phosphoenolpyruvate carboxylase desensitization on glutamic acid production in Corynebacterium glutamicum ATCC 13032.
J Biosci Bioeng.15:S1389-1723.(2015) doi: 10.1016/j.jbiosc.2015.06.008. >>PubMed

Shimizu H, Baba N, Nose T, Taguchi R, Tanaka S, Joe GH, Maseda H, Nomura N, Hagio M, Lee JY, Fukiya S, Yokota A, Ishizuka S, Miyazaki H. Activity of ERK regulates mucin 3 expression and is involved in undifferentiated Caco-2 cell death induced by 3-oxo-C12-homoserine lactone.
Biosci Biotechnol Biochem. 79:937-42.(2015) doi: 10.1080/09168451.2015.1006570.>>PubMed

Sakanaka M, Fukiya S, Kobayashi R, Abe A, Hirayama Y, Kano Y, Yokota A. Isolation and transposition properties of ISBlo11, an active insertion sequence belonging to the IS3 family, from Bifidobacterium longum 105-A.
FEMS Microbiol Lett. 362 (2015) doi: 10.1093/femsle/fnv032. >>PubMed

Matsumoto Y, Yasutake Y, Takeda Y, Tamura T, Yokota A, Wada M. Structural insights into the substrate stereospecificity of D-threo-3-hydroxyaspartate dehydratase from Delftia sp. HT23: a useful enzyme for the synthesis of optically pure L-threo- and D-erythro-3-hydroxyaspartate.
Appl Microbiol Biotechnol. 99 (17):7137-50 (2015) doi: 10.1007/s00253-015-6479-3 >>PubMed


Soma Y, Tsuruno K, Wada M, Yokota A, Hanai T. Metabolic flux redirection from a central metabolic pathway toward a synthetic pathway using a metabolic toggle switch.
Metabolic Engineering 23 :175-184 (2014) doi: 10.1016/j.ymben.2014.02.008. >>PubMed

Kanesaki Y, Masutani H, Sakanaka M, Shiwa Y, Fujisawa T, Nakamura Y, Yokota A, Fukiya S, Suzuki T, Yoshikawa H. Complete Genome Sequence of Bifidobacterium longum 105-A, a Strain with High Transformation Efficiency.
Genome Announc. 18 :01311-14 (2014) doi: 10.1128/genomeA.01311-14. >>PubMed

Hagio M, Shimizu H, Joe GH, Takatsuki M, Shiwaku M, Xu H, Lee JY, Fujii N, Fukiya S, Hara H, Yokota A, Ishizuka S. Diet supplementation with cholic acid promotes intestinal epithelial proliferation in rats exposed to γ-radiation.
Toxicol Lett. 232:246-252 (2014) doi: 10.1016/j.toxlet.2014.10.011. >>PubMed

Sakanaka M, Tamai S, Hirayama Y, Onodera A, Koguchi H, Kano Y, Yokota A, Fukiya S. Functional analysis of bifidobacterial promoters in Bifidobacterium longum and Escherichia coli using the α-galactosidase gene as a reporter.
J Biosci Bioeng. 118:489-95 (2014) doi: 10.1016/j.jbiosc.2014.05.002. >>PubMed

Shimizu H, Hagio M, Iwaya H, Tsuneki I, Lee JY, Fukiya S, Yokota A, Miyazaki H, Hara H, Ishizuka S. Deoxycholic acid is involved in the proliferation and migration of vascular smooth muscle cells.
J Nutr Sci Vitaminol. 60 :450-4 (2014) doi: 10.3177/jnsv.60.450. >>PubMed


Matsumoto Y, Yasutake Y, Takeda Y, Tamura T, Yokota A, Wada M. Crystallization and preliminary X-ray diffraction studies of D-threo-3-hydroxyaspartate dehydratase isolated from Delftia sp. HT23
Acta Crystallogr. Sect. F, 69:1131-1134 (2013) >>PubMed

Lee JY, Arai H, Nakamura Y, Fukiya S, Wada M, Yokota A. Contribution of the 7β-hydroxysteroid dehydrogenase from Ruminococcus gnavus N53 to ursodeoxycholic acid formation in the human colon.
J Lipid Res.(2013). >>PubMed

Sakurama H, Kiyohara M, Wada J, Honda Y, Yamaguchi M, Fukiya S, Yokota A, Ashida H, Kumagai H, Kitaoka M, Yamamoto K, Katayama T. Lacto-N-biosidase Encoded by a Novel Gene of Bifidobacterium longum Subspecies longum Shows Unique Substrate Specificity and Requires a Designated Chaperone for Its Active Expression.
J Biol Chem., 288:25194-25206 (2013) >>PubMed

Shiraishi T, Yokota S, Morita N, Fukiya S, Tomita S, Tanaka N, Okada S, Yokota A. Characterization of a Lactobacillus gasseri JCM 1131T lipoteichoic acid with a novel glycolipid anchor structure.
Appl Environ Microbiol., 79:3315-3318 (2013) >>PubMed


Fukiya S, Hirayama Y, Sakanaka M, KANO Y, Yokota A. Technological Advances in Bifidobacterial Molecular Genetics: Application to Functional Genomics and Medical Treatments
Bioscience of Microbiota, Food and Health, 31:15-25 (2012) >>J-STAGE

Kihira C, Hayashi Y, Azuma N, Noda S, Maeda S, Fukiya S, Wada M, Matsushita K, Yokota A. Alterations of glucose metabolism in Escherichia coli mutants defective in respiratory-chain enzymes.
J Biotechnol, 158:215-223 (2012) >>PubMed

Hirayama Y, Sakanaka M, Fukuma H, Murayama H, Kano Y, Fukiya S, Yokota A. Development of a Double-Crossover Markerless Gene Deletion System in Bifidobacterium longum: Functional Analysis of the α-Galactosidase Gene for Raffinose Assimilation.
Appl Environ Microbiol, 78:4984-4994(2012). >>PubMed

Sawada K, Kato Y, Imai K, Li L, Wada M, Matsushita K, Yokota A. Mechanism of increased respiration in an H+-ATPase-defective mutant of Corynebacterium glutamicum.
J Biosci Bioeng, 113:467-473(2012). >>PubMed

Yokota A, Fukiya S, Ooka T, Ogura Y, Hayashi T, Ishizuka S. Is bile acid a determinant of the gut microbiota on a high-fat diet?
Gut Microbes, 3:epub ahead of print(2012). >>PubMed


Islam KB, Fukiya S, Hagio M, Fujii N, Ishizuka S, Ooka T, Ogura Y, Hayashi T, Yokota A. Bile acid is a host factor that regulates the composition of the cecal microbiota in rats.
Gastroenterology, 141:1773?1781(2011). >>PubMed

Kihira C, Hayashi Y, Azuma N, Noda S, Maeda S, Fukiya S, Wada M, Matsushita K, Yokota A. Alterations of glucose metabolism in Escherichia coli mutants defective in respiratory-chain enzymes.
Journal of Biotechnology, 158:215-223(2011). >>PubMed


Kikuchi H, Sakurai H, Nagura T, Aritsuka T, Tomita F, Yokota A. One-pot conversion of levan prepared from Serratia levanicum NN to difructose anhydride IV by Arthrobacter nicotinovorans levan fructotransferase.
Journal of Bioscience and Bioengineering, 109: 240-243 (2010). >>PubMed

Sawada K, Zen-in S, Wada M, Yokota A. Metabolic changes in a pyruvate kinase gene deletion mutant of Corynebacterium glutamicum ATCC 13032.
Metabolic Engineering, 12: 401-407 (2010). >>PubMed

Fukiya S, Sugiyama T, Kano Y, Yokota A. Characterization of an insertion sequence-like element ISBlo15 identified in a size-increased cryptic plasmid pBK283 harbored in Bifidobacterium longum BK28.
Journal of Bioscience and Bioengineering, 110: 141-146 (2010). >>PubMed

Suzuki T, Nishimukai M, Shinoki A, Taguchi H, Fukiya S, Yokota A, Saburi W, Yamamoto T, Hara H, Matsui H. Ingestion of epilactose, a non-digestible disaccharide, improves postgastrectomy osteopenia and anemia in rats through the promotion of intestinal calcium and iron absorption.
Journal of Agricultural and food chemistry, 58: 10787-10792 (2010). >>PubMed

Maeda T, Takeda Y, Murakami T, Yokota A, Wada M. Purification, characterization and amino acid sequence of a novel enzyme, D-threo-3-hydroxyaspartate dehydratase, from Delftia sp. HT23.
Journal of Biochemistry, 148: 705-712 (2010). >>PubMed


Hiroto Kikuchi, Masanao Inoue, Hidetoshi Saito, Hiroaki Sakurai, Tsutomu Aritsuka, Fusao Tomita, and Atsushi Yokota. Industrial production of difructose anhydride III (DFA III) from crude inulin extracted from chicory roots using Arthrobacter sp. H65-7 fructosyltransferase.
Journal of Bioscience and Bioengineering, 107: 262-265 (2009). >>PubMed

Senoura T, Taguchi H, Ito S, Hamada S, Matsui H, Fukiya S, Yokota A, Watanabe J, Wasaki J, Ito S. Identification of the Cellobiose 2-Epimerase Gene in the Genome of Bacteroides fragilis NCTC 9343.
Bioscience Biotechnology and Biochemistry, 73: 400-406 (2009). >>PubMed

Satoru Fukiya, Miki Arata, Hiroko Kawashima, Daisuke Yoshida, Maki Kaneko, Kimiko Minamida, Jun Watanabe, Yoshio Ogura, Kiyohisa Uchida, Kikuji Itoh, Masaru Wada, Susumu Ito and Atsushi Yokota. Conversion of cholic acid and chenodeoxycholic acid into their 7-oxo derivatives by Bacteroides intestinalis AM-1isolated from human feces.
FEMS Microbiology Letters, 293: 263-270 (2009). >>PubMed

Ogami, Shinichi, Hijikata, Shoichi, Tsukahara, Tamostu, Mie, Yasuhiro, Matsuno, Toshihide, Morita, Naoki, Hara, Isao, Yamazaki, Koji, Inoue, Norio, Yokota, Atsushi, Hoshino, Tamotsu, Yoshimune, Kazuaki, Yumoto, Isao. A membrane-anchored cytochrome c-550 of alkaliphilic Bacillus clarkii K24-1U: Expression, molecular features and properties of redox potential.
Extremophiles, 13(3):491-504 (2009) >>PubMed

Murakami T, Maeda T, Yokota A, Wada M. Gene cloning and expression of pyridoxal 5'-phosphate-dependent L-threo-3-hydroxyaspartate dehydratase from Pseudomonas sp. T62, and characterization of the recombinant enzyme.
Journal of Biochemistry, 145(5):661-668 (2009) >>PubMed

Miki, S., Matsui, K., Kito, H., Otsuka, K., Ashizawa, T., Yasuda, N., Fukiya, S., Sato, J., Hirayae, K., Fujita, Y., Nakajima, T., Tomita, F., and Sone, T. Molecular cloning and characterization of the AVR-Pia locus from a Japanese field isolate of Magnaporthe oryzae.
Molecular Plant Pathology, 10(3): 361-374 (2009). >>PubMed


M. Wada, K. Okabe, M. Kataoka, S. Shimizu, A. Yokota, H. Takagi, Distribution of L-azetidine-2-carboxylate N-acetyltransferese in yeast.
Bioscience Biotechnology and Biochemistry, 72: 582-586, (2008). >>PubMed

E. Yahata, Y. Sawatari, H. Sugiyama, A. Hanakoka, A. Yokota and H. Saruyama. Change of proteins in instant Chinese noodle by the fermentation of Lactobacillus plantarum NRIC0380 affects the noodle quality.
Food Science and Technology Research. 14: 285-292 (2008). >>Journal site

S. Ishizuka, A Iwama, A. Dinoto, A. Suksomcheep, K. Maeta, T. Kasai, H. Hara and A. Yokota. Synbiotic promotion of epithelial proliferation by orally ingested encapsulated Bifidobacterium breve and raffinose in the small intestine of rats.
Molecular Nutrition & Food Research. 2008 Oct 7. >>PubMed

M. Wada, N. Hijikata, R. Aoki, N. Takesue, A. Yokota. Enhanced valine production in Corynebacterium glutamicum with defective H+-ATPase and C-terminal truncated acetohydroxyacid synthase.
Bioscience Biotechnology and Biochemistry, 72: 2959-2965 (2008). >>PubMed


M. Wada, K. Narita, A. Yokota, Alanine production in an H+-ATPase- and lactate dehydrogenase-defective mutant of Escherichia coli expressing alanine dehydrogenase.
Appl. Microbiol. Biotechnol., 76: 819-825 (2007). >>PubMed

L. Li, M. Wada, A. Yokota, A comparative proteomic approach to understand the adaptations of an H+-ATPase-defective mutant of Corynebacterium glutamicum ATCC14067 to energy deficiencies.
Proteomics, 7: 3348-3357 (2007). >>PubMed

L. Li, M. Wada, and A. Yokota, Cytoplasmic proteome reference map for a glutamic acid-producing Corynebacterium glutamicum ATCC14067.
Proteomics, 7: 4317-4322 (2007). >>PubMed

M. P. Ongol, Y. Sawatari, Y. Ebina, T. Sone, M. Tanaka, F. Tomita, A. Yokota and K. Asano. Yoghurt fermented by Lactobacillus delbrueckii subsp. bulgaricus H+-ATPase-defective mutants exhibits enhanced viability of Bifidobacterium breve during storage.
International Journal of Food Microbiology, 116: 358-366 (2007). >>PubMed

Y. Sawatari and A.Yokota. Diversity and mechanisms of alkali tolerance in lactobacilli.
Applied and Environmental Microbiology, 73: 3909-3915 (2007). >>PubMed


P. Kurdi, K. Kawanishi, K. Mizutani, and A. Yokota. Mechanism of growth inhibition by free bile acids in lactobacilli and bifidobacteria.
Journal of Bacteriology, 188: 1979-1986 (2006). >>PubMed

Sakiko Noda, Yuji Takezawa, Tomohiko Mizutani, Tomoaki Asakura, Eiichiro Nishiumi, Kazunori Onoe, Masaru Wada, Fusao Tomita, Kazunobu Matsushita and Atsushi Yokota. Alterations of cellular physiology in Escherichia coli in response to oxidative phosphorylation impaired by defective F1-ATPase.
Journal of Bacteriology, 188: 6869-6876 (2006). >>PubMed

Y. Haitani, N. Awano, M. Yamazaki, M. Wada, S. Nakamori, H. Takagi, Functional analysis of L-serine O-acetyltransferase from Corynebacterium glutamicum.
FEMS Microbiology Letters, 255: 156-163, (2006). >>PubMed

A. Dinoto, A. Suksomcheep, S. Ishizuka, H. Kimura, S. Hanada, Y. Kamagata, K. Asano, F. Tomita, and A. Yokota. Modulation of Rat Cecal Microbiota by the Administration of Raffinose and Encapsulated Bifidobacterium breve.
Applied and Environmental Microbiology, 72: 784-792 (2006). >>PubMed

A. Dinoto, T. M. Marques, K. Sakamoto, S. Fukiya, J. Watanabe, S. Ito and A. Yokota Population dynamics of Bifidobacterium species in human feces during raffinose administration monitored by FISH-flow cytometry.
Appl. Environ. Microbiol. 72: 7739-7747 (2006). >>PubMed

Y. Sawatari, T. Hirano, and A. Yokota. Development of food grade media for the preparation of Lactobacillus plantarum starter culture.
Journal of General and Applied Microbiology. 52: 349-356 (2006). >>PubMed


Central metabolism: sugar uptake and conversion, In: L. Eggeling and M. Bott (eds.), Handbook of Corynebacterium glutamicum, CRC Press, pp.215-240 (2005).

N. Awano, M. Wada, H. Mori, S. Nakamori, H. Takagi, Identification and functional analysis of Escherichia coli cysteine desulfhydrases.
Applied and Environmental Microbiology, 71: 4149-4152 (2005). >>PubMed

C.-C. Hsu, Z. Hong, M. Wada, D. Franke, C.-H. Wong, Directed evolution of D-sialic acid aldolase to L-3-deoxy-manno-2-octulosonic acid (L-KDO) aldolase.
Proceedings of the National Academy of Sciences of the USA, 102: 9122-9126 (2005). >>PubMed

R. Aoki, M. Wada, N. Takesue, K. Tanaka and A. Yokota. Enhanced glutamic acid production by a H+-ATPase-defective mutant of Corynebacterium glutamicum.
Bioscience Biotechnology and Biochemistry, 69: 1466-1472 (2005).

Y. Sawatari, H. Sugiyama, Y. Suzuki, A. Hanaoka, K. Saito,H. Yamauchi, S. Okada and A. Yokota. Development of the fermented instant Chinese noodle using Lactobacillus plantarum.
Food Microbiology, 22: 539-546 (2005).

ASM. Selim, P. Boonkumklao, T. Sone, A. Assavanig, M. Wada and A. Yokota. Development and assessment of a Real-Time PCR assay for the rapid and sensitive detection of a novel thermotolerant bacterium, Lactobacillus thermotolerans, in chicken feces.
Applied and Environmental Microbiology, 71: 4214-4219 (2005). >>PubMed


M. Kataoka, A. Kotaka, R. Thiwthong, M. Wada, S. Nakamori, S. Shimizu. Cloning and overexpression of the old yellow enzyme gene of Candida macedoniensis, and its application to the production of a chiral compound.
J. Biotechnol., 114: 1-9 (2004). >>PubMed


N. Awano, M. Wada, A. Kohdoh, T. Oikawa, H. Takagi, S. Nakamori, Effect of cysteine desulfhydrase gene disruption on L-cysteine overproduction in Escherichia coli.
Applied Microbiology and Biotechnology, 62: 239-243 (2003). >>PubMed

S. Sogabe, A. Yoshizumi, T. A. Fukami, Y. Shiratori, S. Shimizu, H. Takagi, S. Nakamori, M. Wada, The crystal structure and stereospecificity of levodione reductase from Corynebacterium aquaticum M-13
Journal of Biological Chemistry, 278: 19387-19395 (2003). >>PubMed

P. Kurdi, H. Tanaka, H. W. van Veen, K. Asano, F. Tomita and A. Yokota.: Cholic acid accumulation and its diminution by short-chain fatty acids in bifidobacteria.
Microbiology, 149(8): 2031-2037 (2003). >>PubMed

Niamsup, P., Sujaya, I. N., Tanaka, M., Sone, T., Hanada, S., Kamagata, Y., Lumyong, S., Assavanig, A., Asano, K., Tomita, F., and Yokota, A.: Lactobacillus thermotolerans sp. nov., a novel thermotolerant species isolated from chiken faeces.
International Journal of Systematic and Evolutionary Microbiology, 53: 263-268 (2003). >>PubMed

K. Saito, Y. Oda, F. Tomita and A. Yokota. Molecular cloning of the gene for 2,6-beta-D-fructan 6-levanbiohydrolase from Streptomyces exfoliates F3-2.
FEMS Microbiology Letters, 218: 265-270 (2003). >>PubMed

K. Saito, Y. Sumita, Y. Nagasaka, F. Tomita and A. Yokota. Molecular cloning of the gene encoding the di-D-fructofuranose 1,2':2,3' dianhydride hydrolysis enzyme (DFA IIIase) from Arthrobacter sp. H65-7.
Journal of Bioscience and Bioengineering, 95: 538-540 (2003). >>PubMed


M. Kataoka, A. Kotaka, A. Hasegawa, M. Wada, A. Yoshizumi, S. Nakamori, S. Shimizu. Old yellow enzyme from Candida macedoniensis catalyzes the stereospecific reduction of the C=C bond of ketoisophorone.
Bioscience Biotechnology and Biochemistry, 66: 2651-2657 (2002). >>PubMed

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