2023

Ito T, Muto N, Sakagami H, Tanaka M, Hemmi H, Yoshimura T (2023) D-amino acid auxotrophic Escherichia coli strain for in vivo functional cloning of novel D-amino acid synthetic enzyme. The FEBS J (in press)  

2022

・Ito T. (2022). Role of the conserved pyridoxal 5ʹ-phosphate-binding protein YggS/PLPBP in vitamin B6 and amino acid homeostasis. Bioscience, biotechnology, and biochemistry, 86(9):1183-1191

・Yoshimura T. (2022). Molecular basis and functional development of enzymes related to amino acid metabolism. Bioscience, biotechnology, and biochemistry, 86(9):1161-1172 .

・Aoki, M., Vinokur, J., Motoyama, K., Ishikawa, R., Collazo, M., Cascio, D., Sawaya, M. R., Ito, T., Bowie, J. U., & Hemmi, H. (2022). Crystal structure of mevalonate 3,5-bisphosphate decarboxylase reveals insight into the evolution of decarboxylases in the mevalonate metabolic pathways. The Journal of biological chemistry, 98(7):102111

・Tanaka, Y., Yoshimura, T., Hakamata, M., Saito, C., Sumitani, M., Sezutsu, H., Hemmi, H., & Ito, T. (2022). Identification and characterization of a serine racemase in the silkworm Bombyx mori. Journal of biochemistry, 172(1), 17–28.

(Front cover of the jornal!)

・Abe, T., Hakamata, M., Nishiyama, A., Tateishi, Y., Matsumoto, S., Hemmi, H., Ueda, D., & Sato, T. (2022). Identification and functional analysis of a new type of Z,E-mixed prenyl reductase from mycobacteria. The FEBS journal, 10.1111/febs.16412.

・Sompiyachoke, K., Nagasaka, A., Ito, T., & Hemmi, H. (2022). Identification and biochemical characterization of a heteromeric cis-prenyltransferase from the thermophilic archaeon Archaeoglobus fulgidus. Journal of biochemistry, 171(6), 641–651.

・Ashida, H., Murakami, K., Inagaki, K., Sawa, Y., Hemmi, H., Iwasaki, Y., & Yoshimura, T. (2022). Evolution and properties of alanine racemase from Synechocystis sp. PCC6803. Journal of biochemistry, 171(4), 421–428.

・Ito, T., Ogawa, H., Hemmi, H., Downs, D. M., & Yoshimura, T. (2022). Mechanism of Pyridoxine 5'-Phosphate Accumulation in Pyridoxal 5'-Phosphate-Binding Protein Deficiency. Journal of bacteriology, 204(3), e0052121.    

・Ishibashi, Y., Matsushima, N., Ito, T., & Hemmi, H. (2021). Isopentenyl diphosphate/dimethylallyl diphosphate-specific Nudix hydrolase from the methanogenic archaeon Methanosarcina mazei. Bioscience, biotechnology, and biochemistry, 86, 246-253.

2021

・Yasuno, Y., Nakayama, A., Saito, K., Kitsuwa, K., Okamura, H., Komeyama, M., Hemmi, H., & Shinada, T. (2021). Total Synthesis and Structure Confirmation of trans-Anhydromevalonate-5-phosphate, a Key Biosynthetic Intermediate of the Archaeal Mevalonate Pathway. Journal of natural products, 84(10), 2749–2754.

・Ashida, H., Sawa, Y., & Yoshimura, T. (2021). Enzymatic determination of d-alanine with l-alanine dehydrogenase and alanine racemase. Bioscience, biotechnology, and biochemistry, 85(11), 2221–2223.

・Okada M., Unno H., Emi K.-i., Matsumoto M., Hemmi, H. (2021) A versatile cis-prenyltransferase from Methanosarcina mazei catalyzes both C- and O-prenylations. Journal of Biological Chemistry. 296:100679.

・Ito T., Tono M., Kitaura Y., Hemmi H., Yoshimura T. (2021) Urinary L-erythro-β-hydroxyasparagine - a novel serine racemase inhibitor and substrate of the Zn2+-dependent D-serine dehydratase Bioscience Reports 41 (4): BSR20210260.

2020

・Yoshida R., Hemmi H. (2020) Construction of an artificial biosynthetic pathway for hyperextended archaeal membrane lipids in the bacterium Escherichia coli. Synthetic Biology. 5:ysaa018.

・Vu H, Ito T, Downs DM (2020) The role of YggS in vitamin B6 homeostasis in Salmonella enterica is informed by heterologous expression of yeast SNZ3. Journal of Bacteriology. 202(22):e00383-20.  Selected as a Spotlight!

・Ito T, Matsuoka M, Goto M, Watanabe S, Mizobuchi T, Matsushita K, Nasu R, Hemmi H, Yoshimura T. (2020) Mechanism of eukaryotic serine racemase-catalyzed serine dehydration. Biochim Biophys Acta Proteins Proteom. 2020 May 28:140460.

・ Ito T & Downs DM (2020) Pyridoxal reductase, PdxI, is critical for salvage of pyridoxal in Escherichia coli . Journal of Bacteriology. 202. e00056-20.

・ Yoshida R, Yoshimura T, Hemmi H. (2020) Reconstruction of the "Archaeal" Mevalonate Pathway from the Methanogenic Archaeon Methanosarcina mazei in Escherichia coli Cells.  Appl Environ Microbiol. 86. e02889-19.

・ Ito T, Hori R, Hemmi H, Downs DM, Yoshimura T. (2020) Inhibition of glycine cleavage system by pyridoxine 5'-phosphate causes synthetic lethality in glyA yggS and serA yggS in Escherichia coli.  Molecular Microbiology.  2020 113, 270-284.

2019

・ Emi, K.-i., Sompiyachoke, K., Okada, M., & Hemmi, H. (2019) A heteromeric cis-prenyltransferase is responsible for the biosynthesis of glycosyl carrier lipids in Methanosarcina mazei. Biochemical and Biophysical Research Communications. 520, 291-296.

・ Ito, T., Yamamoto, K., Hori, R., Yamauchi, A., Downs, DM., Hemmi, H. & Yoshimura. T. (2019) Conserved pyridoxal 5'-phosphate binding protein YggS impacts amino acid metabolism through pyridoxine 5'-phosphate in Escherichia coli. Applied and Environmental Microbiology. 85, e00430-19.

・ Motoyama, K., Sobue, F., Kawaide, H., Yoshimura, T. & Hemmi, H. (2019) Conversion of mevalonate 3-kinase into 5-phosphomevalonate 3-kinase by single amino acid mutations. Applied and Environmental Microbiology. 85, e00256-19.

・ Iwakawa, H., Makabe, S., Ito, T., Yoshimura, T. & Watanabe H. (2019) Urinary D-serine level as a predictive biomarker for deterioration of renal function in patients with atherosclerotic risk factors. Biomarkers. 24, 159-165.

2018

・ Hayakawa, H., Motoyama, K., Sobue, F., Ito, T., Kawaide, H., Yoshimura, T. & Hemmi, H. (2018) Modified mevalonate pathway of the archaeon Aeropyrum pernix proceeds via trans-anhydromevalonate 5-phosphate. Proceedings of the National Academy of Sciences of the United States of America. 115, 10034-10039.

・ Ito, T., Hamauchi, N., Hagi, T., Morohashi, N., Hemmi, H., Sato, G. Y., Saito, T. & Yoshimura, T. (2018) D-Serine metabolism and its importance in development of Dictyostelium discoideum.  Frontiers in Microbiology. 9: 784

・ Yoshida, R., Yoshimura, T. & Hemmi, H. (2018) Biosynthetic machinery for C₂₅,C₂₅-diether archaeal lipids from the hyperthermophilic archaeon Aeropyrum pernix. Biochemical and Biophysical Research Communications. 497, 87-92

・ Ito, T., Tokoro, M., Hori, R., Hemmi, H., & Yoshimura, T. (2018) Production of ophthalmic acid using engineered Escherichia coli. Applied and Environmental Microbiology. 84: e02806-17.

・ Hayashi, Y., Ito, T., Yoshimura, T. & Hemmi, H. (2018) Utilization of an intermediate of the methylerythritol phosphate pathway, (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate, as the prenyl donor substrate for various prenyltransferases. Bioscience, Biotechnology, and Biochemistry. 82, 993-1002.

2017

・ Ito, T., Yu, Z., Yoshino, I., Hirozawa, Y., Yamamoto, K., Shinoda, K., Watanabe, A., Hemmi, H., Asada, Y., Yoshimura, T. (2017) Occurrence of the (2R,3S)-isomer of 2-amino-3,4-dihydroxybutanoic acid in the mushroom Hypsizygus marmoreus.  Journal of Agricultural and Food Chemistry. 65, 6131–6139

・ Hayakawa, H., Sobue, F., Motoyama, K., Yoshimura, T. & Hemmi, H. (2017) Identification of enzymes involved in the mevalonate pathway of Flavobacterium johnsoniae. Biochemical and Biophysical Research Communications. 487, 702-708.

・ Feng, R., Satoh, Y., Ogasawara, Y., Yoshimura, T. & Dairi, T. (2017) A glycopeptidyl-glutamate epimerase for bacterial peptidoglycan biosynthesis.  Journal of the American Chemical Society. 139. 4243-4245

・ Motoyama, K., Unno, H., Hattori, A., Takaoka, T., Ishikita, H., Kawaide, H., Yoshimura, T. & Hemmi, H. (2017) A single amino acid mutation converts (R)-5-diphosphomevalonate decarboxylase into a kinase. Journal of Biological Chemistry. 292. 2457-2469.

2016

・ Ito, T., Yamauchi, A., Hemmi, H. & Yoshimura, T. (2016) Ophthalmic acid accumulation in an Escherichia coli mutant lacking the conserved PLP-binding protein YggS. Journal of Bioscience and Bioengineering. 122. 689-693

・ Ito, T., Hayashida, M., Kobayashi, S., Muto, N., Hayashi, A., Yoshimura, T. & Mori, H. （2016) Serine racemase is involved in D-aspartate biosynthesis. Journal of Biochemistry. 160. 345-353

・ Ito, T., Gong, C., Kawamoto, J. & Kurihara, T. (2016) Development of a versatile method for targeted gene deletion and insertion by using the pyrF gene in the psychrotrophic bacterium, Shewanella livingstonensis Ac10. Journal of Bioscience and Bioengineering. 122. 645-651

・ Ogawa, T., Emi, K., Koga, K., Yoshimura, T. & Hemmi, H. (2016) A cis-prenyltransferase from Methanosarcina acetivorans catalyzes both head-to-tail and nonhead-to-tail prenyl condensation. FEBS Journal. 283. 2369-2383

・ Zhen, H., Kitaura, Y., Kadota, Y., Ishikawa, T., Kondo, Y., Xu, M., Morishita, Y., Ota, M., Ito, T. & Shimomura, Y. (2016) mTORC1 is involved in the regulation of branched-chain amino acid (BCAA) catabolism in mouse heart. FEBS Open Bio. 6. 43-49

・ Ito, T., Matsuoka, M., Koga, K., Hemmi, H. & Yoshimura, T. (2014) Reaction mechanism of Zn²⁺-dependent D-serine dehydratase: role of a conserved tyrosine residue interacting with pyridine ring nitrogen of pyridoxal 5'-phosphate. Journal of Biochemistry. 156, 173-180

・ Ogawa, T., Isobe, K., Mori, T., Asakawa, S., Yoshimura, T. & Hemmi, H. (2014) A novel geranylgeranyl reductase from the methanogenic archaeon Methanosarcina acetivorans displays unique regiospecificity. FEBS Journal. 281, 3165-3176

・ Azami, Y., Hattori, A., Nishimura, H., Kawaide, H., Yoshimura, T. & Hemmi, H. (2014) (R)-mevalonate 3-phosphate is an intermediate of the mevalonate pathway in Thermoplasma acidophilum. Journal of Biological Chemistry. 289. 15957-15967. (Selected as a paper of the week!)

・ Isobe, K., Ogawa, T., Hirose, K., Yokoi, T., Yoshimura, T. & Hemmi, H. (2014) Geranylgeranyl reductase and ferredoxin from Methanosarcina acetivorans are required for the synthesis of fully reduced archaeal membrane lipid in Escherichia coli cells. Journal of Bacteriology. 196, 417-423.

・ Ito, T., Iimori, J., Takayama, S., Moriyama, A., Yamauchi, A., Hemmi, H. & Yoshimura, T. (2013) Conserved pyridoxal protein that regulates Ile and Val metabolism. Journal of Bacteriology. 195, 5439-5449

・ Mori, T., Ogawa, T., Yoshimura, T. & Hemmi, H. (2013) Substrate specificity of undecaprenyl diphosphate synthase from the hyperthermophilic archaeon Aeropyrum pernix. Biochemical and Biophysical Research Communications. 436, 230-234.

・ Nishimura, H., Azami, Y., Miyagawa, M., Hashimoto, C., Yoshimura, T. & Hemmi, H. (2013) Biochemical evidence supporting the presence of the classical mevalonate pathway in the thermoacidophilic archaeon Sulfolobus solfataricus. Journal of Biochemistry. 153, 415-420.

・ Ito, T., Maekawa, M., Hyashi, S., Goto, M., Hemmi, H. & Yoshimura, T (2013) Catalytic mechanism of serine racemase from Dictyostelium discoideum. Amino Acids. 44, 1073-84

 ・ Kato, S., Hemmi, H. & Yoshimura, T. (2012) Lysine racemase from a lactic acid bacterium, Oenococcus oeni: Structural basis of substrate specificity. Journal of Biochemistry. 76, 2150-2152.

・ Kato, S., Ikuta, T., Hemmi, H., Takahashi, S., Kera, Y. & Yoshimura, T. (2012) Enzymatic assay for D-aspartic acid using D-aspartate oxidase and oxaloacetate decarboxylase. Bioscience, Biotechnology, and Biochemistry. 76, 2150-52

・ Nakatani, H., Goda, S., Unno, H., Nagai, T., Yoshimura, T. & Hemmi, H. (2012) Substrate-induced change in the quaternary structure of type 2 isopentenyl diphosphate isomerase from Sulfolobus shibatae. Journal of Bacteriology. 194,3216-3224

・ Suematsu, T., Yamashita, S., Hemmi, H., Yoshinari, A., Shimoyama, T., Nakayama, T. & Nishino, T. (2012) Quantitative analyses of the behavior of exogenously added bacteria during an acidulocomposting process. Journal of Bioscience and Bioengineering. 114, 70-72.

・ Yokoi, T., Isobe, K., Yoshimura, T. & Hemmi, H. (2012) Archaeal phospholipid biosynthetic pathway reconstructed in Escherichia coli. Archaea. 2012, ID 438931

・ Ito, T., Murase, H., Maekawa, M., Goto, M., Hayashi, S., Saito, H., Maki, M., Hemmi, H., & Yoshimura, T. (2012) Metal ion dependency of serine racemase from Dictyostelium discoideum. Amino Acids. 43, 1567-1576.

・ Ito, T., Koga, K., Hemmi, H., & Yoshimura, T. (2012) Role of Zinc Ion for Catalytic Activity in D-Serine Dehydratase from Saccharomyces cerevisiae. FEBS Journal. 279, 612-624.

・ Nagai T., Unno H., Janczak M.W., Yoshimura T., Poulter C.D. & Hemmi H. (2011) Covalent modification of reduced flavin mononucleotide in type-2 isopentenyl diphosphate isomerase by active-site-directed inhibitors. Proceedings of the National Academy of Sciences of the United States of America. 108, 20461-20466.

・ Kato S., Kito Y., Hemmi H., & Yoshimura T. (2011) Simultaneous determination of D-amino acids by the coupling method of D-amino acid oxidase with high-performance liquid chromatography. Journal of Chromatography B. 111, 104-108.

・ Ogawa T., Yoshimura T. & Hemmi H. (2011) Connected cavity structure enables prenyl elongation across the dimer interface in mutated geranylfarnesyl diphosphate synthase from Methanosarcina mazei. Biochemical and Biophysical Research Communications. 409, 333-337.

・ Sasaki D., Fujihashi M., Iwata Y., Murakami M., Yoshimura T., Hemmi, H. & Miki K. (2011) Structure and mutation analysis of archaeal geranylgeranyl reductase. Journal of Molecular Biology. 409, 543-557.

・ Kato S., Ishihara T., Hemmi H., Kobayashi H. & Yoshimura T. (2011) Alterations in D-amino acid concentrations and microbial community structures during the fermentation of red and white wines. Journal of Bioscience and Bioengineering. 111, 104-108.

・ Naka, T., Ito, T., Hemmi, H. & Yoshimura, T. (2010) A highly sensitive enzymatic assay for D- and total serine detection using D-serine dehydratase from Saccharomyces cerevisiae. Journal of Molecular Catalysis B: Enzymatic. 67, 150-154.

・ Kato, S., Yoshimura, T., Hemmi, H. & Moriyama, R. (2010) Biochemical analysis of a novel lipolytic enzyme YvdO from Bacillus subtilis 168. Bioscience, Biotechnology, and Biochemistry. 74, 701-706.

・ Ogawa, T., Yoshimura, T. & Hemmi, H. (2010) Geranylfarnesyl diphosphate synthase from Methanosarcina mazei: Different role, different evolution. Biochemical and Biophysical Research Communications. 393, 16-20.

・ Masayama, A., Kato, S., Terashima, T., Molgaard, A., Hemmi, H., Yoshimura, T. & Moriyama, R. (2010) Bacillus subtilis spore coat protein LipC is a phospholipase B. Bioscience, Biotechnology, and Biochemistry. 74, 24-30.

・ Goto, M., Yamauchi, T., Kamiya, N., Miyahara, I., Yoshimura, T., Mihara, H., Kurihara, T., Hirotsu, K. & Esaki, N. (2009) Crystal structure of a homolog of mammalian serine racemase from Schizosaccharomyces pombe. J Biol Chem. 284, 25944-25952

・ Yamauchi, T., Goto, M., Wu, H.Y., Uo, T., Yoshimura, T., Mihara, H., Kurihara, T., Miyahara, I., Hirotsu, K. & Esaki, N. (2009) Serine racemase with catalytically active lysinoalanyl residue. J Biochem. 145, 421-424

・ Ito, T., Uozumi, N., Nakamura, T., Takayama, S., Matsuda, N., Aiba, H., Hemmi, H. & Yoshimura, T. (2009) The implication of YggT of Escherichia coli in osmotic regulation. Bioscience, Biotechnology, and Biochemistry. 73, 2698-2704.

・ Kato, S., Masayama, A., Yoshimura, T., Hemmi, H., Tsunoda, H., Kihara, T. & Moriyama, R. (2009) Physiological role of carbon dioxide in spore germination of Clostridium perfringens S40. Journal of Bioscience and Bioengineering. 108, 477-483.

・ Unno, H., Yamashita, S., Ikeda, Y., Sekiguchi, S., Yoshida, N., Yoshimura, T., Kusunoki, M., Nakayama, T., Nishino, T. & Hemmi, H. (2009) Flavinﾕs new role as a general acid-base catalyst with no redox function in type 2 isopentenyl diphosphate isomerase. Journal of Biological Chemistry. 284, 9160-9167.

・ Noike, M., Katagiri, T., Nakayama, T., Nishino, T. & Hemmi, H. (2009) Effect of mutagenesis at the region upstream from the G(Q/E) motif of three types of geranylgeranyl diphosphate synthase on product chain-length. Journal of Bioscience and Bioengineering. 107, 235-239.

・ Uchida, M., Hatayoshi, H., Syuku-nobe, A., Shimoyama, T., Nakayama, T., Okuwaki, A., Nishino, T. & Hemmi, H. (2009) Polymerase chain reaction-denaturing gradient gel electrophoresis analysis of microbial community structure in landfill leachate. Journal of Hazardous Materials. 164, 1503-1508

・ Noike, M., Katagiri, T., Nakayama, T., Koyama, T., Nishino, T. & Hemmi, H. (2008) The product chain length determination mechanism of type II geranylgeranyl diphosphate synthase requires subunit interaction. FEBS Journal. 275, 3921-3933.

・ Sato, S., Murakami, M., Yoshimura, T. & Hemmi, H. (2008) Specific partial reduction of geranylgeranyl diphosphate by an enzyme from the thermoacidophilic archaeon Sulfolobus acidocaldarius yields a reactive prenyl-donor, not a dead-end product. Journal of Bacteriology. 190, 3923-3929.

・ Ito, T., Hemmi, H., Kataoka, K., Mukai, Y. & Yoshimura, T. (2008) A novel zinc-dependent D-serine dehydratase from Saccharomyces cerevisiae, Biochemical Journal. 409, 399-406.

・ Yoshimura T, Goto M (2008) D-amino acids in the brain: structure and function of pyridoxal phosphate-dependent amino acid racemases. FEBS J. 275, 3527-3537

・ Ito, T., Takahashi, K., Naka, T., Hemmi, H. & Yoshimura, T. (2007) Enzyme assay of D-serine dehydratase from Saccharomyces cerevisiae, Analytical Biochemistry. 371, 167-172.

・ Murakami, M., Shibuya, K., Nakayama, T., Nishino, T. Yoshimura, T. & Hemmi, H. (2007) Geranylgeranyl reductase involved in the biosynthesis of archaeal membrane lipids in the hyperthermophilic archaeon Archaeoglobus fulgidus, FEBS Journal. 274, 805-814.

・ Masayama, A., Kuwana, R., Takamatsu, H., Hemmi, H., Yoshimura, T., Watabe, K. & Moriyama, R. (2007) A novel lipolytic enzyme, ycsK (lipC), located in the spore coat of Bacillus subtilis, is involved in spore germination. Journal of Bacteriology. 189, 2369-2375.

・ Doukov, T.I., Hemmi, H., Drennan, C.L., & Ragsdale, S.W. (2007) Structural and kinetic evidence for an extended hydrogen bonding network in catalysis of methyl group transfer: Role of an active site asparagine residue in activation of methyl transfer by methyltransferases. Journal of Biological Chemistry. 282, 6609-6618.