H2NH2N OHPOOO

O

O

O

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EPA-containing phospholipid Unfolded protein

Folded protein Membrane insertion (unfolded)

Synthetic !lipid probe!

Lab. Molecular Microbial Science (Institute for Chemical Research) Prof.: Kurihara, T., Assistant Prof.: Kawamoto, J.

CHEMICAL APPROACH TO MICROORGANISMS

Structures, Functions, and Reaction Mechanisms of Microbial Enzymes

Molecular mechanism of the environmental adaptation of extremophilic microorganisms is under investigation. In particular, cold-adaptation mechanism of psychrotrophs is studied. We are also studying the application of these microorganisms and their cold-active enzymes.

Adaptation of Microorganisms to the Environment

Various microbial systems are investigated by chemical approach, and their applications are developed. In particular, the molecular basis of the environmental adaptation of extremophiles; structures, functions, and reaction mechanisms of microbial enzymes; and organization of biological membranes are studied. Applications of microorganisms for production of useful compounds are also in progress.

C CH

H

Cl

COOHH3C C

HCOOH

Cl

Production of an optically active organohalogen compound (a precursor of herbicides) with a microbial enzyme

Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University 2014.7.11

Microorganisms are capable of converting a great variety of chemicals. They produce various unique enzymes to assimilate or degrade substrates in the environment. Many of these enzymes are attracting a great deal of attention because of their possible industrial applications. We are studying structures, functions, and reaction mechanisms of microbial enzymes and developing their applications.

Functions of Lipids and Proteins in Biological Membrane

Biological membrane separates inside and outside of the cell. Various essential biological processes such as influx of nutrients, efflux of wastes, and signal transduction occur at the membrane. Interaction between phospholipids and proteins is under investigation to understand how biological membrane is constructed and properly functions.

Microorganism, extremophile, psychrotroph, biological membrane, protein, phospholipids, enzyme, coenzyme, polyunsaturated fatty acid, reaction mechanism, environmental adaptation, bioconversion

Keywords

Recent Publications

Characterization of a Thermostable 2,4-Diaminopentanoate Dehydrogenase from Fervidobacterium nodosum Rt17-B1 Fukuyama S, Mihara H, Miyake R, Ueda M, Esaki N, Kurihara T (2014) J Biosci Bioeng 117 (5): 551-556  

Reciprocal Modulation of Surface Expression of Annexin A2 in a Human Umbilical Vein Endothelial Cell-derived Cell Line by Eicosapentaenoic Acid and Docosahexaenoic Acid Park J, Yamaura T, Kawamoto J, Kurihara T, Sato SB (2014) PLoS One. Jan 21; 9(1): e85045

Global Identification of Genes Affecting Iron-sulfur Cluster Biogenesis and Iron Homeostasis Hidese R, Mihara H, Kurihara T, Esaki N (2014) J Bacteriol 196 (6): 1238-1249   Selenocysteine Lyase: Delivering Selenium in Biosynthetic Pathway Mihara H, Kurihara T, Esaki N (2014) Selenium in the Environment and Human Health - Proceedings of the 3rd International Conference on Selenium in the Environment and Human Health 181-182   Inhibition of Constitutive Akt (PKB) Phosphorylation by Docosahexaenoic Acid in the Human Breast Cancer Cell Line MDA-MB-453 Sato S B, Park J, Kawamoto J, Sato S, Kurihara,T (2013) Biochim Biophys Acta 1831: 306-313   Binding Modes of DL-2-Haloacid Dehalogenase Revealed by Crystallography, Modeling and Isotope Effects Studies Siwek A, Omi R, Hirotsu K, Jitsumori K, Esaki N, Kurihara T, Paneth P (2013) Arch Biochem Biophys 540: 26-32 Regulation of Cytochrome c- and Quinol Oxidases, and Piezotolerance of Their Activities in the Deep-Sea Piezophile Shewanella violacea DSS12 in Response to Growth Conditions Ohke Y, Sakoda A, Kato C, Sambongi Y, Kawamoto J, Kurihara T, Tamegai H (2013) Biosci Biotechnol Biochem 77: 1522-1528 Proteins Involved in Cold Adaptation Yoshimune K, Kawamoto J, Kurihara T (2013) Cold-Adapted Microorganisms 97-110

Occurrence of a Bacterial Membrane Microdomain at the Cell Division Site Enriched in Phospholipids with Polyunsaturated Hydrocarbon Chains Sato S, Kawamoto J, Sato S B, Watanabe B, Hiratake J, Esaki N, Kurihara T (2012) J Biol Chem 287: 24113-24121  

Eicosapentaenoic Acid Facilitates the Folding of an Outer Membrane Protein of the Psychrotrophic Bacterium, Shewanella livingstonensis Ac10 Dai X-Z, Kawamoto J, Sato S B, Esaki N, Kurihara T (2012) Biochem Biophys Res Commun. 425: 363-367  

Identification of Cold-Inducible Inner Membrane Proteins of the Psychrotrophic Bacterium, Shewanella livingstonensis Ac10, by Proteomic Analysis Park J, Kawamoto J, Esaki N, Kurihara T (2012) Extremophiles 16: 227-236   Characterization of 1-Acyl-sn-Glycerol-3-Phosphate Acyltransferase from a Polyunsaturated Fatty Acid-Producing Bacterium, Shewanella livingstonensis Ac10 Cho H-N, Kasai W, Kawamoto J, Esaki N, Kurihara T (2012) Trace Nutrients Research 29: 92-99   Functional Analysis of an Eicosapentaenoic Acid Biosynthesis Protein Orf2 from a Psychrotrophic Bacterium, Shewanella livingstonensis Ac10 Gong C, Kawamoto J, Esaki N, Kurihara T (2012) Trace Nutrients Research 29: 84-91   Pseudomonas putida PydR, a RutR-Like Transcriptional Regulator, Represses the Dihydropyrimidine Dehydrogenase Gene in the Pyrimidine Reductive Catabolic Pathway Hidese R, Mihara H, Kurihara T, Esaki N (2012) J Biochem 152: 341-346 Substrate Specificity of Fluoroacetate Dehalogenase: An Insight from Crystallographic Analysis, Fluorescence Spectroscopy, and Theoretical Computations Nakayama T, Kamachi T, Jitsumori K, Omi R, Hirotsu K, Esaki N, Kurihara T, Yoshizawa K (2012) Chemistry 18: 8392-8402   Eicosapentaenoic Acid Plays a Role in Stabilizing Dynamic Membrane Structure in the Deep-Sea Piezophile Shewanella violacea: A Study Employing High-Pressure Time-Resolved Fluorescence Anisotropy Measurement Usui K, Hiraki T, Kawamoto J, Kurihara T, Nogi Y, Kato C, Abe F (2012) Biochim Biophys Acta 1818: 574-583   Favourable effects of Eicosapentaenoic Acid on the Late Step of the Cell Division in a Piezophilic Bacterium, Shewanella violacea DSS12, at High-hydrostatic Pressures Kawamoto J, Sato T, Nakasone K, Kato C, Mihara H, Esaki N, Kurihara T (2011) Environ Microbiol 13: 2293–2298

In vitro Refolding of an OmpA Homolog, a Major Cold-Inducible Outer Membrane Protein, from a Psychrotrophic Bacterium, Shewanella livingstonensis Ac10 Dai X-Z, Kawamoto J, Esaki N, Kurihara T (2011) Journal of Japanese Society for Extremophiles 10: 90-96 Differential Roles of Internal and Terminal Double Bonds in Docosahexaenoic Acid: Comparative Study of Cytotoxicity of Polyunsaturated Fatty Acids to HT-29 Human Colorectal Tumor Cell Line Sato S B, Sato S, Kawamoto J, Kurihara T (2011) Prostaglandins Leukot Essent Fatty Acids 84: 31-37   Function of FADH2-dependent 2-Haloacrylate Hydratase from a 2-Chloroacrylate-utilizing Bacterium, Burkholderia sp. WS Vasudevan A, Fujita M, Kurata A, Kawamoto J, Esaki N, Kurihara T (2011) Trace Nutri Res 28: 58-64  

Thermal Stability of Cytochrome c(5) of Pressure-Sensitive Shewanella livingstonensis Masanari M, Wakai S, Tamegai H, Kurihara T, Kato C, Sambongi Y (2011) Biosci Biotechnol Biochem 75: 1859-1861   Piezotolerance of the Respiratory Terminal Oxidase Activityof the Piezophilic Shewanella violacea DSS12 as Compared with Non-Piezophilic Shewanella Species Tamegai H, Ota Y, Haga M, Fujimori H, Kato C, Nogi Y, Kawamoto J, Kurihara T, Sambongi Y (2011) Biosci Biotechnol Biochem 75: 919-924 Identification of Novel Mammalian Phospholipids Containing Threonine, Aspartate, and Glutamate as the Base Moiety Omori T, Honda A, Mihara H, Kurihara T, Esaki N (2011) J Chromatogr B 879: 3296-3302  

Mammalian Selenocysteine Lyase Is Involved in Selenoprotein Biosynthesis Kurokawa S, Takehashi M, Tanaka H, Mihara H, Kurihara T, Tanaka S, Hill K, Burk R, Esaki N (2011) J Nutr Sci Vitaminol 57: 298-305  

Escherichia coli Dihydropyrimidine Dehydrogenase is a Novel NAD-dependent Heterotetramer Essential for the Production of 5,6-Dihydrouracil Hidese R, Mihara H, Kurihara T, Esaki N (2011) J Bacteriol 193: 989-993 A Mechanistic Analysis of Enzymatic Degradation of Organohalogen Compounds Kurihara T (2011) Biosci Biotechnol Biochem 75: 189-198

IscS Functions as a Primary Sulfur-donating Enzyme by Interacting Specifically with MoeB and MoaD in the Biosynthesis of Molybdopterin in Escherichia coli Zhang W, Urban A, Mihara H, Leimkühler S, Kurihara T, Esaki N (2010) J Biol Chem 285: 2302-2308

Crystallization and Preliminary X-ray Analysis of L-Azetidine-2-Carboxylate Hydrolase from Pseudomonas sp. strain A2C Toyoda M, Jitsumori K, Mikami B, P.Wackett L, Kurihara T, Esaki N (2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 801-804  

The Distribution of Phosphatidyl-D-serine in the Rat Omori T, Mihara H, Kurihara T, Esaki N (2010) Biosci Biotechnol Biochem 74: 1953-1955   Reaction Mechanism and Molecular Basis for Selenium/Sulfur Discrimination of Selenocysteine Lyase Omi R, Kurokawa S, Mihara H, Hayashi H, Goto M, Miyahara I, Kurihara T, Hirotsu K, Esaki N (2010) J Biol Chem 285: 12133-12139   2-Haloacrylate Hydratase, a New Class of Flavoenzyme that Catalyzes the Addition of Water to the Substrate for Dehalogenation Mowafy A M, Kurihara T, Kurata A, Uemura T, Esaki N (2010) Appl Environ Microbiol 76: 6032-6037 2-Haloacrylate Hydratase Is a Bifunctional Enzyme with NADH-Dependent FAD Reductase Activity Mowafy A M, Kurihara T, Esaki N (2010) Trace Nutri Res 27: 52-55   Crystal Structure of a Homolog of Mammalian Serine Racemase from Schizosaccharomyces pombe Goto M, Yamauchi T, Kamiya N, Miyahara I, Yoshimura T, Mihara H, Kurihara T, Hirotsu K, Esaki N (2009) J Biol Chem 284: 25944-25952  

Selenocysteine Is Selectively Taken Up by Red Blood Cells Imai T, Mihara H, Kurihara K, Esaki N (2009) Biosci Biotechnol Biochem 73: 2746-2748. Possible Role of Red Blood Cells in Selenocysteine Metabolism Imai T, Mihara H, Kurihara T, Esaki N (2009) Trace Nutri Res 26: 22-25   The Catalytic Mechanism of Fluoroacetate Dehalogenase: A Computational Exploration of Biological Dehalogenation Kamachi T, Nakayama T, Shitamichi O, Jitsumori K, Kurihara T, Esaki N, Yoshizawa K (2009) Chemistry 15: 7394-7403 Identification of Proteins Interacting with Selenocysteine Lyase Tobe R, Mihara H, Kurihara T, Esaki N (2009) Biosci Biotechnol Biochem 73:1230-1232  

Roles of K151 and D180 in L-2-Haloacid Dehalogenase from Pseudomonas sp. YL: Analysis by Molecular Dynamics and Ab Initio Fragment Molecular Orbital Calculations Nakamura T, Yamaguchi A, Kondo H, Watanabe H, Kurihara T, Esaki N, Hirono S, Tanaka S (2009) J Comput Chem 30: 2625-2634 Serine Racemase with Catalytically Active Lysinoalanyl Residue Yamauchi T, Goto M, Wu H-Y, Uo T, Yoshimura T, Mihara H, Kurihara T, Miyahara I, Hirotsu K, Esaki N (2009) J Biochem 145: 421-424 Occurrence of Phosphatidyl-D-serine in the Rat Cerebrum Omori T, Mihara H, Kurihara T, Esaki N (2009) Biochem Biophys Res Commun 382: 415-418   Eicosapentaenoic Acid Plays a Beneficial Role in Membrane Organization and Cell Division of a Cold-Adapted Bacterium, Shewanella livingstonensis Ac10 Kawamoto J, Kurihara T, Yamamoto K, Nagayasu M, Tani Y, Mihara H, Hosokawa M, Baba T, Sato S B, Esaki N (2009) J Bacteriol 191: 632-640   X-ray Crystallographic and Mutational Studies of Fluoroacetate Dehalogenase from Burkholderia sp. FA1 Jitsumori K, Omi R, Kurihara T, Mihara H, Miyahara I, Hirotsu K, Esaki N (2009) J Bacteriol 191: 2630-2637   Investigation of the Roles of Cysteine Desulfurases in the Molybdopterin Synthesis in Escherichia coli Zhang W, Mihara H, Kurihara T, Esaki N (2008) Trace Nutri Res 25: 152-157   Role of Cysteine Desulfurase IscS in the Biosynthesis of Molybdopterin Zhang W, Mihara H, Kurihara T, Esaki N (2008) Vitamins (Japan) 82: 645-650 Cold Adaptation of Eicosapentaenoic Acid-less Mutant of Shewanella livingstonensis Ac10 Involving Uptake and Remodeling of Synthetic Phospholipids Containing Various Polyunsaturated Fatty Acids Sato S, Kurihara T, Kawamoto J, Hosokawa M, Sato SB, Esaki N (2008) Extremophiles 12: 753-761  

The iscS Gene Deficiency Affects the Expression of Pyrimidine Metabolism Genes Mihara H, Hidese R, Yamane M, Kurihara T, Esaki N (2008) Biochem Biophys Res Commun 372: 407-411 Thioredoxin Reductase 1 Is Important for Selenoprotein Biosynthesis in HeLa Cells Kurokawa S, Mihara H, Yokoyama I, Mochizuki M, Yodoi J, Tamura T, Kurihara T, Esaki N (2008) Biomed Res Trace Elem 19: 84-87

Proteomic Studies of Psychorophilic Microorganisms Kurihara T, Esaki N (2008) Psychrophiles: From Biodiversity to Biotechnology 333-343   Bacterial Hydrolytic Dehalogenases and Related Enzymes: Occurrences, Reaction Mechanisms, and Applications Kurihara T, Esaki N (2008) Chem Rec 8: 67-74   Production of (S)-2-Chloropropionate by Asymmetric Reduction of 2-Chloroacrylate with 2-Haloacrylate Reductase Coupled with Glucose Dehydrogenase Kurata A, Fujita M, Mowafy A M, Kamachi H, Kurihara T, Esaki N (2008) J Biosci Bioeng 105: 429-431