Oda M

References (19)

Title : Improvement of thermostability and activity of PET-degrading enzyme Cut190 towards a detailed understanding and application of the enzymatic reaction mechanism - Numoto_2023_bioRxiv__
Author(s) : Numoto N , Kamiya N , Oda M
Ref : Biorxiv , : , 2023
Abstract : Enzymes capable of hydrolyzing polyethylene terephthalate (PET) and other plastics are attractive catalysts for application to the recycling of plastic waste due to their generally low environmental impact. Cut190 is a cutinase from a thermophilic actinomycete and shows PET-degrading activity and high thermal stability. We developed a series of Cut190 mutants exhibiting further improvements in thermal stability and activity, and showed that the unique stabilization and activation mechanism was dependent on Ca2+ ions. Two of these mutants, Cut190** and Cut190*SS, differed from the previous mutant Cut190* by deletion of the three C-terminal residues and introduction of five substitutions, including two cysteines forming a disulfide-bond, respectively. These mutants exhibit higher thermal stability and activity, which are often mutually exclusive characteristics. Crystallographic studies of these mutants and their inactivated derivatives demonstrated that they could have a novel ejecting form that would be responsible for releasing products. We also determined the crystal structures of ligand-bound complexes, which revealed the molecular mechanisms of the aromatic-ring recognition and the tetrahedral intermediate during the substrate cleaving, although the ligands had no aromatic ring but a cyclic group. This structural information provides insights into the mechanism of the Ca2+ -dependent PET-cleaving activity of Cut190 and provides a useful basis for further mutant design and computational studies.
ESTHER : Numoto_2023_bioRxiv__
PubMedSearch : Numoto_2023_bioRxiv__
PubMedID:
Gene_locus related to this paper: sacvd-c7mve8

Title : Structural basis for Ca(2+)-dependent catalysis of a cutinase-like enzyme and its engineering: application to enzymatic PET depolymerization - Oda_2021_Biophys.Physicobiol_18_168
Author(s) : Oda M
Ref : Biophys Physicobiol , 18 :168 , 2021
Abstract : A cutinase-like enzyme from Saccharomonospora viridis AHK190, Cut190, can depolymerize polyethylene terephthalate (PET). As high activity at approximately 70 degreesC is required for PET depolymerization, structure-based protein engineering of Cut190 was carried out. Crystal structure information of the Cut190 mutants was used for protein engineering and for evaluating the molecular basis of activity and thermal stability. A variety of biophysical methods were employed to unveil the mechanisms underlying the unique features of Cut190, which included the regulation of its activity and thermal stability by Ca(2+). Ca(2+) association and dissociation can change the enzyme conformation to regulate catalytic activity. Weak metal-ion binding would be required for the naive conformational change of Cut190, while maintaining its fluctuation, to "switch" the enzyme on and off. The activity of Cut190 is regulated by the weak Ca(2+) binding to the specific site, Site 1, while thermal stability is mainly regulated by binding to another Site 2, where a disulfide bond could be introduced to increase the stability. Recent results on the structure-activity relationship of engineered Cut190 are reviewed, including the application for PET depolymerization by enzymes.
ESTHER : Oda_2021_Biophys.Physicobiol_18_168
PubMedSearch : Oda_2021_Biophys.Physicobiol_18_168
PubMedID: 34386313
Gene_locus related to this paper: sacvd-c7mve8

Title : Structural basis of mutants of PET-degrading enzyme from Saccharomonospora viridis AHK190 with high activity and thermal stability - Emori_2021_Proteins_89_502
Author(s) : Emori M , Numoto N , Senga A , Bekker GJ , Kamiya N , Kobayashi Y , Ito N , Kawai F , Oda M
Ref : Proteins , 89 :502 , 2021
Abstract : The cutinase-like enzyme from the thermophile Saccharomonospora viridis AHK190, Cut190, is a good candidate to depolymerize polyethylene terephthalate (PET) efficiently. We previously developed a mutant of Cut190 (S226P/R228S), which we designated as Cut190* that has both increased activity and stability and solved its crystal structure. Recently, we showed that mutation of D250C/E296C on one of the Ca(2+) -binding sites resulted in a higher thermal stability while retaining its polyesterase activity. In this study, we solved the crystal structures of Cut190* mutants, Q138A/D250C-E296C/Q123H/N202H, designated as Cut190*SS, and its inactive S176A mutant, Cut190*SS_S176A, at high resolution. The overall structures were similar to those of Cut190* and Cut190*S176A reported previously. As expected, Cys250 and Cys296 were closely located to form a disulfide bond, which would assuredly contribute to increase the stability. Isothermal titration calorimetry experiments and 3D Reference Interaction Site Model calculations showed that the metal-binding properties of the Cut190*SS series were different from those of the Cut190* series. However, our results show that binding of Ca(2+) to the weak binding site, site 1, would be retained, enabling Cut190*SS to keep its ability to use Ca(2+) to accelerate the conformational change from the closed (inactive) to the open (active) form. While increasing the thermal stability, Cut190*SS could still express its enzymatic function. Even after incubation at 70 degreesC, which corresponds to the glass transition temperature of PET, the enzyme retained its activity well, implying a high applicability for industrial PET depolymerization using Cut190*SS.
ESTHER : Emori_2021_Proteins_89_502
PubMedSearch : Emori_2021_Proteins_89_502
PubMedID: 33340163
Gene_locus related to this paper: sacvd-c7mve8

Title : Cutinases from thermophilic bacteria (actinomycetes): From identification to functional and structural characterization - Oda_2021_Methods.Enzymol_648_159
Author(s) : Oda M , Numoto N , Bekker GJ , Kamiya N , Kawai F
Ref : Methods Enzymol , 648 :159 , 2021
Abstract : Thermophilic cutinases are mainly obtained from thermophilic actinomycetes, and are categorized into two groups, i.e., those with higher (>70 degreesC) or lower (<70 degreesC) thermostabilities. The thermostabilities of cutinases are highly relevant to their ability to degrade polyethylene terephthalate (PET). Many crystal structures of thermophilic cutinases have been solved, showing that their overall backbone structures are identical, irrespective of their ability to hydrolyze PET. One of the unique properties of cutinases is that metal ion-binding on the enzyme's surface both elevates their melting temperatures and activates the enzyme. In this chapter, we introduce the methodology for the identification and cloning of thermophilic cutinases from actinomycetes. For detailed characterization of cutinases, we describe the approach to analyze the intricate dynamics of the enzyme, based on its crystal structures complexed with metal ions and model substrates using a combination of experimental and computational techniques.
ESTHER : Oda_2021_Methods.Enzymol_648_159
PubMedSearch : Oda_2021_Methods.Enzymol_648_159
PubMedID: 33579402

Title : Multiple structural states of Ca2+-regulated PET hydrolase, Cut190, and its correlation with activity and stability - Senga_2021_J.Biochem_169_207
Author(s) : Senga A , Numoto N , Yamashita M , Iida A , Ito N , Kawai F , Oda M
Ref : J Biochem , 169 :207 , 2021
Abstract : An enzyme, Cut190, from a thermophilic isolate, Saccharomonospora viridis AHK190 could depolymerize polyethylene terephthalate (PET). The catalytic activity and stability of Cut190 and its S226P/R228S mutant, Cut190*, are regulated by Ca2+ binding. We previously determined the crystal structures of the inactive mutant of Cut190*, Cut190*S176A, in complex with metal ions, Ca2+ and Zn2+, and substrates, monoethyl succinate and monoethyl adipate. In this study, we determined the crystal structures of another mutant of Cut190*, Cut190**, in which the three C-terminal residues of Cut190* are deleted, and the inactive mutant, Cut190**S176A, in complex with metal ions. In addition to the previously observed closed, open and engaged forms, we determined the ejecting form, which would allow the product to irreversibly dissociate, followed by proceeding to the next cycle of reaction. These multiple forms would be stable or sub-stable states of Cut190, regulated by Ca2+ binding, and would be closely correlated with the enzyme function. Upon the deletion of the C-terminal residues, we found that the thermal stability increased while retaining the activity. The increased stability could be applied for the protein engineering of Cut190 for PET depolymerization as it requires the reaction above the glass transition temperature of PET.
ESTHER : Senga_2021_J.Biochem_169_207
PubMedSearch : Senga_2021_J.Biochem_169_207
PubMedID: 32882044
Gene_locus related to this paper: sacvd-c7mve8

Title : Current knowledge on enzymatic PET degradation and its possible application to waste stream management and other fields - Kawai_2019_Appl.Microbiol.Biotechnol_103_4253
Author(s) : Kawai F , Kawabata T , Oda M
Ref : Applied Microbiology & Biotechnology , 103 :4253 , 2019
Abstract : Enzymatic hydrolysis of polyethylene terephthalate (PET) has been the subject of extensive previous research that can be grouped into two categories, viz. enzymatic surface modification of polyester fibers and management of PET waste by enzymatic hydrolysis. Different enzymes with rather specific properties are required for these two processes. Enzymatic surface modification is possible with several hydrolases, such as lipases, carboxylesterases, cutinases, and proteases. These enzymes should be designated as PET surface-modifying enzymes and should not degrade the building blocks of PET but should hydrolyze the surface polymer chain so that the intensity of PET is not weakened. Conversely, management of PET waste requires substantial degradation of the building blocks of PET; therefore, only a limited number of cutinases have been recognized as PET hydrolases since the first PET hydrolase was discovered by Muller et al. (Macromol Rapid Commun 26:1400-1405, 2005). Here, we introduce current knowledge on enzymatic degradation of PET with a focus on the key class of enzymes, PET hydrolases, pertaining to the definition of enzymatic requirements for PET hydrolysis, structural analyses of PET hydrolases, and the reaction mechanisms. This review gives a deep insight into the structural basis and dynamics of PET hydrolases based on the recent progress in X-ray crystallography. Based on the knowledge accumulated to date, we discuss the potential for PET hydrolysis applications, such as in designing waste stream management.
ESTHER : Kawai_2019_Appl.Microbiol.Biotechnol_103_4253
PubMedSearch : Kawai_2019_Appl.Microbiol.Biotechnol_103_4253
PubMedID: 30957199

Title : Metal binding to cutinase-like enzyme from Saccharomonospora viridis AHK190 and its effects on enzyme activity and stability - Senga_2019_J.Biochem_166_149
Author(s) : Senga A , Hantani Y , Bekker GJ , Kamiya N , Kimura Y , Kawai F , Oda M
Ref : J Biochem , 166 :149 , 2019
Abstract : A cutinase from Saccharomonospora viridis AHK190, Cut190, can hydrolyze polyethylene terephthalate and has a unique feature that the activity and stability are regulated by Ca2+ binding. Our recent structural and functional analyses showed three Ca2+ binding sites and their respective roles. Here, we analysed the binding thermodynamics of Mn2+, Zn2+ and Mg2+ to Cut190 and their effects on the catalytic activity and thermal stability. The binding affinities of Mn2+ and Zn2+ were higher than that of Mg2+ and are all entropy driven with a binding stoichiometry of three, one and one for Zn2+, Mn2+ and Mg2+, respectively. The catalytic activity was measured in the presence of the respective metals, where the activity of 0.25 mM Mn2+ was comparable to that of 2.5 mM Ca2+. Our 3D Reference Interaction Site Model calculations suggested that all the ions exhibited a high occupancy rate for Site 2. Thus, Mn2+ and Mg2+ would most likely bind to Site 2 (contributes to stability) with high affinity, while to Sites 1 and 3 (contributes to activity) with low affinity. We elucidate the metal-dependent structural and functional properties of Cut190 and show the subtle balance on structure stability and flexibility is controlled by specific metal ions.
ESTHER : Senga_2019_J.Biochem_166_149
PubMedSearch : Senga_2019_J.Biochem_166_149
PubMedID: 30825308
Gene_locus related to this paper: sacvd-c7mve8

Title : Structural Dynamics of the PET-Degrading Cutinase-like Enzyme from Saccharomonospora viridis AHK190 in Substrate-Bound States Elucidates the Ca(2+)-Driven Catalytic Cycle - Numoto_2018_Biochemistry_57_5289
Author(s) : Numoto N , Kamiya N , Bekker GJ , Yamagami Y , Inaba S , Ishii K , Uchiyama S , Kawai F , Ito N , Oda M
Ref : Biochemistry , 57 :5289 , 2018
Abstract : A cutinase-type polyesterase from Saccharomonospora viridis AHK190 (Cut190) has been shown to degrade the inner block of polyethylene terephthalate. A unique feature of Cut190 is that its function and stability are regulated by Ca(2+) binding. Our previous crystal structure analysis of Cut190S226P showed that one Ca(2+) binds to the enzyme, which induces large conformational changes in several loop regions to stabilize an open conformation [Miyakawa, T., et al. (2015) Appl. Microbiol. Biotechnol. 99, 4297]. In this study, to analyze the substrate recognition mechanism of Cut190, we determined the crystal structure of the inactive form of a Cut190 mutant, Cut190*S176A, in complex with calcium ions and/or substrates. We found that three calcium ions bind to Cut190*S176A, which is supported by analysis using native mass spectrometry experiments and 3D Reference Interaction Site Model calculations. The complex structures with the two substrates, monoethyl succinate and monoethyl adipate (engaged and open forms), presumably correspond to the pre- and post-reaction states, as the ester bond is close to the active site and pointing outward from the active site, respectively, for the two complexes. Ca(2+) binding induces the pocket to open, enabling the substrate to access the pocket more easily. Molecular dynamics simulations suggest that a post-reaction state in the engaged form presumably exists between the experimentally observed forms, indicating that the substrate would be cleaved in the engaged form and then requires the enzyme to change to the open form to release the product, a process that Ca(2+) can greatly accelerate.
ESTHER : Numoto_2018_Biochemistry_57_5289
PubMedSearch : Numoto_2018_Biochemistry_57_5289
PubMedID: 30110540
Gene_locus related to this paper: sacvd-c7mve8

Title : Enzymatic hydrolysis of PET: functional roles of three Ca(2+) ions bound to a cutinase-like enzyme, Cut190*, and its engineering for improved activity - Oda_2018_Appl.Microbiol.Biotechnol_102_10067
Author(s) : Oda M , Yamagami Y , Inaba S , Oida T , Yamamoto M , Kitajima S , Kawai F
Ref : Applied Microbiology & Biotechnology , 102 :10067 , 2018
Abstract : Cut190 from Saccharomonospora viridis AHK190 (Cut190) is the only cutinase that exhibits inactive (Ca(2+)-free) and active (Ca(2+)-bound) states, although other homologous cutinases always maintain the active states (Ca(2+)-free and bound). The X-ray crystallography of the S176A mutant of Cut190* (Cut190_S226P/R228S) showed that three Ca(2+) ions were bound at sites 1-3 of the mutant. We analyzed the roles of three Ca(2+) ions by mutation and concluded that they play different roles in Cut190* for activation (sites 1 and 3) and structural and thermal stabilization (sites 2 and 3). Based on these analyses, we elucidated the mechanism for the conformational change from the Ca(2+)-free inactive state to the Ca(2+)-bound active state, proposing the novel Ca(2+) effect on structural dynamics of protein. The introduction of a disulfide bond at Asp250 and Glu296 in site 2 remarkably increased the melting temperatures of the mutant enzymes by more than 20-30 degrees C (while Ca(2+)-bound) and 4-14 degrees C (while Ca(2+)-free), indicating that a disulfide bond mimics the Ca(2+) effect. Replacement of surface asparagine and glutamine with aspartic acid, glutamic acid, or histidine increased the melting temperatures. Engineered mutant enzymes were evaluated by an increase in melting temperatures and kinetic values, based on the hydrolysis of poly(butylene succinate-co-adipate) and microfiber polyethylene terephthalate (PET). A combined mutation, Q138A/D250C-E296C/Q123H/N202H, resulted in the highest thermostability, leading to the maximum degradation of PET film (more than 30%; approximately threefold at 70 degrees C, compared with that of Cut190* at 63 degrees C).
ESTHER : Oda_2018_Appl.Microbiol.Biotechnol_102_10067
PubMedSearch : Oda_2018_Appl.Microbiol.Biotechnol_102_10067
PubMedID: 30250976
Gene_locus related to this paper: sacvd-c7mve8

Title : Mutational analysis of cutinase-like enzyme, Cut190, based on the 3D docking structure with model compounds of polyethylene terephthalate - Kawabata_2017_J.Biosci.Bioeng_124_28
Author(s) : Kawabata T , Oda M , Kawai F
Ref : J Biosci Bioeng , 124 :28 , 2017
Abstract : The cutinase-like enzyme, Cut190, from Saccharomonospora viridis AHK190 can degrade the inner block of polyethylene terephthalate (PET) in the presence of Ca2+, and its mutant, S226P/R228S, exhibited increased activity and higher thermostability. The crystal structures of the Cut190 S226P mutant in the absence and presence of Ca2+ were determined, and revealed the large conformational change induced upon Ca2+ binding. However, the substrate-bound 3D structures of Cut190 remained unknown. In this study, to determine the substrate-binding site and improve the enzyme activity, we first built 3D structures of a PET model compound bound to the crystal structures, using the distance restraints between the scissile carbonyl group of the compound and the catalytic site of the enzyme. We then mutated the putative substrate-binding site predicted from the models, and experimentally determined the enzymatic activities of the mutants for the model substrate poly(butylene succinate-co-adipate). The mutated sites with decreased activity were consistent with the putative binding sites predicted by the 3D model from the Ca2+-bound crystal structure, suggesting that the structure of the Ca2+-bound state represents the active state. Notably, we generated two mutants with significantly increased activities.
ESTHER : Kawabata_2017_J.Biosci.Bioeng_124_28
PubMedSearch : Kawabata_2017_J.Biosci.Bioeng_124_28
PubMedID: 28259444
Gene_locus related to this paper: sacvd-c7mve8

Title : Significance of Cholinergic and Peptidergic Nerves in Stress-Induced Ulcer and MALT Lymphoma Formation - Nakamura_2017_Curr.Pharm.Des_23_3993
Author(s) : Nakamura M , Overby A , Uehara A , Oda M , Takahashi S , Murayama SY , Matsui H
Ref : Curr Pharm Des , 23 :3993 , 2017
Abstract : Backgound: The role of enteric nerves has previously been demonstrated in the formation of several gastric diseases. In the present review, the significance of the cholinergic nerves in stress-induced ulcer formation as well as the importance of substance P in the formation of gastric MALT lymphoma is discussed. METHODS: The stress-induced ulcer was induced by the plaster bandage methods in rats. The gastric MALT lymphoma was formed by the peroral infection of gastric mucosal homogenate of the infected mouse in C57BL/6 mice. For the stress-induced ulcer, the distribution of the cholinergic nerves and muscarinic acetylcholine receptors was investigated by acetylcholinesterase histochemistry and autoradiography of water soluble compounds using 3H-quinuclidinyl benzilate was performed. To the MALT lymphoma study, the distribution of the substance P and effect of substance P antagonist, spantide II, was investigated by immunohistochemical studies. RESULTS: The stress induced ulcer formation was shown to be related to the hyperactivity of the cholinergic nerves. The gastric MALT lymphoma was shown to be related to the increased localization of substance P. CONCLUSION: Stress-induced ulceration as a model of hyperactivity of the cholinergic nerves was proved to be a useful approach, while substance P and its role in MALT lymphoma formation may serve as a tool to clarify the neuroimmune modulation of chronic infectious diseases.
ESTHER : Nakamura_2017_Curr.Pharm.Des_23_3993
PubMedSearch : Nakamura_2017_Curr.Pharm.Des_23_3993
PubMedID: 28190393

Title : Structural basis for the Ca(2+)-enhanced thermostability and activity of PET-degrading cutinase-like enzyme from Saccharomonospora viridis AHK190 - Miyakawa_2015_Appl.Microbiol.Biotechnol_99_4297
Author(s) : Miyakawa T , Mizushima H , Ohtsuka J , Oda M , Kawai F , Tanokura M
Ref : Applied Microbiology & Biotechnology , 99 :4297 , 2015
Abstract : A cutinase-like enzyme from Saccharomonospora viridis AHK190, Cut190, hydrolyzes the inner block of polyethylene terephthalate (PET); this enzyme is a member of the lipase family, which contains an alpha/beta hydrolase fold and a Ser-His-Asp catalytic triad. The thermostability and activity of Cut190 are enhanced by high concentrations of calcium ions, which is essential for the efficient enzymatic hydrolysis of amorphous PET. Although Ca(2+)-induced thermostabilization and activation of enzymes have been well explored in alpha-amylases, the mechanism for PET-degrading cutinase-like enzymes remains poorly understood. We focused on the mechanisms by which Ca(2+) enhances these properties, and we determined the crystal structures of a Cut190 S226P mutant (Cut190(S226P)) in the Ca(2+)-bound and free states at 1.75 and 1.45 A resolution, respectively. Based on the crystallographic data, a Ca(2+) ion was coordinated by four residues within loop regions (the Ca(2+) site) and two water molecules in a tetragonal bipyramidal array. Furthermore, the binding of Ca(2+) to Cut190(S226P) induced large conformational changes in three loops, which were accompanied by the formation of additional interactions. The binding of Ca(2+) not only stabilized a region that is flexible in the Ca(2+)-free state but also modified the substrate-binding groove by stabilizing an open conformation that allows the substrate to bind easily. Thus, our study explains the structural basis of Ca(2+)-enhanced thermostability and activity in PET-degrading cutinase-like enzyme for the first time and found that the inactive state of Cut190(S226P) is activated by a conformational change in the active-site sealing residue, F106.
ESTHER : Miyakawa_2015_Appl.Microbiol.Biotechnol_99_4297
PubMedSearch : Miyakawa_2015_Appl.Microbiol.Biotechnol_99_4297
PubMedID: 25492421
Gene_locus related to this paper: sacvd-c7mve8

Title : A novel Ca-activated, thermostabilized polyesterase capable of hydrolyzing polyethylene terephthalate from Saccharomonospora viridis AHK190 - Kawai_2014_Appl.Microbiol.Biotechnol_98_10053
Author(s) : Kawai F , Oda M , Tamashiro T , Waku T , Tanaka N , Yamamoto M , Mizushima H , Miyakawa T , Tanokura M
Ref : Applied Microbiology & Biotechnology , 98 :10053 , 2014
Abstract : Only two polyethylene glycol terephthalate (PET)-degrading enzymes have been reported, and their mechanism for the biochemical degradation of PET remains unclear. To identify a novel PET-degrading enzyme, a putative cutinase gene (cut190) was cloned from the thermophile Saccharomonospora viridis AHK190 and expressed in Escherichia coli Rosetta-gami B (DE3). Mutational analysis indicated that substitution of Ser226 with Pro and Arg228 with Ser yielded the highest activity and thermostability. The Ca2+ ion enhanced the enzyme activity and thermostability of the wild-type and mutant Cut190. Circular dichroism suggested that the Ca2+ changes the tertiary structure of the Cut190 (S226P/R228S), which has optimal activity at 65-75 degrees C and pH 6.5-8.0 in the presence of 20 % glycerol. The enzyme was stable over a pH range of 5-9 and at temperatures up to 65 degrees C for 24 h with 40 % activity remaining after incubation for 1 h at 70 degrees C. The Cut190 (S226P/R228S) efficiently hydrolyzed various aliphatic and aliphatic-co-aromatic polyester films. Furthermore, the enzyme degraded the PET film above 60 degrees C. Therefore, Cut190 is the novel-reported PET-degrading enzyme with the potential for industrial applications in polyester degradation, monomer recycling, and PET surface modification. Thus, the Cut190 will be a useful tool to elucidate the molecular mechanisms of the PET degradation, Ca2+ activation, and stabilization.
ESTHER : Kawai_2014_Appl.Microbiol.Biotechnol_98_10053
PubMedSearch : Kawai_2014_Appl.Microbiol.Biotechnol_98_10053
PubMedID: 24929560
Gene_locus related to this paper: sacvd-c7mve8

Title : Complete sequencing and pan-genomic analysis of Lactobacillus delbrueckii subsp. bulgaricus reveal its genetic basis for industrial yogurt production - Hao_2011_PLoS.One_6_e15964
Author(s) : Hao P , Zheng H , Yu Y , Ding G , Gu W , Chen S , Yu Z , Ren S , Oda M , Konno T , Wang S , Li X , Ji ZS , Zhao G
Ref : PLoS ONE , 6 :e15964 , 2011
Abstract : Lactobacillus delbrueckii subsp. bulgaricus (Lb. bulgaricus) is an important species of Lactic Acid Bacteria (LAB) used for cheese and yogurt fermentation. The genome of Lb. bulgaricus 2038, an industrial strain mainly used for yogurt production, was completely sequenced and compared against the other two ATCC collection strains of the same subspecies. Specific physiological properties of strain 2038, such as lysine biosynthesis, formate production, aspartate-related carbon-skeleton intermediate metabolism, unique EPS synthesis and efficient DNA restriction/modification systems, are all different from those of the collection strains that might benefit the industrial production of yogurt. Other common features shared by Lb. bulgaricus strains, such as efficient protocooperation with Streptococcus thermophilus and lactate production as well as well-equipped stress tolerance mechanisms may account for it being selected originally for yogurt fermentation industry. Multiple lines of evidence suggested that Lb. bulgaricus 2038 was genetically closer to the common ancestor of the subspecies than the other two sequenced collection strains, probably due to a strict industrial maintenance process for strain 2038 that might have halted its genome decay and sustained a gene network suitable for large scale yogurt production.
ESTHER : Hao_2011_PLoS.One_6_e15964
PubMedSearch : Hao_2011_PLoS.One_6_e15964
PubMedID: 21264216
Gene_locus related to this paper: lacda-q1g8l1 , lacdl-pip

Title : Nafamostat is hydrolysed by human liver cytosolic long-chain acyl-CoA hydrolase - Yamaori_2007_Xenobiotica_37_260
Author(s) : Yamaori S , Ukena E , Fujiyama N , Funahashi T , Kimura T , Yamamoto I , Ohshima T , Matsumura K , Oda M , Watanabe K
Ref : Xenobiotica , 37 :260 , 2007
Abstract : Although the authors recently reported that nafamostat, a clinically used serine protease inhibitor, was mainly hydrolysed by carboxylesterase in human liver microsomes, the involvement of human liver cytosol has not been elucidated. The current study examined the in vitro metabolism of nafamostat with human liver cytosols. Kinetic analysis indicated that the Vmax and Km values in the liver cytosols were 9.82 nmolmin(-1) mg(-1) protein and 197 microM for a liver sample HL-1, and 15.1 nmolmin(-1) mg(-1) protein and 157 microM for HL-2, respectively. The Vmax/Km values in both cytosols were at least threefold higher than those in the corresponding microsomes. The liver cytosolic activity for nafamostat hydrolysis was inhibited by phenylmethylsulfonyl fluoride (PMSF) (43% inhibition at 100 microM), whereas diisopropyl fluorophosphate (DFP) and bis(p-nitrophenyl)phosphate (BNPP) failed to inhibit the activity. Furthermore, the hydrolytic activity was also reduced by palmitoyl-CoA (67% inhibition at 100 microM) but not by acetyl-CoA. Effects of PMSF, DFP and BNPP on cytosolic palmitoyl-CoA hydrolytic activity were comparable with those of the cytosolic nafamostat hydrolytic activity. In addition, the palmitoyl-CoA hydrolytic activity was competitively inhibited by nafamostat with the apparent Ki value of 164 microM for the liver cytosol from HL-2. These results suggest that an isoform of long-chain acyl-CoA hydrolase may be responsible for the nafamostat hydrolysis in human liver cytosol.
ESTHER : Yamaori_2007_Xenobiotica_37_260
PubMedSearch : Yamaori_2007_Xenobiotica_37_260
PubMedID: 17624024

Title : Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences - Mikkelsen_2007_Nature_447_167
Author(s) : Mikkelsen TS , Wakefield MJ , Aken B , Amemiya CT , Chang JL , Duke S , Garber M , Gentles AJ , Goodstadt L , Heger A , Jurka J , Kamal M , Mauceli E , Searle SM , Sharpe T , Baker ML , Batzer MA , Benos PV , Belov K , Clamp M , Cook A , Cuff J , Das R , Davidow L , Deakin JE , Fazzari MJ , Glass JL , Grabherr M , Greally JM , Gu W , Hore TA , Huttley GA , Kleber M , Jirtle RL , Koina E , Lee JT , Mahony S , Marra MA , Miller RD , Nicholls RD , Oda M , Papenfuss AT , Parra ZE , Pollock DD , Ray DA , Schein JE , Speed TP , Thompson K , Vandeberg JL , Wade CM , Walker JA , Waters PD , Webber C , Weidman JR , Xie X , Zody MC , Graves JA , Ponting CP , Breen M , Samollow PB , Lander ES , Lindblad-Toh K
Ref : Nature , 447 :167 , 2007
Abstract : We report a high-quality draft of the genome sequence of the grey, short-tailed opossum (Monodelphis domestica). As the first metatherian ('marsupial') species to be sequenced, the opossum provides a unique perspective on the organization and evolution of mammalian genomes. Distinctive features of the opossum chromosomes provide support for recent theories about genome evolution and function, including a strong influence of biased gene conversion on nucleotide sequence composition, and a relationship between chromosomal characteristics and X chromosome inactivation. Comparison of opossum and eutherian genomes also reveals a sharp difference in evolutionary innovation between protein-coding and non-coding functional elements. True innovation in protein-coding genes seems to be relatively rare, with lineage-specific differences being largely due to diversification and rapid turnover in gene families involved in environmental interactions. In contrast, about 20% of eutherian conserved non-coding elements (CNEs) are recent inventions that postdate the divergence of Eutheria and Metatheria. A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation.
ESTHER : Mikkelsen_2007_Nature_447_167
PubMedSearch : Mikkelsen_2007_Nature_447_167
PubMedID: 17495919
Gene_locus related to this paper: mondo-ACHE , mondo-b2bsf5 , mondo-b2bsz5 , mondo-BCHE , mondo-d2x2i6 , mondo-d2x2i8 , mondo-f6slk2 , mondo-f6wu00 , mondo-f6wuf2 , mondo-f6xfj4 , mondo-f6yt13 , mondo-f7c7p0 , mondo-f7ckd0 , mondo-f7cvq8 , mondo-f7cvr5 , mondo-f7eil6 , mondo-f7ez13 , mondo-f7f0i7 , mondo-f7fg16 , mondo-f7gcv7 , mondo-f7gep4 , mondo-f7gly2 , mondo-f6u7q2 , mondo-f7fw54 , mondo-f7dpf6 , mondo-f6pgj5 , mondo-f6yg68 , mondo-f7g8u4 , mondo-f7eyv1 , mondo-f6pq73 , mondo-f7cre0 , mondo-f7fdj0 , mondo-f7fdj5 , mondo-f7ft63 , mondo-f7ge99 , mondo-f7gea2 , mondo-f6pxq2 , mondo-f7awc1 , mondo-f7c412 , mondo-f7ev24 , mondo-f7b6s6 , mondo-f6vcx0 , mondo-f7g148 , mondo-f6tlv9 , mondo-f6tdm5 , mondo-f7f3w0 , mondo-f7fg39 , mondo-f7d6c2 , mondo-f6sdn0 , mondo-f7gi08 , mondo-f6xss6 , mondo-f6sa37 , mondo-f7gd97 , mondo-f6z6x9

Title : Involvement of human blood arylesterases and liver microsomal carboxylesterases in nafamostat hydrolysis - Yamaori_2006_Drug.Metab.Pharmacokinet_21_147
Author(s) : Yamaori S , Fujiyama N , Kushihara M , Funahashi T , Kimura T , Yamamoto I , Sone T , Isobe M , Ohshima T , Matsumura K , Oda M , Watanabe K
Ref : Drug Metab Pharmacokinet , 21 :147 , 2006
Abstract : Metabolism of nafamostat, a clinically used serine protease inhibitor, was investigated with human blood and liver enzyme sources. All the enzyme sources examined (whole blood, erythrocytes, plasma and liver microsomes) showed nafamostat hydrolytic activity. V(max) and K(m) values for the nafamostat hydrolysis in erythrocytes were 278 nmol/min/mL blood fraction and 628 microM; those in plasma were 160 nmol/min/mL blood fraction and 8890 microM, respectively. Human liver microsomes exhibited a V(max) value of 26.9 nmol/min/mg protein and a K(m) value of 1790 microM. Hydrolytic activity of the erythrocytes and plasma was inhibited by 5, 5'-dithiobis(2-nitrobenzoic acid), an arylesterase inhibitor, in a concentration-dependent manner. In contrast, little or no suppression of these activities was seen with phenylmethylsulfonyl fluoride (PMSF), diisopropyl fluorophosphate (DFP), bis(p-nitrophenyl)phosphate (BNPP), BW284C51 and ethopropazine. The liver microsomal activity was markedly inhibited by PMSF, DFP and BNPP, indicating that carboxylesterase was involved in the nafamostat hydrolysis. Human carboxylesterase 2 expressed in COS-1 cells was capable of hydrolyzing nafamostat at 10 and 100 microM, whereas recombinant carboxylesterase 1 showed significant activity only at a higher substrate concentration (100 microM). The nafamostat hydrolysis in 18 human liver microsomes correlated with aspirin hydrolytic activity specific for carboxylesterase 2 (r=0.815, p<0.01) but not with imidapril hydrolysis catalyzed by carboxylesterase 1 (r=0.156, p=0.54). These results suggest that human arylesterases and carboxylesterase 2 may be predominantly responsible for the metabolism of nafamostat in the blood and liver, respectively.
ESTHER : Yamaori_2006_Drug.Metab.Pharmacokinet_21_147
PubMedSearch : Yamaori_2006_Drug.Metab.Pharmacokinet_21_147
PubMedID: 16702735

Title : [Pathophysiology and treatment of vascular dementia] -
Author(s) : Udaka F , Oda M , Kameyama M
Ref : Nihon Ronen Igakkai Zasshi , 41 :1 , 2004
PubMedID: 14999902

Title : Vascular endothelial growth factor increases fenestral permeability in hepatic sinusoidal endothelial cells - Yokomori_2003_Liver.Int_23_467
Author(s) : Yokomori H , Oda M , Yoshimura K , Nagai T , Ogi M , Nomura M , Ishii H
Ref : Liver Int , 23 :467 , 2003
Abstract : Vascular endothelial growth factor (VEGF) is an important regulator of vasculogenesis and vascular permeability. Hepatic sinusoidal endothelial cells (SECs) possess sieve-like pores that form an anastomosing labyrinth structure by the deeply invaginated plasma membrane. Caveolin is the principal structural protein in caveolae. In this study, we examined the role of VEGF on the fenestration and permeability of SECs and the relation with caveolin-1. SECs isolated from rat livers by collagenase infusion method were cultured for 24 h with (10 or 100 ng/ml) or without VEGF. The cells were then examined by transmission and scanning electron microscopy (EM). The expression of caveolin was investigated by confocal immunofluorescence, immunogold EM, and Western blot. Endocytosis and intracellular traffic was studied using horseradish peroxidase (HRP) reaction as a marker of fluid phase transport in SECs. Both transmission and scanning EM showed an increased number of sinusoidal endothelial fenestrae (SEF) in SECs cultured with VEGF. By confocal immunofluorescence, SECs cultured with VEGF displayed prominent caveolin-l-positive aggregates in the cytoplasm, especially surrounding the nucleus region. Immunogold EM depicted increased caveolin-1 reactivity on vesicles and vacuoles of VEGF-treated SECs compared with VEGF-nontreated cells. However, there was no change in the level of caveolin-1 protein expression on Western blot. After HRP injection, an increase of electron-dense tracer filled the SEF in cells treated with VEGF. Our results suggested that VEGF induced fenestration in SECs, accompanied by an increased number of caveolae-like vesicles. Increased caveolin-1 might be associated with vesicle formation but not with fenestration. Increased fenestration may augment hepatic sinusoidal permeability and transendothelial transport.
ESTHER : Yokomori_2003_Liver.Int_23_467
PubMedSearch : Yokomori_2003_Liver.Int_23_467
PubMedID: 14986821