Yuichi Kobayashi

Tokyo Institute of Technology, Tokyo, Tokyo-to, Japan

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Publications (48)249.97 Total impact

  • Article: Inhibition of arabidopsis hypocotyl elongation by jasmonates is enhanced under red light in phytochrome B dependent manner.
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    ABSTRACT: Jasmonates are phytohormones derived from oxygenated fatty acids that regulate a broad range of plant defense and developmental processes. In Arabidopsis, hypocotyl elongation under various light conditions was suppressed by exogenously supplied methyl jasmonate (MeJA). Moreover, this suppression by MeJA was particularly effective under red light condition. Mutant analyses suggested that SCF(COI1)-mediated proteolysis was involved in this function. However, MeJA action still remained in the coi1 mutant, and (+)-7-iso-JA-L-Ile, a well-known active form of jasmonate, had a weaker effect than MeJA under the red light condition, suggesting that unknown signaling pathway are present in MeJA-mediated inhibition of hypocotyl elongation. EMS mutant screening identified two MeJA-insensitive hypocotyl elongation mutants, jasmonate resistance long hypocotyl 1 (jal1) and jal36, which had mutations in the phytochrome B (PHYB) gene. These analyses suggested that inhibition of hypocotyl elongation by jasmonates is enhanced under red light in phyB dependent manner.
    Journal of Plant Research 07/2012; · 1.75 Impact Factor
  • Article: Allylic substitution on cyclopentene and -hexene rings with alkynylcopper reagents.
    Qian Wang, Yuichi Kobayashi
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    ABSTRACT: Substitution of cyclic allylic picolinates with a reagent derived from TMS-C≡CMgBr and a copper salt was investigated. Although the previous type of reagent (TMSC≡CMgBr and CuBr·Me(2)S) developed for linear allylic picolinates was less product selective and regioselective, the Cu(acac)(2)-derived reagent was highly selective (94-95%) to afford the S(N)2' product in good yields. As an application, several C-C bond formations at the acetylenic carbon and the synthesis of the PG intermediate were studied with success.
    Organic Letters 11/2011; 13(23):6252-5. · 5.86 Impact Factor
  • Article: Synthesis of coronafacic acid via TBAF-assisted elimination of the mesylate and its conversion to the isoleucine conjugate.
    Yusuke Kosaki, Narihito Ogawa, Qian Wang, Yuichi Kobayashi
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    ABSTRACT: An aldol reaction followed by elimination of the derived mesylate was used to construct the side chain that was designed to afford the cyclohexene ring of coronafacic acid via intramolecular alkylation. Elimination of the mesylate proceeded with TBAF. The alkylation was achieved with t-BuOK in THF, and then hydrolysis afforded coronafacic acid, which upon condensation with unprotected L-isoleucine using ClCO(2)Bu(i) furnished coronafacoyl-L-isoleucine, the L-Ile conjugate.
    Organic Letters 08/2011; 13(16):4232-5. · 5.86 Impact Factor
  • Article: High-performance affinity purification for identification of 15-deoxy-Δ 12,14 -PGJ₂ interacting factors using magnetic nanobeads.
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    ABSTRACT: Prostaglandin J₂ (PGJ₂) family have been reported to show various kinds of biological activities. Considerable progress has been made toward understanding the mechanism of adipogenesis, however, the mechanisms of other actions of PGJ₂ family remain controversial. The 15-deoxy-Δ(12,14) -PGJ₂ (15d-PGJ₂) is one of the members of PGJ₂ family, and is known as a ligand for peroxisome proliferator-activated receptor γ (PPARγ), which promotes the expression of the crucial genes for adipogenesis. In this study, we found that 15d-PGJ₂ did not stimulate PPARγ-mediated gene expression in HEK293 cells whereas 15d-PGJ₂ transactivated PPARγ-dependent transcription in other cell lines. Moreover, we confirmed that 15d-PGJ₂ suppressed the growth of HEK293 cells. These observations suggest that 15d-PGJ₂ shows another biological activity e.g. growth inhibition in HEK293 cells via unknown receptor for 15d-PGJ₂. The aim of this study is to develop and validate effective purification system for PGJ₂ interacting factors (PGJIFs). We have recently developed high performance magnetic nanobeads. In this study, we have newly developed 15d-PGJ₂-immobilized beads by conjugating 15d-PGJ₂ to the surface of these nanobeads. Firstly, we showed that PPARγ specifically bound to 15d-PGJ₂-immobilized beads. Secondly, we newly identified voltage dependent anionic channel 1 (VDAC1) as new PGJIF from crude extracts of HEK293 cells using this affinity purification system. These data presented here demonstrate that 15d-PGJ₂-immobilized beads are effective tool for purification of PGJIFs directly from crude cell extracts.
    Biomedical Chromatography 04/2011; 25(4):466-71. · 1.97 Impact Factor
  • Article: Stereoselective synthesis of epi-jasmonic acid, tuberonic acid, and 12-oxo-PDA.
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    ABSTRACT: epi-Jasmonic acid (epi-JA) and tuberonic acid (TA) were synthesized from the key aldehyde, all cis-2-(2-hydroxy-5-vinylcyclopentyl)acetaldehyde (14), which was in turn prepared stereoselectively from the (1R)-acetate of 4-cyclopentene-1,3-diol (10) through S(N)2-type allylic substitution with CH(2)[double bond, length as m-dash]CHMgBr followed by Mitsunobu inversion, Eschenmoser-Claisen rearrangement, and regioselective Swern oxidation of the corresponding bis-TES ether (13). Wittig reaction of the aldehyde 14 with [Ph(3)P(CH(2))Me](+)Br(-) followed by oxidation afforded epi-JA (3) stereoselectivity over the trans isomer. Similarly, TA (5) was synthesized. Furthermore, the above findings were applied successfully to improve the total efficiency of the previous synthesis of 12-oxo-PDA (1).
    Organic & Biomolecular Chemistry 11/2010; 8(22):5212-23. · 3.70 Impact Factor
  • Article: Jasmonate perception by inositol-phosphate-potentiated COI1-JAZ co-receptor.
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    ABSTRACT: Jasmonates are a family of plant hormones that regulate plant growth, development and responses to stress. The F-box protein CORONATINE INSENSITIVE 1 (COI1) mediates jasmonate signalling by promoting hormone-dependent ubiquitylation and degradation of transcriptional repressor JAZ proteins. Despite its importance, the mechanism of jasmonate perception remains unclear. Here we present structural and pharmacological data to show that the true Arabidopsis jasmonate receptor is a complex of both COI1 and JAZ. COI1 contains an open pocket that recognizes the bioactive hormone (3R,7S)-jasmonoyl-l-isoleucine (JA-Ile) with high specificity. High-affinity hormone binding requires a bipartite JAZ degron sequence consisting of a conserved α-helix for COI1 docking and a loop region to trap the hormone in its binding pocket. In addition, we identify a third critical component of the jasmonate co-receptor complex, inositol pentakisphosphate, which interacts with both COI1 and JAZ adjacent to the ligand. Our results unravel the mechanism of jasmonate perception and highlight the ability of F-box proteins to evolve as multi-component signalling hubs.
    Nature 10/2010; 468(7322):400-5. · 36.28 Impact Factor
  • Article: Construction of a quaternary carbon at the carbonyl carbon of the cyclohexane ring.
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    ABSTRACT: High S(N)2' selectivity in the allylic substitution of cyclohexylidene ethyl picolinates with copper reagents prepared from RMgBr and CuBr.Me(2)S was realized by addition of ZnX(2) (X = I, Br, Cl). Furthermore, ZnX(2) accelerated the reaction with the bulky iPr reagent.
    Chemical Communications 08/2010; 46(30):5482-4. · 6.17 Impact Factor
  • Article: Alternative splicing expands the repertoire of dominant JAZ repressors of jasmonate signaling.
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    ABSTRACT: Jasmonates (JAs) are fatty acid-derived signaling compounds that control diverse aspects of plant growth, development and immunity. The F-box protein COI1 functions both as a receptor for jasmonoyl-l-isoleucine (JA-Ile) and as the component of an E3-ubiquitin ligase complex (SCF(COI1) ) that targets JAZ transcriptional regulators for degradation. A key feature of JAZ proteins is the C-terminal Jas motif that mediates the JA-Ile-dependent interaction with COI1. Here, we show that most JAZ genes from evolutionarily diverse plants contain a conserved intron that splits the Jas motif into 20 N-terminal and seven C-terminal (X(5) PY) amino acid submotifs. In most members of the Arabidopsis JAZ family, alternative splicing events involving retention of this intron generate proteins that are truncated before the X(5) PY sequence. In vitro pull-down and yeast two-hybrid assays indicate that these splice variants have reduced capacity to form stable complexes with COI1 in the presence of the bioactive stereoisomer of the hormone (3R,7S)-JA-Ile. cDNA overexpression studies showed that some, but not all, truncated splice variants are dominant repressors of JA signaling. We also show that strong constitutive expression of an intron-containing JAZ10 genomic clone is sufficient to repress JA responses. These findings provide evidence for functional differences between JAZ isoforms, and establish a direct link between the alternative splicing of JAZ pre-mRNA and the dominant repression of JA signal output. We propose that production of dominant JAZ repressors by alternative splicing reduces the negative consequences associated with inappropriate or hyperactivation of the JA response pathway.
    The Plant Journal 08/2010; 63(4):613-22. · 6.16 Impact Factor
  • Article: High‐performance affinity purification for identification of 15‐deoxy‐Δ12,14‐PGJ2 interacting factors using magnetic nanobeads
    [show abstract] [hide abstract]
    ABSTRACT: Prostaglandin J2 (PGJ2) family have been reported to show various kinds of biological activities. Considerable progress has been made toward understanding the mechanism of adipogenesis, however, the mechanisms of other actions of PGJ2 family remain controversial. The 15-deoxy-Δ12,14-PGJ2 (15d-PGJ2) is one of the members of PGJ2 family, and is known as a ligand for peroxisome proliferator-activated receptor γ (PPARγ), which promotes the expression of the crucial genes for adipogenesis. In this study, we found that 15d-PGJ2 did not stimulate PPARγ-mediated gene expression in HEK293 cells whereas 15d-PGJ2 transactivated PPARγ-dependent transcription in other cell lines. Moreover, we confirmed that 15d-PGJ2 suppressed the growth of HEK293 cells. These observations suggest that 15d-PGJ2 shows another biological activity e.g. growth inhibition in HEK293 cells via unknown receptor for 15d-PGJ2.The aim of this study is to develop and validate effective purification system for PGJ2 interacting factors (PGJIFs). We have recently developed high performance magnetic nanobeads. In this study, we have newly developed 15d-PGJ2-immobilized beads by conjugating 15d-PGJ2 to the surface of these nanobeads. Firstly, we showed that PPARγ specifically bound to 15d-PGJ2-immobilized beads. Secondly, we newly identified voltage dependent anionic channel 1 (VDAC1) as new PGJIF from crude extracts of HEK293 cells using this affinity purification system. These data presented here demonstrate that 15d-PGJ2-immobilized beads are effective tool for purification of PGJIFs directly from crude cell extracts. Copyright © 2010 John Wiley & Sons, Ltd.
    Biomedical Chromatography 06/2010; 25(4):466 - 471. · 1.97 Impact Factor
  • Article: Formation of chiral C(sp3)-C(sp) bond by allylic substitution of secondary allylic picolinates and alkynyl copper reagents.
    Yohei Kiyotsuka, Yuichi Kobayashi
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    ABSTRACT: To establish allylic substitution of secondary allylic alcohol derivatives with alkynyl copper reagents, allylic esters bearing the (2-pyridine)CO2-, (2-pyrazine)CO2-, (EtO)2PO2-, C6F5CO2-, o-(Ph2P)C6H4CO2-, MeOCO2-, or AcO- group were examined. First, picolinate (R1 = Me, R2 = CH2OPMB) was subjected to reaction with (TMS-C[triple bond]C)2CuLi.LiBr at 0degreesC. Although no substitution took place, MgBr2 (3 equiv) was found to promote the reaction to produce the anti SN2' product in 93% yield with 94% regioselectivity and 99% chirality transfer. In contrast, substitution of the other esters with the copper reagent in the presence of MgBr2 were less reactive ((2-pyrazine)CO2-) or marginally reactive (other cases). Generality of the substitution using picolinates was established with five picolinates (R1 = Me, Ph(CH2)2, PMBO(CH2)3; R2 = Me, CH2OPMB, CH2OTBS, C5H11, c-C6H11) and seven alkynyl copper reagents (R3 = TMS, Ph, p-TBSOC6H4, p- and o-MeOC6H4, p-MeC6H4, p-FC6H4), furnishing anti SN2' products in 61-93% yields with high regioselectivity (usually >90%) and high chirality transfer (usually >95%). In addition, transformation of the products was briefly studied.
    The Journal of Organic Chemistry 10/2009; 74(19):7489-95. · 4.45 Impact Factor
  • Article: Synthesis of (S)-imperanene by using allylic substitution.
    Yuji Takashima, Yuichi Kobayashi
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    ABSTRACT: Synthesis of (S)-imperanene (1) was studied by using copper-assisted allylic substitution of ArCH=CHCH(L)CH(2)Ar (L: leaving group) and (i-PrO)Me(2)SiCH(2)MgCl. Preliminary substitution between PhCH=CHCH(L)Me (L = AcO, PivO, MeOCO(2), (2-Py)CO(2)) and Bu copper reagents derived from BuMgX (X = Br, Cl) and CuBr.Me(2)S or CuCl in 1:1-40:1 ratios suggested acetate 28 as the best substrate. To prepare 28, kinetic resolution of racemic (E)-TMSCH=CHCH(OH)CH(2)Ar(2) (Ar(2) = (p-TBSO)(m-MeO)C(6)H(3)) carried out by using the asymmetric epoxidation with (-)-DIPT afforded the corresponding epoxy alcohol and (S)-allylic alcohol. After separation by chromatography, these products were converted to (S,E)-Bu(3)SnCH=CHCH(OH)CH(2)Ar(2), which upon palladium-catalyzed coupling with Ar(2)-I followed by acetylation gave 28 (95-98% ee). Substitution of 28 with (i-PrO)Me(2)SiCH(2)MgCl and CuBr.Me(2)S in a 4:1 ratio at 0 degrees C proceeded cleanly to produce 29 with 100% inversion in 92% yield. Finally, Tamao oxidation furnished 1.
    The Journal of Organic Chemistry 08/2009; 74(16):5920-6. · 4.45 Impact Factor
  • Article: Synthesis of the active form of loxoprofen by using allylic substitutions in two steps.
    Tomonori Hyodo, Yohei Kiyotsuka, Yuichi Kobayashi
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    ABSTRACT: High regioselectivity for allylic substitution of the cyclopentenyl picolinate 5 with benzylcopper reagent was attained with ZnBr(2), and the finding was applied to the p-BrC(6)H(4)CH(2) reagent. The cyclopentene moiety in the product was reduced to the cyclopentane, and the p-BrC(6)H(4) was converted to the "Cu"C(6)H(4) for the second allylic substitution with picolinate 8 to furnish the title compound after oxidative cleavage of the resulting olefin moiety.
    Organic Letters 03/2009; 11(5):1103-6. · 5.86 Impact Factor
  • Article: New general method for regio- and stereoselective allylic substitution with aryl and alkenyl coppers derived from Grignard reagents.
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    ABSTRACT: Allylic substitution with sp(2)-carbon reagents (aryl and alkenyl anions) was realized by using allylic picolinates and copper reagents derived from RMgBr and CuBr x Me(2)S to afford anti S(N)2' products regio- and stereoselectively. Steric and electronic factors in the reagents and the size of the methylene substituents around the allylic moiety marginally affected the selectivity. The reaction system was compatible with alkyl reagents as well. Furthermore, the substitution was applied to construction of a quaternary center and synthesis of (-)-sesquichamaenol. Electron-withdrawing nature of the pyridyl group and chelation of the C(=O)-C(5)H(4)N to MgBr(2) generated in situ were found to be responsible for the high efficiency of the substitution.
    The Journal of Organic Chemistry 03/2009; 74(5):1939-51. · 4.45 Impact Factor
  • Article: Picolinoxy group, a new leaving group for anti SN2' selective allylic substitution with aryl anions based on Grignard reagents.
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    ABSTRACT: The picolinoxy group was found to be an extremely powerful leaving group for allylic substitution with aryl nucleophiles derived from ArMgBr and CuBr*Me2S. The substitution proceeds with anti SN2' pathway and with high chirality transfer. The electron-withdrawing effect of the pyridyl group and chelation to MgBr2 are likely the origin of success. Results suggesting these effects were obtained.
    Organic Letters 06/2008; 10(9):1719-22. · 5.86 Impact Factor
  • Article: Realization of anti-SN2' selective allylation of 4-cyclopentene-1,3-diol monoester with aryl- and alkenyl-zinc reagents.
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    ABSTRACT: Anti-SN2' mode of allylation of the monoester of 4-cyclopentene-1,3-diol with aryl and alkenyl anions was achieved, for the first time, with the MeOCH2CO2- group as a leaving group to which R-ZnBr and CuCl (as a catalyst) were best fitted. The aryl groups successfully installed were Ph, o- and p-MeC6H4, o-MOMOC6H4, o-MeOC6H4, and p-F-C6H4, while cis and trans alkenyl groups were attached with retention of the olefinic stereochemistries.
    Organic Letters 05/2008; 10(7):1345-8. · 5.86 Impact Factor
  • Article: Mercury-free preparation and selective reactions of propargyl (and propargylic) Grignard reagents.
    Hukum P Acharya, Kei Miyoshi, Yuichi Kobayashi
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    ABSTRACT: ZnBr2 was found to catalyze formation of propargyl and propargylic Grignard reagents, and thus put an end to the standard method using a mercury catalyst. The Grignard reagents were submitted to addition reaction with carbonyl compounds and allylation with the cyclic monoacetate to afford the propargyl-type products selectively. Furthermore, the product from the monoacetate was transformed to an acetylene analogue of 2-(5,6-epoxyisoprostane A2)phosphorylcholines.
    Organic Letters 09/2007; 9(18):3535-8. · 5.86 Impact Factor
  • Article: Nickel-catalyzed coupling producing (2Z)-2,4-alkadien-1-ols, conversion to (E)-3-alkene-1,2,5-triol derivatives, and synthesis of decarestrictine D.
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    ABSTRACT: The 3-alkene-1,2,5-triol structure is not only a major framework of biologically important molecules but also a new functional-group-rich unit for synthesis of polyols and sugars. A method furnishing such triol derivatives 8 was developed and successfully applied to synthesis of decarestrictine D (18). First, coupling reaction of the unprotected alcohols 2 with borates 4 was investigated to produce the dienyl alcohols 6 with NiCl2(dppf) in Et2O/THF (5:1) at room temperature. The hydroxyl-group-directed epoxidation of 6 followed by palladium-catalyzed reaction with AcOH (Scheme 1) furnished 3-alkene-1,2,5-triol derivatives 8. Since each step proceeded with high stereo- and regioselectivities, the stereochemistry of 8 has been correlated with the olefin geometry of 6. With the above transformation in mind, synthesis of the full carbon skeleton of decarestrictine D (18) could be designed easily and was completed successfully. Furthermore, a new seco acid 19b with the MOM protective group for the three hydroxyl groups was found to afford macrolide 48 in a yield higher than those reported previously.
    The Journal of Organic Chemistry 04/2007; 72(5):1707-16. · 4.45 Impact Factor
  • Article: Identification of a peroxisomal acyl-activating enzyme involved in the biosynthesis of jasmonic acid in Arabidopsis.
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    ABSTRACT: Jasmonic acid (JA) is a lipid-derived signal that regulates a wide variety of developmental and defense-related processes in higher plants. JA is synthesized from linolenic acid via an enzymatic pathway that initiates in the plastid and terminates in peroxisomes. The C18 JA precursor 12-oxo-phytodienoic acid (OPDA) is converted in the peroxisome to 3-oxo-2-(2'-[Z]-pentenyl)cyclopentane-1-octanoic acid (OPC-8:0), which subsequently undergoes three rounds of beta-oxidation to yield JA. Although most JA biosynthetic enzymes have been identified, several key steps in the pathway remain to be elucidated. To address this knowledge gap, we employed co-expression analysis to identify genes that are coordinately regulated with known JA biosynthetic components in Arabidopsis. Among the candidate genes uncovered by this approach was a 4-coumarate-CoA ligase-like member of the acyl-activating enzyme (AAE) gene family, which we have named OPC-8:0 CoA Ligase1 (OPCL1). In response to wounding, opcl1 null mutants exhibited reduced levels of JA and hyperaccumulation of OPC-8:0. Recombinant OPCL1 was active against both OPDA and OPC-8:0, as well as medium-to-long straight-chain fatty acids. Subcellular localization studies with green fluorescent protein-tagged OPCL1 showed that the protein is targeted to peroxisomes. These findings establish a physiological role for OPCL1 in the activation of JA biosynthetic precursors in leaf peroxisomes, and further indicate that OPC-8:0 is a physiological substrate for the activation step. The results also demonstrate the utility of co-expression analysis for identification of factors that contribute to jasmonate homeostasis.
    Journal of Biological Chemistry 12/2006; 281(44):33511-20. · 4.77 Impact Factor
  • Article: Synthesis of cannabidiols via alkenylation of cyclohexenyl monoacetate.
    Yuichi Kobayashi, Akira Takeuchi, Yong-Gang Wang
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    ABSTRACT: [reaction: see text] Because of the lack of potency binding to the receptors responsible for psychoactivity, cannabidiol has received much attention as a lead compound to develop a nonpsychotropic drug. Herein, we establish a method to access not only cannabidiol but also its analogues. The key reaction is nickel-catalyzed allylation of 2-cyclohexene-1,4-diol monoacetate with a new reagent, (alkenyl)ZnCl/TMEDA, which gives a S(N)2-type product with 94% regioselectivity in good yield.
    Organic Letters 07/2006; 8(13):2699-702. · 5.86 Impact Factor
  • Article: Total synthesis of phoslactomycin B and its biosynthetic deamino precursor.
    Yong-Gang Wang, Ryuichi Takeyama, Yuichi Kobayashi
    Angewandte Chemie International Edition 06/2006; 45(20):3320-3. · 13.45 Impact Factor