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김창선,유승헌,Akira Nakagiri,Takashi Shirouzu,Kozue Sotome,김선철,Nitaro Maekawa 한국식물병리학회 2012 Plant Pathology Journal Vol.28 No.4
Shiitake (Lentinula edodes) is the most economically important cultivated mushroom, but yields are impacted by its competitor, Trichoderma spp. We previously found two unidentified Trichoderma species growing in bedlogs and sawdust shiitake media in Korea. Here, we identify and re-describe those two species based on molecular sequence data, morphology, and culture characteristics. Well-supported clades based on phylogenetic analyses of internal transcribed spacer, translation elongation factor 1-α, and RNA polymerase subunit II sequences grouped one of the unidentified Trichoderma spp. with Hypocrea pseudogelatinosa and the other with Hypocrea pseudostraminea, and their morphologies matched well with the original descriptions of the two Hypocrea species. This study reports the first phylogenetic analyses of H. pseudogelatinosa and Japanese strains of H. pseudostraminea. Based on the phylogenetic results, we redescribed these two species using modern taxonomic concepts in Hypocrea/Trichoderma.
Kim, Chang Sun,Yu, Seung Hun,Nakagiri, Akira,Shirouzu, Takashi,Sotome, Kozue,Kim, Seon Cheol,Maekawa, Nitaro The Korean Society of Plant Pathology 2012 Plant Pathology Journal Vol.28 No.4
Shiitake (Lentinula edodes) is the most economically important cultivated mushroom, but yields are impacted by its competitor, Trichoderma spp. We previously found two unidentified Trichoderma species growing in bedlogs and sawdust shiitake media in Korea. Here, we identify and re-describe those two species based on molecular sequence data, morphology, and culture characteristics. Well-supported clades based on phylogenetic analyses of internal transcribed spacer, translation elongation factor 1-${\alpha}$, and RNA polymerase subunit II sequences grouped one of the unidentified Trichoderma spp. with Hypocrea pseudogelatinosa and the other with Hypocrea pseudostraminea, and their morphologies matched well with the original descriptions of the two Hypocrea species. This study reports the first phylogenetic analyses of H. pseudogelatinosa and Japanese strains of H. pseudostraminea. Based on the phylogenetic results, we redescribed these two species using modern taxonomic concepts in Hypocrea/Trichoderma.
Kikukawa, Takashi,Shimono, Kazumi,Tamogami, Jun,Miyauchi, Seiji,Kim, So Young,Kimura-Someya, Tomomi,Shirouzu, Mikako,Jung, Kwang-Hwan,Yokoyama, Shigeyuki,Kamo, Naoki American ChemicalSociety 2011 Biochemistry Vol.50 No.41
<P><I>Acetabularia</I> rhodopsins are the firstmicrobialrhodopsins discovered in a marine plant organism, <I>Acetabulariaacetabulum</I>. Previously, we expressed <I>Acetabularia</I> rhodopsin II (ARII) by a cell-free system from one of two opsingenes in <I>A. acetabulum</I> cDNA and showed that ARIIis a light-driven proton pump [Wada, T., et al. (2011) <I>J.Mol. Biol.</I><I>411</I>, 986–998]. In thisstudy, the photochemistry of ARII was examined using the flash-photolysistechnique, and data were analyzed using a sequential irreversiblemodel. Five photochemically defined intermediates (P<SUB><I>i</I></SUB>) were sufficient to simulate the data. Noticeably, both P<SUB>3</SUB> and P<SUB>4</SUB> contain an equilibrium mixture of M, N,and O. Using a transparent indium tin oxide electrode, the photoinducedproton transfer was measured over a wide pH range. Analysis of thepH-dependent proton transfer allowed estimation of the p<I>K</I><SUB>a</SUB> values of some amino acid residues. The estimated valueswere 2.6, 5.9 (or 6.3), 8.4, 9.3, 10.5, and 11.3. These values wereassigned as the p<I>K</I><SUB>a</SUB> of Asp81 (Asp85<SUP>BR</SUP>) in the dark, Asp92 (Asp96<SUP>BR</SUP>) at N, Glu199 (Glu204<SUP>BR</SUP>) at M, Glu199 in the dark, an undetermined proton-releasingresidue at the release, and the pH to start denaturation, respectively.Following this analysis, the proton transfer of ARII is discussed.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/2011/bichaw.2011.50.issue-41/bi2009932/production/images/medium/bi-2011-009932_0006.gif'></P>
Bin, Bum-Ho,Hojyo, Shintaro,Hosaka, Toshiaki,Bhin, Jinhyuk,Kano, Hiroki,Miyai, Tomohiro,Ikeda, Mariko,Kimura-Someya, Tomomi,Shirouzu, Mikako,Cho, Eun-Gyung,Fukue, Kazuhisa,Kambe, Taiho,Ohashi, Wakana BlackWell Publishing Ltd 2014 EMBO molecular medicine Vol.6 No.8
<P>The zinc transporter protein ZIP13 plays critical roles in bone, tooth, and connective tissue development, and its dysfunction is responsible for the spondylocheirodysplastic form of Ehlers-Danlos syndrome (SCD-EDS, OMIM 612350). Here, we report the molecular pathogenic mechanism of SCD-EDS caused by two different mutant ZIP13 proteins found in human patients: ZIP13<SUP>G64D</SUP>, in which Gly at amino acid position 64 is replaced by Asp, and ZIP13<SUP>ΔFLA</SUP>, which contains a deletion of Phe-Leu-Ala. We demonstrated that both the ZIP13<SUP>G64D</SUP> and ZIP13<SUP>ΔFLA</SUP> protein levels are decreased by degradation via the valosin-containing protein (VCP)-linked ubiquitin proteasome pathway. The inhibition of degradation pathways rescued the protein expression levels, resulting in improved intracellular Zn homeostasis. Our findings uncover the pathogenic mechanisms elicited by mutant ZIP13 proteins. Further elucidation of these degradation processes may lead to novel therapeutic targets for SCD-EDS.</P>
High-resolution crystal structure of the catalytic domain of human dual-specificity phosphatase 26.
Won, Eun Young,Xie, Yong,Takemoto, Chie,Chen, Lirong,Liu, Zhi Jie,Wang, Bi Cheng,Lee, Daeyoup,Woo, Eui Jeon,Park, Sung Goo,Shirouzu, Mikako,Yokoyama, Shigeyuki,Kim, Seung Jun,Chi, Seung Wook Wiley-Blackwell 2013 Acta crystallographica. Section D, Biological crys Vol.69 No.6
<P>Dual-specificity phosphatases (DUSPs) play an important role in regulating cellular signalling pathways governing cell growth, differentiation and apoptosis. Human DUSP26 inhibits the apoptosis of cancer cells by dephosphorylating substrates such as p38 and p53. High-resolution crystal structures of the DUSP26 catalytic domain (DUSP26-C) and its C152S mutant [DUSP26-C (C152S)] have been determined at 1.67 and 2.20 ? resolution, respectively. The structure of DUSP26-C showed a novel type of domain-swapped dimer formed by extensive crossover of the C-terminal α7 helix. Taken together with the results of a phosphatase-activity assay, structural comparison with other DUSPs revealed that DUSP26-C adopts a catalytically inactive conformation of the protein tyrosine phosphate-binding loop which significantly deviates from that of canonical DUSP structures. In particular, a noticeable difference exists between DUSP26-C and the active forms of other DUSPs at the hinge region of a swapped C-terminal domain. Additionally, two significant gaps were identified between the catalytic core and its surrounding loops in DUSP26-C, which can be exploited as additional binding sites for allosteric enzyme regulation. The high-resolution structure of DUSP26-C may thus provide structural insights into the rational design of DUSP26-targeted anticancer drugs.</P>