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  • 51. Henriksson, Marielle
    et al.
    Berglund, Lars A.
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Bulone, Vincent
    KTH, School of Biotechnology (BIO), Glycoscience.
    Zhou, Qi
    KTH, School of Biotechnology (BIO), Glycoscience.
    Method of producing and the use of microfibrillated paper2009Patent (Other (popular science, discussion, etc.))
    Abstract [en]

    The present invention relates to a method of producing a cellulose based paper, the paper itself and the use thereof where the paper exhibits enhanced mechanical properties. The method involves providing a suspension of well dispersed modified cellulose at a low concentration. The properties and the chemical structure of the paper make it suitable for in vivo applications such as implant material.

  • 52.
    Henriksson, Marielle
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology, Biocomposites.
    Berglund, Lars
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology, Biocomposites.
    Bulone, Vincent
    KTH, School of Biotechnology (BIO), Glycoscience.
    Zhou, Qi
    KTH, School of Biotechnology (BIO), Glycoscience.
    Producing paper, useful as e.g. filter paper, speaker membrane and suture, comprises providing modified nanofibrils of cellulose, providing suspension of modified nanofibrils, and filtering, dewatering and drying the nanofibrils2009Patent (Other (popular science, discussion, etc.))
    Abstract [en]

    The present invention relates to a method of producing a cellulose based paper, the paper itself and the use thereof where the paper exhibits enhanced mechanical properties. The method involves providing a suspension of well dispersed modified cellulose at a low concentration. The properties and the chemical structure of the paper make it suitable for in vivo applications such as implant material.

  • 53. Him, J. L. K.
    et al.
    Chanzy, H.
    Pelosi, L.
    Putaux, J. L.
    Bulone, Vincent
    KTH, Superseded Departments, Biotechnology.
    Recent developments in the field of in vitro biosynthesis of plant beta-glucans2003In: American Chemical Society Symposium Series (ACS), ISSN 0097-6156, E-ISSN 1947-5918, Vol. 840, p. 65-77Article, review/survey (Refereed)
    Abstract [en]

    This chapter reports the use of various detergents for the preparation of vesicles and micelles from plant plasma membranes bearing beta-glucan synthases. The effects of these detergents and other parameters on the in vitro activity of cellulose and (1-->3)-beta-glucan synthases are described. Morphological and structural aspects of the vesicles and micelles; are presented together with the characterization of the products synthesized in vitro by the detergent-extracted beta-glucan synthases. The possible involvement of porins for extrusion of cell wall glucans through plasma membranes as well as future developments for the study of in vitro biosynthesis of these polysaccharides are discussed in relation to these results.

  • 54. Him, J. L. K.
    et al.
    Pelosi, L.
    Chanzy, H.
    Putaux, J. L.
    Bulone, Vincent
    KTH, Superseded Departments, Biotechnology.
    Biosynthesis of (1 -> 3)-beta-D-glucan (callose) by detergent extracts of a microsomal fraction from Arabidopsis thaliana2001In: European Journal of Biochemistry, ISSN 0014-2956, E-ISSN 1432-1033, Vol. 268, no 17, p. 4628-4638Article in journal (Refereed)
    Abstract [en]

    The aim of this work was to develop a biochemical approach to study (1-->3)-beta -D-glucan (callose) biosynthesis using suspension cultures of Arabidopsis thaliana. Optimal conditions for in vitro synthesis of callose corresponded to an assay mixture containing 50 mM Mops buffer, pH6.8, 1 mM UDP-glucose, 8 mM Ca2+ and 20 mM cellobiose. The enzyme was Ca2+-dependent, and addition of Mg2+ to the reaction mixture did not favour cellulose biosynthesis. Enzyme kinetics suggested the existence of positive. homotropic cooperativity of (1-->3)-beta -D-glucan synthase for the substrate UDP-glucose, in agreement with the hypothesis that callose synthase consists of a multimeric complex containing several catalytic subunits. Detergents belonging to different families were tested for their ability to extract and preserve membrane-bound (1-->3)-beta -D-glucan synthase activity. Cryo-transmission electron microscopy experiments showed that n-octyl-beta -D-glucopyranoside allowed the production of micelle-like structures, whereas vesicles were obtained with Chaps and Zwittergent 3-12. The morphology and size of the (1-->3)-beta -D-glucans synthesized in vitro by fractions obtained with different detergents were affected by the nature of the detergent tested. These data suggest that the general organization of the glucan synthase complexes and the properties of them in vitro products are influenced by the detergent used for protein extraction. The reaction products synthesized by different detergent extracts were characterized by infrared spectroscopy, methylation analysis, C-13-N-MR spectroscopy, electron microscopy and X-ray diffraction. These products were identified as linear (1-->3)-beta -D-glucans having a degree of polymerization higher than 100, a microfibrillar structure, and a low degree of crystallinity.

  • 55.
    Horikawa, Yoshiki
    et al.
    Kyoto Univ, Res Inst Sustainable Humanosphere, Kyoto 6110011, Japan..
    Ito, Chiori
    Kyoto Univ, Res Inst Sustainable Humanosphere, Kyoto 6110011, Japan..
    Imai, Tomoya
    Kyoto Univ, Res Inst Sustainable Humanosphere, Kyoto 6110011, Japan..
    Bulone, Vincent
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience.
    Sugiyama, Junji
    Kyoto Univ, Res Inst Sustainable Humanosphere, Kyoto 6110011, Japan..
    In vitro beta-glucan synthesis of plant cells.2009In: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 237Article in journal (Other academic)
  • 56. Hrmova, M.
    et al.
    Imai, T.
    Rutten, S. J.
    Fairweather, J. K.
    Pelosi, L.
    Bulone, Vincent
    KTH, Superseded Departments, Biotechnology.
    Driguez, H.
    Fincher, G. B.
    Mutated barley (1,3)-beta-D-glucan endohydrolases synthesize crystalline (1,3)-beta-D-glucans2002In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 277, no 33, p. 30102-30111Article in journal (Refereed)
    Abstract [en]

    Barley (1,3)-beta-D-glucan endohydrolases (EC 3.2.1.39), inactivated by site-directed mutagenesis of their catalytic nucleophiles, show autocondensation glucosynthetic activity with alpha-laminaribiosyl fluoride and heterocondensation glycosynthetic activity with a-laminaribiosyl fluoride and 4'-nitrophenyl beta-D-glucopyranoside. The native enzyme is a retaining endohydrolase of the family 17 group and catalyzes glycosyl transfer reactions at high substrate concentrations. Catalytic efficiencies (k(cat) K-m(-1)) of mutants E231G, E231S, and E231A as glycosynthases are 28.9, 0.9, and 0.5 x 10(-4) M-1 s(-1), respectively. Glycosynthase reactions appear to be processive and proceed with pH optima of 6-8 and yields of up to 75%. Insoluble products formed during the glycosynthase reaction appear as lamellar, hexagonal crystals when observed by electron microscopy. Methylation, NMR, and matrix-assisted laser desorption ionization time-of-flight analyses show that the reaction products are linear (1,3)-beta-D-glucans with a degree of polymerization of 30-34, whereas electron and x-ray diffraction patterns indicate that these (1,3)-beta-D-glucan chains adopt a parallel, triple helical conformation. The (1,3)-beta-D-glucan triple helices are orientated perpendicularly to the plane of the lamellar crystals. The barley (1,3)-beta-D-glucan glycosynthases have considerable potential for tailored and high efficiency synthesis of (1,3)-beta-D-linked oligo- and polysaccharides, some of which could have immunomodulating activity, or for the coupling of (1,3)-beta-D-linked glucosyl residues onto other oligosaccharides or glycoproteins.

  • 57.
    Hsieh, Yves S. Y.
    et al.
    KTH, School of Biotechnology (BIO), Glycoscience. Univ Adelaide, Australia.
    Zhang, Qisen
    Yap, Kuok
    Shirley, Neil J.
    Lahnstein, Jelle
    Nelson, Clark J.
    Burton, Rachel A.
    Millar, A. Harvey
    Bulone, Vincent
    KTH, School of Biotechnology (BIO), Glycoscience. Univ Adelaide, Australia.
    Fincher, Geoffrey B.
    Genetics, Transcriptional Profiles, and Catalytic Properties of the UDP-Arabinose Mutase Family from Barley2016In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 55, no 2, p. 322-334Article in journal (Refereed)
    Abstract [en]

    Four members of the UDP-Ara mutase (UAM) gene family from barley have been isolated and characterized, and their map positions on chromosomes 2H, 3H, and 4H have been defined. When the genes are expressed in Escherichia coli, the corresponding HvUAM1, HvUAM2, and HvUAM3 proteins exhibit UAM activity, and the kinetic properties of the enzymes have been determined, including K-m, K-cat, and catalytic efficiencies. However, the expressed HvUAM4 protein shows no mutase activity against UDP-Ara or against a broad range of other nucleotide sugars and related molecules. The enzymic data indicate therefore that the HvUAM4 protein may not be a mutase. However, the HvUAM4 gene is transcribed at high levels in all the barley tissues examined, and its transcript abundance is correlated with transcript levels for other genes involved in cell wall biosynthesis. The UDP-L-Arap -> UDP-L-Araf reaction, which is essential for the generation of the UDP-Araf substrate for arabinoxylan, arabinogalactan protein, and pectic polysaccharide biosynthesis, is thermodynamically unfavorable and has an equilibrium constant of 0.02. Nevertheless, the incorporation of Araf residues into nascent polysaccharides clearly occurs at biologically appropriate rates. The characterization of the HvUAM genes opens the way for the manipulation of both the amounts and fine structures of heteroxylans in cereals, grasses, and other crop plants, with a view toward enhancing their value in human health and nutrition, and in renewable biofuel production.

  • 58.
    Iversen, Tommy
    et al.
    STFI Packforsk, SE-11486 Stockholm, Sweden..
    Larsson, Per Tomas
    STFI Packforsk, SE-11486 Stockholm, Sweden..
    Wickholm, Kristina
    STFI Packforsk, SE-11486 Stockholm, Sweden..
    Bulone, Vincent
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience.
    CELL 157-Surface structure of native cellulose fibrils2008In: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 235Article in journal (Other academic)
  • 59. Jaeger, Diana
    et al.
    Ndi, Chi P.
    Crocoll, Christoph
    Simpson, Bradley S.
    Khakimov, Bekzod
    Guzman-Genuino, Ruth Marian
    Hayball, John D.
    Xing, Xiaohui
    KTH, School of Biotechnology (BIO), Glycoscience. School of Biotechnology, AlbaNova University Centre, Stockholm, SE-10691, Sweden; ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, 5064, Australia.
    Bulone, Vincent
    KTH, School of Biotechnology (BIO), Glycoscience. School of Biotechnology, AlbaNova University Centre, Stockholm, SE-10691, Sweden; ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, 5064, Australia.
    Weinstein, Philip
    Moller, Birger L.
    Semple, Susan J.
    Isolation and Structural Characterization of Echinocystic Acid Triterpenoid Saponins from the Australian Medicinal and Food Plant Acacia ligulata2017In: Journal of natural products (Print), ISSN 0163-3864, E-ISSN 1520-6025, Vol. 80, no 10, p. 2692-2698Article in journal (Refereed)
    Abstract [en]

    The Australian plant Acacia ligulata has a number of traditional food and medicinal uses by Australian Aboriginal people, although no bioactive compounds have previously been isolated from this species. Bioassay-guided fractionation of an ethanolic extract of the mature pods of A. ligulata led to the isolation of the two new echinocystic acid triterpenoid saponins, ligulatasides A (1) and B (2), which differ in the fine structure of their glycan substituents. Their structures were elucidated on the basis of 1D and 2D NMR, GC-MS, LC-MS/MS, and saccharide linkage analysis. These are the first isolated compounds from A. ligulata and the first fully elucidated structures of triterpenoid saponins from Acacia sensu stricto having echinocystic acid reported as the aglycone. Compounds 1 and 2 were evaluated for cytotoxic activity against a human melanoma cancer cell line (SK-MEL28) and a diploid fibroblast cell line (HFF), but showed only weak activity.

  • 60. Jiang, Rays H. Y.
    et al.
    de Bruijn, Irene
    Haas, Brian J.
    Belmonte, Rodrigo
    Loebach, Lars
    Christie, James
    van den Ackerveken, Guido
    Bottin, Arnaud
    Bulone, Vincent
    KTH, School of Biotechnology (BIO), Glycoscience.
    Diaz-Moreno, Sara M.
    KTH, School of Biotechnology (BIO), Glycoscience.
    Dumas, Bernard
    Fan, Lin
    Gaulin, Elodie
    Govers, Francine
    Grenville-Briggs, Laura J.
    KTH, School of Biotechnology (BIO), Glycoscience.
    Horner, Neil R.
    Levin, Joshua Z.
    Mammella, Marco
    Meijer, Harold J. G.
    Morris, Paul
    Nusbaum, Chad
    Oome, Stan
    Phillips, Andrew J.
    van Rooyen, David
    Rzeszutek, Elzbieta
    KTH, School of Biotechnology (BIO), Glycoscience.
    Saraiva, Marcia
    Secombes, Chris J.
    Seidl, Michael F.
    Snel, Berend
    Stassen, Joost H. M.
    Sykes, Sean
    Tripathy, Sucheta
    van den Berg, Herbert
    Vega-Arreguin, Julio C.
    Wawra, Stephan
    Young, Sarah K.
    Zeng, Qiandong
    Dieguez-Uribeondo, Javier
    Russ, Carsten
    Tyler, Brett M.
    van West, Pieter
    Distinctive Expansion of Potential Virulence Genes in the Genome of the Oomycete Fish Pathogen Saprolegnia parasitica2013In: PLOS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 9, no 6, p. e1003272-Article in journal (Refereed)
    Abstract [en]

    Oomycetes in the class Saprolegniomycetidae of the Eukaryotic kingdom Stramenopila have evolved as severe pathogens of amphibians, crustaceans, fish and insects, resulting in major losses in aquaculture and damage to aquatic ecosystems. We have sequenced the 63 Mb genome of the fresh water fish pathogen, Saprolegnia parasitica. Approximately 1/3 of the assembled genome exhibits loss of heterozygosity, indicating an efficient mechanism for revealing new variation. Comparison of S. parasitica with plant pathogenic oomycetes suggests that during evolution the host cellular environment has driven distinct patterns of gene expansion and loss in the genomes of plant and animal pathogens. S. parasitica possesses one of the largest repertoires of proteases (270) among eukaryotes that are deployed in waves at different points during infection as determined from RNA-Seq data. In contrast, despite being capable of living saprotrophically, parasitism has led to loss of inorganic nitrogen and sulfur assimilation pathways, strikingly similar to losses in obligate plant pathogenic oomycetes and fungi. The large gene families that are hallmarks of plant pathogenic oomycetes such as Phytophthora appear to be lacking in S. parasitica, including those encoding RXLR effectors, Crinkler's, and Necrosis Inducing-Like Proteins (NLP). S. parasitica also has a very large kinome of 543 kinases, 10% of which is induced upon infection. Moreover, S. parasitica encodes several genes typical of animals or animal-pathogens and lacking from other oomycetes, including disintegrins and galactose-binding lectins, whose expression and evolutionary origins implicate horizontal gene transfer in the evolution of animal pathogenesis in S. parasitica.

  • 61. Kaida, Rumi
    et al.
    Satoh, Yumi
    Bulone, Vincent
    KTH, School of Biotechnology (BIO), Glycoscience.
    Yamada, Yohko
    Kaku, Tomomi
    Hayashi, Takahisa
    Kaneko, Takako S.
    Activation of beta-Glucan Synthases by Wall-Bound Purple Acid Phosphatase in Tobacco Cells2009In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 150, no 4, p. 1822-1830Article in journal (Refereed)
    Abstract [en]

    Wall-bound purple acid phosphatases have been shown to be potentially involved in the regulation of plant cell growth. The aim of this work was to further investigate the function of one of these phosphatases in tobacco (Nicotiana tabacum), NtPAP12, using transgenic cells overexpressing the enzyme. The transgenic cells exhibited a higher level of phosphatase activity in their walls. The corresponding protoplasts regenerating a cell wall exhibited a higher rate of beta-glucan synthesis and cellulose deposition was increased in the walls of the transgenic cells. A higher level of plasma membrane glucan synthase activities was also measured in detergent extracts of membrane fractions from the transgenic line, while no activation of Golgi-bound glycan synthases was detected. Enzymatic hydrolysis and methylation analysis were performed on the products synthesized in vitro by the plasma membrane enzymes from the wild-type and transgenic lines extracted with digitonin and incubated with radioactive UDP-glucose. The data showed that the glucans consisted of callose and cellulose and that the amount of each glucan synthesized by the enzyme preparation from the transgenic cells was significantly higher than in the case of the wildtype cells. The demonstration that callose and cellulose synthases are activated in cells overexpressing the wall-bound phosphatase NtPAP12 suggests a regulation of these carbohydrate synthases by a phosphorylation/dephosphorylation process, as well as a role of wall-bound phosphatases in the regulation of cell wall biosynthesis.

  • 62.
    Kallas, Åsa M.
    et al.
    KTH, School of Biotechnology (BIO).
    Coutinho, Pedro
    Bulone, Vincent
    KTH, School of Biotechnology (BIO).
    Mellerowicz, Ewa J.
    Gilbert, Harry J.
    Henrissat, Bernard
    Teeri, Tuula T.
    KTH, School of Biotechnology (BIO).
    Characterization of a CBM43 module from hybrid aspen (Populus tremula x tremuloides): specificity of polysaccharide interaction and bioinformatic analysisManuscript (Other academic)
  • 63.
    Klinter, Stefan
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience.
    Bulone, Vincent
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience. Univ Adelaide, ARC Ctr Excellence Plant Cell Walls, Waite Campus, Urrbrae, SA 5064, Australia.;Univ Adelaide, Sch Agr Food & Wine, Waite Campus, Urrbrae, SA 5064, Australia..
    Arvestad, Lars
    Stockholm Univ, Dept Math, Swedish E Sci Res Ctr, Sci Life Lab, S-10691 Stockholm, Sweden..
    Diversity and evolution of chitin synthases in oomycetes (Straminipila: Oomycota)2019In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 139, article id 106558Article in journal (Refereed)
    Abstract [en]

    The oomycetes are filamentous eukaryotic microorganisms, distinct from true fungi, many of which act as crop or fish pathogens that cause devastating losses in agriculture and aquaculture. Chitin is present in all true fungi, but it occurs in only small amounts in some Saprolegniomycetes and it is absent in Peronosporomycetes. However, the growth of several oomycetes is severely impacted by competitive chitin synthase (CHS) inhibitors. Here, we shed light on the diversity, evolution and function of oomycete CHS proteins. We show by phylogenetic analysis of 93 putative CHSs from 48 highly diverse oomycetes, including the early diverging Ewychasma dicksonii, that all available oomycete genomes contain at least one putative CHS gene. All gene products contain conserved CHS motifs essential for enzymatic activity and form two Peronosporomycete-specific and six Saprolegniale-specific clades. Proteins of all clades, except one, contain an N-terminal microtubule interacting and trafficking (MIT) domain as predicted by protein domain databases or manual analysis, which is supported by homology modelling and comparison of conserved structural features from sequence logos. We identified at least three groups of CHSs conserved among all oomycete lineages and used phylogenetic reconciliation analysis to infer the dynamic evolution of CHSs in oomycetes. The evolutionary aspects of CHS diversity in modern-day oomycetes are discussed. In addition, we observed hyphal tip rupture in Phytophthora infestans upon treatment with the CHS inhibitor nikkomycin Z. Combining data on phylogeny, gene expression, and response to CHS inhibitors, we propose the association of different CHS clades with certain developmental stages.

  • 64.
    Koskela, Salla
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Centres, Wallenberg Wood Science Center.
    Wang, Shennan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience.
    Xu, Dingfeng
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience.
    Yang, Xuan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Centres, Wallenberg Wood Science Center.
    Li, Kai
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Centres, Wallenberg Wood Science Center.
    Berglund, Lars
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Centres, Wallenberg Wood Science Center.
    McKee, Lauren S.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Centres, Wallenberg Wood Science Center.
    Bulone, Vincent
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience.
    Zhou, Qi
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Centres, Wallenberg Wood Science Center.
    Lytic polysaccharide monooxygenase (LPMO) mediated production of ultra-fine cellulose nanofibres from delignified softwood fibres2019In: Green Chemistry, ISSN 1463-9262, E-ISSN 1463-9270Article in journal (Refereed)
    Abstract [en]

    The production of cellulose nanofibres (CNFs) typically requires harsh chemistry and strong mechanical fibrillation, both of which have negative environmental impacts. A possible solution is offered by lytic polysaccharide monooxygenases (LPMOs), oxidative enzymes that boost cellulose fibrillation. Although the role of LPMOs in oxidative modification of cellulosic substrates is rather well established, their use in the production of cellulose nanomaterials is not fully explored, and the effect of the carbohydrate-binding module (CBM) on nanofibrillation has not yet been reported. Herein, we studied the activity of two LPMOs, one of which was appended to a CBM, on delignified softwood fibres for green and energy-efficient production of CNFs. The CNFs were used to prepare cellulose nanopapers, and the structure and properties of both nanofibres and nanopapers were determined. Both enzymes were able to facilitate nanocellulose fibrillation and increase colloidal stability of the produced CNFs. However, the CBM-lacking LPMO was more efficient in introducing carboxyl groups (0.53 mmol/g) on the cellulose fibre surfaces and releasing CNFs with thinner width (4.3 ± 1.5 nm) from delignified spruce fibres than the modular LPMO (carboxylate content of 0.38 mmol/g and nanofibre width of 6.7± 2.5 nm through LPMO pretreatment followed by mild homogenisation. The prepared nanopapers showed improved mechanical properties (tensile strength of 262 MPa, and modulus of 16.2 GPa) compared to conventional CNFs preparation methods, demonstrating the potential of LPMOs as green alternatives for cellulose nanomaterials preparation.

  • 65.
    Koskela, Salla
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience.
    Wang, Shennan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience.
    Yang, Xuan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology.
    Li, Kai
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience.
    Srivastava, Vaibhav
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience.
    McKee, Lauren S.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience.
    Berglund, Lars
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology.
    Bulone, Vincent
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience.
    Zhou, Qi
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience.
    Enzyme-assisted preparation of nanocellulose from wood holocellulose fibers2019Other (Other academic)
  • 66.
    Kuang, Guanglin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Bulone, Vincent
    KTH, School of Biotechnology (BIO), Glycoscience.
    Tu, Yaoquan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Computational studies of the binding profile of phosphoinositide PtdIns (3,4,5) P-3 with the pleckstrin homology domain of an oomycete cellulose synthase2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 20555Article in journal (Refereed)
    Abstract [en]

    Saprolegnia monoica is a model organism to investigate Saprolegnia parasitica, an important oomycete which causes considerable loss in aquaculture every year. S. monoica contains cellulose synthases vital for oomycete growth. However, the molecular mechanism of the cellulose biosynthesis process in the oomycete growth is still poorly understood. Some cellulose synthases of S. monoica, such as SmCesA2, are found to contain a plecsktrin homology (PH) domain, which is a protein module widely found in nature and known to bind to phosphoinositides, a class of signaling compounds involved in many biological processes. Understanding the molecular interactions between the PH domain and phosphoinositides would help to unravel the cellulose biosynthesis process of oomycetes. In this work, the binding profile of PtdIns (3,4,5) P-3, a typical phosphoinositide, with SmCesA2-PH was studied by molecular docking, molecular dynamics and metadynamics simulations. PtdIns (3,4,5) P-3 is found to bind at a specific site located at beta 1, beta 2 and beta 1-beta 2 loop of SmCesA2-PH. The high affinity of PtdIns (3,4,5) P-3 to SmCesA2-PH is contributed by the free phosphate groups, which have electrostatic and hydrogenbond interactions with Lys88, Lys100 and Arg102 in the binding site.

  • 67.
    Kuang, Guanglin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Liang, Lijun
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Zhejiang University, China.
    Brown, Christian
    KTH, School of Biotechnology (BIO), Glycoscience.
    Wang, Qi
    Bulone, Vincent
    KTH, School of Biotechnology (BIO), Glycoscience. Univ Adelaide, Australia.
    Tu, Yaoquan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Insight into the adsorption profiles of the Saprolegnia monoica chitin synthase MIT domain on POPA and POPC membranes by molecular dynamics simulation studies2016In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 18, no 7, p. 5281-5290Article in journal (Refereed)
    Abstract [en]

    The critical role of chitin synthases in oomycete hyphal tip growth has been established. A microtubule interacting and trafficking (MIT) domain was discovered in the chitin synthases of the oomycete model organism, Saprolegnia monoica. MIT domains have been identified in diverse proteins and may play a role in intracellular trafficking. The structure of the Saprolegnia monoica chitin synthase 1 (SmChs1) MIT domain has been recently determined by our group. However, although our in vitro assay identified increased strength in interactions between the MIT domain and phosphatidic acid (PA) relative to other phospholipids including phosphatidylcholine (PC), the mechanism used by the MIT domain remains unknown. In this work, the adsorption behavior of the SmChs1 MIT domain on POPA and POPC membranes was systematically investigated by molecular dynamics simulations. Our results indicate that the MIT domain can adsorb onto the tested membranes in varying orientations. Interestingly, due to the specific interactions between MIT residues and lipid molecules, the binding affinity to the POPA membrane is much higher than that to the POPC membrane. A binding hotspot, which is critical for the adsorption of the MIT domain onto the POPA membrane, was also identified. The lower binding affinity to the POPC membrane can be attributed to the self-saturated membrane surface, which is unfavorable for hydrogen-bond and electrostatic interactions. The present study provides insight into the adsorption profile of SmChs1 and additionally has the potential to improve our understanding of other proteins containing MIT domains.

  • 68.
    Kuang, Guanglin
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Liang, Lijun
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Brown, Christian
    KTH, School of Biotechnology (BIO), Glycoscience.
    Wang, Qi
    Tu, Yaoquan
    Bulone, Vincent
    KTH, School of Biotechnology (BIO), Glycoscience.
    Tu, Yaoquan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Insight into the adsorption profiles of the Saprolegnia practica chitin synthase MIT domain on POPA and POPC membranes by molecular dynamics simulation studiesManuscript (preprint) (Other academic)
  • 69. Kumar, Manoj
    et al.
    Thammannagowda, Shivegowda
    Bulone, Vincent
    KTH, School of Biotechnology (BIO), Wood Biotechnology.
    Chiang, Vincent
    Han, Kyung-Hwan
    Joshi, Chandrashekhar P.
    Mansfield, Shawn D.
    Mellerowicz, Ewa
    Sundberg, Bjorn
    Teeri, Tuula T.
    KTH, School of Biotechnology (BIO), Wood Biotechnology.
    Ellis, Brian E.
    An update on the nomenclature for the cellulose synthase genes in Populus2009In: Trends in Plant Science, ISSN 1360-1385, E-ISSN 1878-4372, Vol. 14, no 5, p. 248-254Article, review/survey (Refereed)
    Abstract [en]

    Cellulose synthase (CesA) is a central catalyst in the generation of the plant cell wall biomass and is, therefore, the focus of intense research. Characterization of individual CesA genes from Populus species has led to the publication of several different naming conventions for CesA gene family members in this model tree. To help reduce the resulting confusion, we propose here a new phylogeny-based CesA nomenclature that aligns the Populus CesA gene family with the established Arabidopsis thaliana CesA family structure.

  • 70. Lai-Kee-Him, J.
    et al.
    Chanzy, H.
    Muller, M.
    Putaux, J. L.
    Imai, T.
    Bulone, Vincent
    KTH, Superseded Departments, Biotechnology.
    In vitro versus in vivo cellulose microfibrils from plant primary wall synthases: Structural differences2002In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 277, no 40, p. 36931-36939Article in journal (Refereed)
    Abstract [en]

    Detergent extracts of microsomal fractions from suspension cultured cells of Rubus fruticosus (blackberry) were tested for their ability to synthesize in vitro sizable quantities of cellulose from UDP-glucose. Both Brij 58 and taurocholate were effective and yielded a substantial percentage of cellulose microfibrils together with (1-->3)-beta-D-glucan (callose). The taurocholate extracts, which did not require the addition of Mg2+, were the most efficient, yielding roughly 20% of cellulose. This cellulose was characterized after callose removal by methylation analysis, electron microscopy, and electron and x-ray synchrotron diffractions; its resistance toward the acid Updegraff reagent was also evaluated. The cellulose microfibrils synthesized in vitro had the same diameter as the endogenous microfibrils isolated from primary cell walls. Both polymers diffracted as cellulose IVI, a disorganized form of cellulose I. Besides these similarities, the in vitro microfibrils had a higher perfection and crystallinity as well as a better resistance toward the Updegraff reagent. These differences can be attributed to the mode of synthesis of the in vitro microfibrils that are able to grow independently in a neighbor-free environment, as opposed to the cellulose in the parent cell walls where new microfibrils have to interweave with the already laid polymers, with the result of a number of structural defects.

  • 71. Larsbrink, Johan
    et al.
    Tuveng, Tina R.
    Pope, Phillip B.
    Bulone, Vincent
    KTH, School of Biotechnology (BIO), Glycoscience.
    Eijsink, Vincent G.H.
    Brumer, Harry
    KTH, School of Biotechnology (BIO), Glycoscience. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center.
    McKee, Lauren S.
    KTH, School of Biotechnology (BIO), Glycoscience. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center.
    Proteomic data on enzyme secretion and activity in the bacterium Chitinophaga pinensis2017In: Data in Brief, E-ISSN 2352-3409, Vol. 11, p. 484-490Article in journal (Refereed)
    Abstract [en]

    The secretion of carbohydrate-degrading enzymes by a bacterium sourced from a softwood forest environment has been investigated by mass spectrometry. The findings are discussed in full in the research article “Proteomic insights into mannan degradation and protein secretion by the forest floor bacterium Chitinophaga pinensis” in Journal of Proteomics by Larsbrink et al. ([1], doi: 10.1016/j.jprot.2017.01.003). The bacterium was grown on three carbon sources (glucose, glucomannan, and galactomannan) which are likely to be nutrient sources or carbohydrate degradation products found in its natural habitat. The bacterium was grown on solid agarose plates to mimic the natural behaviour of growth on a solid surface. Secreted proteins were collected from the agarose following trypsin-mediated hydrolysis to peptides. The different carbon sources led to the secretion of different numbers and types of proteins. Most carbohydrate-degrading enzymes were found in the glucomannan-induced cultures. Several of these enzymes may have biotechnological potential in plant cell wall deconstruction for biofuel or biomaterial production, and several may have novel activities. A subset of carbohydrate-active enzymes (CAZymes) with predicted activities not obviously related to the growth substrates were also found in samples grown on each of the three carbohydrates. The full dataset is accessible at the PRIDE partner repository (ProteomeXchange Consortium) with the identifier PXD004305, and the full list of proteins detected is given in the supplementary material attached to this report.

  • 72.
    Le Normand, Myriam
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology, Wood Chemistry and Pulp Technology.
    Mélida, Hugo
    KTH, School of Biotechnology (BIO), Glycoscience.
    Holmbom, Bjarne
    Åbo Akademi.
    Michaelsen, Terje E.
    Unversity of Oslo.
    Inngjerdingen, Marit
    University of Oslo.
    Bulone, Vincent
    KTH, School of Biotechnology (BIO), Glycoscience.
    Paulsen, B.S.
    Ek, Monica
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology, Wood Chemistry and Pulp Technology.
    Hot-water extracts from the inner bark of Norway spruce with immunomodulating activities2014In: Carbohydrate Polymers, ISSN 0144-8617, E-ISSN 1879-1344, Vol. 101, no 1, p. 699-704Article in journal (Refereed)
    Abstract [en]

    The inner bark of Norway spruce (Picea abies) was sequentially extracted with hot water at 100 degrees C, 140 C and 160 degrees C. The hot-water extracts (IB 100 degrees C, IB 140 degrees C and IB 160 degrees C) contained pectic polysaccharides and showed immunostimulating activities. Structural analyses of their carbohydrate content, including glycosidic linkage analyses, revealed the presence of pectins with a large rhamnogalacturonan RG-I domain ramified with highly-branched arabinans. IB 100 degrees C also contained a large amount of terminal glucosyl residues, indicating the presence of highly substituted polymers. IB 160 degrees C was mainly composed of starch. The hot-water extracts were tested for two biological activities, namely complement fixation and macrophage stimulation. IB 100 degrees C exhibited the highest complement fixation activity, with a 1.7-times higher IC(H)50 than the control pectin, while IB 140 degrees C and IB 160 degrees C gave similar IC(H)50 values as the control. Macrophages were stimulated by IB 100 degrees C and IB 140 degrees C in a dose-dependent manner, but not by IB 160 degrees C. IB 100 degrees C presented the highest activity toward macrophages, comparable to the control pectin.

  • 73.
    Leijon, Felicia
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience.
    Melida, Hugo
    Melzer, Michael
    Larsson, Per Tomas
    Srivastava, Vaibhav
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience.
    Gomez, Leonardo
    Guerriero, Gea
    McQueen-Mason, Simon
    Bulone, Vincent
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience.
    The effect of carbohydrate-binding modules (CBMs) on plant cell wall properties: an in vivo approachManuscript (preprint) (Other academic)
  • 74.
    Leijon, Felicia
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience.
    Melzer, Michael
    Zhou, Qi
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience.
    Srivastava, Vaibhav
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience.
    Bulone, Vincent
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience. ARC Centre of Excellence in Plant Cell Walls and School of Agriculture, Food and Wine, The University of Adelaide.
    Proteomic Analysis of Plasmodesmata From Populus Cell Suspension Cultures in Relation With Callose Biosynthesis.2018In: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 9, article id 1681Article in journal (Refereed)
    Abstract [en]

    Plasmodesmata are channels that link adjacent cells in plant tissues through which molecular exchanges take place. They are involved in multiple processes vital to plant cells, such as responses to hormonal signaling or environmental challenges including osmotic stress, wounding and pathogen attack. Despite the importance of plasmodesmata, their proteome is not well-defined. Here, we have isolated fractions enriched in plasmodesmata from cell suspension cultures of Populus trichocarpa and identified 201 proteins that are enriched in these fractions, thereby providing further insight on the multiple functions of plasmodesmata. Proteomics analysis revealed an enrichment of proteins specifically involved in responses to stress, transport, metabolism and signal transduction. Consistent with the role of callose deposition and turnover in the closure and aperture of the plasmodesmata and our proteomic analysis, we demonstrate the enrichment of callose synthase activity in the plasmodesmata represented by several gene products. A new form of calcium-independent callose synthase activity was detected, in addition to the typical calcium-dependent enzyme activity, suggesting a role of calcium in the regulation of plasmodesmata through two forms of callose synthase activities. Our report provides the first proteomic investigation of the plasmodesmata from a tree species and the direct biochemical evidence for the occurrence of several forms of active callose synthases in these structures. Data are available via ProteomeXchange with identifier PXD010692.

  • 75.
    Li, Jing
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience.
    Wang, Damao
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience.
    Xing, Xiaohui
    Adelaide Glycomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia.
    Cheng, Ting-Jen Rachel
    Genomics Research Centre, Academia Sinica, Sec. 2, 128 Academia Road, Nankang, Taipei 115, Taiwan.
    Liang, Pi-Hui
    School of Pharmacy, College of Medicine, National Taiwan University, Taipei 100, Taiwan.
    Bulone, Vincent
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience. Adelaide Glycomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia.
    Park, Jeong Hill
    College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
    Hsieh, Yves S. Y.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Centres, Wallenberg Wood Science Center.
    Structural analysis and biological activity of cell wall polysaccharides extracted from Panax ginseng marc2019In: International Journal of Biological Macromolecules, ISSN 0141-8130, E-ISSN 1879-0003, Vol. 135, p. 29-37Article in journal (Refereed)
    Abstract [en]

    Ginseng marc is a major by-product of the ginseng industry currently used as animal feed or fertilizer. This fibrous, insoluble waste stream is rich in cell wall polysaccharides and therefore a potential source of ingredients for functional food with health-promoting properties. However, the extraction of these polysaccharides has proved problematic and their exact composition remains unknown. Here we have analysed the composition, structure and biological activity of polysaccharides from ginseng root, stem and leaf marc fractionated using a chelator and alkali solutions. The pectic fraction has been extracted from root marc in high abundance and can activate the production of interleukine-1α and the hematopoietic growth factor by RAW 264.7 murine macrophage cells, which are important immune regulators of T-cells during inflammatory responses and infection processes. Our study reveals the potential to increase the value of ginseng marc by generating carbohydrate-based products with a higher value than animal feed.

  • 76.
    Liljeblad, Jonathan F. D.
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Surface and Corrosion Science.
    Bulone, Vincent
    KTH, School of Biotechnology (BIO), Glycoscience.
    Tyrode, Eric C.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Surface and Corrosion Science.
    Johnson, Magnus C.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Surface and Corrosion Science.
    Rutland, Mark W.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Surface and Corrosion Science.
    Molecular Structure and Stability of Phospholipid Monolayers Probed by Vibrational Sum Frequency Spectroscopy (VSFS)2012In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 102, no 3, p. 591A-591AArticle in journal (Other academic)
  • 77.
    Liljeblad, Jonathan F.D.
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Surface and Corrosion Science. KTH, School of Chemical Science and Engineering (CHE), Centres, Swedish Center for Biomimetic Fiber Engineering, BioMime.
    Bulone, Vincent
    KTH, School of Biotechnology (BIO), Glycoscience. KTH, School of Chemical Science and Engineering (CHE), Centres, Swedish Center for Biomimetic Fiber Engineering, BioMime.
    Rutland, Mark W.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Surface and Corrosion Science. KTH, School of Chemical Science and Engineering (CHE), Centres, Swedish Center for Biomimetic Fiber Engineering, BioMime.
    Johnson, Magnus C.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Surface and Corrosion Science. KTH, School of Chemical Science and Engineering (CHE), Centres, Swedish Center for Biomimetic Fiber Engineering, BioMime.
    Supported Phospholipid Monolayers: The Molecular Structure Investigated by Vibrational Sum Frequency Spectroscopy2011In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 115, no 21, p. 10617-10629Article in journal (Refereed)
    Abstract [en]

    The molecular structure, packing properties, and hydrating water of Langmuir-Blodgett monolayers of the phospholipids 1,2-distearoyl-sn-glyercophosphatidylcholine (DSPC, 18:0 PC), its deuterated analogue (18:0 PC-d83), and 1,2-distearoyl-sn-glyerco-phosphatidylserine (DSPC, 18:0 PS) deposited on planar calcium fluoride (CaF2) substrates have been investigated using the surface-specific nonlinear optical technique vibrational sum frequency spectroscopy (VSFS). Compression isotherms were recorded before the deposition of the monolayers at a surface pressure of 35 mN/m, mimicking the conditions of biological cell membranes. The CH and CD stretch regions, the water region, and the lower wavenumber region, containing phosphate, ester, carboxylate, and amine signals, thus partly covering the fingerprint region, were probed to obtain a complete map of the molecules. The data indicate that all deposited monolayers formed a well-ordered and stable film, and probing the water region revealed significant differences in hydration for the different headgroups. In addition, the tilt angle of the aliphatic chains relative to the surface normal was estimated to be approximately 4 degrees to 10 degrees based on orientational analysis using the antisymmetric methyl stretching vibration. Orientational analysis of the ester C=O groups was also performed, and the result was consistent with the estimated tilt angle of the aliphatic chains.

  • 78.
    Liljeblad, Jonathan F.D.
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Surface and Corrosion Science.
    Bulone, Vincent
    KTH, School of Biotechnology (BIO), Glycoscience.
    Tyrode, Eric
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Surface and Corrosion Science.
    Rutland, Mark W.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Surface and Corrosion Science. Institute for Surface Chemistry, Stockholm, Sweden.
    Johnson, Magnus C.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Surface and Corrosion Science.
    Phospholipid Monolayers Probed by Vibrational Sum Frequency Spectroscopy: Instability of Unsaturated Phospholipids2010In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 98, p. L50-L52Article in journal (Refereed)
    Abstract [en]

    The surface specific technique vibrational sum frequency spectroscopy has been applied to in situ studies of the degradation of Langmuir monolayers of 1,2-diacyl-phosphocholines with various degrees of unsaturation in the aliphatic chains. To monitor the degradation of the phospholipids, the time-dependent change of the monolayer area at constant surface pressure and the sum frequency intensity of the vinyl CH stretch at the carbon-carbon double bonds were measured. The data show a rapid degradation of monolayers of phospholipids carrying unsaturated aliphatic chains compared to the stable lipids carrying fully saturated chains when exposed to the ambient laboratory air. In addition, the degradation of the phospholipids can be inhibited by purging the ambient air with nitrogen. This instability may be attributed to spontaneous degradation by oxidation mediated by various reactive species in the air. To further elucidate the process of lipid oxidation in biological membranes artificial Langmuir monolayers probed by a surface specific spectroscopic technique as in this study can serve as a model system for studying the degradation/oxidation of cell membrane constituents.

  • 79.
    Liljeblad, Jonathan F.D.
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Surface and Corrosion Science.
    Rutland, Mark W.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Surface and Corrosion Science.
    Bulone, Vincent
    KTH, School of Biotechnology (BIO), Glycoscience.
    Johnson, C. Magnus
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Surface and Corrosion Science.
    Stability and structure of phospholipid monolayers probed by vibrational sum frequency spectroscopy (VSFS)2010In: Abstracts of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 239Article in journal (Other academic)
  • 80.
    Liljeblad, Jonathan F.D.
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Surface and Corrosion Science.
    Rutland, Mark W.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Surface and Corrosion Science.
    Bulone, Vincent
    KTH, School of Biotechnology (BIO), Glycoscience.
    Johnson, Magnus C.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Surface and Corrosion Science.
    The Structure of Model Membranes Studied by Vibrational Sum Frequency Spectroscopy2010In: Progress in Colloid and Polymer Science, ISSN 0340-255X, E-ISSN 1437-8027, Vol. 137, p. 9-12Article in journal (Refereed)
    Abstract [en]

    The structure and order of insoluble Langmuir monolayers consisting of 1,2-distearoyl-sn-glycero-3-phosphatidylcholine (DSPC or 18:0 PC) and the surrounding water molecules have been investigated by vibrational sum frequency spectroscopy (VSFS). At surface pressures of 1, 15, and 57 mN/m corresponding to molecular areas of 53, 50, and 43 Å2, respectively, the DSPC molecules formed a well ordered film. Both the VSF signal from the methyl stretching vibrations of the lipid and the surrounding water increased with enhanced surface pressure, as a result of the higher surface density and increased order of the system. Water molecules hydrating the polar parts of the headgroup and in close contact to the hydrocarbon groups of the lipid were observed in all three polarization combinations of the laser beams, and distinguished by their different vibrational frequencies.

  • 81. Liu, Yiying
    et al.
    Rzeszutek, Elzbieta
    KTH, School of Biotechnology (BIO), Glycoscience.
    van der Voort, Menno
    Wu, Cheng-Hsuan
    Thoen, Even
    Skaar, Ida
    Bulone, Vincent
    KTH, School of Biotechnology (BIO), Glycoscience.
    Dorrestein, Pieter C.
    Raaijmakers, Jos M.
    de Bruijn, Irene
    Diversity of Aquatic Pseudomonas Species and Their Activity against the Fish Pathogenic Oomycete Saprolegnia2015In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 10, no 8, article id e0136241Article in journal (Refereed)
    Abstract [en]

    Emerging fungal and oomycete pathogens are increasingly threatening animals and plants globally. Amongst oomycetes, Saprolegnia species adversely affect wild and cultivated populations of amphibians and fish, leading to substantial reductions in biodiversity and food productivity. With the ban of several chemical control measures, new sustainable methods are needed to mitigate Saprolegnia infections in aquaculture. Here, PhyloChip-based community analyses showed that the Pseudomonadales, particularly Pseudomonas species, represent one of the largest bacterial orders associated with salmon eggs from a commercial hatchery. Among the Pseudomonas species isolated from salmon eggs, significantly more biosurfactant producers were retrieved from healthy salmon eggs than from Saprolegnia-infected eggs. Subsequent in vivo activity bioassays showed that Pseudomonas isolate H6 significantly reduced salmon egg mortality caused by Saprolegnia diclina. Live colony mass spectrometry showed that strain H6 produces a viscosin-like lipopeptide surfactant. This biosurfactant inhibited growth of Saprolegnia in vitro, but no significant protection of salmon eggs against Saprolegniosis was observed. These results indicate that live inocula of aquatic Pseudomonas strains, instead of their bioactive compound, can provide new (micro) biological and sustainable means to mitigate oomycete diseases in aquaculture.

  • 82.
    Malm, Erik
    et al.
    KTH, School of Biotechnology (BIO), Glycoscience.
    Bulone, Vincent
    KTH, School of Biotechnology (BIO), Glycoscience.
    Wickholm, Kristina
    Larsson, Per Tomas
    Iversen, Tommy
    The surface structure of well-ordered native cellulose fibrils in contact with water2010In: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 345, no 1, p. 97-100Article in journal (Refereed)
    Abstract [en]

    CP/MAS C-13 NMR spectroscopy was used in combination with spectral fitting to examine the surface structure of hydrated cellulose I fibrils from Halocynthia and Gluconoacetobacter xylinus. To increase the spectral intensities and minimize signal overlap, G. xylinus celluloses site-specifically enriched in C-13 either on C4 or on both C1 and C6 were examined. The experimental data showed multiple C4 and C6 signals for the water accessible fibril surfaces in the highly crystalline celluloses. These signal multiplicities were attributed to structural features in the surface layers induced by the fibril interior, and could not be extracted by spectral fitting in celluloses with a lower degree of crystallinity such as cellulose from cotton.

  • 83.
    Malm, Erik
    et al.
    KTH, School of Biotechnology (BIO), Glycoscience.
    Srivastava, Vaibhav
    KTH, School of Biotechnology (BIO), Glycoscience.
    Sundqvist, Gustav
    KTH, School of Biotechnology (BIO), Glycoscience.
    Bulone, Vincent
    KTH, School of Biotechnology (BIO), Glycoscience.
    APP: An Automated Proteomics Pipeline for the analysis of mass spectrometry data based on multiple open access tools2014In: BMC Bioinformatics, ISSN 1471-2105, E-ISSN 1471-2105, Vol. 15, no 1, article id 345Article in journal (Refereed)
    Abstract [en]

    Background: Mass spectrometry analyses of complex protein samples yield large amounts of data and specific expertise is needed for data analysis, in addition to a dedicated computer infrastructure. Furthermore, the identification of proteins and their specific properties require the use of multiple independent bioinformatics tools and several database search algorithms to process the same datasets. In order to facilitate and increase the speed of data analysis, there is a need for an integrated platform that would allow a comprehensive profiling of thousands of peptides and proteins in a single process through the simultaneous exploitation of multiple complementary algorithms. Results: We have established a new proteomics pipeline designated as APP that fulfills these objectives using a complete series of tools freely available from open sources. APP automates the processing of proteomics tasks such as peptide identification, validation and quantitation from LC-MS/MS data and allows easy integration of many separate proteomics tools. Distributed processing is at the core of APP, allowing the processing of very large datasets using any combination of Windows/Linux physical or virtual computing resources. Conclusions: APP provides distributed computing nodes that are simple to set up, greatly relieving the need for separate IT competence when handling large datasets. The modular nature of APP allows complex workflows to be managed and distributed, speeding up throughput and setup. Additionally, APP logs execution information on all executed tasks and generated results, simplifying information management and validation.

  • 84.
    Martins, Antonio
    et al.
    Stockholm Univ, Wenner Gren Inst, Dept Mol Biosci, SE-10691 Stockholm, Sweden..
    Pfirrmann, Thorsten
    Stockholm Univ, Wenner Gren Inst, Dept Mol Biosci, SE-10691 Stockholm, Sweden.;Martin Luther Univ Halle Wittenberg, Inst Physiol Chem, D-06114 Halle, Germany..
    Heessen, Stijn
    Stockholm Univ, Wenner Gren Inst, Dept Mol Biosci, SE-10691 Stockholm, Sweden.;Sanofi Aventis Deutschland GmbH, Global Business Dev & Licensing Consumer Healthca, D-65926 Frankfurt, Germany..
    Sundqvist, Gustav
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience.
    Bulone, Vincent
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience.
    Andreasson, Claes
    Stockholm Univ, Wenner Gren Inst, Dept Mol Biosci, SE-10691 Stockholm, Sweden..
    Ljungdahl, Per O.
    Stockholm Univ, Wenner Gren Inst, Dept Mol Biosci, SE-10691 Stockholm, Sweden..
    Ssy5 is a signaling serine protease that exhibits atypical biogenesis and marked S1 specificity2018In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 293, no 22, p. 8362-8378Article in journal (Refereed)
    Abstract [en]

    Ssy5 is a signaling endoprotease that plays a key role in regulating central metabolism, cellular aging, and morphological transitions important for growth and survival of yeast (Saccharomyces cerevisiae) cells. In response to extracellular amino acids, Ssy5 proteolytically activates the transcription factors Stp1 and Stp2, leading to enhanced Ssy1-Ptr3-Ssy5 (SPS) sensor-regulated gene expression. Ssy5 comprises a catalytic (Cat) domain and an extensive regulatory prodomain. Ssy5 is refractory to both broad-spectrum and serine protease-specific inhibitors, confounding its classification as a protease, and no information about Ssy5's cleavage-site preferences and its mechanism of substrate selection is available. Here, using mutational and inhibition experiments, we investigated the biogenesis and catalytic properties of Ssy5 and conclusively show that it is a serine protease. Atypical for the majority of serine proteases, Ssy5's prodomain was obligatorily required in cis during biogenesis for the maturation of the proteolytic activity of the Cat domain. Autolysis and Stp1 and Stp2 cleavage occurred between a cysteine (at the P1 site) and a serine or alanine (at the P1 site) and required residues with short side chains at the P1 site. Substitutions in the Cat domain affecting substrate specificity revealed that residues Phe-634, His-661, and Gly-671 in the S1-binding pocket of this domain are important for Ssy5 catalytic function. This study confirms that the signaling protease Ssy5 is a serine protease and provides a detailed understanding of the biogenesis and intrinsic properties of this key enzyme in yeast.

  • 85.
    McKee, Lauren S.
    et al.
    KTH, School of Biotechnology (BIO), Glycoscience. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center.
    Sunner, Hampus
    Anasontzis, George E.
    Toriz, Guillermo
    Gatenholm, Paul
    Bulone, Vincent
    KTH, School of Biotechnology (BIO), Glycoscience. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center. Univ Adelaide, Australia.
    Vilaplana, Francisco
    KTH, School of Biotechnology (BIO), Glycoscience. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center.
    Olsson, Lisbeth
    A GH115 alpha-glucuronidase from Schizophyllum commune contributes to the synergistic enzymatic deconstruction of softwood glucuronoarabinoxylan2016In: Biotechnology for Biofuels, ISSN 1754-6834, E-ISSN 1754-6834, Vol. 9, article id 2Article in journal (Refereed)
    Abstract [en]

    Background: Lignocellulosic biomass from softwood represents a valuable resource for the production of biofuels and bio-based materials as alternatives to traditional pulp and paper products. Hemicelluloses constitute an extremely heterogeneous fraction of the plant cell wall, as their molecular structures involve multiple monosaccharide components, glycosidic linkages, and decoration patterns. The complete enzymatic hydrolysis of wood hemicelluloses into monosaccharides is therefore a complex biochemical process that requires the activities of multiple degradative enzymes with complementary activities tailored to the structural features of a particular substrate. Glucuronoarabinoxylan (GAX) is a major hemicellulose component in softwood, and its structural complexity requires more enzyme specificities to achieve complete hydrolysis compared to glucuronoxylans from hardwood and arabinoxylans from grasses. Results: We report the characterisation of a recombinant alpha-glucuronidase (Agu115) from Schizophyllum commune capable of removing (4-O-methyl)-glucuronic acid ((Me) GlcA) residues from polymeric and oligomeric xylan. The enzyme is required for the complete deconstruction of spruce glucuronoarabinoxylan (GAX) and acts synergistically with other xylan-degrading enzymes, specifically a xylanase (Xyn10C), an alpha-l-arabinofuranosidase (AbfA), and a beta-xylosidase (XynB). Each enzyme in this mixture showed varying degrees of potentiation by the other activities, likely due to increased physical access to their respective target monosaccharides. The exo-acting Agu115 and AbfA were unable to remove all of their respective target side chain decorations from GAX, but their specific activity was significantly boosted by the addition of the endo-Xyn10C xylanase. We demonstrate that the proposed enzymatic cocktail (Agu115 with AbfA, Xyn10C and XynB) achieved almost complete conversion of GAX to arabinofuranose (Araf), xylopyranose (Xylp), and MeGlcA monosaccharides. Addition of Agu115 to the enzymatic cocktail contributes specifically to 25 % of the conversion. However, traces of residual oligosaccharides resistant to this combination of enzymes were still present after deconstruction, due to steric hindrances to enzyme access to the substrate. Conclusions: Our GH115 alpha-glucuronidase is capable of finely tailoring the molecular structure of softwood GAX, and contributes to the almost complete saccharification of GAX in synergy with other exo- and endo-xylan-acting enzymes. This has great relevance for the cost-efficient production of biofuels from softwood lignocellulose.

  • 86. Monegal, A.
    et al.
    Bulone, Vincent
    KTH, School of Biotechnology (BIO), Glycoscience.
    Planas, A.
    Enzymatic characterization of bovine alpha-1,3-galactosyltransferase. Validation of a radiometric assay and kinetic mechanism2005In: Afinidad, ISSN 0001-9704, Vol. 62, no 519, p. 505-512Article in journal (Refereed)
    Abstract [es]

    alpha 3-Galactosyltransferase (alpha 3GT) transfers galactose from UDP-Gal (sugar nucleotide donor) to the N-acetyllactosaminyl or lactosyl terminal groups of glycoproteins and glycolipids, catalyzing the formation of an alpha-1,3 glycosidic bond. The terminal saccharide Gal alpha 3NAcGal beta 4Glu-R is the main antigenic determinant responsible of the hyperaccute rejection in xenotransplantation. A radiometric assay for the determination of alpha 3GT activity is implemented and validated. The recombinant enzyme (catalytic domain) expressed in Eschericia coli follows a bi bi sequential ordered kinetic mechanism with binding of donor substrate (UDP-Gal) first and acceptor substrate to form a productive ternary complex. K-M values are 30 mu M for UDP-Gal, and 1.2 mM for lactose.

  • 87.
    Mélida, Hugo
    et al.
    KTH, School of Biotechnology (BIO), Glycoscience.
    Sain, D.
    Stajich, J. E.
    Bulone, Vincent
    KTH, School of Biotechnology (BIO), Glycoscience.
    Deciphering the uniqueness of Mucoromycotina cell walls by combining biochemical and phylogenomic approaches2015In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 17, no 5, p. 1649-1662Article in journal (Refereed)
    Abstract [en]

    Most fungi from the Mucoromycotina lineage occur in ecosystems as saprobes, although some species are phytopathogens or may induce human mycosis. Mucoromycotina represent early diverging models that are most valuable for understanding fungal evolution. Here we reveal the uniqueness of the cell wall structure of the Mucoromycotina Rhizopus oryzae and Phycomyces blakesleeanus compared with the better characterized cell wall of the ascomycete Neurospora crassa. We have analysed the corresponding polysaccharide biosynthetic and modifying pathways, and highlight their evolutionary features and higher complexity in terms of gene copy numbers compared with species from other lineages. This work uncovers the presence in Mucoromycotina of abundant fucose-based polysaccharides similar to algal fucoidans. These unexpected polymers are associated with unusually low amounts of glucans and a higher proportion of chitin compared with N.crassa. The specific structural features are supported by the identification of genes potentially involved in the corresponding metabolic pathways. Phylogenomic analyses of genes encoding carbohydrate synthases, polysaccharide modifying enzymes and enzymes involved in nucleotide-sugar formation provide evidence for duplication events during evolution of cell wall metabolism in fungi. Altogether, the data highlight the specificity of Mucoromycotina cell walls and pave the way for a finer understanding of their metabolism.

  • 88.
    Mélida, Hugo
    et al.
    KTH, School of Biotechnology (BIO), Glycoscience.
    Sandoval-Sierra, Jose V.
    Dieguez-Uribeondo, Javier
    Bulone, Vincent
    KTH, School of Biotechnology (BIO), Glycoscience.
    Analyses of Extracellular Carbohydrates in Oomycetes Unveil the Existence of Three Different Cell Wall Types2013In: Eukaryotic Cell, ISSN 1535-9778, E-ISSN 1535-9786, Vol. 12, no 2, p. 194-203Article in journal (Refereed)
    Abstract [en]

    Some of the most devastating plant and animal pathogens belong to the oomycete class. The cell walls of these microorganisms represent an excellent target for disease control, but their carbohydrate composition is elusive. We have undertaken a detailed cell wall analysis in 10 species from 2 major oomycete orders, the Peronosporales and the Saprolegniales, thereby unveiling the existence of 3 clearly different cell wall types: type I is devoid of N-acetylglucosamine (GlcNAc) but contains glucuronic acid and mannose; type II contains up to 5% GlcNAc and residues indicative of cross-links between cellulose and 1,3-beta-glucans; type III is characterized by the highest GlcNAc content (>5%) and the occurrence of unusual carbohydrates that consist of 1,6-linked GlcNAc residues. These 3 cell wall types are also distinguishable by their cellulose content and the fine structure of their 1,3-beta-glucans. We propose a cell wall paradigm for oomycetes that can serve as a basis for the establishment of cell wall architectural models and the further identification of cell wall subtypes. This paradigm is complementary to morphological and molecular criteria for taxonomic grouping and provides useful information for unraveling poorly understood cell wall carbohydrate biosynthetic pathways through the identification and characterization of the corresponding enzymes.

  • 89. Nars, A.
    et al.
    Lafitte, C.
    Chabaud, M.
    Drouillard, S.
    Mélida, Hugo
    KTH, School of Biotechnology (BIO), Glycoscience.
    Danoun, S.
    Le Costaouëc, T.
    Rey, T.
    Benedetti, J.
    Bulone, Vincent
    KTH, School of Biotechnology (BIO), Glycoscience.
    Barker, D. G.
    Bono, J. -J
    Dumas, B.
    Jacquet, C.
    Heux, L.
    Fliegmann, J.
    Bottin, A.
    Aphanomyces euteiches Cell Wall Fractions Containing Novel Glucan-Chitosaccharides Induce Defense Genes and Nuclear Calcium Oscillations in the Plant Host Medicago truncatula2013In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, no 9, p. e75039-Article in journal (Refereed)
    Abstract [en]

    N-acetylglucosamine-based saccharides (chitosaccharides) are components of microbial cell walls and act as molecular signals during host-microbe interactions. In the legume plant Medicago truncatula, the perception of lipochitooligosaccharide signals produced by symbiotic rhizobia and arbuscular mycorrhizal fungi involves the Nod Factor Perception (NFP) lysin motif receptor-like protein and leads to the activation of the so-called common symbiotic pathway. In rice and Arabidopsis, lysin motif receptors are involved in the perception of chitooligosaccharides released by pathogenic fungi, resulting in the activation of plant immunity. Here we report the structural characterization of atypical chitosaccharides from the oomycete pathogen Aphanomyces euteiches, and their biological activity on the host Medicago truncatula. Using a combination of biochemical and biophysical approaches, we show that these chitosaccharides are linked to β-1,6-glucans, and contain a β-(1,3;1,4)-glucan backbone whose β-1,3-linked glucose units are substituted on their C-6 carbon by either glucose or N-acetylglucosamine residues. This is the first description of this type of structural motif in eukaryotic cell walls. Glucan-chitosaccharide fractions of A. euteiches induced the expression of defense marker genes in Medicago truncatula seedlings independently from the presence of a functional Nod Factor Perception protein. Furthermore, one of the glucan-chitosaccharide fractions elicited calcium oscillations in the nucleus of root cells. In contrast to the asymmetric oscillatory calcium spiking induced by symbiotic lipochitooligosaccharides, this response depends neither on the Nod Factor Perception protein nor on the common symbiotic pathway. These findings open new perspectives in oomycete cell wall biology and elicitor recognition and signaling in legumes.

  • 90. Niculaes, Claudiu
    et al.
    Morreel, Kris
    Kim, Hoon
    Lu, Fachuang
    Mckee, Lauren S.
    KTH, School of Biotechnology (BIO), Glycoscience.
    Ivens, Bart
    Haustraete, Jurgen
    Vanholme, Bartel
    De Rycke, Riet
    Hertzberg, Magnus
    Fromm, Jörg
    Bulone, Vincent
    KTH, School of Biotechnology (BIO), Glycoscience.
    Polle, Andrea
    Ralph, John
    Boerjan, Wout
    Phenylcoumaran Benzylic Ether Reductase Prevents Accumulation of Compounds Formed under Oxidative Conditions in Poplar Xylem2014In: The Plant Cell, ISSN 1040-4651, E-ISSN 1532-298X, Vol. 26, no 9, p. 3775-3791Article in journal (Refereed)
    Abstract [en]

    Phenylcoumaran benzylic ether reductase (PCBER) is one of the most abundant proteins in poplar (Populus spp) xylem, but its biological role has remained obscure. In this work, metabolite profiling of transgenic poplar trees downregulated in PCBER revealed both the in vivo substrate and product of PCBER. Based on mass spectrometry and NMR data, the substrate was identified as a hexosylated 8-5-coupling product between sinapyl alcohol and guaiacylglycerol, and the product was identified as its benzyl-reduced form. This activity was confirmed in vitro using a purified recombinant PCBER expressed in Escherichia coli. Assays performed on 20 synthetic substrate analogs revealed the enzyme specificity. In addition, the xylem of PCBER-downregulated trees accumulated over 2000-fold higher levels of cysteine adducts of monolignol dimers. These compounds could be generated in vitro by simple oxidative coupling assays involving monolignols and cysteine. Altogether, our data suggest that the function of PCBER is to reduce phenylpropanoid dimers in planta to form antioxidants that protect the plant against oxidative damage. In addition to describing the catalytic activity of one of the most abundant enzymes in wood, we provide experimental evidence for the antioxidant role of a phenylpropanoid coupling product in planta.

  • 91. Omadjela, Okako
    et al.
    Narahari, Adishesh
    Strumillo, Joanna
    Mélida, Hugo
    KTH, School of Biotechnology (BIO), Glycoscience.
    Mazur, Olga
    Bulone, Vincent
    KTH, School of Biotechnology (BIO), Glycoscience.
    Zimmer, Jochen
    BcsA and BcsB form the catalytically active core of bacterial cellulose synthase sufficient for in vitro cellulose synthesis2013In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 110, no 44, p. 17856-17861Article in journal (Refereed)
    Abstract [en]

    Cellulose is a linear extracellular polysaccharide. It is synthesized by membrane-embedded glycosyltransferases that processively polymerize UDP-activated glucose. Polymer synthesis is coupled to membrane translocation through a channel formed by the cellulose synthase. Although eukaryotic cellulose synthases function in macromolecular complexes containing several different enzyme isoforms, prokaryotic synthases associate with additional subunits to bridge the periplasm and the outer membrane. In bacteria, cellulose synthesis and translocation is catalyzed by the inner membrane-associated bacterial cellulose synthase (Bcs) A and BcsB subunits. Similar to alginate and poly-beta-1,6 N-acetylglucosamine, bacterial cellulose is implicated in the formation of sessile bacterial communities, termed biofilms, and its synthesis is likewise stimulated by cyclic-di-GMP. Biochemical studies of exopolysaccharide synthesis are hampered by difficulties in purifying and reconstituting functional enzymes. We demonstrate robust in vitro cellulose synthesis reconstituted from purified BcsA and BcsB proteins from Rhodobacter sphaeroides. Although BcsA is the catalytically active subunit, the membrane-anchored BcsB subunit is essential for catalysis. The purified BcsA-B complex produces cellulose chains of a degree of polymerization in the range 200-300. Catalytic activity critically depends on the presence of the allosteric activator cyclic-di-GMP, but is independent of lipid-linked reactants. Our data reveal feedback inhibition of cellulose synthase by UDP but not by the accumulating cellulose polymer and highlight the strict substrate specificity of cellulose synthase for UDP-glucose. A truncation analysis of BcsB localizes the region required for activity of BcsA within its C-terminal membrane-associated domain. The reconstituted reaction provides a foundation for the synthesis of biofilm exopolysaccharides, as well as its activation by cyclic-di-GMP.

  • 92. Pacheco-Villalobos, David
    et al.
    Diaz-Moreno, Sara M.
    KTH, School of Biotechnology (BIO), Glycoscience.
    van der Schuren, Alja
    Tamaki, Takayuki
    Kang, Yeon Hee
    Gujas, Bojan
    Novak, Ondrej
    Jaspert, Nina
    Li, Zhenni
    Wolf, Sebastian
    Oecking, Claudia
    Ljung, Karin
    Bulone, Vincent
    KTH, School of Biotechnology (BIO), Glycoscience.
    Hardtke, Christian S.
    The Effects of High Steady State Auxin Levels on Root Cell Elongation in Brachypodium2016In: The Plant Cell, ISSN 1040-4651, E-ISSN 1532-298X, Vol. 28, no 5, p. 1009-1024Article in journal (Refereed)
    Abstract [en]

    The long-standing Acid Growth Theory of plant cell elongation posits that auxin promotes cell elongation by stimulating cell wall acidification and thus expansin action. To date, the paucity of pertinent genetic materials has precluded thorough analysis of the importance of this concept in roots. The recent isolation of mutants of the model grass species Brachypodium distachyon with dramatically enhanced root cell elongation due to increased cellular auxin levels has allowed us to address this question. We found that the primary transcriptomic effect associated with elevated steady state auxin concentration in elongating root cells is upregulation of cell wall remodeling factors, notably expansins, while plant hormone signaling pathways maintain remarkable homeostasis. These changes are specifically accompanied by reduced cell wall arabinogalactan complexity but not by increased proton excretion. On the contrary, we observed a tendency for decreased rather than increased proton extrusion from root elongation zones with higher cellular auxin levels. Moreover, similar to Brachypodium, root cell elongation is, in general, robustly buffered against external pH fluctuation in Arabidopsis thaliana. However, forced acidification through artificial proton pump activation inhibits root cell elongation. Thus, the interplay between auxin, proton pump activation, and expansin action may be more flexible in roots than in shoots.

  • 93.
    Pallinti, Purushotham Naidu
    et al.
    Univ Virginia, Charlottesville, VA USA..
    Cho, Sung Hyun
    Penn State, Biochem & Mol Biol, University Pk, PA USA..
    Diaz-Moreno, Sara M.
    KTH, School of Biotechnology (BIO), Glycoscience.
    Kumar, Manish
    Penn State, Dept Chem Engn, University Pk, PA USA..
    Nixon, B. Tracy
    Penn State, Biochem & Mol Biol, University Pk, PA USA..
    Bulone, Vincent
    KTH, School of Biotechnology (BIO), Glycoscience. Royal Inst Technol, Div Glycosci, Stockholm, Sweden.;Australian Res Council Ctr Excellence Plant Cell, Sch Agr Food & Wine, Urrbrae, SA, Australia..
    Zimmer, Jochen
    Univ Virginia, Charlottesville, VA USA..
    Cellulose microfibril formation in vitro by a single heterologously expressed plant cellulose synthase isoform2017In: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 253Article in journal (Other academic)
  • 94.
    Pang, Zhili
    et al.
    KTH, School of Biotechnology (BIO), Glycoscience. China Agricultural University, China.
    Chen, Lei
    Miao, Jianqiang
    Wang, Zhiwen
    Bulone, Vincent
    KTH, School of Biotechnology (BIO), Glycoscience. University of Adelaide, Australia.
    Liu, Xili
    Proteomic profile of the plant-pathogenic oomycete Phytophthora capsici in response to the fungicide pyrimorph2015In: Proteomics, ISSN 1615-9853, E-ISSN 1615-9861, Vol. 15, no 17, p. 2972-2982Article in journal (Refereed)
    Abstract [en]

    Pyrimorph is a novel fungicide from the carboxylic acid amide (CAA) family used to control plant-pathogenic oomycetes such as Phytophthora capsici. The proteomic response of P. capsici to pyrimorph was investigated using the iTRAQ technology to determine the target site of the fungicide and potential biomarker candidates of drug efficacy. A total of 1336 unique proteins were identified from the mycelium of wild-type P. capsici isolate (Hd3) and two pyrimorphresistantmutants (R3-1 and R3-2) grown in the presence or absence of pyrimorph. Comparative analysis revealed that the three P. capsici isolates Hd3, R3-1, and R3-2 produced 163, 77, and 13 unique proteins, respectively, which exhibited altered levels of abundance in response to the pyrimorph treatment. Further investigations, using Cluster of Orthologous Groups of Proteins (COG) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis identified 35 proteins related to the mode of action of pyrimorph against P. capsici and 62 proteins involved in the stress response of P. capsici to pyrimorph. Many of the proteins with altered expression were associated with glucose and energy metabolism. Biochemical analysis using D-[U-C-14] glucose verified the proteomics data, suggesting that the major mode of action of pyrimorph in P. capsici is the inhibition of cell wall biosynthesis. These results also illustrate that proteomics approaches are useful tools for determining the pathways targeted by novel fungicides as well as for evaluating the tolerance of plant pathogens to environmental challenges, such as the presence of fungicides.

  • 95.
    Pang, Zhili
    et al.
    KTH, School of Biotechnology (BIO), Glycoscience.
    Srivastava, Vaibhav
    KTH, School of Biotechnology (BIO), Glycoscience.
    Liu, X.
    Bulone, Vincent
    KTH, School of Biotechnology (BIO), Glycoscience.
    Quantitative proteomics links metabolic pathways to specific developmental stages of the plant-pathogenic oomycete Phytophthora capsici2016In: Molecular plant pathology, ISSN 1464-6722, E-ISSN 1364-3703Article in journal (Refereed)
    Abstract [en]

    The oomycete Phytophthora capsici is a plant pathogen responsible for important losses to vegetable production worldwide. Its asexual reproduction plays an important role in the rapid propagation and spread of the disease in the field. A global proteomics study was conducted to compare two key asexual life stages of P. capsici, i.e. the mycelium and cysts, to identify stage-specific biochemical processes. A total of 1200 proteins was identified using qualitative and quantitative proteomics. The transcript abundance of some of the enriched proteins was also analysed by quantitative real-time polymerase chain reaction. Seventy-three proteins exhibited different levels of abundance between the mycelium and cysts. The proteins enriched in the mycelium are mainly associated with glycolysis, the tricarboxylic acid (or citric acid) cycle and the pentose phosphate pathway, providing the energy required for the biosynthesis of cellular building blocks and hyphal growth. In contrast, the proteins that are predominant in cysts are essentially involved in fatty acid degradation, suggesting that the early infection stage of the pathogen relies primarily on fatty acid degradation for energy production. The data provide a better understanding of P. capsici biology and suggest potential metabolic targets at the two different developmental stages for disease control. © 2016 BSPP AND JOHN WILEY & SONS LTD.

  • 96. Park, Eunsook
    et al.
    Diaz-Moreno, Sara M.
    KTH, School of Biotechnology (BIO), Glycoscience.
    Davis, Destiny J.
    Wilkop, Thomas E.
    Bulone, Vincent
    KTH, School of Biotechnology (BIO), Glycoscience.
    Drakakaki, Georgia
    Endosidin 7 Specifically Arrests Late Cytokinesis and Inhibits Callose Biosynthesis, Revealing Distinct Trafficking Events during Cell Plate Maturation2014In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 165, no 3, p. 1019-1034Article in journal (Refereed)
    Abstract [en]

    Although cytokinesis is vital for plant growth and development, our mechanistic understanding of the highly regulated membrane and cargo transport mechanisms in relation to polysaccharide deposition during this process is limited. Here, we present an in-depth characterization of the small molecule endosidin 7 (ES7) inhibiting callose synthase activity and arresting late cytokinesis both in vitro and in vivo in Arabidopsis (Arabidopsis thaliana). ES7 is a specific inhibitor for plant callose deposition during cytokinesis that does not affect endomembrane trafficking during interphase or cytoskeletal organization. The specificity of ES7 was demonstrated (1) by comparing its action with that of known inhibitors such as caffeine, flufenacet, and concanamycin A and (2) across kingdoms with a comparison in yeast. The interplay between cell plate-specific post-Golgi vesicle traffic and callose accumulation was analyzed using ES7, and it revealed unique and temporal contributions of secretory and endosomal vesicles in cell plate maturation. While RABA2A-labeled vesicles, which accumulate at the early stage of cell plate formation, were not affected by ES7, KNOLLE was differentially altered by the small molecule. In addition, the presence of clathrin-coated vesicles in cells containing elevated levels of callose and their reduction under ES7 treatment further support the role of endocytic membrane remodeling in the maturing cell plate while the plate is stabilized by callose. Taken together, these data show the essential role of callose during the late stages of cell plate maturation and establish the temporal relationship between vesicles and regulatory proteins at the cell plate assembly matrix during polysaccharide deposition.

  • 97.
    Pavankumar, Asalapuram R.
    et al.
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Kayathri, Rajarathinam
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Murugan, Natarajan Arul
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Zhang, Qiong
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Srivastava, Vaibhav
    KTH, School of Biotechnology (BIO), Glycoscience.
    Okoli, Chuka
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Bulone, Vincent
    KTH, School of Biotechnology (BIO), Glycoscience.
    Rajarao, Gunaratna K.
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Dimerization of a flocculent protein from Moringa oleifera: experimental evidence and in silico interpretation2014In: Journal of Biomolecular Structure and Dynamics, ISSN 0739-1102, E-ISSN 1538-0254, Vol. 32, no 3, p. 406-415Article in journal (Refereed)
    Abstract [en]

    Many proteins exist in dimeric and other oligomeric forms to gain stability and functional advantages. In this study, the dimerization property of a coagulant protein (MO2.1) from Moringa oleifera seeds was addressed through laboratory experiments, protein-protein docking studies and binding free energy calculations. The structure of MO2.1 was predicted by homology modelling, while binding free energy and residues-distance profile analyses provided insight into the energetics and structural factors for dimer formation. Since the coagulation activities of the monomeric and dimeric forms of MO2.1 were comparable, it was concluded that oligomerization does not affect the biological activity of the protein.

  • 98. Pelosi, L.
    et al.
    Imai, T.
    Chanzy, H.
    Heux, L.
    Buhler, E.
    Bulone, Vincent
    KTH, Superseded Departments, Biotechnology.
    Structural and morphological diversity of (1 -> 3)-beta-D-glucans synthesized in vitro by enzymes from Saprolegnia monoica. Comparison with a corresponding in vitro product from blackberry (Rubus fruticosus)2003In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 42, no 20, p. 6264-6274Article in journal (Refereed)
    Abstract [en]

    Detergent extracts of microsomal fractions from Saprolegnia monoica and blackberry (Rubus fruticosus) cells were incubated with UDP-glucose to yield in vitro (1-->3)-beta-D-glucans. The insoluble products were analyzed by conventional and cryo transmission electron microscopy, X-ray diffraction, and C-13 CP/MAS NMR, and their molecular weights were determined by light scattering experiments. All the products were microfibrillar, but for the detergent extracts from S. monoica, important morphological differences were observed when the pH of the synthesizing medium was modified. At pH 6, the product had a weight average degree of polymerization ((DPw) over bar) exceeding 20 000 and consisted of endless ribbon-like microfibrils. The microfibrils obtained at pH 9 had a length of only 200-300 nm, and their (DPw) over bar was similar to5000. Of all the in vitro (1-->3)-beta-D-glucans, the one from R. fruticosus had the shortest length and the smallest (DPw) over bar. Crystallographic and spectroscopic data showed that the three in vitro samples consisted of triple helices of (1-->3)-beta-D-glucans and contained substantial amounts of water molecules in their structure, the shortest microfibrils being more hydrated. In addition, the long microfibrils from S. monoica synthesized at pH 6 were more resistant toward the action of an endo-(1-->3)-beta-D-glucanase than the shorter ones obtained at pH 9. These results are discussed in terms of molecular biosynthetic mechanisms of fungal and plant (1-->3)-beta-D-glucans, and in relation with the possible existence of several (1-->3)-beta-D-glucan synthases in a given organism. The interpretation and discussion of these observations integrate the current knowledge of the structure and function of (1-->3)-beta-D-glucans.

  • 99. Pelosi, Ludovic
    et al.
    Bulone, Vincent
    KTH, School of Biotechnology (BIO), Glycoscience.
    Heux, Laurent
    Polymorphism of curdlan and (1 -> 3)-beta-D-glucans synthesized in vitro: A C-13 CP-MAS and X-ray diffraction analysis2006In: Carbohydrate Polymers, ISSN 0144-8617, E-ISSN 1879-1344, Vol. 66, no 2, p. 199-207Article in journal (Refereed)
    Abstract [en]

    The polymorphism of three different forms of curdlan and four (1 -> 3)-beta-D-glucans synthesized in vitro was investigated by C-13 cross-polarization/magic angle spinning nuclear magnetic resonance (CP/MAS NMR) spectroscopy and X-ray powder diffraction. Dried samples of curdlan presented a disordered state whereas two distinct hydrated crystalline structures were evidenced for the polymer after hydrothermal treatment or swelling in water at room temperature. The samples synthesized in vitro by detergent extracts of plasma membranes from Rubus fruticosus and Saprolegnia monoica and by a mutated barley (1 -> 3)-beta-D-glucan endohydrolase exhibited a structural heterogeneity that can be explained in the light of the results obtained on standard samples. A 76-ppm resonance signal corresponding to carbon five was identified by CP/MAS NMR spectroscopy. The relative importance of this peak was shown to be linked to the proportion of the different crystalline allomorphs in a given sample. This peak can be considered as a new marker of the degree of organization of (1 -> 3)-beta-D-glucans. The observed polymorphism provides further detailed information on the conformation of the different (1 -> 3)P-D-glucan allomorphs.

  • 100. Pham, Trang A.T.
    et al.
    Schwerdt, Julian G.
    Shirley, Neil J.
    Xing, Xiaohui
    Hsieh, Yves S. Y.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Centres, Wallenberg Wood Science Center.
    Srivastava, Vaibhav
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience.
    Bulone, Vincent
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience.
    Little, Alan
    Analysis of cell wall synthesis and metabolism during early germination of Blumeria graminis f. sp. hordei conidial cells induced in vitro2019In: The Cell Surface, ISSN 2468-2330, Vol. 5, p. 100030-Article in journal (Refereed)
    Abstract [en]

    As an obligate biotroph, Blumeria graminis f. sp. hordei (Bgh) cannot be grown in an axenic culture, and instead must be cultivated on its host species, Hordeum vulgare (barley). In this study an in vitro system utilizing n-hexacosanal, a constituent of the barley cuticle and known inducer of Bgh germination, was used to cultivate Bgh and differentiate conidia up to the appressorial germ tube stage for analysis. Transcriptomic and proteomic profiling of the appressorial germ tube stage revealed that there was a significant shift towards energy and protein production during the pre-penetrative phase of development, with an up-regulation of enzymes associated with cellular respiration and protein synthesis, modification and transport. Glycosidic linkage analysis of the cell wall polysaccharides demonstrated that during appressorial development an increase in 1,3- and 1,4-linked glucosyl residues and xylosyl residues was detected along with a significant decrease in galactosyl residues. The use of this in vitro cultivation method demonstrates that it is possible to analyse the pre-penetrative processes of Bgh development in the absence of a plant host.

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