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  • 1. Becker, D.
    et al.
    Braet, C.
    Brumer, Harry
    KTH, Superseded Departments, Biotechnology.
    Claeyssens, M.
    Divne, Christina
    KTH, Superseded Departments, Biotechnology.
    Fagerstrom, B. R.
    Harris, M.
    Jones, T. A.
    Kleywegt, G. J.
    Koivula, A.
    Mahdi, S.
    Piens, K.
    Sinnott, M. L.
    Stahlberg, J.
    Teeri, Tuula T.
    KTH, Superseded Departments, Biotechnology.
    Underwood, M.
    Wohlfahrt, G.
    Engineering of a glycosidase Family 7 cellobiohydrolase to more alkaline pH optimum: the pH behaviour of Trichoderma reesei CeI7A and its E223S/A224H/L225V/T226A/D262G mutant2001In: Biochemical Journal, ISSN 0264-6021, E-ISSN 1470-8728, Vol. 356, p. 19-30Article in journal (Refereed)
    Abstract [en]

    The crystal structures of Family 7 glycohydrolases suggest that a histidine residue near the acid/base catalyst could account for the higher pH optimum of the Humicola insolens endoglucanase Cel7B, than the corresponding Trichoderma reesei enzymes. Modelling studies indicated that introduction of histidine at the homologous position in T. reesei Cel7A (Ala(224)) required additional changes to accommodate the bulkier histidine side chain. X-ray crystallography of the catalytic domain of the E223S/A224H/L225V/T226A/D262G mutant reveals that major differences from the wild-type are confined to the mutations themselves, The introduced histidine residue is in plane with its counterpart in H. insolens Cel7B, but is 1.0 Angstrom (= 0.1 nm) closer to the acid/base Glu(217) residue, with a 3.1 Angstrom contact between N-2 and O'(1). The pH variation of k(cat)/K-m for 3,4-dinitrophenyl lactoside hydrolysis was accurately bell-shaped for both wildtype and mutant, with pK(1) shifting from 2.22+/-0.03 in the wild-type to 3.19+/-0.03 in the mutant, and pK(2) shifting from 5.99+/-0.02 to 6.78+/-0.02. With this poor substrate, the ionizations probably represent those of the free enzyme. The relative k(cat) for 2-chloro-4-nitrophenyl lactoside showed similar behaviour. The shift in the mutant pH optimum was associated with lower k(cat)/K-m values for both lactosides and cellobiosides, and a marginally lower stability. However, k(cat) values for cellobiosides are higher for the mutant. This we attribute to reduced nonproductive binding in the +1 and +2 subsites; inhibition by cellobiose is certainly relieved in the mutant. The weaker binding of cellobiose is due to the loss of two water-mediated hydrogen bonds.

  • 2. Bessueille, Laurence
    et al.
    Sindt, Nicolas
    Guichardant, Michel
    Djerbi, Soraya
    Teeri, Tuula T.
    KTH, School of Biotechnology (BIO), Glycoscience.
    Bulone, Vincent
    KTH, School of Biotechnology (BIO), Glycoscience.
    Plasma membrane microdomains from hybrid aspen cells are involved in cell wall polysaccharide biosynthesis2009In: Biochemical Journal, ISSN 0264-6021, E-ISSN 1470-8728, Vol. 420, p. 93-103Article in journal (Refereed)
    Abstract [en]

    Detergent-resistant plasma membrane microdomains [DRMs (detergent-resistant membranes)] were isolated recently from several plant species. As for animal cells, a large range of cellular functions, such as signal transduction, endocytosis and protein trafficking, have been attributed to plant lipid rafts and DRMs. The data available are essentially based on protcomics and more approaches need to be undertaken to elucidate the precise function of individual populations of DRMs in plants. We report here the first isolation of DRMs from purified plasma membranes of a tree species, the hybrid aspen Populus tremula x tremuloides, and their biochemical characterization. Plasma membranes were solubilized with Triton X-100 and the resulting DRMs were isolated by flotation in sucrose density gradients. The DRMs were enriched in sterols, sphingolipids and glycosylphosphatidylinositol-anchored proteins and thus exhibited similar properties to DRMs from other species. However, they contained key carbohydrate synthases involved in cell wall polysaccharide biosynthesis, namely callose [(1 -> 3)-beta-D-glucan] and cellulose synthases. The association of these enzymes with DRMs was demonstrated using specific glucan synthase assays and antibodies, as well as biochemical and chemical approaches for the characterization of the polysaccharides synthesized in vitro by the isolated DRMs. More than 70% of the total glucan synthase activities present in the original plasma membranes was associated with the DRM fraction. In addition to shedding light on the lipid environment of callose and cellulose synthases, our results demonstrate the involvement of DRMs in the biosynthesis of important cell wall polysaccharides. This novel concept suggests a function of plant membrane microdomains in cell growth and morphogenesis.

  • 3. Faijes, M.
    et al.
    Ima, T.
    Bulone, Vincent
    KTH, Superseded Departments, Biotechnology.
    Planas, A.
    In vitro synthesis of a crystalline (1 -> 3,1 -> 4)-beta-D-glucan by a mutated (1 -> 3,1 -> 4)-beta-D-glucanase from Bacillus2004In: Biochemical Journal, ISSN 0264-6021, E-ISSN 1470-8728, Vol. 380, p. 635-641Article in journal (Refereed)
    Abstract [en]

    Oligo- and poly-saccharides have a large number of important biological functions, and they occur in natural composite materials, such as plant cell walls, where they self-assemble during biosynthesis in a poorly understood manner. They can also be used for the formation of artificial composite materials with industrial applications. Fundamental and applied research in biology and nanobiotechnology would benefit from the possibility of synthesizing tailor-made oligo-/poly-saccharides. In the present paper, we demonstrate that such syntheses are possible using genetically modified glycoside hydrolases, i.e. glycosynthases. The ability of the endoglycosynthase derived from Bacillus ( 1 --> 3,1 --> 4)-beta-D-glucanase to catalyse self-condensation of sugar donors was exploited for the in vitro synthesis of a regular polysaccharicle. The specificity of the enzyme allowed the polymerization of alpha-laminaribiosyl fluoride via the formation of (1 --> 4)-beta-linkages to yield a new linear crystalline (1 --> 3,1 --> 4)-beta-D-glucan with a repeating 4betaG3betaG unit. MS and methylation analyses indicated that the in vitro product consisted of a mixture of oligosaccharides, the one having a degree of polymerization of 12 being the most abundant. Morphological characterization revealed that the (1 --> 3,1 --> 4)-beta-D-glucan forms spherulites which are composed of platelet crystals. X-ray and electron diffraction analyses allowed the proposition of a putative crystallographic structure which corresponds to a monoclinic unit cell with a = 0.834 nm, b = 0.825 nm, c = 2.04 nm and gamma = 90.5degrees. The dimensions of the ab plane are similar to those of cellulose I-beta, but the length of the c-axis is nearly twice that of cellulose I. It is proposed that four glucose residues are present in an extended conformation along the c-axis of the unit cell. The data presented show that glycosynthases represent promising enzymic systems for the synthesis of novel polysaccharides with specific and controlled structures, and for the analysis in vitro of the mechanisms of polymerization and crystallization of potysaccharides.

  • 4. Henriksson, G
    et al.
    Salumets, A
    Divne, Christina
    KTH, School of Biotechnology (BIO).
    Pettersson, G
    Studies of cellulose binding by cellobiose dehydrogenase and a comparison with cellobiohydrolase 11997In: Biochemical Journal, ISSN 0264-6021, E-ISSN 1470-8728, Vol. 324, p. 833-838Article in journal (Refereed)
  • 5. Henriksson, H.
    et al.
    Denman, S. E.
    Campuzano, I. D. G.
    Ademark, P.
    Master, E. R.
    Teeri, Tuula T.
    KTH, Superseded Departments, Biotechnology.
    Brumer, Harry
    KTH, Superseded Departments, Biotechnology.
    N-linked glycosylation of native and recombinant cauliflower xyloglucan endotransglycosylase 16A2003In: Biochemical Journal, ISSN 0264-6021, E-ISSN 1470-8728, Vol. 375, p. 61-73Article in journal (Refereed)
    Abstract [en]

    The gene encoding a XET (xyloglucan endotransglycosylase) from cauliflower (Brassica oleracea var. botrytis) florets has been cloned and sequenced. Sequence analysis indicated a high degree of similarity to other XET enzymes belonging to glycosyl hydrolase family 16 (GH16). In addition to the conserved GH16 catalytic sequence motif EIDFE, there exists one potential N-linked glycosylation site. which is also highly conserved in XET enzymes from this family. Purification of the corresponding protein from extracts of cauliflower florets allowed the fractionation of a single, pure glycoform. which was analysed by MS techniques. Accurate protein mass determination following the enzymic deglycosylation of this glycoform indicated the presence of a high-mannose-type glycan of the general structure GlcNAc(2)Man(6). LC/MS and MS/MS (tandem MS) analysis provided supporting evidence for this structure and confirmed that the glycosylation site (underlined) was situated close to the predicted catalytic residues in the conserved sequence YLSSTNNEHDEIDFEFLGNRTGQPVILQTNVFTGGK. Heterologous expression in Pichia pastoris produced a range of protein glycoforms, which were, on average, more highly mannosylated than the purified native enzyme. This difference in glycosylation did not influence the apparent enzymic activity of the enzyme significantly. However, the removal of high-mannose glycosylation in recombinant cauliflower XET by endoglycosidase H, quantified by electrospray-ionization MS, caused a 40 % decrease in the transglycosylation activity of the enzyme. No hydrolytic activity was detected in native or heterologously expressed BobXET16A, even when almost completely deglycosylated.

  • 6. Knorpp, Carina
    et al.
    Szigyarto, Cristina
    Glaser, Elzbieta
    Evidence for a novel ATP-dependent membrane-associated protease in spinach leaf mitochondria.1995In: Biochemical Journal, ISSN 0264-6021, E-ISSN 1470-8728, Vol. 310 ( Pt 2)Article in journal (Refereed)
    Abstract [en]

    We report the presence of an ATP-dependent proteolytic activity in spinach (Spinacia oleracea) leaf mitochondria. The proteolysis was observed as degradation of newly imported precursor protein. The precursor studied was that of the ATP synthase F1 beta subunit of Nicotiana plumbaginifolia, transcribed and translated in vitro. Degradation of pre-F1 beta was observed during kinetic studies of import in vitro. The degradation was characterized in chase experiments in which the precursor was imported into mitochondria. The import reaction was subsequently stopped by the addition of valinomycin and oligomycin. The fate of the imported precursor inside the mitochondria was monitored under different experimental conditions. There was no proteolytic degradation of the newly imported precursor at 15 degrees C, whereas 50% of the precursor was degraded after a 45 min incubation at 25 degrees C. The proteolytic activity was found to be ATP-dependent and was partially inhibited by a metal chelator, o-phenanthroline. Fractionation of mitochondria prior to degradation showed that all the ATP-dependent degradative activity was associated with the mitochondrial membrane fraction. The membrane-bound protease was inhibited by Pefabloc [4-(2-aminoethyl)-benzenesulphonyl fluoride hypochloride], an inhibitor of serine-type proteases and by N-ethylmaleimide, a thiol group reagent. Our studies thus describe a novel ATP-dependent membrane-associated serine-type protease in plant mitochondria that is capable of degrading newly imported non-assembled proteins.

  • 7.
    Knorpp, Carina
    et al.
    Stockholm University.
    Szigyarto, Cristina
    Stockholm University.
    Glaser, Elzbieta
    Stockholm University.
    Evidence for a novel ATP-dependent membrane-associated protease in spinach leaf mitochondria1995In: Biochemical Journal, ISSN 0264-6021, E-ISSN 1470-8728, Vol. 310, p. 527-531Article in journal (Refereed)
    Abstract [en]

    We report the presence of an ATP-dependent proteolytic activity in spinach (Spinacia oleracea) leaf mitochondria. The proteolysis was observed as degradation of newly imported precursor protein. The precursor studied was that of the ATP synthase F1 beta subunit of Nicotiana plumbaginifolia, transcribed and translated in vitro. Degradation of pre-F1 beta was observed during kinetic studies of import in vitro. The degradation was characterized in chase experiments in which the precursor was imported into mitochondria. The import reaction was subsequently stopped by the addition of valinomycin and oligomycin. The fate of the imported precursor inside the mitochondria was monitored under different experimental conditions. There was no proteolytic degradation of the newly imported precursor at 15 degrees C, whereas 50% of the precursor was degraded after a 45 min incubation at 25 degrees C. The proteolytic activity was found to be ATP-dependent and was partially inhibited by a metal chelator, o-phenanthroline. Fractionation of mitochondria prior to degradation showed that all the ATP-dependent degradative activity was associated with the mitochondrial membrane fraction. The membrane-bound protease was inhibited by Pefabloc [4-(2-aminoethyl)-benzenesulphonyl fluoride hypochloride], an inhibitor of serine-type proteases and by N-ethylmaleimide, a thiol group reagent. Our studies thus describe a novel ATP-dependent membrane-associated serine-type protease in plant mitochondria that is capable of degrading newly imported non-assembled proteins.

  • 8.
    Larsbrink, Johan
    et al.
    KTH, School of Biotechnology (BIO), Glycoscience.
    Izumi, Atsushi
    Ibatullin, Farid M.
    KTH, School of Biotechnology (BIO), Glycoscience.
    Nakhai, Azadeh
    KTH, School of Biotechnology (BIO), Glycoscience.
    Gilbert, Harry J.
    Davies, Gideon J.
    Brumer, Harry
    KTH, School of Biotechnology (BIO), Glycoscience.
    Structural and enzymatic characterization of a glycoside hydrolase family 31 alpha-xylosidase from Cellvibrio japonicus involved in xyloglucan saccharification2011In: Biochemical Journal, ISSN 0264-6021, E-ISSN 1470-8728, Vol. 436, p. 567-580Article in journal (Refereed)
    Abstract [en]

    The desire for improved methods of biomass conversion into fuels and feedstocks has re-awakened interest in the enzymology of plant cell wall degradation. The complex polysaccharide xyloglucan is abundant in plant matter, where it may account for up to 20% of the total primary cell wall carbohydrates. Despite this, few studies have focused on xyloglucan saccharification, which requires a consortium of enzymes including endo-xyloglucanases, alpha-xylosidases, beta-galactosidases and alpha-L-fucosidases, among others. In the present paper, we show the characterization of Xy131A, a key alpha-xylosidase in xyloglucan utilization by the model Gram-negative soil saprophyte Cellvibrio japonicus. CjXy131A exhibits high regiospecificity for the hydrolysis of XGOs (xylogluco-oligosaccharides), with a particular preference for longer substrates. Crystallographic structures of both the apo enzyme and the trapped covalent 5-fluoro-beta-xylosyl-enzyme intermediate, together with docking studies with the XXXG heptasaccharide, revealed, for the first time in GH31 (glycoside hydrolase family 31), the importance of PA14 domain insert in the recognition of longer oligosaccharides by extension of the active-site pocket. The observation that CjXy131A was localized to the outer membrane provided support for a biological model of xyloglucan utilization by C. japonicas, in which XGOs generated by the action of a secreted endo-xyloglucanase are ultimately degraded in close proximity to the cell surface. Moreover, the present study diversifies the toolbox of glycosidases for the specific modification and saccharification of cell wall polymers for biotechnological applications.

  • 9. Lombard, Vincent
    et al.
    Bernard, Thomas
    Rancurel, Corinne
    Brumer, Harry
    KTH, School of Biotechnology (BIO), Glycoscience.
    Coutinho, Pedro M.
    Henrissat, Bernard
    A hierarchical classification of polysaccharide lyases for glycogenomics2010In: Biochemical Journal, ISSN 0264-6021, E-ISSN 1470-8728, Vol. 432, p. 437-444Article in journal (Refereed)
    Abstract [en]

    Carbohydrate-active enzymes face huge substrate diversity in a highly selective manner using only a limited number of available folds. They are therefore subjected to multiple divergent and convergent evolutionary events. This and their frequent modularity render their functional annotation in genomes difficult in a number of cases. In the present paper, a classification of polysaccharide lyases (the enzymes that cleave polysaccharides using an elimination instead of a hydrolytic mechanism) is shown thoroughly for the first time. Based on the analysis of a large panel of experimentally characterized polysaccharide lyases, we examined the correlation of various enzyme properties with the three levels of the classification: fold, family and subfamily. The resulting hierarchical classification, which should help annotate relevant genes in genomic efforts, is available and constantly updated at the Carbohydrate-Active Enzymes Database (http://www.cazy.org).

  • 10. Mackenzie, L F
    et al.
    Sulzenbacher, G
    Divne, Christina
    KTH, School of Biotechnology (BIO).
    Jones, T A
    Woldike, H F
    Schulein, M
    Withers, S G
    Davies, G J
    Crystal structure of the family 7 endoglucanase I (Cel7B) from Humicola insolens at 2.2 angstrom resolution and identification of the catalytic nucleophile by trapping of the covalent glycosyl-enzyme intermediate1998In: Biochemical Journal, ISSN 0264-6021, E-ISSN 1470-8728, Vol. 335, p. 409-416Article in journal (Refereed)
  • 11. Saura-Valls, M.
    et al.
    Faure, R.
    Ragas, S.
    Piens, K.
    Brumer, Harry
    KTH, School of Biotechnology (BIO), Glycoscience.
    Teeri, Tuula T.
    KTH, School of Biotechnology (BIO), Glycoscience.
    Cottaz, S.
    Driguez, H.
    Planas, A.
    Kinetic analysis using low-molecular mass xyloglucan oligosaccharides defines the catalytic mechanism of a Populus xyloglucan endotransglycosylase2006In: Biochemical Journal, ISSN 0264-6021, E-ISSN 1470-8728, Vol. 395, p. 99-106Article in journal (Refereed)
    Abstract [en]

    Plant XETs [XG (xyloglucan) endotransglycosylases] catalyse the transglycosylation front a XG donor to a XG or low-molecular-mass XG fragment Lis the acceptor, and are thought to be important enzymes in the formation and remodelling of the cellulose-XG three-dimensional network in the primary plant cell wall. Current methods to assay XET activity use the XG polysaccharide as the donor substrate, and present limitations for kinetic and mechanistic studies of XET action due to the polymeric and polydisperse nature of the substrate. A novel activity assay based oil HPCE (high performance capillary electrophoresis), in con, junction with a defined low-molecular-mass XGO {XG oligosaccharicle; (XXXGXXXG, where G = Glc beta 1,4- and X = [Xyl alpha 1,6]Glc beta 1,4-)l as the glycosyl donor and a heptasaccharide derivatized with ANTS [8-aminonaphthalene-1,3,6-trisulphonic acid; (XXXG-ANTS)] as the acceptor substrate was developed and validated. The recombinant enzyme PttXET16A from Popidus tremula x tremuloides (hybrid aspen) was characterized using file donor/acceptor pair indicated above, for which preparative scale syntheses have been optimized. The low-molecular-mass donor underwent a single transglycosylation reaction to the acceptor substrate under initial-rate conditions. with a pH optimum at 5.0 and maximal activity between 30 and 40 degrees C. Kinetic data are best explained by a ping-pong bi-bi mechanism With Substrate inhibition by both donor and acceptor. This is the first assay for XETs using a donor Substrate other than polymeric XG, enabling quantitative kinetic analysis of different XGO donors for specificity, and subsite mapping studies of XET enzymes.

  • 12. Selles, Benjamin
    et al.
    Hugo, Martin
    Trujillo, Madia
    Srivastava, Vaibhav
    Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå Plant Science Center.
    Wingsle, Gunnar
    Jacquot, Jean-Pierre
    Radi, Rafael
    Rouhier, Nicolas
    Hydroperoxide and peroxynitrite reductase activity of poplar thioredoxin-dependent glutathione peroxidase 5: kinetics, catalytic mechanism and oxidative inactivation.2012In: Biochemical Journal, ISSN 0264-6021, E-ISSN 1470-8728, Vol. 442, p. 369-380Article in journal (Refereed)
    Abstract [en]

    Glutathione peroxidases constitute a family of peroxidases, including selenocysteine- or cysteine-containing isoforms ((SeCys- or Cys-Gpxs) which are regenerated by glutathione or thioredoxins, (Trxs) respectively. We present here new data concerning the substrates of poplar Gpx5 and the residues involved in its catalytic mechanism. This study establishes the capacity of this Cys-Gpx to reduce peroxynitrite with a catalytic efficiency of 106 M-1 s-1. In PtGpx5, Glu79, which replaces the Gln usually found in Gpx catalytic tetrad, is likely involved in substrate selectivity. Although the redox midpoint potential of the Cys44-Cys92 disulfide and the pKa of Cys44 are not modified in the E79Q variant, it exhibited significantly improved kinetic parameters (Kperoxide and kcat) with tert-butyl hydroperoxide. The characterization of the monomeric Y151R variant demonstrated that PtGpx5 is not an obligate homodimer. Also, we show that the conserved Phe90 is important for Trx recognition and that Trx-mediated recycling of PtGpx5 occurs via the formation of a transient disulfide between the Trx catalytic cysteine and the Gpx5 resolving cysteine. Finally, we demonstrate that the conformational changes observed during the transition from the reduced to the oxidized form of PtGpx5 are primarily determined by the oxidation of the peroxidatic cysteine into sulfenic acid. Besides, mass spectrometry analysis of in vitro oxidized PtGpx5 demonstrated that the peroxidatic cysteine can be over-oxidized into sulfinic or sulfonic acids. This suggests that some isoforms could have dual functions potentially acting as hydrogen peroxide- and peroxynitrite-scavenging systems and/or as mediators of peroxide signalling as proposed for 2-Cys peroxiredoxins.

  • 13. Stahl, A.
    et al.
    Pavlov, P. F.
    Al-Khalili Szigyarto, Cristina
    Glaser, E.
    Rapid degradation of the presequence of the F-1 beta precursor of the ATP synthase inside mitochondria2000In: Biochemical Journal, ISSN 0264-6021, E-ISSN 1470-8728, Vol. 349, p. 703-707Article in journal (Refereed)
    Abstract [en]

    We have investigated the fate of the presequence of an overexpressed protein derived from the precursor of the F(1)beta subunit of ATP synthase after import and processing in mitochondria. Our studies revealed a rapid degradation of the presequence inside mitochondria catalysed by matrix-located protease(s). In contrast, the mature portion of the precursor was not degraded. This is the first experimental evidence of the rapid degradation of the F(1)beta a mitochondrial presequence in organello after in vitro import and processing.

  • 14.
    Woestenenk, Esmeralda A.
    et al.
    KTH, Superseded Departments, Biotechnology.
    Gongadze, George M.
    Shcherbakov, Dmitry V.
    Rak, Alexey V.
    Garber, Maria B.
    Härd, Torleif
    KTH, Superseded Departments, Biotechnology.
    Berglund, Helena
    KTH, Superseded Departments, Biotechnology.
    The solution structure of ribosomal protein L18 from Thermus thermophilus reveals a conserved RNA-binding fold2002In: Biochemical Journal, ISSN 0264-6021, E-ISSN 1470-8728, Vol. 363, no 3, p. 553-561Article in journal (Refereed)
    Abstract [en]

    We have determined the solution structure of ribosomal protein L18 from Thermus thermophilus. L18 is a 12.5 kDa protein of the large subunit of the ribosome and binds to both 5 S and 23 S rRNA. In the uncomplexed state L18 folds to a mixed α/β globular structure with a long disordered N-terminal region. We compared our high-resolution structure with RNA-complexed L 18 from Haloarcula marismortui and T. thermophilus to examine RNA-induced as well as species-dependent structural differences. We also identified T. thermophilus S11 as a structural homologue and found that the structures of the RNA-recognition sites are conserved. Important features, for instance a bulge in the RNA-contacting β-sheet, are conserved in both proteins. We suggest that the L18 fold recognizes a specific RNA motif and that the resulting RNA-protein-recognition module is tolerant to variations in sequence.

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