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  • 1.
    Aspeborg, Henrik
    et al.
    KTH, School of Biotechnology (BIO), Glycoscience.
    Coutinho, Pedro M.
    Wang, Yang
    KTH, School of Biotechnology (BIO), Glycoscience.
    Brumer, Harry
    KTH, School of Biotechnology (BIO), Glycoscience.
    Henrissat, Bernard
    Evolution, substrate specificity and subfamily classification of glycoside hydrolase family 5 (GH5)2012In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 12, no 1, p. 186-Article in journal (Refereed)
    Abstract [en]

    Background: The large Glycoside Hydrolase family 5 (GH5) groups together a wide range of enzymes acting on beta-linked oligo- and polysaccharides, and glycoconjugates from a large spectrum of organisms. The long and complex evolution of this family of enzymes and its broad sequence diversity limits functional prediction. With the objective of improving the differentiation of enzyme specificities in a knowledge-based context, and to obtain new evolutionary insights, we present here a new, robust subfamily classification of family GH5. Results: About 80% of the current sequences were assigned into 51 subfamilies in a global analysis of all publicly available GH5 sequences and associated biochemical data. Examination of subfamilies with catalytically-active members revealed that one third are monospecific (containing a single enzyme activity), although new functions may be discovered with biochemical characterization in the future. Furthermore, twenty subfamilies presently have no characterization whatsoever and many others have only limited structural and biochemical data. Mapping of functional knowledge onto the GH5 phylogenetic tree revealed that the sequence space of this historical and industrially important family is far from well dispersed, highlighting targets in need of further study. The analysis also uncovered a number of GH5 proteins which have lost their catalytic machinery, indicating evolution towards novel functions. Conclusion: Overall, the subfamily division of GH5 provides an actively curated resource for large-scale protein sequence annotation for glycogenomics; the subfamily assignments are openly accessible via the Carbohydrate-Active Enzyme database at http://www.cazy.org/GH5.html.

  • 2.
    Chen, Zhi-Hui
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics. Taiyuan University of Technology, China; Beijing University of Posts and Telecommunications, China .
    Wang, Yang
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Yang, Yibiao
    Qiao, Na
    Wang, Yuncai
    Yu, Zhongyuan
    Enhanced normal-direction excitation and emission of dual-emitting quantum dots on a cascaded photonic crystal surface2014In: Nanoscale, ISSN 2040-3364, E-ISSN 2040-3372, Vol. 6, no 24, p. 14708-14715Article in journal (Refereed)
    Abstract [en]

    Large normal-direction excitation and emission of dual-emitting quantum dots (QDs) are essential for practical application of QD sensors based on the ratiometric fluorescence response. We have numerically demonstrated an all-dielectric four-layer cascaded photonic crystal (CPC) structure (alternating TiO2 and SiO2/SU8 layers with two dimensional nanoscale patterns in each layer) which is capable of providing normal-direction high Q-factor leaky modes at excitation wavelengths of QDs and two low Q-factor leaky modes coinciding with the two emission peaks of a dual-emitting QD. Normal-direction excitation and far-field emission of the dual-emitting QDs are enhanced significantly when QDs are distributed on/in the top TiO2 layer of the CPC structure, especially in the spatial distribution areas of the resonant leaky modes. QDs can be positioned differently depending on the applications. Positioning QDs on the top TiO2 layer will improve the signal-to-noise ratios of QD biomedical/chemical/temperature sensors, while embedding QDs in the top TiO2 layer will increase the light extraction from the QD light emitting device, making our CPC a versatile optical coupling structure. Our CPC-QD structure is experimentally feasible and robust against the parameter perturbation in real fabrication.

  • 3.
    Wang, Lei
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Duan, Lele
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Wang, Ying
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ahlquist, Mårten
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Sun, Licheng
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry. State Key Lab of Fine Chemicals, DUT-KTH Joint Education and Research Center on Molecular Devices, Dalian University of Technology (DUT)Dalian, China .
    Highly efficient and robust molecular water oxidation catalysts based on ruthenium complexes2014In: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, Vol. 50, no 85, p. 12947-12950Article in journal (Refereed)
    Abstract [en]

    Two monomeric ruthenium molecular catalysts for water oxidation have been prepared, and both of them show high activities in pH 1.0 aqueous solutions, with an initial rate of over 1000 turnover s(-1) by complex 1, and a turnover number of more than 100 000 by complex 2.

  • 4.
    Wang, Yang
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Discovery and investigation of glycoside hydrolase family 5 enzymes with potential use in biomass conversion2015Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Glycoside hydrolases (GHs) cleave glycosidic bonds in glycoconjugates, oligosaccharides and polysaccharides such as cellulose and various hemicelluloses. Mannan is a major group of hemicelluloses. In higher plants, they usually serve as storage carbohydrates in seeds and tubers or as structural polysaccharides cross-linking with cellulose/lignin in cell walls. In industrial fields, this renewable biomass component can be used in various areas such as production of biofuels and health-benefit manno-oligosaccharides; and mannan degrading enzymes, especially mannanases, are important molecular tools for controlling mannan polysaccharides properties in biomass conversion. In this thesis, the evolution, substrate specificity and subfamily classification of the most important GH family, i.e., glycoside hydrolase family 5 (GH5), are presented providing a powerful tool for exploring GH5 enzymes in search for enzymes with interesting properties for sustainable biomass conversion. Additionally, three GH5_7 mannanases from Arabidopsis thaliana (AtMan5-1, AtMan5-2 and AtMan5-6) were investigated in the present study. Bioinformatics tools, heterologous expression, and enzymology were applied in order to reveal the catalytic properties of the target enzymes, increase understanding of plant mannanase evolution, and evaluate their potential use in biomass conversion. This approach revealed: (1) AtMan5-1 exhibits mannan hydrolase/transglycosylase activity (MHT), (2) AtMan5-2 preferably degrades mannans with a glucomannan backbone, and (3) AtMan5-6 is a relatively thermotolerant enzyme showing high catalytic efficiency for conversion of glucomannan and galactomannan making this plant mannanase an interesting candidate for biotechnological applications of digesting various mannans. Moreover, these studies suggest an evolutionary diversification of plant mannanase enzymatic function.

  • 5.
    Wang, Yang
    KTH, School of Biotechnology (BIO), Glycoscience.
    Exploring glycoside hydrolase family 5 (GH5) enzymes2013Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    In 1990, the classification of carbohydrate-active enzymes (CAZymes) was introduced by the scientist Bernard Henrissat. According to sequence similarity, these enzymes were separated into families with conserved structures and reaction mechanisms. One interesting class of CAZymes is the group of glycoside hydrolases (GHs) containing more than 138000 modules divided into 131 families as of February 2013. One of the most versatile and the largest of these GH families, containing enzymes with numerous biomass-deconstructing activities, is glycoside hydrolase family 5 (GH5). However, for large and diverse families like the GH5 family, another layer of classification is required to get a better understanding of the evolution of diverse enzyme activities. In Paper I, a new subfamily classification of GH5 is presented in order to sort the family members into distinct groups with predictive power. In total, 51 subfamilies were defined. Despite the fact that several hundred GH5 enzymes have been characterized, 20 subfamilies lacking biochemically characterized enzymes and 38 subfamilies without structural data were identified. These highlighted subfamilies contain interesting targets for future investigation.

    The GH5 family includes endo-β-mannanases catalyzing the hydrolysis of the β-1,4-linked backbone of mannan polysaccharides, which are common hemicelluloses found as storage and structural polymers in plant cell walls. Mannans are commonly utilized as raw biomaterials in food, feed, paper, textile and cosmetic industries, and mannanases are often applied for modifying and controlling the property of mannan polysaccharides in such applications. The overwhelming majority of characterized mannanases are from microbial origin. The situation for plant mannanases is quite different, as the catalytic properties for only a handful have been determined. Paper II describes the first characterization of a heterologously expressed Arabidopsis β-mannanase.

  • 6.
    Wang, Yang
    et al.
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Azhar, Shoaib
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Gandini, Rosaria
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Divne, Christina
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Ezcurra, Ines
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Aspeborg, Henrik
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Biochemical characterization of the novel endo-β-mannanase AtMan5-2 from Arabidopsis thalianaManuscript (preprint) (Other academic)
  • 7.
    Wang, Yang
    et al.
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Azhar, Shoaib
    KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center. KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Gandini, Rosaria
    KTH, School of Biotechnology (BIO), Industrial Biotechnology. Karolinska Institutet, Stockholm.
    Divne, Christina
    KTH, School of Biotechnology (BIO), Industrial Biotechnology. Karolinska Institutet, Stockholm.
    Ezcurra, Ines
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Aspeborg, Henrik
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Biochemical characterization of the novel endo-β-mannanase AtMan5-2 from Arabidopsis thaliana2015In: Plant Science, ISSN 0168-9452, E-ISSN 1873-2259, Vol. 241, p. 151-163Article in journal (Refereed)
    Abstract [en]

    Plant mannanases are enzymes that carry out fundamentally important functions in cell wall metabolism during plant growth and development by digesting manno-polysaccharides. In this work, the Arabidopsis mannanase 5-2 (AtMan5-2) from a previously uncharacterized subclade of glycoside hydrolase family 5 subfamily 7 (GH5_7) has been heterologously produced in Pichia pastoris. Purified recombinant AtMan5-2 is a glycosylated protein with an apparent molecular mass of 50 kDa, a pH optimum of 5.5-6.0 and a temperature optimum of 25 degrees C. The enzyme exhibits high substrate affinity and catalytic efficiency on mannan substrates with main chains containing both glucose and mannose units such as konjac glucomannan and spruce galactoglucomannan. Product analysis of manno-oligosaccharide hydrolysis shows that AtMan5-2 requires at least six substrate-binding subsites. No transglycosylation activity for the recombinant enzyme was detected in the present study. Our results demonstrate diversification of catalytic function among members in the Arabidopsis GH5_7 subfamily.

  • 8.
    Wang, Yang
    et al.
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Azhar, Shoaib
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Gandini, Rosaria
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Divne, Christina
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Ezcurra, Ines
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Aspeborg, Henrik
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Investigating the function and biochemical properties of Arabidopsis mannanase 5-6Manuscript (preprint) (Other academic)
  • 9.
    Wang, Yang
    et al.
    KTH, School of Biotechnology (BIO), Glycoscience.
    Vilaplana, Francisco
    KTH, School of Biotechnology (BIO), Glycoscience.
    Brumer, Harry
    Aspeborg, Henrik
    KTH, School of Biotechnology (BIO), Glycoscience.
    Enzymatic characterization of a GH5_7 mannanase from Arabidopsis thalianaManuscript (preprint) (Other academic)
  • 10.
    Wang, Yang
    et al.
    KTH, School of Biotechnology (BIO), Glycoscience. KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Vilaplana, Francisco
    KTH, School of Biotechnology (BIO), Glycoscience. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center.
    Brumer, Harry
    KTH, School of Biotechnology (BIO), Glycoscience.
    Aspeborg, Henrik
    KTH, School of Biotechnology (BIO), Glycoscience. KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Enzymatic characterization of a glycoside hydrolase family 5 subfamily 7 (GH5_7) mannanase from Arabidopsis thaliana2014In: Planta, ISSN 0032-0935, E-ISSN 1432-2048, Vol. 239, no 3, p. 653-665Article in journal (Refereed)
    Abstract [en]

    Each plant genome contains a repertoire of beta-mannanase genes belonging to glycoside hydrolase family 5 subfamily 7 (GH5_7), putatively involved in the degradation and modification of various plant mannan polysaccharides, but very few have been characterized at the gene product level. The current study presents recombinant production and in vitro characterization of AtMan5-1 as a first step towards the exploration of the catalytic capacity of Arabidopsis thaliana beta-mannanase. The target enzyme was expressed in both E. coli (AtMan5-1e) and P. pastoris (AtMan5-1p). The main difference between the two forms was a higher observed thermal stability for AtMan5-1p, presumably due to glycosylation of that particular variant. AtMan5-1 displayed optimal activity at pH 5 and 35 A degrees C and hydrolyzed polymeric carob galactomannan, konjac glucomannan, and spruce galactoglucomannan as well as oligomeric mannopentaose and mannohexaose. However, the galactose-rich and highly branched guar gum was not as efficiently degraded. AtMan5-1 activity was enhanced by Co2+ and inhibited by Mn2+. The catalytic efficiency values for carob galactomannan were 426.8 and 368.1 min(-1) mg(-1) mL for AtMan5-1e and AtMan5-1p, respectively. Product analysis of AtMan5-1p suggested that at least five substrate-binding sites were required for manno-oligosaccharide hydrolysis, and that the enzyme also can act as a transglycosylase.

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