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Biochemical Characterization of Β-Xylan Acting Glycoside

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BIOCHEMICAL CHARACTERIZATION OF β-XYLAN ACTING GLYCOSIDE HYDROLASES FROM THE THERMOPHILIC BACTERIUM Caldicellulosiruptor saccharolyticus Thesis Submitted to The School of Engineering of the UNIVERSITY OF DAYTON In Partial Fulfillment of the Requirements for The Degree of Master of Science in Chemical Engineering By Jin Cao Dayton, Ohio December, 2012 BIOCHEMICAL CHARACTERIZATION OF β-XYLAN ACTING GLYCOSIDE HYDROLASES FROM THE THERMOPHILIC BACTERIUM Caldicellulosiruptor saccharolyticus Name: Cao, Jin APPROVED BY: ______________________ ________________________ Donald A. Comfort, Ph.D. Amy Ciric, Ph.D. Advisory Committee Chairman Committee Member Research Advisor & Assistant Professor Lecturer Department of Department of Chemical & Materials Engineering Chemical & Materials Engineering ________________________ Karolyn Hansen, Ph.D. Committee Member Assistant Professor Department of Biology _______________________ ________________________ John G. Weber, Ph.D. Tony E. Saliba, Ph.D. Associate Dean Dean, School of Engineering School of Engineering & Wilke Distinguished Professor ii ABSTRACT BIOCHEMICAL CHARACTERIZATION OF Β-XYLAN ACTING GLYCOSIDE HYDROLASES FROM THE THERMOPHILIC BACTERIUM Caldicellulosiruptor saccharolyticus Name: Cao, Jin University of Dayton Research Advisor: Donald A. Comfort Fossil fuels have been the dominant source for energy around the world since the industrial revolution, however, with the increasing demand for energy and decreasing fossil fuel reserves alternative energy sources must be exploited. Bio-ethanol is a promising prospect for an alternative energy source to petroleum, especially when plant biomass is used as the replacement carbon source. This gives greater benefit for implementation of bioethanol as a viable alternative transport fuel than food stocks such as starch from corn. The implementation of this next generation of bioethanol requires more robust and environmentally friendly methods for degrading cellulose and hemicellulose, the two major components of plant biomass. This work looks to understand the role and mechanism of xylan degradation by glycoside hydrolases from the thermophilic bacterium Caldicellulosiruptor saccharolyticus. The degradation of xylan is achieved through multiple glycoside hydrolase enzymes working synergistically. iii Among these genes is the β-xlyosidase from C. saccharolyticus, XynD (Csac_2409), which was characterized to determine the optimal temperature, pH value, kinetic properties, hydrolysis pattern of oligosaccharides, and effects of inhibition by xylose. This biochemical characterization of the enzyme provides insight into its role in hydrolyzing xylan oligosaccharides by C. saccharolyticus and also potential biotechnological applications of the enzyme for upstream processing of hemicellulose for bioenergy application. iv ACKNOWLEDGEMENTS I sincerely thank Dr. Donald Comfort, my advisor, for all the help he has given to me since I started my study in UD. He provided a great stage to let me show my thinking and exchange ideas with him. His patient and open-minding make me never feel tough for my research. I have obtained a great deal of encouragement and approval from him that makes me feel confident to overcome the difficulties and burdens in research. I would like to thank all faculty and staff from Chemical Engineering Department. Your wonderful classes give me the opportunities to further understand what an engineer truly is. Thanks my defense committee, Dr. Ciric and Dr. Hansen for their direction and invaluable advice along this project. Thank you to all my friends, without your supports, either from the academic or daily life, I could not stand here today. This is thesis dedicated to my parents and bother. Your love is my power to face all the difficulties. v TABLE OF CONTENTS ABSTRACT ....................................................................................................................... iii ACKNOWLEDGEMENTS ................................................................................................ v TABLE OF CONTENTS ................................................................................................... vi LIST OF FIGURES ......................................................................................................... viii LIST OF TABLES .............................................................................................................. x CHAPTER 1 LIGNOCELLULOSIC BIOMASS FOR BIOETHANOL PRODUCTION ............................................................................................................................................. 1 Introduction ..................................................................................................................... 1 Bioethanol for Fuel.......................................................................................................... 4 Bioethanol Production ..................................................................................................... 7 Pretreatment and separation of lignin .......................................................................... 8 Hydrolyzing lignocellulosic biomass ........................................................................ 10 Caldicellulosiruptor saccharolyticus .......................................................................... 15 Research Goals .............................................................................................................. 16 vi CHAPTER 2 BIOCHEMICAL CHARACTERIZATION OF β-XYLODIDASE FROM THE THERMOPHILIC BATERIUM Caldicellulosiruptor saccharolyticus ................ 17 Introduction ................................................................................................................... 17 Materials and Methods .................................................................................................. 19 PCR, cloning and expression ..................................................................................... 19 Purification of recombinant xylan 1,4-β- xylosidase XynD ...................................... 21 Determination of the molecular weight of xylan 1,4-β- xylosidase .......................... 22 Enzyme assay and kinetics characterization using synthetic substrates .................... 22 Hydrolysis of Natural Substrates and Thin-Layer chromatography (TLC) .............. 23 Results ........................................................................................................................... 24 CHAPTER 3 CONCLUSION........................................................................................... 37 Conclusion ..................................................................................................................... 37 Future Work .................................................................................................................. 38 REFERENCES ................................................................................................................. 40 APPENDIX A PRIMER SEQUENCE AND RELEVANT PCR MATERIALS ............. 52 APPENDIX B LIQUID AND SOLID MEDIA ................................................................ 54 APPENDIX C LIGATION ............................................................................................... 57 vii LIST OF FIGURES Figure 1: Lignocellulosic Ethanol Pathway ........................................................................ 8 Figure 2: Cellulose hydrolysis procedure by three major types of cellulases. .................. 12 Figure 3 : General structure of xylan. ............................................................................... 14 Figure 4: Structure of xylo-oligosaccharide. .................................................................... 14 Figure 5: Procedure for gene cloning................................................................................ 21 Figure 6: SDS-PAGE analysis of purified XynD from C. saccharolyticus. ..................... 24 Figure 7: a) Lineweaver-Burk plot for XynD incubated with substrate pNP--D- xylopyranoside; b) Plot of experimental initial velocity versus substrate concentration. 26 Figure 8: a) Lineweaver-Burk inhibition plot of xylose on XynD, and b) Michaelis- Menten plot of the same data showing the increase in the corresponding half-maximal . 29 Figure 9: Thin layer chromatography of the products formed from the hydrolysis of xylo- oligosaccharides incubated with XynD ............................................................................. 31 Figure 10: Estimated quaternary structure 3D model of the XynD, from C. saccharolyticus. ................................................................................................................ 33 viii Figure 11: Amino acid sequence XynD, from C. saccharolyticus, aligned with protein XynB, from T. saccharolyticum, XynB, from G. stearothermophilus and XynB2, from C. crescentus. ......................................................................................................................... 34 Figure 12: a) (β/α)8- barrel fold 3D secondary structure of XynD, from C. saccharolyticus and the active and b) overlayed 3D structure for Csac_XynD, T. saccharolyticum, XynB, G. stearothermophilus XynB2, and C. crescentus XynB2 ................................................. 36 ix LIST OF TABLES Table 1: The composition of potential lignocellulosic materials ........................................ 6 Table 2: Heating cycle parameters for PCR ....................................................................
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    bioRxiv preprint doi: https://doi.org/10.1101/2020.06.30.179523; this version posted July 1, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 CLASSIFICATION: Biological Sciences / Physical Sciences (Chemistry) TITLE: Structure of human endo-α-1,2-mannosidase (MANEA), an antiviral host- glycosylation target AUTHORS: Łukasz F. Sobala1, Pearl Z Fernandes2, Zalihe Hakki2, Andrew J Thompson1, Jonathon D Howe3, Michelle Hill3, Nicole Zitzmann3, Scott Davies4, Zania Stamataki4, Terry D. Butters3, Dominic S. Alonzi3, Spencer J Williams2,*, Gideon J Davies1,* AFFILIATIONS: 1. Department of Chemistry, University of York, YO10 5DD, United Kingdom. 2. School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia. 3. Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road Oxford OX1 3QU, United Kingdom. 4. Institute for Immunology and Immunotherapy, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom. CORRESPONDING AUTHOR: [email protected], ORCID 0000-0001-6341-4364 [email protected] ORCID 0000-0002-7343-776X bioRxiv preprint doi: https://doi.org/10.1101/2020.06.30.179523; this version posted July 1, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license.