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Investigation of the Energy Metabolism and Stress Defence Pathways of the Emerging Pathogen Campylobacter Concisus and Other Human Hosted Campylobacter Species

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Investigation of the Energy Metabolism and Stress Defence Pathways of the Emerging Pathogen Campylobacter Concisus and Other Human Hosted Campylobacter Species Investigation of the energy metabolism and stress defence pathways of the emerging pathogen Campylobacter concisus and other human hosted Campylobacter species Melissa Yeow A thesis submitted in fulfilment of the requirements for the degree of Masters by Research (Biotechnology) Supervisor: Dr Li Zhang School of Biotechnology and Biomolecular Sciences Faculty of Science The University of New South Wales 2020 ORIGINALITY STATEMENT ‘I hereby declare that this submission is my own work and to the best of my knowledge it contains no materials previously published or written by another person, or substantial proportions of material which have been accepted for the award of any other degree or diploma at UNSW or any other educational institution, except where due acknowledgement is made in the thesis. Any contribution made to the research by others, with whom I have worked at UNSW or elsewhere, is explicitly acknowledged in the thesis. I also declare that the intellectual content of this thesis is the product of my own work, except to the extent that assistance from others in the project's design and conception or in style, presentation and linguistic expression is acknowledged.’ Signed …………………………………………….............. Date ……………………………5/3/2020.……….............. I Thesis/Dissertation Sheet Surname/Family Name : Yeow Given Name/s : Melissa, Wei Bao Abbreviation for degree as given in the University : MSc – Biotechnology (2036) calendar Faculty : Science School : School of Biotechnology and Biomolecular Sciences Investigation of the energy metabolism and stress defence pathways of the Thesis Title : emerging pathogen Campylobacter concisus and other human hosted Campylobacter species Abstract 350 words maximum: (PLEASE TYPE) Campylobacter species have historically been considered non-saccharyolytic and unable to ferment sugars for energy. Recent evidence refutes this, as several species have been found to use fucose, or glucose via the Entner Doudoroff pathway. Additionally, all human-hosted Campylobacter species have been observed to require hydrogen for growth, but little information is available about their energy metabolisms. Thus, this project examines the pathways of central carbon metabolism and energy metabolism of human-hosted Campylobacter species, using the model organism Escherichia coli, and the most well-studied Campylobacter species, Campylobacter jejuni as references for BLASTp comparison. This project also investigates their oxidative and nitrosative stress mechanisms, which protect bacteria from reactive oxygen and nitrogen species generated by the electron transport chain during respiration and host immune defense. This study found that key enzymes from glycolytic pathways, the tricarboxylic acid cycle and fucose use pathways were not identified in human-hosted Campylobacter species, providing a molecular basis for their non-saccharyolytic nature. Analysis of human-hosted Campylobacter species found that they had branched electron transport chains similar to C. jejuni, but with fewer possible electron donors and acceptors. Enzymes for use of hydrogen were encoded in all species. Unlike in C. jejuni, enzymes for use of lactate, sulfite and gluconate were not encoded in all species examined, and enzymes for use of fumarate, nitrite and tetrathionate were uncommon. Dimethylsulphoxide and fumarate were proven experimentally to be used as electron acceptors by Campylobacter concisus, as their addition to media significantly increased growth of C. concisus. Likely fewer possible amino acids are used, as enzymes for use of proline, serine and branched chain amino acids were not encoded. Fewer oxidative and nitrosative stress defence genes were encoded, and the key enzyme catalase was not encoded in most species, suggesting that they are more sensitive to oxidative and nitrosative stress than C. jejuni. However, the nitric oxide reductase NorZ and nitrous oxide reductase NosZ previously reported in C. concisus are present in most species. In summary, this project provides a molecular basis for the non-saccharolytic and hydrogen-dependent nature of human-hosted Campylobacter species, presenting insights into their growth requirements and pathogenicity. Declaration relating to disposition of project thesis/dissertation I hereby grant to the University of New South Wales or its agents a non-exclusive licence to archive and to make available (including to members of the public) my thesis or dissertation in whole or in part in the University libraries in all forms of media, now or here after known. I acknowledge that I retain all intellectual property rights which subsist in my thesis or dissertation, such as copyright and patent rights, subject to applicable law. I also retain the right to use all or part of my thesis or dissertation in future works (such as articles or books). …………………………………………………………… Signature 5/3/2020 ……….……………………...…….…………………………. Date The University recognises that there may be exceptional circumstances requiring restrictions on copying or conditions on use. Requests for restriction for a period of up to 2 years can be made when submitting the final copies of your thesis to the UNSW Library. Requests for a longer period of restriction may be considered in exceptional circumstances and require the approval of the Dean of Graduate Research. II COPYRIGHT STATEMENT ‘I hereby grant the University of New South Wales or its agents a non-exclusive licence to archive and to make available (including to members of the public) my thesis or dissertation in whole or part in the University libraries in all forms of media, now or here after known. I acknowledge that I retain all intellectual property rights which subsist in my thesis or dissertation, such as copyright and patent rights, subject to applicable law. I also retain the right to use all or part of my thesis or dissertation in future works (such as articles or books).’ ‘For any substantial portions of copyright material used in this thesis, written permission for use has been obtained, or the copyright material is removed from the final public version of the thesis.’ Signed …………………………........................... Date …………………………17/06/2020…….............................. AUTHENTICITY STATEMENT ‘I certify that the Library deposit digital copy is a direct equivalent of the final officially approved version of my thesis.’ Signed …………………………........................... Date …………………………17/06/2020…….............................. INCLUSION OF PUBLICATIONS STATEMENT UNSW is supportive of candidates publishing their research results during their candidature as detailed in the UNSW Thesis Examination Procedure. Publications can be used in their thesis in lieu of a Chapter if: • The candidate contributed greater than 50% of the content in the publication and is the “primary author”, ie. the candidate was responsible primarily for the planning, execution and preparation of the work for publication • The candidate has approval to include the publication in their thesis in lieu of a Chapter from their supervisor and Postgraduate Coordinator. • The publication is not subject to any obligations or contractual agreements with a third party that would constrain its inclusion in the thesis Please indicate whether this thesis contains published material or not: This thesis contains no publications, either published or submitted for publication ☐ (if this box is checked, you may delete all the material on page 2) Some of the work described in this thesis has been published and it has ☐ been documented in the relevant Chapters with acknowledgement (if this box is checked, you may delete all the material on page 2) This thesis has publications (either published or submitted for publication) incorporated into it in lieu of a chapter and the details are presented ☒ below CANDIDATE’S DECLARATION I declare that: • I have complied with the UNSW Thesis Examination Procedure • where I have used a publication in lieu of a Chapter, the listed publication(s) below meet(s) the requirements to be included in the thesis. Candidate’s Name Signature Date (dd/mm/yy) Melissa Yeow 06/03/2020 III POSTGRADUATE COORDINATOR’S DECLARATION I declare that: • the information below is accurate • where listed publication(s) have been used in lieu of Chapter(s), their use complies with the UNSW Thesis Examination Procedure • the minimum requirements for the format of the thesis have been met. PGC’s Name PGC’s Signature Date (dd/mm/yy) Michael Janitz 07/03/2020 For each publication incorporated into the thesis in lieu of a Chapter, provide all of the requested details and signatures required Details of publication #1: Full title: Analyses of energy metabolism and stress defence provide insights into Campylobacter concisus growth and pathogenicity Authors: Melissa Yeow, Fang Liu, Rena Ma, Timothy J. Williams, Stephen M. Riordan and Li Zhang Journal or book name: Gut Pathogens Volume/page numbers: Volume 12 Article 13 Date accepted/ published:05/03/2020 Status Published X Accepted and In In progress press (submitted) The Candidate’s Contribution to the Work Conducted bioinformatics analysis, analyzed data and wrote manuscript Location of the work in the thesis and/or how the work is incorporated in the thesis: Chapter 2 PRIMARY SUPERVISOR’S DECLARATION I declare that: • the information above is accurate • this has been discussed with the PGC and it is agreed that this publication can be included in this thesis in lieu of a Chapter • All of the co-authors of the publication have reviewed the above information and have
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