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University of Alberta University of Alberta Tripartite-motif family members in the White Pekin duck (Anas platyrhynchos) modulate antiviral gene expression by Alysson Heather Blaine A thesis submitted to the Faculty of Graduate Studies and Research in partial fulfillment of the requirements for the degree of Master of Science in Physiology, Cell and Developmental Biology Biological Sciences ©Alysson Heather Blaine Fall 2013 Edmonton, Alberta Permission is hereby granted to the University of Alberta Libraries to reproduce single copies of this thesis and to lend or sell such copies for private, scholarly or scientific research purposes only. Where the thesis is converted to, or otherwise made available in digital form, the University of Alberta will advise potential users of the thesis of these terms. The author reserves all other publication and other rights in association with the copyright in the thesis and, except as herein before provided, neither the thesis nor any substantial portion thereof may be printed or otherwise reproduced in any material form whatsoever without the author's prior written permission. Abstract Wild waterfowl, including mallard ducks, are the natural reservoir of avian influenza A virus and are resistant to highly pathogenic strains. This is primarily due to the robust innate immune response of ducks. Shortly after exposure to both highly pathogenic (A/Viet Nam/1203/04 (H5N1)) and low pathogenic (A/mallard/BC/500/05 (H5N2)) avian influenza, many immune genes are upregulated including members of the diverse tripartite-motif (TRIM) family. TRIM proteins have species-specific antiviral roles in a variety of viral infections. I have identified a contig of TRIM genes located adjacent to the MHC locus in the White Pekin duck (Anas platyrhynchos) genome. A duplication of the TRIM27.1 gene (TRIM27.1a and TRIM27.1b) has occurred. Using quantitative real-time PCR (qPCR) I determined that both TRIM27.1a and TRIM27.1b are upregulated 34- and 5-fold, respectively, at 1 day post-infection with VN1203. In a co- transfection experiment I determined that TRIM27.1a and TRIM27.1b have opposite effects on expression, decreasing and increasing transcription of antiviral genes, respectively. Acknowledgements Firstly, I would like to thank my supervisor, Dr. Kathy Magor for inviting me to join her lab and giving me the tools and opportunities rarely offered to a M.Sc. I am grateful for the support, direction and encouragement I have received throughout my degree from you and know that you have made me a better scientist, student and presenter. I could not have chosen a better lab or environment to work in and know that I have had amazing experiences in my three years in your lab, so thank you. Thank you also to my committee members, Dr. James Stafford and Dr. Jim Smiley for your guidance. To Dr. Miodrag Belosevic for both your time and your constructive feedback. Thank you to Dr. Brad Magor for your expertise in cell culture and for the use of your equipment. Domingo, thank you for your guidance in planning experiments and the motivation you provided me with. Megan, although I only overlapped for a short period of time, I cherish that time and connection and your help and confidence in me that I sometimes lacked. Thank you for being you, and being me, all at the same time. Ximena, for being so generous with your technical skills and for your friendship, I thank you. Hillary and Kristina, you were both supportive in times of need and willing to help whenever I needed it. Thank you for all the good times, you both made grad school fun. Thank you to Laura, Graham, Bianca, and Michelle for your friendship and support. Finally, I would like to thank and acknowledge all the members of the K. Magor lab, past and present and from the ether of BioSci - Brittany, Herman, Emmanuel and Barb I have learned so much from each and every one of you. And thank you to everyone at CanBiocin. Without the training and exposure I received, and continue to receive, from the company and everyone involved, I would not have pursued graduate studies. Thank you to my funding sources, NSERC for funding this work, Alberta Innovates Technology Futures, the department, the GSA and FGSR for the financial support in completion of this degree. Finally, and perhaps most profoundly, I would like to thank my family; both blood and chosen. Thank you Mum for being a pillar of strength and constancy and for trying to keep me sane and grounded throughout this endeavour. And thank you Mum for the ongoing encouragement, pride and for embracing my need for furry companions. Thanks to my sister, Amanda for the laughs and for listening. To Aunt Mary for her belief and support and the reminders of how proud Uncle Eric would have been. To my adopted families; Christina, Amy (and all the Pura and Higgins family) and Erin. Under no circumstance could I have made it through this without you three. Table of Contents Chapter 1. INTRODUCTION ..................................................................................... 1 1.1 Overview ................................................................................................................. 1 1.2 Characteristics of TRIMs and their roles in innate immunity .................................. 3 1.2.1 The tripartite-motif and classifications of TRIMs ............................................ 3 1.2.2 Functional implications of the RING domain as an E3-ligase .......................... 4 1.2.3 Protein-protein interactions can be mediated by the B-box and coiled-coil domains ..................................................................................................................... 5 1.2.4 Immune relevance of the C-terminal PRY/SPRY (B30.2) domain ................... 6 1.3 Intracellular detection of influenza and the intracellular immune signaling pathways ....................................................................................................................... 8 1.3.1 Signaling components downstream of RIG-I and TLR7 PAMP recognition .... 9 1.3.2 The importance of RIG-I in differential susceptibility ................................... 12 1.3.3 The RIG-I bioset in ducks and the antiviral program during IAV infection ... 13 1.4 TRIMs and innate immune pathways .................................................................... 15 1.4.1 TRIM25 is integral to RIG-I signaling ........................................................... 16 1.4.2 TRIM19/PML is a transcriptional modifier that localizes to nuclear bodies .. 16 1.4.3 TRIM14 is a newly identified signaling component of AP-1 ......................... 18 1.5 The TRIMs, the MHC and evolution..................................................................... 18 1.5.1 The chicken and turkey MHC has TRIM rich regions .................................... 21 1.6 TRIM27/Ret finger protein (RFP) ......................................................................... 22 1.6.1 TRIM27/RFP, cancer development and intracellular signaling ...................... 22 1.6.2 Human TRIM27/RFP interacts with the IKKs to supress IFN ....................... 24 1.7 Research aims ....................................................................................................... 26 Chapter 2. MATERIALS AND METHODS ................................................................... 32 2.1 In silico analysis and annotation of the TRIM genes in the draft duck genome .... 32 2.2 RNA extraction of infected tissues and cDNA synthesis....................................... 32 2.3 Expression analysis by reverse-transcription (RT-PCR) and qPCR ...................... 33 2.4 Cloning and sequencing ........................................................................................ 35 2.5 Amplification of TRIM27.1a and TRIM27.1b and allele screening ....................... 35 2.6 Expression constructs and design .......................................................................... 36 2.7 Transfection and expression .................................................................................. 37 2.8 RNA extractions from tissue culture ..................................................................... 38 2.9 Protein extraction from tissue culture and GST-pulldown .................................... 39 2.10 Western blotting and imaging ............................................................................. 40 2.11 Chicken interferon-2 promoter activation ........................................................... 40 Chapter 3. RESULTS AIM 1 AND AIM 2 ..................................................................... 52 3.1 Repertoire of TRIM genes in White Pekin ducks .................................................. 52 3.1.1 Annotation of the predicted duck MHC TRIM-rich region ............................ 53 3.1.2 Duck scaffold618 predicts four TRIM27 genes .............................................. 55 3.1.3 RT-PCR amplification of TRIM7.1 and annotation of TRIM7.1 and TRIM39.2 ................................................................................................................................ 56 3.1.4 TRIM39.1-like/BR gene is not a member of the TRIM family ........................ 56 3.1.5 Analysis of TRIM14 as a candidate antiviral TRIM ....................................... 57 3.1.6 Ducks have two TRIM19 or TRIM19-like genes ............................................. 58 3.2 Expression of immune relevant TRIM genes during influenza A infection. .......... 60 3.2.1 Quantification of expression of TRIM27.1a in infected ducks ......................
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