This Thesis Has Been Submitted in Fulfilment of the Requirements for a Postgraduate Degree (E.G
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This thesis has been submitted in fulfilment of the requirements for a postgraduate degree (e.g. PhD, MPhil, DClinPsychol) at the University of Edinburgh. Please note the following terms and conditions of use: • This work is protected by copyright and other intellectual property rights, which are retained by the thesis author, unless otherwise stated. • A copy can be downloaded for personal non-commercial research or study, without prior permission or charge. • This thesis cannot be reproduced or quoted extensively from without first obtaining permission in writing from the author. • The content must not be changed in any way or sold commercially in any format or medium without the formal permission of the author. • When referring to this work, full bibliographic details including the author, title, awarding institution and date of the thesis must be given. Expression and Characterisation of a Novel Poly(A)-Binding Protein, PABP5 Ross C. Anderson PhD The University of Edinburgh 2010 Abstract The poly(A)-binding proteins (PABPs) are a family of eukaryotic RNA-binding proteins with key roles in mRNA translation and stability. The molecular function of PABPs have been largely revealed through study of the prototypical cytoplasmic poly(A)-binding protein, PABP1. Thus, little is known regarding other PABP family members. PABP5 contains four RNA-recognition motifs characteristic of the cytoplasmic PABPs yet is structurally distinct as it lacks a portion of the C-terminus. This region contains a proline-rich section linked to a globular domain that facilitates a number of protein-protein interactions. To date, little information has been presented regarding the expression of PABP5 and there is no data pertaining to the function of this protein, despite being mapped to a region of the X-chromosome associated with human pathological conditions. In this thesis, I present the first data documenting the expression of PABP5 within mouse tissues, and find it to be expressed at the highest levels within the brain, ovary, and testis. The limited data available suggests that gonads may be the only tissue to contain all PABPs therefore I additionally describe the expression of PABP1 and PABP4 to ascertain their cellular distribution within these tissues. This revealed that PABPs have overlapping yet distinct expression patterns in mouse gonads. The distinct structure of PABP5 suggested that its function may vary from PABP1. Characterisation of its activities in translational regulation was therefore investigated. When tethered to a reporter mRNA PABP5 had limited translational stimulatory activity, and in addition could not be isolated via m7G cap chromatography and failed to interact with translation initiation factors including eIF4G and PAIP-1. These factors interact with PABP1 to positively promote translation, implying that PABP5 function in translational regulation differs from other PABPs investigated. ii Examining why PABP5 failed to display translational stimulatory activity also revealed an interaction with the negative regulator of translation, PAIP-2. In summary, I present the first description of PABP5 cellular localisation, and have gone some way towards elucidating the molecular function of this uncharacterised protein. iii Declaration I declare that the work presented in this PhD is my own and has not been submitted for any other degree. Ross C. Anderson iv Acknowledgements The last 4 years have been the source of much stress, pain and anxiety, filled with many periods where I wondered if I would ever finish, and yet seeing the following 300 pages come together as a coherent thesis is incredibly satisfying. There are so many people to thank I don’t know where to start – special thanks to Niki, who after 7 years of working together I would prefer to call a friend rather than a boss. I am forever indebted as I know this thesis caused you no small amount of trauma! Thank you to Matt for the lab supervision and opening my eyes to the world of curry (maybe one day I will be able to eat a chilli without fainting). Thanks to Hannah and Pedro for sharing the PhD pain, and to Barbara for keeping me in line! Richard – has been an excellent drinking buddy and a source of infinite wisdom in the lab. Finally, William (aka the Beef from Dalkeith), - it’s your round mate. Outside the lab, I wanted to say thanks to Niall and Euan for the distracting weekends of drinking which have been excellent fun. I’d like to say a huge thank you to Claire – you have been amazing and I‘ll never forget the support you have given me. This thesis would not have been finished and handed in without your help. Finally, I’d like to save the biggest thank you for Babs and Stu – I know I don’t pick up the phone or jump in the car often enough (unless of course I need money or food!) but you have supported me through thick and thin and I wish there was some way I could repay you. I love you both very much and I want to dedicate this thesis to you both. To my parents. Cheers! v Abbreviations µg.............................. microgram µl............................... microlitre µM............................ micromolar µm................. .......... micrometre 3’-UTR.......... ........... 3’ untranslated region 4E-BP............ ........... eukaryotic initiation factor 4E binding protein 5’-UTR.......... ........... 5’ untranslated region A................................ adenosine aa-tRNA................... aminoacyl-transfer ribonucleic acid ActD.............. .......... actinomycin D AD................. .......... activation domain Ago........................... argonaute protein ARE............... ........... adenosine/uracil-rich element ARE-BP.................... adenosine/uracil-rich element binding protein ARS.......................... autoregulatory sequence A-site........................ aminoacyl site ATP........................... adenosine triphosphate BD............................. binding domain C............................... cytosine cDNA........................ complementary DNA vi Co-IP........................ protein complex immunoprecipitation CPE.......................... cytoplasmic polyadenylation element CPEB........................ cytoplasmic polyadenylation element binding protein CrPV......................... cricket paralysis virus CT............................. threshold cycle C-terminus............... carboxyl terminus CTP........................... cytosine triphosphate DAB.......................... diaminobenzidinetrahydrochloride DAP5........................ death associated protein 5 DAPI........................ 4’, 6-diamidino-2-phenylindole DCP1........................ decapping protein 1 DCP2........................ decapping protein 2 Dcps.......................... scavenger decapping protein ddH2O...................... double distilled water dH2O........................ distilled water DMEM..................... Dulbecco’s minimal essential medium DNA......................... deoxyribonucleic acid DNase....................... deoxyribonucleic acid nuclease dsRNA...................... double stranded ribonucleic acid E. coli........................ Escherichia coli EDTA....................... ethylene diamine tetraacetic acid eEF........................... eukaryotic elongation factor vii EGFP........................ enhanced green fluorescent protein eIF............................. eukaryotic initiation factor EJC........................... exon junction complex EMCV...................... encephalomyocarditis virus EMSA....................... electrophoresis mobility shift assay ePABP...................... embryonic polyadenylate binding protein ePABP2.................... embryonic polyadenylate binding protein 2 ER............................ endoplasmic reticulum eRF........................... eukaryotic release factor E-site........................ exit site FCS........................... fetal calf serum FMDV...................... foot and mouth disease virus G............................... guanosine g................................ gram GAC......................... guanosine triphosphatase associated centre GAP.......................... guanosine triphosphatase activating protein GCN4....................... general control nonderepressible 4 GEF.......................... guanine nucleotide exchange factor GST.......................... glutathione S-transferase GTP.......................... guanosine triphosphate GTPase..................... guanosine triphosphatase H2O.......................... water viii HCV......................... hepatitis C virus HeLa cell................... Henrietta Lacks cell His............................ histidine hnRNP...................... heterogeneous nuclear ribonucleoprotein HRI........................... heme-regulated eukaryotic initiation factor 2 alpha kinase HRP.......................... horse radish peroxidase iPABP....................... inducible polyadenylate binding protein IPTG........................ isopropyl β-D-1-thiogalactopyranoside IRE........................... iron regulatory element IRES......................... internal ribosome entry site IRP........................... iron regulatory protein ISH........................... in-situ hybridisation ITAF........................ internal ribosome entry site trans-acting factor ITC........................... isothermal titration calorimetry Kb............................. kilobase Kd............................. dissociation constant kDa........................... kilodalton L................................ litre