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Elucidating the role of Mitoferrin (Mfrn), Iron Regulatory Proteins (IRP1 and IRP2) and Hephaestin (Heph) in Iron Metabolism by tagSNP and Protein-Protein Interaction (PPI) analysis Velaga M Ravindranath A thesis submitted for the degree of Doctor of Philosophy to London Metropolitan University First supervisor: Dr. Kenneth White Second supervisor: Dr. Una Fairbrother 1 ABSTRACT Precisely how Hephaestin (Heph) facilitate iron release from cells is poorly understood. The work in this thesis tried to establish the role of different iron metabolic proteins, Mitoferrin (Mfrn), IRPs and Heph in iron homeostasis. Analysis of 18 tagSNPs in the Mfrn gene was carried out in an Asian-Caucasian population to establish any correlation between the Mfrn tagSNPs, haemoglobin levels and birth weight in the presence of covariates such as sex of the fetus, gestational age and mother's booking weight. Two-way ANCOVA analysis was carried out to check if the covariates have any influence on the dependent variable in the presence of fixed factors. From the ANCOVA analysis of Mfrn tagSNPs it can be concluded that neither the haemoglobin levels nor the birth weight are dependent on the genotype, fetal sex, nor on their interaction. Owing to the significance in identifying the interacting partners of IRPs and Heph to understand more about their role in iron metabolism, protein-protein interaction studies were also carried out. IRPs and Heph genes were successfully cloned with One-Strep tag. Full length clones were sequence confirmed for any variation after PCR. Before carrying out immunoprecipitation to identify the interacting partners, transfection efficiency, viability and the role of magnetic particles on K562 cells was performed by using IRPs and Heph cloned with One-Strep tag. Lipofectamine-LTX plus transfection had more viable cells and higher efficiency compared with magnetic-assisted transfection. Also, this study confirms that magnetic nanoparticles do not have any adverse or significant effect on IRPs during the transfection. An unsuccessful attempt was made to identify the interacting partners of IRPs and Heph by immunoprecipitation. The current thesis work also involved identification of a potential ferroxidase. Ceruloplasmin (Cp) was used as a postive control. Non-denaturing gel eletrophoresis of the K562, MDA-MB-231 and PNT2-C2 cell fractions confirmed the presence of the extra band establishing the ubiquitous nature of the band. Mass spectrometry analysis identified the excised band as Calreticulin (CALR). This is the first report of calreticulin having ferroxidase activity. 2 DEDICATION This thesis is dedicated to“TIME” 3 ACKNOWLEDGEMENTS If I hadn’t met Dr. Kenneth White, I wonder how and where I would have ended up. Meeting you has been a very fortunate time of the journey. I have learned from you so much in terms of research, personality development and how calmly one can take things when going gets tougher. Thank you for all the opportunities you gave me whenever I wanted to learn or explore. Without your support I would not have met Dr. Wolfgang. I would like to thank you from the bottom of my heart for all your time and for being there when ever I needed as a guiding figure. Thank you Dr. White. Dr. Wolfgang, you inspired me, taught me and been there every time I knocked your door for the support. Even with all your busy schedules in US you replied at the first possible opportunity as you know I will be waiting for you feedback across the Atlantic. I sometimes wonder and feel so fortunate to have that one conversation in front of the Medical centre which you let me have, though when you were busy going to see someone else. Thank you Dr. Wolfgang. I would like to thank Prof. Rob Evans for his kind collaboration during CALR work in Imperial College, UK, for exchange of ideas and literature help. My best mates, Syam Kommana, Kasyap Bhogaraju, Subhakar Suryadevara, Amit Thotakura, Venkat Pappula, JJ Sivala, Bhavani Kommineni and Hamid Reza Khalatbari without whom, it would not have been possible to see this day. Because of you, I realised how important friendships for life are. Thank you very much for being there in every possible way guys. Thank you Ephraim, Muy, Ed, Samireh, Sharad, Katia, Amara and Laura. Without you being around in the lab, we would not have those technical and personal (stress busters) discussions which sometimes lasted for hours. But never felt hours have passed by and I am confident you are and will have great times ahead. Without the help of Brigitte Awamaria, John Morgan, Arun, Ruth, Pam, Sophie, and Suresh it would not have been easy at all to get hands on lab resources. You always walked an extra mile to help me. Thank you guys. Thank you to Dr. Una for being a second supervisor and for your support. Special thanks to Prof. Chris Palmer for all the energy and radiant smile whenever I came across you. Prof. Jameel, thank you for your encouraging words in the summer of 2007. 4 My heartfelt thank you to Simon Williams from exams office who has been very kind in considering me towards the semester end exam invigilation duties. Thank you Mom and Dad. I know this is late to say a thank you. No thanks will count for what you have been in my life. I do not think I can repay your patience, but surely can try to be a good human being. Thank you. My dear brothers, Dattu and Venu, I know you have thought, suggested, guided and motivated a lot for my own good. Sure we had our own hard times and thanks for the emotional kicks you gave me all the while. I surely can understand why you guys were tough. No hard feelings. I am sure; I do not even need to mention that without your presence in my life I would have lost long time ago. Thank you for your support and patience which again can never be paid back like Dad’s and Mom’s. 5 Table of Contents ABSTRACT .......................................................................................................................................................... 2 DEDICATION ....................................................................................................................................................... 3 ACKNOWLEDGEMENTS...................................................................................................................................... 4 LIST OF FIGURES .............................................................................................................................................. 11 LIST OF TABLES ................................................................................................................................................ 14 CHAPTER 1 ....................................................................................................................................................... 15 INTRODUCTION ....................................................................................................................................... 15 1.01 Significance of Iron ...................................................................................................................... 16 1.02 Availability of Iron ........................................................................................................................ 16 1.03 Body Iron Requirements .................................................................................................................. 17 1.04 Bioavailability of iron ....................................................................................................................... 18 1.04.001 Non-haem iron ......................................................................................................................... 19 1.04.002 Haem iron ................................................................................................................................. 19 1.05 Intestinal Iron absorption ................................................................................................................ 20 1.05.001 Intestinal iron absorption ......................................................................................................... 21 1.05.002 Export of iron into plasma ........................................................................................................ 23 1.05.003 Iron transport to Mitochondria ................................................................................................ 26 1.05.004 Mitochondrial iron storage and export .................................................................................... 29 1.06 Cellular iron regulation .................................................................................................................... 31 1.06.001 Regulation of iron in stores ...................................................................................................... 32 1.06.001.1 Molecules involved in the regulation of cellular iron ............................................................ 35 1.06.001.2 Regulation by Inflammatory and Stress Signals .................................................................... 38 1.06.001.3 Regulation of iron absorption by erythropoiesis ................................................................... 40 1.07 Current study ................................................................................................................................... 41 1.07.001.1 Mitoferrin, a solute carrier in SLC25 super family ................................................................. 42 1.07.001.2 Phylogenetic analysis of SLC25
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  • Electronic Supplementary Material (ESI) for Molecular Omics

    Electronic Supplementary Material (ESI) for Molecular Omics

    Electronic Supplementary Material (ESI) for Molecular Omics. This journal is © The Royal Society of Chemistry 2020 SUPPLEMENTARY INFORMATION Supplementary Table S2. GO analysis for the 289 overlapping genes based on DAVID database. ID Category Term Genes PValue HSD3B2, CYP24A1, ME3, SORD, ADHFE1, CYP2C44, PAH, HIBADH, MTHFD1, ALDH1A1, PECR, CYP4A12A, FMO1, MIOX, CYP2J11, HAAO, BC089597, ALDH4A1, BDH2, DAO, NQO1, BDH1, SARDH, HPD, 1 BP GO:0055114~oxidation reduction 1.18E-17 NOX4, GCDH, SUOX, AKR1E1, QDPR, CMAH, HGD, FADS2, AKR1C21, PPARGC1A, TET1, DDO, NNT, HAO2, CYP2D26, HSD11B2, DIO1, RDH16, CYP4A14, STEAP1, DCXR, PRODH SLC12A6, SLC2A13, SLC5A2, SLC12A1, SLC5A1, SLC22A7, SLC22A8, RHBG, SLC7A9, AQP6, SLC26A4, GO:0055085~transmembrane 2 BP SLC23A1, SLC16A7, SLC2A4, RHCG, SLC7A1, 1.28E-07 transport SLC25A10, SLC2A2, SLC16A9, SLC5A9, SLC13A2, SLC25A37, SLC13A3, SLC46A1, SLC5A12 PDK2, SLC37A4, PDK4, CMAH, PGAM2, ADIPOQ, GO:0005996~monosaccharide 3 BP HIBADH, PCK1, GALM, G6PC, PPP1R1A, GYS2, MYC, 1.25E-06 metabolic process DCXR, XYLB SLC12A6, SLC5A2, SLC23A1, SLC12A1, SLC5A1, 4 BP GO:0006814~sodium ion transport SLC9A3, SLC5A9, SLC13A2, SLC13A3, SLC10A2, 3.05E-06 SLC4A4, SLC5A12 SLC5A2, G6PC, SLC2A4, SLC2A2, SLC5A1, SLC37A4, 5 BP GO:0015758~glucose transport 3.22E-06 STXBP4 SLC5A2, G6PC, SLC2A4, SLC2A2, SLC5A1, SLC37A4, 6 BP GO:0008645~hexose transport 4.95E-06 STXBP4 GO:0015749~monosaccharide SLC5A2, G6PC, SLC2A4, SLC2A2, SLC5A1, SLC37A4, 7 BP 6.06E-06 transport STXBP4 GO:0006006~glucose metabolic PDK2, G6PC, PPP1R1A, PDK4, SLC37A4, GYS2,