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Dissertation Submitted to the Combined Faculty of Natural Sciences and Mathematics of the Ruperto Carola University Heidelberg Dissertation submitted to the Combined Faculty of Natural Sciences and Mathematics of the Ruperto Carola University Heidelberg, Germany for the degree of Doctor of Natural Sciences Presented by M.Sc. Kathrin Bajak Born in: Heilbronn, Germany Oral examination: 12th of July 2019 Networks of gene expression control in Trypanosoma brucei Referees: Prof. Dr. Christine Clayton Prof. Dr. Dr. Georg Stoecklin Acknowledgment I would like to kindly thank Prof. Dr. Christine Clayton for giving me the opportunity to work in her laboratory, for great scientific input, thoughtful guidance and many inspiring discussions. Dr. Esteban Erben for his supervision, numerous fruitful, critical as well as inspiring discussions, for technical help, for proofreading this thesis, for your belief in my work and all your support. Prof. Dr. Nina Papavasiliou and Dr. Erec Stebbins for giving me the opportunity to work in their lab for the last year of my PhD. Prof. Dr. Luise Krauth-Siegel and Prof. Dr. Dr. Georg Stoecklin for scientific support and inspiring discussions in the TAC meetings. Prof. Dr. Dr. Georg Stoecklin and Dr. Susanne Kramer for providing cell lines, reagents and equipment. Dr. Esteban Erben and Kevin Leiss for their research on the ZC3H5 project on which I could built up my work. Pia Hartwig for her assistance and contribution in the BFR1L project during her lab rotation. The whole Papavasiliou/Stebbins lab for the friendly atmosphere and the great time that we shared in and outside the lab. Dr. Thomas Ruppert and Sabine Merker from the Core Facility for Mass Spectrometry & Proteomics at the ZMBH and David Ibberson from the Cell Networks Deep Sequencing Core Facility at the University of Heidelberg for useful discussions and analysis of our samples. Dr. Holger Lorenz and Christian Hoerth from the Imaging facility at the ZMBH for their help with microscopy and image analysis and Tobias Rubner from the FACS facility at the DKFZ for his help and support. Ute and Claudia from the Clayton lab for the technical support, which made my live in the lab much easier. Larissa Melo Do Nascimento from the Clayton lab for all the scientific and non-scientific discussions. And Daniela Begolo for your great friendship, it was a pleasure having you around in the lab and spending fun leisure time together. Katharina Haneke for your friendship, endless support and advise during the PhD time. To all my friends for their support, motivation and the great time we spent. Girls from riding stable for distracting me from the lab work and spending time with the horses; friends from university that we are still in contact, even if we are spread around the world; friends from home for the amazing weekend times. My parents and my sister for their patience, care, love and support. For all the lovely family time we spent together. For their belief in me and my work; for encouraging and motivating me. Table of contents List of abbreviations .................................................................................................... VIII List of figures .................................................................................................................. X List of tables.................................................................................................................. XII Summary ...................................................................................................................... XIII Zusammenfassung ...................................................................................................... XIV 1. Introduction ............................................................................................................. 1 1.1. Trypanosomes- disease and model organism ..................................................... 1 1.2. The life cycle of Trypanosoma brucei .................................................................. 2 1.3. The cell cycle in T. brucei and its regulation ........................................................ 3 1.4. Regulation of gene expression in T. brucei ......................................................... 4 1.4.1. Transcription ................................................................................................ 4 1.4.2. Export of mRNA from the nucleus ................................................................ 5 1.4.3. mRNA decay in Trypanosomes ................................................................... 5 1.4.4. Localization of mRNAs in Trypanosomes .................................................... 6 1.4.5. Translation ................................................................................................... 7 1.4.6. Influence of codon usage on the regulation of gene expression ................... 7 1.5. RNA-binding proteins and their role in regulation of gene expression in T. brucei 8 1.5.1. RRM domain containing proteins ................................................................. 8 1.5.2. ALBA domain containing proteins ................................................................ 9 1.5.3. PUF domain containing proteins .................................................................. 9 1.5.4. Zinc finger domain containing proteins........................................................10 1.5.5. Non-canonical RBPs ...................................................................................10 1.6. Identification of new putative post-transcriptional regulators ..............................12 1.7. Aim of the study .................................................................................................13 2. mRNAs encoding ribosomal proteins might be regulated by BFR1L .................14 2.1. Results ...............................................................................................................14 2.1.1. Knock-down of Tb927.10.14150 affects cell growth in the bloodstream form ............................................................................................................14 2.1.2. BFR1L localizes to ER and partially to mitochondria ...................................17 2.1.3. Protein interactome of BFR1L .....................................................................21 2.1.4. Most of the mRNAs associated with BFR1L encode ribosomal proteins .....24 2.1.5. BFR1L does not colocalize with the stress granule marker Scd6 under starvation stress .........................................................................................25 2.2. Discussion .........................................................................................................28 V 3. ZC3H5 is required for cytokinesis .........................................................................32 3.1. Results ...............................................................................................................32 3.1.1. Downregulation of ZC3H5 rapidly kills bloodstream form cells ....................32 3.1.2. Proteins interacting with ZC3H5 form a complex ........................................33 3.1.3. Knock-down of proteins interacting with ZC3H5 results in reduced growth .38 3.1.4. RIP-Seq identifies mRNAs encoding cytoskeleton proteins as ZC3H5 targets ........................................................................................................40 3.1.5. Short-term down-regulation of ZC3H5 results in a minor effect on the transcriptome ..............................................................................................42 3.1.6. Effect of ZC3H5 down-regulation on ribosomal biogenesis, transcription and mRNA processing................................................................................42 3.1.7. Short-term down-regulation of ZC3H5 leads to an increase in monosomes ................................................................................................46 3.2. Discussion .........................................................................................................52 4. Material and Methods .............................................................................................57 4.1. Trypanosoma cell culture ...................................................................................57 4.1.1. Bloodstream form cells ...............................................................................57 4.1.2. Procyclic cells .............................................................................................57 4.1.3. Antibiotics ...................................................................................................57 4.1.4. Transfection of bloodstream-form trypanosomes ........................................58 4.1.5. Transfection of procyclic trypanosomes ......................................................58 4.2. Cloning ..............................................................................................................59 4.3. SDS-PAGE and Western Blotting ......................................................................59 4.4. Digitonin Titration ...............................................................................................60 4.5. Tandem affinity purification ................................................................................61 4.5.1. 1st step of TAP ............................................................................................61 4.5.2. 2nd step of TAP ...........................................................................................61 4.6. Trichloroacetic acid (TCA)-Acetone precipitation ...............................................62 4.7. decrosslinking
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