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REDOX REGULATION of PROTEIN TRANSLATION in EUKARYOTES Maxim Gerashchenko University of Nebraska-Lincoln, [email protected]

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REDOX REGULATION of PROTEIN TRANSLATION in EUKARYOTES Maxim Gerashchenko University of Nebraska-Lincoln, Germaximus@Gmail.Com University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Theses and Dissertations in Biochemistry Biochemistry, Department of 4-2014 REDOX REGULATION OF PROTEIN TRANSLATION IN EUKARYOTES Maxim Gerashchenko University of Nebraska-Lincoln, [email protected] Follow this and additional works at: http://digitalcommons.unl.edu/biochemdiss Part of the Biochemistry Commons, and the Genetics Commons Gerashchenko, Maxim, "REDOX REGULATION OF PROTEIN TRANSLATION IN EUKARYOTES" (2014). Theses and Dissertations in Biochemistry. 16. http://digitalcommons.unl.edu/biochemdiss/16 This Article is brought to you for free and open access by the Biochemistry, Department of at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Theses and Dissertations in Biochemistry by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. REDOX REGULATION OF PROTEIN TRANSLATION IN EUKARYOTES by Maxim Gerashchenko A DISSERTATION Presented to the Faculty of The Graduate College at the University of Nebraska In Partial Fulfillment of Requirements For the Degree of Doctor of Philosophy Major: Biochemistry Under the Supervision of Professors Dmitri E. Fomenko and Vadim N. Gladyshev Lincoln, Nebraska April, 2014 REDOX REGULATION OF PROTEIN TRANSLATION IN EUKARYOTES Maxim Gerashchenko, PhD. University of Nebraska, 2014 Advisors: Vadim N. Gladyshev and Dmitri E. Fomenko Gene expression may be controlled at multiple levels, e.g., through genomic architecture, transcription and translation. In the current work, we focused on regulation of protein synthesis. Historically, the investigation of the regulation of gene expression at the level of translation lagged behind the transcriptional control because of the lack of accessible high-throughput methods. Our research has begun with the finding of the use of alternative non-AUG start codon in thioredoxin-glutathione reductase (TGR), a selenoprotein involved in redox control during male reproduction. The use of this codon, CUG, relies on the Kozak consensus sequence and ribosomal scanning mechanism. However, the CUG serves as an inefficient start codon that allows downstream in-frame initiation, generating two isoforms of the enzyme in vivo and in vitro from the same mRNA. These findings were extended with the use of systemic, proteome-wide approaches, that supported targeted discovery of initiation start sites. For this purpose, a new technology, ribosomal profiling, was employed. It embraced high-throughput sequencing and offered analyses of ribosome occupancy along the mRNA at a single nucleotide resolution. We applied this technique to examine the interplay between transcription and translation under conditions of hydrogen peroxide treatment in Saccharomyces cerevisiae. Oxidative stress elicited by hydrogen peroxide led to a massive and rapid increase in ribosome occupancy of short upstream open reading frames (uORFs), including those with non-AUG translational starts, and N-terminal regions of ORFs that preceded the transcriptional response. In addition, this treatment induced the synthesis of N-terminally extended proteins and elevated stop codon read-through and frameshift events. It also increased ribosome occupancy at the beginning of ORFs and potentially duration of the elongation step. We identified proteins whose synthesis was rapidly regulated by hydrogen peroxide post-transcriptionally; however, for the majority of genes increased protein synthesis followed transcriptional regulation. Nevertheless, a number of proteins were regulated post-transcriptionally even at the 5 min time point. These data defined the landscape of genome-wide regulation of translation in response to hydrogen peroxide and suggested that "potentiation" (co-regulation of the transcript level and translation) is a feature of oxidative stress. Finally, we expanded this research to better define conditions for ribosome profiling, which are broadly applicable for studies on regulation of translation. ACKNOWLEDGEMENTS I would like to express my deepest gratitude to my advisor, Dr. Vadim Gladyshev, for giving me the opportunity to work in his lab, as well as for his support and continuous guidance during my years as a graduate student. A special thanks goes to Dr. Alexey Lobanov for his guidance on bioinformatics tools. I would like to thank my supervisory committee members, Dr. Audrey Atkin, Dr. Mark Wilson, Dr. Dmitri Fomenko, and Dr. Jaekwon Lee, for their support, assistance and suggestions. I would like to thank all my friends and colleagues for advice and assistance. TABLE OF CONTENTS CHAPTER 1. Introduction.................................................................................................. 1 1.1 Translation .............................................................................................................. 1 1.2 Ribosome ................................................................................................................ 2 1.3 Structure of the catalytic center of the ribosome .................................................... 4 1.4 Selenocysteine as a unique amino acid ................................................................... 4 1.5 Cap-dependent and cap-independent translation .................................................... 5 1.6 Selection of a start codon in open reading frame .................................................... 5 1.7 Short upstream reading frames as translational regulators ..................................... 7 1.8 Translational regulation of gene expression ........................................................... 8 CHAPTER 2. CUG start codon generates thioredoxin/glutathione reductase isoforms in mouse testes ...................................................................................................................... 12 2.1 Abstract ................................................................................................................. 12 2.2 Introduction ........................................................................................................... 13 2.3 Methods................................................................................................................. 15 2.4 Results ................................................................................................................... 19 2.5 Discussion ............................................................................................................. 30 CHAPTER 3 Genome-wide ribosomal profiling reveals complex translational regulation in response to oxidative stress........................................................................................... 34 3.1 Abstract ................................................................................................................. 34 3.2 Introduction ........................................................................................................... 35 3.3 Methods................................................................................................................. 37 3.4 Results ................................................................................................................... 45 3.5 Discussion ............................................................................................................. 62 CHAPTER 4 Reassessing eukaryotic translation by ribosomal profiling ........................ 67 4.1 Abstract ................................................................................................................. 67 4.2 Introduction ........................................................................................................... 67 4.3 Methods................................................................................................................. 69 4.4 Results and Discussion ......................................................................................... 76 CHAPTER 5 Future perspectives ..................................................................................... 82 5.1 Ribosomal profiling in systems with extremely low net translation ..................... 82 5.2 Specialized ribosome hypothesis .......................................................................... 86 ABBREVIATIONS 3' UTR three prime untranslated region 5' UTR five prime untranslated region GFP green fluorescent protein GR glutathione reductase Grx glutaredoxin IRES internal ribosome entry site miRNA micro ribonucleic acid mRNA messenger ribonucleic acid mRNA-seq mRNA sequencing NGS next generation sequencing ORF open reading frame Ribo-seq sequencing of ribosome protected footprints Rpkm reads per kilobase per million rRNA ribosomal ribonucleic acid SECIS selenocysteine insertion sequence SGD Saccharomyces genome database TE translation efficiency TGR thioredoxin glutathione reductase TR thioredoxin reductase tRNA transport ribonucleic acid Trx thioredoxin uORF upstream open reading frame nt nucleotide/s CHAPTER 1 INTRODUCTION 1.1 Translation Genetic information contained in a form of linear nucleotide sequences has to be interpreted to generate proteins. The central dogma in biology states that DNA serves as a matrix for RNA and the latter bears information to be converted into proteins. Not all RNAs encode proteins; those that do are named mRNA (messenger). Transcription is a process of synthesizing RNA whereas translation is synthesizing protein. Unlike transcription, translation represents a bigger challenge. With some exceptions, all proteins consist of 20
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