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Characterization of a New Ribosome Associated Quality

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Characterization of a New Ribosome Associated Quality CHARACTERIZATION OF A NEW RIBOSOME ASSOCIATED QUALITY CONTROL PATHWAY by William Barbeau A Senior Honors Thesis Submitted to the Faculty of The University of Utah In Partial Fulfillment of the Requirements for the Honors Degree in Bachelor of Science In Biology Approved: ______________________________ _____________________________ Markus Babst, PhD Denise Dearing, PhD Thesis Faculty Supervisor Chair, Department of Biology _______________________________ _____________________________ Martin Horvath, PhD Sylvia D. Torti, PhD Honors Faculty Advisor Dean, Honors College December 2016 Copyright © 2016 All Rights Reserved ABSTRACT Proteins are life’s double edged sword. Proteins are essential macromolecules of life, and the tasks that some proteins accomplish are quite marvelous. At the same time, if proteins misfold they have the potential to kill the cell that harbors them. It is becoming increasingly clear that proteins have the potential to misfold from the very beginning of their life, during translation. To strike a balance between translational efficiency and accuracy, cells choose between various synonymous codons to regulate translation. Frequent codons are translated more quickly than rare codons, and the usage of frequent and rare codons is used to regulate translation dynamics. The balance between the usage of frequent and rare codons is fine, as synonymous mutations can disrupt the translational machinery enough to abort translation and degrade the nascent protein. Surprisingly, disruption of the ribosome happens quite frequently, and requires the response of ribosome associated quality control (RQC) to degrade the potentially misfolded proteins. So far only one RQC pathway has been described that responds to ribosomes that have been stalled for prolonged periods of time. In this study I present a novel RQC pathway where the ribosome is able to recover from stalling. Despite ribosome recovery, the nascent protein is still targeted for degradation with ubiquitin. I found that previously described RQC components, Ltn1 and Rqc1 are involved in this pathway. Additionally, I begin to characterize how the nascent protein is trafficked from the ribosome to the vacuole. This new RQC pathway further highlights the importance codon usage plays in protein folding and adds a more nuanced view of the genetic code and translation. ii TABLE OF CONTENTS ABSTRACT ii INTRODUCTION 1 METHODS 18 RESULTS 20 DISCUSSION 41 ACKNOLWEDGMENTS 51 REFERENCES 52 iii 1 INTRODUCTION Proteins have many different functions in the cell including, catalyzing chemical reactions, providing structural support, transporting substances, and much more. Unfolded proteins can be detrimental to the cell such as a leaky nutrient transporter that disrupts the cell’s ability to maintain osmotic homeostasis (Keener and Babst, 2013). Beyond the particular function of a protein, misfolded proteins can arrange themselves into aggregates that cause other properly folded proteins to unfold. It is becoming increasingly clear that the cytotoxicity of protein misfolding and aggregation is the basis of many human diseases (Stefani, 2004). Due to the functional importance of proteins to cell physiology, and the harm that comes from their unfolding, cells invest a considerable amount of energy to ensure proteins are made without mistakes. Translation is the process of protein synthesis by decoding the four letter code of mRNA into the twenty amino acid language of proteins. In 1958 Francis Crick proposed the adaptor hypothesis, where a molecule of RNA is associated with a specific amino acid and can decode mRNA by forming Watson-Crick hydrogen bonds (Crick, 1958). Crick was later proved right with the existence of tRNA. mRNA is read from 5’-3’ one codon, or three nucleotides, at a time. A molecule of tRNA contains an anticodon at one end that can hydrogen bond with a select number of codons. At the other end of the tRNA molecule is an amino acid that is specific to that tRNA molecule (Hoagland et al., 1958). Since a codon is composed of three out of four possible nucleotides, there is a total of 64 possible permutations. There are 61 codons that code for an amino acid. The remaining three are signals for the end of protein synthesis. However, there are only 20 amino acids, which means there is codon redundancy with multiple codons representing a 2 given amino acid. This in turn allows some amino acids to have more than one tRNA, and for some tRNAs to recognize multiple codons. The fact that a single tRNA can recognize more than one codon is explained by the wobble hypothesis. When an anticodon of a tRNA base pairs with a codon of an mRNA, the first two nucleotides of the codon always form Watson-Crick base pairs. The third nucleotide of the codon however does not always form Watson-Crick base pairs. Watson-Crick base pairs do not form when tRNAs contain inosine (I), uracil (U), or guanine (G) as the first nucleotide of the anticodon (which base pairs with the third nucleotide of the codon). The resulting hydrogen bonds formed with wobble base pairing are weaker than Watson-Crick bonds. Even though wobble results in weaker base pairing between the codon and anticodon, it allows the genetic code to be read by a minimum of 32 tRNAs (Crick, 1966). Translation takes place at the ribosome, which serves as a platform for tRNAs to read mRNA, and for peptide bonds to form between amino acids. The ribosome is large structure composed of rRNA and protein, and is arranged in a way that has the RNA in the center and the proteins on the periphery. While ribosomes in bacteria and eukaryotes have diverged, with eukaryotic ribosomes being larger and having a structurally distinct periphery, the core of the ribosome is conserved across all domains of life (Melnikov et al., 2012). The ribosome is composed of two subunits, small (40S in eukaryotes) and large (60S in eukaryotes). The small subunit contains the path for mRNA to transverse, and the decoding center where tRNA hydrogen bonds with mRNA. The small subunit also contains parts of the three tRNA binding sites, the aminoacyl (A) site, peptidyl (P) site, 3 and exit (E) site. The large subunit also contains parts of the three tRNA binding sites. Most notably, the large subunit is the location of the active site of peptide bond catalysis, also known as the peptidyl transferase center (PTC). Near the PTC is the opening of the peptide exit tunnel, which allows nascent proteins to leave the ribosome (Melnikov et al., 2012). The exit tunnel is composed of rRNA and protein, and is 80-100Å long and 10- 20Å wide. The length of the exit tunnel can accommodate about 30-40 amino acids if the polypeptide is unfolded, and about 60 amino acids if the polypeptide is folded into an a helix (Blobel and Sabatini, 1970; Cabrita et al., 2010; Kramer et al., 2009; Nissen et al., 2000). The process of translation is divided into four steps, initiation, elongation, termination, and recycling. The goal of initiation is to assemble the ribosome and guide it to the start codon (AUG, Met), which marks the beginning of the protein coding portion of mRNA. In eukaryotes, initiation is aided by twelve protein factors, only a few of which will be described here. Initiation begins when initiation factors eIF1A and eIF3 bind to the 40S subunit. eIF1A binds to the A site to prevent tRNA from binding, and eIF3 prevents the 60S subunit from binding. The next step involves the initiator tRNA, which recognizes the start codon, and is charged with Met. The initiator tRNA bound with eIF2-GTP binds to the 40S subunit at the P site. The resulting complex of the small ribosomal subunit, eIF1A, eIF3, the initiator tRNA, and eIF2-GTP is called the 43S preinitiation complex (Lopez-Lastra et al., 2005). eIF4F is a ternary complex and helps mRNA associate with the 43S preinitation complex by binding to eIF3 (part of the preinitation complex). Importantly, eIF4F binds to the 5’ cap of mRNA. As a result, eIF4F correctly positions the ribosome at the 5’ end 4 of the mRNA. The addition of mRNA and eIF4F to the preinitation complex results in a 48S complex (Lopez-Lastra et al., 2005). With the 48S correctly positioned at the 5’ end of mRNA, this complex scans the mRNA until it reaches the start codon, which is signaled by the RNA-RNA interaction between the start codon and the anticodon of the initiator tRNA. This codon-anticodon interaction is communicated throughout the subunits of the initiation complex and signals the hydrolysis of GTP bound to eIF2 into GDP and phosphate. This hydrolysis triggers the dissociation of the initiation factors from the small subunit and the binding of the 60S subunit to the 40S subunit. The resulting 80S ribosome contains the initiator tRNA correctly paired with the start codon in the P site (Lopez-Lastra et al., 2005). During elongation, the ribosome adds amino acids to the growing polypeptide chain by moving along the mRNA, decoding it one codon at a time. Elongation is a cyclical process, with the completion of one cycle resulting in the addition of one amino acid to the nascent protein. This cycle begins with a tRNA bonded to the nascent protein in the P site, and the A and E sites empty. Next, a charged tRNA bound to eEF1A-GTP enters the A site. If the anticodon of the tRNA matches the codon of the mRNA, eEF1A hydrolyzes GTP, and leaves the ribosome. If the tRNA does not match the codon, then GTP is not hydrolyzed, and the aminoacyl-tRNA leaves the A site. Successful hydrolysis of GTP by eEF1A positions the 3’ ends of the tRNA in the A and P site close together so that catalysis of the peptide bond can occur (Dever and Green, 2012).
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