Molecular Biology Commons^™

Effects Of Trans-Acting Factors On The Translational Machinery In Yeast, Brandon M. Trainor

Graduate School of Biomedical Sciences Theses and Dissertations

Synthesis of proteins, or translation, is a complex biological process requiring the coordinated effort of numerous protein and RNA factors. Central to translation is the ribosome, a complex macromolecular complex consisting of both ribosomal RNA (rRNA) and ribosomal protein (r-protein). Ribosomes are essential and are one of the oldest and most abundant biomolecules across all forms of life. In addition to the ribosome, translation requires messenger RNA (mRNA), transfer-RNA conjugated to an amino acid (aa-tRNA), translation factors, and energy in the form of ATP and GTP. Translation universally occurs in four major stages, initiation, elongation, termination, and recycling, with initiation …

Identification Of Ires Activity In Cellular Mrnas And Viral Rna Using A Circular Rna Construct, Priyanka Sehta

Legacy Theses & Dissertations (2009 - 2024)

Translation initiation is a critical step in the process of protein synthesis. The canonical way of translation initiation involves ribosomes being recruited to the 7-methyl guanosine cap present at the 5’end of the untranslated region (5’ UTR) of the RNAs. However, viral RNAs and some cellular mRNAs lack this 5’ cap structure and thus deploy an alternate non-canonical translation initiation mechanism. In non-canonical translation initiation, ribosome recruitment is facilitated by the RNA secondary structures called Internal Ribosome Entry Site (IRES) present most often in the 5’ UTR. To measure IRES-mediated translation, the dual luciferase assay has been the gold standard. …

Regulation Of Gene Expression Through Ribosome-Associated Proteins, Clare Margaret Miller

Legacy Theses & Dissertations (2009 - 2024)

Translation is a crucial mechanism for generating proteins to carry out cellular processes and for ensuring proper cell functions. Ribosomes are at the center of translation and are complex pieces of machinery. They consist of at least 80 core eukaryotic ribosomal proteins, which are conserved from prokaryotes, and four ribosomal RNAs (rRNAs): 18S, 28S, 5,8A 5S. In addition, numerous translation factors aid the ribosome in protein production. While ribosomes are typically described by these core features, they are known to exist in a heterogenous pool with variations in protein composition, modifications of rRNA, and an assortment of non-ribosomal proteins that …

Transcriptional Regulation Of Dksa In E. Coli, Daniel Thomas Woods

Legacy Theses & Dissertations (2009 - 2024)

DksA is a global transcription factor that binds RNAP directly to regulate the expression of many genes and operons, including ribosomal RNA, in a ppGpp-dependent or ppGpp–independent manner. It is also involved in facilitating the process of DNA replication by removing stalled transcription elongation complexes that could block the progress of the replication fork. In addition, DksA is important for colonization, establishment of biofilms, and pathogenesis. In order to sustain these various functions, an adequate level of cellular DksA is required. This work tested the hypothesis that the E. coli dksA is substantially regulated at the level of transcription. Using …

Inhibition Of Ribosome Biogenesis Through Genetic And Chemical Approaches, Leonid Anikin

Graduate School of Biomedical Sciences Theses and Dissertations

In order to maintain the ability to generate proteins, proliferating cells must continuously generate ribosomes, designating up to 80% of their energy to ribosome biogenesis (RBG). RBG involves transcription of rDNA by RNA polymerases I (Pol I) and III (Pol III), expression of approximately 80 ribosomal proteins, and assembly of these components in a process referred to as ribosome maturation. During maturation, the Pol I transcribed 47S pre-rRNA undergoes a number of processing events, while simultaneously interacting with processing factors and ribosomal proteins that drive pre-ribosome assembly. Inhibition of RBG has become one of the pursued targets for cancer therapy …

Rack1 Is A Critical Component In Ires-Mediated Translation, Ethan Asher Lafontaine

Legacy Theses & Dissertations (2009 - 2024)

Due to its sheer number of interacting partners, core ribosomal protein RACK1 is a key player in many cellular processes and has been shown to play a vital role of translation initiation of the Hepatitis C virus RNA. The HCV 5′ untranslated region contains an internal ribosome entry site. IRES-mediated translation is a process employed in eukaryotes by select viruses and some cellular mRNAs by which translation initiation bypasses the canonical mRNA cap-dependent pathway by means of an RNA secondary structure (the IRES). While cap-dependent translation requires the recruitment of a suite of initiation factors, IRES-mediated translation requires few to …

Regulation Of Ty1 Retrovirus-Like Transposon Rna Localization And Translation, Ryan Joseph Palumbo

Legacy Theses & Dissertations (2009 - 2024)

Replication of the Ty1 retrovirus-like transposon of the yeast Saccharomyces cerevisiae is stringently regulated to reduce the frequency of deleterious retrotransposition events. However, under stress conditions, Ty1 retrotransposition can lead to adaptive genomic alterations. To characterize host regulation of Ty1 retrotransposition, I analyzed ribosome profiling data and showed that Ty1 RNA is efficiently translated. Moreover, the ribosome biogenesis factors BUD21, DBP7, HCR1, LOC1, MRT4, and PUF6 are required for optimal expression of the Ty1 protein Gag.

Global And Specific Controls Of Protein Synthesis In Hibernators, Peipei Pan

UNLV Theses, Dissertations, Professional Papers, and Capstones

Mammalian hibernation is a highly dynamic physiological process that is composed of a series of torpor bouts, wherein hibernators oscillate between periods of torpor and interbout arousal. Although normally vital to homeostasis, many energetically consumptive processes such as translation or protein synthesis are virtually ceased during hibernation. Earlier studies indicated that protein synthesis had fallen to almost negligible levels. Cap-dependent initiation of translation is well regulated by eukaryotic translation initiation factor 4E (eIF4E) and its binding partner eIF4E-binding protein 1 (4E-BP1) when hibernators cycle in and out the torpor state. Herein, I investigated well-characterized regulatory mechanisms of global and specific …

The Mitospecific Region Of Mrp20 And Its Importance For The Assembly Of Mitochondrial Ribosomes In Saccharomyces Cerevisiae, Jasvinder Kaur

Dissertations (1934 -)

Yeast mitochondrial ribosomes are composed of an rRNA scaffold, encoded by the mitochondrial genome and many different proteins, which, with the exception of one, are encoded by nuclear genes. These ribosomal proteins are imported into the mitochondrial matrix following their synthesis in the cytosol, however, little is known about the subsequent events which result in an assembled, translationally-competent ribosome. Many of the mitochondrial ribosomal proteins bear homology to bacterial ancestors. In addition to the acquisition of mitochondrial targeting signals, a number of these nuclearly-encoded ribosomal proteins have acquired additional domains, often at their C-termini, which are termed "mitochondrial-specific domains". The …

Study Of Dynamic Processes In Protein Synthesis Using Heterogeneous Ribosome Specimens, Jie Fu

Legacy Theses & Dissertations (2009 - 2024)

Single-particle reconstruction from cryo-electron microscopy (cryo-EM) images is a widely used technique in studying the structure of macromolecular complexes. This technique allows the visualization of molecules in their native hydrated state. The heterogeneity of two-dimensional projection images, resulting from the co-existence of different states of a macromolecular complex, remains a major obstacle, as it impairs the validity of reconstruction and limits the progress toward higher resolution. On the other hand, co-existing structures, if successfully extracted from a single dataset, can provide valuable information about the equilibrium and dynamics of the biological system being studied.

A Molecular Basis For Erythromycin Sensitivity And Resistance In Escherichia Coli, Harold S. Chittum

Electronic Theses and Dissertations

The effect of erythromycin on the 50S ribosomal subunit during cell growth has been extensively investigated. Sucrose density gradient analysis of ribosomes formed in the presence and absence of the drug revealed a 50S specific assembly defect is partially responsible for erythromycin's inhibitory effects on wild type cells. Examination of two erythromycin-resistant mutants of E. coli (N281 and N282) revealed that mutant N281 (L22 mutant) but not N282 (L4 mutant) was assembly defective in the presence of the drug, although only at much higher drug concentrations (300 ug/ml vs. 75 ug/ml for wild type cells). The altered genes from each …

The Association Of 5.8 S With 28s Ribosomal Rna, Nandita Banerjee

Chemistry & Biochemistry Theses & Dissertations

5.8S rRNA is a low molecular weight ribosomal RNA which is noncovalently bonded to the larger ribosomal subunit 28S rRNA; through its 3' end and through its 5' end. This interaction is an integral part of the ribosome, and plays an important role in the ribosome structure and function.

There is a high degree of homology between the 5.8S rRNA primary structures of rat, turtle and chicken. The base sequence of rat 5.8S rRNA differs only in one position from that of turtle and in three positions fr.om that of cl1.icken. Tl1ere is a single purine substitution at the 5' …