RNA recognition by SAM domains
By: by Tzvi Aviv.
Published: 2006
Language: eng
Number of pages: 142
ISBN-13: 9780494158487
Description: Anteroposterior patterning in Drosophila melanogaster is dependent upon the sequence-specific RNA binding protein Smaug, which binds to and regulates the translation of nanos mRNA. In this thesis, I demonstrate that the s&barbelow;terile-a&barbelow;lpha m&barbelow;otif (SAM) domain of Smaug functions as an RNA recognition domain. This represents a new function for the SAM domain family, which is well characterized for mediating protein-protein interactions. Using homology modeling and site-directed mutagenesis, I have localized the RNA binding surface of the Smaug SAM domain. The conservation of these surface residues in a group of SAM domain containing proteins present from yeast to human suggested that these proteins share a common RNA binding function. I proved this point by demonstrating that the SAM domain of the Smaug homolog in Saccharomyces cerevisiae (Vts1) binds RNA hairpins with essentially the same affinity and sequence specificity as Smaug. In addition, I solved the crystal structures of the Vts1 SAM domain in its unliganded state and in complex with an RNA hairpin. The two structures are essentially identical, implying that no major structural rearrangements occur upon RNA binding. Specificity of hairpin binding arises from the association of a guanosine base of the hairpin loop with a shallow pocket on the SAM domain and from multiple contacts made to the unique backbone structure of the hairpin. Using a reporter gene, I demonstrated that Vts1 induces transcript degradation through a mechanism involving the cytoplasmic deadenylase CCR4. Subsequentially, I validated NNF1  as an endogenous target of Vts1 among 79 transcripts that co-purify with epitope tagged Vts1. Together my work uncovers the molecular details of sequence-specific RNA recognition by a conserved subfamily of SAM domains and define a class of post-transcriptional regulators that act in part through a common RNA binding mechanism.
Notes: Source: Dissertation Abstracts International, Volume: 67-07, Section: B, page: 3585.

Thesis (Ph.D.)--University of Toronto, 2006.

Includes bibliographic references.

Electronic version licensed for access by U. of T. users.