PhD

dissertationRecoding is the programmed alteration of translation, a dynamic process in which specific signals within the mRNA act as stimulators to alter the ribosomes reading of the genetic code. There are three broad classes of recoding including translational frameshifting, redefinition of codons, and translational bypass. In frameshifting the translational machinery acts on signals from stimulators contained in the mRNA to shift into the -1 or +1 frame. Redefinition of codon meaning is a specific case in which the stop codons UAG or UGA are used to code for an amino acid and, as with frameshifting, signals found within the mRNA direct the recoding event. Translational bypass is defined by the skipping of relatively long stretches of a gene. Again, signals found within the mRNA direct the bypass event. Stimulators for recoding events include elements located either 3' or 5' of the recoding site. These signals include but are not limited to RNA secondary structures, Shine-Dalgamo sequences, stop codons, and the nascent polypeptide chain. In this study we have used structural and genetic methods to investigate the stimulatory signals involved in two recoding events: the -1 frameshifting in bacterial insertion sequence IS977 and the translational bypass in bacteriophage T4 gene