UBC Theses and Dissertations
The S1 domains of Escherichia coli mRNA degradation Edge, Robert Edward
The S1 domain is a recurring theme in the enzymes of mRNA decay in Escherichia coli, occurring in polynucleotide phosphorylase (PNPase), ribonuclease II (RNase II), ribonuclease E (RNase E) and ribonuclease G (RNase G). This thesis focuses on the function of the S1 domain of PNPase and RNase E. In the former, the hypothesis examined was that the domain provides an RNA -substrate contact that imparts processive phosphorylysis to the enzyme. Results show that PNPase lacking this domain still possesses catalytic activity, although at an extremely reduced rate, but appears to retain processive phosphorylysis of RNA substrates. In addition, the isolated PNPase domain has a Kd for RNA that is very high, suggesting that this domain may not play a role in the interactions between PNPase and its substrate. The S1 domain of RNase E was studied as an isolated domain. NMR experiments conducted by Dr. Mario Schubert revealed the solution structure of this isolated domain as well as potential dimerization contacts and identified residues implicated in nucleic acid interaction. Crosslinking data confirmed the dimerization of this domain. CD spectroscopy showed that a classical temperature -sensitive mutation in this domain alters its structure. The work on the RNase E S1 domain also tested the hypothesis that the domain confers the preference of RNase E for monophosphorylated substrates. The data suggest that this domain indeed binds to RNA (Kd 2 μM to 5 μM); however, it displays no increased affinity for differentially phosphorylated RNAs or detectable sequence specificity.
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