Genetic and biochemical analysis of the endoribonuclease E/G family in RNA metabolism in Escherichia coli K-12
Chung, Dae Hwan
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Degradation of mRNA and maturation of stable RNAs provide important mechanisms for controlling gene expression at post-transcriptional level. In Escherichia coli, the RNase E/G endoribonuclease family plays a central role in the initiation of both processes. This dissertation research was an attempt to broaden our understanding of physiological roles and functional relationships of RNase E and RNase G by using a combination of genetic and biochemical analysis. The rng-219 and rng-248 alleles, comprising single amino acid substitutions within the predicted RNase H domain of RNase G, are able to support cell viability in the total absence of RNase E when present at physiologically relevant protein levels. These observations suggest that the difference in biological activities between the two enzymes is governed by their RNase H domains to some extent. The in vivo characterization of rneD1018/rng-219 and rneD1018/rng-248 double mutants allowed critical examination of the distinct physiological roles of RNase E and RNase G in E. coli RNA metabolism. The degradation of certain mRNAs and the processing of some tRNA precursors are absolutely dependent on RNase E activity. In contrast, 9S rRNA processing is effectively restored by the altered RNase G proteins in the absence of RNase E. We also examined the biochemical properties of purified RNase E, RNase G and Rng-219 proteins. The purified RNase G and Rng-219 proteins cleave structured RNA substrates, such as 9S rRNA and tRNAs, at identical sites as RNase E. Although, both RNase E/G prefer RNA substrates with 5’-monophosphate termini, the presence of a 5’-triphosphate affects the efficiency of RNase E much more than RNase G. A surprising result is the greater catalytic 2+2+activity of RNase G and Rng-219 proteins in the presence of Mn than Mg.