Decreased Expression of Stable RNA Can Alleviate the Lethality Associated with RNase E Deficiency in Escherichia coli.
The endoribonuclease RNase E participates in mRNA degradation, rRNA processing, and tRNA maturation inEscherichia coli, but the precise reasons for its essentiality are unclear and much debated. The enzyme is most active on RNA substrates with a 5'-terminal monophosphate, which is sensed by a domain in the enzyme that includes residue R169;E. colialso possesses a 5'-pyrophosphohydrolase, RppH, that catalyzes conversion of 5'-terminal triphosphate to 5'-terminal monophosphate on RNAs. Although the C-terminal half (CTH), beyond residue approximately 500, of RNase E is dispensable for viability, deletion of the CTH is lethal when combined with an R169Q mutation or with deletion ofrppHIn this work, we show that both these lethalities can be rescued in derivatives in which four or five of the sevenrrnoperons in the genome have been deleted. We hypothesize that the reduced stable RNA levels under these conditions minimize the need of RNase E to process them, thereby allowing for its diversion for mRNA degradation. In support of this hypothesis, we have found that other conditions that are known to reduce stable RNA levels also suppress one or both lethalities: (i) alterations inrelAandspoT, which are expected to lead to increased basal ppGpp levels; (ii) stringentrpoBmutations, which mimic high intracellular ppGpp levels; and (iii) overexpression of DksA. Lethality suppression by these perturbations was RNase R dependent. Our work therefore suggests that its actions on the various substrates (mRNA, rRNA, and tRNA) jointly contribute to the essentiality of RNase E inE. coliIMPORTANCEThe endoribonuclease RNase E is essential for viability in many Gram-negative bacteria, includingEscherichia coliDifferent explanations have been offered for its essentiality, including its roles in global mRNA degradation or in the processing of several tRNA and rRNA species. Our work suggests that, rather than its role in the processing of any one particular substrate, its distributed functions on all the different substrates (mRNA, rRNA, and tRNA) are responsible for the essentiality of RNase E inE. coli.
Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India.
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Himabindu
Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India anu@cdfd.org.in.
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Anupama
D004722:Endoribonucleases / Q000235:genetics / Q000378:metabolism*; D004926:Escherichia coli / Q000201:enzymology* / Q000235:genetics / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism; D017353:Gene Deletion; D015964:Gene Expression Regulation, Bacterial / Q000502:physiology*; D005838:Genotype; D009154:Mutation; D009876:Operon; D012329:RNA, Bacterial / Q000235:genetics / Q000378:metabolism*
D029968:Escherichia coli Proteins; D012329:RNA, Bacterial; C090751:dksA protein, E coli; D004722:Endoribonucleases; C022537:ribonuclease E
RNA processing and decay; RNase E; ppGpp; stable RNA expression; stringent rpoB mutants