RNase E plays an essential role in the maturation of Escherichia coli tRNA precursors

Abstract

Conversion of tRNA precursors to their mature forms requires the action of both endo-and exoribonucleases. Although studies over many years identified the endoribonuclease, RNase P, and several exoribonucleases as the enzymes responsible for generating the mature 59 and 39 termini, respectively, of Escherichia coli tRNAs, relatively little is known about how tRNAs are separated from long multimeric or multifunction transcripts, or from long leader and trailer sequences. To examine this question, the tRNA products that accumulate in mutant strains devoid of multiple exoribonucleases plus one or several endoribonucleases were analyzed by northern analysis. We find that the multifunction tyrT transcript, which contains two tRNA 1Tyr sequences separated by a 209-nt spacer region plus a downstream mRNA, is cleaved at three sites in the spacer region by the endoribonuclease, RNase E. When both RNase E and RNase P are absent, a product containing both tRNAs accumulates. Two multimeric tRNA transcripts, those for tRNA Arg-His-Leu-Pro and tRNA Gly-Cys-Leu also require RNase E for maturation. For the former transcript, products with long 39 extensions on tRNA Arg , tRNA His , and tRNA Pro , as well as the primary transcript, accumulate in the absence of RNase E. For the latter transcript, RNase E cleaves downstream of each tRNA. Little processing of either multimeric transcript occurs in the absence of both RNase E and RNase P. These data indicate that RNase E is a major contributor to the initial processing of E. coli tRNA transcripts, providing substrates for final maturation by RNase P and the 39 exoribonucleases. Based on this new information, a detailed model for tRNA maturation is proposed.

Transfer RNA instability as a stress response inEscherichia coli: Rapid dynamics of the tRNA pool as a function of demand

“…24 It is also a major endoribonuclease in tRNA 49 and rRNA 50 maturation. Furthermore, RNase E is a core member of the degradosome which is a multiprotein complex involved in RNA degradation 48 assembled on RNase E through PNPase, RhlB, and enolase binding to the C-terminal half of RNase E. 51-53 The degradosome is effective in structured RNA decay from duplex unwinding by the helicase RhIB.…”

Novel One-step Mechanism for tRNA 3′-End Maturation by the Exoribonuclease RNase R of Mycoplasma genitalium

“…In E. coli, for example, the shortening of the long 3Ј-trailer in a tRNA precursor and the generation of the mature 3Ј-end are carried out by different RNases. The endoribonuclease RNase E and the processive exoribonucleases RNase II and polynucleotide phosphorylase can efficiently remove the long 3Ј-trailer, leaving a few extra residues at the 3Ј-end (3). The last few 3Ј extra residues are removed by any of the five exoribonucleases RNases T, PH, D, II, and BN, with T and PH being the most efficient enzymes.…”

“…In bacteria, tRNA 3Ј-processing may be accomplished by the actions of endo-or exoribonucleases or both (1,2). In Escherichia coli, the primary tRNA transcript undergoes an initial cleavage by RNase E in its 3Ј-trailer downstream of the CCA sequence (3,4), followed by stepwise trimming reactions of the extra residues by multiple exoribonucleases, including RNases T, PH, D, II, and BN and polynucleotide phosphorylase (5,6). In Bacillus subtilis, pre-tRNAs with an encoded CCA sequence are matured by exonucleolytic action at the 3Ј-end, whereas CCAless tRNA precursors are cleaved by RNase Z after the discriminator base, followed by CCA addition (7).…”

tDNA locus polymorphism and ecto-chromosomal DNA insertion hot-spots are related to the phylogenetic group of Escherichia coli strains

“…Several tDNA loci (either monocistronic or polycistronic) have been shown to be cotranscribed with downstream genes (Bosl & Kersten, 1991;Fournier & Ozeki, 1985;Li & Deutscher, 2002). Disruption of such transcriptional units could therefore be detrimental to the bacteria.…”