Showing papers by "Murray P. Deutscher published in 1998"

3‧ Exoribonucleolytic trimming is a common feature of the maturation of small, stable RNAs in Escherichia coli

Abstract: In addition to tRNA and 5S RNA, Escherichia coli contains several other small, stable RNA species; these are M1, 10Sa, 6S, and 4.5S RNA. Although these RNAs are initially synthesized as precursor molecules, relatively little is known about their maturation. The data presented here show that 3′ exoribonucleolytic trimming is required for the final maturation of each of these molecules. As found previously with tRNA, but not 5S RNA, any one of a number of exoribonucleases can carry out the trimming reaction in vivo, although RNases T and PH are most effective. In their absence, large amounts of immature molecules accumulate for most of the RNAs, and these can be converted to the mature forms in vitro by the purified RNases. A model is proposed that identifies a structural feature present in all the small, stable RNAs of E. coli, and describes how this structure together with the RNases influences the common mechanism for 3′ maturation.

Polyadenylation of stable RNA precursors in vivo

Abstract: Polyadenylation at the 3′ terminus has long been considered a specific feature of mRNA and a few other unstable RNA species. Here we show that stable RNAs in Escherichia coli can be polyadenylated as well. RNA molecules with poly(A) tails are the major products that accumulate for essentially all stable RNA precursors when RNA maturation is slowed because of the absence of processing exoribonucleases; poly(A) tails vary from one to seven residues in length. The polyadenylation process depends on the presence of poly(A) polymerase I. A stochastic competition between the exoribonucleases and poly(A) polymerase is proposed to explain the accumulation of polyadenylated RNAs. These data indicate that polyadenylation is not unique to mRNA, and its widespread occurrence suggests that it serves a more general function in RNA metabolism.

Oligoribonuclease Is Encoded by a Highly Conserved Gene in the 3′-5′ Exonuclease Superfamily

Abstract: Oligoribonuclease, a 3′-to-5′ exoribonuclease specific for small oligoribonucleotides, was purified to homogeneity from extracts of Escherichia coli. The purified protein is an α2 dimer of 40 kDa. NH2-terminal sequence analysis of the protein identified the gene encoding oligoribonuclease as yjeR (o204a), a previously reported open reading frame located at 94 min on the E. coli chromosome. However, as a consequence of the sequence information, the translation start site of this open reading frame has been revised. Cloning of yjeR led to overexpression of oligoribonuclease activity, and interruption of the cloned gene with a kanamycin resistance cassette eliminated the overexpression. On the basis of these data, we propose that yjeR be renamed orn. Orthologs of oligoribonuclease are present in a wide range of organisms, extending up to humans.