tRNA 3′ End Maturation in Archaea has Eukaryotic Features: the RNase Z from Haloferax volcanii

Schierling, Karina; Rösch, Sylvia; Rupprecht, Renate; Schiffer, Steffen; Marchfelder, Anita

doi:10.1006/jmbi.2001.5395

Cited by 59 publications

(52 citation statements)

References 31 publications

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“…Specifically, ElaC is capable of processing tRNA precursors lacking a chromosomally encoded CCA determinant both in vivo and in vitro ( Figs 1B, 1C, and 6A), in agreement with published data for RNase Z found in B. subtilis, archaea and eukaryotes (Schierling et al, 2002;Schiffer et al, 2002;Pellegrini et al, 2003;Dubrovsky et al, 2004). In addition, as predicted from the experiments in B. subtilis (Pellegrini et al, 2003), the enzyme does not process a B. subtilis tRNA precursor sibly RNase Z and RNase LS, the most likely explanation for their apparent supporting role in mRNA decay in single mutants (Table 1, Ow et al, 2003;Otsuka and Yonesaki, 2005) arises from the relatively low abundance of these proteins.…”

Section: Discussionsupporting

confidence: 91%

“…Fifty nanograms of RNase E and 100 ng of RNase Z were used in 80 µl reaction volumes. (Schierling et al, 2002;Schiffer et al, 2002;Pellegrini et al, 2003;Dubrovsky et al, 2004), the results presented in Figs 5, 6C and 7 and Table 1 clearly indicate that it plays a significant role in mRNA decay, an activity not previously observed for this enzyme. In particular, when both RNase E and RNase Z were inactivated in the rne-1 rnz∆500::kan double mutant, five different mRNAs were dramatically stabilized compared with both the rne-1 strain and the wild-type control (Fig.…”

Section: Optimum Reaction Conditions For Rnase Bn Inhibit Rnase Z Actsupporting

confidence: 67%

“…Finally, it should be noted that Ezraty et al (2005) have claimed that the E. coli elaC gene encodes the previously characterized 3′→5′ exonuclease RNase BN, an activity implicated in tRNA maturation (Schmidt and McClain, 1978;Kelly and Deutscher, 1992). Although RNase BN was identified prior to the genetic, biochemical and crystallographic characterization of the endonuclease RNase Z (Schierling et al, 2002;Schiffer et al, 2002;Pellegrini et al, 2003;Dubrovsky et al, 2004;Ishii et al, 2005;Schilling et al, 2005), the overwhelming body of evidence suggests that the RNase Z family of enzymes act primarily as endoribonucleases. In fact, RNase Z-specific endonucleolytic cleavages were observed with nanogram amounts of purified enzyme (Fig.…”

Section: Discussionmentioning

confidence: 99%

“…A variety of experiments have demonstrated that representatives of the ELAC1/2 family from Arabadopsis, Bacillus subtilis, Haloferax volcanii and Drosophila melanogaster encode an endoribonuclease, designated RNase Z, which is involved in the processing of tRNA precursors lacking an encoded CCA 3 ′ terminus (Schierling et al ., 2002;Schiffer et al ., 2002;Pellegrini et al ., 2003;Dubrovsky et al ., 2004). However, it is not active on tRNA precursors that contain a chromosomally encoded CCA (Pellegrini et al ., 2003).…”

Section: Introductionmentioning

confidence: 99%

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RNase Z in Escherichia coli plays a significant role in mRNA decay

Perwez

Kushner²

2006

Molecular Microbiology

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SummaryGenetic and biochemical analysis of RNase Z in eukaryotes, such as Arabadopsis thaliana , and prokaryotes like Bacillus subtilis have demonstrated that this endoribonuclease is essential for the maturation of tRNA precursors that do not contain a chromosomally encoded CCA determinant. As all Escherichia coli tRNA transcripts have chromosomally encoded CCA determinants, the function of its putative RNase Z homologue, the product of the elaC gene, is not clear. Here we demonstrate that the E. coli ElaC protein (RNase Z) endonucleolytically processes B. subtilis tRNA precursors lacking a CCA determinant both in vivo and in vitro . More importantly, E. coli RNase Z plays a significant role in mRNA decay, a previously unidentified activity for the enzyme. The purified RNase Z protein cleaves the rpsT mRNA at locations distinct from those obtained with RNase E. As expected, under physiological conditions E. coli and B. subtilis tRNA precursors containing a CCA determinant are not substrates. These results suggest a potentially important new role for the RNase Z family of proteins in RNA metabolism, particularly in organisms lacking RNase E.

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Section: Discussionsupporting

confidence: 91%

Section: Optimum Reaction Conditions For Rnase Bn Inhibit Rnase Z Actsupporting

confidence: 67%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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RNase Z in Escherichia coli plays a significant role in mRNA decay

Perwez

Kushner²

2006

Molecular Microbiology

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“…On the other hand, the removal of the 3Ј extension is a more complex process. In archaea and eukaryotes, the 3Ј extension sequence is removed by RNase Z in a single step reaction (6,7), whereas in bacteria a number of RNases perform this function in multistep reactions (2)(3)(4). In Escherichia coli, the proposed 3Ј processing pathway involves the following steps (2)(3)(4).…”

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confidence: 99%

Crystal Structure of the tRNA Processing Enzyme RNase PH from Aquifex aeolicus

Ishii

Nureki

Yokoyama

2003

Journal of Biological Chemistry

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RNase PH is one of the exoribonucleases that catalyze the 3 end processing of tRNA in bacteria. RNase PH removes nucleotides following the CCA sequence of tRNA precursors by phosphorolysis and generates mature tRNAs with amino acid acceptor activity. In this study, we determined the crystal structure of Aquifex aeolicus RNase PH bound with a phosphate, a co-substrate, in the active site at 2.3-Å resolution. RNase PH has the typical ␣/␤ fold, which forms a hexameric ring structure as a trimer of dimers. This ring structure resembles that of the polynucleotide phosphorylase core domain homotrimer, another phosphorolytic exoribonuclease. Four amino acid residues, Arg-86, Gly-124, Thr-125, and Arg-126, of RNase PH are involved in the phosphate-binding site. Mutational analyses of these residues showed their importance in the phosphorolysis reaction. A docking model with the tRNA acceptor stem suggests how RNase PH accommodates substrate RNAs.The processing of tRNA precursors into mature tRNAs involves several steps, including the removal of the 5Ј and 3Ј extension sequences (1-4). This removal of the 5Ј and 3Ј extension sequences is necessary for producing the CCA sequence, which is essential for tRNA aminoacylation and subsequent protein synthesis (2-4). The 5Ј extension is removed, in a single step reaction, by the ribonucleoprotein RNase P, which is conserved in all organisms (5). On the other hand, the removal of the 3Ј extension is a more complex process. In archaea and eukaryotes, the 3Ј extension sequence is removed by RNase Z in a single step reaction (6, 7), whereas in bacteria a number of RNases perform this function in multistep reactions (2-4). In Escherichia coli, the proposed 3Ј processing pathway involves the following steps (2-4). First, an endonucleolytic cleavage occurs downstream of the CCA sequence. RNases E and III have been identified as participating in this first step. Then the endonucleolytic reaction is followed by the 5Ј-terminal processing by RNase P, if the 3Ј trailer sequence of the tRNA precursor is short. However, if the tRNA precursor has a long 3Ј trailer sequence, an exonucleolytic reaction removes some nucleotides from the 3Ј end before RNase P processes the 5Ј end. This exonucleolytic reaction involves RNases PH, T, BN, D, II, and polynucleotide phosphorylase. Finally, these exonucleases remove all of the nucleotides downstream of the CCA sequence; RNase PH and RNase T are usually most effective (8).In this final trimming, RNase PH catalyzes a 3Ј exonucleolytic, phosphorolytic reaction, which needs a phosphate as the co-substrate, and produces a nucleoside diphosphate (9, 10). RNase PH was shown to catalyze the reverse reaction in vitro,

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