Nucleotides in precursor tRNAs that are required intact for catalysis by RNase P RNAs

Thurlow, David L.; Shilowski, Deborah; Marsh, Terence L.

doi:10.1093/nar/19.4.885

Cited by 58 publications

(41 citation statements)

References 29 publications

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“…In contrast, the enzymes from HeLa (Yuan and Altman, 1994, 199.5) and Xenopus nuclei (Carrara et al, 1995) tolerate alterations of the substrate structure, including disruption or deletion of D-stem and anticodon-stem domains, as long as the acceptorstem and T-loop remain unchanged. The requirement of eukaryotic RNases P for an intact, contiguous acceptor-stem and Tstem helix terminating with the correct T-loop sequence implies that the conserved T-loop might bind to the enzyme and thus aid in the correct positioning of the cleavage site, as has been postulated for E. coli RNase P (Kahle et al, 1990;Thurlow et al, 1991). Compared to the more relaxed specificity of the vertebrate enzymes, the substrate recognition by plant RNase P thus seems to be more strictly confined to the conserved three-dimensional pre-tRNA structure.…”

Section: Discussionmentioning

confidence: 96%

Partial Purification and Characterization of Nuclear Ribonuclease P from Wheat

Arends

Schön

1997

European Journal of Biochemistry

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Ribonuclease P (RNase P) from wheat nuclei has been purified over 1000-fold, using wheat germ extract as starting material and a combination of poly(ethylenglyco1) precipitation and column chromatography. The enzyme was shown to be of nuclear origin by its characteristic ionic requirements; for optimum activity it requires 0.5-1.5 mM Mg", which can be partly replaced by MnZ+. With about 100 kDa, wheat nuclear RNase P has the lowest molecular mass reported so far for a eukaryotic RNase P. The enzyme has an isoelectric point of 5.0 and a buoyant density of 1.34 g/ml in CsCl, suggesting the presence of a nucleic acid component; it is, however, insensitive against treatment with micrococcal nuclease. Wheat germ RNase P requires an intact tertiary structure of the pre-tRNA substrate; its cleavage efficiency is also influenced by the presence of an intron, and by the nature of the 3' terminus of the substrate. The apparent K,,, and V,,, for an intronless plant pre-tRNATYr are 10.3 nM and 1.12 fmol/min, respectively.Keywords: enzyme purification; nuclear ribonuclease P; pre-tRNA processing ; substrate specificity ; Triticum aestivum.RNase P is the ubiquitous endonuclease required for the maturation of the 5' end of tRNAs. In all cases where the composition of this enzyme has been investigated in detail, it was found to consist of both protein and RNA subunits (Kmpp et al., 1986;Bartkiewicz et al., 1989;Lee and Engelke, 1989;Morales et al., 1989;Doria et al., 1991;Nieuwlandt et al., 1991 ; LaGrandeur et al., 1993;Marchfelder and Brennicke, 1994;Baum et al., 1996; Lee et al., 1996a,b; for the bacterial enzymes, see reviews by Altman et al., 1993a;Pace and Brown, 1995). RNase P RNAs from bacteria show enzymatic activity in vitro without the protein subunit; however, RNase P from archaebacteria or eukaryotes is only active as a holoenzyme. In contrast to our current knowledge on RNase P from bacteria and most eukaryotic cellular compartments, no detailed information is available on cleavage mechanism, substrate requirements, or subunit composition of RNase P from plant nuclei. Previous studies performed with a complete processing system from wheat germ did not allow unambigous determination of the order of cleavage events involved in end maturation of tRNAs (e.g. Stange and Beier, 1987). Similarly, although investigation of a variety of pre-tRNAs indicated that mutations disrupting the tRNA structure severely impair overall processing in this plant in vitro system (Stange et al., 1991 ;Fuchs et al., 1992;Teichmann et al., 1994), it is not clear at present which of the enzymes involved is most sensitive to these changes. To approach these questions, and to gain insight into the molecular composition and substrate requirements of nuclear RNase P from higher (EC 3.1.31.1).plants, we have purified and characterized this enzyme from wheat germ. Although an RNA component could not yet be identified in wheat germ RNase P, several properties of the enzyme indicate that it might be a ribonucleoprotein. The availability of a high...

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Section: Discussionmentioning

confidence: 96%

Partial Purification and Characterization of Nuclear Ribonuclease P from Wheat

Arends

Schön

1997

European Journal of Biochemistry

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“…In all organisms studied so far, the 5Ј leader of a tRNA precursor is removed by the site-specific RNase P, which cleaves precisely at the 5Ј end of the mature tRNA (for a review, see e.g., reference 1). Structural studies have already indicated that (i) the conformation of the tRNA in the precursor is approximately the same as that in the final mature state and (ii) the correct cloverleaf folding and L-shaped threedimensional structure of the tRNA moiety in the precursor are essential for recognition and cleavage by RNase P. Two domains, one near the cleavage site at the 5Ј end of the tRNA and the other one in the T stem and loop, were shown to be important for the interaction between the eubacterial RNase P RNA and the tRNA precursor (36). The residue at position 4 was part of the 6 nt of the acceptor stem involved in this interaction.…”

Section: Discussionmentioning

confidence: 99%

A Single Editing Event Is a Prerequisite for Efficient Processing of Potato Mitochondrial Phenylalanine tRNA

Maréchal-Drouard

Cosset

Remacle

et al. 1996

Molecular and Cellular Biology

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In bean, potato, and Oenothera plants, the C encoded at position 4 (C 4 ) in the mitochondrial tRNA GAA Phe gene is converted into a U in the mature tRNA. This nucleotide change corrects a mismatched C 4 -A 69 base pair which appears when the gene sequence is folded into the cloverleaf structure. C-to-U conversions constitute the most common editing events occurring in plant mitochondrial mRNAs. While most of these conversions introduce changes in the amino acids specified by the mRNA and appear to be essential for the synthesis of functional proteins in plant mitochondria, the putative role of mitochondrial tRNA editing has not yet been defined. Since the edited form of the tRNA has the correct secondary and tertiary structures compared with the nonedited form, the two main processes which might be affected by a nucleotide conversion are aminoacylation and maturation. To test these possibilities, we determined the aminoacylation properties of unedited and edited potato mitochondrial tRNA Phe in vitro transcripts, as well as the processing efficiency of in vitrosynthesized potato mitochondrial tRNA Phe precursors. Reverse transcription-PCR amplification of natural precursors followed by cDNA sequencing was also used to investigate the influence of editing on processing. Our results show that C-to-U conversion at position 4 in the potato mitochondrial tRNA GAA Phe is not required for aminoacylation with phenylalanine but is likely to be essential for efficient processing of this tRNA.

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“…pre-tRNA recognition by bacterial RNase P The regions of precursor tRNA recognized by bacterial RNase P include the TCC stem-loop, D-loop, and the acceptor stem (McClain et al 1987;Green and Vold 1988;Kahle et al 1990;Thurlow et al 1991;Pan et al 1995;Pan 1997, 1998;Chen et al 1998); the 59-leader also plays a role in substrate recognition and substrate/product discrimination (Brannvall et al 1998;Crary et al 1998;Niranjanakumari et al 1998;Zahler et al 2003Zahler et al , 2005Rueda et al 2005;Pettersson and Kirsebom 2008;Cuzic-Feltens et al 2009). In addition, bacterial RNase P typically interacts with the 39-end RCCA sequence found in most bacterial pre-tRNA transcripts (Sprinzl and Vassilenko 2005), and the disruption of this interaction has a negative effect on the substrate cleavage in vitro, although it does not abolish it (Guerrier-Takada et al 1984;McClain et al 1987;Kirsebom and Svard 1994;LaGrandeur et al 1994;Oh and Pace 1994;Svard et al 1996;Oh et al 1998;Heide et al 1999;Busch et al 2000;.…”

Section: The Known Functions and Substrates Of Rnase P Rnase P Is A Mmentioning

confidence: 99%

Of proteins and RNA: The RNase P/MRP family

Esakova¹,

Krasilnikov²

2010

RNA

199

230

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Nuclear ribonuclease (RNase) P is a ubiquitous essential ribonucleoprotein complex, one of only two known RNA-based enzymes found in all three domains of life. The RNA component is the catalytic moiety of RNases P across all phylogenetic domains; it contains a well-conserved core, whereas peripheral structural elements are diverse. RNA components of eukaryotic RNases P tend to be less complex than their bacterial counterparts, a simplification that is accompanied by a dramatic reduction of their catalytic ability in the absence of protein. The size and complexity of the protein moieties increase dramatically from bacterial to archaeal to eukaryotic enzymes, apparently reflecting the delegation of some structural functions from RNA to proteins and, perhaps, in response to the increased complexity of the cellular environment in the more evolutionarily advanced organisms; the reasons for the increased dependence on proteins are not clear. We review current information on RNase P and the closely related universal eukaryotic enzyme RNase MRP, focusing on their functions and structural organization.

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Nucleotides in precursor tRNAs that are required intact for catalysis by RNase P RNAs

Cited by 58 publications

References 29 publications

Partial Purification and Characterization of Nuclear Ribonuclease P from Wheat

Partial Purification and Characterization of Nuclear Ribonuclease P from Wheat

A Single Editing Event Is a Prerequisite for Efficient Processing of Potato Mitochondrial Phenylalanine tRNA

Of proteins and RNA: The RNase P/MRP family

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