M1 RNA, the RNA subunit of Escherichia coli ribonuclease P, can undergo a pH-sensitive conformational change

Altman, Sidney; Guerrier-Takada, Cecilia

doi:10.1021/bi00354a002

Cited by 26 publications

(13 citation statements)

References 9 publications

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“…Antisense transcripts of the cDNA encoding S. cerevisiae RNase P-associated RNA (37) were used to screen an S. cerevisiae genomic library in YCp5O by filter hybridization (2). Twenty-three positive clones that encompassed the cDNA sequence were identified.…”

Section: Resultsmentioning

confidence: 99%

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Characterization of RPR1, an essential gene encoding the RNA component of Saccharomyces cerevisiae nuclear RNase P.

Lee¹,

Rohlman²,

Molony³

et al. 1991

Mol. Cell. Biol.

115

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RNA components have been identified in preparations of RNase P from a number of eucaryotic sources, but final proof that these RNAs are true RNase P subunits has been elusive because the eucaryotic RNAs, unlike the procaryotic RNase P ribozymes, have not been shown to have catalytic activity in the absence of protein.We previously identified such an RNA component in Saccharomyces cerevisiae nuclear RNase P preparations and have now characterized the corresponding, chromosomal gene, called RPRI (RNase P ribonucleoprotein 1). Gene disruption experiments showed RPR1 to be single copy and essential. Characterization of the gene region located RPRI 600 bp downstream of the URA3 coding region on chromosome V. We have sequenced 400 bp upstream and 550 bp downstream of the region encoding the major 369-nucleotide RPRI RNA. The presence of less abundant, potential precursor RNAs with an extra 84 nucleotides of 5' leader and up to 30 nucleotides of 3' trailing sequences suggests that the primary RPRI transcript is subjected to multiple processing steps to obtain the 369-nucleotide form. Complementation of RPRI-disrupted haploids with one variant of RPRI gave a slow-growth and temperature-sensitive phenotype. This strain accumulates tRNA precursors that lack the 5' end maturation performed by RNase P, providing direct evidence that RPRI RNA is an essential component of this enzyme.RNase P from both procaryotic and eucaryotic sources is an endonuclease that cleaves pre-tRNA substrates to yield mature 5' termini. In procaryotes, both the RNA and protein components of the ribonucleoprotein enzymes are required for in vivo activity (15,27,29,33,43,49,57,58), but the RNA component alone is capable of efficiently catalyzing the correct reaction under some conditions in vitro (3,18,21,22,52). Extensive phylogenetic sequence comparisons of these RNAs (30), combined with folding energy calculations and cleavage sensitivity studies (6, 19, 51, 52), suggest a conserved, highly ordered secondary structure. Most if not all of the key contacts with the substrates depend on this structure, with the protein contributing to efficiency through secondary effects such as charge shielding between RNA chain phosphate backbones. The mechanism by which pretRNA substrates are recognized is not clearly understood, however, since there are no obvious regions of required Watson-Crick base pairing between the enzyme and substrate RNAs (20,36).Studies of eucaryotic RNase Ps have suggested that they also contain essential RNA subunits, although the role of the RNA components has not been firmly established. RNAs that copurify with both nuclear and organelle RNase Ps have been characterized (1,7,9,11,12,14,24,32,34,35,37,38,40,42) and shown to have sequence and structural similarities to each other and to a lesser degree to the procaryotic RNAs (5, 37). The identification of the eucaryotic RNAs as essential RNase P subunits has not been rigorously confirmed, however, since there are no reports of the eucaryotic RNAs having enzyme activity in the absence ...

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Section: Resultsmentioning

confidence: 99%

“…The Styl site used to prepare the 3' end S1 probe is indicated. nuclease analysis was then performed as previously described (2). Size markers for the Si-protected fragments were unrelated dideoxynucleotide chain termination reactions in adjacent lanes (not shown).…”

Section: Methodsmentioning

confidence: 99%

Characterization of RPR1, an essential gene encoding the RNA component of Saccharomyces cerevisiae nuclear RNase P.

Lee¹,

Rohlman²,

Molony³

et al. 1991

Mol. Cell. Biol.

115

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“…Although temperature-sensitive mutations in these individual components have shown that both are required for RNase P activity in vivo (24,25,31,38,41,46,47), each RNA component alone can recognize and cleave substrates under some conditions in vitro (2,16,19,20,44). The enzymic RNAs can form extensively base-paired secondary structures as judged by theoretical calculations and cleavage sensitivity structure analyses (3,17,43,44).…”

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confidence: 99%

Partial characterization of an RNA component that copurifies with Saccharomyces cerevisiae RNase P.

Lee¹,

Engelke²

1989

Mol. Cell. Biol.

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Saccharomyces cerevisiae cellular RNase P is composed of both protein and RNA components that are essential for activity. The isolated holoenzyme contains a highly structured RNA of 369 nucleotides that has extensive sequence similarities to the 286-nucleotide RNA associated with Schizosaccharomyces pombe RNase P but bears little resemblance to the analogous RNA sequences in procaryotes or S. cerevisiae mitochondria. Even so, the predicted secondary structure of S. cerevisiae RNA is strikingly similar to the bacterial phylogenetic consensus rather than to previously predicted structures of other eucaryotic RNase P RNAs.Mature 5' termini of tRNAs in both procaryotes and eucaryotes are generated by cleavage with a structurespecific endonuclease, RNase P. Extensive study of RNase P activities from Escherichia coli and Bacillus siubtilis has shown that both enzymes consist of single RNA and protein species (14,16,19,21,25,[29][30][31]38,43,44,51). Although temperature-sensitive mutations in these individual components have shown that both are required for RNase P activity in vivo (24,25,31,38,41,46,47), each RNA component alone can recognize and cleave substrates under some conditions in vitro (2,16,19,20,44). The enzymic RNAs can form extensively base-paired secondary structures as judged by theoretical calculations and cleavage sensitivity structure analyses (3,17,43,44). Extensive phylogenetic sequence comparisons among the bacterial RNAs suggest several short domains of conserved sequences and a conserved secondary structure (26). This structure, rather than Watson-Crick base pairing with the substrates, is suspected of being primarily responsible for recognition of pre-tRNAs, since several RNA structural disruptions have been shown to reduce catalytic activity. A sequence originally thought to contribute to substrate recognition through complementarity to the invariant T4JCG sequence in tRNAs is dispensable (18,34).RNase P RNA activities have been reported in a number of eucaryotes (1,5,6,8,11,13,22,28,32,33,35,36), but there has been significant disagreement as to the nature of the enzymes. In particular, the RNase P from Xenopis laevis has been reported to be insensitive to micrococcal nuclease and found as part of a large polypeptide complex (6). For all other nuclear and mitochondrial enzymes tested, RNA components have been shown to be essential on the basis of either nuclease sensitivity of the enzyme or genetic evidence. Other than one report on HeLa cell RNase P (15), the ability to denature and reconstitute the eucaryotic components has not been reported and there have been no instances of RNA components having catalytic activity in the absence of protein (39). RNA subunits essential for the activity of the enzyme (28, 37) in SchiZosaccharomnvces pombe and Saccharomvces cerev'isiae mitochondria have been identified and their sequences have been determined (33,37). Surprisingly, neither the nucleotide sequences nor the predicted secondary structures of these RNAs bear any striking resemblance to each o...

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“…It is likely that a 2—3 unit pH difference (from pH 7) could cause the RNA to fold differently as the pK a 's of some functional groups present in RNA bases can be in this range (67). Perturbations of RNA structures due to pH changes have been observed in the Hepatitis δ virus (68) and E. coli RNase P RNA (18). Many single-stranded nucleases, such as S1, Mung Bean and the single-stranded nucleases from Neurospora crassa and Schizopyllum commune , also require divalent transition metal ions such Zn 2+ or Co 2+ (66,69), which can also affect folding.…”

Section: Discussionmentioning

confidence: 99%

Improvement of RNA secondary structure prediction using RNase H cleavage and randomized oligonucleotides

Kauffmann

Campagna

Bartels

et al. 2009

Nucleic Acids Research

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RNA secondary structure prediction using free energy minimization is one method to gain an approximation of structure. Constraints generated by enzymatic mapping or chemical modification can improve the accuracy of secondary structure prediction. We report a facile method that identifies single-stranded regions in RNA using short, randomized DNA oligonucleotides and RNase H cleavage. These regions are then used as constraints in secondary structure prediction. This method was used to improve the secondary structure prediction of Escherichia coli 5S rRNA. The lowest free energy structure without constraints has only 27% of the base pairs present in the phylogenetic structure. The addition of constraints from RNase H cleavage improves the prediction to 100% of base pairs. The same method was used to generate secondary structure constraints for yeast tRNAPhe, which is accurately predicted in the absence of constraints (95%). Although RNase H mapping does not improve secondary structure prediction, it does eliminate all other suboptimal structures predicted within 10% of the lowest free energy structure. The method is advantageous over other single-stranded nucleases since RNase H is functional in physiological conditions. Moreover, it can be used for any RNA to identify accessible binding sites for oligonucleotides or small molecules.

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M1 RNA, the RNA subunit of Escherichia coli ribonuclease P, can undergo a pH-sensitive conformational change

Cited by 26 publications

References 9 publications

Characterization of RPR1, an essential gene encoding the RNA component of Saccharomyces cerevisiae nuclear RNase P.

Characterization of RPR1, an essential gene encoding the RNA component of Saccharomyces cerevisiae nuclear RNase P.

Partial characterization of an RNA component that copurifies with Saccharomyces cerevisiae RNase P.

Improvement of RNA secondary structure prediction using RNase H cleavage and randomized oligonucleotides

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