RNase MRP/RNase P: a structure‐function relation conserved in evolution?

Karwan, Robert

doi:10.1016/0014-5793(93)80025-p

Cited by 21 publications

(14 citation statements)

References 66 publications

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“…(Saccharomyces diastaticus)+ It is interesting to compare the pairwise sequence identity among RNase MRP and P RNAs+ The sequences between the two strands of the P4 helix are known for both RNase P and RNase MRP RNAs for 15 species+ The mean sequence identity between the RNAs of each species and S. cerevisiae is 73% for RNase MRP RNA, but only 59% for RNase P RNA, indicating that within the fungi analyzed here, the RNase P RNA has undergone more extensive evolution than has RNase MRP RNA+ Much of the variation in RNase P is due to sporadic presence of helices (Frank et al+, 2000)+ The structures in Figure 1 and the sequences shown in Figure 2 indicate that much of the sequence variation that exists between the RNA species is localized to putative helical elements, with variable lengths+ Consequently, the sequences in Figure 2 are aligned only in regions where homology is evident by sequence similarities+ Helical regions that vary in length are not necessarily aligned (e+g+, helices ymP6, 7, 8, and eP19)+ Individual instances of the proposed structures of these variable length helices are depicted in Figure 1+ Despite many base substitutions within the variable helices, compensatory mutations maintain the integrity of the proposed pairings+ The sequence covariation found in both the complete and the partial MRP genes supports the existence of all MRP helices shown in Figures 1 and 2+ As expected, the structures of the four helices proposed in Domain 1 (labeled P1, P2, P3, and P4; Fig+ 1) conform, in general, to previously proposed models for RNase MRP RNA (Forster & Altman, 1990;Karwan, 1993;Reilly & Schmitt, 1996)+ Indeed, homologous structures are also present in all known examples of cellular RNase P RNA, including those of Archaea and Bacteria (Chen & Pace, 1997)+ In keeping with the nomenclature used for RNase P RNA, we refer to these regions as P1-P4 (for paired regions 1-4)+ A fifth helix in Domain 1, eP19 (Fig+ 1), was also proposed previously and occupies a position equivalent to eP19 in eukaryotic RNase P RNA (Frank et al+, 2000)+ This helix also occurs in some, but not all, RNase P RNAs from Bacteria and Archaea+…”

Section: Phylogenetic Analysissupporting

confidence: 78%

Phylogenetic analysis of the structure of RNase MRP RNA in yeasts

Frank

Pace

et al. 2002

RNA

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RNase MRP is a ribonucleoprotein enzyme involved in processing precursor rRNA in eukaryotes. To facilitate our structure-function analysis of RNase MRP from Saccharomyces cerevisiae, we have determined the likely secondary structure of the RNA component by a phylogenetic approach in which we sequenced all or part of the RNase MRP RNAs from 17 additional species of the Saccharomycetaceae family. The structure deduced from these sequences contains the helices previously suggested to be common to the RNA subunit of RNase MRP and the related RNA subunit of RNase P, an enzyme cleaving tRNA precursors. However, outside this common region, the structure of RNase MRP RNA determined here differs from a previously proposed universal structure for RNase MRPs. Chemical and enzymatic structure probing analyses were consistent with our revised secondary structure. Comparison of all known RNase MRP RNA sequences revealed three regions with highly conserved nucleotides. Two of these regions are part of a helix implicated in RNA catalysis in RNase P, suggesting that RNase MRP may cleave rRNA using a similar catalytic mechanism.

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Section: Phylogenetic Analysissupporting

confidence: 78%

Phylogenetic analysis of the structure of RNase MRP RNA in yeasts

Frank

Pace

et al. 2002

RNA

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“…The Th protein has not been sequenced or cloned but may have epitopes in common with the bacterial RNase P proteins, as antibodies against the E. coli protein cross-react with a 40-kD protein component of human RNase P (Mamula et al 1989), which may well be the Th protein. The buoyant density reported for human RNase P (Bartkiewicz et al 1989) and the sedimentation velocity of the RNase MRP (Karwan 1993) would not be consistent with the presence of only the RNA and a protein of 40 kD, indicating that other protein components are likely to be present. POPlp is the first nuclear RNase P and the only RNase MRP protein for which the gene has been cloned.…”

Section: Pop1 Is a Component Of Rnase P And Rnase Mrpmentioning

confidence: 90%

“…This protein has a molecular mass of 105 kD and is essential for mitochondrial RNase P function in vivo but has no significant homology to POPlp. The protein composition of RNase P and RNase MRP from higher eukaryotes is less well defined, but they may share a protein of 40 kD, referred to as the Th protein Yuan et al 1989;Karwan 1993). The Th protein has not been sequenced or cloned but may have epitopes in common with the bacterial RNase P proteins, as antibodies against the E. coli protein cross-react with a 40-kD protein component of human RNase P (Mamula et al 1989), which may well be the Th protein.…”

Section: Pop1 Is a Component Of Rnase P And Rnase Mrpmentioning

confidence: 99%

“…Both RNase P and endonuclease G have also been reported to cleave the mitochondrial RNA in vitro at some of the sites cleaved by RNase MRP (C6t6 and Ruiz-Carrillo 1993;Potuschak et al 1993). The RNA components of RNase P and MRP have considerable structural homology, with a conserved core region termed the cage structure (for review, see Altman 1989;Darr et al 1992;Altman et al 1993;Karwan 1993;. This, together with the existence of a common epitope or polypeptide, suggests that these RNPs have substantial similarities.…”

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confidence: 99%

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The POP1 gene encodes a protein component common to the RNase MRP and RNase P ribonucleoproteins.

Lygerou¹,

Mitchell²,

Petfalski³

et al. 1994

Genes Dev.

198

214

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Two forms of the yeast 5.8S rRNA are generated from a large precursor by distinct processing pathways. Cleavage at site A3 is required for synthesis of the major, short form, designated 5.8S(S), but not for synthesis of the long form, 5.8S(L). To identify components required for A3 cleavage, a bank of temperature-sensitive lethal mutants was screened for those with a reduced ratio of 5.8S(S):5.8S(L). The pop1-1 mutation (for processing of precursor RNAs) shows this phenotype and also inhibits A3 cleavage. The pre-rRNA processing defect of pop1-1 strains is similar to that reported for mutations in the RNA component of RNase MRP; we show that a mutation in the RNase MRP RNA also inhibits cleavage at site A3. This is the first site shown to require RNase MRP for cleavage in vivo. The pop1-1 mutation also leads to a block in the processing of pre-tRNA that is identical to that reported for mutations in the RNA component of RNase P. The RNA components of both RNase MRP and RNase P are underaccumulated in pop1-1 strains at the nonpermissive temperature, and immunoprecipitation demonstrates that POPlp is a component of both ribonucleoproteins.The POP1 gene encodes a protein with a predicted molecular mass of 100.5 kD and is essential for viability.POPlp is the first protein component of the nuclear RNase P or RNase MRP for which the gene has been cloned.[Key Words: POP1 gene; RNase MRP; RNase P; S. cerevisiae; RNA processing] Received April 4, 1994; revised version accepted May 9, 1994.Two ribonucleoprotein (RNP) complexes are known to have endoribonuclease (RNase) activity. These are the RNase P and RNase mitochondrial RNA processing (MRP) RNPs.All pre-tRNAs are transcribed with 5' and 3' extensions, and some contain intervening sequences that are removed to produce the mature tRNAs. RNase P is responsible for the 5' processing of pre-tRNAs in eubacteria, archaebacteria, and eukaryotes (for review, see Altman 1989;Dart et al. 1992;Altman et al. 1993). RNase P also processes the precursor of the 4.5S RNA in Escherichia coli (for review, see by Altman et al. 1993) but has not been reported to have substrates other than pretRNAs in archaebacteria or eukaryotes. The RNA component of eubacterial RNase P has catalytic activity in vitro in the absence of protein cofactors. In contrast, the RNA components of archaebacterial (Nieuwlandt et al. 1991;LaGrandeur et al. 1993) and eukaryotic RNase P have not been found to be catalytic in the absence of proteins, despite their considerable structural homology to the eubacterial RNAs. E. coli RNase P contains a single protein, designated C5, which is small (119 amino acids, 13.8 kD) and highly basic. This protein cofactor is required for RNase P activity in vivo and greatly stimulates activity in vitro. The protein plays important roles in the release of the product, the mature tRNA, from the enzyme, which is the rate-limiting step for the RNA catalyzed reaction in vitro (Reich et al. 1988;Tallsj6 and Kirsebom 1993), and in the binding of suboptimal substrates, including the 4.5S RN...

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“…There is evidence that another ribonuclease in eukaryotes, RNase MRP, is closely related, and perhaps homologous (i.e., evolutionarily related), to RNase P (reviewed by [62,63]). It is a ribonucleoprotein complex that participates in nucleolar pre-rRNA processing.…”

Section: Rnase Pmentioning

confidence: 99%

Ribozymes: the characteristics and properties of catalytic RNAs

Tanner¹

1999

FEMS Microbiology Reviews

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Ribozymes, or catalytic RNAs, were discovered a little more than 15 years ago. They are found in the organelles of plants and lower eukaryotes, in amphibians, in prokaryotes, in bacteriophages, and in viroids and satellite viruses that infect plants. An example is also known of a ribozyme in hepatitis delta virus, a serious human pathogen. Additional ribozymes are bound to be found in the future, and it is tempting to regard the RNA component(s) of various ribonucleoprotein complexes as the catalytic engine, while the proteins serve as mere scaffolding^an unheard-of notion 15 years ago! In nature, ribozymes are involved in the processing of RNA precursors. However, all the characterized ribozymes have been converted, with some clever engineering, into RNA enzymes that can cleave or modify targeted RNAs (or even DNAs) without becoming altered themselves. While their success in vitro is unquestioned, ribozymes are increasingly used in vivo as valuable tools for studying and regulating gene expression. This review is intended as a brief introduction to the characteristics of the different identified ribozymes and their properties. ß

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RNase MRP/RNase P: a structure‐function relation conserved in evolution?

Cited by 21 publications

References 66 publications

Phylogenetic analysis of the structure of RNase MRP RNA in yeasts

Phylogenetic analysis of the structure of RNase MRP RNA in yeasts

The POP1 gene encodes a protein component common to the RNase MRP and RNase P ribonucleoproteins.

Ribozymes: the characteristics and properties of catalytic RNAs

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