Domain Architecture of the DRpp29 Protein and Its Interaction with the RNA Subunit of <i>Dictyostelium discoideum</i> RNase P

Stamatopoulou, Vassiliki; Toumpeki, Chrisavgi; Tzakos, Andreas G.; Vourekas, Anastassios; Drainas, Denis

doi:10.1021/bi101297z

Cited by 7 publications

(8 citation statements)

References 59 publications

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“…In fact, the proximity of binding of Rpp29 to P4, which is essential for the formation of the catalytic center of RNase P RNA (16), is consistent with this protein being a co-factor in catalysis. This role is corroborated by the ability of Rpp29 from human and Dictyostelium discoideum to associate and activate M1 RNA in vitro (37,42). UV crosslinking experiments and oligonucleotide interference assays reveal that Rpp29 recognizes precursor tRNA and not its mature tRNA form (37).…”

Section: Discussionmentioning

confidence: 78%

RNA binding properties of conserved protein subunits of human RNase P

Reiner

Alfiya-Mor

Berrebi-Demma

et al. 2011

Nucleic Acids Research

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Human nuclear RNase P is required for transcription and processing of tRNA. This catalytic RNP has an H1 RNA moiety associated with ten distinct protein subunits. Five (Rpp20, Rpp21, Rpp25, Rpp29 and Pop5) out of eight of these protein subunits, prepared in refolded recombinant forms, bind to H1 RNA in vitro. Rpp20 and Rpp25 bind jointly to H1 RNA, even though each protein can interact independently with this transcript. Nuclease footprinting analysis reveals that Rpp20 and Rpp25 recognize overlapping regions in the P2 and P3 domains of H1 RNA. Rpp21 and Rpp29, which are sufficient for reconstitution of the endonucleolytic activity, bind to separate regions in the catalytic domain of H1 RNA. Common themes and discrepancies in the RNA-protein interactions between human nuclear RNase P and its related yeast and archaeal counterparts provide a rationale for the assembly of the fully active form of this enzyme.

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Section: Discussionmentioning

confidence: 78%

RNA binding properties of conserved protein subunits of human RNase P

Reiner

Alfiya-Mor

Berrebi-Demma

et al. 2011

Nucleic Acids Research

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“…In addition, we used RPP21, RPP29, POP5, and RPP30 from the set of 71 genomes as well as their homologs from Saccharomyces cerevisiae [ 10 ], Dictyostelium discoideum [ 57 , 58 , 59 ] , Xenopus laevis , and Homo sapiens [ 38 ] as input for the web-based Multiple EM for Motif Elicitation (MEME) sequence analysis tool [ 60 , 61 ] to uncover ungapped motifs common to archaeal and eukaryotic RPPs; L7Ae was excluded from MEME profiling given the extensive structural studies and previous analyses (see 47 and references therein). The MEME search parameters used for each RPP family were zero to eight motifs of 10–30 amino acids long.…”

Section: Resultsmentioning

confidence: 99%

Sequence Analysis and Comparative Study of the Protein Subunits of Archaeal RNase P

Samanta¹,

Lai

Daniels

et al. 2016

Biomolecules

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RNase P, a ribozyme-based ribonucleoprotein (RNP) complex that catalyzes tRNA 5′-maturation, is ubiquitous in all domains of life, but the evolution of its protein components (RNase P proteins, RPPs) is not well understood. Archaeal RPPs may provide clues on how the complex evolved from an ancient ribozyme to an RNP with multiple archaeal and eukaryotic (homologous) RPPs, which are unrelated to the single bacterial RPP. Here, we analyzed the sequence and structure of archaeal RPPs from over 600 available genomes. All five RPPs are found in eight archaeal phyla, suggesting that these RPPs arose early in archaeal evolutionary history. The putative ancestral genomic loci of archaeal RPPs include genes encoding several members of ribosome, exosome, and proteasome complexes, which may indicate coevolution/coordinate regulation of RNase P with other core cellular machineries. Despite being ancient, RPPs generally lack sequence conservation compared to other universal proteins. By analyzing the relative frequency of residues at every position in the context of the high-resolution structures of each of the RPPs (either alone or as functional binary complexes), we suggest residues for mutational analysis that may help uncover structure-function relationships in RPPs.

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“…Similar observations were made for protein‐rich nuclear RNase P enzymes from Eukarya. Enzymes from Homo sapiens sapiens , Saccharomyces cerevisiae and Dictyostelium discoideum ,28 all three consisting of an RNA subunit plus multiple different protein components,2, 29 were strongly inhibited by Cd 2+ ions, and to some extent also by Mn 2+ ions, despite the presence of an excess of Mg 2+ ions. Thus, although all three enzymes were strongly inhibited by an R p‐ or S p‐phosphorothioate modification at the canonical RNase P cleavage site, in line with what has been observed for bacterial RNase P,9, 10 no clear rescue effects by thiophilic metal ions could be demonstrated.…”

Section: Discussionmentioning

confidence: 99%

tRNA Processing by Protein‐Only versus RNA‐Based RNase P: Kinetic Analysis Reveals Mechanistic Differences

et al. 2012

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In Arabidopsis thaliana, RNase P function, that is, endonucleolytic tRNA 5'-end maturation, is carried out by three homologous polypeptides ("proteinaceous RNase P" (PRORP) 1, 2 and 3). Here we present the first kinetic analysis of these enzymes. For PRORP1, a specificity constant (k(react)/K(m(sto))) of 3×10(6) M(-1) min(-1) was determined under single-turnover conditions. We demonstrate a fundamentally different sensitivity of PRORP enzymes to an Rp-phosphorothioate modification at the canonical cleavage site in a 5'-precursor tRNA substrate; whereas processing by bacterial RNase P is inhibited by three orders of magnitude in the presence of this sulfur substitution and Mg(2+) as the metal-ion cofactor, the PRORP enzymes are affected by not more than a factor of five under the same conditions, without significantly increased miscleavage. These findings indicate that the catalytic mechanism utilized by proteinaceous RNase P is different from that of RNA-based bacterial RNase P, taking place without a direct metal-ion coordination to the (pro-)Rp substituent. As Rp-phosphorothioate and inosine modification at all 26 G residues of the tRNA body had only minor effects on processing by PRORP, we conclude that productive PRORP-substrate interaction is not critically dependent on any of the affected (pro-)Rp oxygens or guanosine 2-amino groups.

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Domain Architecture of the DRpp29 Protein and Its Interaction with the RNA Subunit of Dictyostelium discoideum RNase P

Cited by 7 publications

References 59 publications

RNA binding properties of conserved protein subunits of human RNase P

RNA binding properties of conserved protein subunits of human RNase P

Sequence Analysis and Comparative Study of the Protein Subunits of Archaeal RNase P

tRNA Processing by Protein‐Only versus RNA‐Based RNase P: Kinetic Analysis Reveals Mechanistic Differences

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