Archaeal Guide RNAs Function in rRNA Modification in the Eukaryotic Nucleus

Speckmann, Wayne A.; Li, Zhu-Hong; Lowe, Todd M.; Eddy, Sean R.; Terns, Rebecca M.; Terns, Michael P.

doi:10.1016/s0960-9822(02)00655-3

Cited by 19 publications

(12 citation statements)

References 34 publications

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“…The identities of the 40, 62 and 66 kDa proteins were verified by immunoprecipitation of the RNase‐digested, cross‐linked samples with antibodies targeting the predicted box C/D snoRNP components (Speckmann et al ., 2002). The specificity of these antibodies for Xenopus fibrillarin, Nop56 and Nop58 is confirmed by immunoprecipitation and western blot in Figure 2A and B.…”

Section: Resultsmentioning

confidence: 99%

Site-specific cross-linking analyses reveal an asymmetric protein distribution for a box C/D snoRNP

2002

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Methylation of the ribose 2¢-hydroxyl, the most widespread modi®cation of ribosomal and splicesomal RNAs, is guided by the box C/D class of small nucleolar RNAs (snoRNAs). Box C/D small nucleolar ribonucleoproteins (snoRNPs) contain four core proteins: ®brillarin, Nop56, Nop58 and 15.5 kDa. We constructed U25 snoRNAs containing a single photoactivatable 4-thiouridine at each U position within the conserved box C/D and C¢/D¢ motifs. Proteins assembled on the snoRNA after injection into Xenopus oocyte nuclei were identi®ed by cross-linking, and reconstituted particles characterized by functional rescue and mutational analyses. Our data argue that box C/D snoRNPs are asymmetric, with the C¢ box contacting Nop56 and ®brillarin, the C box interacting with Nop58, and the D and D¢ boxes contacting ®bril-larin. No cross-link to 15.5 kDa was detected; its binding is disrupted by 4-thiouridine substitution in position 1 of the C box. Repositioning the guide sequence of U25 upstream of box D instead of D¢ revealed that both C/D motifs have the potential to function as guide centers, but, surprisingly, there was no alteration in protein cross-linking.

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Section: Resultsmentioning

confidence: 99%

Site-specific cross-linking analyses reveal an asymmetric protein distribution for a box C/D snoRNP

2002

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“…The PCR products were cloned into the pCR2.1-TOPO vector (Invitrogen) and were confirmed by DNA sequence analysis. DNA templates encoding sR2 and sR29 (Speckmann et al 2002) and human tRNA i Met (Narayanan et al 1999) were generated as described. The template for in vitro transcription of the substrate RNA (corresponding to nucleotides 905-917 of P. furiosus 16S rRNA with uridines 915-917 replaced by adenosines, and flanked by three nucleotide extensions at each end) was generated by direct annealing of two oligonucleotides (see Supplementary Tables 1, 3).…”

Section: Synthesis Of Dna Templates For In Vitro Transcription Of Rnasmentioning

confidence: 99%

RNA-Guided RNA modification: functional organization of the archaeal H/ACA RNP

Baker¹,

Youssef²,

Chastkofsky³

et al. 2005

Genes Dev.

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In eukaryotes and archaea, uridines in various RNAs. The RNA-guided RNA modification system alters the primary sequence and modulates the function of target RNAs that include rRNAs, snRNAs, tRNAs, and perhaps mRNAs (Yu et al. 1998(Yu et al. , 2005Cavaille et al. 2000;King et al. 2003;Omer et al. 2003). In humans it is currently estimated that >200 2Ј-O-methylations and pseudouridylations are introduced into rRNA and other RNAs by this system (Maden 1990;Bachellerie and Cavaille 1998;Ofengand and Fournier 1998;Vitali et al. 2003).There are two large families of modification guide RNAs found in both eukaryotes and archaea: C/D RNAs that guide 2Ј-O-ribose methylation (Kiss-Laszlo et al. 1996;Omer et al. 2000) and H/ACA RNAs that guide pseudouridylation (Balakin et al. 1996; Ganot et al. 1997a,b;Tang et al. 2002). Both families of guide RNAs function in the context of RNA-protein complexes (RNPs) that include the enzyme responsible for modification (Filipowicz and Pogacic 2002;Terns and Terns 2002). The functional organization of modification guide RNPs, including the mechanism by which the enzyme associates with a guide RNA and the roles of the other essential proteins in the complex, is a subject of great interest. In C/D RNPs the 2Ј-O-methyltransferase, fibrillarin, associates with a guide RNA primarily via a bridge formed by the other proteins in the complex, Nop56/58 and L7Ae (or Nop56, Nop58, and p15.5 in eukaryotes).

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“…Archaeal rRNA modification seems to be more similar to that found in eukaryotic organisms, with snoRNAs guiding pseudouridylationand ribose methylation ( Omer et al 2003). Indeed,g uideR NAs from archaeal organisms can direct methylation of Xenopus laevis RNA (Speckmann et al 2002). Although archaeal cells lack anuclear membrane,atleast one archaeal genome contains putative homologs to nuclear and nucleolar structural genes from eukaryotes (Pace1 997).…”

Section: Introductionmentioning

confidence: 99%

Recognition of a complex substrate by the KsgA/Dim1 family of enzymes has been conserved throughout evolution

O′Farrell¹,

Pulicherla²,

Desai³

et al. 2006

RNA

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Ribosome biogenesis is ac omplicated process, involving numerous cleavage, base modification and assembly steps. All ribosomes share the same general architecture, with small and large subunits made up of roughly similar rRNA species and av ariety of ribosomal proteins. However, the fundamental assembly process differs significantly between eukaryotes and eubacteria, not only in distribution and mechanism of modifications but also in organization of assembly steps. Despite these differences, members of the KsgA/Dim1 methyltransferase family and their resultant modification of small-subunit rRNA are found throughout evolution and therefore were present in the last common ancestor. In this paper we report that KsgA orthologs from archaeabacteria and eukaryotes are able to complement for KsgA function in bacteria, both in vivo and in vitro. This indicates that all of these enzymes can recognize acommon ribosomal substrate, and that the recognition elements must be largely unchanged since the evolutionary split between the three domains of life.

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Archaeal Guide RNAs Function in rRNA Modification in the Eukaryotic Nucleus

Cited by 19 publications

References 34 publications

Site-specific cross-linking analyses reveal an asymmetric protein distribution for a box C/D snoRNP

Site-specific cross-linking analyses reveal an asymmetric protein distribution for a box C/D snoRNP

RNA-Guided RNA modification: functional organization of the archaeal H/ACA RNP

Recognition of a complex substrate by the KsgA/Dim1 family of enzymes has been conserved throughout evolution

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