RNA‐modifying machines in archaea

Omer, Arina D.; Ziesche, Sonia; Decatur, Wayne A.; Fournier, Maurille J.; Dennis, Patrick P.

doi:10.1046/j.1365-2958.2003.03483.x

Cited by 88 publications

(76 citation statements)

References 79 publications

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“…YLR022C was found to co-purify with snoRNAs and exhibited a profile that is similar to that of YHR040W (BCD1), an RNA-associating protein. snoRNPs, which contain these non-coding snoRNAs, have been implicated in the cleavage, modification, and folding of precursor rRNA substrates (61).…”

Section: Resultsmentioning

confidence: 99%

The Shwachman-Bodian-Diamond Syndrome Protein Family Is Involved in RNA Metabolism

Savchenko¹,

Krogan

Cort

et al. 2005

Journal of Biological Chemistry

102

104

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A combination of structural, biochemical, and genetic studies in model organisms was used to infer a cellular role for the human protein (SBDS) responsible for Shwachman-Bodian-Diamond syndrome. The crystal structure of the SBDS homologue in Archaeoglobus fulgidus, AF0491, revealed a three domain protein. The N-terminal domain, which harbors the majority of diseaselinked mutations, has a novel three-dimensional fold. The central domain has the common winged helix-turn-helix motif, and the C-terminal domain shares structural homology with known RNA-binding domains. Proteomic analysis of the SBDS sequence homologue in Saccharomyces cerevisiae, YLR022C, revealed an association with over 20 proteins involved in ribosome biosynthesis. NMR structural genomics revealed another yeast protein, YHR087W, to be a structural homologue of the AF0491 N-terminal domain. Sequence analysis confirmed them as distant sequence homologues, therefore related by divergent evolution. Synthetic genetic array analysis of YHR087W revealed genetic interactions with proteins involved in RNA and rRNA processing including Mdm20/ Nat3, Nsr1, and Npl3. Our observations, taken together with previous reports, support the conclusion that SBDS and its homologues play a role in RNA metabolism.

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Section: Resultsmentioning

confidence: 99%

The Shwachman-Bodian-Diamond Syndrome Protein Family Is Involved in RNA Metabolism

Savchenko¹,

Krogan

Cort

et al. 2005

Journal of Biological Chemistry

102

104

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“…Box H͞ACA RNAs and all of the known tRNAs, rRNAs, RNase P RNA, and 7S RNA were identified, but none of the Ͼ50 known box C͞D RNAs in P. furiosus were identified (unless they were directly adjacent to another structured noncoding RNA). One structural element found in box C͞D RNAs and recognized for its importance in the stability and function of the box C͞D RNAs in eukaryotes is the terminal stem (1,2,4,5,7,30). The 5Ј and 3Ј termini of linear box C͞D RNAs are normally tethered by base-pairing.…”

Section: Resultsmentioning

confidence: 99%

“…B ox C͞D RNAs function as the guide components of RNAprotein complexes [box C͞D ribonucleoproteins (RNPs)] that 2Ј-O-methylate rRNA and small nuclear RNA in eukaryotes and tRNA in archaea (1)(2)(3)(4)(5)(6)(7). The RNAs are characterized by the presence of one or two sets of the short, conserved sequence elements termed box C and box D. Base-pairing of the guide region of a box C͞D RNA to the target RNA establishes a site of 2Ј-O-methylation of the target RNA.…”

mentioning

confidence: 99%

Circular box C/D RNAs in Pyrococcus furiosus

Starostina

Marshburn

Johnson

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

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In eukaryotes, box C͞D modification guide RNAs are made by two primary pathways (2, 5, 10, 11). Some are found in the introns of host genes, and the linear box C͞D RNAs are processed from debranched lariats. In other cases, linear box C͞D RNAs are processed from mono-or polycistronic transcripts synthesized from independent promoters. Box C͞D RNAs were found only recently in archaea (12, 13). The pathway by which archaeal box C͞D RNAs are made is unknown. The archaeal box C͞D RNAs are located primarily in intergenic regions of the genome, sometimes overlapping the 3Ј or 5Ј end of flanking ORFs (1, 4, 12, 13). Independent promoters have not been identified.In the course of analyzing a cDNA library of small RNAs from P. furiosus, we observed an interesting incongruence between the linear sequence of some box C͞D RNA clones

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“…In Archaea, homologs of box C/D snoRNPs (box C/D sRNPs) consist of box C/D sRNAs, fibrillarin, Nop5p (a single homolog of Nop56/58p), and L7Ae proteins (3,8). The box C/D RNAs are responsible for the recognition of methylation target RNAs via base pairing of their antisense regions with the target.…”

mentioning

confidence: 99%

Structural and Thermodynamic Evidence for a Stabilizing Role of Nop5p in S-Adenosyl-L-methionine Binding to Fibrillarin

Aittaleb¹,

Visone²,

Fenley

2004

Journal of Biological Chemistry

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In Archaea, fibrillarin and Nop5p form the core complex of box C/D small ribonucleoprotein particles, which are responsible for site-specific 2 -hydroxyl methylation of ribosomal and transfer RNAs. Fibrillarin has a conserved methyltransferase fold and employs S-adenosyl-L-methionine (AdoMet) as the cofactor in methyl transfer reactions. Comparison between recently determined crystal structures of free fibrillarin and fibrillarinNop5p-AdoMet tertiary complex revealed large conformational differences at the cofactor-binding site in fibrillarin. To identify the structural elements responsible for these large conformational differences, we refined a crystal structure of Archaeoglobus fulgidus fibrillarin-Nop5p binary complex at 3.5 Å. This structure exhibited a pre-formed backbone geometry at the cofactor binding site similar to that when the cofactor is bound, suggesting that binding of Nop5p alone to fibrillarin is sufficient to stabilize the AdoMet-binding pocket. Calorimetry studies of cofactor binding to fibrillarin alone and to fibrillarin-Nop5p binary complex provided further support for this role of Nop5p. Mutagenesis and thermodynamic data showed that a cationbridge formed between Tyr-89 of fibrillarin and Arg-169 of Nop5p, although dispensable for in vitro methylation activity, could partially account for the enhanced binding of cofactor to fibrillarin by Nop5p. Finally, assessment of cofactor-binding thermodynamics and catalytic activities of enzyme mutants identified three additional fibrillarin residues (Thr-70, Glu-88, and Asp-133) to be important for cofactor binding and for catalysis.

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RNA‐modifying machines in archaea

Cited by 88 publications

References 79 publications

The Shwachman-Bodian-Diamond Syndrome Protein Family Is Involved in RNA Metabolism

The Shwachman-Bodian-Diamond Syndrome Protein Family Is Involved in RNA Metabolism

Circular box C/D RNAs in Pyrococcus furiosus

Structural and Thermodynamic Evidence for a Stabilizing Role of Nop5p in S-Adenosyl-L-methionine Binding to Fibrillarin

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