A Subset of Yeast snRNA's Contains Functional Binding Sites for the Highly Conserved Sm Antigen

Riedel, Nora; Wolin, Sandra L.; Guthrie, Christine

doi:10.1126/science.2948278

Cited by 87 publications

(60 citation statements)

References 30 publications

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“…This sequence (GAU 3-4 G) is different from the conserved Sm sites found in the Kluyveromyces (ANU 5 G) or Saccharomyces (AAU 5 G) TERs. However, it is consistent with the budding yeasts Sm consensus sequence (AU 3-6 G; Riedel et al 1987). Interestingly, two additional conserved sequences, termed CS8 and CS9, were identified downstream from the Sm site (Supplemental Figs.…”

Section: Sm Site and Downstream Splicing Consensus Sequencessupporting

confidence: 57%

Identification and comparative analysis of telomerase RNAs from Candida species reveal conservation of functional elements

Gunišová

Elboher²,

Nosek³

et al. 2009

RNA

134

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The RNA component of telomerase (telomerase RNA; TER) varies substantially both in sequence composition and size (from ;150 nucleotides [nt] to >1500 nt) across species. This dramatic divergence has hampered the identification of TER genes and a large-scale comparative analysis of TER sequences and structures among distantly related species. To identify by phylogenetic analysis conserved sequences and structural features of TER that are of general importance, it is essential to obtain TER sequences from evolutionarily distant groups of species, providing enough conservation within each group and enough variation among the groups. To this end, we identified TER genes in several yeast species with relatively large (>20 base pairs) and nonvariant telomeric repeats, mostly from the genus Candida. Interestingly, several of the TERs reported here are longer than all other yeast TERs known to date. Within these TERs, we predicted a pseudoknot containing U-AÁU base triples (conserved in vertebrates, budding yeasts, and ciliates) and a three-way junction element (conserved in vertebrates and budding yeasts). In addition, we identified a novel conserved sequence (CS2a) predicted to reside within an internal-loop structure, in all the budding yeast TERs examined. CS2a is located near the Est1p-binding bulge-stem previously identified in Saccharomyces cerevisiae. Mutational analyses in both budding yeasts S. cerevisiae and Kluyveromyces lactis demonstrate that CS2a is essential for in vivo telomerase function. The comparative and mutational analyses of conserved TER elements reported here provide novel insights into the structure and function of the telomerase ribonucleoprotein complex.

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Section: Sm Site and Downstream Splicing Consensus Sequencessupporting

confidence: 57%

Identification and comparative analysis of telomerase RNAs from Candida species reveal conservation of functional elements

Gunišová

Elboher²,

Nosek³

et al. 2009

RNA

134

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“…Examination of snRNAs annotated in Flybase (http://www.flybase.org) revealed a total of seven nonredundant U5-like RNA sequences in addition to the canonical U5 snRNA. These eight RNAs are all 125 nucleotides (nt) in length and consist of an identical 5 0 85-nt sequence followed by a variable 3 0 sequence that in each case has the potential to form a single-hairpin secondary structure preceded by a short pyrimidine-rich region resembling the Sm protein binding site of canonical snRNAs (Wooley et al 1982;Riedel et al 1987; Fig. 1).…”

Section: Resultsmentioning

confidence: 99%

Identification and analysis of U5 snRNA variants in Drosophila

CHEN¹

2005

RNA

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Distinct isoforms of spliceosomal RNAs may be involved in regulating pre-messenger RNA splicing in eukaryotic cells. During a large-scale effort to identify small noncoding RNAs in Drosophila, we isolated a U5 snRNA-like molecule containing a 5 0 segment identical to that of the canonical (major) U5 snRNA but with a variant Sm binding site and a distinct 3 0 hairpin sequence. Based on this finding, another six similar U5 snRNA-like sequences were identified within the Drosophila genome by sequence similarity to the invariant loop in the 5 0 half of U5. Interestingly, although all of these variants are expressed in vivo, each shows a distinct temporal expression profile during Drosophila development, and one is expressed primarily in fly heads. The presence of these U5 snRNA variants within RNP particles suggests their role in splicing and implies a possible connection to regulation of developmental and tissue-specific gene expression.

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“…After washing strips in 50 mM Tris/HCl, pH 7.5, 200 mM NaCl and 0.05% Tween 20, bound antibody was eluted with 5 mM glycine, pH 2.3, and 1% bovine serum albumin for 2 min. The solution was neutralized immediately by the addition of 1 .O M KC1, pH 7, to a final concentration of 50 mM. This procedure was repeated over 30 times with the same strips without loss of binding capacity or specificity.…”

Section: Immunoblot Analysismentioning

confidence: 99%

Purification, primary structure, bacterial expression and subcellular distribution of an oocyte‐specific protein in Xenopus

Rother

Frank

Thomas

1992

European Journal of Biochemistry

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This study defines a novel Xenopus luevis protein (PIOO) that has recently been shown to be recognized by scleroderma patient sera. Using a combination of differential solubility in detergents, hydroxyapatite chromatography and one-dimensional PAGE, PlOO was purified to apparent homogeneity and the amino acid sequence was obtained. An oligonucleotide derived from this sequence was used to clone PlOO cDNA through a polymerase-chain-reaction cloning strategy. The entire PlOO cDNA sequence was determined, identifying a novel 83000-Da protein. Two alleles for PlOO were transcribed in the oocyte, with only one predicted amino acid change between them. Bacterial expression of a clone containing the entire PlOO coding region produced a protein that migrated at a mass 15% greater than that predicted from the amino acid sequence, indicating an aberrant electrophoretic mobility. The mRNA transcript for PlOO was only expressed during the previtellogenic stages of oogenesis (stages I and 11) and was absent from other Xenopus tissues. Similarly, the PlOO protein was found only in Xenopus oocytes and was localized to the cytoplasm of these cells. PlOO irreversibly bound single-stranded-DNA -cellulose but not double-stranded-DNA -cellulose. These data demonstrate the presence of a novel oocyte-specific protein in Xenopus.Autoantibodies in rheumatic diseases target a variety of highly conserved intracellular proteins, including those involved in RNA polymerase I and 111 transcription, heteronuclear RNA splicing, aminoacylation of certain tRNA species, DNA replication, DNA supercoiling and mitosis (review in [l]). The Xenopus oocyte and embryo have provided valuable systems for the characterization of many of these proteins. One example is the ribonucleoproteins targeted by systemic lupus erythematosus patient sera [2]. Antibodies against Sm and RNP were shown to inhibit intron excision from ribosomal genes when injected into germinal vesicles of oocytes, confirming that the RNA-splicing function of these particles demonstrated in vitro also occurred in vivo [3-51. Furthermore, Xenopus Sm and RNP were able to package exogenous small-nuclear RNA from mouse, Drosophila and yeast [6, 71. The Xenopus egg and early embryo were also shown to contain a large store of the U1 small nuclear RNA [6]. Fibrillarin, a ribonucleoprotein associated with U3 small nuclear RNA and recognized by scleroderma patient antibodies, was first cloned and sequenced from a Xenopus cDNA library [8, 91. Other autoantigenic proteins characterized in the Xenopus system include the proliferating cell nuclear antigen and the histones 130-131.Recent experiments in our laboratory have shown that scleroderma sera recognize a 100-kDa protein (P100) which is expressed in Xenopus luevis ovary [14]. Preliminary work also suggests a low level of expression in HeLa cells; however, attempts to clone a 100-kDa protein from a HeLa cell cDNA expression library with such sera have proven to be unsuccessful. In light of the abundance of a 100-kDa protein in X . luevis oocytes...

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A Subset of Yeast snRNA's Contains Functional Binding Sites for the Highly Conserved Sm Antigen

Cited by 87 publications

References 30 publications

Identification and comparative analysis of telomerase RNAs from Candida species reveal conservation of functional elements

Identification and comparative analysis of telomerase RNAs from Candida species reveal conservation of functional elements

Identification and analysis of U5 snRNA variants in Drosophila

Purification, primary structure, bacterial expression and subcellular distribution of an oocyte‐specific protein in Xenopus

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