Precursors of ribosomal RNA in yeast nucleus

Smitt, W.W. Sillevis; Vlak, J.M.; Schiphof, R.; Rozijn, Th.H.

doi:10.1016/0014-4827(72)90259-5

Cited by 22 publications

(2 citation statements)

References 30 publications

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“…Newly synthesized 5S rRNA was detected in apparent excess over 5.8S rRNA in nuclear fractions while cytoplasmic fractions contained similar amounts of both pulse labelled LSU rRNA species. These results agree with conclusions drawn from similar experiments that in yeast cells nascent LSUs containing 25S rRNA, 5.8S rRNA (or its functional equivalent 3′ extended forms, see above) and 5S rRNA are adequate substrates of the nuclear export machinery [50], [51], [52].…”

Section: Resultssupporting

confidence: 92%

rRNA Maturation in Yeast Cells Depleted of Large Ribosomal Subunit Proteins

et al. 2009

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The structural constituents of the large eukaryotic ribosomal subunit are 3 ribosomal RNAs, namely the 25S, 5.8S and 5S rRNA and about 46 ribosomal proteins (r-proteins). They assemble and mature in a highly dynamic process that involves more than 150 proteins and 70 small RNAs. Ribosome biogenesis starts in the nucleolus, continues in the nucleoplasm and is completed after nucleo-cytoplasmic translocation of the subunits in the cytoplasm. In this work we created 26 yeast strains, each of which conditionally expresses one of the large ribosomal subunit (LSU) proteins. In vivo depletion of the analysed LSU r-proteins was lethal and led to destabilisation and degradation of the LSU and/or its precursors. Detailed steady state and metabolic pulse labelling analyses of rRNA precursors in these mutant strains showed that LSU r-proteins can be grouped according to their requirement for efficient progression of different steps of large ribosomal subunit maturation. Comparative analyses of the observed phenotypes and the nature of r-protein – rRNA interactions as predicted by current atomic LSU structure models led us to discuss working hypotheses on i) how individual r-proteins control the productive processing of the major 5′ end of 5.8S rRNA precursors by exonucleases Rat1p and Xrn1p, and ii) the nature of structural characteristics of nascent LSUs that are required for cytoplasmic accumulation of nascent subunits but are nonessential for most of the nuclear LSU pre-rRNA processing events.

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Section: Resultssupporting

confidence: 92%

rRNA Maturation in Yeast Cells Depleted of Large Ribosomal Subunit Proteins

et al. 2009

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“…They are composed in part of highly conserved RNA sequences (2) usually coded on DNA in operons of three subunits (16S, 23S and 5S) in Bacteria and Archaea (3,4) and in tandem repeats of longer operons that ultimately mature to four subunits (18S, 25/28S, 5.8S and 5S) in Eukaryotes (5,6). The complete primary nucleotide sequences of representative rRNA subunits in the seven duplicated rRNA operons of Escherichia coli were published between 1967 and 1978 (7–10).…”

Section: Introductionmentioning

confidence: 99%

Misannotations of rRNA can now generate 90% false positive protein matches in metatranscriptomic studies

Tripp

Hewson

Boyarsky

et al. 2011

Nucleic Acids Research

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In the course of analyzing 9 522 746 pyrosequencing reads from 23 stations in the Southwestern Pacific and equatorial Atlantic oceans, it came to our attention that misannotations of rRNA as proteins is now so widespread that false positive matching of rRNA pyrosequencing reads to the National Center for Biotechnology Information (NCBI) non-redundant protein database approaches 90%. One conserved portion of 23S rRNA was consistently misannotated often enough to prompt curators at Pfam to create a spurious protein family. Detailed examination of the annotation history of each seed sequence in the spurious Pfam protein family (PF10695, ‘Cw-hydrolase’) uncovered issues in the standard operating procedures and quality assurance programs of major sequencing centers, and other issues relating to the curation practices of those managing public databases such as GenBank and SwissProt. We offer recommendations for all these issues, and recommend as well that workers in the field of metatranscriptomics take extra care to avoid including false positive matches in their datasets.

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Non-radioactive In Vivo Labeling of RNA with 4-Thiouracil

Braun

Knüppel

Pérez-Fernández

et al. 2022

Ribosome Biogenesis

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RNA molecules and their expression dynamics play essential roles in the establishment of complex cellular phenotypes and/or in the rapid cellular adaption to environmental changes. Accordingly, analyzing RNA expression remains an important step to understand the molecular basis controlling the formation of cellular phenotypes, cellular homeostasis or disease progression. Steady-state RNA levels in the cells are controlled by the sum of highly dynamic molecular processes contributing to RNA expression and can be classified in transcription, maturation and degradation. The main goal of analyzing RNA dynamics is to disentangle the individual contribution of these molecular processes to the life cycle of a given RNA under different physiological conditions. In the recent years, the use of nonradioactive nucleotide/nucleoside analogs and improved chemistry, in combination with time-dependent and high-throughput analysis, have greatly expanded our understanding of RNA metabolism across various cell types, organisms, and growth conditions.In this chapter, we describe a step-by-step protocol allowing pulse labeling of RNA with the nonradioactive nucleotide analog, 4-thiouracil, in the eukaryotic model organism Saccharomyces cerevisiae and the model archaeon Haloferax volcanii.

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Precursors of ribosomal RNA in yeast nucleus

Cited by 22 publications

References 30 publications

rRNA Maturation in Yeast Cells Depleted of Large Ribosomal Subunit Proteins

rRNA Maturation in Yeast Cells Depleted of Large Ribosomal Subunit Proteins

Misannotations of rRNA can now generate 90% false positive protein matches in metatranscriptomic studies

Non-radioactive In Vivo Labeling of RNA with 4-Thiouracil

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