Trans-acting factors in yeast pre-rRNA and pre-snoRNA processing

1995 ◽  
Vol 73 (11-12) ◽  
pp. 803-812 ◽  
Author(s):  
Denis Lafontaine ◽  
David Tollervey
Keyword(s):  
Rna Processing ◽  
Ribosome Biogenesis ◽  
Complex Mixture ◽  
Current View ◽  
Small Nucleolar Rnas ◽  
Rrna Processing ◽  
In Trans ◽  
Biochemical Analyses ◽  
Nucleolar Rnas ◽  
Processing Steps

The major intermediates in the pathway of pre-rRNA processing in yeast and other eukaryotes were originally identified by biochemical analyses. However, as a result of the analysis of the effects of mutations in trans-acting factors, the yeast pre-rRNA processing pathway is now characterized in far more detail than that of other eukaryotes. These analyses have led to the identification of processing sites and intermediates that were either too close in size or too short lived to be detected by biochemical analyses alone. In addition, it was generally unclear whether pre-rRNA processing steps were endonucleolytic or exonucleolytic; analyses of trans-acting factors is now revealing a complex mixture of endonucleolytic and exonucleolytic processing steps. Many of the small nucleolar RNAs (snoRNAs) are excised from larger precursors. Analyses of trans-acting factors are also revealing details of pre-snoRNA processing in yeast. Interestingly, factors involved in pre-snoRNA processing turn out to be components that also function in pre-rRNA processing, suggesting a potential mechanism for the coregulation of rRNA and snoRNA synthesis. In general, very little is known about the regulation of pre-rRNA processing steps. The best candidate for a system regulating specific pre-rRNA processing reactions has recently been revealed by the analysis of a yeast pre-RNA methylase. Here we will review recent data on the trans-acting factors involved in yeast ribosome synthesis and discuss how these analyses have contributed to our current view of this complex process.Key words: RNA processing, ribosome biogenesis, rRNA, exonuclease, methylation, yeast.

Small nucleolar RNA

1995 ◽  
Vol 73 (11-12) ◽  
pp. 845-858 ◽  
Author(s):  
Susan A. Gerbi
Keyword(s):  
Rna Polymerase Ii ◽  
Binding Sites ◽  
Ribosome Biogenesis ◽  
Internal Transcribed Spacers ◽  
28S Rrna ◽  
Small Nucleolar Rnas ◽  
Rrna Processing ◽  
Conserved Sequence ◽  
Nucleolar Rna ◽  
Nucleolar Rnas

A growing list of small nucleolar RNAs (snoRNAs) has been characterized in eukaryotes. They are transcribed by RNA polymerase II or III; some snoRNAs are encoded in the introns of other genes. The nonintronic polymerase II transcribed snoRNAs receive a trimethylguanosine cap, probably in the nucleus, and move to the nucleolus. snoRNAs are complexed with proteins, sometimes including fibrillarin. Localization and maintenance in the nucleolus of some snoRNAs requires the presence of initial precursor rRNA (pre-rRNA). Many snoRNAs have conserved sequence boxes C and D and a 3′ terminal stem; the roles of these features are discussed. Functional assays done for a few snoRNAs indicate their roles in rRNA processing for cleavage of the external and internal transcribed spacers (ETS and ITS). U3 is the most abundant snoRNA and is needed for cleavage of ETS1 and ITS1; experimental results on U3 binding sites in pre-rRNA are reviewed. 18S rRNA production also needs U14, U22, and snR30 snoRNAs, whereas U8 snoRNA is needed for 5.8S and 28S rRNA production. Other snoRNAs that are complementary to 18S or 28S rRNA might act as chaperones to mediate RNA folding. Whether snoRNAs join together in a large rRNA processing complex (the "processome") is not yet clear. It has been hypothesized that such complexes could anchor the ends of loops in pre-rRNA containing 18S or 28S rRNA, thereby replacing base-paired stems found in pre-rRNA of prokaryotes.Key words: RNA processing, small nucleolar RNAs, nucleolus, ribosome biogenesis, rRNA processing complex.

scholarly journals Knock-Down of a Novel snoRNA in Tetrahymena Reveals a Dual Role in 5.8S rRNA Processing and Generation of a 26S rRNA Fragment

Biomolecules ◽  
2018 ◽  
Vol 8 (4) ◽  
pp. 128
Author(s):  
Kasper Andersen ◽  
Henrik Nielsen
Keyword(s):  
Small Nucleolar Rnas ◽  
Rrna Processing ◽  
Specific Chemical ◽  
Knock Down ◽  
5.8S Rrna ◽  
Rrna Species ◽  
26S Rrna ◽  
Precursor Molecules ◽  
Nucleolar Rnas ◽  
Function Sequence

In eukaryotes, 18S, 5.8S, and 28S rRNAs are transcribed as precursor molecules that undergo extensive modification and nucleolytic processing to form the mature rRNA species. Central in the process are the small nucleolar RNAs (snoRNAs). The majority of snoRNAs guide site specific chemical modifications but a few are involved in defining pre-rRNA cleavages. Here, we describe an unusual snoRNA (TtnuCD32) belonging to the box C/D subgroup from the ciliate Tetrahymena thermophila. We show that TtnuCD32 is unlikely to function as a modification guide snoRNA and that it is critical for cell viability. Cell lines with genetic knock-down of TtnuCD32 were impaired in growth and displayed two novel and apparently unrelated phenotypes. The most prominent phenotype is the accumulation of processing intermediates of 5.8S rRNA. The second phenotype is the decrease in abundance of a ~100 nt 26S rRNA fragment of unknown function. Sequence analysis demonstrated that TtnuCD32 share features with the essential snoRNA U14 but an alternative candidate (TtnuCD25) was more closely related to other U14 sequences. This, together with the fact that the observed rRNA processing phenotypes were not similar to what has been observed in U14 depleted cells, suggests that TtnuCD32 is a U14 homolog that has gained novel functions.

scholarly journals Controlling the material properties and rRNA processing function of the nucleolus using light

2019 ◽  
Vol 116 (35) ◽  
pp. 17330-17335 ◽  
Author(s):  
Lian Zhu ◽  
Tiffany M. Richardson ◽  
Ludivine Wacheul ◽  
Ming-Tzo Wei ◽  
Marina Feric ◽  
...  
Keyword(s):  
Phase Behavior ◽  
Ribosomal Rna ◽  
Material Properties ◽  
Viscoelastic Properties ◽  
Ribosome Biogenesis ◽  
Threshold Concentration ◽  
Rrna Processing ◽  
Small Proteins ◽  
Nucleolar Material ◽  
Processing Steps

The nucleolus is a prominent nuclear condensate that plays a central role in ribosome biogenesis by facilitating the transcription and processing of nascent ribosomal RNA (rRNA). A number of studies have highlighted the active viscoelastic nature of the nucleolus, whose material properties and phase behavior are a consequence of underlying molecular interactions. However, the ways in which the material properties of the nucleolus impact its function in rRNA biogenesis are not understood. Here we utilize the Cry2olig optogenetic system to modulate the viscoelastic properties of the nucleolus. We show that above a threshold concentration of Cry2olig protein, the nucleolus can be gelled into a tightly linked, low mobility meshwork. Gelled nucleoli no longer coalesce and relax into spheres but nonetheless permit continued internal molecular mobility of small proteins. These changes in nucleolar material properties manifest in specific alterations in rRNA processing steps, including a buildup of larger rRNA precursors and a depletion of smaller rRNA precursors. We propose that the flux of processed rRNA may be actively tuned by the cell through modulating nucleolar material properties, which suggests the potential of materials-based approaches for therapeutic intervention in ribosomopathies.

scholarly journals Processing of the Precursors to Small Nucleolar RNAs and rRNAs Requires Common Components

1998 ◽  
Vol 18 (3) ◽  
pp. 1181-1189 ◽  
Author(s):  
Elisabeth Petfalski ◽  
Thomas Dandekar ◽  
Yves Henry ◽  
David Tollervey
Keyword(s):  
Small Nucleolar Rnas ◽  
Rrna Processing ◽  
5.8S Rrna ◽  
Genes Encoding ◽  
Sequences Analysis ◽  
Upstream Processing ◽  
Exonuclease Digestion ◽  
Nucleolar Rna ◽  
Nucleolar Rnas ◽  
Common Components

ABSTRACT The genes encoding the small nucleolar RNA (snoRNA) species snR190 and U14 are located close together in the genome of Saccharomyces cerevisiae. Here we report that these two snoRNAs are synthesized by processing of a larger common transcript. In strains mutant for two 5′→3′ exonucleases, Xrn1p and Rat1p, families of 5′-extended forms of snR190 and U14 accumulate; these have 5′ extensions of up to 42 and 55 nucleotides, respectively. We conclude that the 5′ ends of both snR190 and U14 are generated by exonuclease digestion from upstream processing sites. In contrast to snR190 and U14, the snoRNAs U18 and U24 are excised from the introns of pre-mRNAs which encode proteins in their exonic sequences. Analysis of RNA extracted from a dbr1-Δ strain, which lacks intron lariat-debranching activity, shows that U24 can be synthesized only from the debranched lariat. In contrast, a substantial level of U18 can be synthesized in the absence of debranching activity. The 5′ ends of these snoRNAs are also generated by Xrn1p and Rat1p. The same exonucleases are responsible for the degradation of several excised fragments of the pre-rRNA spacer regions, in addition to generating the 5′ end of the 5.8S rRNA. Processing of the pre-rRNA and both intronic and polycistronic snoRNAs therefore involves common components.

scholarly journals SnoRNA microarray analysis reveals changes in H/ACA and C/D RNA levels caused by dyskerin ablation in mouse liver

2010 ◽  
Vol 429 (1) ◽  
pp. 33-41 ◽  
Author(s):  
Jingping Ge ◽  
Seth D. Crosby ◽  
Michael E. Heinz ◽  
Monica Bessler ◽  
Philip J. Mason
Keyword(s):  
Microarray Analysis ◽  
Mouse Liver ◽  
Cellular Response ◽  
Ribosome Biogenesis ◽  
Microarray Platform ◽  
Protein Component ◽  
Small Nucleolar Rnas ◽  
Ribosome Synthesis ◽  
Nucleolar Rnas ◽  
Host Genes

snoRNAs (small nucleolar RNAs) are key components of snoRNP (small nucleolar ribonucleoprotein) particles involved in modifying specific residues of ribosomal and other RNAs by pseudouridylation (H/ACA snoRNAs) or methylation (C/D snoRNAs). They are encoded within the introns of host genes, which tend to be genes whose products are involved in ribosome biogenesis or function. Although snoRNPs are abundant, ubiquitous and their components highly conserved, information concerning their expression during development or how their expression is altered in diseased states is sparse. To facilitate these studies we have developed a snoRNA microarray platform for the analysis of the abundance of snoRNAs in different RNA samples. In the present study we show that the microarray is sensitive and specific for the detection of snoRNAs. A mouse snoRNA microarray was used to monitor changes in abundance of snoRNAs after ablation of dyskerin, an H/ACA snoRNA protein component, from mouse liver, which causes a decrease in ribosome production. H/ACA snoRNAs were decreased in abundance in these livers while, unexpectedly, C/D snoRNAs were increased. The increase in C/D snoRNAs corresponded with an increase in the abundance of the mRNAs transcribed from snoRNA host genes, suggesting the increase may be part of a cellular response to defective ribosome synthesis.

scholarly journals Identification of Genes That Function in the Biogenesis and Localization of Small Nucleolar RNAs in Saccharomyces cerevisiae

2008 ◽  
Vol 28 (11) ◽  
pp. 3686-3699 ◽  
Author(s):  
Hui Qiu ◽  
Julia Eifert ◽  
Ludivine Wacheul ◽  
Marc Thiry ◽  
Adam C. Berger ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Ribosome Biogenesis ◽  
Large Scale ◽  
Cajal Body ◽  
Temperature Sensitive ◽  
Small Nucleolar Rnas ◽  
Animal Cells ◽  
U3 Snorna ◽  
Genes Encoding ◽  
Nucleolar Rnas

ABSTRACT Small nucleolar RNAs (snoRNAs) orchestrate the modification and cleavage of pre-rRNA and are essential for ribosome biogenesis. Recent data suggest that after nucleoplasmic synthesis, snoRNAs transiently localize to the Cajal body (in plant and animal cells) or the homologous nucleolar body (in budding yeast) for maturation and assembly into snoRNPs prior to accumulation in their primary functional site, the nucleolus. However, little is known about the trans-acting factors important for the intranuclear trafficking and nucleolar localization of snoRNAs. Here, we describe a large-scale genetic screen to identify proteins important for snoRNA transport in Saccharomyces cerevisiae. We performed fluorescence in situ hybridization analysis to visualize U3 snoRNA localization in a collection of temperature-sensitive yeast mutants. We have identified Nop4, Prp21, Tao3, Sec14, and Htl1 as proteins important for the proper localization of U3 snoRNA. Mutations in genes encoding these proteins lead to specific defects in the targeting or retention of the snoRNA to either the nucleolar body or the nucleolus. Additional characterization of the mutants revealed impairment in specific steps of U3 snoRNA processing, demonstrating that snoRNA maturation and trafficking are linked processes.

scholarly journals Intranucleolar sites of ribosome biogenesis defined by the localization of early binding ribosomal proteins

2007 ◽  
Vol 177 (4) ◽  
pp. 573-578 ◽  
Author(s):  
Tim Krüger ◽  
Hanswalter Zentgraf ◽  
Ulrich Scheer
Keyword(s):  
Ribosomal Rna ◽  
Ribosomal Proteins ◽  
Live Cell Imaging ◽  
Ribosome Biogenesis ◽  
Cell Imaging ◽  
Rrna Processing ◽  
Dense Fibrillar Component ◽  
Assembly Pathway ◽  
Fibrillar Component ◽  
Processing Steps

Considerable efforts are being undertaken to elucidate the processes of ribosome biogenesis. Although various preribosomal RNP complexes have been isolated and molecularly characterized, the order of ribosomal protein (r-protein) addition to the emerging ribosome subunits is largely unknown. Furthermore, the correlation between the ribosome assembly pathway and the structural organization of the dedicated ribosome factory, the nucleolus, is not well established. We have analyzed the nucleolar localization of several early binding r-proteins in human cells, applying various methods, including live-cell imaging and electron microscopy. We have located all examined r-proteins (S4, S6, S7, S9, S14, and L4) in the granular component (GC), which is the nucleolar region where later pre-ribosomal RNA (rRNA) processing steps take place. These results imply that early binding r-proteins do not assemble with nascent pre-rRNA transcripts in the dense fibrillar component (DFC), as is generally believed, and provide a link between r-protein assembly and the emergence of distinct granules at the DFC–GC interface.

scholarly journals Synthesis and Assembly of the Box C+D Small Nucleolar RNPs

2000 ◽  
Vol 20 (8) ◽  
pp. 2650-2659 ◽  
Author(s):  
Denis L. J. Lafontaine ◽  
David Tollervey
Keyword(s):  
18S Rrna ◽  
Protein A ◽  
Small Nucleolar Rnas ◽  
Rrna Processing ◽  
Bona Fide ◽  
Polycistronic Transcripts ◽  
Nucleolar Rnas

ABSTRACT Two core small nucleolar RNP (snoRNP) proteins, Nop1p (fibrillarin in vertebrates) and Nop58p (also known as Nop5p) have previously been reported to be specifically associated with the box C+D class of small nucleolar RNAs (snoRNAs). Here we report that Nop56p, a protein related in sequence to Nop58p, is a bona fide box C+D snoRNP component; all tested box C+D snoRNAs were coprecipitated with protein A-tagged Nop56p. Analysis of in vivo snoRNP assembly indicated that Nop56p was stably associated with the snoRNAs only in the presence of Nop1p. In contrast, Nop58p and Nop1p associate independently with the snoRNAs. Genetic depletion of Nop56p resulted in inhibition of early pre-rRNA processing events at sites A0, A1, and A2 and mild depletion of 18S rRNA. However, Nop56p depletion did not lead to codepletion of the box C+D snoRNAs. This is in contrast to Nop58p, which was required for the accumulation of all tested box C+D snoRNAs. Unexpectedly, we found that Nop1p was specifically required for the synthesis and accumulation of box C+D snoRNAs processed from pre-mRNA introns and polycistronic transcripts.

scholarly journals The Arabidopsis 2′-O-Ribose-Methylation and Pseudouridylation Landscape of rRNA in Comparison to Human and Yeast

2021 ◽  
Vol 12 ◽  
Author(s):  
Deniz Streit ◽  
Enrico Schleiff
Keyword(s):  
Arabidopsis Thaliana ◽  
Ribosomal Rna ◽  
Ribosomal Dna ◽  
Ribosomal Proteins ◽  
Ribosome Biogenesis ◽  
Ribosome Assembly ◽  
Small Nucleolar Rnas ◽  
General Process ◽  
Specific Factors ◽  
Nucleolar Rnas

Eukaryotic ribosome assembly starts in the nucleolus, where the ribosomal DNA (rDNA) is transcribed into the 35S pre-ribosomal RNA (pre-rRNA). More than two-hundred ribosome biogenesis factors (RBFs) and more than two-hundred small nucleolar RNAs (snoRNA) catalyze the processing, folding and modification of the rRNA in Arabidopsis thaliana. The initial pre-ribosomal 90S complex is formed already during transcription by association of ribosomal proteins (RPs) and RBFs. In addition, small nucleolar ribonucleoprotein particles (snoRNPs) composed of snoRNAs and RBFs catalyze the two major rRNA modification types, 2′-O-ribose-methylation and pseudouridylation. Besides these two modifications, rRNAs can also undergo base methylations and acetylation. However, the latter two modifications have not yet been systematically explored in plants. The snoRNAs of these snoRNPs serve as targeting factors to direct modifications to specific rRNA regions by antisense elements. Today, hundreds of different sites of modifications in the rRNA have been described for eukaryotic ribosomes in general. While our understanding of the general process of ribosome biogenesis has advanced rapidly, the diversities appearing during plant ribosome biogenesis is beginning to emerge. Today, more than two-hundred RBFs were identified by bioinformatics or biochemical approaches, including several plant specific factors. Similarly, more than two hundred snoRNA were predicted based on RNA sequencing experiments. Here, we discuss the predicted and verified rRNA modification sites and the corresponding identified snoRNAs on the example of the model plant Arabidopsis thaliana. Our summary uncovers the plant modification sites in comparison to the human and yeast modification sites.

scholarly journals Principles of 60S ribosomal subunit assembly emerging from recent studies in yeast

2017 ◽  
Vol 474 (2) ◽  
pp. 195-214 ◽  
Author(s):  
Salini Konikkat ◽  
John L. Woolford,
Keyword(s):  
Ribosomal Rna ◽  
Ribosomal Proteins ◽  
Ribosome Biogenesis ◽  
Ribosomal Subunit ◽  
Ribosome Assembly ◽  
Small Nucleolar Rnas ◽  
Large Ribosomal Subunit ◽  
Yeast Saccharomyces Cerevisiae ◽  
Subunit Assembly ◽  
Nucleolar Rnas

Ribosome biogenesis requires the intertwined processes of folding, modification, and processing of ribosomal RNA, together with binding of ribosomal proteins. In eukaryotic cells, ribosome assembly begins in the nucleolus, continues in the nucleoplasm, and is not completed until after nascent particles are exported to the cytoplasm. The efficiency and fidelity of ribosome biogenesis are facilitated by >200 assembly factors and ∼76 different small nucleolar RNAs. The pathway is driven forward by numerous remodeling events to rearrange the ribonucleoprotein architecture of pre-ribosomes. Here, we describe principles of ribosome assembly that have emerged from recent studies of biogenesis of the large ribosomal subunit in the yeast Saccharomyces cerevisiae. We describe tools that have empowered investigations of ribosome biogenesis, and then summarize recent discoveries about each of the consecutive steps of subunit assembly.

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