New bioinformatic tools for analysis of nucleotide modifications in eukaryotic rRNA

Piekna‐Przybylska, Dorota; Decatur, Wayne A.; Fournier, Maurille J.

doi:10.1261/rna.373107

Cited by 97 publications

(119 citation statements)

References 53 publications

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“…These snoRNAs fall into two classes based on their integration into C/D-box or H/ACA-box small nucleolar ribonucleoprotein particles (snoRNPs), which have methyltransferase or pseudouridine synthase activity, respectively [50]. In yeast, 42 [ 4 2 3 _ T D $ D I F F ] C/D-box snoRNAs and 28 H/ACA-box snoRNAs target around 100 different nucleotides for modification [51]. To allow accurate folding of pre-rRNA and its assembly with r-proteins, snoRNAs must dissociate from the rRNA.…”

Section: Assembly Of the Ssumentioning

confidence: 99%

A Puzzle of Life: Crafting Ribosomal Subunits

Kressler

Hurt

Baßler

2017

Trends in Biochemical Sciences

165

127

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The biogenesis of eukaryotic ribosomes is a complicated process during which the transcription, modification, folding, and processing of the rRNA is coupled with the ordered assembly of $80 ribosomal proteins (r-proteins). Ribosome synthesis is catalyzed and coordinated by more than 200 biogenesis factors as the preribosomal subunits acquire maturity on their path from the nucleolus to the cytoplasm. Several biogenesis factors also interconnect the progression of ribosome assembly with quality control of important domains, ensuring that only functional subunits engage in translation. With the recent visualization of several assembly intermediates by cryoelectron microscopy (cryo-EM), a structural view of ribosome assembly begins to emerge. In this review we integrate these first structural insights into an updated overview of the consecutive ribosome assembly steps. Synopsis of Eukaryotic Ribosome AssemblyRibosomes are the molecular machines that translate the genetic information from the intermediary mRNA templates into proteins [1]. Eukaryotic 80S ribosomes comprise two unequal subunits that contain four different rRNAs and around 80 r-proteins ( Figure 1). The small 40S subunit (SSU) comprises the 18S rRNA and 33 r-proteins (referred to as RPS or S). The large 60S subunit (LSU) comprises the 25S/28S, 5.8S, and 5S rRNA and, in most eukaryotic species, 47 r-proteins (RPL or L); a notable exception is budding yeasts, which lack eL28The act of building a ribosome begins in the nucleolus, where the ribosomal DNA (rDNA) is transcribed into a long pre-rRNA precursor (35S pre-rRNA in yeast) and involves the ordered assembly of the r-proteins with the pre-rRNA, which is concomitantly processed into the mature rRNA species [5][6][7][8] (Figure 1 and Box 1). These assembly and processing events are tightly coupled and occur within preribosomal particles (see Glossary) that travel, as maturation progresses, from the nucleus across nuclear pore complexes (NPCs) to the cytoplasm, where they are ultimately converted into translation-competent ribosomal subunits [5,[9][10][11][12][13] (Figure 2, Key Figure). Given the gargantuan complexity of this process, it is unsurprising that the assembly of eukaryotic ribosomes strictly requires the assistance of a plethora (>200) of mostly essential ribosome biogenesis factors, which are also called trans-acting or assembly factors [5,14,15].Our current knowledge has been mainly obtained by studying ribosome biogenesis in the yeast Saccharomyces cerevisiae. Research conducted in the 1970s defined the r-protein composition of ribosomes, revealed the major pre-rRNA processing intermediates, and uncovered the existence of the 90S, 43S, and 66S preribosomal particles. The following 25 years witnessed the identification of numerous biogenesis factors and attributed functional roles TrendsCryoelectron microscopy analyses of the 90S preribosome show that the biogenesis factors create a casting mold that encloses the nascent pre-40S subunit.Structures of nuclear pre-60S particles reveal that a...

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Section: Assembly Of the Ssumentioning

confidence: 99%

A Puzzle of Life: Crafting Ribosomal Subunits

Kressler

Hurt

Baßler

2017

Trends in Biochemical Sciences

165

127

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“…First we consulted the Rfam, SGD, the LncRNAdb, and the yeast snoRNA databases (Piekna-Przybylska et al 2007;Cherry et al 2012;Nawrocki et al 2015;Quek et al 2015) in addition to the published literature, to draw up a complete list of S. cerevisiae ncRNAs. We then retrieved relevant articles by searching PubMed for abstracts containing at least one ncRNA name and "yeast" or "S. cerevisiae" terms.…”

Section: Data Collection and Curation: Yeast Noncoding Rnasmentioning

confidence: 99%

The yeast noncoding RNA interaction network

Panni

Prakash

Bateman

et al. 2017

RNA

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This article describes the creation of the first expert manually curated noncoding RNA interaction networks for S. cerevisiae. The RNA-RNA and RNA-protein interaction networks have been carefully extracted from the experimental literature and made available through the IntAct database (www.ebi.ac.uk/intact). We provide an initial network analysis and compare their properties to the much larger protein-protein interaction network. We find that the proteins that bind to ncRNAs in the network contain only a small proportion of classical RNA binding domains. We also see an enrichment of WD40 domains suggesting their direct involvement in ncRNA interactions. We discuss the challenges in collecting noncoding RNA interaction data and the opportunities for worldwide collaboration to fill the unmet need for this data.

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“…Additional nucleotides between H70 and H71 are methylated in all organisms. In yeast, the three ribose methylations in H70/71 are guided by two snoRNAs, snR13 (A2280m and A2281m), and snR75 (G2288m) (Lowe and Eddy 1999;Piekna-Przybylska et al 2007). The cytosine-5 methyltransferase for C2278 in yeast was unknown prior to this study.…”

Section: Introductionmentioning

confidence: 99%

A cluster of methylations in the domain IV of 25S rRNA is required for ribosome stability

Gigova

Duggimpudi

Pollex

et al. 2014

RNA

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In all three domains of life ribosomal RNAs are extensively modified at functionally important sites of the ribosome. These modifications are believed to fine-tune the ribosome structure for optimal translation. However, the precise mechanistic effect of modifications on ribosome function remains largely unknown. Here we show that a cluster of methylated nucleotides in domain IV of 25S rRNA is critical for integrity of the large ribosomal subunit. We identified the elusive cytosine-5 methyltransferase for C2278 in yeast as Rcm1 and found that a combined loss of cytosine-5 methylation at C2278 and ribose methylation at G2288 caused dramatic ribosome instability, resulting in loss of 60S ribosomal subunits. Structural and biochemical analyses revealed that this instability was caused by changes in the structure of 25S rRNA and a consequent loss of multiple ribosomal proteins from the large ribosomal subunit. Our data demonstrate that individual RNA modifications can strongly affect structure of large ribonucleoprotein complexes.

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New bioinformatic tools for analysis of nucleotide modifications in eukaryotic rRNA

Cited by 97 publications

References 53 publications

A Puzzle of Life: Crafting Ribosomal Subunits

A Puzzle of Life: Crafting Ribosomal Subunits

The yeast noncoding RNA interaction network

A cluster of methylations in the domain IV of 25S rRNA is required for ribosome stability

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