Multiple Regions of Yeast Ribosomal Protein L1 Are Important for Its Interaction with 5 S rRNA and Assembly into Ribosomes

Deshmukh, Mohanish; Stark, Jeremy M.; Yeh, Lee Chuan C; Lee, John C.; Woolford, John L.

doi:10.1074/jbc.270.50.30148

Cited by 42 publications

(12 citation statements)

References 55 publications

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“…Although ribosomal protein L5 (rpL5) is far from the decoding center, it has been shown to interact with eEF3 [13]. Previous studies have characterized five temperature-sensitive alleles of the yeast RPL5 gene encoding rpL5 [28], [29]. A preliminary assay of five rpl5 mutant strains using the near- (AGC) and non- (UCU) cognate reporters indicated that the K27E mutant of L5 tended to be generally hyperaccurate (data not shown).…”

Section: Resultsmentioning

confidence: 99%

Differentiating between Near- and Non-Cognate Codons in Saccharomyces cerevisiae

et al. 2007

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BackgroundDecoding of mRNAs is performed by aminoacyl tRNAs (aa-tRNAs). This process is highly accurate, however, at low frequencies (10−3 – 10−4) the wrong aa-tRNA can be selected, leading to incorporation of aberrant amino acids. Although our understanding of what constitutes the correct or cognate aa-tRNA:mRNA interaction is well defined, a functional distinction between near-cognate or single mismatched, and unpaired or non-cognate interactions is lacking.Methodology/Principal FindingsMisreading of several synonymous codon substitutions at the catalytic site of firefly luciferase was assayed in Saccharomyces cerevisiae. Analysis of the results in the context of current kinetic and biophysical models of aa-tRNA selection suggests that the defining feature of near-cognate aa-tRNAs is their potential to form mini-helical structures with A-site codons, enabling stimulation of GTPase activity of eukaryotic Elongation Factor 1A (eEF1A). Paromomycin specifically stimulated misreading of near-cognate but not of non-cognate aa-tRNAs, providing a functional probe to distinguish between these two classes. Deletion of the accessory elongation factor eEF1Bγ promoted increased misreading of near-cognate, but hyperaccurate reading of non-cognate codons, suggesting that this factor also has a role in tRNA discrimination. A mutant of eEF1Bα, the nucleotide exchange factor for eEF1A, promoted a general increase in fidelity, suggesting that the decreased rates of elongation may provide more time for discrimination between aa-tRNAs. A mutant form of ribosomal protein L5 promoted hyperaccurate decoding of both types of codons, even though it is topologically distant from the decoding center.Conclusions/SignficanceIt is important to distinguish between near-cognate and non-cognate mRNA:tRNA interactions, because such a definition may be important for informing therapeutic strategies for suppressing these two different categories of mutations underlying many human diseases. This study suggests that the defining feature of near-cognate aa-tRNAs is their potential to form mini-helical structures with A-site codons in the ribosomal decoding center. An aminoglycoside and a ribosomal factor can be used to distinguish between near-cognate and non-cognate interactions.

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Section: Resultsmentioning

confidence: 99%

Differentiating between Near- and Non-Cognate Codons in Saccharomyces cerevisiae

et al. 2007

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“…Mutations in these basic amino acids reduced or obliterated 5S rRNA stability and cell viability. Deletions within the L5 C-terminal domain also interfere with assembly of functional ribosomes [23].…”

Section: Discussionmentioning

confidence: 99%

“…Studies were performed as previously described [11] using 500 µg of nuclear extracts and polyclonal sera directed against P34 and P37 or polyclonal sera directed against the yeast L5 protein (formerly L1) [23]. 1 µL of RNAseOUT (Invitrogen) was included in the precipitation reactions.…”

Section: Methodsmentioning

confidence: 99%

A Novel Association between Two Trypanosome-Specific Factors and the Conserved L5-5S rRNA Complex

Ciganda

Prohaska²,

Hellman³

et al. 2012

PLoS ONE

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P34 and P37 are two previously identified RNA binding proteins in the flagellate protozoan Trypanosoma brucei. RNA interference studies have determined that the proteins are involved in and essential for ribosome biogenesis. The proteins interact with the 5S rRNA with nearly identical binding characteristics. We have shown that this interaction is achieved mainly through the LoopA region of the RNA, but P34 and P37 also protect the L5 binding site located on LoopC. We now provide evidence to show that these factors form a novel pre-ribosomal particle through interactions with both 5S rRNA and the L5 ribosomal protein. Further in silico and in vitro analysis of T. brucei L5 indicates a lower affinity for 5S rRNA than expected, based on other eukaryotic L5 proteins. We hypothesize that P34 and P37 complement L5 and bridge the interaction with 5S rRNA, stabilizing it and aiding in the early steps of ribosome biogenesis.

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“…However, equivalent analyses for the 60S r-proteins have not yet been reported. To date, only functional analyses on ribosome maturation have been reported for a few 60S r-proteins, such as Rpl3 (32), Rpl5 (33), Rpl10 (21,34,35), Rpl11 (36), Rpl25 (37) and Rpl33 (38). …”

Section: Introductionmentioning

confidence: 99%

Role and dynamics of the ribosomal protein P0 and its related trans -acting factor Mrt4 during ribosome assembly in Saccharomyces cerevisiae

Rodríguez-Mateos

García-Gómez

Francisco‐Velilla

et al. 2009

Nucleic Acids Research

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Mrt4 is a nucleolar component of the ribosome assembly machinery that shares notable similarity and competes for binding to the 25S rRNA GAR domain with the ribosomal protein P0. Here, we show that loss of function of either P0 or Mrt4 results in a deficit in 60S subunits, which is apparently due to impaired rRNA processing of 27S precursors. Mrt4, which shuttles between the nucleus and the cytoplasm, defines medium pre-60S particles. In contrast, P0 is absent from medium but present in late/cytoplasmic pre-60S complexes. The absence of Mrt4 notably increased the amount of P0 in nuclear Nop7–TAP complexes and causes P0 assembly to medium pre-60S particles. Upon P0 depletion, Mrt4 is relocated to the cytoplasm within aberrant 60S subunits. We conclude that Mrt4 controls the position and timing of P0 assembly. In turn, P0 is required for the release of Mrt4 and exchanges with this factor at the cytoplasm. Our results also suggest other P0 assembly alternatives.

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Multiple Regions of Yeast Ribosomal Protein L1 Are Important for Its Interaction with 5 S rRNA and Assembly into Ribosomes

Cited by 42 publications

References 55 publications

Differentiating between Near- and Non-Cognate Codons in Saccharomyces cerevisiae

Differentiating between Near- and Non-Cognate Codons in Saccharomyces cerevisiae

A Novel Association between Two Trypanosome-Specific Factors and the Conserved L5-5S rRNA Complex

Role and dynamics of the ribosomal protein P0 and its related trans -acting factor Mrt4 during ribosome assembly in Saccharomyces cerevisiae

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