The eukaryotic ribosomal protein S15/uS19 is involved in fungal development and its C-terminal tail contributes to stop codon recognition

SummaryS15/uS19 is one of the fifteen universally conserved ribosomal proteins of the small ribosomal subunit. While prokaryotic uS19 is located away from the mRNA decoding site, cross-linking studies identified eukaryotic uS19 C-terminal tail as contacting the A site on the 80S ribosome. Here, we study the effects of uS19 mutations isolated as translation accuracy mutations in the filamentous fungus Podospora anserina. All mutations alter residues of uS19 C-terminal tail, and cluster to the eukaryote-specific decapeptide 138-PGIGATHSSR-147. All mutations modify fungal development and cytosolic translation, albeit differently. Two mutations (P138S and S145F) increase fungus longevity and display mild effects on translation, while others (G139D and G139C) decrease longevity, have stronger effects on translation and confer hypersensitivity to paromomycin. By mimicking P. anserina mutations in the yeast Saccharomyces cerevisiae RPS15 gene, we further show that P138S and S145F induce hyperaccurate recognition of the three stop codons, whereas G139D and G139C impair UAG and UAA codon recognition. Noteworthy, in P. anserina, uS19 genetically interacts with the eRF1 and eRF3 release factors. All together, our data indicate that uS19 C-terminal tail contributes in vivo to eukaryotic translation termination, and identify key amino acids of uS19 that potentially modulate eRF1-eRF3 interaction in the pre-termination complex.Graphical abstractAbbreviated SummaryS15/uS19 is a conserved small ribosomal protein that in eukaryotes harbors a flexible C-terminal extension proposed to interact with the A site mRNA codon during translation. Here, we describe how C-terminal variants variously affect Podospora anserina development and longevity and impact fungal ribosome and polysome formation. We reveal that stop codon recognition is significantly altered by the presence of those C-terminal variants, which either expand or on the contrary restrict termination ambiguity.

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Atomic mutagenesis of stop codon nucleotides reveals the chemical prerequisites for release factor-mediated peptide release

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1714554115 ◽

2018 ◽

Vol 115 (3) ◽

pp. E382-E389 ◽

Cited By ~ 7

Author(s):

Thomas Philipp Hoernes ◽

Nina Clementi ◽

Michael Andreas Juen ◽

Xinying Shi ◽

Klaus Faserl ◽

...

Keyword(s):

Stop Codon ◽

Release Factor ◽

Stop Codons ◽

Codon Recognition ◽

Chemically Modified ◽

Peptide Release ◽

Stop Codon Recognition ◽

A Site ◽

Chemical Groups ◽

Insight Into

Termination of protein synthesis is triggered by the recognition of a stop codon at the ribosomal A site and is mediated by class I release factors (RFs). Whereas in bacteria, RF1 and RF2 promote termination at UAA/UAG and UAA/UGA stop codons, respectively, eukaryotes only depend on one RF (eRF1) to initiate peptide release at all three stop codons. Based on several structural as well as biochemical studies, interactions between mRNA, tRNA, and rRNA have been proposed to be required for stop codon recognition. In this study, the influence of these interactions was investigated by using chemically modified stop codons. Single functional groups within stop codon nucleotides were substituted to weaken or completely eliminate specific interactions between the respective mRNA and RFs. Our findings provide detailed insight into the recognition mode of bacterial and eukaryotic RFs, thereby revealing the chemical groups of nucleotides that define the identity of stop codons and provide the means to discriminate against noncognate stop codons or UGG sense codons.

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Conformational control of translation termination on the 70S ribosome

10.1101/226837 ◽

2017 ◽

Cited By ~ 1

Author(s):

Egor Svidritskiy ◽

Andrei A. Korostelev

Keyword(s):

Conformational Changes ◽

Catalytic Domain ◽

Stop Codon ◽

Translation Termination ◽

Release Factor ◽

Codon Recognition ◽

Peptide Release ◽

Stop Codon Recognition ◽

70S Ribosome ◽

A Site

AbstractTranslation termination ensures proper lengths of cellular proteins. During termination, release factor (RF) recognizes a stop codon and catalyzes peptide release. Conformational changes in RF are thought to underlie accurate translation termination. If true, the release factor should bind the A-site codon in inactive (compact) conformation(s), but structural studies of ribosome termination complexes have only captured RFs in an extended, active conformation. Here, we identify a hyper-accurate RF1 variant, and present crystal structures of 70S termination complexes that suggest a structural pathway for RF1 activation. In the presence of blasticidin S, the catalytic domain of RF1 is removed from the peptidyl-transferase center, whereas the codon-recognition domain is fully engaged in stop-codon recognition in the decoding center. RF1 codon recognition induces decoding-center rearrangements that precede accommodation of the catalytic domain. Our findings suggest how structural dynamics of RF1 and the ribosome coordinate stop-codon recognition with peptide release, ensuring accurate translation termination.

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Eukaryotic Release Factor 1 Phosphorylation by CK2 Protein Kinase Is Dynamic but Has Little Effect on the Efficiency of Translation Termination in Saccharomyces cerevisiae

Eukaryotic Cell ◽

10.1128/ec.00073-06 ◽

2006 ◽

Vol 5 (8) ◽

pp. 1378-1387 ◽

Cited By ~ 12

Author(s):

Adam K. Kallmeyer ◽

Kim M. Keeling ◽

David M. Bedwell

Keyword(s):

Saccharomyces Cerevisiae ◽

Protein Synthesis ◽

Protein Kinase ◽

Stop Codon ◽

Translation Termination ◽

Release Factor ◽

Codon Recognition ◽

Number Of Factors ◽

Stop Codon Recognition

ABSTRACT Protein synthesis requires a large commitment of cellular resources and is highly regulated. Previous studies have shown that a number of factors that mediate the initiation and elongation steps of translation are regulated by phosphorylation. In this report, we show that a factor involved in the termination step of protein synthesis is also subject to phosphorylation. Our results indicate that eukaryotic release factor 1 (eRF1) is phosphorylated in vivo at serine 421 and serine 432 by the CK2 protein kinase (previously casein kinase II) in the budding yeast Saccharomyces cerevisiae. Phosphorylation of eRF1 has little effect on the efficiency of stop codon recognition or nonsense-mediated mRNA decay. Also, phosphorylation is not required for eRF1 binding to the other translation termination factor, eRF3. In addition, we provide evidence that the putative phosphatase Sal6p does not dephosphorylate eRF1 and that the state of eRF1 phosphorylation does not influence the allosuppressor phenotype associated with a sal6Δ mutation. Finally, we show that phosphorylation of eRF1 is a dynamic process that is dependent upon carbon source availability. Since many other proteins involved in protein synthesis have a CK2 protein kinase motif near their extreme C termini, we propose that this represents a common regulatory mechanism that is shared by factors involved in all three stages of protein synthesis.

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Halobacterium cutirubrum ribosomes. Properties of the ribosomal proteins and ribonucleic acid

Biochemical Journal ◽

10.1042/bj1300103 ◽

1972 ◽

Vol 130 (1) ◽

pp. 103-110 ◽

Cited By ~ 51

Author(s):

L. P. Visentin ◽

C. Chow ◽

A. T. Matheson ◽

M. Yaguchi ◽

F. Rollin

Keyword(s):

Ribosomal Protein ◽

Ribosomal Proteins ◽

Soluble Fraction ◽

Ribosomal Subunit ◽

23S Rrna ◽

Core Particle ◽

Fractionation Procedure ◽

Additional Protein ◽

70S Ribosome ◽

Low Ionic Strength

1. The 30S ribosomal subunit of the extreme halophile Halobacterium cutirubrum is unstable and loses 75% of its ribosomal protein when the 70S ribosome is dissociated into the two subunits. A stable 30S subunit is obtained if the dissociation of the 70S particle is carried out in the presence of the soluble fraction. 2. A fractionation procedure was developed for the selective removal of groups of proteins from the 30S and 50S subunits. When the ribosomes, which are stable in 4m-K+ and 0.1m-Mg2+, were extracted with low-ionic-strength buffer 75–80% of the 30S proteins and 60–65% of the 50S proteins as well as the 5S rRNA were released. The proteins in this fraction are the most acidic of the H. cutirubrum ribosomal proteins. Further extraction with Li+–EDTA releases additional protein, leaving a core particle containing either 16S rRNA or 23S rRNA and about 5% of the total ribosomal protein. The amino acid composition, mobility on polyacrylamide gels at pH4.5 and 8.7, and the molecular-weight distribution of the various protein fractions were determined. 3. The s values of the rRNA are 5S, 16S and 23S. The C+G contents of the 16S and 23S rRNA were 56.1 and 58.8% respectively and these are higher than C+G contents of the corresponding Escherichia coli rRNA (53.8 and 54.1%).

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Ribosomal protein S14 is altered by two-step emetine resistance mutations in Chinese hamster cells

Molecular and Cellular Biology ◽

10.1128/mcb.3.2.190-197.1983 ◽

1983 ◽

Vol 3 (2) ◽

pp. 190-197

Author(s):

J J Madjar ◽

M Frahm ◽

S McGill ◽

D J Roufa

Keyword(s):

Ribosomal Protein ◽

Ribosomal Proteins ◽

Ribosomal Subunit ◽

Chinese Hamster ◽

Complementation Group ◽

Resistance Mutations ◽

Cho Cell ◽

Ribosomal Subunits ◽

40S Ribosomal Subunit ◽

One Step

Four two-dimensional polyacrylamide gel electrophoresis systems were used to identify 78 Chinese hamster cell ribosomal proteins by the uniform nomenclature based on rat liver ribosomal proteins. The 40S ribosomal subunit protein affected by Chinese hamster ovary (CHO) cell one-step emetine resistance mutations is designated S14 in the standard nomenclature. To seek unambiguous genetic evidence for a cause and effect relationship between CHO cell emetine resistance and mutations in the S14 gene, we mutagenized a one-step CHO cell mutant and isolated second-step mutant clones resistant to 10-fold-higher concentrations of emetine. All of the highly resistant, two-step CHO cell mutants obtained displayed additional alterations in ribosomal protein S14. Hybridization complementation tests revealed that the two-step CHO cell emetine resistance mutants were members of the same complementation group defined by one-step CHO cell mutants, EmtB. Two-step mutants obtained from a Chinese hamster lung cell emetine-resistant clone belong to the EmtA complementation group. The two-step and EmtB mutants elaborated 40S ribosomal subunits, which dissociated to 32S and 40S core particles in buffers containing 0.5 M KCl at 4 degrees C. In contrast, 40S ribosomal subunits purified from all EmtA, one-step EmtB EmtC mutants, and wild-type CHO and lung cells were stable at this temperature in buffers containing substantially higher concentrations of salt. Thus, two-step emtB mutations affect the structure of S14 protein directly and the stability of the 40S ribosomal subunit indirectly.

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