Proteobacterial ArfA Peptides Are Synthesized from Non-stop Messenger RNAs

Schaub, Ryan E.; Poole, Stephen J.; Garza-Sánchez, Fernando; Benbow, Sarah J.; Hayes, Christopher S.

doi:10.1074/jbc.m112.374074

Cited by 41 publications

(58 citation statements)

References 43 publications

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“…In the absence of the tmRNA-SmpB system, the C-terminal 17 amino acids truncated protein ArfAΔ17C is produced, and it has been suggested that this is the form of the protein that recruits RF2 to rescue the stalled ribosome (Garza-Sanchez et al 2011;Schaub et al 2012). Different truncated ArfA proteins that lack C-terminal 12, 17, 22, 25, and 32 amino acids were constructed, and these variants all showed a similar ribosome-rescuing activity, except for ArfAΔ32C .…”

Section: Resultsmentioning

confidence: 99%

“…The expression of the wild-type ArfA in the cell is subject to the regulation of RNase III and tmRNA-SmpB activity Garza-Sanchez et al 2011;Schaub et al 2012). In the absence of the tmRNA-SmpB system, the C-terminal 17 amino acids truncated protein ArfAΔ17C is produced, and it has been suggested that this is the form of the protein that recruits RF2 to rescue the stalled ribosome (Garza-Sanchez et al 2011;Schaub et al 2012).…”

Section: Resultsmentioning

confidence: 99%

“…Chadani et al (2010) discovered that ArfA is essential for the viability of E. coli in the absence of tmRNA-mediated trans-translation system using a synthetic lethal screen. The expression of ArfA in E. coli and ArfA-homolog proteins in other bacteria species is regulated by RNase III and tmRNA Garza-Sanchez et al 2011;Schaub et al 2012). Class I release factor RF2 is essential for ArfA's function in the cell (Chadani et al 2012;Shimizu 2012).…”

Section: Introductionmentioning

confidence: 99%

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Peptide release promoted by methylated RF2 and ArfA in nonstop translation is achieved by an induced-fit mechanism

Zeng

Jin

2015

RNA

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Here we report that the specificity of peptide release in the ribosome on a nonstop mRNA by ArfA and RF2 is achieved by an induced-fit mechanism. Using RF2 that is methylated on the glutamine of its GGQ motif (RF2 m ), we show that methylation substantially increases the rate of ArfA/RF2-catalyzed peptide release on a nonstop mRNA that does not occupy the ribosomal A site, but has only a modest effect on k cat by the same proteins on longer nonstop mRNAs occupying the A site of the mRNA channel in the ribosome. Our data suggest that enhancement in the k cat of peptide release by ArfA and RF2 under the cognate decoding condition is the result of favorable conformational changes in the nonstop complex. We demonstrate a shared mechanism between canonical and nonstop termination, supported by similarities in the kinetic mechanisms in antibiotic inhibition and methylation-correlated enhancement in the rate of peptide release. Despite these similarities, our data suggest that nonstop termination differs from canonical pathway in the downstream event of recycling.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Peptide release promoted by methylated RF2 and ArfA in nonstop translation is achieved by an induced-fit mechanism

Zeng

Jin

2015

RNA

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“…Individual proteins are also targeted for trans-translation through truncation of the cognate mRNAs. Nuclease cleavage sites or transcriptional terminators 5= of the stop codon have been found in some arfA and kinA genes (58)(59)(60). Translation of these genes results in proteins that are rapidly degraded unless trans-translation is impaired, making the encoded protein activity dependent on the state of trans-translation.…”

Section: Substrates For Trans-translationmentioning

confidence: 99%

Resolving Nonstop Translation Complexes Is a Matter of Life or Death

Keiler

Feaga

2014

J Bacteriol

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Problems during gene expression can result in a ribosome that has translated to the 3= end of an mRNA without terminating at a stop codon, forming a nonstop translation complex. The nonstop translation complex contains a ribosome with the mRNA and peptidyl-tRNA engaged, but because there is no codon in the A site, the ribosome cannot elongate or terminate the nascent chain. Recent work has illuminated the importance of resolving these nonstop complexes in bacteria. Transfer-messenger RNA (tmRNA)-SmpB specifically recognizes and resolves nonstop translation complexes in a reaction known as trans-translation. trans-Translation releases the ribosome and promotes degradation of the incomplete nascent polypeptide and problematic mRNA. tmRNA and SmpB have been found in all bacteria and are essential in some species. However, other bacteria can live without trans-translation because they have one of the alternative release factors, ArfA or ArfB. ArfA recruits RF2 to nonstop translation complexes to promote hydrolysis of the peptidyl-tRNAs. ArfB recognizes nonstop translation complexes in a manner similar to tmRNA-SmpB recognition and directly hydrolyzes the peptidyl-tRNAs to release the stalled ribosomes. Genetic studies indicate that most or all species require at least one mechanism to resolve nonstop translation complexes. Consistent with such a requirement, small molecules that inhibit resolution of nonstop translation complexes have broad-spectrum antibacterial activity. These results suggest that resolving nonstop translation complexes is a matter of life or death for bacteria.

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“…Lorsque l'ARNtm et SmPB sont actifs, ils dégradent ArfA en ajoutant le signal de dégradation à la protéine et son ARNm est détruit. En revanche, si la trans-traduction devient inefficace, ArfA n'est plus trans-traduit, et il peut alors prendre le relais [16,17]. Le second système alternatif, ArfB, est une petite protéine mimant le domaine catalytique de RF2.…”

Section: Quand La Traduction Se Grippe…unclassified

La synthèse des protéines par le ribosome

Macé¹,

Giudice²,

Gillet³

2015

Med Sci (Paris)

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> La synthèse des protéines, également appelée traduction, est assurée dans chaque cellule par des machines moléculaires très sophistiquées : les ribosomes. Compte tenu de l'immense quantité de données biologiques à traiter, il arrive régulièrement que ces machines se bloquent et mettent en péril la survie de la cellule. Chez les bactéries, le principal processus de sauvetage des ribosomes bloqués est la trans-traduction. Il est assuré par un acide ribonucléique (ARN) hybride, l'ARN transfert-messager (ARNtm), associé à une petite protéine basique, SmpB (small protein B). Plusieurs autres systèmes de contrôle qualité ont récemment été mis en évidence, révélant un réseau de maintien de la survie cellulaire très sophistiqué. Cette machinerie du contrôle qualité de la synthèse protéique est une cible très prometteuse pour le développement de futurs antibiotiques. < d'un alphabet de quatre lettres (les nucléotides qui composent l'ADN et l'ARNm) à un alphabet de vingt-deux lettres (les acides aminés qui composent les protéines). Elle est portée par une machine molé-culaire très complexe et dynamique : le ribosome [1]. Les ribosomes sont constitués de deux sous-unités distinctes, elles-mêmes composées d'ARN ribosomiques (ARNr) et de protéines. La petite sous-unité permet le décodage de l'information génétique portée par les ARNm, tandis que la grande sous-unité est le siège de la synthèse des protéines via la catalyse des liaisons entre acides aminés (les liaisons peptidiques). Le ribosome possède trois sites de liaison aux ARN de transfert (ARNt), chargés de lui apporter les acides aminés. Le site A, auquel les ARNt aminoacylés se lient après reconnaissance spéci-fique des codons, le site P, qui est occupé par un ARNt lié à la chaîne polypeptidique naissante, et le site E, par lequel les ARNt déacylés transitent avant d'être éjectés. La traduction s'effectue en quatre étapes majeures (Figure 1) : le démarrage (ou initiation), l'élongation, la terminaison et le recyclage (pour une description détaillée du processus voir [2]). Chez les bactéries, le démarrage débute par la fixation de l'ARNm à la petite sous-unité ribosomique 30S, via une séquence riche en purines, dite de Shine-Dalgarno (SD). Cette fixation, assistée par trois facteurs d'initiation (IF1, IF2 et IF3), permet de placer précisément le codon de démarrage (AUG, ou, moins communément, GUG ou UUG) dans le site P du ribosome, afin qu'il soit reconnu par un ARNt porteur de l'acide aminé formyl-méthionine. L'arrimage de la grande sous-unité 50S à ce complexe de démarrage permet de reconstituer le ribosome complet 70S, signant ainsi le début de la phase d'élongation. Dans un processus itératif, les codons de l'ARNm sont ensuite décodés dans

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Proteobacterial ArfA Peptides Are Synthesized from Non-stop Messenger RNAs

Cited by 41 publications

References 43 publications

Peptide release promoted by methylated RF2 and ArfA in nonstop translation is achieved by an induced-fit mechanism

Peptide release promoted by methylated RF2 and ArfA in nonstop translation is achieved by an induced-fit mechanism

Resolving Nonstop Translation Complexes Is a Matter of Life or Death

La synthèse des protéines par le ribosome

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