Start Codon Recognition in Eukaryotic and Archaeal Translation Initiation: A Common Structural Core

Schmitt, Emmanuelle; Coureux, Pierre‐Damien; Monestier, Auriane; Dubiez, Etienne; Mechulam, Yves

doi:10.3390/ijms20040939

Cited by 18 publications

(30 citation statements)

References 169 publications

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“…In this view, it is notable that eS26 is absent in euryarchaotes but present in crenarchaeota/lokiarchaeota genomes 7,81 . Because the archaeal version of the exit chamber is a simplified version of the eukaryotic one, this argues in favor of the controversial hypothesis that eukaryotic ribosomes have evolved from within the archaeal version 10,82 .…”

Section: Discussionmentioning

confidence: 99%

“…Despite this, a local search of the mRNA by the IC (termed as "local scanning" in ref. 10 ) is necessary to allow precise positioning of the start codon in the P site. Thus, even if the recruitment of the PIC on the mRNA is different in eukaryotes and archaea, start codon selection is achieved within a common structural core made up of the small ribosomal subunit, the mRNA, the methionylated initiator tRNA (Met-tRNA i Met ) and the three IFs e/aIF1, e/aIF1A and e/aIF2 10 .…”

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confidence: 99%

“…10 ) is necessary to allow precise positioning of the start codon in the P site. Thus, even if the recruitment of the PIC on the mRNA is different in eukaryotes and archaea, start codon selection is achieved within a common structural core made up of the small ribosomal subunit, the mRNA, the methionylated initiator tRNA (Met-tRNA i Met ) and the three IFs e/aIF1, e/aIF1A and e/aIF2 10 . e/aIF2 is a specific eukaryotic and archaeal heterotrimeric protein that binds the initiator tRNA in the presence of GTP 11 .…”

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confidence: 99%

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Cryo-EM study of an archaeal 30S initiation complex gives insights into evolution of translation initiation

et al. 2020

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Archaeal translation initiation occurs within a macromolecular complex containing the small ribosomal subunit (30S) bound to mRNA, initiation factors aIF1, aIF1A and the ternary complex aIF2:GDPNP:Met-tRNA i Met. Here, we determine the cryo-EM structure of a 30S: mRNA:aIF1A:aIF2:GTP:Met-tRNA i Met complex from Pyrococcus abyssi at 3.2 Å resolution. It highlights archaeal features in ribosomal proteins and rRNA modifications. We find an aS21 protein, at the location of eS21 in eukaryotic ribosomes. Moreover, we identify an N-terminal extension of archaeal eL41 contacting the P site. We characterize 34 N 4-acetylcytidines distributed throughout 16S rRNA, likely contributing to hyperthermostability. Without aIF1, the 30S head is stabilized and initiator tRNA is tightly bound to the P site. A network of interactions involving tRNA, mRNA, rRNA modified nucleotides and C-terminal tails of uS9, uS13 and uS19 is observed. Universal features and domain-specific idiosyncrasies of translation initiation are discussed in light of ribosomal structures from representatives of each domain of life.

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Section: Discussionmentioning

confidence: 99%

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Cryo-EM study of an archaeal 30S initiation complex gives insights into evolution of translation initiation

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“…The 'translational initiation' GO annotation term is also highly enriched within the Critical proteins. 'Translational initiation' is a complex process that involves eukaryotic conserved initiation factors (such as EIF1B, EIF2S3, EIF4A2 and ribosomes) and regulation mechanisms that select the start codon on the mRNA 33 .…”

Section: Criticalmentioning

confidence: 99%

Conservation motifs - a novel evolutionary-based classification of proteins

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Sherill-Rofe

Unterman

et al. 2020

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Cross-species protein conservation patterns, as directed by natural selection, are indicative of the interplay between protein function, protein-protein interaction and evolution. Since the beginning of the genomic era, proteins were characterized as either conserved or not conserved. This simple classification became archaic and cursory once data on protein orthologs became available for thousands of species.To enrich the language used to describe protein conservation patterns, and to understand their biological significance, we classified 20,294 human proteins against 1096 species. Analyses of the conservation patterns of human proteins in different eukaryotic clades yielded extremely variable and rich patterns that had never been characterized or studied before. Using mathematical classifications, we defined seven conservation motifs: Steps, Critical, Lately Developed, Plateau, Clade Loss, Trait Loss and Gain, which describe the evolution of human proteins.One type of motif, which we termed Gain, describes the human proteins that are highly conserved in a small number of organisms but are not found in most other species.Interestingly, this pattern predicts 73 possible instances of horizontal gene transfer in eukaryotes.Overall, our work offers novel terms for conservation patterns and defines a new language intended to classify proteins based on evolution, reveal aspects of protein evolution, and improve the understanding of protein functions.

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“…Indeed, aIF1, aIF1A, aIF2, and aIF5B homologous to the corresponding eukaryotic factors are present (Figures 1, 2; Dennis, 1997;Kyrpides and Woese, 1998;Benelli and Londei, 2011;Gäbel et al, 2013;Schmitt et al, 2019). Thus, even if there are obvious differences between archaea and eukaryotes, in particular for the recruitment of mRNA, via SD sequences vs. long-range scanning, the selection of the start codon is carried out within a same structural core composed of the small ribosomal subunit, mRNA, methionylated initiator tRNA (Met-tRNA i Met ), and the three initiation factors e/aIF1, e/aIF1A, and e/aIF2 (Schmitt et al, 2019). Finally, the late steps of TI preceding the formation of a ribosome competent for elongation are controlled by initiation factors that are conserved in the three domains of life, IF1-e/aIF1A, and IF2-e/aIF5B.…”

Section: Introductionmentioning

confidence: 99%

Recent Advances in Archaeal Translation Initiation

et al. 2020

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Translation initiation (TI) allows accurate selection of the initiation codon on a messenger RNA (mRNA) and defines the reading frame. In all domains of life, translation initiation generally occurs within a macromolecular complex made up of the small ribosomal subunit, the mRNA, a specialized methionylated initiator tRNA, and translation initiation factors (IFs). Once the start codon is selected at the P site of the ribosome and the large subunit is associated, the IFs are released and a ribosome competent for elongation is formed. However, even if the general principles are the same in the three domains of life, the molecular mechanisms are different in bacteria, eukaryotes, and archaea and may also vary depending on the mRNA. Because TI mechanisms have evolved lately, their studies bring important information about the evolutionary relationships between extant organisms. In this context, recent structural data on ribosomal complexes and genomewide studies are particularly valuable. This review focuses on archaeal translation initiation highlighting its relationships with either the eukaryotic or the bacterial world. Eukaryotic features of the archaeal small ribosomal subunit are presented. Ribosome evolution and TI mechanisms diversity in archaeal branches are discussed. Next, the use of leaderless mRNAs and that of leadered mRNAs having Shine-Dalgarno sequences is analyzed. Finally, the current knowledge on TI mechanisms of SD-leadered and leaderless mRNAs is detailed.

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Start Codon Recognition in Eukaryotic and Archaeal Translation Initiation: A Common Structural Core

Cited by 18 publications

References 169 publications

Cryo-EM study of an archaeal 30S initiation complex gives insights into evolution of translation initiation

Cryo-EM study of an archaeal 30S initiation complex gives insights into evolution of translation initiation

Conservation motifs - a novel evolutionary-based classification of proteins

Recent Advances in Archaeal Translation Initiation

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