RNA Mimicry by the Fap7 Adenylate Kinase in Ribosome Biogenesis

Loc'h, J.; Blaud, Magali; Réty, S.; Lebaron, Simon; Deschamps, P; Bareille, Joseph; Jombart, Julie; Robert-Paganin, Julien; Delbos, Lila; Chardon, Florian; Zhang, Elodie; Charenton, Clément; Tollervey, David; Leulliot, Nicolas

doi:10.1371/journal.pbio.1001860

Cited by 40 publications

(66 citation statements)

References 69 publications

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“…80S-like ribosomes accumulate in the absence of the essential ATPase Fap7 (Strunk et al, 2012), which also interacts with, and is activated by the small ribosomal protein Rps14 (Granneman et al, 2005; Hellmich et al, 2013; Loc’h et al, 2014). Furthermore, Fap7 was crosslinked to the AF Dim1 in vivo (Strunk et al, 2012).…”

Section: (Introduction)mentioning

confidence: 99%

The ATPase Fap7 Tests the Ability to Carry Out Translocation-like Conformational Changes and Releases Dim1 during 40S Ribosome Maturation

et al. 2017

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SUMMARY Late in their maturation, nascent small (40S) ribosomal subunits bind 60S subunits to produce 80S-like ribosomes. Due to the analogy of this translation-like cycle to actual translation, and because 80S-like ribosomes do not produce any protein, it was suggested that this represents a quality-control mechanism for subunit functionality. Here, we use genetic and biochemical experiments to show that the essential ATPase Fap7 promotes formation of the rotated state, a key intermediate in translocation, thereby releasing the essential assembly factor Dim1 from pre-40S subunits. Bypassing this quality control step produces defects in reading frame maintenance. These results show how progress in the maturation cascade is linked to a test for a key functionality of 40S ribosomes, their ability to translocate the mRNA•tRNA pair. Furthermore, our data demonstrate for the first time that the translation-like cycle is a quality control mechanism that ensures the fidelity of the cellular ribosome pool.

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Section: (Introduction)mentioning

confidence: 99%

The ATPase Fap7 Tests the Ability to Carry Out Translocation-like Conformational Changes and Releases Dim1 during 40S Ribosome Maturation

et al. 2017

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“…S20, S29, and S31 are incorporated around the time of export, and at least S20 and S29 appear to be only partially occupied in a purified cytoplasmic intermediate (57). S10, S26, and Asc1 are completely absent, and S3 and S14 appear not to be positioned at their final location (32, 55). This assembly intermediate also contains seven stably bound assembly factors: Enp1 and Ltv1, bound to the beak structure; Rio2, Tsr1, and Dim1, located at the subunit interface; and Nob1 and Pno1 on the platform (57).…”

Section: Cytoplasmic Steps Of 40s Ribosomal Subunit Maturationmentioning

confidence: 96%

“…In developing models for the roles of r-proteins in ribosome assembly, the known locations of r-proteins within mature subunits have provided powerful platforms that are guiding our thinking. Although one assumes that the locations of most r-proteins are similar in assembling particles, one keeps in mind examples of the differences discussed in the next sections (32, 55–57). …”

Section: What Might the Structure Of The Ribosome Tell Us About R-promentioning

confidence: 99%

Functions of Ribosomal Proteins in Assembly of Eukaryotic Ribosomes In Vivo

Cruz

Karbstein

Woolford

2015

Annu. Rev. Biochem.

332

241

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The proteome of cells is synthesized by ribosomes, complex ribonucleoproteins that in eukaryotes contain 79–80 proteins and four ribosomal RNAs (rRNAs) more than 5,400 nucleotides long. How these molecules assemble together and how their assembly is regulated in concert with the growth and proliferation of cells remain important unanswered questions. Here, we review recently emerging principles to understand how eukaryotic ribosomal proteins drive ribosome assembly in vivo. Most ribosomal proteins assemble with rRNA cotranscriptionally; their association with nascent particles is strengthened as assembly proceeds. Each subunit is assembled hierarchically by sequential stabilization of their subdomains. The active sites of both subunits are constructed last, perhaps to prevent premature engagement of immature ribosomes with active subunits. Late-assembly intermediates undergo quality-control checks for proper function. Mutations in ribosomal proteins that affect mostly late steps lead to ribosomopathies, diseases that include a spectrum of cell type–specific disorders that often transition from hypoproliferative to hyperproliferative growth.

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“…The cases of protein-nucleic acid mimicry are now known to be more extensive and multifaceted [60,61,62]. The emergent consensus for the cases of tRNA mimicry in translation factors is that it refers mostly to the shapes of the tRNAs, necessary to fit the pockets and tunnels of the ribosome, while some of the functional details may differ from the expected if they would be substituting the tRNA functions [63,64].…”

Section: Rnp World Instead Of Rna Worldmentioning

confidence: 99%

Self-Referential Encoding on Modules of Anticodon Pairs—Roots of the Biological Flow System

Guimarães

2017

Preprint

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Abstract:The proposal that the genetic code was formed on the basis of protein synthesis directed by tRNA dimers is reviewed and updated. The tRNAs paired through the anticodon loops are an indication on the process. Dimers are considered mimics of the ribosomes -structures that hold tRNAs together and facilitate the transferase reaction, and of the translation process -anticodons are at the same time codons for each other. The primitive protein synthesis system gets stabilized when the product peptides are able to bind the producers therewith establishing a self-stimulating production cycle. The chronology of amino acid encoding starts with Glycine and Serine, indicating the metabolic support of the Glycine-Serine C1-assimilation pathway, which is also consistent with evidence on origins of bioenergetics mechanisms. Since it is not possible to reach for substrates simpler than C1 and compounds in the identified pathway are apt for generating the other central metabolic routes, it is considered that protein synthesis is the beginning and center of a succession of sinkeffective mechanisms that drive the formation and evolution of the metabolic flow system. Plasticity and diversification of proteins construct the cellular system following the orientation given by the flow and implementing it. Nucleic acid monomers participate in bioenergetics and the polymers are conservative memory systems for the synthesis of proteins. Protoplasmic fission is the final sink-effective mechanism, part of cell reproduction, guaranteeing that proteins don't accumulate to saturation, which would trigger inhibition.Keywords: genetic code; tRNA dimers; self-reference; modularity; error-compensation; metabolism chronology; protein stability; punctuation system Living beings are metabolic flow systems that self-construct on the basis of memories and adapt / evolve on the basis of constitutive plasticity. Life is the ontogenetic and evolutionary process instantiated by living beings. ContextCellular structures and functions are composed by a network that may be divided into a mostly internal segment of macromolecules, the proteins and the nucleic acids, and another of micromolecules, that communicate and exchange intimately with the environment. The genetic encoding/decoding system is a key mechanism in both of these processes. It participates in the informational, the polymer sequence order-based self-referential cycle that is the cellular nucleoprotein core, the specifically endogenous and molecular identifier of living beings (Figure 1). The decoding system mediates the translation of genetic sequences -string memories -into proteins, which are the main functional working components of the cell system. The protein synthesis machinery is centered on ribosomes, while the mRNAs, tRNAs and synthetases carry the translation signals, Preprints (www.preprints.org) | NOT PEER-REVIEWED |

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RNA Mimicry by the Fap7 Adenylate Kinase in Ribosome Biogenesis

Abstract: The structure of a ribosome assembly factor in complex bound to a ribosomal protein uncovers a chaperoning function that uses RNA mimicry and is regulated by ATP hydrolysis.

Cited by 40 publications

References 69 publications

The ATPase Fap7 Tests the Ability to Carry Out Translocation-like Conformational Changes and Releases Dim1 during 40S Ribosome Maturation

The ATPase Fap7 Tests the Ability to Carry Out Translocation-like Conformational Changes and Releases Dim1 during 40S Ribosome Maturation

Functions of Ribosomal Proteins in Assembly of Eukaryotic Ribosomes In Vivo

Self-Referential Encoding on Modules of Anticodon Pairs—Roots of the Biological Flow System

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RNA Mimicry by the Fap7 Adenylate Kinase in Ribosome Biogenesis

Abstract: The structure of a ribosome assembly factor in complex bound to a ribosomal protein uncovers a chaperoning function that uses RNA mimicry and is regulated by ATP hydrolysis.

Cited by 40 publications

References 69 publications

The ATPase Fap7 Tests the Ability to Carry Out Translocation-like Conformational Changes and Releases Dim1 during 40S Ribosome Maturation

The ATPase Fap7 Tests the Ability to Carry Out Translocation-like Conformational Changes and Releases Dim1 during 40S Ribosome Maturation

Functions of Ribosomal Proteins in Assembly of Eukaryotic Ribosomes In Vivo

Self-Referential Encoding on Modules of Anticodon Pairs&mdash;Roots of the Biological Flow System

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Self-Referential Encoding on Modules of Anticodon Pairs—Roots of the Biological Flow System