The final step of 40S ribosomal subunit maturation is controlled by a dual key lock

Plassart, Laura; Shayan, Ramtin; Montellese, Christian; Rinaldi, Daniel; Larburu, Natacha; Pichereaux, Carole; Froment, Carine; Lebaron, Simon; O’Donohue, Marie-Françoise; Kutay, Ulrike; Marcoux, Julien; Gleizes, Pierre‐Emmanuel; Plisson‐Chastang, Célia

doi:10.7554/elife.61254

Cited by 31 publications

(39 citation statements)

References 67 publications

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“…These proteins are functionally related through their known roles in ribosomal function. LARS is leucine tRNA synthase, POLR3A is a subunit of specialized RNA polymerase III responsible for the synthesis of tRNAs, ribosomal 5S rRNA, and other small RNAs, POLR1B is a subunit of RNA polymerase I responsible for the production of ribosomal RNAs, whereas RIOK1 (RIO kinase 1) plays essential role in maturation of 40S ribosomal subunits ( 38 ). Phylogenetic profiles of all four domains across the whole tree of life ( Supplementary Figure S3 ) share a strong similarity beyond eukaryotes: they have similar levels of conservation among their homologs in Archaea and a drop of conservation signal in Bacteria .…”

Section: Resultsmentioning

confidence: 99%

DEPCOD: a tool to detect and visualize co-evolution of protein domains

Sadreyev

2022

Nucleic Acids Research

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Proteins with similar phylogenetic patterns of conservation or loss across evolutionary taxa are strong candidates to work in the same cellular pathways or engage in physical or functional interactions. Our previously published tools implemented our method of normalized phylogenetic sequence profiling to detect functional associations between non-homologous proteins. However, many proteins consist of multiple protein domains subjected to different selective pressures, so using protein domain as the unit of analysis improves the detection of similar phylogenetic patterns. Here we analyze sequence conservation patterns across the whole tree of life for every protein domain from a set of widely studied organisms. The resulting new interactive webserver, DEPCOD (DEtection of Phylogenetically COrrelated Domains), performs searches with either a selected pre-defined protein domain or a user-supplied sequence as a query to detect other domains from the same organism that have similar conservation patterns. Top similarities on two evolutionary scales (the whole tree of life or eukaryotic genomes) are displayed along with known protein interactions and shared complexes, pathway enrichment among the hits, and detailed visualization of sources of detected similarities. DEPCOD reveals functional relationships between often non-homologous domains that could not be detected using whole-protein sequences. The web server is accessible at http://genetics.mgh.harvard.edu/DEPCOD.

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Section: Resultsmentioning

confidence: 99%

DEPCOD: a tool to detect and visualize co-evolution of protein domains

Sadreyev

2022

Nucleic Acids Research

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“…To gain a greater understanding of how ORF11 interacts with pre-40S ribosomal subunits during biogenesis, we mapped the abundance of the small subunit ribosomal proteins identified from the quantitative proteomic affinity pulldowns to the structure of the pre-40S ribosomal subunit (Plassart et al 2021, PDB: 6ZUO) 37 . The most highly abundant 40S ribosomal proteins interacting with GFP-ORF11 localise around the rRNA on the subunit interface side of the pre-40S ribosomal subunit, which include eS30, uS19, uS13, eS19, eS8, and uS15 (Fig.…”

Section: The Kshv Orf11 Protein Interacts With Pre-ribosome Complexes...mentioning

confidence: 99%

Kaposi’s sarcoma-associated herpesvirus induces specialised ribosomes to efficiently translate viral lytic mRNAs

Murphy

Schumann

Harrington

et al. 2022

Preprint

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Historically, ribosomes have been viewed as unchanged homogeneous macromolecular machines with no intrinsic regulatory capacity for mRNA translation. However, an emerging concept is that heterogeneity of ribosomal composition exists, which can exert a regulatory function or specificity in translational control. This is supported by recent discoveries identifying compositionally distinct specialised ribosomes that actively regulate mRNA translation. Viruses lack their own translational machinery and impose a high translational demand on the host cell during replication. Here we explore the possibility that Kaposi sarcoma associated herpesvirus can manipulate host ribosome biogenesis during infection to produce specialised ribosomes which preferentially translate viral transcripts. Quantitative proteomic analysis has identified changes in the stoichiometry and composition of precursor ribosomal complexes during the switch from latent to lytic KSHV replication. Intriguingly, we demonstrate the enhanced association of ribosomal biogenesis factors BUD23 and NOC4L, and a previously uncharacterised KSHV lytic protein, ORF11, with small ribosomal subunit precursor complexes during lytic KSHV infection. Notably, BUD23 depletion resulted in significantly reduced viral gene expression and progression through the lytic cascade, culminating in a dramatic reduction of infectious virion production. Importantly, ribosome profiling demonstrated that BUD23 is essential for the reduced association of ribosomes with KSHV uORFs in late lytic genes, required for the efficient translation of the main open reading frame. Together our results provide new mechanistic insights into KSHV-mediated manipulation of cellular ribosome composition inducing a population of specialised ribosomes to facilitate efficient translation of viral mRNAs.

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“…The RNA-binding protein Pno1 masks a cleavage site at the 3’-end of the mature 18S rRNA. Conformational rearrangement and interaction of the pre-40S subunit with the mature 60S subunit are the checking steps required for interaction with Nob1, which converts the 20S pre-rRNA into the 18S rRNA [ 5 , 38 , 133 , 134 , 135 , 136 , 137 ]. A Cryo-EM analysis of human, late pre-40S particles supports a model where Rio1-ATP interacts with the ribosomal protein RPS26 and displaces Dim2 from the 3’-end of the 20S pre-rRNA.…”

Section: Ribosome Biogenesismentioning

confidence: 99%

Eukaryotic Ribosome Biogenesis: The 40S Subunit

et al. 2022

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The formation of eukaryotic ribosomes is a sequential process of ribosomal precursors maturation in the nucleolus, nucleoplasm, and cytoplasm. Hundreds of ribosomal biogenesis factors ensure the accurate processing and formation of the ribosomal RNAs tertiary structure, and they interact with ribosomal proteins. Most of what we know about the ribosome assembly has been derived from yeast cell studies, and the mechanisms of ribosome biogenesis in eukaryotes are considered quite conservative. Although the main stages of ribosome biogenesis are similar across different groups of eukaryotes, this process in humans is much more complicated owing to the larger size of the ribosomes and pre-ribosomes and the emergence of regulatory pathways that affect their assembly and function. Many of the factors involved in the biogenesis of human ribosomes have been identified using genome-wide screening based on RNA interference. This review addresses the key aspects of yeast and human ribosome biogenesis, using the 40S subunit as an example. The mechanisms underlying these differences are still not well understood, because, unlike yeast, there are no effective methods for characterizing pre-ribosomal complexes in humans. Understanding the mechanisms of human ribosome assembly would have an incidence on a growing number of genetic diseases (ribosomopathies) caused by mutations in the genes encoding ribosomal proteins and ribosome biogenesis factors. In addition, there is evidence that ribosome assembly is regulated by oncogenic signaling pathways, and that defects in the ribosome biogenesis are linked to the activation of tumor suppressors.

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The final step of 40S ribosomal subunit maturation is controlled by a dual key lock

Cited by 31 publications

References 67 publications

DEPCOD: a tool to detect and visualize co-evolution of protein domains

DEPCOD: a tool to detect and visualize co-evolution of protein domains

Kaposi’s sarcoma-associated herpesvirus induces specialised ribosomes to efficiently translate viral lytic mRNAs

Eukaryotic Ribosome Biogenesis: The 40S Subunit

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