Structures of the eukaryotic ribosome and its translational states in situ

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: Dec. 2, 2022

Ribosomes translate genetic information into primary structure. During translation, various cofactors transiently bind to the ribosome that undergoes prominent conformational and structural changes. Different translational states of ribosomes have been well characterized in vitro. However, which extent known are representative native situation inside cells has thus far only addressed prokaryotes. Here, we apply cryo-electron tomography cryo-FIB milled Dictyostelium discoideum combined with subtomogram averaging classification. We obtain an situ structure is locally resolved up 3 Angstrom, distribution eukaryotic states, unique arrangement rRNA expansion segments. Our work demonstrates use biology techniques for identifying distinct within cellular environment.

Language: Английский

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A new family of bacterial ribosome hibernation factors

Nature, Journal Year: 2024, Volume and Issue: 626(8001), P. 1125 - 1132

Published: Feb. 14, 2024

Abstract To conserve energy during starvation and stress, many organisms use hibernation factor proteins to inhibit protein synthesis protect their ribosomes from damage 1,2 . In bacteria, two families of factors have been described, but the low conservation these huge diversity species, habitats environmental stressors confounded discovery 3–6 Here, by combining cryogenic electron microscopy, genetics biochemistry, we identify Balon, a new in cold-adapted bacterium Psychrobacter urativorans We show that Balon is distant homologue archaeo-eukaryotic translation aeRF1 found 20% representative bacteria. During cold shock or stationary phase, occupies ribosomal A site both vacant actively translating complex with EF-Tu, highlighting an unexpected role for EF-Tu cellular stress response. Unlike typical A-site substrates, binds mRNA-independent manner, initiating mode ribosome can commence while are still engaged synthesis. Our work suggests Balon–EF-Tu-regulated ubiquitous bacterial stress-response mechanism, demonstrate putative homologues Mycobacteria bind similar fashion. This finding calls revision current model inferred common holds numerous implications how understand study hibernation.

Language: Английский

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Ultrastructural insights into the microsporidian infection apparatus reveal the kinetics and morphological transitions of polar tube and cargo during host cell invasion

PLoS Biology, Journal Year: 2024, Volume and Issue: 22(2), P. e3002533 - e3002533

Published: Feb. 29, 2024

During host cell invasion, microsporidian spores translocate their entire cytoplasmic content through a thin, hollow superstructure known as the polar tube. To achieve this, tube transitions from compact spring-like state inside environmental spore to long needle-like capable of long-range sporoplasm delivery. The unique mechanical properties building blocks allow for an explosive transition extended and support rapid cargo translocation process. molecular structural factors enabling this ultrafast process changes during delivery are unknown. Here, we employ light microscopy in situ cryo-electron tomography visualize multiple ultrastructural states Vairimorpha necatrix tube, allowing us evaluate kinetics its germination characterize underlying morphological transitions. We describe cargo-filled with ordered arrangement ribosomes, which cluster along thin wall, empty post-translocation reduced diameter but thicker wall. Together proteomic analysis endogenously affinity-purified tubes, our work provides comprehensive data on infection apparatus microsporidia uncovers new aspects ribosome regulation transport.

Language: Английский

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Genomic and phenotypic evolution of nematode-infecting microsporidia

PLoS Pathogens, Journal Year: 2023, Volume and Issue: 19(7), P. e1011510 - e1011510

Published: July 20, 2023

Microsporidia are a large phylum of intracellular parasites that can infect most types animals. Species in the Nematocida genus nematodes including Caenorhabditis elegans, which has become an important model to study mechanisms microsporidia infection. To understand genomic properties and evolution nematode-infecting microsporidia, we sequenced genomes nine species two genera, Enteropsectra Pancytospora, without any previously genomes. Core cellular processes, metabolic pathways, mostly conserved across genera microsporidia. Each encodes unique proteins belonging gene families likely used interact with host cells. Most strikingly, observed one such family, NemLGF1, is present both Pancytospora species, but not other how phenotypic traits evolved, measured range, tissue specificity, spore size, polar tube length several genus. Our phylogenetic analysis shows composed groups distinct longer tubes multiple tissues. Together, our work details trait between related provides useful resource for further understanding infection mechanisms.

Language: Английский

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Structures of Saccharolobus solfataricus initiation complexes with leaderless mRNAs highlight archaeal features and eukaryotic proximity

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: Jan. 2, 2025

Language: Английский

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The space between notes: emerging roles for translationally silent ribosomes

Trends in Biochemical Sciences, Journal Year: 2022, Volume and Issue: 47(6), P. 477 - 491

Published: March 1, 2022

Language: Английский

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Structure of the reduced microsporidian proteasome bound by PI31-like peptides in dormant spores

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: Nov. 15, 2022

Proteasomes play an essential role in the life cycle of intracellular pathogens with extracellular stages by ensuring proteostasis environments limited resources. In microsporidia, divergent parasites extraordinarily streamlined genomes, proteasome complexity and structure are unknown, which limits our understanding how these unique adapt compact eukaryotic complexes. We present cryo-electron microscopy structures microsporidian 20S 26S isolated from dormant or germinated Vairimorpha necatrix spores. The discovery PI31-like peptides, known to inhibit activity, bound simultaneously all six active sites within central cavity spore proteasome, suggests reduced activity environmental stage. contrast, absence peptides existence particles post-germination presence ATP indicates that proteasomes reactivated nutrient-rich conditions. Structural phylogenetic analyses reveal have undergone extensive reductive evolution, lost at least two regulatory proteins, compacted nearly every subunit. highly derived minimized version PI31 presented here, reinforce feasibility development specific inhibitors provide insight into evolution biology medically economically important pathogens.

Language: Английский

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Insights into translocation mechanism and ribosome evolution from cryo-EM structures of translocation intermediates of Giardia intestinalis

Nucleic Acids Research, Journal Year: 2023, Volume and Issue: 51(7), P. 3436 - 3451

Published: March 13, 2023

Giardia intestinalis is a protozoan parasite that causes diarrhea in humans. Using single-particle cryo-electron microscopy, we have determined high-resolution structures of six naturally populated translocation intermediates, from ribosomes isolated directly actively growing cells. The highly compact and uniquely GC-rich possess eukaryotic rRNAs ribosomal proteins, but retain some bacterial features. with bound tRNAs elongation factor 2 (eEF2), display characteristic intersubunit rotation small subunit's head swiveling-universal for translocation. In addition, observe the eukaryote-specific 'subunit rolling' dynamics, albeit limited Finally, eEF2·GDP state features positioned 'leaving phosphate (Pi)' proposes hitherto unknown molecular events Pi eEF2 release ribosome at final stage summary, our study elucidates mechanism protists illustrates evolution translation machinery bacteria to eukaryotes both structural mechanistic perspectives.

Language: Английский

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CryoEM reveals that ribosomes in microsporidian spores are locked in a dimeric hibernating state

Nature Microbiology, Journal Year: 2023, Volume and Issue: 8(10), P. 1834 - 1845

Published: Sept. 14, 2023

Abstract Translational control is an essential process for the cell to adapt varying physiological or environmental conditions. To survive adverse conditions such as low nutrient levels, translation can be shut down almost entirely by inhibiting ribosomal function. Here we investigated eukaryotic hibernating ribosomes from microsporidian parasite Spraguea lophii in situ a combination of electron cryo-tomography and single-particle cryo-microscopy. We show that spores contain are locked dimeric (100S) state, which formed unique dimerization mechanism involving beak region. The within dimer fully assembled, suggesting they ready activated once host invaded. This study provides structural evidence acting hibernation microsporidia, therefore demonstrates eukaryotes utilize this translational control.

Language: Английский

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Rippling life on a dormant planet: hibernation of ribosomes, RNA polymerases, and other essential enzymes

Frontiers in Microbiology, Journal Year: 2024, Volume and Issue: 15

Published: May 6, 2024

Throughout the tree of life, cells and organisms enter states dormancy or hibernation as a key feature their biology: from bacterium arresting its growth in response to starvation, plant seed anticipating placement fertile ground, human oocyte poised for fertilization create new life. Recent research shows that when hibernate, many essential enzymes hibernate too: they disengage substrates associate with specialized group proteins known factors. Here, we summarize how factors protect cellular undesired activity irreparable damage hibernating cells. We show molecular hibernation, once viewed rare exclusive certain molecules like ribosomes, is fact widespread property biological required sustained persistence life on Earth.

Language: Английский

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