A general mechanism of ribosome dimerization revealed by single-particle cryo-electron microscopy

Franken, Linda E.; Oostergetel, Gert T.; Pijning, Tjaard; Puri, Pranav; Arkhipova, Valentina; Boekema, Egbert J.; Poolman, Berend; Guskov, Albert

doi:10.1038/s41467-017-00718-x

Cited by 62 publications

(87 citation statements)

References 56 publications

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“…A similar interaction between uS2 and h26 was also observed in S. aureus 100S; however, in this structure bS18 does not seem to be involved in the dimer interface connections; instead, h40 interacts with HPF long -CTD [34]. Instead it interacts with the h26 of the opposite ribosome [32], like in the second 100S structure. The finding that two independent studies on the same particle yielded different structure suggests that the 100S may adopt various conformations, thus further illustrating the flexibility of the dimer interface.…”

Section: Resultssupporting

confidence: 66%

“…A for the whole dimer) [30][31][32][33][34][35][36]. These demonstrated that in all systems dimer formation benefits from the ribosomal inherent flexibility.…”

Section: Resultsmentioning

confidence: 99%

“…The sequences of both NTD and CTD domains of HPF long are rather conserved among different bacteria, whereas the sequence and composition of the linker is hardy conserved [32]. This finding has been attributed to the flexibility of this linker.…”

Section: Resultsmentioning

confidence: 99%

“…Long version of HPF is a homodimer in solution [10, 14,[30][31][32][33][34]. Therefore, it has been suggested that , S. aureus [33], L. lectococcus and T. thermpophilus, respectively.…”

Section: Mechanisms For Dimerizationmentioning

confidence: 99%

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Stress response as implemented by hibernating ribosomes: a structural overview

et al. 2019

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Protein synthesis is one of the most energy demanding cellular processes. The ability to regulate protein synthesis is essential for cells under normal as well as stress conditions, such as nutrient deficiencies. One mechanism for protein synthesis suppression is the dimerization of ribosomes into hibernation complexes. In most cells, this process is promoted by the hibernating promoting factor (HPF) and in a small group of Gram‐negative bacteria (γ‐proteobacteria), the dimer formation is induced by a shorter version of HPF (HPFshort) and by an additional protein, the ribosome modulation factor. In most bacteria, the product of this process is the 100S ribosome complex. Recent advances in cryogenic electron microscopy methods resulted in an abundance of detailed structures of near atomic resolutions 100S complexes that allow for a better understanding of the dimerization process and the way it inhibits protein synthesis. As ribosomal dimerization is vital for cell survival, this process is an attractive target for the development of novel antimicrobial substances that might inhibit or stabilize the complex formation. As different dimerization processes exist among bacteria, including pathogens, this process may provide the basis for species‐specific design of antimicrobial agents. Here, we review in detail the various dimerization mechanisms and discuss how they affect the overall dimer structures of the bacterial ribosomes.

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Section: Resultssupporting

confidence: 66%

“…A for the whole dimer) [30][31][32][33][34][35][36]. These demonstrated that in all systems dimer formation benefits from the ribosomal inherent flexibility.…”

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

“…Long version of HPF is a homodimer in solution [10, 14,[30][31][32][33][34]. Therefore, it has been suggested that , S. aureus [33], L. lectococcus and T. thermpophilus, respectively.…”

Section: Mechanisms For Dimerizationmentioning

confidence: 99%

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Stress response as implemented by hibernating ribosomes: a structural overview

et al. 2019

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“…The bipartite HPF long proteins consist of the translational silencing N-terminal domain (NTD) and a dimerizing C-terminal domain (CTD) linked by an unstructured region composed of 16–62 residues (Franken et al 2017) (Figs. 1, 2).…”

Section: The Many Flavors Of Ribosome Hibernation Factorsmentioning

confidence: 99%

Survival of the drowsiest: the hibernating 100S ribosome in bacterial stress management

Gohara

Yap

2017

Curr Genet

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In response to nutrient deprivation and environmental insults, bacteria conjoin two copies of non-translating 70S ribosomes that form the translationally inactive 100S dimer. This widespread phenomenon is believed to prevent ribosome turnover and serves as a reservoir that, when conditions become favorable, allows the hibernating ribosomes to be disassembled and recycled for translation. New structural studies have revealed two distinct mechanisms for dimerizing 70S ribosomes, but the molecular basis of the disassembly process is still in its infancy. Many details regarding the sequence of dimerization-dissociation events with respect to the binding and departure of the hibernation factor and its antagonizing disassembly factor remain unclear.

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Chemical Crosslinking‐Mass Spectrometry (CXL‐MS) for Proteomics, Antibody‐Drug Conjugates (ADCs) and Cryo‐Electron Microscopy (cryo‐EM)

2018

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Chemical crosslinking-mass spectrometry (CXL-MS) has emerged as a powerful tool in structural biology to elucidate protein-protein interactions. This review throws light on the advent of these technologies incorporating chemical crosslinking in proteomics, structural biology and extended to studies and applications of antibody-drug conjugates (ADCs). Monoclonal ASCs are known to target their specific receptors, where the drug could be released for vastly improved therapeutic effect. Cryo-electron microscopy (cryo-EM) is being referred to as the "revolution of the century" as it can help attain almost atomic resolution, while preserving the biological samples at near-native state and has been recognized by the Nobel award 2017. CXL-MS and appropriate bioinformatics tools in combination with cryo-EM reveal better 3D information about dynamic interactions in proteins, interactive domains and motifs, among others in ADCs and in viruses like Zika virus, Rota virus, Dengue virus and also spliceosomes at resolutions, especially below 3 Å. © 2018 IUBMB Life, 70(10):947-960, 2018.

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A general mechanism of ribosome dimerization revealed by single-particle cryo-electron microscopy

Cited by 62 publications

References 56 publications

Stress response as implemented by hibernating ribosomes: a structural overview

Stress response as implemented by hibernating ribosomes: a structural overview

Survival of the drowsiest: the hibernating 100S ribosome in bacterial stress management

Chemical Crosslinking‐Mass Spectrometry (CXL‐MS) for Proteomics, Antibody‐Drug Conjugates (ADCs) and Cryo‐Electron Microscopy (cryo‐EM)

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