Cryo-EM structures of the 80S ribosomes from human parasites Trichomonas vaginalis and Toxoplasma gondii

Li, Zhifei; Guo, Qiang; Zheng, Lvqin; Ji, Yongchang; Xie, Yiting; Lai, De‐Hua; Lun, Zhao‐Rong; Suo, Xun; Gao, Ning

doi:10.1038/cr.2017.104

Cited by 26 publications

(28 citation statements)

References 92 publications

(134 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Among eukaryotes, T. vaginalis is rather special in that it clustered with archaea (P. furiosus and H. marismortui), which then grouped together with a cluster of trypanosomes (L. donovani and T. cruzi); separated from these, the remaining eukaryotes formed a larger cluster. This separation of T. vaginalis is supported by the properties of its rRNAs, which are comparable in size to prokaryotic counterparts, and with nearly all the eukaryote-specific rRNA expansion segments missing [24]. More generally, the separations of T. vaginalis and trypanosomes from the other eukaryotes is also consistent with the evolutionary relationships obtained from 16S-like rRNA sequences (from the ribosome small subunit) [24].…”

Section: Hierarchical Clustering Of Tunnel Radius Variation Plots Refsupporting

confidence: 68%

“…This separation of T. vaginalis is supported by the properties of its rRNAs, which are comparable in size to prokaryotic counterparts, and with nearly all the eukaryote-specific rRNA expansion segments missing [24]. More generally, the separations of T. vaginalis and trypanosomes from the other eukaryotes is also consistent with the evolutionary relationships obtained from 16S-like rRNA sequences (from the ribosome small subunit) [24]. We confirmed this result by carrying out a phylogenetic analysis for the species in our dataset, based on their 16S/18S rRNA sequences (see Figure S2A).…”

Section: Hierarchical Clustering Of Tunnel Radius Variation Plots Refmentioning

confidence: 93%

“…Plotting this frequency as a function of d for all the species, we observed in Figure 6B a global decrease in the frequency of CNEs as d increases, which means that nucleotides located farther from the tunnel are less conserved. For much divergent rRNAs such as the ones from organelles or T. vaginalis [24], the low number of CNEs yields no association with the distance to the tunnel. For bacteria, archaea, and eukaryotic trypanosomes, we found that the frequency of CNEs within 25 Å from the tunnel is 21 ± 5%, which is more than the double the frequency of CNEs located between 25 and 50 Å (10 ± 2%) and also that located farther than 50 Å from the tunnel (8 ± 2%).…”

Section: Association Between Rrna Sequence Conservation and The Exit mentioning

confidence: 99%

See 2 more Smart Citations

Differences in the path to exit the ribosome across the three domains of life

Duc

Batra

Bhattacharya

et al. 2018

Preprint

View full text Add to dashboard Cite

Recent advances in biological imaging have led to a surge of fine-resolution structures of the ribosome from diverse organisms. Comparing these structures, especially the exit tunnel, to characterize the key similarities and differences across species is essential for various important applications, such as designing antibiotic drugs and understanding the intricate details of translation dynamics. Here, we compile and compare 20 fine-resolution cryo-EM and X-ray crystallography structures of the ribosome recently obtained from all three domains of life (bacteria, archaea and eukarya). We first show that a hierarchical clustering of tunnel shapes closely reflects the species phylogeny. Then, by analyzing the ribosomal RNAs and proteins localized near the tunnel, we explain the observed geometric variations and show direct association between the conservations of the geometry, structure, and sequence. We find that the tunnel is more conserved in its upper part, from the polypeptide transferase center to the constriction site. In the lower part, tunnels are significantly narrower in eukaryotes than in bacteria, and we provide evidence for the existence of a second constriction site in eukaryotic tunnels. We also show that ribosomal RNA and protein sequences are more likely to be conserved closer to the tunnel, as is the presence of positively charged amino acids. Overall, our comparative analysis shows how the geometric and biophysical properties of the exit tunnel play an important role in ensuring proper transit of the nascent polypeptide chain, and may explain the differences observed in several co-translational processes across species.

show abstract

Section: Hierarchical Clustering Of Tunnel Radius Variation Plots Refsupporting

confidence: 68%

Section: Hierarchical Clustering Of Tunnel Radius Variation Plots Refmentioning

confidence: 93%

Section: Association Between Rrna Sequence Conservation and The Exit mentioning

confidence: 99%

See 1 more Smart Citation

Differences in the path to exit the ribosome across the three domains of life

Duc

Batra

Bhattacharya

et al. 2018

Preprint

View full text Add to dashboard Cite

show abstract

“…Recent studies of the ribosome composition and structure for diverse species have contributed to draw a more intricate picture of the ribosome evolution. An important example of divergence among eukaryotes is the kinetoplastid family, which has been the object of several structural studies [ 21 , 22 , 23 , 24 ], showing ribosomes with fragmented rRNA’s that are comparable in size to prokaryotic counterparts, with nearly all the eukaryote-specific rRNA expansion segments missing. Similarly, during their evolution into organisms with highly compacted genomes, microsporidia have removed essentially all eukaryotic expansion segments and repurposed several ribosomal proteins to compensate for the extensive rRNA reduction [ 25 ].…”

Section: The Multiple Sources Of Heterogeneity In Ribosome Structumentioning

confidence: 99%

Structural Heterogeneities of the Ribosome: New Frontiers and Opportunities for Cryo-EM

Poitevin

Kushner

et al. 2020

Molecules

View full text Add to dashboard Cite

The extent of ribosomal heterogeneity has caught increasing interest over the past few years, as recent studies have highlighted the presence of structural variations of the ribosome. More precisely, the heterogeneity of the ribosome covers multiple scales, including the dynamical aspects of ribosomal motion at the single particle level, specialization at the cellular and subcellular scale, or evolutionary differences across species. Upon solving the ribosome atomic structure at medium to high resolution, cryogenic electron microscopy (cryo-EM) has enabled investigating all these forms of heterogeneity. In this review, we present some recent advances in quantifying ribosome heterogeneity, with a focus on the conformational and evolutionary variations of the ribosome and their functional implications. These efforts highlight the need for new computational methods and comparative tools, to comprehensively model the continuous conformational transition pathways of the ribosome, as well as its evolution. While developing these methods presents some important challenges, it also provides an opportunity to extend our interpretation and usage of cryo-EM data, which would more generally benefit the study of molecular dynamics and evolution of proteins and other complexes.

show abstract

“…conserved core of 216 eukaryotic ES39, which we call the ES39 217 signature fold. We compared experimental 218 three-dimensional structures of rRNAs in a 219 wide range of eukaryotic ribosomes(Ben- 220 Shem, et al 2010;Klinge, et al 2011; 221 Khatter, et al 2015;Li, et al 2017). The 222 ES39 signature fold, which is common to 223 all eukaryotic ES39s, consists of helix 98 224 (H98; 20-30 nts), helix b (Hb; 40-50 nts), 225 and their linkage by three unpaired 15 nts 226 long segments of rRNA (supplementary 227 figure S4).…”

mentioning

confidence: 99%

Supersized ribosomal RNA expansion segments in Asgard archaea

Penev

Fakhretaha-Aval

Patel

et al. 2019

Preprint

View full text Add to dashboard Cite

12The ribosome's common core connects all life back to a common ancestor and serves as a 13 window to relationships among organisms. In eukaryotes, the common core contains expansion 14 segments (ES's) that vastly increase ribosomal RNA size. Supersized ES's have not been 15 observed previously in Bacteria or Archaea, and the origin of eukaryotic ES's remains enigmatic. 16We discovered that the large subunit rRNA of Lokiarchaeota, the closest modern cell lineage to 17 the last common ancestor of Archaea and Eukarya, bridges the gap in size between prokaryotic 18 and eukaryotic rRNA. The long large subunit rRNA in Lokiarchaeota is largely due to the 19 presence of two eukaryotic-like, supersized ES's, ES9 and ES39, which are transcribed in situ. 20We applied computational models, covariation analysis, and chemical footprinting experiments 21 to study the structure and evolution of Lokiarchaeota ES9 and ES39. We also defined the 22 eukaryotic ES39 fold for comparison. We found that Lokiarchaeota and eukaryotic ES's are 23 structurally distinct: Lokiarchaeota ES39 has more and longer helices than the eukaryotic ES39 24 fold. Despite their structural differences, we found that Lokiarchaeota and eukaryotic ES's 25 originated from a common ancestor that was "primed" for evolution of larger and more complex 26 rRNAs than those found in Bacteria and other archaea. 27

show abstract

Cryo-EM structures of the 80S ribosomes from human parasites Trichomonas vaginalis and Toxoplasma gondii

Cited by 26 publications

References 92 publications

Differences in the path to exit the ribosome across the three domains of life

Differences in the path to exit the ribosome across the three domains of life

Structural Heterogeneities of the Ribosome: New Frontiers and Opportunities for Cryo-EM

Supersized ribosomal RNA expansion segments in Asgard archaea

Contact Info

Product

Resources

About