scholarly journals Structure and assembly model for the Trypanosoma cruzi 60S ribosomal subunit

2016 ◽  
Vol 113 (43) ◽  
pp. 12174-12179 ◽  
Author(s):  
Zheng Liu ◽  
Cristina Gutierrez-Vargas ◽  
Jia Wei ◽  
Robert A. Grassucci ◽  
Madhumitha Ramesh ◽  
...  
Keyword(s):  
Trypanosoma Cruzi ◽  
Large Subunit ◽  
Level Structure ◽  
Ribosomal Subunit ◽  
28S Rrna ◽  
Assembly Model ◽  
Ribosomal Assembly ◽  
Assembly Pathway ◽  
Glue Proteins ◽  
Stepwise Assembly

Ribosomes of trypanosomatids, a family of protozoan parasites causing debilitating human diseases, possess multiply fragmented rRNAs that together are analogous to 28S rRNA, unusually large rRNA expansion segments, and r-protein variations compared with other eukaryotic ribosomes. To investigate the architecture of the trypanosomatid ribosomes, we determined the 2.5-Å structure of the Trypanosoma cruzi ribosome large subunit by single-particle cryo-EM. Examination of this structure and comparative analysis of the yeast ribosomal assembly pathway allowed us to develop a stepwise assembly model for the eight pieces of the large subunit rRNAs and a number of ancillary “glue” proteins. This model can be applied to the characterization of Trypanosoma brucei and Leishmania spp. ribosomes as well. Together with other details, our atomic-level structure may provide a foundation for structure-based design of antitrypanosome drugs.

Structure and assembly model for the Trypanosoma cruzi 60S ribosomal subunit

2018 ◽  
pp. 526-531
Author(s):  
Zheng Liu ◽  
Cristina Gutierrez-Vargas ◽  
Jia Wei ◽  
Robert A. Grassucci ◽  
Madhumitha Ramesh ◽  
...  
Keyword(s):  
Trypanosoma Cruzi ◽  
Ribosomal Subunit ◽  
Assembly Model

scholarly journals A distinct assembly pathway of the human 39S late pre-mitoribosome

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jingdong Cheng ◽  
Otto Berninghausen ◽  
Roland Beckmann
Keyword(s):  
16S Rrna ◽  
Affinity Purification ◽  
Large Subunit ◽  
Assembly Pathway ◽  
Assembly Factors ◽  
Peptidyltransferase Center

AbstractAssembly of the mitoribosome is largely enigmatic and involves numerous assembly factors. Little is known about their function and the architectural transitions of the pre-ribosomal intermediates. Here, we solve cryo-EM structures of the human 39S large subunit pre-ribosomes, representing five distinct late states. Besides the MALSU1 complex used as bait for affinity purification, we identify several assembly factors, including the DDX28 helicase, MRM3, GTPBP10 and the NSUN4-mTERF4 complex, all of which keep the 16S rRNA in immature conformations. The late transitions mainly involve rRNA domains IV and V, which form the central protuberance, the intersubunit side and the peptidyltransferase center of the 39S subunit. Unexpectedly, we find deacylated tRNA in the ribosomal E-site, suggesting a role in 39S assembly. Taken together, our study provides an architectural inventory of the distinct late assembly phase of the human 39S mitoribosome.

scholarly journals Characterization of the nuclear export adaptor protein Nmd3 in association with the 60S ribosomal subunit

2010 ◽  
Vol 189 (7) ◽  
pp. 1079-1086 ◽  
Author(s):  
Jayati Sengupta ◽  
Cyril Bussiere ◽  
Jesper Pallesen ◽  
Matthew West ◽  
Arlen W. Johnson ◽  
...  
Keyword(s):  
Binding Site ◽  
Nuclear Export ◽  
Large Subunit ◽  
Ribosomal Subunit ◽  
Adaptor Protein ◽  
Structural Data ◽  
Release Mechanism ◽  
Nuclear Pore ◽  
Subunit Joining

The nucleocytoplasmic shuttling protein Nmd3 is an adaptor for export of the 60S ribosomal subunit from the nucleus. Nmd3 binds to nascent 60S subunits in the nucleus and recruits the export receptor Crm1 to facilitate passage through the nuclear pore complex. In this study, we present a cryoelectron microscopy (cryo-EM) reconstruction of the 60S subunit in complex with Nmd3 from Saccharomyces cerevisiae. The density corresponding to Nmd3 is directly visible in the cryo-EM map and is attached to the regions around helices 38, 69, and 95 of the 25S ribosomal RNA (rRNA), the helix 95 region being adjacent to the protein Rpl10. We identify the intersubunit side of the large subunit as the binding site for Nmd3. rRNA protection experiments corroborate the structural data. Furthermore, Nmd3 binding to 60S subunits is blocked in 80S ribosomes, which is consistent with the assigned binding site on the subunit joining face. This cryo-EM map is a first step toward a molecular understanding of the functional role and release mechanism of Nmd3.

scholarly journals The molecular basis for ANE syndrome revealed by the large ribosomal subunit processome interactome

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Kathleen L McCann ◽  
Takamasa Teramoto ◽  
Jun Zhang ◽  
Traci M Tanaka Hall ◽  
Susan J Baserga
Keyword(s):  
Protein Interactions ◽  
Molecular Basis ◽  
Large Subunit ◽  
Ribosomal Subunit ◽  
Rna Recognition Motif ◽  
Rna Recognition ◽  
Rrna Processing ◽  
Protein Protein Interactions ◽  
Recognition Motif ◽  
Processing Defects

ANE syndrome is a ribosomopathy caused by a mutation in an RNA recognition motif of RBM28, a nucleolar protein conserved to yeast (Nop4). While patients with ANE syndrome have fewer mature ribosomes, it is unclear how this mutation disrupts ribosome assembly. Here we use yeast as a model system and show that the mutation confers growth and pre-rRNA processing defects. Recently, we found that Nop4 is a hub protein in the nucleolar large subunit (LSU) processome interactome. Here we demonstrate that the ANE syndrome mutation disrupts Nop4’s hub function by abrogating several of Nop4’s protein-protein interactions. Circular dichroism and NMR demonstrate that the ANE syndrome mutation in RRM3 of human RBM28 disrupts domain folding. We conclude that the ANE syndrome mutation generates defective protein folding which abrogates protein-protein interactions and causes faulty pre-LSU rRNA processing, thus revealing one aspect of the molecular basis of this human disease.

scholarly journals Structural consequences of the interaction of RbgA with a 50S ribosomal subunit assembly intermediate

2019 ◽  
Vol 47 (19) ◽  
pp. 10414-10425 ◽  
Author(s):  
Amal Seffouh ◽  
Nikhil Jain ◽  
Dushyant Jahagirdar ◽  
Kaustuv Basu ◽  
Aida Razi ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Large Subunit ◽  
Ribosomal Subunit ◽  
Catalytic Residue ◽  
Gtp Hydrolysis ◽  
Subunit Assembly ◽  
Cryo Electron Microscopy ◽  
Assembly Factor ◽  
Assembly Intermediate ◽  
Immature Particle

Abstract Bacteria harbor a number GTPases that function in the assembly of the ribosome and are essential for growth. RbgA is one of these GTPases and is required for the assembly of the 50S subunit in most bacteria. Homologs of this protein are also implicated in the assembly of the large subunit of the mitochondrial and eukaryotic ribosome. We present here the cryo-electron microscopy structure of RbgA bound to a Bacillus subtilis 50S subunit assembly intermediate (45SRbgA particle) that accumulates in cells upon RbgA depletion. Binding of RbgA at the P site of the immature particle stabilizes functionally important rRNA helices in the A and P-sites, prior to the completion of the maturation process of the subunit. The structure also reveals the location of the highly conserved N-terminal end of RbgA containing the catalytic residue Histidine 9. The derived model supports a mechanism of GTP hydrolysis, and it shows that upon interaction of RbgA with the 45SRbgA particle, Histidine 9 positions itself near the nucleotide potentially acting as the catalytic residue with minimal rearrangements. This structure represents the first visualization of the conformational changes induced by an assembly factor in a bacterial subunit intermediate.

scholarly journals A DEAD-box protein regulates ribosome assembly through control of ribosomal protein synthesis

2019 ◽  
Vol 47 (15) ◽  
pp. 8193-8206 ◽  
Author(s):  
Isabelle Iost ◽  
Chaitanya Jain
Keyword(s):  
Protein Synthesis ◽  
Ribosomal Proteins ◽  
Ribosomal Subunit ◽  
Large Family ◽  
Ribosome Assembly ◽  
Protein Abundance ◽  
Ribosomal Assembly ◽  
Dead Box ◽  
Ribosomal Protein Synthesis ◽  
Intrinsic Transcription Termination

Abstract DEAD-box proteins (DBPs) comprise a large family of proteins that most commonly have been identified as regulators of ribosome assembly. The Escherichia coli DBP, SrmB, represents a model bacterial DBP whose absence impairs formation of the large ribosomal subunit (LSU). To define the basis for SrmB function, suppressors of the ribosomal defect of ΔsrmB strains were isolated. The major class of suppressors was found to map to the 5′ untranslated region (UTR) of the rplM-rpsI operon, which encodes the ribosomal proteins (r-proteins) L13 and S9. An analysis of protein abundance indicated that both r-proteins are under-produced in the ΔsrmB strain, but are increased in these suppressors, implicating r-protein underproduction as the molecular basis for the observed ribosomal defects. Reduced r-protein synthesis was determined to be caused by intrinsic transcription termination within the rplM 5′ UTR that is abrogated by SrmB. These results reveal a specific mechanism for DBP regulation of ribosomal assembly, indirectly mediated through its effects on r-protein expression.

scholarly journals Morphological and molecular rates of evolution in post-Paleozoic echinoids

1992 ◽  
Vol 6 ◽  
pp. 273-273
Author(s):  
Andrew B. Smith ◽  
R. Christen
Keyword(s):  
Morphological Evolution ◽  
Large Subunit ◽  
Rank Correlation ◽  
Great Majority ◽  
Data Matrix ◽  
Time Interval ◽  
28S Rrna ◽  
Geological Time ◽  
Molecular Change ◽  
Rates Of Evolution

Phylogenetic analysis of a data matrix of 86 skeletal characteristics, and of the first 400 bases of the 5’ end of the large subunit ribosomal RNA gene produce congruent cladograms for 11 extant echinoids. Based on these cladistic analyses the great majority of morphologic and molecular apomorphies can be placed in one of 18 independent geological time intervals. When the cladogram is calibrated using the fossil record of post-Paleozoic echinoids, rates of molecular change in 28S rRNA can be calculated and compared with estimated rates of morphological evolution.Morphological and molecular apomorphies acquired in each time interval both correlate moderately strongly with time elapsed, but less strongly with one another. As expected, morphological rates vary considerably over time and between sister groups, but so too do molecular rates. When averaged over all echinoids studied, the number of morphological apomorphies accrued yields a slightly higher Spearman Rank correlation coefficient with time elapsed than does the number of molecular apomorphies accrued. This is because there is a three-fold difference in the rate of molecular change amongst the echinoid lineages studied.

scholarly journals Taxonomical considerations and molecular phylogeny of the closely related genera Bitylenchus, Sauertylenchus and Tylenchorhynchus (Nematoda: Telotylenchinae), with one new and four known species from Iran

2020 ◽  
Vol 94 ◽  
Author(s):  
M. Hosseinvand ◽  
A. Eskandari ◽  
S. Ganjkhanloo ◽  
R. Ghaderi ◽  
P. Castillo ◽  
...  
Keyword(s):  
New Species ◽  
Anterior Part ◽  
Phylogenetic Analyses ◽  
Ribosomal Subunit ◽  
Molecular Data ◽  
28S Rrna ◽  
Natural Habitats ◽  
Morphometric Characters ◽  
Molecular Approaches ◽  
Tail Tip

Abstract During several nematological surveys in cultivated and natural habitats in Khuzestan and Zanjan provinces of Iran, a new species, Bitylenchus parvulus n. sp., two new records for Iran – namely, Tylenchorhynchus agri and Tylenchorhynchus graciliformis – and a population of Bitylenchus parvus and one of Sauertylenchus maximus were recovered and characterized based upon morphological and molecular approaches. The new species is characterized by lip region with five to seven annuli, stylet 17.7 (17.0–18.5) μm long, sub-cylindrical tail narrowing abruptly near terminus giving a bluntly digitate shape to the tail tip, cuticle near anterior part of vulva wrinkled and post-rectal sac occupies whole of tail cavity. The phylogenetic analyses were carried out using molecular data from D2–D3 expansion segments of large ribosomal subunit (28S rRNA) for all studied species and the partial small ribosomal subunit (18S rRNA) for the new species. The representatives of Bitylenchus and Sauertylenchus formed distinct clades from Tylenchorhynchus members, supporting the hypothesis in which Bitylenchus and Sauertylenchus could be considered as valid genera, but rejecting the ‘large-genus’ concept for Tylenchorhynchus. Also, Sauertylenchus ibericus was proposed as a junior synonym of S. maximus based on the results from morphological and phylogenetic analysis. Furthermore, an identification key for all known species included in the three genera Bitylenchus, Tylenchorhynchus and Sauertylenchus is presented herein. The number of transverse annuli on the lip region and presence/absence of post-rectal sac were considered as the main diagnostic characters for classifying the species into seven groups, and other morphological and morphometric characters were subsequently used for distinguishing species in each group.

scholarly journals Stress induces the assembly of RNA granules in the chloroplast of Chlamydomonas reinhardtii

2008 ◽  
Vol 182 (4) ◽  
pp. 641-646 ◽  
Author(s):  
James Uniacke ◽  
William Zerges
Keyword(s):  
Oxidative Stress ◽  
Chlamydomonas Reinhardtii ◽  
Large Subunit ◽  
Ribosomal Subunit ◽  
Stress Granules ◽  
Mrna Localization ◽  
Messenger Rnas ◽  
Rna Granules ◽  
Cytoplasmic Rna ◽  
Ribulosebisphosphate Carboxylase

Eukaryotic cells under stress repress translation and localize these messenger RNAs (mRNAs) to cytoplasmic RNA granules. We show that specific stress stimuli induce the assembly of RNA granules in an organelle with bacterial ancestry, the chloroplast of Chlamydomonas reinhardtii. These chloroplast stress granules (cpSGs) form during oxidative stress and disassemble during recovery from stress. Like mammalian stress granules, cpSGs contain poly(A)-binding protein and the small, but not the large, ribosomal subunit. In addition, mRNAs are in continuous flux between polysomes and cpSGs during stress. Localization of cpSGs within the pyrenoid reveals that this chloroplast compartment functions in this stress response. The large subunit of ribulosebisphosphate carboxylase/oxygenase also assembles into cpSGs and is known to bind mRNAs during oxidative stress, raising the possibility that it plays a role in cpSG assembly. This discovery within such an organelle suggests that mRNA localization to granules during stress is a more general phenomenon than currently realized.

scholarly journals Unusual pattern of ribonucleic acid components in the ribosome of Crithidia fasciculata, a trypanosomatid protozoan.

1981 ◽  
Vol 1 (4) ◽  
pp. 347-357 ◽  
Author(s):  
M W Gray
Keyword(s):  
Ribosomal Rna ◽  
Ribonucleic Acid ◽  
Large Subunit ◽  
Ribosomal Subunit ◽  
Ribosomal Rnas ◽  
High Potassium ◽  
Intact Cells ◽  
Crithidia Fasciculata ◽  
Low Magnesium ◽  
Chain Lengths

In a previous study from this laboratory, presumptive ribosomal ribonucleic acid (RNA) species were identified in the total cellular RNA directly extracted from intact cells of the trypanosomatid protozoan Crithidia fasciculata (M. W. Gray, Can. J. Biochem. 57:914-926, 1979). The results suggested that the C. fasciculata ribosome might be unusual in containing three novel, low-molecular-weight ribosomal RNA components, designated e, f, and g (apparent chain lengths 240, 195, and 135 nucleotides, respectively), in addition to analogs of eucaryotic 5S (species h) and 5.8S (species i) ribosomal RNAs. In the present study, all of the presumptive ribosomal RNAs were indeed found to be associated with purified C. fasciculata ribosomes, and their localization was investigated in subunits produced under different conditions of ribosome dissociation. When ribosomes were dissociated in a high-potassium (880 mM K+, 12.5 mM Mg2+) medium, species e to i were all found in the large ribosomal subunit, which also contained an additional, transfer RNA-sized component (species j). However, when subunits were prepared in a low-magnesium (60 mM K+, 0.1 mM Mg2+) medium, two of the novel species (e and g) did not remain with the large subunit, but were released, apparently as free RNAs. Control experiments have eliminated the possibility that the small RNAs are generated by quantitative and highly specific (albeit artifactual) ribonuclease cleavage of large ribosomal RNAs during isolation. In terms of RNA composition and dissociation properties, therefore, the ribosome of C. fasciculata is the most "atypical" eucaryotic ribosome yet described. These observations raise interesting questions about the function and evolutionary origin of C. fasciculata ribosomes and about the organization and expression of ribosomal RNA genes in this organism.

Sign in / Sign up

Export Citation Format

Share Document