scholarly journals RsmG forms stable complexes with premature small subunit rRNA during bacterial ribosome biogenesis

RSC Advances ◽  
2020 ◽  
Vol 10 (38) ◽  
pp. 22361-22369
Author(s):  
Sudeshi M. Abedeera ◽  
Caitlin M. Hawkins ◽  
Sanjaya C. Abeysirigunawardena
Keyword(s):  
16S Rrna ◽  
Ribosomal Proteins ◽  
Ribosome Biogenesis ◽  
Small Subunit ◽  
Small Subunit Rrna ◽  
Bacterial Ribosome ◽  
The Stability

RsmG is the methyltransferase responsible for the N7 methylation of G527 of 16S rRNA. Here we show that RsmG binds preferably to premature bacterial small subunit rRNA. The presence of ribosomal proteins also influences the stability of RsmG–rRNA complexes.

scholarly journals Release of the ribosome biogenesis factor Bud23 from small subunit precursors in yeast

RNA ◽  
2021 ◽  
pp. rna.079025.121
Author(s):  
Joshua J Black ◽  
Arlen W Johnson
Keyword(s):  
Binding Site ◽  
Ribosomal Proteins ◽  
Ribosome Biogenesis ◽  
Assembly Line ◽  
Small Subunit ◽  
Nucleotide Hydrolysis ◽  
Ribonucleoprotein Complexes ◽  
Intermediate States ◽  
Ssu Processome

Ribosomes are the universally conserved ribonucleoprotein complexes that synthesize proteins. The two subunits of the eukaryotic ribosome are produced through a quasi-independent assembly-line-like pathway involving the hierarchical actions of numerous trans-acting biogenesis factors and the incorporation of ribosomal proteins. The factors work together to shape the nascent subunits through a series of intermediate states into their functional architectures. The earliest intermediate of the small subunit (SSU or 40S) is the SSU Processome which is subsequently transformed into the pre-40S intermediate. This transformation is, in part, facilitated by the binding of the methyltransferase Bud23. How Bud23 is released from the resultant pre-40S is not known. The ribosomal proteins Rps0, Rps2, and Rps21, termed the Rps0-cluster proteins, and several biogenesis factors are known to bind the pre-40S around the time that Bud23 is released, suggesting that one or more of these factors induce Bud23 release. Here, we systematically examined the requirement of these factors for the release of Bud23 from pre-40S particles. We found that the Rps0-cluster proteins are needed but not sufficient for Bud23 release. The atypical kinase/ATPase Rio2 shares a binding site with Bud23 and is thought to be recruited to pre-40S after the Rps0-cluster proteins. Depletion of Rio2 prevented the release of Bud23 from the pre-40S. More importantly, the addition of recombinant Rio2 to pre-40S particles affinity-purified from Rio2-depleted cells was sufficient for Bud23 release in vitro. The ability of Rio2 to displace Bud23 was independent of nucleotide hydrolysis. We propose a novel role for Rio2 in which its binding to the pre-40S actively displaces Bud23 from the pre-40S, and we suggest a model in which the binding of the Rps0-cluster proteins and Rio2 promote the release of Bud23.

Requirements for the nuclear export of the small ribosomal subunit

2002 ◽  
Vol 115 (14) ◽  
pp. 2985-2995 ◽  
Author(s):  
Terence I. Moy ◽  
Pamela A. Silver
Keyword(s):  
Nuclear Export ◽  
Ribosome Biogenesis ◽  
Large Scale ◽  
Ribosomal Subunit ◽  
Small Subunit ◽  
Temperature Sensitive ◽  
Yeast Saccharomyces Cerevisiae ◽  
Small Ribosomal Subunit ◽  
Factors Affecting ◽  
The Stability

Eukaryotic ribosome biogenesis requires multiple steps of nuclear transport because ribosomes are assembled in the nucleus while protein synthesis occurs in the cytoplasm. Using an in situ RNA localization assay in the yeast Saccharomyces cerevisiae, we determined that efficient nuclear export of the small ribosomal subunit requires Yrb2, a factor involved in Crm1-mediated export. Furthermore, in cells lacking YRB2, the stability and abundance of the small ribosomal subunit is decreased in comparison with the large ribosomal subunit. To identify additional factors affecting small subunit export, we performed a large-scale screen of temperature-sensitive mutants. We isolated new alleles of several nucleoporins and Ran-GTPase regulators. Together with further analysis of existing mutants,we show that nucleoporins previously shown to be defective in ribosomal assembly are also defective in export of the small ribosomal subunit.

scholarly journals An evolutionarily conserved element in initiator tRNAs prompts ultimate steps in ribosome maturation

2016 ◽  
Vol 113 (41) ◽  
pp. E6126-E6134 ◽  
Author(s):  
Sunil Shetty ◽  
Umesh Varshney
Keyword(s):  
Escherichia Coli ◽  
16S Rrna ◽  
Ribosomal Proteins ◽  
Ribosome Biogenesis ◽  
Complex Function ◽  
Cold Sensitivity ◽  
Base Pairs ◽  
Initiation Complex ◽  
Evolutionarily Conserved ◽  
Multistep Process

Ribosome biogenesis, a complex multistep process, results in correct folding of rRNAs, incorporation of >50 ribosomal proteins, and their maturation. Deficiencies in ribosome biogenesis may result in varied faults in translation of mRNAs causing cellular toxicities and ribosomopathies in higher organisms. How cells ensure quality control in ribosome biogenesis for the fidelity of its complex function remains unclear. Using Escherichia coli, we show that initiator tRNA (i-tRNA), specifically the evolutionarily conserved three consecutive GC base pairs in its anticodon stem, play a crucial role in ribosome maturation. Deficiencies in cellular contents of i-tRNA confer cold sensitivity and result in accumulation of ribosomes with immature 3′ and 5′ ends of the 16S rRNA. Overexpression of i-tRNA in various strains rescues biogenesis defects. Participation of i-tRNA in the first round of initiation complex formation licenses the final steps of ribosome maturation by signaling RNases to trim the terminal extensions of immature 16S rRNA.

scholarly journals Succession of Microbial Communities during Hot Composting as Detected by PCR–Single-Strand-Conformation Polymorphism-Based Genetic Profiles of Small-Subunit rRNA Genes

2000 ◽  
Vol 66 (3) ◽  
pp. 930-936 ◽  
Author(s):  
Sabine Peters ◽  
Stefanie Koschinsky ◽  
Frank Schwieger ◽  
Christoph C. Tebbe
Keyword(s):  
16S Rrna ◽  
18S Rrna ◽  
Single Strand Conformation Polymorphism ◽  
Small Subunit ◽  
Ssu Rdna ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Small Subunit Rrna ◽  
Genetic Profiles ◽  
Conformation Polymorphism

ABSTRACT A cultivation-independent technique for genetic profiling of PCR-amplified small-subunit rRNA genes (SSU rDNA) was chosen to characterize the diversity and succession of microbial communities during composting of an organic agricultural substrate. PCR amplifications were performed with DNA directly extracted from compost samples and with primers targeting either (i) the V4–V5 region of eubacterial 16S rRNA genes, (ii) the V3 region in the 16S rRNA genes of actinomycetes, or (iii) the V8–V9 region of fungal 18S rRNA genes. Homologous PCR products were converted to single-stranded DNA molecules by exonuclease digestion and were subsequently electrophoretically separated by their single-strand-conformation polymorphism (SSCP). Genetic profiles obtained by this technique showed a succession and increasing diversity of microbial populations with all primers. A total of 19 single products were isolated from the profiles by PCR reamplification and cloning. DNA sequencing of these molecular isolates showed similarities in the range of 92.3 to 100% to known gram-positive bacteria with a low or high G+C DNA content and to the SSU rDNA of γ-Proteobacteria. The amplified 18S rRNA gene sequences were related to the respective gene regions of Candida krusei and Candida tropicalis. Specific molecular isolates could be attributed to different composting stages. The diversity of cultivated bacteria isolated from samples taken at the end of the composting process was low. A total of 290 isolates were related to only 6 different species. Two or three of these species were also detectable in the SSCP community profiles. Our study indicates that community SSCP profiles can be highly useful for the monitoring of bacterial diversity and community successions in a biotechnologically relevant process.

scholarly journals Shape changes and cooperativity in the folding of the central domain of the 16S ribosomal RNA

2021 ◽  
Vol 118 (10) ◽  
pp. e2020837118
Author(s):  
Naoto Hori ◽  
Natalia A. Denesyuk ◽  
D. Thirumalai
Keyword(s):  
16S Rrna ◽  
Ribosomal Proteins ◽  
Quantitative Description ◽  
Small Subunit ◽  
Coarse Grained ◽  
Radius Of Gyration ◽  
Central Domain ◽  
Induced Folding ◽  
Starting Point ◽  
Hydroxyl Radical Footprinting

Both the small and large subunits of the ribosome, the molecular machine that synthesizes proteins, are complexes of ribosomal RNAs (rRNAs) and a number of proteins. In bacteria, the small subunit has a single 16S rRNA whose folding is the first step in its assembly. The central domain of the 16S rRNA folds independently, driven either by Mg2+ ions or by interaction with ribosomal proteins. To provide a quantitative description of ion-induced folding of the ∼350-nucleotide rRNA, we carried out extensive coarse-grained molecular simulations spanning Mg2+ concentration between 0 and 30 mM. The Mg2+ dependence of the radius of gyration shows that globally the rRNA folds cooperatively. Surprisingly, various structural elements order at different Mg2+ concentrations, indicative of the heterogeneous assembly even within a single domain of the rRNA. Binding of Mg2+ ions is highly specific, with successive ion condensation resulting in nucleation of tertiary structures. We also predict the Mg2+-dependent protection factors, measurable in hydroxyl radical footprinting experiments, which corroborate the specificity of Mg2+-induced folding. The simulations, which agree quantitatively with several experiments on the folding of a three-way junction, show that its folding is preceded by formation of other tertiary contacts in the central junction. Our work provides a starting point in simulating the early events in the assembly of the small subunit of the ribosome.

scholarly journals Ribosome biogenesis factor Ltv1 chaperones the assembly of the small subunit head

2018 ◽  
Vol 217 (12) ◽  
pp. 4141-4154 ◽  
Author(s):  
Jason C. Collins ◽  
Homa Ghalei ◽  
Joanne R. Doherty ◽  
Haina Huang ◽  
Rebecca N. Culver ◽  
...  
Keyword(s):  
Cancer Cells ◽  
Ribosomal Proteins ◽  
Ribosome Biogenesis ◽  
Breast Cancer Cells ◽  
Ribosomal Subunit ◽  
Small Subunit ◽  
Yeast Genetics ◽  
Structure Probing ◽  
Rna Quality Control ◽  
Assembly Factor

The correct assembly of ribosomes from ribosomal RNAs (rRNAs) and ribosomal proteins (RPs) is critical, as indicated by the diseases caused by RP haploinsufficiency and loss of RP stoichiometry in cancer cells. Nevertheless, how assembly of each RP is ensured remains poorly understood. We use yeast genetics, biochemistry, and structure probing to show that the assembly factor Ltv1 facilitates the incorporation of Rps3, Rps10, and Asc1/RACK1 into the small ribosomal subunit head. Ribosomes from Ltv1-deficient yeast have substoichiometric amounts of Rps10 and Asc1 and show defects in translational fidelity and ribosome-mediated RNA quality control. These defects provide a growth advantage under some conditions but sensitize the cells to oxidative stress. Intriguingly, relative to glioma cell lines, breast cancer cells have reduced levels of LTV1 and produce ribosomes lacking RPS3, RPS10, and RACK1. These data describe a mechanism to ensure RP assembly and demonstrate how cancer cells circumvent this mechanism to generate diverse ribosome populations that can promote survival under stress.

scholarly journals Release of the ribosome biogenesis factor Bud23 from small subunit precursors in yeast

2021 ◽  
Author(s):  
Joshua J Black ◽  
Arlen W Johnson
Keyword(s):  
Binding Site ◽  
Ribosomal Proteins ◽  
Ribosome Biogenesis ◽  
Assembly Line ◽  
Small Subunit ◽  
Nucleotide Hydrolysis ◽  
Ribonucleoprotein Complexes ◽  
Intermediate States ◽  
Ssu Processome

Ribosomes are the universally conserved ribonucleoprotein complexes that synthesize proteins. The two subunits of the eukaryotic ribosome are produced through a quasi-independent assembly-line-like pathway involving the hierarchical actions of numerous trans-acting biogenesis factors and the incorporation of ribosomal proteins. The factors work together to shape the nascent subunits through a series of intermediate states into their functional architectures. The earliest intermediate of the small subunit (SSU or 40S) is the SSU Processome which is subsequently transformed into the pre-40S intermediate. This transformation is, in part, facilitated by the binding of the methyltransferase Bud23. How Bud23 is released from the resultant pre-40S is not known. The ribosomal proteins Rps0, Rps2, and Rps21, termed the Rps0-cluster proteins, and several biogenesis factors are known to bind the pre-40S around the time that Bud23 is released, suggesting that one or more of these factors induce Bud23 release. Here, we systematically examined the requirement of these factors for the release of Bud23 from pre-40S particles. We found that the Rps0-cluster proteins are needed but not sufficient for Bud23 release. The atypical kinase/ATPase Rio2 shares a binding site with Bud23 and is thought to be recruited to pre-40S after the Rps0-cluster proteins. Depletion of Rio2 prevented the release of Bud23 from the pre-40S. More importantly, the addition of recombinant Rio2 to pre-40S particles affinity-purified from Rio2-depleted cells was sufficient for Bud23 release in vitro. The ability of Rio2 to displace Bud23 was independent of nucleotide hydrolysis. We propose a novel role for Rio2 in which its binding to the pre-40S actively displaces Bud23 from the pre-40S, and we suggest a model in which the binding of the Rps0-cluster proteins and Rio2 promote the release of Bud23.

scholarly journals In Situ Accessibility of Small-Subunit rRNA of Members of the Domains Bacteria, Archaea, and Eucarya to Cy3-Labeled Oligonucleotide Probes

2003 ◽  
Vol 69 (3) ◽  
pp. 1748-1758 ◽  
Author(s):  
Sebastian Behrens ◽  
Caroline Rühland ◽  
João Inácio ◽  
Harald Huber ◽  
Á. Fonseca ◽  
...  
Keyword(s):  
16S Rrna ◽  
18S Rrna ◽  
Small Subunit ◽  
Oligonucleotide Probes ◽  
Consensus Model ◽  
Class Iii ◽  
Small Subunit Rrna ◽  
Data Set ◽  
Secondary Structure Models

ABSTRACT Low accessibility of the rRNA is together with cell wall impermeability and low cellular ribosome content a frequent reason for failure of whole-cell fluorescence hybridization with fluorescently labeled oligonucleotide probes. In this study we compare accessibility data for the 16S rRNA of Escherichia coli (gamma Proteobacteria, Bacteria) with the phylogenetically distantly related organisms Pirellula sp. strain 1 (Planctomycetes, Bacteria) and Metallosphaera sedula (Crenarchaeota, Archaea) and the 18S rRNA accessibility of Saccharomyces cerevisiae (Eucarya). For a total of 537 Cy3-labeled probes, the signal intensities of hybridized cells were quantified under standardized conditions by flow cytometry. The relative probe-conferred fluorescence intensities are shown on color-coded small-subunit rRNA secondary-structure models. For Pirellula sp., most of the probes belong to class II and III (72% of the whole data set), whereas most of the probes targeting sites on M. sedula were grouped into class V and VI (46% of the whole data set). For E. coli, 45% of all probes of the data set belong to class III and IV. A consensus model for the accessibility of the small-subunit rRNA to oligonucleotide probes is proposed which uses 60 homolog target sites of the three prokaryotic 16S rRNA molecules. In general, open regions were localized around helices 13 and 14 including target positions 285 to 338, whereas helix 22 (positions 585 to 656) and the 3′ half of helix 47 (positions 1320 to 1345) were generally inaccessible. Finally, the 16S rRNA consensus model was compared to data on the in situ accessibility of the 18S rRNA of S. cerevisiae.

scholarly journals The hierarchical system of the ‘Alphaproteobacteria’: description of Hyphomonadaceae fam. nov., Xanthobacteraceae fam. nov. and Erythrobacteraceae fam. nov.

2005 ◽  
Vol 55 (5) ◽  
pp. 1907-1919 ◽  
Author(s):  
Kyung-Bum Lee ◽  
Chi-Te Liu ◽  
Yojiro Anzai ◽  
Hongik Kim ◽  
Toshihiro Aono ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Tree ◽  
Small Subunit ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Likelihood Analysis ◽  
The 16S Rrna Gene

Phylogenetic analysis of the class ‘Alphaproteobacteria’, including physiologically diverse species, was conducted by using small-subunit rRNA gene sequences. The 16S rRNA gene sequences of 261 species in the class ‘Alphaproteobacteria’ were obtained from GenBank/EMBL/DDBJ for constructing a phylogenetic tree by using maximum-likelihood analysis. In the resulting tree, members of the class ‘Alphaproteobacteria’ were subdivided into five major clusters, which were compared with the taxonomic outline of Bergey's Manual of Systematic Biology and the arb tree. Based on this phylogenetic tree, three novel families are proposed: Hyphomonadaceae fam. nov. to accommodate the bacterial genera Hyphomonas, Hirschia, Maricaulis and Oceanicaulis, Xanthobacteraceae fam. nov. to include the genera Xanthobacter, Azorhizobium, Ancylobacter, Labrys and Starkeya, and Erythrobacteraceae fam. nov. to accommodate the genera Erythrobacter, Porphyrobacter and Erythromicrobium. The phylogenetic tree of 16S rRNA gene sequences established in this study may provide a sound basis for future taxonomic reconstruction of the class ‘Alphaproteobacteria’.

scholarly journals Interaction of Hsp90 with Ribosomal Proteins Protects from Ubiquitination and Proteasome-dependent Degradation

2006 ◽  
Vol 17 (2) ◽  
pp. 824-833 ◽  
Author(s):  
Tae-Sung Kim ◽  
Chang-Young Jang ◽  
Hag Dong Kim ◽  
Jae Yung Lee ◽  
Byung-Yoon Ahn ◽  
...  
Keyword(s):  
Ribosomal Protein ◽  
Molecular Chaperone ◽  
Ribosomal Proteins ◽  
Heat Shock Protein 90 ◽  
Small Subunit ◽  
Hsp90 Inhibitors ◽  
Ribosomal Protein S6 ◽  
Hsp90 Activity ◽  
Ribosomal Protein S3 ◽  
The Stability

Heat-shock protein 90 (Hsp90) is a molecular chaperone that plays a key role in the conformational maturation of various transcription factors and protein kinases in signal transduction. Multifunctional ribosomal protein S3 (rpS3), a component of the ribosomal small subunit, is involved in DNA repair and apoptosis. Our data show that Hsp90 binds directly to rpS3 and the functional consequence of Hsp90-rpS3 interaction results in the prevention of the ubiquitination and the proteasome-dependent degradation of rpS3, subsequently retaining the function and the biogenesis of the ribosome. Interference of Hsp90 activity by Hsp90 inhibitors appears to dissociate rpS3 from Hsp90, associate the protein with Hsp70, and induce the degradation of free forms of rpS3. Furthermore, ribosomal protein S6 (rpS6) also interacted with Hsp90 and exhibited a similar effect upon treatment with Hsp90 inhibitors. Therefore, we conclude that Hsp90 regulates the function of ribosomes by maintaining the stability of 40S ribosomal proteins such as rpS3 and rpS6.

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