ABSTRACT
Ribosome biogenesis proceeds along a multifaceted pathway from the nucleolus to the cytoplasm that is extensively coupled to several quality control mechanisms. However, the mode by which 5S ribosomal RNA is incorporated into the developing pre-60S ribosome, which in humans links ribosome biogenesis to cell proliferation by surveillance by factors such as p53-MDM2, is poorly understood. Here, we report nine nucleolar pre-60S cryo-EM structures from Chaetomium thermophilum, one of which clarifies the mechanism of 5S RNP incorporation into the early pre-60S. Successive assembly states then represent how helicases Dbp10 and Spb4, and the Pumilio domain factor Puf6 act in series to surveil the gradual folding of the nearby 25S rRNA domain IV. Finally, the methyltransferase Spb1 methylates a universally conserved guanine nucleotide in the A-loop of the peptidyl transferase center, thereby licensing further maturation. Our findings provide insight into the hierarchical action of helicases in safeguarding rRNA tertiary structure folding and coupling to surveillance mechanisms that culminate in local RNA modification.
Subject(s)
RNA, Ribosomal , Saccharomyces cerevisiae Proteins , Humans , RNA, Ribosomal/genetics , RNA, Ribosomal/metabolism , Ribosomes/genetics , RNA, Ribosomal, 5S/genetics , RNA, Ribosomal, 5S/metabolism , DNA Helicases/metabolism , Protein Binding , Ribosomal Proteins/metabolism , Saccharomyces cerevisiae Proteins/metabolismABSTRACT
Ribonucleases (RNases) play critical roles in RNA metabolism and are collectively essential for cell viability. However, most knowledge about bacterial RNases comes from the studies on Escherichia coli; very little is known about the RNases in plant pathogens. The crucifer black rot pathogen Xanthomonas campestris pv. campestris (Xcc) encodes 15 RNases, but none of them has been functionally characterized. Here, we report the physiological function of the exoribonuclease RNase D in Xcc and provide evidence demonstrating that the Xcc RNase D is involved in 5S rRNA degradation and exopolysaccharide (EPS) production. Our work shows that the growth and virulence of Xcc were not affected by deletion of RNase D but were severely attenuated by RNase D overexpression. However, deletion of RNase D in Xcc resulted in a significant reduction in EPS production. In addition, either deletion or overexpression of RNase D in Xcc did not influence the tRNAs tested, inconsistent with the finding in E. coli that the primary function of RNase D is to participate in tRNA maturation and its overexpression degrades tRNAs. More importantly, deletion, overexpression, and in vitro enzymatic analyses revealed that the Xcc RNase D degrades 5S rRNA but not 16S and 23S rRNAs that share an operon with 5S rRNA. Our results suggest that Xcc employs RNase D to realize specific modulation of the cellular 5S rRNA content after transcription and maturation whenever necessary. The finding expands our knowledge about the function of RNase D in bacteria.
Subject(s)
Xanthomonas campestris , Xanthomonas campestris/metabolism , RNA, Ribosomal, 5S/metabolism , Ribonuclease III/metabolism , Escherichia coli/genetics , Escherichia coli/metabolism , Plant Diseases/microbiology , Bacterial Proteins/genetics , Bacterial Proteins/metabolismABSTRACT
BACKGROUND: Trypanosomes are single-celled eukaryotes that rely heavily on post-transcriptional mechanisms to regulate gene expression. RNA-binding proteins play essential roles in regulating the fate, abundance and translation of messenger RNAs (mRNAs). Among these, zinc finger proteins of the cysteine3histidine (CCCH) class have been shown to be key players in cellular processes as diverse as differentiation, regulation of the cell cycle and translation. ZC3H41 is an essential zinc finger protein that has been described as a component of spliced leader RNA granules and nutritional stress granules, but its role in RNA metabolism is unknown. METHODS: Cell cycle analysis in ZC3H41- and Z41AP-depleted cells was carried out using 4',6-diamidino-2-phenylindole staining, microscopic examination and flow cytometry. The identification of ZC3H41 protein partners was done using tandem affinity purification and mass spectrometry. Next-generation sequencing was used to evaluate the effect of ZC3H41 depletion on the transcriptome of procyclic Trypanosoma brucei cells, and also to identify the cohort of mRNAs associated with the ZC3H41/Z41AP complex. Levels of 5S ribosomal RNA (rRNA) species in ZC3H41- and Z41AP-depleted cells were assessed by quantitative reverse transcription-polymerase chain reaction. Surface sensing of translation assays were used to monitor global translation. RESULTS: We showed that depletion of the zinc finger protein ZC3H41 resulted in marked cell cycle defects and abnormal cell morphologies. ZC3H41 was found associated with an essential protein, which we named Z41AP, forming a stable heterodimer, and also with proteins of the poly(A)-binding protein 1 complex. The identification of mRNAs associated with the ZC3H41/Z41AP complex revealed that it is primarily composed of ribosomal protein mRNAs, and that binding to target transcripts is diminished upon nutritional stress. In addition, we observed that mRNAs encoding several proteins involved in the maturation of 5S rRNA are also associated with the ZC3H41/Z41AP complex. Finally, we showed that depletion of either ZC3H41 or Z41AP led to the accumulation of 5S rRNA precursors and a decrease of protein translation. CONCLUSIONS: We propose that ZC3H41 and Z41AP play important roles in controlling the fate of ribosomal components in response to environmental cues.
Subject(s)
Ribosomal Proteins , Trypanosoma brucei brucei , Humans , RNA, Messenger/genetics , RNA, Messenger/metabolism , Ribosomal Proteins/genetics , RNA, Ribosomal, 5S/metabolism , RNA-Binding Proteins/genetics , RNA-Binding Proteins/metabolism , Trypanosoma brucei brucei/genetics , Trypanosoma brucei brucei/metabolism , Protozoan Proteins/metabolismABSTRACT
Ribosome biogenesis occurs co-transcriptionally and entails rRNA folding, ribosomal protein binding, rRNA processing, and rRNA modification. In most bacteria, the 16S, 23S and 5S rRNAs are co-transcribed, often with one or more tRNAs. Transcription involves a modified RNA polymerase, called the antitermination complex, which forms in response to cis-acting elements (boxB, boxA and boxC) in the nascent pre-rRNA. Sequences flanking the rRNAs are complementary and form long helices known as leader-trailer helices. Here, we employed an orthogonal translation system to interrogate the functional roles of these RNA elements in 30S subunit biogenesis in Escherichia coli. Mutations that disrupt the leader-trailer helix caused complete loss of translation activity, indicating that this helix is absolutely essential for active subunit formation in the cell. Mutations of boxA also reduced translation activity, but by only 2- to 3-fold, suggesting a smaller role for the antitermination complex. Similarly modest drops in activity were seen upon deletion of either or both of two leader helices, termed here hA and hB. Interestingly, subunits formed in the absence of these leader features exhibited defects in translational fidelity. These data suggest that the antitermination complex and precursor RNA elements help to ensure quality control during ribosome biogenesis.
Subject(s)
Escherichia coli Proteins , RNA, Ribosomal , RNA, Ribosomal/metabolism , Ribosomes/metabolism , Escherichia coli/genetics , Escherichia coli/metabolism , Escherichia coli Proteins/metabolism , Ribosomal Proteins/metabolism , Ribosome Subunits, Small/metabolism , RNA, Ribosomal, 5S/metabolism , RNA, Ribosomal, 16S/metabolism , RNA, Ribosomal, 23S/metabolismABSTRACT
5S rRNA is highly transcribed in fish oocytes and this transcription levels can be used to identify the presence of oocytes in the intersex testes of fish exposed to xenoestrogens. Similar to 5S rRNA, tRNAs are transcribed by RNA polymerase III (Pol-III) in eukaryotes, so this study focuses in the analysis of the levels of expression of tRNAs in the gonads (ovaries and testes) of eight teleost species as a possible new oocyte molecular marker. Total RNA extracted from gonads of six commercial teleost species in the Biscay Bay, from the pollution sentinel species thicklip grey mullet (Chelon labrosus) known present intersex testes in response to xenoestrogens in Gernika estuary and from the laboratory model species Danio rerio were analysed through capillary electrophoresis. Bioanalyzer electropherograms were used to quantify the concentrations of tRNAs, 5S and 5.8S rRNA. All studied ovaries expressed significantly higher levels of tRNAs and 5S rRNA than testes. A tRNA to 5.8S rRNA index was calculated which differentiates ovaries from testes, and identifies some intersex testes in between testes and ovaries in mullets. The tRNA/5.8S ratio was highest in ovaries in previtellogenic stage, decreasing towards maturity. Thus, strong oocyte expression of tRNAs is an additional proof of high activity levels of Pol-III during early stages of oocyte development in teleost ovaries. Incidentally, we observed that miRNA concentrations were always higher in testes than ovaries. The indexing approach developed in the present study could have multiple applications in teleost reproduction research and in the development of early molecular markers of intersex condition.
Subject(s)
Disorders of Sex Development , Smegmamorpha , Animals , Male , Female , Ovary/metabolism , Testis/metabolism , RNA, Ribosomal, 5S/genetics , RNA, Ribosomal, 5S/metabolism , RNA, Ribosomal, 5.8S/metabolism , Oocytes/metabolism , Zebrafish/genetics , Zebrafish/metabolism , Disorders of Sex Development/veterinaryABSTRACT
BACKGROUND AND AIMS: Interferon (IFN) signaling is critical to the pathogenesis of alcohol-associated hepatitis (AH), yet the mechanisms for activation of this system are elusive. We hypothesize that host-derived 5S rRNA pseudogene (RNA5SP) transcripts regulate IFN production and modify immunity in AH. APPROACH AND RESULTS: Mining of transcriptomic datasets revealed that in patients with severe alcohol-associated hepatitis (sAH), hepatic expression of genes regulated by IFNs was perturbed and gene sets involved in IFN production were enriched. RNA5SP transcripts were also increased and correlated with expression of type I IFNs. Interestingly, inflammatory mediators upregulated in sAH, but not in other liver diseases, were positively correlated with certain RNA5SP transcripts. Real-time quantitative PCR demonstrated that RNA5SP transcripts were upregulated in peripheral blood mononuclear cells (PBMCs) from patients with sAH. In sAH livers, increased 5S rRNA and reduced nuclear MAF1 (MAF1 homolog, negative regulator of RNA polymerase III) protein suggested a higher activity of RNA polymerase III (Pol III); inhibition of Pol III reduced RNA5SP expression in monocytic THP-1 cells. Expression of several RNA5SP transcript-interacting proteins was downregulated in sAH, potentially unmasking transcripts to immunosensors. Indeed, siRNA knockdown of interacting proteins potentiated the immunostimulatory activity of RNA5SP transcripts. Molecular interaction and cell viability assays demonstrated that RNA5SP transcripts adopted Z-conformation and contributed to ZBP1-mediated caspase-independent cell death. CONCLUSIONS: Increased expression and binding availability of RNA5SP transcripts was associated with hepatic IFN production and inflammation in sAH. These data identify RNA5SP transcripts as a potential target to mitigate inflammation and hepatocellular injury in AH.
Subject(s)
Biosensing Techniques , Hepatitis, Alcoholic , Interferon Type I , Humans , RNA, Ribosomal, 5S/genetics , RNA, Ribosomal, 5S/metabolism , Pseudogenes , RNA Polymerase III/genetics , RNA Polymerase III/metabolism , Leukocytes, Mononuclear , Immunoassay , Inflammation/genetics , Hepatitis, Alcoholic/genetics , Interferon Type I/geneticsABSTRACT
Mitoribosomes of green algae display a great structural divergence from their tracheophyte relatives, with fragmentation of both rRNA and proteins as a defining feature. Here, we report a 2.9 Å resolution structure of the mitoribosome from the alga Polytomella magna harbouring a reduced rRNA split into 13 fragments. We found that the rRNA contains a non-canonical reduced form of the 5S, as well as a permutation of the LSU domain I. The mt-5S rRNA is stabilised by mL40 that is also found in mitoribosomes lacking the 5S, which suggests an evolutionary pathway. Through comparison to other ribosomes with fragmented rRNAs, we observe that the pattern is shared across large evolutionary distances, and between cellular compartments, indicating an evolutionary convergence and supporting the concept of a primordial fragmented ribosome. On the protein level, eleven peripherally associated HEAT-repeat proteins are involved in the binding of 3' rRNA termini, and the structure features a prominent pseudo-trimer of one of them (mL116). Finally, in the exit tunnel, mL128 constricts the tunnel width of the vestibular area, and mL105, a homolog of a membrane targeting component mediates contacts with an inner membrane bound insertase. Together, the structural analysis provides insight into the evolution of the ribosomal machinery in mitochondria.
Subject(s)
Chlorophyta , Mitochondrial Ribosomes , Chlorophyta/metabolism , Mitochondria/metabolism , Mitochondrial Ribosomes/metabolism , RNA, Ribosomal/metabolism , RNA, Ribosomal, 5S/metabolism , Ribosomes/metabolismABSTRACT
The candidate phyla radiation (CPR) is a large bacterial group consisting mainly of uncultured lineages. They have small cells and small genomes, and they often lack ribosomal proteins uL1, bL9, and/or uL30, which are basically ubiquitous in non-CPR bacteria. Here, we comprehensively analyzed the genomic information on CPR bacteria and identified their unique properties. The distribution of protein lengths in CPR bacteria peaks at around 100-150 amino acids, whereas the position of the peak varies in the range of 100-300 amino acids in free-living non-CPR bacteria, and at around 100-200 amino acids in most symbiotic non-CPR bacteria. These results show that the proteins of CPR bacteria are smaller, on average, than those of free-living non-CPR bacteria, like those of symbiotic non-CPR bacteria. We found that ribosomal proteins bL28, uL29, bL32, and bL33 have been lost in CPR bacteria in a taxonomic lineage-specific manner. Moreover, the sequences of approximately half of all ribosomal proteins of CPR differ, in part, from those of non-CPR bacteria, with missing regions or specifically added regions. We also found that several regions in the 16S, 23S, and 5S rRNAs of CPR bacteria are lacking, which presumably caused the total predicted lengths of the three rRNAs of CPR bacteria to be smaller than those of non-CPR bacteria. The regions missing in the CPR ribosomal proteins and rRNAs are located near the surface of the ribosome, and some are close to one another. These observations suggest that ribosomes are smaller in CPR bacteria than those in free-living non-CPR bacteria, with simplified surface structures.
Subject(s)
Bacteria , Ribosomes , Amino Acids/metabolism , Bacteria/metabolism , RNA, Ribosomal, 5S/metabolism , Ribosomal Proteins/genetics , Ribosomal Proteins/metabolism , Ribosomes/genetics , Ribosomes/metabolismABSTRACT
Acinetobacter baumannii is an important pathogen in hospital acquired infections. Although tigecycline currently remains a potent antibiotic for treating infections caused by multidrug resistant A. baumannii (MDRAB) strains, reports of tigecycline resistant isolates have substantially increased. The resistance mechanisms to tigecycline in A. baumannii are far more complicated and diverse than what has been described in the literature so far. Here, we characterize in vitro-selected MDRAB strains obtained by increasing concentrations of tigecycline. We have identiï¬ed mutations in adeS, rrf and rpoB that result in reduced susceptibility to tigecycline. Using in situ complementation experiments, we confirm that mutations in rrf, rpoB, and two types of mutations in adeS correlate with tigecycline resistance. By Western blot and polysome profile analysis, we demonstrate that the rrf mutation results in decreased expression of RRF, which affects the process of ribosome recycling ultimately leading to increased tigecycline tolerance. A transcriptional analysis shows that the mutated rpoB gene plays a role in regulating the expression of the SAM-dependent methyltransferase (trm) and transcriptional regulators, to confer moderate tigecycline resistance. This study provides direct in vitro evidence that mutations in the adeS, rpoB and rrf are associated with tigecycline resistance in A. baumannii.
Subject(s)
Acinetobacter Infections/microbiology , Acinetobacter baumannii/drug effects , Acinetobacter baumannii/genetics , Anti-Bacterial Agents/pharmacology , Bacterial Proteins/genetics , RNA, Ribosomal, 5S/genetics , Tigecycline/pharmacology , Acinetobacter Infections/drug therapy , Acinetobacter baumannii/metabolism , Bacterial Proteins/metabolism , Drug Resistance, Bacterial , Humans , Microbial Sensitivity Tests , Mutation , RNA, Ribosomal, 5S/metabolismABSTRACT
Folding of RNA can produce elaborate tertiary structures, corresponding to their diverse roles in the regulation of biological activities. Direct observation of RNA structures at high resolution in their native form however remains a challenge. The large vestibule and the narrow constriction of a Mycobacterium smegmatis porin A (MspA) suggests a sensing mode called nanopore trapping/translocation, which clearly distinguishes between microRNA, small interfering RNA (siRNA), transfer RNA (tRNA) and 5 S ribosomal RNA (rRNA). To further profit from the acquired event characteristics, a custom machine learning algorithm is developed. Events from measurements with a mixture of RNA analytes can be automatically classified, reporting a general accuracy of ~93.4%. tRNAs, which possess a unique tertiary structure, report a highly distinguishable sensing feature, different from all other RNA types tested in this study. With this strategy, tRNAs from different sources are measured and a high structural conservation across different species is observed in single molecule.
Subject(s)
Mycobacterium smegmatis/metabolism , Nanopores , Porins/metabolism , RNA/metabolism , Machine Learning , MicroRNAs/chemistry , MicroRNAs/genetics , MicroRNAs/metabolism , Molecular Dynamics Simulation , Molecular Weight , Mycobacterium smegmatis/genetics , Nucleic Acid Conformation , Porins/chemistry , Porins/genetics , RNA/chemistry , RNA/genetics , RNA Folding , RNA Transport , RNA, Ribosomal, 5S/chemistry , RNA, Ribosomal, 5S/genetics , RNA, Ribosomal, 5S/metabolism , RNA, Small Interfering/chemistry , RNA, Small Interfering/genetics , RNA, Small Interfering/metabolism , RNA, Transfer/chemistry , RNA, Transfer/genetics , RNA, Transfer/metabolismABSTRACT
Ribonucleases are central players in post-transcriptional regulation, a major level of gene expression regulation in all cells. Here, we characterized the 3'-5' exoribonuclease RNase R from the bacterial pathogen Helicobacter pylori. The 'prototypical' Escherichia coli RNase R displays both exoribonuclease and helicase activities, but whether this latter RNA unwinding function is a general feature of bacterial RNase R had not been addressed. We observed that H. pylori HpRNase R protein does not carry the domains responsible for helicase activity and accordingly the purified protein is unable to degrade in vitro RNA molecules with secondary structures. The lack of RNase R helicase domains is widespread among the Campylobacterota, which include Helicobacter and Campylobacter genera, and this loss occurred gradually during their evolution. An in vivo interaction between HpRNase R and RhpA, the sole DEAD-box RNA helicase of H. pylori was discovered. Purified RhpA facilitates the degradation of double stranded RNA by HpRNase R, showing that this complex is functional. HpRNase R has a minor role in 5S rRNA maturation and few targets in H. pylori, all included in the RhpA regulon. We concluded that during evolution, HpRNase R has co-opted the RhpA helicase to compensate for its lack of helicase activity.
Subject(s)
DEAD-box RNA Helicases/metabolism , Exoribonucleases/metabolism , Helicobacter pylori/enzymology , Amino Acid Motifs , Epsilonproteobacteria/enzymology , Exoribonucleases/chemistry , RNA, Double-Stranded/metabolism , RNA, Ribosomal, 5S/metabolismABSTRACT
All species transcribe ribosomal RNA in an immature form that requires several enzymes for processing into mature rRNA. The number and types of enzymes utilized for these processes vary greatly between different species. In low G + C Gram-positive bacteria including Bacillus subtilis and Geobacillus stearothermophilus, the endoribonuclease (RNase) M5 performs the final step in 5S rRNA maturation, by removing the 3'- and 5'-extensions from precursor (pre) 5S rRNA. This cleavage activity requires initial complex formation between the pre-rRNA and a ribosomal protein, uL18, making the full M5 substrate a ribonucleoprotein particle (RNP). M5 contains a catalytic N-terminal Toprim domain and an RNA-binding C-terminal domain, respectively, shown to assist in processing and binding of the RNP. Here, we present structural data that show how two Mg2+ ions are accommodated in the active site pocket of the catalytic Toprim domain and investigate the importance of these ions for catalysis. We further perform solution studies that support the previously proposed 3'-before-5' order of removal of the pre-5S rRNA extensions and map the corresponding M5 structural rearrangements during catalysis.
Subject(s)
Bacillus subtilis/enzymology , Endoribonucleases/chemistry , Endoribonucleases/metabolism , Geobacillus stearothermophilus/enzymology , Magnesium/metabolism , RNA Precursors/metabolism , RNA, Double-Stranded/metabolism , RNA, Ribosomal, 5S/metabolism , Amino Acid Sequence , Endoribonucleases/genetics , Nucleic Acid Conformation , RNA Precursors/genetics , RNA, Double-Stranded/genetics , RNA, Ribosomal, 5S/genetics , Ribosomes/genetics , Ribosomes/metabolism , Substrate SpecificityABSTRACT
The large ribosomal RNAs of eukaryotes frequently contain expansion sequences that add to the size of the rRNAs but do not affect their overall structural layout and are compatible with major ribosomal function as an mRNA translation machine. The expansion of prokaryotic ribosomal RNAs is much less explored. In order to obtain more insight into the structural variability of these conserved molecules, we herein report the results of a comprehensive search for the expansion sequences in prokaryotic 5S rRNAs. Overall, 89 expanded 5S rRNAs of 15 structural types were identified in 15 archaeal and 36 bacterial genomes. Expansion segments ranging in length from 13 to 109 residues were found to be distributed among 17 insertion sites. The strains harboring the expanded 5S rRNAs belong to the bacterial orders Clostridiales, Halanaerobiales, Thermoanaerobacterales, and Alteromonadales as well as the archael order Halobacterales When several copies of a 5S rRNA gene are present in a genome, the expanded versions may coexist with normal 5S rRNA genes. The insertion sequences are typically capable of forming extended helices, which do not seemingly interfere with folding of the conserved core. The expanded 5S rRNAs have largely been overlooked in 5S rRNA databases.
Subject(s)
Genome, Archaeal , Genome, Bacterial , RNA, Archaeal/genetics , RNA, Bacterial/genetics , RNA, Ribosomal, 5S/genetics , Alteromonadaceae/classification , Alteromonadaceae/genetics , Alteromonadaceae/metabolism , Base Pairing , Base Sequence , Clostridiales/classification , Clostridiales/genetics , Clostridiales/metabolism , Firmicutes/classification , Firmicutes/genetics , Firmicutes/metabolism , Halobacteriales/classification , Halobacteriales/genetics , Halobacteriales/metabolism , Nucleic Acid Conformation , Phylogeny , RNA, Archaeal/chemistry , RNA, Archaeal/metabolism , RNA, Bacterial/chemistry , RNA, Bacterial/metabolism , RNA, Ribosomal, 5S/chemistry , RNA, Ribosomal, 5S/metabolism , Thermoanaerobacterium/classification , Thermoanaerobacterium/genetics , Thermoanaerobacterium/metabolismABSTRACT
Production and expression of RNA requires the action of multiple RNA-binding proteins (RBPs). New RBPs are most often created by novel combinations of dedicated RNA-binding modules. However, recruiting existing genes to create new RBPs is also an important evolutionary strategy. In this report, we analyzed the eight-member uL18 ribosomal protein family in Arabidopsis uL18 proteins share a short structurally conserved domain that binds the 5S ribosomal RNA (rRNA) and allows its incorporation into ribosomes. Our results indicate that Arabidopsis uL18-Like proteins are targeted to either mitochondria or chloroplasts. While two members of the family are found in organelle ribosomes, we show here that two uL18-type proteins function as factors necessary for the splicing of certain mitochondrial and plastid group II introns. These two proteins do not cosediment with mitochondrial or plastid ribosomes but instead associate with the introns whose splicing they promote. Our study thus reveals that the RNA-binding capacity of uL18 ribosomal proteins has been repurposed to create factors that facilitate the splicing of organellar introns.
Subject(s)
Arabidopsis Proteins/metabolism , Arabidopsis/genetics , Chloroplasts/metabolism , Mitochondria/metabolism , RNA Splicing , Ribosomal Proteins/metabolism , Arabidopsis/metabolism , Arabidopsis Proteins/genetics , Introns/genetics , Mutation , Plants, Genetically Modified , RNA, Ribosomal, 5S/metabolism , Ribosomal Proteins/geneticsABSTRACT
Dynamic protein maturation, such as localization, folding, and complex formation, can occur co-translationally. To what extent do nascent polypeptides engage in the co-translational dynamics to produce the functional proteome's complement? We address this question using a protein-dynamics reporter (DR) module comprising a force-sensitive arrest sequence (Bacillus subtilis MifM) followed in frame by LacZ. An engineered transposon, TnDR, carrying DR, is transposed into the B. subtilis chromosome to create translational fusions between N-terminal regions of proteins and the C-terminal DR module. By looking for LacZ+ colonies, we identify hundreds of proteins that cancel the elongation arrest, most probably reflecting their ability to initiate the maturation/localization process co-translationally. Case studies identify B. subtilis proteins that initiate assembly with a partner molecule before completion of translation. These results suggest that co-translational maturation is a frequently occurring event in protein biogenesis.
Subject(s)
Bacillus subtilis/metabolism , Bacterial Proteins/metabolism , DNA Transposable Elements/genetics , Genes, Reporter , Protein Biosynthesis , Proteome/metabolism , Cytosol/metabolism , Genetic Testing , Protein Transport , RNA, Ribosomal, 5S/metabolismABSTRACT
Recently, mutations in the RNA polymerase III subunit A (POLR3A) have been described as the cause of the neonatal progeria or Wiedemann-Rautenstrauch syndrome (WRS). POLR3A has important roles in transcription regulation of small RNAs, including tRNA, 5S rRNA, and 7SK rRNA. We aim to describe the cellular and molecular features of WRS fibroblasts. Cultures of primary fibroblasts from one WRS patient [monoallelic POLR3A variant c.3772_3773delCT (p.Leu1258Glyfs*12)] and one control patient were cultured in vitro. The mutation caused a decrease in the expression of wildtype POLR3A mRNA and POLR3A protein and a sharp increase in mutant protein expression. In addition, there was an increase in the nuclear localization of the mutant protein. These changes were associated with an increase in the number and area of nucleoli and to a high increase in the expression of pP53 and pH2AX. All these changes were associated with premature senescence. The present observations add to our understanding of the differences between Hutchinson-Gilford progeria syndrome and WRS and opens new alternatives to study cell senesce and human aging.
Subject(s)
Fetal Growth Retardation , Fibroblasts , Progeria , RNA Polymerase III , Tumor Suppressor Protein p53/metabolism , Cell Nucleolus/physiology , Cells, Cultured , Cellular Senescence/physiology , DNA Damage , Fetal Growth Retardation/genetics , Fetal Growth Retardation/pathology , Fibroblasts/physiology , Fibroblasts/ultrastructure , Gene Expression , Humans , Mutation , Progeria/genetics , Progeria/pathology , RNA Polymerase III/genetics , RNA Polymerase III/metabolism , RNA, Ribosomal, 5S/metabolismABSTRACT
Ribosome biogenesis is an elaborate and energetically expensive program that involve two hundred protein factors in eukaryotes. Nuclear export of pre-ribosomal particles is one central step which also serves as an internal structural checkpoint to ensure the proper completion of nuclear assembly events. Here we present four structures of human pre-60S particles isolated through a nuclear export factor NMD3, representing assembly stages immediately before and after nuclear export. These structures reveal locations of a dozen of human factors, including an uncharacterized factor TMA16 localized between the 5S RNA and the P0 stalk. Comparison of these structures shows a progressive maturation for the functional regions, such as peptidyl transferase centre and peptide exit tunnel, and illustrate a sequence of factor-assisted rRNA maturation events. These data facilitate our understanding of the global conservation of ribosome assembly in eukaryotes and species-specific features of human assembly factors.
Subject(s)
Cell Nucleus/metabolism , Models, Molecular , RNA, Ribosomal, 5S/ultrastructure , Ribosomal Proteins/ultrastructure , Ribosome Subunits, Large, Eukaryotic/metabolism , Cryoelectron Microscopy , Humans , RNA, Ribosomal, 5S/isolation & purification , RNA, Ribosomal, 5S/metabolism , RNA-Binding Proteins/isolation & purification , RNA-Binding Proteins/metabolism , RNA-Binding Proteins/ultrastructure , Ribosomal Proteins/isolation & purification , Ribosomal Proteins/metabolism , Ribosome Subunits, Large, Eukaryotic/ultrastructureABSTRACT
5S rRNA is an indispensable component of cytoplasmic ribosomes in all species. The functions of 5S rRNA and the reasons for its evolutionary preservation as an independent molecule remain unclear. Here we used ribosome engineering to investigate whether 5S rRNA autonomy is critical for ribosome function and cell survival. By linking circularly permutated 5S rRNA with 23S rRNA we generated a bacterial strain devoid of free 5S rRNA. Viability of the engineered cells demonstrates that autonomous 5S rRNA is dispensable for cell growth under standard conditions and is unlikely to have essential functions outside the ribosome. The fully assembled ribosomes carrying 23S-5S rRNA are highly active in translation. However, the engineered cells accumulate aberrant 50S subunits unable to form stable 70S ribosomes. Cryo-EM analysis revealed a malformed peptidyl transferase center in the misassembled 50S subunits. Our results argue that the autonomy of 5S rRNA is preserved due to its role in ribosome biogenesis.
Subject(s)
RNA, Ribosomal, 5S/metabolism , Ribosomes/metabolism , Catalytic Domain , Cryoelectron Microscopy , DNA-Binding Proteins/metabolism , Escherichia coli/metabolism , Escherichia coli Proteins/metabolism , Gene Expression Regulation , Genetic Engineering , Mutation , Nucleic Acid Conformation , Peptidyl Transferases/metabolism , RNA, Bacterial , RNA, Ribosomal, 23S/metabolism , Rec A Recombinases/metabolism , Ribosomal Proteins/metabolism , Ribosome Subunits, Large, Bacterial/metabolismABSTRACT
Bacterial ribosomal RNAs (rRNAs) are transcribed as precursors and require processing by Ribonucleases (RNases) to generate mature and functional rRNAs. Although the initial steps of rRNA processing in Escherichia coli (E. coli) were described several decades ago, the enzymes responsible for the final steps of 5S and 23S rRNA 5'-end maturation have remained unknown. Here, I show that RNase AM, a recently identified 5' to 3' exonuclease, performs the last step of 5S rRNA 5'-end maturation. RNase AM was also found to generate the mature 5' end of 23S rRNA, subsequent to a newly identified prior processing step. Additionally, RNase AM was found to mature the 5' end of 16S rRNA, a reaction previously attributed to RNase G. These findings indicate a major role for RNase AM in cellular RNA metabolism and establish a biological role for the first 5' to 3' RNA exonuclease identified in E. coli.
Subject(s)
Escherichia coli Proteins/metabolism , Escherichia coli/enzymology , Exoribonucleases/metabolism , RNA Processing, Post-Transcriptional , RNA, Ribosomal, 16S/metabolism , RNA, Ribosomal, 23S/metabolism , RNA, Ribosomal, 5S/metabolism , Escherichia coli/geneticsABSTRACT
Ribosome biogenesis is the fine-tuned, essential process that generates mature ribosomal subunits and ultimately enables all protein synthesis within a cell. Novel regulators of ribosome biogenesis continue to be discovered in higher eukaryotes. While many known regulatory factors are proteins or small nucleolar ribonucleoproteins, microRNAs (miRNAs), and long non-coding RNAs (lncRNAs) are emerging as a novel modulatory layer controlling ribosome production. Here, we summarize work uncovering non-coding RNAs (ncRNAs) as novel regulators of ribosome biogenesis and highlight their links to diseases of defective ribosome biogenesis. It is still unclear how many miRNAs or lncRNAs are involved in phenotypic or pathological disease outcomes caused by impaired ribosome production, as in the ribosomopathies, or by increased ribosome production, as in cancer. In time, we hypothesize that many more ncRNA regulators of ribosome biogenesis will be discovered, which will be followed by an effort to establish connections between disease pathologies and the molecular mechanisms of this additional layer of ribosome biogenesis control.