Ribosomal translocation: one step closer to the molecular mechanism

Dysregulated ribosome quality control in human diseases

Precise regulation of mRNA translation is of fundamental importance for maintaining homeostasis. Conversely, dysregulated general or transcript-specific translation, as well as abnormal translation events, have been linked to a multitude of diseases. However, driven by the misconception that the transient nature of mRNAs renders their abnormalities inconsequential, the importance of mechanisms that monitor the quality and fidelity of the translation process has been largely overlooked. In recent years, there has been a dramatic shift in this paradigm, evidenced by several seminal discoveries on the role of a key mechanism in monitoring the quality of mRNA translation - namely, Ribosome Quality Control (RQC) - in the maintenance of homeostasis and the prevention of diseases. Here, we will review recent advances in the field and emphasize the biological significance of the RQC mechanism, particularly its implications in human diseases.

On the response of elongating ribosomes to forces opposing translocation

The elongation phase of protein synthesis is a cyclic, steady-state process. It follows that its directionality is determined by the thermodynamics of the accompanying chemical reactions, which strongly favor elongation. Its irreversibility is guaranteed by its coupling to those reactions, rather being a consequence of any of the conformational changes that occur as it unfolds. It also follows that, in general, the rate of elongation is not proportional to the forward rate constants of any of its steps, including its final, mechano-chemical step, translocation. Instead, the reciprocal of the rate of elongation should be linearly related to the reciprocal of those rate constants. When the results of experiments done a decade ago to measure the effect that forces opposing translocation have on the rate of elongation are reinterpreted in light of these findings, it becomes clear that translocation was rate limiting under conditions in which those experiments were done, and that it is likely to be a Brownian ratchet process, as was concluded earlier.

Eukaryotic ribosome display for antibody discovery: A review

Monoclonal antibody biologics have significantly transformed the therapeutic landscape within the biopharmaceutical industry, partly due to the utilisation of discovery technologies such as the hybridoma method and phage display. While these established platforms have streamlined the development process to date, their reliance on cell transformation for antibody identification faces limitations related to library diversification and the constraints of host cell physiology. Cell-free systems like ribosome display offer a complementary approach, enabling antibody selection in a completely in vitro setting while harnessing enriched cellular molecular machinery. This review aims to provide an overview of the fundamental principles underlying the ribosome display method and its potential for advancing antibody discovery and development.

How biological codes break causal chains to enable autonomy for organisms

Autonomy, meaning freedom from exogenous control, requires independence of both constitution and cybernetic regulation. Here, the necessity of biological codes to achieve both is explained, assuming that Aristotelian efficient cause is 'formal cause empowered by physical force'. Constitutive independence requires closure to efficient causation (in the Rosen sense); cybernetic independence requires transformation of cause-effect into signal-response relations at the organism boundary; the combination of both kinds of independence enables adaptation and evolution. Codes and cyphers translate information from one form of physical embodiment (domain) to another. Because information can only contribute as formal cause to efficient cause within the domain of its embodiment, translation can extend or restrict the range over which information is effective. Closure to efficient causation requires internalised information to be isolated from the cycle of efficient causes that it informs: e.g. Von Neumann self-replicator requires a (template) source of information that is causally isolated from the physical replication system. Life operationalises this isolation with the genetic code translating from the (isolated) domain of codons to that of protein interactions. Separately, cybernetic freedom is achieved at the cell boundary because transducers, which embody molecular coding, translate exogenous information into a domain where it no longer has the power of efficient cause. Information, not efficient cause, passes through the boundary to serve as stimulus for an internally generated response. Coding further extends freedom by enabling historically accumulated information to be selectively transformed into efficient cause under internal control, leaving it otherwise stored inactive. Code-based translation thus enables selective causal isolation, controlling the flow from cause to effect. Genetic code, cell-signalling codes and, in eukaryotes, the histone code, signal sequence based protein sorting and other code-dependent processes all regulate and separate causal chains. The existence of life can be seen as an expression of the power of molecular codes to selectively isolate and thereby organise causal relations among molecular interactions to form an organism.

Efficient fluorescent recognition of ATP/GTP by a water-soluble bisquinolinium pyridine-2,6-dicarboxamide compound. Crystal structures, spectroscopic studies and interaction mode with DNA

The new dicationic pyridine-2,6-dicarboxamide-based compound 1 bearing two N-alkylquinolinium units was synthesized, structurally determined by single-crystal X-ray diffraction, and studied in-depth as a fluorescent receptor for nucleotides and inorganic phosphorylated anions in pure water. The addition of nucleotides to 1 at pH = 7.0 quenches its blue emission with a selective affinity towards adenosine 5'-triphosphate (ATP) and guanosine 5'-tripohosphate (GTP) over other nucleotides such CTP, UTP, ADP, AMP, dicarboxylates and inorganic anions. On the basis of the spectroscopic tools (1H, 31P NMR, UV-vis, fluorescence), MS measurements and DFT calculations, receptor 1 binds ATP with high affinity (log K = 5.04) through the simultaneous formation of strong hydrogen bonds and π-π interactions between the adenosine fragment and quinolinium ring with binding energy calculated in 8.7 kcal mol-1. High affinity for ATP/GTP is attributed to the high acidity of amides and preorganized rigid structure of 1. Receptor 1 is an order of magnitude more selective for ATP than GTP. An efficient photoinduced electron transfer quenching mechanism with simultaneous receptor-ATP complexation in both the excited and ground states is proposed. Additionally, multiple spectroscopic studies and molecular dynamics simulations showed that 1 can intercalate into DNA base pairs.

Assessment of Intracellular GTP Levels Using Genetically Encoded Fluorescent Sensors

Changes in intracellular GTP levels, even incremental ones, profoundly affect the activity of several GTP-binding proteins ultimately resulting in alteration of several basal cellular phenotypes including cell motility, invasion, and tumorigenesis. However, until recently, no tools were available for GTP quantification in live cells. Therefore, in the current chapter, we describe the methodology for the quantitative assessment of spatiotemporal changes in GTP levels in the cells using genetically encoded fluorescent ratiometric GTP sensors termed GEVALs for GTP evaluators.

COVID-19: Mechanisms of the Antiviral Activities of Selective Antibiotics Targeting the Human 80S Ribosome

Background:

The majority of scientists, physicians, and healthcare professionals were trained with the paradigm: “antibiotics are for bacteria only !”, because they misunderstood the definition of the ribosome targeting antibiotics. In the context of the current worldwide COVID-19 pandemic, it might be useful to recall as precisely as possible the definition of the word antibiotic and provide evidence that some classes of antibiotics could offer excellent means to counteract viral infections via specific mechanisms.

Methods:

Molecular modeling and docking studies were used, as well as the tRNAox labeling reaction of the ribosomal protein eL42 in situ on human 80S ribosomes to demonstrate that cycloheximide and its thiosemicarbazone analogues bind to the catalytic Lys-53 residue of the human large subunit ribosomal protein eL42.

Results:

Comparison of the binding sites for Cycloheximide (CHX) and Sparsomycin (SPS) on the evolutionarily conserved E. coli bL12 and S. cerevisiae eL42 by means of molecular modeling and docking studies showed that: (i) SPS binds in proximity to the catalytic Lys-65 residue of the GANK motif of rp bL12 and to the catalytic Lys-55 residue of the GGQTKP motif of rp eL42; (ii) CHX failed to bind to the GANK motif, while the glutarimide moiety of SPS and CHX was found to make contact with Lys-55 of the GGQTKP motif of rp eL42.

Conclusion:

In this report, we demonstrate that cycloheximide and its thiosemicarbazone analogues are capable of inhibiting the human 80S ribosomes selectively through their binding to the ε-amino group of the side chain of Lys-53. As a consequence, these small-molecule inhibitors of translation are susceptible to exhibit antiviral activities by preventing the human ribosomes of the SARS-CoV-2 infected cells from synthesizing the viral proteins and enzymes.

Multifaceted control of mRNA translation machinery in cancer

The mRNA translation machinery is tightly regulated through several, at times overlapping, mechanisms that modulate its efficiency and accuracy. Due to their fast rate of growth and metabolism, cancer cells require an excessive amount of mRNA translation and protein synthesis. However, unfavorable conditions, such as hypoxia, amino acid starvation, and oxidative stress, which are abundant in cancer, as well as many anti-cancer treatments inhibit mRNA translation. Cancer cells adapt to the various internal and environmental stresses by employing specialised transcript-specific translation to survive and gain a proliferative advantage. We will highlight the major signaling pathways and mechanisms of translation that regulate the global or mRNA-specific translation in response to the intra- or extra-cellular signals and stresses that are key components in the process of tumourigenesis.

Acetylation of translation machinery affected protein translation in E. coli

Reversible lysine acetylation (RLA) of translation machinery components, such as ribosomal proteins (RPs) and translation factors (TFs), was identified in many microorganisms, while knowledge of its function and effect on translation remains limited. Herein, we show that translation machinery is regulated by acetylation. Using the cell-free translation system of E. coli, we found that AcP-driven acetylation significantly reduced the relative translation rate, and deacetylation partially restored the translation activity. Hyperacetylation caused by intracellular AcP accumulation or carbon/nitrogen fluctuation (carbon overflow or nitrogen limitation) modulated protein translation in vivo. These results uncovered a critical role of acetylation in translation regulation and indicated that carbon/nitrogen imbalance induced acetylation of ribosome in E. coli and dynamically affected translation rate via a global, uniform manner. KEY POINTS: • Acetylation of translation machinery directly regulated global translation. • K618 of EF-G, K411, and K464 of S1 are the key points influencing translation rate. • Carbon/nitrogen imbalance triggers AcP-dependent acetylation.

Phosphorothioate Modification of mRNA Accelerates the Rate of Translation Initiation to Provide More Efficient Protein Synthesis

Messenger RNAs (mRNAs) with phosphorothioate modification (PS-mRNA) to the phosphate site of A, G, C, and U with all 16 possible combinations were prepared, and the translation reaction was evaluated using an E. coli cell-free translation system. Protein synthesis from PS-mRNA increased in 12 of 15 patterns when compared with that of unmodified mRNA. The protein yield increased 22-fold when the phosphorothioate modification at A/C sites was introduced into the region from the 5'-end to the initiation codon. Single-turnover analysis of PS-mRNA translation showed that phosphorothioate modification increases the number of translating ribosomes, thus suggesting that the rate of translation initiation (rate of ribosome complex formation) is positively affected by the modification. The method provides a new strategy for improving translation by using non-natural mRNA.

A Ribosome Interaction Surface Sensitive to mRNA GCN Periodicity

A longstanding challenge is to understand how ribosomes parse mRNA open reading frames (ORFs). Significantly, GCN codons are over-represented in the initial codons of ORFs of prokaryote and eukaryote mRNAs. We describe a ribosome rRNA-protein surface that interacts with an mRNA GCN codon when next in line for the ribosome A-site. The interaction surface is comprised of the edges of two stacked rRNA bases: the Watson-Crick edge of 16S/18S rRNA C1054 and the adjacent Hoogsteen edge of A1196 (Escherichia coli 16S rRNA numbering). Also part of the interaction surface, the planar guanidinium group of a conserved Arginine (R146 of yeast ribosomal protein Rps3) is stacked adjacent to A1196. On its other side, the interaction surface is anchored to the ribosome A-site through base stacking of C1054 with the wobble anticodon base of the A-site tRNA. Using molecular dynamics simulations of a 495-residue subsystem of translocating ribosomes, we observed base pairing of C1054 to nucleotide G at position 1 of the next-in-line codon, consistent with previous cryo-EM observations, and hydrogen bonding of A1196 and R146 to C at position 2. Hydrogen bonding to both of these codon positions is significantly weakened when C at position 2 is changed to G, A or U. These sequence-sensitive mRNA-ribosome interactions at the C1054-A1196-R146 (CAR) surface potentially contribute to the GCN-mediated regulation of protein translation.

Chemosensing of Guanosine Triphosphate Based on a Fluorescent Dinuclear Zn(II)-Dipicolylamine Complex in Water

Guanosine triphosphate (GTP) is a key biomarker of multiple cellular processes and human diseases. The new fluorescent dinuclear complex [Zn₂(L)(S)][OTf]₄, 1 (asymmetric ligand, L = 5,8-Bis{[bis(2-pyridylmethyl)amino] methyl}quinoline, S = solvent, and OTf = triflate anion) was synthesized and studied in-depth as a chemosensor for nucleoside polyphosphates and inorganic anions in pure water. Additions at neutral pH of nucleoside triphosphates, guanosine diphosphate, guanosine monophosphate, and pyrophosphate (PPi) to 1 quench its blue emission (λ_em = 410 nm) with a pronounced selectivity toward GTP over other anions, including adenosine triphosphate (ATP), uridine triphosphate (UTP), and cytidine triphosphate (CTP). The efficient quenching response by the addition of GTP was observed in the presence of coexisting species in blood plasma and urine with a detection limit of 9.2 μmol L^-1. GTP also shows much tighter binding to the receptor 1 on a submicromolar level. On the basis of multiple spectroscopic tools (¹H, ³¹P NMR, UV-vis, and fluorescence) and DFT calculations, the binding mode is proposed through three-point recognition involving the simultaneous coordination of the N⁷ atom of the guanosine motif and two phosphate groups to the two Zn(II) atoms. Spectroscopic studies, MS-ESI, and DFT suggested that GTP bound to 1 in 1:1 and 2:2 models with high overall binding constants of log β_1 (1:1) = 6.05 ± 0.01 and log β₂ = 10.91 ± 0.03, respectively. The optical change and selectivity are attributed to the efficient binding of GTP to 1 by the combination of a strong electrostatic contribution and synergic effects of coordination bonds. Such GTP selectivity of an asymmetric metal-based receptor in water is still rare.

Development of a multi-locus sequence typing system helps reveal the evolution of Cardinium hertigii, a reproductive manipulator symbiont of insects

Background

Cardinium is an intracellular bacterial symbiont in the phylum Bacteroidetes that is found in many different species of arthropods and some nematodes. This symbiont is known to be able to induce three reproductive manipulation phenotypes, including cytoplasmic incompatibility. Placing individual strains of Cardinium within a larger evolutionary context has been challenging because only two, relatively slowly evolving genes, 16S rRNA gene and Gyrase B, have been used to generate phylogenetic trees, and consequently, the relationship of different strains has been elucidated in only its roughest form.

Results

We developed a Multi Locus Sequence Typing (MLST) system that provides researchers with three new genes in addition to Gyrase B for inferring phylogenies and delineating Cardinium strains. From our Cardinium phylogeny, we confirmed the presence of a new group D, a Cardinium clade that resides in the arachnid order harvestmen (Opiliones). Many Cardinium clades appear to display a high degree of host affinity, while some show evidence of host shifts to phylogenetically distant hosts, likely associated with ecological opportunity. Like the unrelated reproductive manipulator Wolbachia, the Cardinium phylogeny also shows no clear phylogenetic signal associated with particular reproductive manipulations.

Conclusions

The Cardinium phylogeny shows evidence of diversification within particular host lineages, and also of host shifts among trophic levels within parasitoid-host communities. Like Wolbachia, the relatedness of Cardinium strains does not necessarily predict their reproductive phenotypes. Lastly, the genetic tools proposed in this study may help future authors to characterize new strains and add to our understanding of Cardinium evolution.

Proteomic analysis revealed the survival strategy of Coxiella burnetii to doxycycline exposure

Antibiotic resistance is a global threat with a top concern in healthcare. Doxycycline is an antibiotic highly permeable to cell membrane used for treating a broad variety of bacteria, including Coxiella burnetii. This intracellular pathogen is the causative agent of Q fever, a re-emerging zoonosis found worldwide. Hence, C. burnetii has a considerable impact on the farming industry and public health, it is essential to explore its antibiotic adaptation/tolerance strategy to ensure effective therapy. Herein, we tracked changes in the bacterium induced by doxycycline exposure. Our proteomic analysis detected fifteen significantly altered proteins. Adjustments of some key proteins were verified by gene expression analysis. We also observed an increasing in hydrogen peroxide as a consequence of treatment, indicating deregulation of redox balance. Thus, our data suggests the reduction of protein synthesis to minimal levels, activation of the defense mechanism against oxidative stress and maintenance of cell envelope integrity as the key processes ensuring C. burnetii survival under doxycycline exposure. SIGNIFICANCE: Infection by intracellular microorganisms like C. burnetii requires long periods of treatment, thus antibiotic resistance development is a risk. In this report, 2-DE quantitative proteomics was used to identify changes in the proteome that occurs when C. burnetii is exposed to high concentrations of doxycycline. The identification of pathways impacted by doxycycline could be helpful to understand the mechanism of how C. burnetii is dealing with antibiotic stress.

One-Pot Production of RNA Nanoparticles via Automated Processing and Self-Assembly

From the original sequencing of the human genome, it was found that about 98.5% of the genome did not code for proteins. Subsequent studies have now revealed that a much larger portion of the genome is related to short or long noncoding RNAs that regulate cellular activities. In addition to the milestones of chemical and protein drugs, it has been proposed that RNA drugs or drugs targeting RNA will become the third milestone in drug development ( Shu , Y. ; Adv. Drug Deliv. Rev. 2014 , 66 , 74 . ). Currently, the yield and cost for RNA nanoparticle or RNA drug production requires improvement in order to advance the RNA field in both research and clinical translation by reducing the multiple tedious manufacturing steps. For example, with 98.5% incorporation efficiency of chemical synthesis of a 100 nucleotide RNA strand, RNA oligos will result with 78% contamination of aborted byproducts. Thus, RNA nanotechnology is one of the remedies, because large RNA can be assembled from small RNA fragments via bottom-up self-assembly. Here we report the one-pot production of RNA nanoparticles via automated processing and self-assembly. The continuous production of RNA by rolling circle transcription (RCT) using a circular dsDNA template is coupled with self-cleaving ribozymes encoded in the concatemeric RNA transcripts. Production was monitored in real-time. Automatic production of RNA fragments enabled their assembly either in situ or via one-pot co-transcription to obtain RNA nanoparticles of desired motifs and functionalities from bottom-up assembly of multiple RNA fragments. In combination with the RNA nanoparticle construction process, a purification method using a large-scale electrophoresis column was also developed.

The uncharacterized bacterial protein YejG has the same architecture as domain III of elongation factor G

InterPro family IPR020489 comprises ~1000 uncharacterized bacterial proteins. Previously we showed that overexpressing the Escherichia coli representative of this family, EcYejG, conferred low-level resistance to aminoglycoside antibiotics. In an attempt to shed light on the biochemical function of EcYejG, we have solved its structure using multinuclear solution NMR spectroscopy. The structure most closely resembles that of domain III from elongation factor G (EF-G). EF-G catalyzes ribosomal translocation and mutations in EF-G have also been associated with aminoglycoside resistance. While we were unable to demonstrate a direct interaction between EcYejG and the ribosome, the protein might play a role in translation.

Roles of specific aminoglycoside-ribosome interactions in the inhibition of translation

Aminoglycosides containing a 2-deoxystreptamine core (AGs) represent a large family of antibiotics that target the ribosome. These compounds promote miscoding, inhibit translocation, and inhibit ribosome recycling. AG binding to helix h44 of the small subunit induces rearrangement of A-site nucleotides A1492 and A1493, which promotes a key open-to-closed conformational change of the subunit and thereby increases miscoding. Mechanisms by which AGs inhibit translocation and recycling remain less clear. Structural studies have revealed a secondary AG binding site in H69 of the large subunit, and it has been proposed that interaction at this site is crucial for inhibition of translocation and recycling. Here, we analyze ribosomes with mutations targeting either or both AG binding sites. Assaying translocation, we find that ablation of the h44 site increases the IC₅₀ values for AGs dramatically, while removal of the H69 site increases these values modestly. This suggests that the AG-h44 interaction is primarily responsible for inhibition, with H69 playing a minor role. Assaying recycling, we find that mutation of h44 has no effect on AG inhibition, consistent with a primary role for AG-H69 interaction. Collectively, these findings help clarify the roles of the two AG binding sites in mechanisms of inhibition by these compounds.

Dynamics of tRNA dissociation in early and later cycles of translation elongation by the ribosome

Deacylated tRNA dissociation from E site and aminoacyl-tRNA binding to the A site of the ribosome play a critical role in repetitive cycles of protein synthesis. Available experimental data showed that in the small range of aminoacyl-tRNA concentrations, during the first few cycles of translation elongation (initiation phase of translation) the E-site tRNA can be dissociated either before or after the A-site tRNA binding, while during the later cycles of elongation (elongation phase) the E-site tRNA is mostly dissociated before the A-site tRNA binding. Here, based on our proposed model of translation elongation we study analytically the dynamics of the E-site tRNA dissociation and A-site tRNA binding, providing quantitative explanations of the available experimental data in both the initiation and elongation phases. In our model there exist two routes of state transitions within an elongation cycle in the initiation phase, with each route having stochastic E-site tRNA dissociation but with different dissociation rates. Thus, the E-site tRNA dissociation is governed by a stochastic competition between the tRNA dissociation and A-site tRNA association reactions, although in the small range of aminoacyl-tRNA concentrations used in the experiments it seems that such stochastic competition does not exist. Moreover, the detailed comparisons between the dynamics of tRNA dissociation in the initiation phase and that in the elongation phase are made.

Roadblocks and resolutions in eukaryotic translation

During protein synthesis, ribosomes encounter many roadblocks, the outcomes of which are largely determined by substrate availability, amino acid features and reaction kinetics. Prolonged ribosome stalling is likely to be resolved by ribosome rescue or quality control pathways, whereas shorter stalling is likely to be resolved by ongoing productive translation. How ribosome function is affected by such hindrances can therefore have a profound impact on the translational output (yield) of a particular mRNA. In this Review, we focus on these roadblocks and the resumption of normal translation elongation rather than on alternative fates wherein the stalled ribosome triggers degradation of the mRNA and the incomplete protein product. We discuss the fundamental stages of the translation process in eukaryotes, from elongation through ribosome recycling, with particular attention to recent discoveries of the complexity of the genetic code and regulatory elements that control gene expression, including ribosome stalling during elongation, the role of mRNA context in translation termination and mechanisms of ribosome rescue that resemble recycling.

Super-resolution force spectroscopy reveals ribosomal motion at sub-nucleotide steps

Probing biomolecular motion beyond a single nucleotide is technically challenging but fundamentally significant. We have developed super-resolution force spectroscopy (SURFS) with 0.5 pN force resolution and revealed that the ribosome moves by half a nucleotide upon the formation of the pre-translocation complex, which is beyond the resolution of other techniques.

The Ribosome as an Allosterically Regulated Molecular Machine

The ribosome as a complex molecular machine undergoes significant conformational rearrangements during the synthesis of polypeptide chains of proteins. In this review, information obtained using various experimental methods on the internal consistency of such rearrangements is discussed. It is demonstrated that allosteric regulation involves all the main stages of the operation of the ribosome and connects functional elements remote by tens and even hundreds of angstroms. Data obtained using Förster resonance energy transfer (FRET) show that translocation is controlled in general by internal mechanisms of the ribosome, and not by the position of the ligands. Chemical probing data revealed the relationship of such remote sites as the decoding, peptidyl transferase, and GTPase centers of the ribosome. Nevertheless, despite the large amount of experimental data accumulated to date, many details and mechanisms of these phenomena are still not understood. Analysis of these data demonstrates that the development of new approaches is necessary for deciphering the mechanisms of allosteric regulation of the operation of the ribosome.

The kinetic mechanism of bacterial ribosome recycling

Bacterial ribosome recycling requires breakdown of the post-termination complex (PoTC), comprising a messenger RNA (mRNA) and an uncharged transfer RNA (tRNA) cognate to the terminal mRNA codon bound to the 70S ribosome. The translation factors, elongation factor G and ribosome recycling factor, are known to be required for recycling, but there is controversy concerning whether these factors act primarily to effect the release of mRNA and tRNA from the ribosome, with the splitting of the ribosome into subunits being somewhat dispensable, or whether their main function is to catalyze the splitting reaction, which necessarily precedes mRNA and tRNA release. Here, we utilize three assays directly measuring the rates of mRNA and tRNA release and of ribosome splitting in several model PoTCs. Our results largely reconcile these previously held views. We demonstrate that, in the absence of an upstream Shine–Dalgarno (SD) sequence, PoTC breakdown proceeds in the order: mRNA release followed by tRNA release and then by 70S splitting. By contrast, in the presence of an SD sequence all three processes proceed with identical apparent rates, with the splitting step likely being rate-determining. Our results are consistent with ribosome profiling results demonstrating the influence of upstream SD-like sequences on ribosome occupancy at or just before the mRNA stop codon.

Internally ratiometric fluorescent sensors for evaluation of intracellular GTP levels and distribution

GTP is a major regulator of multiple cellular processes, but tools for quantitative evaluation of GTP levels in live cells have not been available. We report the development and characterization of genetically encoded GTP sensors, which we constructed by inserting a circularly permuted yellow fluorescent protein (cpYFP) into a region of the bacterial G protein FeoB that undergoes a GTP-driven conformational change. GTP binding to these sensors results in a ratiometric change in their fluorescence, thereby providing an internally normalized response to changes in GTP levels while minimally perturbing those levels. Mutations introduced into FeoB to alter its affinity for GTP created a series of sensors with a wide dynamic range. Critically, in mammalian cells the sensors showed consistent changes in ratiometric signal upon depletion or restoration of GTP pools. We show that these GTP evaluators (GEVALs) are suitable for detection of spatiotemporal changes in GTP levels in living cells and for high-throughput screening of molecules that modulate GTP levels.

Miscoding-induced stalling of substrate translocation on the bacterial ribosome

Directional transit of the ribosome along the messenger RNA (mRNA) template is a key determinant of the rate and processivity of protein synthesis. Imaging of the multistep translocation mechanism using single-molecule FRET has led to the hypothesis that substrate movements relative to the ribosome resolve through relatively long-lived late intermediates wherein peptidyl-tRNA enters the P site of the small ribosomal subunit via reversible, swivel-like motions of the small subunit head domain within the elongation factor G (GDP)-bound ribosome complex. Consistent with translocation being rate-limited by recognition and productive engagement of peptidyl-tRNA within the P site, we now show that base-pairing mismatches between the peptidyl-tRNA anticodon and the mRNA codon dramatically delay this rate-limiting, intramolecular process. This unexpected relationship between aminoacyl-tRNA decoding and translocation suggests that miscoding antibiotics may impact protein synthesis by impairing the recognition of peptidyl-tRNA in the small subunit P site during EF-G-catalyzed translocation. Strikingly, we show that elongation factor P (EF-P), traditionally known to alleviate ribosome stalling at polyproline motifs, can efficiently rescue translocation defects arising from miscoding. These findings help reveal the nature and origin of the rate-limiting steps in substrate translocation on the bacterial ribosome and indicate that EF-P can aid in resuming translation elongation stalled by miscoding errors.

Translation and folding of single proteins in real time

Protein biosynthesis is inherently coupled to cotranslational protein folding. Folding of the nascent chain already occurs during synthesis and is mediated by spatial constraints imposed by the ribosomal exit tunnel as well as self-interactions. The polypeptide's vectorial emergence from the ribosomal tunnel establishes the possible folding pathways leading to its native tertiary structure. How cotranslational protein folding and the rate of synthesis are linked to a protein's amino acid sequence is still not well defined. Here, we follow synthesis by individual ribosomes using dual-trap optical tweezers and observe simultaneous folding of the nascent polypeptide chain in real time. We show that observed stalling during translation correlates with slowed peptide bond formation at successive proline sequence positions and electrostatic interactions between positively charged amino acids and the ribosomal tunnel. We also determine possible cotranslational folding sites initiated by hydrophobic collapse for an unstructured and two globular proteins while directly measuring initial cotranslational folding forces. Our study elucidates the intricate relationship among a protein's amino acid sequence, its cotranslational nascent-chain elongation rate, and folding.

Computational Discovery of Putative Leads for Drug Repositioning through Drug-Target Interaction Prediction

De novo experimental drug discovery is an expensive and time-consuming task. It requires the identification of drug-target interactions (DTIs) towards targets of biological interest, either to inhibit or enhance a specific molecular function. Dedicated computational models for protein simulation and DTI prediction are crucial for speed and to reduce the costs associated with DTI identification. In this paper we present a computational pipeline that enables the discovery of putative leads for drug repositioning that can be applied to any microbial proteome, as long as the interactome of interest is at least partially known. Network metrics calculated for the interactome of the bacterial organism of interest were used to identify putative drug-targets. Then, a random forest classification model for DTI prediction was constructed using known DTI data from publicly available databases, resulting in an area under the ROC curve of 0.91 for classification of out-of-sampling data. A drug-target network was created by combining 3,081 unique ligands and the expected ten best drug targets. This network was used to predict new DTIs and to calculate the probability of the positive class, allowing the scoring of the predicted instances. Molecular docking experiments were performed on the best scoring DTI pairs and the results were compared with those of the same ligands with their original targets. The results obtained suggest that the proposed pipeline can be used in the identification of new leads for drug repositioning. The proposed classification model is available at http://bioinformatics.ua.pt/software/dtipred/.

The emergence of multi-resistant bacterial strains and the existing void in the discovery and development of new classes of antibiotics is a growing concern. Indeed, some bacterial strains are now resistant to last-line antibiotics and considered untreatable. Drug repositioning has been suggested as a strategy to minimize time and cost expenses until the drug reaches the market, compared to traditional drug design. Drug-target interactions (DTIs) are the basis of rational drug design and thus, we proposed a computational approach to predict DTIs solely based on the primary sequence of the protein and the simplified molecular-input line-entry system of the ligand. In addition, network metrics are used to identify vital putative drug-targets in bacteria. Molecular docking experiments were performed to compare the binding affinities between a given ligand and a putative drug-target, as well as with their original targets. According to the docking results, the predicted DTIs have better or similar binding activities than the ligand and their real target, indicating the validity of the proposed model.

On the pathway of ribosomal translocation

The translocation of tRNAs coupled with mRNA in the ribosome is a critical process in the elongation cycle of protein synthesis. The translocation entails large-scale conformational changes of the ribosome and involves several intermediate states with tRNAs in different positions with respect to 30S and 50S ribosomal subunits. However, the detailed role of the intermediate states is unknown and the detailed mechanism and pathway of translocation is unclear. Here based on previous structural, biochemical and single-molecule data we present a translocation pathway by incorporating several intermediate states. With the pathway, we study theoretically (i) the kinetics of 30S head rotation associated with translocation catalyzed by wild-type EF-G, (ii) the dynamics of fluctuations between different tRNA states during translocation interfered with EF-G mutants and translocation-specific antibiotics, (iii) the kinetics of tRNA movement in 50S subunit and mRNA movement in 30S subunit in the presence of wild-type EF-G, EF-G mutants and translocation-specific antibiotics, (iv) the dynamics of EF-G sampling to the ribosome during translocation, etc., providing consistent and quantitative explanations of various available biochemical and single-molecule experimental data published in the literature. Moreover, we study the kinetics of 30S head rotation in the presence of EF-G mutants, providing predicted results. These have significant implications for the molecular mechanism and pathway of ribosomal translocation.

Non-canonical roles of tRNAs and tRNA mimics in bacterial cell biology

Transfer RNAs (tRNAs) are the macromolecules that transfer activated amino acids from aminoacyl-tRNA synthetases to the ribosome, where they are used for the mRNA guided synthesis of proteins. Transfer RNAs are ancient molecules, perhaps even predating the existence of the translation machinery. Albeit old, these molecules are tremendously conserved, a characteristic that is well illustrated by the fact that some bacterial tRNAs are efficient and specific substrates of eukaryotic aminoacyl-tRNA synthetases and ribosomes. Considering their ancient origin and high structural conservation, it is not surprising that tRNAs have been hijacked during evolution for functions outside of translation. These roles beyond translation include synthetic, regulatory and information functions within the cell. Here we provide an overview of the non-canonical roles of tRNAs and their mimics in bacteria, and discuss some of the common themes that arise when comparing these different functions.

Mechanical insights into ribosomal progression overcoming RNA G-quadruplex from periodical translation suppression in cells

G-quadruplexes formed on DNA and RNA can be roadblocks to movement of polymerases and ribosome on template nucleotides. Although folding and unfolding processes of the G-quadruplexes are deliberately studied in vitro, how the mechanical and physical properties of the G-quadruplexes affect intracellular biological systems is still unclear. In this study, mRNAs with G-quadruplex forming sequences located either in the 5′ untranslated region (UTR) or in the open reading frame (ORF) were constructed to evaluate positional effects of the G-quadruplex on translation suppression in cells. Periodic fluctuation of translation suppression was observed at every three nucleotides within the ORF but not within the 5′ UTR. The results suggested that difference in motion of ribosome at the 5′ UTR and the ORF determined the ability of the G-quadruplex structure to act as a roadblock to translation in cells and provided mechanical insights into ribosomal progression to overcome the roadblock.

Multiperspective smFRET reveals rate-determining late intermediates of ribosomal translocation

Directional translocation of the ribosome through the messenger RNA open reading frame is a critical determinant of translational fidelity. This process entails a complex interplay of large-scale conformational changes within the actively translating particle, which together coordinate the movement of transfer and messenger RNA substrates with respect to the large and small ribosomal subunits. Using pre-steady state, single-molecule fluorescence resonance energy transfer imaging, we have tracked the nature and timing of these conformational events within the Escherichia coli ribosome from five structural perspectives. Our investigations reveal direct evidence of structurally and kinetically distinct, late intermediates during substrate movement, whose resolution is rate-determining to the translocation mechanism. These steps involve intra-molecular events within the EFG(GDP)-bound ribosome, including exaggerated, reversible fluctuations of the small subunit head domain, which ultimately facilitate peptidyl-tRNA’s movement into its final post-translocation position.

Nucleobase-Modified PNA Suppresses Translation by Forming a Triple Helix with a Hairpin Structure in mRNA In Vitro and in Cells

Compounds that bind specifically to double-stranded regions of RNA have potential as regulators of structure-based RNA function; however, sequence-selective recognition of double-stranded RNA is challenging. The modification of peptide nucleic acid (PNA) with unnatural nucleobases enables the formation of PNA-RNA triplexes. Herein, we demonstrate that a 9-mer PNA forms a sequence-specific PNA-RNA triplex with a dissociation constant of less than 1 nm at physiological pH. The triplex formed within the 5' untranslated region of an mRNA reduces the protein expression levels both in vitro and in cells. A single triplet mismatch destabilizes the complex, and in this case, no translation suppression is observed. The triplex-forming PNAs are unique and potent compounds that hold promise as inhibitors of cellular functions that are controlled by double-stranded RNAs, such as RNA interference, RNA editing, and RNA localization mediated by protein-RNA interactions.

Ribosome utilizes the minimum free energy changes to achieve the highest decoding rate and fidelity

The performance of ribosome translation can be characterized by two factors, the translation rate and fidelity. Here, we provide analytical studies of the effect of the near-cognate tRNAs on the two factors. It is shown that the increase of the concentration of the near-cognate tRNAs relative to that of the cognate tRNA has negative effects on the ribosome translation by reducing both the translation rate and the translation fidelity. The effect of the near-cognate ternary complexes on the translation rate results mainly from the initial selection phase, whereas the proofreading phase has a minor effect. By contrast, the effect of the near-cognate ternary complexes on the fidelity results almost equally from the two phases. By using two successive phases, the initial selection and the proofreading, the ribosome can achieve higher translation fidelity than the product of the fidelity when only the initial selection is included and when only the proofreading is included, especially at the large ratio of the concentration of the near-cognate tRNAs compared to that of the cognate tRNA. Moreover, we study the changes of the free energy landscape in the tRNA decoding step. It is found that the rate constants of the tRNA decoding step measured experimentally give the minimum energy changes for the ribosomal complex to attain the optimal performance with both the highest decoding rate and fidelity and/or with the maximum value of the decoding fitness function. This suggests that the ribosome has evolved to utilize the minimum free energy changes gained from the conformational changes of the ribosome, EF-Tu, and tRNA to achieve the optimal performance in the tRNA decoding.

Quantitative Connection between Ensemble Thermodynamics and Single-Molecule Kinetics: A Case Study Using Cryogenic Electron Microscopy and Single-Molecule Fluorescence Resonance Energy Transfer Investigations of the Ribosome

At equilibrium, thermodynamic and kinetic information can be extracted from biomolecular energy landscapes by many techniques. However, while static, ensemble techniques yield thermodynamic data, often only dynamic, single-molecule techniques can yield the kinetic data that describe transition-state energy barriers. Here we present a generalized framework based upon dwell-time distributions that can be used to connect such static, ensemble techniques with dynamic, single-molecule techniques, and thus characterize energy landscapes to greater resolutions. We demonstrate the utility of this framework by applying it to cryogenic electron microscopy (cryo-EM) and single-molecule fluorescence resonance energy transfer (smFRET) studies of the bacterial ribosomal pre-translocation complex. Among other benefits, application of this framework to these data explains why two transient, intermediate conformations of the pre-translocation complex, which are observed in a cryo-EM study, may not be observed in several smFRET studies.

Overexpression of ribosome elongation factor G and recycling factor increases L-isoleucine production in Corynebacterium glutamicum

Ribosome elongation factor G encoded by fusA promotes the translocation step of protein synthesis in bacteria; ribosome recycling factor encoded by frr, together with the elongation factor G, dissociates ribosomes from messenger RNA after the termination of translation. Both factors play important roles during protein synthesis in bacteria. In this study, we found that overexpression of fusA and/or frr led to the increase of L-isoleucine production in Corynebacterium glutamicum IWJ001, an L-isoleucine production strain generated by random mutagenesis. Reverse transcription polymerase chain reaction analysis showed that transcriptional levels of genes lysC, hom, thrB, ilvA, ilvBN, and ilvE encoding the key enzymes in the biosynthetic pathway of L-isoleucine increased in C. glutamicum IWJ001 when fusA and/or frr were overexpressed. Co-overexpression of fusA and frr, together with genes ilvA, ilvB, ilvN, and ppnk in C. glutamicum IWJ001, led to 76.5 % increase of L-isoleucine production in flask cultivation and produced 28.5 g/L L-isoleucine in 72-h fed-batch fermentation. The results demonstrate that overexpressing ribosome elongation factor G and ribosome recycling factor is an efficient approach to enhance L-isoleucine production in C. glutamicum.

Simple Method for Constructing RNA Triangle, Square, Pentagon by Tuning Interior RNA 3WJ Angle from 60° to 90° or 108°

Precise shape control of architectures at the nanometer scale is an intriguing but extremely challenging facet. RNA has recently emerged as a unique material and thermostable building block for use in nanoparticle construction. Here, we describe a simple method from design to synthesis of RNA triangle, square, and pentagon by stretching RNA 3WJ native angle from 60° to 90° and 108°, using the three-way junction (3WJ) of the pRNA from bacteriophage phi29 dsDNA packaging motor. These methods for the construction of elegant polygons can be applied to other RNA building blocks including the utilization and application of RNA 4-way, 5-way, and other multi-way junctions.

Biphasic character of ribosomal translocation and non-Michaelis-Menten kinetics of translation

We study theoretically the kinetics of mRNA translocation in the wild-type (WT) Escherichia coli ribosome, which is composed of a small 30S and large 50S subunit, and the ribosomes with mutations to some intersubunit bridges such as B1a, B4, B7a, and B8. The theoretical results reproduce well the available in vitro experimental data on the biphasic kinetics of the forward mRNA translocation catalyzed by elongation factor G (EF-G) hydrolyzing GTP, which can be best fit by the sum of two exponentials, and the monophasic kinetics of the spontaneous reverse mRNA translocation in the absence of the elongation factor, which can be best fit by a single-exponential function, in both the WT and mutant ribosomes. We show that both the mutation-induced increase in the maximal rate of the slow phase for the forward mRNA translocation and that in the rate of the spontaneous reverse mRNA translocation result from a reduction in the intrinsic energy barrier to resist the rotational movements between the two subunits, giving the same degree of increase in the two rates. The mutation-induced increase in the maximal rate of the fast phase for the forward mRNA translocation results mainly from the increase in the rate of the ribosomal unlocking, a conformational change in the ribosome that widens the mRNA channel for the mRNA translocation to take place, which could be partly due to the effect of the mutation on the intrasubunit 30S head rotation. Moreover, we study the translation rate of the WT and mutant ribosomes. It is shown that the translation rate versus the concentration of EF-G-GTP does not follow the Michaelis-Menten (MM) kinetics, which is in sharp contrast to the general property of other enzymes that the rate of the enzymatic reaction versus the concentration of a substrate follows the MM kinetics. The physical origin of this non-MM kinetics for the ribosome is revealed.

Movement of elongation factor G between compact and extended conformations

Previous structural studies suggested that ribosomal translocation is accompanied by large interdomain rearrangements of elongation factor G (EF-G). Here, we follow the movement of domain IV of EF-G relative to domain II of EF-G using ensemble and single-molecule Förster resonance energy transfer. Our results indicate that ribosome-free EF-G predominantly adopts a compact conformation that can also, albeit infrequently, transition into a more extended conformation in which domain IV moves away from domain II. By contrast, ribosome-bound EF-G predominantly adopts an extended conformation regardless of whether it is interacting with pretranslocation ribosomes or with posttranslocation ribosomes. Our data suggest that ribosome-bound EF-G may also occasionally sample at least one more compact conformation. GTP hydrolysis catalyzed by EF-G does not affect the relative stability of the observed conformations in ribosome-free and ribosome-bound EF-G. Our data support a model suggesting that, upon binding to a pretranslocation ribosome, EF-G moves from a compact to a more extended conformation. This transition is not coupled to but likely precedes both GTP hydrolysis and mRNA/tRNA translocation.

The ribosome uses cooperative conformational changes to maximize and regulate the efficiency of translation

One of the most challenging unanswered questions regarding the structural biology of biomolecular machines such as the two-subunit ribosome is whether and how these machines coordinate seemingly independent and random conformational fluctuations to maximize and regulate their functional efficiencies. To address this question, we have used ribosome mutagenesis or a ribosome-targeting antibiotic to predictably perturb the dynamics of intersubunit rotation, a structural rearrangement of the ribosome that is essential for the translocation and ejection of ribosome-bound tRNAs during translation. Concomitantly, we have used single-molecule fluorescence resonance energy transfer (smFRET) to characterize the effects of these perturbations on the dynamics of ribosomal L1 stalk movements and ribosome-bound tRNA reconfigurations, conformational changes that are likewise essential for the translocation and ejection of tRNAs during translation. Together with the results of complementary biochemical studies, our smFRET studies demonstrate that the ribosome uses cooperative conformational changes to maximize and regulate the efficiency with which it translocates and ejects tRNAs during translation. We propose that the ribosome employs cooperative conformational changes to efficiently populate global conformational states that are productive for translation, that translation factors exploit this cooperativity as part of their mechanisms of action, and that antibiotics exploit it to maximize the potency with which they inhibit translation. It is likely that similar cooperative conformational changes underlie the function and regulation of other biomolecular machines.

Model of EF4-induced ribosomal state transitions and mRNA translocation

EF4, a highly conserved protein present in bacteria, mitochondria and chloroplasts, can bind to both the posttranslocation and pretranslocation ribosomal complexes. When binding to the posttranslocation state, it catalyzes backward translocation to a pretranslocation state. When binding to the pretranslocation state, it catalyzes transition to another pretranslocation state that is similar and possibly identical to that resulting from the posttranslocation state bound by EF4, and competes with EF-G to regulate the elongation cycle. However, the molecular mechanism on how EF4 induces state transitions and mRNA translocation remains unclear. Here, we present both the model for state transitions induced by EF4 binding to the posttranslocation state and that by EF4 binding to the pretranslocation state, based on which we study the kinetics of EF4-induced state transitions and mRNA translocation, giving quantitative explanations of the available experimental data. Moreover, we present some predicted results on state transitions and mRNA translocation induced by EF4 binding to the pretranslocation state complexed with the mRNA containing a duplex region.

Free-energy landscape of reverse tRNA translocation through the ribosome analyzed by electron microscopy density maps and molecular dynamics simulations

To understand the mechanism of reverse tRNA translocation in the ribosome, all-atom molecular dynamics simulations of the ribosome-tRNAs-mRNA-EFG complex were performed. The complex at the post-translocational state was directed towards the translocational and pre-translocational states by fitting the complex into cryo-EM density maps. Between a series of the fitting simulations, umbrella sampling simulations were performed to obtain the free-energy landscape. Multistep structural changes, such as a ratchet-like motion and rotation of the head of the small subunit were observed. The free-energy landscape showed that there were two main free-energy barriers: one between the post-translocational and intermediate states, and the other between the pre-translocational and intermediate states. The former corresponded to a clockwise rotation, which was coupled to the movement of P-tRNA over the P/E-gate made of G1338, A1339 and A790 in the small subunit. The latter corresponded to an anticlockwise rotation of the head, which was coupled to the location of the two tRNAs in the hybrid state. This indicates that the coupled motion of the head rotation and tRNA translocation plays an important role in opening and closing of the P/E-gate during the ratchet-like movement in the ribosome. Conformational change of EF-G was interpreted to be the result of the combination of the external motion by L12 around an axis passing near the sarcin-ricin loop, and internal hinge-bending motion. These motions contributed to the movement of domain IV of EF-G to maintain its interaction with A/P-tRNA.

EF-G and EF4: translocation and back-translocation on the bacterial ribosome

Ribosomes translate the codon sequence of an mRNA into the amino acid sequence of the corresponding protein. One of the most crucial events is the translocation reaction, which involves movement of both the mRNA and the attached tRNAs by one codon length and is catalysed by the GTPase elongation factor G (EF-G). Interestingly, recent studies have identified a structurally related GTPase, EF4, that catalyses movement of the tRNA2-mRNA complex in the opposite direction when the ribosome stalls, which is known as back-translocation. In this Review, we describe recent insights into the mechanistic basis of both translocation and back-translocation.