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.     

Differential effects of thiopeptide and orthosomycin antibiotics on translational GTPases

The ribosome is a major target in the bacterial cell for antibiotics. Here, we dissect the effects that the thiopeptide antibiotics thiostrepton (ThS) and micrococcin (MiC) as well as the orthosomycin antibiotic evernimicin (Evn) have on translational GTPases. We demonstrate that, like ThS, MiC is a translocation inhibitor, and that the activation by MiC of the ribosome-dependent GTPase activity of EF-G is dependent on the presence of the ribosomal proteins L7/L12 as well as the G' subdomain of EF-G. In contrast, Evn does not inhibit translocation but is a potent inhibitor of back-translocation as well as IF2-dependent 70S-initiation complex formation. Collectively, these results shed insight not only into fundamental aspects of translation but also into the unappreciated specificities of these classes of translational inhibitors.     

Unifying the Aminohexopyranose‐ and Peptidyl‐Nucleoside Antibiotics: Implications for Antibiotic Design

In search of new anti‐tuberculars compatible with anti‐retroviral therapy we re‐identified amicetin as a lead compound. Amicetin's binding to the 70S ribosomal subunit of Thermus thermophilus (Tth) has been unambiguously determined by crystallography and reveals it to occupy the peptidyl transferase center P‐site of the ribosome. The amicetin binding site overlaps significantly with that of the well‐known protein synthesis inhibitor balsticidin S. Amicetin, however, is the first compound structurally characterized to bind to the P‐site with demonstrated selectivity for the inhibition of prokaryotic translation. The natural product‐ribosome structure enabled the synthesis of simplified analogues that retained both potency and selectivity for the inhibition of prokaryotic translation.     

Homogenous time resolved fluorescence assay to identify modulators of cap-dependent translation initiation

Eukaryotic initiation factor (eIF) 4F plays a key role in recruiting 40S ribosomes and associated factors to mRNA templates during translation initiation. The function of this heterotrimeric complex is to deliver an RNA helicase to the 5' cap proximal region of mRNAs in preparation for ribosome binding. To study the interaction between subunits of this complex, as well as identify small molecules that could interfere with their association, we developed a time resolved fluorescence assay that allows monitoring of interactions between two subunits of eIF4F. We have performed a small molecule chemical screen of >73,000 compounds using this assay.     

Traveling Time of a translating ribosome along messenger RNA monitored directly on a quartz crystal microbalance

During translation, the biosynthesis of polypeptides is dynamically regulated. The translation rate along messenger RNA (mRNA), which is dependent on the codon, structure, and sequence, is not always constant. However, methods for measuring the duration required for polypeptide elongation on an mRNA of interest have not been developed. In this work, we used a quartz crystal microbalance (QCM) technique to monitor mRNA translation in an Escherichia coli cell-free translation system in real time. This method permitted us to evaluate the translation of proteins of interest fused upstream of a streptavidin-binding peptide (SBP) fusion protein. The translation of mRNA encoding the SBP fusion protein alone was observed as a mass increase on a streptavidin-modified QCM plate. Addition of the protein of interest resulted in a delay in the mass change corresponding to the traveling time of the ribosome along the coding region of the protein of interest. With this technique, the lengths of coding sequences, codon usages, influences of unique sequences, and various protein-coding sequences were evaluated. The results showed that the traveling time of the translating ribosome depends on the length of the coding region translated but is also affected by the sequence itself. Differences in the time lags for various proteins imply that mRNA coding sequences may regulate gene expression.     

Probing conformational states of modified helix 69 in 50S ribosomes

The movement of the small ribosomal subunit (30S) relative to the large ribosomal subunit (50S) during translation is widely known, but many molecular details and roles of rRNA and proteins in this process are still undefined, especially in solution models. The functional relationship of modified nucleotides to ribosome activity is one such enigma. To better understand ribosome dynamics and the influence of modified nucleotides on such processes, the focus of this work was helix 69 of 23S rRNA, which contains three pseudouridine residues in its loop region. Ribosome probing experiments with dimethylsulfate revealed that specific base accessibilities and individual nucleotide conformations in helix 69 are influenced differently by pH, temperature, magnesium, and the presence of pseudouridine modifications.     

The ribosome through the looking glass

For almost 20 years crystallographers have sought to solve the structure of the ribosome, the largest and most complicated RNA-protein complex in the cell. All ribosomes are composed of a large and small subunit which for the humble bacterial ribosome comprise more than 4000 ribonucleotides, 54 different proteins, and have a molecular mass totaling over 2.5 million Daltons. The past few years have seen the resolution of structures at the atomic level for both large and small subunits and of the complete 70S ribosome from Thermus thermophilus at a resolution of 5.5-A. Soaking of small ligands (such as antibiotics, substrate analogues, and small translational factors) into the crystals of the subunits has revolutionized our understanding of the central functions of the ribosome. Coupled with the power of cryo-electron microscopic studies of translation complexes, a collection of snap-shots is accumulating, which can be assembled to create a likely motion picture of the bacterial ribosome during translation. Recent analyses show yeast ribosomes have a remarkable structural similarity to bacterial ribosomes. This Review aims to follow the bacterial ribosome through each sequential "frame" of the translation cycle, emphasizing at each point the features that are found in all organisms.     

Effects of solvent,casting temperature,and guest/host stoichiometries on the properties of shape memory material based on partial α‐CD‐PEG inclusion complex

A series of supramolecular inclusion complex (IC) films were formed by threading α‐cyclodextrin (α‐CD) molecules over poly(ethylene glycol) (PEG), according to the designed ratio of α‐CD/PEG. Because of containing α‐CD‐PEG inclusion crystallites as physical crosslinks and uncovered PEG crystallites as “switch phase”, the resulting supramolecular α‐CD‐PEG partial ICs displayed a shape memory effect. The properties of the materials were investigated by ¹H‐NMR, X‐ray diffraction (XRD), differential scanning calorimetry (DSC), dynamic mechanical analysis (DMA), and swelling measurement. It was found that the casting temperature, solvent, and the ratio of α‐CD‐PEG inclusion/PEG had great influence on the formation and properties of α‐CD‐PEG partial ICs. The modes of complexes on different conditions were proposed. © 2010 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 48: 951–957, 2010     

Simultaneous characterization of isoflavonoids and astragalosides in two Astragalus species by high-performance liquid chromatography coupled with atmospheric pressure chemical ionization tandem mass spectrometry

A method was developed for the simultaneous identification of astragalosides (AGs) and isoflavonoids (IFs) in the roots of Astragalus membranaceus and Astragalus mongholicus by HPLC coupled with atmospheric pressure chemical ionization MS/MS (HPLC-APCI-MS/MS). Diagnostic fragment ions of AGs and different group of IFs were obtained with one AG and eight IF standards analyzed by CID-MS, which were adopted as characteristic MS/MS fingerprints for further identification of these compounds in the two Astragalus species by using HPLC-APCI-MS/MS. A total of 20 IFs and 10 AGs were identified or tentatively identified. Among them, six IFs were detected in A. membranaceus for the first time and five IFs were firstly identified in A. mongholicus. The results indicate that HPLC-APCI-MS/MS is a powerful tool for the simultaneous characterization of IFs and AGs in complex matrix.     

Partial miscibility in a nylon‐6/nylon‐66 blend coalesced from their common α‐cyclodextrin inclusion complex

We successfully formed a series of inclusion complexes (ICs) between an α‐cyclodextrin (α‐CD) host and two kinds of guest polymers, nylon‐6 and nylon‐66. An attempt to achieve an intimate blend between nylon‐6 and nylon‐66 through the formation and dissociation of their common α‐CD IC was made. The formation of all nylon ICs was verified with wide‐angle X‐ray diffraction, differential scanning calorimetry (DSC), and Fourier transform infrared (FTIR) and cross‐polarized/magic‐angle‐spinning ¹³C NMR spectroscopy. The experimental results demonstrated that α‐CD could only host single nylon polymer chains in the IC channels, either nylon‐6 or nylon‐66 in their own complexes, and presumably either nylon in neighboring channels of their common IC. The IC‐coalesced blend of nylon‐6 and nylon‐66 was obtained after the removal of the host cyclodextrin from their common IC with dimethyl sulfoxide. The spectroscopic results (FTIR and ¹³C NMR) illustrated that there was a degree of intimate miscibility existing in the IC‐coalesced blend, but not in the solution‐cast physical blend, although X‐ray diffraction patterns showed that the crystal structure of the IC‐coalesced blend was similar to that of the physical blend. DSC thermal profiles suggested that nylon‐66 first formed crystals during coalescence and that the subsequent crystallization of nylon‐6 was greatly affected by the nylon‐66 crystallites because of the close proximity of the two components in portions of the coalesced blend. DSC observations also demonstrated that the melting of the coalesced blend did not lead to complete phase separation of the nylon‐6 and nylon‐66 components. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 1369–1378, 2004     

Molecular mixing of incompatible polymers through formation of and coalescence from their common crystalline cyclodextrin inclusion compounds

We describe the successful mixing of polymer pairs and triplets that are normally incompatible to form blends that possess molecular‐level homogeneity. This is achieved by the simultaneous formation of crystalline inclusion compounds (ICs) between host cyclodextrins (CDs) and two or more guest polymers, followed by coalescing the included guest polymers from their common CD–ICs to form blends. Several such CD–IC fabricated blends, including both polymer1/polymer2 binary and polymer1/ polymer2/polymer3 ternary blends, are described and examined by means of X‐ray diffraction, differential scanning calorimetry, thermogravimetric analysis, Fourier transform infrared spectroscopy, and solid‐state NMR to probe their levels of mixing. It is generally observed that homogeneous blends with a molecular‐level mixing of blend components is achieved, even when the blend components are normally immiscible by the usual solution and melt blending techniques. In addition, when block copolymers composed of inherently immiscible blocks are coalesced from their CD–ICs, significant suppression of their normal phase‐segregated morphologies generally occurs. Preliminary observations of the thermal and temporal stabilities of the CD–IC coalesced blends and block copolymers are reported, and CD–IC fabrication of polymer blends and reorganization of block copolymers are suggested as a potentially novel means to achieve a significant expansion of the range of useful polymer materials. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 4207–4224, 2004     

A highly efficient heterogeneous rhodium(I)‐catalyzed C–S coupling reaction of thiols with polychloroalkanes or alkyl halides under mild conditions

Heterogeneous C–S coupling reaction of thiols with polychloroalkanes or alkyl halides was achieved at 30 or 80 °C in the presence of 5 mol% of an MCM‐41‐immobilized bidentate phosphine rhodium complex (MCM‐41‐2P‐RhCl(PPh₃)) and triethylamine, yielding a variety of formaldehyde dithioacetals, ethylenedithioethers and unsymmetric thioethers in good to excellent yields. This heterogeneous rhodium catalyst can be easily recovered and recycled by simple filtration of the reaction solution and used for at least 10 consecutive trials without significant loss of activity. Copyright © 2015 John Wiley & Sons, Ltd.     

Photoliquefiable Ionic Crystals: A Phase Crossover Approach for Photon Energy Storage Materials with Functional Multiplicity

Ionic crystals (ICs) of the azobenzene derivatives show photoinduced IC–ionic liquid (IL) phase transition (photoliquefaction) upon UV‐irradiation, and the resulting cis‐azobenzene ILs are reversibly photocrystallized by illumination with visible light. The photoliquefaction of ICs is accompanied by a significant increase in ionic conductivity at ambient temperature. The photoliquefaction also brings the azobenzene ICs further significance as photon energy storage materials. The cis‐IL shows thermally induced crystallization to the trans‐IC phase. This transition is accompanied by exothermic peaks with a total ΔH of 97.1 kJ mol^?1, which is almost double the conformational energy stored in cis‐azobenzene chromophores. Thus, the integration of photoresponsive ILs and self‐assembly pushes the limit of solar thermal batteries.     

Two-phase channel structures based on alpha-cyclodextrin-polyethylene glycol inclusion complexes

Wide-angle X-ray scattering observations of alpha-cyclodextrin (CD)-poly(ethylene glycol) (PEG) inclusion complexes (ICs) have shown for the first time that two crystalline columnar modifications (forms I and II) are produced in the process of their formation. This was made possible by precise azimuthal X-ray diffraction scanning of oriented IC samples. Form I is characterized by CDs threaded onto PEG chains and arranged along channels in the order head-to-head/tail-to-tail, while form II is formed by unbound CDs also arranged into columns in a head-to-tail and also possibly a head-to-head/tail-to-tail manner, probably as a result of template crystallization on the form I IC crystals. It was shown that similar structural peculiarities are inherent for channel structures based on ICs obtained with PEG with a wide range of molecular weights (MWs). The characteristic feature of ICs based on PEG, especially with MW > 8000, is the presence of unbound polymer in the composition of the complex. The amount of unbound PEG was shown to rise with increasing MW of PEG, resulting in greater imperfections in the IC crystalline structure. The polyblock structure of ICs based on alpha-CD and PEG was therefore proposed.     

Structure and function of bacterial initiation factors

Bacteria require three initiation factors, IF1, IF2 and IF3, to start protein synthesis. In the last few years the elucidation of both structural and mechanistic aspects pertaining to these proteins has made substantial progress. In this article we outline the translation initiation process in bacteria and review these recent developments giving a summary of the main features of the structure and function of the initiation factors.     

Creation of novel polymer materials by processing with inclusion compounds

The processing of polymer materials from their inclusion compounds (ICs) formed with urea (U) and cyclodextrin (CD) hosts is described. Several examples are presented and serve to demonstrate the fabrication of unique polymer‐polymer composites and blends, including intimate blends of normally incompatible polymers, and the delivery of additives to polymers by means of embedding polymer‐ or additive‐U and CD‐ ICs into carrier polymer films and fibers, followed by coalescence of the IC guest, or by coalescence of two polymers or a polymer and an additive from their common CD‐IC crystals.     

Insect‐Derived Proline‐Rich Antimicrobial Peptides Kill Bacteria by Inhibiting Bacterial Protein Translation at the 70 S Ribosome

Proline‐rich antimicrobial peptides (PrAMPs) have been investigated and optimized by several research groups and companies as promising lead compounds to treat systemic infections caused by Gram‐negative bacteria. PrAMPs, such as apidaecins and oncocins, enter the bacteria and kill them apparently through inhibition of specific targets without a lytic effect on the membranes. Both apidaecins and oncocins were shown to bind with nanomolar dissociation constants to the 70S ribosome. In apidaecins, at least the two C‐terminal residues (Arg17 and Leu18) interact strongly with the 70S ribosome, whereas residues Lys3, Tyr6, Leu7, and Arg11 are the major interaction sites in oncocins. Oncocins inhibited protein biosynthesis very efficiently in vitro with half maximal inhibitory concentrations (IC₅₀ values) of 150 to 240 nmol L ^?1. The chaperone DnaK is most likely not the main target of PrAMPs but it binds them with lower affinity.     

Three-dimensional electron cryomicroscopy of ribosomes

Single particle electron cryomicroscopy is nowadays routinely used to generate three-dimensional structural information of ribosomal complexes without the need of crystallization. A large number of structures of functional important ribosomal complexes have thus been determined using this technique. In E. coli 70S ribosomes all three tRNA binding sites could be localized. The ternary complex of EF-TutRNAGTP that delivers the tRNA to the ribosome was directly visualized in a ribosomal complex blocked by the antibiotic kirromycin. Three different functional states of translocation have been studied and the respective EF-G binding sites have been mapped. The level of resolution achievable with electron cryomicroscopy allows conformational changes in the domain structures of elongation factors to be modelled in terms of rigid body movements. Structural information on eukaryotic ribosomes is also available for yeast and mammalian 80S ribosomes. The structural differences between rabbit 80S and E. coli 70S ribosomes could be interpreted in terms of ribosomal RNA expansion segments in the 18S and 23S RNA. The EF-G homologue EF2 was mapped analysing the structure of an 80SEF2sodarin complex and most recently the binding of a hepatitis C virus IRES element to a yeast 40S subunit has been studied. The first electron cryomicroscopical 3D reconstructions have further been used to overcome the initial phasing problems in X-ray crystallographic studies of the ribosome facilitating structure determination of the recent atomic resolution structures of the 30S and 50S ribosomal subunits. In turn, the knowledge of the atomic structure of the ribosome makes detailed interpretations of cryo-EM maps possible at approximately 20 A resolution.     

Is tRNA binding or tRNA mimicry mandatory for translation factors?

tRNA is the adaptor in the translation process. The ribosome has three sites for tRNA, the A-, P-, and E-sites. The tRNAs bridge between the ribosomal subunits with the decoding site and the mRNA on the small or 30S subunit and the peptidyl transfer site on the large or 50S subunit. The possibility that translation release factors could mimic tRNA has been discussed for a long time, since their function is very similar to that of tRNA. They identify stop codons of the mRNA presented in the decoding site and hydrolyse the nascent peptide from the peptidyl tRNA in the peptidyl transfer site. The structures of eubacterial release factors are not yet known, and the first example of tRNA mimicry was discovered when elongation factor G (EF-G) was found to have a closely similar shape to a complex of elongation factor Tu (EF-Tu) with aminoacyl-tRNA. An even closer imitation of the tRNA shape is seen in ribosome recycling factor (RRF). The number of proteins mimicking tRNA is rapidly increasing. This primarily concerns translation factors. It is now evident that in some sense they are either tRNA mimics, GTPases or possibly both.