eEF2 diphthamide modification restrains spurious frameshifting to maintain translational fidelity.

Diphthamide (DPH), a conserved amino acid modification on eukaryotic translation elongation factor eEF2, is synthesized via a complex, multi-enzyme pathway. While DPH is non-essential for cell viability and its function has not been resolved, diphtheria and other bacterial toxins ADP-ribosylate DPH to inhibit translation. Characterizing Saccharomyces cerevisiae mutants that lack DPH or show synthetic growth defects in the absence of DPH, we show that loss of DPH increases resistance to the fungal translation inhibitor sordarin and increases -1 ribosomal frameshifting at non-programmed sites during normal translation elongation and at viral programmed frameshifting sites. Ribosome profiling of yeast and mammalian cells lacking DPH reveals increased ribosomal drop-off during elongation, and removal of out-of-frame stop codons restores ribosomal processivity on the ultralong yeast MDN1 mRNA. Finally, we show that ADP-ribosylation of DPH impairs the productive binding of eEF2 to elongating ribosomes. Our results reveal that loss of DPH impairs the fidelity of translocation during translation elongation resulting in increased rates of ribosomal frameshifting throughout elongation and leading to premature termination at out-of-frame stop codons. We propose that the costly, yet non-essential, DPH modification has been conserved through evolution to maintain translational fidelity despite being a target for inactivation by bacterial toxins.

Rapid 40S scanning and its regulation by mRNA structure during eukaryotic translation initiation.

How the eukaryotic 43S preinitiation complex scans along the 5' untranslated region (5' UTR) of a capped mRNA to locate the correct start codon remains elusive. Here, we directly track yeast 43S-mRNA binding, scanning, and 60S subunit joining by real-time single-molecule fluorescence spectroscopy. 43S engagement with mRNA occurs through a slow, ATP-dependent process driven by multiple initiation factors including the helicase eIF4A. Once engaged, 43S scanning occurs rapidly and directionally at ∼100 nucleotides per second, independent of multiple cycles of ATP hydrolysis by RNA helicases post ribosomal loading. Scanning ribosomes can proceed through RNA secondary structures, but 5' UTR hairpin sequences near start codons drive scanning ribosomes at start codons backward in the 5' direction, requiring rescanning to arrive once more at a start codon. Direct observation of scanning ribosomes provides a mechanistic framework for translational regulation by 5' UTR structures and upstream near-cognate start codons.

Structural basis for the transition from translation initiation to elongation by an 80S-eIF5B complex.

Recognition of a start codon by the initiator aminoacyl-tRNA determines the reading frame of messenger RNA (mRNA) translation by the ribosome. In eukaryotes, the GTPase eIF5B collaborates in the correct positioning of the initiator Met-tRNAiMet on the ribosome in the later stages of translation initiation, gating entrance into elongation. Leveraging the long residence time of eIF5B on the ribosome recently identified by single-molecule fluorescence measurements, we determine the cryoEM structure of the naturally long-lived ribosome complex with eIF5B and Met-tRNAiMet immediately before transition into elongation. The structure uncovers an unexpected, eukaryotic specific and dynamic fidelity checkpoint implemented by eIF5B in concert with components of the large ribosomal subunit.

Retraction: Kim, J.R. and Kim, J.J. Epoxy Resins Toughened with Surface Modified Epoxidized Natural Rubber Fibers by One-Step Electrospinning. Materials 2017, 10, 464, doi:10.3390/ma10050464.

The published article [...].

Epoxy Resins Toughened with Surface Modified Epoxidized Natural Rubber Fibers by One-Step Electrospinning.

Epoxidized natural rubber fibers (ERFs) are developed through one-step electrospinning and directly deposited into epoxy resins without collecting and distributing of fibers. The shape of ERFs shows rough surface due to different evaporation rate of solvent mixture consisting of chloroform and dichloromethane and the average diameter of ERFs is 6.2 µm. The increase of ERFs loading from 0 to 20 wt % into the epoxy resin increases the fracture strain significantly from 1.2% to 13% and toughness from 0.3 MPa to 1.9 MPa by a factor of 7. However, the tensile strength and Young's modulus decrease about 34% from 58 MPa to 34 MPa and from 1.4 GPa to 0.9 GPa, respectively. Due to the crosslinking reactions between oxirane groups of ERFs and amine groups in the resin, surface roughness and the high aspect ratio of ERFs, ERFs result in more effective toughening effect with the minimum loss of tensile properties in epoxy resins.

Eco-Friendly Acaricidal Effects of Nylon 66 Nanofibers via Grafted Clove Bud Oil-Loaded Capsules on House Dust Mites.

Acaricidal nylon 66 fabrics (AN66Fs) grafted with clove oil-loaded microcapsules (COMCs) were developed against Dermatophagoides farina (D. gallinae). The average diameter was about 2.9 µm with a range of 100 nm-8.5 µm. COMCs carried clove oil loading of about 65 vol %. COMCs were chemically grafted to electrospun nylon nanofibers by the chemical reactions between -OH groups of COMCs and -COOH end groups of nylon fabrics to form ester linkages. AN66Fs had an effect on D. farinae depending on COMCs loadings. The increase in COMCs loading of AN66Fs from 5 to 15 wt % increased from 22% to 93% mortality against D. farinae within 72 h. However, AN66Fs containing over 20 wt % COMCs were more effective, showing up to 100% mortality within 24 h because the large amount of monoterpene alcohol, eugenol. This research suggests the use of clove oil and its major constituent eugenol as eco-friendly bioactive agents that can serve as a replacement for synthetic acaricides in controlling the population of D. farinae.

Amino acid substrates impose polyamine, eIF5A, or hypusine requirement for peptide synthesis.

Whereas ribosomes efficiently catalyze peptide bond synthesis by most amino acids, the imino acid proline is a poor substrate for protein synthesis. Previous studies have shown that the translation factor eIF5A and its bacterial ortholog EF-P bind in the E site of the ribosome where they contact the peptidyl-tRNA in the P site and play a critical role in promoting the synthesis of polyproline peptides. Using misacylated Pro-tRNAPhe and Phe-tRNAPro, we show that the imino acid proline and not tRNAPro imposes the primary eIF5A requirement for polyproline synthesis. Though most proline analogs require eIF5A for efficient peptide synthesis, azetidine-2-caboxylic acid, a more flexible four-membered ring derivative of proline, shows relaxed eIF5A dependency, indicating that the structural rigidity of proline might contribute to the requirement for eIF5A. Finally, we examine the interplay between eIF5A and polyamines in promoting translation elongation. We show that eIF5A can obviate the polyamine requirement for general translation elongation, and that this activity is independent of the conserved hypusine modification on eIF5A. Thus, we propose that the body of eIF5A functionally substitutes for polyamines to promote general protein synthesis and that the hypusine modification on eIF5A is critically important for poor substrates like proline.

Eucalyptus oil-loaded microcapsules grafted to cotton fabrics for acaricidal effect against Dermatophagoides farinae.

The purpose of this study was to develop acaricidal cotton fabrics grafted with eucalyptus oil-loaded microcapsules (EOMCs) produced from green resources. EOMCs showed a broad size distribution between 0.5 and 6.5 µm, and had the average diameter 1.8 µm. EOMCs exhibited nonporous spherical shapes and individually remained on cotton fibres. Through AATCC mortality tests against house dust mites (HDMs) (Dermatophagoides farinae), the treated cotton fabric containing EOMCs resulted in 98.7% mortality. Acaricidal efficiency was due to the large amount of oxygenated monoterpene, 1,8-eucalyptol (75.8%) and hydroxylated monoterpenes such as α-terpineol (3.6%), terpinen-4-ol (0.4%) and linalool (0.3%) found in eucalyptus oil. These compounds are effective in enhancing penetration into HDMs. EOMCs produced from safe and natural sources can serve as a replacement for synthetic acaricides in controlling the population of HDM, leading to positive impacts on the human health and environment.

EIF2S3 Mutations Associated with Severe X-Linked Intellectual Disability Syndrome MEHMO.

Impairment of translation initiation and its regulation within the integrated stress response (ISR) and related unfolded-protein response has been identified as a cause of several multisystemic syndromes. Here, we link MEHMO syndrome, whose genetic etiology was unknown, to this group of disorders. MEHMO is a rare X-linked syndrome characterized by profound intellectual disability, epilepsy, hypogonadism and hypogenitalism, microcephaly, and obesity. We have identified a C-terminal frameshift mutation (Ile465Serfs) in the EIF2S3 gene in three families with MEHMO syndrome and a novel maternally inherited missense EIF2S3 variant (c.324T>A; p.Ser108Arg) in another male patient with less severe clinical symptoms. The EIF2S3 gene encodes the γ subunit of eukaryotic translation initiation factor 2 (eIF2), crucial for initiation of protein synthesis and regulation of the ISR. Studies in patient fibroblasts confirm increased ISR activation due to the Ile465Serfs mutation and functional assays in yeast demonstrate that the Ile465Serfs mutation impairs eIF2γ function to a greater extent than tested missense mutations, consistent with the more severe clinical phenotype of the Ile465Serfs male mutation carriers. Thus, we propose that more severe EIF2S3 mutations cause the full MEHMO phenotype, while less deleterious mutations cause a milder form of the syndrome with only a subset of the symptoms.

Synthesis of Antifungal Agents from Xanthene and Thiazine Dyes and Analysis of Their Effects.

Indoor fungi growth is an increasing home health problem as our homes are more tightly sealed. One thing that limits durability of the antifungal agents is the scarcity of reactive sites on many surfaces to attach these agents. In order to increase graft yield of photosensitizers to the fabrics, poly(acrylic acid-co-styrene sulfonic acid-co-vinyl benzyl rose bengal or phloxine B) were polymerized and then grafted to electrospun fabrics. In an alternative process, azure A or toluidine blue O were grafted to poly(acrylic acid), which was subsequently grafted to nanofiber-based and microfiber-based fabrics. The fabrics grafted with photosensitizers induced antifungal effects on all seven types of fungi in the order of rose bengal > phloxine B > toluidine blue O > azure A, which follows the quantum yield production of singlet oxygen for these photoactive dyes. Their inhibition rates for inactivating fungal spores decreased in the order of P. cinnamomi, T. viride, A. niger, A. fumigatus, C. globosum, P. funiculosum, and M. grisea, which is associated with lipid composition in membrane and the morphology of fungal spores. The antifungal activity was also correlated with the surface area of fabric types which grafted the photosensitizer covalently on the surface as determined by the bound color strength.

Photodynamic activity of nanostructured fabrics grafted with xanthene and thiazine dyes against opportunistic fungi.

Fungi are an important class of human pathogens for which considerable research has gone into defeating them. The photodynamic effects of rose bengal (RB), phloxine B (PB), azure A (AA), and toluidine blue O (TBO) dyes to inhibit Aspergillus fumigatus, Aspergillus niger, Trichoderma viride, Penicillium funiculosum, and Chaetomium globosum were investigated grafted to nano- and micro-structured fabrics. Three antifungal tests conducted: broth microdilution test of free dyes, zone of inhibition and quantitative antifungal assays on fabrics grafted with dyes. In the broth microdilution test, free RB displayed the lowest MIC at 32 µM to inhibit visible hyphal growth and germination but the antifungal ability of MIC for other photosensitizers below 63 µM was insignificant. RB and PB showed lower MIC than AA and TBO. In the inhibition zone tests, nanostructured fabrics grafted with RB and PB did not display fungal growth on the surface. Most microstructured fabrics grafted with AA and TBO showed little inhibition. In quantitative antifungal assay, nanostructured fabrics grafted with RB has the largest inhibition rate on T. viride and the lowest inhibition rate on P. funiculosum and the results showed the increasing inhibition rate in the order of AA < TBO < PB < RB.

eIF5A promotes translation of polyproline motifs.

Translation factor eIF5A, containing the unique amino acid hypusine, was originally shown to stimulate Met-puromycin synthesis, a model assay for peptide bond formation. More recently, eIF5A was shown to promote translation elongation; however, its precise requirement in protein synthesis remains elusive. We use in vivo assays in yeast and in vitro reconstituted translation assays to reveal a specific requirement for eIF5A to promote peptide bond formation between consecutive Pro residues. Addition of eIF5A relieves ribosomal stalling during translation of three consecutive Pro residues in vitro, and loss of eIF5A function impairs translation of polyproline-containing proteins in vivo. Hydroxyl radical probing experiments localized eIF5A near the E site of the ribosome with its hypusine residue adjacent to the acceptor stem of the P site tRNA. Thus, eIF5A, like its bacterial ortholog EFP, is proposed to stimulate the peptidyl transferase activity of the ribosome and facilitate the reactivity of poor substrates like Pro.

Tetraarsenic oxide and cisplatin induce apoptotic synergism in cervical cancer.

Tetraarsenic oxide (As4O6, TAO) is a new arsenic compound that inhibits cell growth and induces apoptosis in human cervical cancer cell lines. In the present study, we report that the growth of tumor cells (CaSki) was inhibited by treatment with TAO alone or in combination with cisplatin or paclitaxel in vitro and in vivo. Proliferation was assessed by WST-1 assay, and apoptosis was assessed by Annexin-V/PI FACS analysis in the CaSki cell line treated with a single agent or with the combinations of two agents. Expression of apoptosis-related proteins was analyzed by western blot analysis. A mouse xenograft model using CaSki cells was used to determine the in vivo activity of tetraarsenic oxide alone and in combination with cisplatin or paclitaxel by estimation of tumor size. At the end of the experiment, tumor tissue from each mouse was removed and processed for TUNEL analysis for confirmation of apoptotic cells. TAO was able to inhibit cell proliferation in a time- and dose-dependent manner. A combination of TAO and cisplatin effectively induced apoptosis by activating caspase-3. Using a mouse xenograft model, the sizes of tumors which were treated with a single agent and with a combination of agents decreased in a time-dependent manner. A combination of TAO and cisplatin resulted in a significantly reduced tumor size (P<0.05). The data for the histochemical staining of TUNEL-positive cells showed that the number of apoptotic cells was significantly increased by the combination of TAO and cisplatin. Thus, TAO is a good candidate for use in a combined regimen with cisplatin for patients with cervical cancer.

eIF2γ mutation that disrupts eIF2 complex integrity links intellectual disability to impaired translation initiation.

Together with GTP and initiator methionyl-tRNA, translation initiation factor eIF2 forms a ternary complex that binds the 40S ribosome and then scans an mRNA to select the AUG start codon for protein synthesis. Here, we show that a human X-chromosomal neurological disorder characterized by intellectual disability and microcephaly is caused by a missense mutation in eIF2γ (encoded by EIF2S3), the core subunit of the heterotrimeric eIF2 complex. Biochemical studies of human cells overexpressing the eIF2γ mutant and of yeast eIF2γ with the analogous mutation revealed a defect in binding the eIF2ß subunit to eIF2γ. Consistent with this loss of eIF2 integrity, the yeast eIF2γ mutation impaired translation start codon selection and eIF2 function in vivo in a manner that was suppressed by overexpressing eIF2ß. These findings directly link intellectual disability to impaired translation initiation, and provide a mechanistic basis for the human disease due to partial loss of eIF2 function.

Initiation factor eIF2γ promotes eIF2-GTP-Met-tRNAi(Met) ternary complex binding to the 40S ribosome.

In contrast to prokaryotic elongation factor EF-Tu, which delivers aminoacyl-tRNAs to the ribosomal A-site, eukaryotic initiation factor eIF2 binds methionyl initiator transfer RNA (Met-tRNA(i)(Met)) to the P-site of the 40S ribosomal subunit. The results of directed hydroxyl radical probing experiments to map binding of Saccharomyces cerevisiae eIF2 on the ribosome and on Met-tRNA(i)(Met) revealed that eIF2γ primarily contacts the acceptor stem of Met-tRNA(i)(Met) and identified a key binding interface between domain III of eIF2γ and 18S rRNA helix h44 on the 40S subunit. Whereas the analogous domain III of EF-Tu contacts the T stem of tRNAs, biochemical analyses demonstrated that eIF2γ domain III is important for ribosome, not Met-tRNA(i)(Met). Thus, despite their structural similarity, eIF2 and EF-Tu bind tRNAs in substantially different manners, and we propose that the tRNA-binding domain III of EF-Tu has acquired a new ribosome-binding function in eIF2γ.

Structural integrity of {alpha}-helix H12 in translation initiation factor eIF5B is critical for 80S complex stability.

Translation initiation factor eIF5B promotes GTP-dependent ribosomal subunit joining in the final step of the translation initiation pathway. The protein resembles a chalice with the α-helix H12 forming the stem connecting the GTP-binding domain cup to the domain IV base. Helix H12 has been proposed to function as a rigid lever arm governing domain IV movements in response to nucleotide binding and as a molecular ruler fixing the distance between domain IV and the G domain of the factor. To investigate its function, helix H12 was lengthened or shortened by one or two turns. In addition, six consecutive residues in the helix were substituted by Gly to alter the helical rigidity. Whereas the mutations had minimal impacts on the factor's binding to the ribosome and its GTP binding and hydrolysis activities, shortening the helix by six residues impaired the rate of subunit joining in vitro and both this mutation and the Gly substitution mutation lowered the yield of Met-tRNA(i)(Met) bound to 80S complexes formed in the presence of nonhydrolyzable GTP. Thus, these two mutations, which impair yeast cell growth and enhance ribosome leaky scanning in vivo, impair the rate of formation and stability of the 80S product of subunit joining. These data support the notion that helix H12 functions as a ruler connecting the GTPase center of the ribosome to the P site where Met-tRNA(i)(Met) is bound and that helix H12 rigidity is required to stabilize Met-tRNA(i)(Met) binding.

Acaricidal activities of clove bud oil and red thyme oil using microencapsulation against HDMs.

The purpose of this study was to produce a safer microcapsule loaded with clove bud oil and red thyme oil to reduce the population of house dust mites (HDMs). Gelatin-based microcapsules 4-85 µm in size were created, with agitation speed and type of oil playing a critical role in governing their size. Microcapsules made up of single spherical units less than 30 µm in diameter remained separate on the fibre, whereas larger microcapsules of over 30 µm ruptured or aggregated. Thermogravimetric analysis (TGA) demonstrated that microcapsules containing red thyme oil showed a more consistent range of oil loading, from 50 to 80%, than microcapsules containing clove bud oil, which ranged from 30 to 80% (more deviated). Mortality tests on Dermatophagoides farinae conducted on fabric with attached microcapsules showed that clove bud oil, containing a more phenolic monoterpenoid (eugenol), was more effective at reducing the live HDMs (94% mortality).

rRNA suppressor of a eukaryotic translation initiation factor 5B/initiation factor 2 mutant reveals a binding site for translational GTPases on the small ribosomal subunit.

The translational GTPases promote initiation, elongation, and termination of protein synthesis by interacting with the ribosome. Mutations that impair GTP hydrolysis by eukaryotic translation initiation factor 5B/initiation factor 2 (eIF5B/IF2) impair yeast cell growth due to failure to dissociate from the ribosome following subunit joining. A mutation in helix h5 of the 18S rRNA in the 40S ribosomal subunit and intragenic mutations in domain II of eIF5B suppress the toxic effects associated with expression of the eIF5B-H480I GTPase-deficient mutant in yeast by lowering the ribosome binding affinity of eIF5B. Hydroxyl radical mapping experiments reveal that the domain II suppressors interface with the body of the 40S subunit in the vicinity of helix h5. As the helix h5 mutation also impairs elongation factor function, the rRNA and eIF5B suppressor mutations provide in vivo evidence supporting a functionally important docking of domain II of the translational GTPases on the body of the small ribosomal subunit.

Intragenic suppressor mutations restore GTPase and translation functions of a eukaryotic initiation factor 5B switch II mutant.

Structural studies of GTP-binding proteins identified the Switch I and Switch II elements as contacting the gamma-phosphate of GTP and undergoing marked conformational changes upon GTP versus GDP binding. Movement of a universally conserved Gly at the N terminus of Switch II is thought to trigger the structural rearrangement of this element. Consistently, we found that mutation of this Gly in the Switch II element of the eukaryotic translation initiation factor 5B (eIF5B) from Saccharomyces cerevisiae impaired cell growth and the guanine nucleotide-binding, GTPase, and ribosomal subunit joining activities of eIF5B. In a screen for mutations that bypassed the critical requirement for this Switch II Gly in eIF5B, intragenic suppressors were identified in the Switch I element and at a residue in domain II of eIF5B that interacts with Switch II. The intragenic suppressors restored yeast cell growth and eIF5B nucleotide-binding, GTP hydrolysis, and subunit joining activities. We propose that the Switch II mutation distorts the geometry of the GTP-binding active site, impairing nucleotide binding and the eIF5B domain movements associated with GTP binding. Accordingly, the Switch I and domain II suppressor mutations induce Switch II to adopt a conformation favorable for nucleotide binding and hydrolysis and thereby reestablish coupling between GTP binding and eIF5B domain movements.