tRNAVal allows four-way decoding with unmodified uridine at the wobble position in Lactobacillus casei.

Modifications at the wobble position (position 34) of tRNA facilitate interactions that enable or stabilize non-Watson-Crick basepairs. In bacterial tRNA, 5-hydroxyuridine (ho5U) derivatives xo5U [x: methyl (mo5U), carboxymethyl (cmo5U), and methoxycarbonylmethyl (mcmo5U)] present at the wobble positions of tRNAs are responsible for recognition of NYN codon families. These modifications of U34 allow basepairing not only with A and G but also with U and in some cases C. mo5U was originally found in Gram-positive bacteria, and cmo5U and mcmo5U were found in Gram-negative bacteria. tRNAs of Mycoplasma species, mitochondria, and chloroplasts adopt four-way decoding in which unmodified U34 recognizes codons ending in A, G, C, and U. Lactobacillus casei, Gram-positive bacteria and lactic acid bacteria, lacks the modification enzyme genes for xo5U biosynthesis. Nevertheless, L. casei has only one type of tRNAVal with the anticodon UAC [tRNAVal(UAC)]. However, the genome of L. casei encodes an undetermined tRNA (tRNAUnd) gene, and the sequence corresponding to the anticodon region is GAC. Here, we confirm that U34 in L. casei tRNAVal is unmodified and that there is no tRNAUnd expression in the cells. In addition, in vitro transcribed tRNAUnd was not aminoacylated by L. casei valyl-tRNA synthetase suggesting that tRNAUnd is not able to accept valine, even if expressed in cells. Correspondingly, native tRNAVal(UAC) with unmodified U34 bound to all four valine codons in the ribosome A site. This suggests that L. casei tRNAVal decodes all valine codons by four-way decoding, similarly to tRNAs from Mycoplasma species, mitochondria, and chloroplasts.

Spin and charge interactions between nanographene host and ferrocene.

Ferrocene (FeCp2) was introduced as a non-magnetic guest molecule to activated carbon fibers (ACFs) as a nanographene-based host having localized spins originating from zigzag edges of graphene. The introduction of the guest molecule was confirmed by FTIR for ACFs-FeCp2 introduced at 55 (150) °C (FeCp2-ACFs-55(150)). The appearance of satellite Fe2p peaks and the increase in shake-up peak intensity of the C1s in the XPS spectrum proved the emergence of charge-transfer host-guest interaction in FeCp2-ACFs-150, supported by the red-shift of the G-band in the Raman spectrum. The six-times enhancement in the spin concentration in FeCp2-ACFs-150 compared with ACFs indicates the spin magnetism of the non-magnetic guest FeCp2+ molecule induced by a charge-transfer host-guest interaction in the nanographene host. The larger ESR linewidth than that expected from the dipolar interaction estimated by the localized spin concentration suggests the exchange interaction between the nanographene and FeCp2 spins. The narrowing of the ESR linewidth of FeCp2-ACFs-55 upon higher excitation microwave power suggests the inhomogeneity of the environment for FeCp2+ molecules in the nanographene host. The observed induction of spin magnetism by the interfacial interactions between the nanographene host and the guest molecules will be a promising strategy for developing a new class of molecular magnets.

Recombinant expression and purification of phenylalanyl-tRNA synthetase from wheat: a long-lasting poly(U)-dependent poly(Phe) synthesis system.

Synthetic genes for the two subunits of phenylalanyl-tRNA synthetase (PheRS) from wheat were expressed in Escherichia coli. When each gene was induced individually, the α subunit with a cleavable 6 × His tag at the amino terminus was largely soluble, while the ß subunit was almost completely insoluble. When the two subunits were co-expressed, a soluble fraction containing the two subunits were obtained. This was purified by a standard method in which the tag was cleaved off with a specific protease after affinity purification. As the sample contained slightly more PheRSα than PheRSß, we further resolved the sample by gel filtration to obtain the fraction that showed the size of the conventional α2ß2 tetrameric complex and contains an almost equal amount of the two subunits. The final yield was 0.6 mg per 1 liter of the culture medium, and the specific activity was 28 nmol min-1 mg-1, which was higher than that of a fraction purified from wheat germ. This recombinant PheRS was used, along with purified samples of the elongation factors and the ribosomes from wheat germ, for a poly(U)-dependent poly(Phe) synthesis reaction. The reaction was dependent on the added components and lasted for more than several hours.

Isolated Spin-7/2 Species of Gadolinium (III) Chelate Complexes on the Surface of 5-nm Diamond Particles.

The magnetic characteristics of a system of triply charged gadolinium ions Gd3+ chelated with carboxyls on the surface of detonation nanodiamond (DND) particles have been studied. Gd3+ ions demonstrate almost perfect spin (S = 7/2) paramagnetism with negligible antiferromagnetic interaction between spins (Weiss temperature about -0.35 K) for a wide range of concentrations up to ~18 ions per 5 nm particle. The study of the concentration dependence of the electron paramagnetic resonance signal for DND intrinsic defects with spin ½ (g = 2.0027) shows that Gd3+ ions are located on average at a distance of no more than 1.4 nm from shallow subsurface defects with spin 1/2. At the same time, they are located (according to density functional theory calculations) at a distance of about or at least 0.28 nm from the particle surface. Magnetic studies also confirm the isolated nature of the gadolinium chelate complexes on the surface of DND particles. DND particles turn out to be an optimal carrier for high-spin 4f- ions (gadolinium) in a highly concentrated isolated state. This property makes DND-Gd particles a candidate for the role of a contrast agent for magnetic resonance imaging.

Mechanism of tRNA recognition by heterotetrameric glycyl-tRNA synthetase from lactic acid bacteria.

Glycyl-tRNA synthetases (GlyRSs) have different oligomeric structures depending on the organisms. While a dimeric α2 GlyRS species is present in archaea, eukaryotes and some eubacteria, a heterotetrameric α2ß2 GlyRS species is found in most eubacteria. Here, we present the crystal structure of heterotetrameric α2ß2 GlyRS, consisting of the full-length α and ß subunits, from Lactobacillus plantarum (LpGlyRS), gram-positive lactic bacteria. The α2ß2LpGlyRS adopts the same X-shaped structure as the recently reported Escherichia coli α2ß2 GlyRS. A tRNA docking model onto LpGlyRS suggests that the α and ß subunits of LpGlyRS together recognize the L-shaped tRNA structure. The α and ß subunits of LpGlyRS together interact with the 3'-end and the acceptor region of tRNAGly, and the C-terminal domain of the ß subunit interacts with the anticodon region of tRNAGly. The biochemical analysis using tRNA variants showed that in addition to the previously defined determinants G1C72 and C2G71 base pairs, C35, C36 and U73 in eubacterial tRNAGly, the identification of bases at positions 4 and 69 in tRNAGly is required for efficient glycylation by LpGlyRS. In this case, the combination of a purine base at Position 4 and a pyrimidine base at Position 69 in tRNAGly is preferred.

Correlation between charge density wave phase transition and hydrogen adsorption in 1T-TaS2thin film devices.

Thin films of tantalum disulfide in the 1T-polytype structural phase (1T-TaS2), a type of metallic two-dimensional (2D) transition metal dichalcogenides (TMDs), are reactive to H2. Interestingly, in the incommensurate charge-density wave (ICCDW) phase with a metallic state, the electrical resistance of the 1T-TaS2thin film decreases when H2is adsorbed on it and returns to its initial value upon desorption. In contrast, the electrical resistance of the film in the nearly commensurate CDW (NCCDW) phase, which has a subtle band overlap or a small bandgap, does not change upon H2adsorption/desorption. This difference in H2reactivity is a result of differences in the electronic structure of the two 1T-TaS2phases, namely, the ICCDW and NCCDW phases. Compared to other semiconductor 2D-TMDs such as MoS2and WS2, the metallic TaS2has been theoretically proven to capture gas molecules more easily because Ta has a stronger positive charge than Mo or W. Our experimental results provide evidence of this. Notably, this study is the first example of H2sensing using 1T-TaS2thin films and demonstrates the possibility of controlling the reactivity of the sensors to the gas by changing the electronic structure via CDW phase transitions.

Intron-Dependent or Independent Pseudouridylation of Precursor tRNA Containing Atypical Introns in Cyanidioschyzon merolae.

Eukaryotic precursor tRNAs (pre-tRNAs) often have an intron between positions 37 and 38 of the anticodon loop. However, atypical introns are found in some eukaryotes and archaea. In an early-diverged red alga Cyanidioschyzon merolae, the tRNAIle(UAU) gene contains three intron coding regions, located in the D-, anticodon, and T-arms. In this study, we focused on the relationship between the intron removal and formation of pseudouridine (Ψ), one of the most universally modified nucleosides. It had been reported that yeast Pus1 is a multiple-site-specific enzyme that synthesizes Ψ34 and Ψ36 in tRNAIle(UAU) in an intron-dependent manner. Unexpectedly, our biochemical experiments showed that the C. merolae ortholog of Pus1 pseudouridylated an intronless tRNAIle(UAU) and that the modification position was determined to be 55 which is the target of Pus4 but not Pus1 in yeast. Furthermore, unlike yeast Pus1, cmPus1 mediates Ψ modification at positions 34, 36, and/or 55 only in some specific intron-containing pre-tRNAIle(UAU) variants. cmPus4 was confirmed to be a single-site-specific enzyme that only converts U55 to Ψ, in a similar manner to yeast Pus4. cmPus4 did not catalyze the pseudouridine formation in pre-tRNAs containing an intron in the T-arm.

Recognition of tRNAIle with a UAU anticodon by isoleucyl-tRNA synthetase in lactic acid bacteria.

In almost all eubacteria, the AUA codon is translated by tRNAIle2 bearing lysidine at the wobble position. Lysidine is introduced by tRNAIle lysidine synthetase (TilS) via post-transcriptional modification of the cytidine of tRNAIle2 (CAU). Lactobacillus casei and Lactobacillus plantarum have tilS homologues and tRNAIle2 (CAU) genes. In addition, L. casei also has another tRNAIle2 gene with an UAU anticodon. L. plantarum has a tRNAIle (UAU)-like RNA. Here, we demonstrate that L. casei tRNAIle2 (UAU) is charged with isoleucine by L. casei isoleucyl-tRNA synthetase (IleRS) but not by L. plantarum IleRS, even though the amino acid identity of these two enzymes is over 60%. It has been reported that, in Mycoplasma mobile, which has its tRNAIle2 (UAU) but no tilS homologue, an Arg residue at position 865 of the IleRS is required for recognition of the UAU anticodon. This position is occupied by an Arg also in the IleRSs from both of the Lactobacillus species. Thus, other residues in L. casei, IleRS should also contribute to the recognition of tRNAIle2 (UAU). We found that a chimeric L. casei IleRS in which the N-terminal domain was replaced by the corresponding region of L. plantatarum IleRS has very low aminoacylation activity towards both tRNAIle2 (UAU) and tRNAIle1 (GAU). The A18G mutant had barely detectable aminoacylation activity towards either of the tRNAsIle . However, a double point mutant of A18G and G19N aminoacylated tRNAIle1 (GAU), but not tRNAIle2 (UAU). Our results suggest that, for L. casei IleRS, Ala18 and Gly19 also play a critical role in recognition of tRNAIle2 (UAU).

The uridine to pseudouridine modification at the wobble position of eukaryotic isoleucine tRNA species is unlikely to induce mistranslation.

Replacement of a U in an RNA duplex with a pseudouridine (Ψ), in general, stabilize the duplex because of the stronger stacking interaction, even concerning the wobble pair with G. The tRNA species specific to the AUA isoleucine codon in many eukaryotes have a Ψ at the first position of the anticodon. This tRNAIle would cause mistranslation if it could recognize the AUG codon through formation of a Ψ-G base pair. Here, I propose rationales for the minimal promotive effect of the U to Ψ modification on the mistranslation of the AUG codon.

Anomalous spin relaxation in graphene nanostructures on the high temperature annealed surface of hydrogenated diamond nanoparticles.

The electronic and magnetic structures of diamond nanoparticles with a hydrogenated surface are investigated as a function of annealing temperature under vacuum annealing up to 800-1000 °C. Near edge X-ray absorption fine structure (NEXAFS) spectra together with elemental analysis show successive creation of defect-induced nonbonding surface states at the expense of surface-hydrogen atoms as the annealing temperature is increased above 800 °C. Magnetization and ESR spectra confirm the increase in the concentration of localized spins assigned to the nonbonding surface states upon the increase of the annealing temperature. Around 800 °C, surface defects collectively created upon the annealing result in the formation of graphene nano-islands which possess magnetic nonbonding edge states of π-electron origin. Interestingly, extremely slow spin relaxation is observed in the magnetization of the edge state spins at low temperatures. The relaxation time is well explained in terms of a lognormal distribution of magnetic anisotropy energies instead of the classical Néel relaxation mechanism with a unique magnetic anisotropy energy, in addition to the contribution of the quantum mechanical tunnelling mechanism. The spin-orbit interaction enhanced by the electrostatic potential gradient created at the interface between the core diamond particle and surface graphene nano-islands is responsible for the slow spin relaxation.

High-Quality Green-Emitting Nanodiamonds Fabricated by HPHT Sintering of Polycrystalline Shockwave Diamonds.

We demonstrate a high-pressure, high-temperature sintering technique to form nitrogen-vacancy-nitrogen centres in nanodiamonds. Polycrystalline diamond nanoparticle precursors, with mean size of 25 nm, are produced by the shock wave from an explosion. These nanoparticles are sintered in the presence of ethanol, at a pressure of 7 GPa and temperature of 1300 °C, to produce substantially larger (3-4 times) diamond crystallites. The recorded spectral properties demonstrate the improved crystalline quality. The types of defects present are also observed to change; the characteristic spectral features of nitrogen-vacancy and silicon-vacancy centres present for the precursor material disappear. Two new characteristic features appear: (1) paramagnetic substitutional nitrogen (P1 centres with spin ½) with an electron paramagnetic resonance characteristic triplet hyperfine structure due to the I = 1 magnetic moment of the nitrogen nuclear spin and (2) the green spectral photoluminescence signature of the nitrogen-vacancy-nitrogen centres. This production method is a strong alternative to conventional high-energy particle beam irradiation. It can be used to easily produce purely green fluorescing nanodiamonds with advantageous properties for optical biolabelling applications.

Photoluminescence from NV- Centres in 5 nm Detonation Nanodiamonds: Identification and High Sensitivity to Magnetic Field.

The content of nitrogen-vacancy (NV-) colour centres in the nanodiamonds (DNDs) produced during the detonation of nitrogen-containing explosives was found to be 1.1 ± 0.3 ppm. This value is impressive for nanodiamonds of size < 10 nm with intentionally created NV- centres. The concentration was estimated from the electron paramagnetic resonance as determined from the integrated intensity of the g = 4.27 line. This line is related with "forbidden" ∆ms = 2 transitions between the Zeeman levels of a NV- centre's ground triplet state. Confocal fluorescence microscopy enables detection of the red photoluminescence (PL) of the NV- colour centres in nanoscale DND aggregates formed from the 5-nm nanoparticles. Subwavelength emitters consisting of NV- with sizes a few times smaller than the diffraction-limited spot are clearly distinguished. We have further observed an abrupt drop in the PL intensity when mixing and anti-crossing of the ground and excited states spin levels in NV- occurs under an applied external magnetic field. This effect is a unique quantum feature of NV- centres, which cannot be observed for other visible domain light-emitting colour centres in a diamond lattice.

Kinetic characterization of substrate-binding sites of thermostable tRNA methyltransferase (TrmB).

TrmB is a eubacterial tRNA methyltransferase which catalyzes the formation of N7-methylguanosine at position 46 (m7G46) in tRNA consuming S-adenosyl-L-methionine (AdoMet) as the methyl group donor during the reaction. Previously, we purified TrmB from Aquifex aeolicus, a hyper-thermophilic eubacterium, and clarified the recognition sites in tRNA. Furthermore, we reported that an additional C-terminal region of A. aeolicus TrmB is required for protein stability at high temperatures. In the current study, we devised a new purification method to remove contaminating RNA completely. The purified enzyme is mainly in a monomeric form. We prepared 17 mutant A. aeolicus TrmB proteins and performed kinetic studies. Our analyses reveal that Glu47, Tyr95, Arg108, Thr165 and Tyr167 residues are important for AdoMet binding and that Asp74, Asp97, and Thr132 are important for the methyltransfer reaction. Furthermore, substitution of Asp133 by alanine caused complete loss of enzymatic activity. Based on the results of our current studies and previous bioinformatic, biochemical and structural studies by others, a reaction mechanism for TrmB is proposed.

Characterization of redundant tRNAIles with CAU and UAU anticodons in Lactobacillus plantarum.

In most eubacteria, the minor AUA isoleucine codon is decoded by tRNAIle2, which has a lysidine (L) in the anticodon loop. The lysidine is introduced by tRNAIle-lysidine synthetase (TilS) through post-transcriptional modification of cytidine to yield an LAU anticodon. Some bacteria, Lactobacillus plantarum for example, possess two tRNAIle2(UAU) genes in addition to, two tRNAIle2(CAU) genes and the tilS gene. tRNA expression from all these genes would generate redundancy in a tRNA that decodes a rare AUA codon. In this study, we investigated the tRNA expression from these genes in L. plantarum and characterized the corresponding tRNAs. The tRNAIle2(CAU) gene products are modified by TilS to produce tRNAIle2(LAU), while tRNAIle2(UAU) lacks modification especially in the anticodon sequence. We found that tRNAIle2(LAU) is charged with isoleucine but tRNAIle2(UAU) is not. Our results suggest that the tRNAIle2 redundancy may be related to different roles of these tRNAs in the cell.

Translational resistivity/conductivity of coding sequences during exponential growth of Escherichia coli.

Codon adaptation index (CAI) has been widely used for prediction of expression of recombinant genes in Escherichia coli and other organisms. However, CAI has no mechanistic basis that rationalizes its application to estimation of translational efficiency. Here, I propose a model based on which we could consider how codon usage is related to the level of expression during exponential growth of bacteria. In this model, translation of a gene is considered as an analog of electric current, and an analog of electric resistance corresponding to each gene is considered. "Translational resistance" is dependent on the steady-state concentration and the sequence of the mRNA species, and "translational resistivity" is dependent only on the mRNA sequence. The latter is the sum of two parts: one is the resistivity for the elongation reaction (coding sequence resistivity), and the other comes from all of the other steps of the decoding reaction. This electric circuit model clearly shows that some conditions should be met for codon composition of a coding sequence to correlate well with its expression level. On the other hand, I calculated relative frequency of each of the 61 sense codon triplets translated during exponential growth of E. coli from a proteomic dataset covering over 2600 proteins. A tentative method for estimating relative coding sequence resistivity based on the data is presented.

CodHonEditor: Spreadsheets for Codon Optimization and Editing of Protein Coding Sequences.

Gene synthesis is getting more important with the growing availability of low-cost commercial services. The coding sequences are often "optimized" as for the relative synonymous codon usage (RSCU) before synthesis, which is generally included in the commercial services. However, the codon optimization processes are different among different providers and are often hidden from the users. Here, the d'Hondt method, which is widely adopted as a method for determining the number of seats for each party in proportional-representation public elections, is applied to RSCU fitting. This allowed me to make a set of electronic spreadsheets for manual design of protein coding sequences for expression in Escherichia coli, with which users can see the process of codon optimization and can manually edit the codons after the automatic optimization. The spreadsheets may also be useful for molecular biology education.

SfiNX: a method for assembly of protein coding sequences with high success rates.

OBJECTIVE: Concatenation of two NdeI-XhoI gene fragments via an oligonucleotide linker on a plasmid vector with an SfiI site was performed to evaluate success rates in construction of polycistronic genes expressible in Escherichia coli. RESULTS: A series of plasmids with an SfiI site between the selection marker and the replication origin were constructed. The three wheat eEF1B subunit genes inserted between the NdeI and XhoI sites of pET-22b were transferred to the SfiI-containing plasmid with a spectinomycin-resistance gene. Then, the marker gene in the resultant plasmids was substituted with the ampicillin-resistance gene. These plasmids were used for concatenation of two different genes via a linker oligonucleotide containing a ribosome-binding site. During these operations, 42 clones were picked up out of which 41 had the intended product plasmid. CONCLUSION: This method, named as the SfiNX method, is useful for trial-and-error based testing of different combinations of fusion and co-expression partners for optimization of recombinant protein production.

Preferential oxidation-induced etching of zigzag edges in nanographene.

We investigated the thermal oxidation process of nanographene using activated carbon fibers (ACFs) by thermogravimetry (TG), X-ray photoemission spectroscopy (XPS), near-edge X-ray absorption fine structure (NEXAFS), and electrical conductance measurements. The oxidation process started from the edge of nanographene with the formation of phenol (-OH) or ether (C-O-C) groups attached to edge carbon atoms, as verified by the XPS and NEXAFS results. While the TG results indicated a decrease in the size of the nanographene sheet during the oxidation process, the intensity of the edge-state peak, i.e., the signature of the zigzag edge, decreased in the C K-edge NEXAFS spectra. This suggests that the zigzag edge preferentially reacted with oxygen and that the nanographene terminated with the thermodynamically unstable zigzag edges converted to one terminated with stable armchair edges. As the oxidation temperature increased, the activation energy for the electron hopping transport governed by the Coulomb gap variable range hopping between the nanographene sheets increased, and the tunneling barrier decreased. This change can be understood on the basis of the decrease in the size of the nanographene sheets together with the preferential etching of nanographene edges and the decrease in the inter-nanographene-sheet distance.

Heat treatment effect on the electronic and magnetic structures of nanographene sheets investigated through electron spectroscopy and conductance measurements.

The heat treatment effect on the electronic and magnetic structures of a disordered network of nanographene sheets has been investigated by in situ measurements of X-ray photoemission spectroscopy, near-edge X-ray absorption fine structure (NEXAFS), and electrical conductance, together with temperature-programmed desorption measurements. Oxygen-containing functional groups bonded to nanographene edges in the pristine sample are almost completely decomposed under heat treatment up to 1300-1500 K, resulting in the formation of edges primarily terminated by hydrogen. The removal of the oxygen-containing groups enhances the conductance owing to the decrease in the electron transport barriers between nanographene sheets. Heat treatment above 1500 K removes also the hydrogen atoms from the edges, promoting the successive fusion of nanographene sheets at the expense of edges. The decrease in the π* peak width in NEXAFS indicates the progress of the fusion reaction, that is, the extension of the π-conjugation, which agrees with the increase in the orbital susceptibility previously reported. The fusion leads to the formation of local π/sp(2) bridges between nanographene sheets and brings about an insulator-to-metal transition at 1500-1600 K, at which the bridge network becomes infinite. As for the magnetism, the intensity of the edge state peak in NEXAFS, which corresponds to the number of the spin-polarized edge states, decreases above 1500 K, though the effective edge-state spin density per edge state starts decreasing at approximately 200 K lower than the temperature of the edge state peak change. This disagreement indicates the development of antiferromagnetic short range ordering as a precursor of a spin glass state near the insulator-metal transition, at which the random network of inter-nanographene-sheet exchange interactions strengthened with the formation of the π/sp(2) bridges becomes infinite.

Magnetic edge-states in nanographene, HNO3-doped nanographene and its residue compounds of nanographene-based nanoporous carbon.

We investigated the magnetic and electronic properties of nanographene and its charge transfer effect, using near edge X-ray absorption fine structure (NEXAFS), magnetic susceptibility and ESR measurements, and elemental analysis, with the employment of nanoporous carbon, which consists of a three dimensional disordered network of loosely stacked nanographene sheets, in relation to the host-guest interaction with HNO3 as the electron-accepting guest. The adsorption of electron acceptor HNO3 decreases the intensity of the edge state peak in NEXAFS as a result of the charge-transfer-induced Fermi energy downshift, in agreement with the decrease in the edge-state spin concentration, and it also induces the structural expansion, which makes the inter-nanographene sheet distance elongated, resulting in weakening of the inter-nanographene-sheet antiferromagnetic interaction as evidenced by the decrease in the Weiss temperature. In addition, the decomposition of HNO3, which takes place with the electron-rich edge state as an oxidation catalyst, results in the creation of oxygen/nitrogen-containing functional groups bonded to the periphery of the nanographene sheets. Heat-treatment of the HNO3-ACFs under evacuation desorbs the HNO3 molecules completely, though a part of the oxygen/nitrogen-containing species remains strongly bonded to the edge even at a high temperature of ∼800 °C, according to NEXAFS and elemental analysis results. These remaining species participate in the charge transfer, modifying the electronic structure as observed with the decrease in the orbital susceptibility and the strengthening of the inter-nanographene-sheet antiferromagnetic interaction.