Purification and characterization of 3-(5-oxo-2-thioxoimidazolidin-4-yl) propionic acid desulfhydrase involved in ergothioneine utilization in Burkholderia sp. HME13

Recombinant 3-(5-oxo-2-thioxoimidazolidin-4-yl) propionic acid desulfhydrase (ErtC) derived from Burkholderia sp. HME13 was purified to homogeneity. Here, ErtC's kinetic parameters, optimum reaction temperature and pH, and stability at varying temperatures and pH and the effects of various additives on ErtC activity were determined. Real-time polymerase chain reaction and enzyme assays suggested that ergothioneine induced the expression of ertC.

Isomerism tunes the diradical character of difluorenopyrroles at constant Hückel-level anti-aromaticity

A new diradical based on diindenocarbazole or difluorenopyrrole was synthesized and experimentally characterized by optical, electrochemical, and magnetic techniques, as well as quantum chemical calculations. The isomerism of these structures tunes the diradical character and the associated properties, representing a unique case of such important modulation. A full study of the electronic structure was carried out considering the perturbative interactions between different canonical forms as well as the anti-aromatic character of the molecular cores. Such a study reveals how we can tune diradical character simply by reorganizing the bonding patterns at constant chemical costs (composition).

A series of boron difluoride complexes of azinylcarbazoles: synthesis and structure-property relationships

A series of boron difluoride (BF₂) complexes of azinylcarbazoles 1b-1h were synthesized, and the effects of the structure of azine moieties on the photophysical and electrochemical properties of the BF₂ complexes were clarified. UV-vis analysis of 1b with quinoline, 1c with isoquinoline, and fully fused 1d revealed that fusion with a benzene ring to a pyridylcarbazole BF₂ complex (1a) resulted in red shifts of longest-maximum absorption wavelengths (λ_max). UV-vis analysis of 1e and 1f with pyrimidine, 1g with pyridazine, and 1h with pyrazine revealed that substitution of a carbon atom to a nitrogen atom in 1a also resulted in red shifts of λ_max. The fluorescence quantum yields (Φ_f) decreased from 1a to 1b-1h, and especially, the fluorescence of 1e, 1g, and 1h was quenched in solution. At 77 K, the emission intensities of 1b-1h were significantly increased compared with those at ambient temperature, and they also exhibited phosphorescence with relatively narrow energy gaps between the singlet and triplet excited states. These results on the emission at 77 K indicate that the quench of fluorescence from 1e, 1g, and 1h at ambient temperature originates from both internal conversions and intersystem crossing. In the solid state, all of the complexes including 1e, 1g, and 1h exhibited emission. Distinctive aggregation-induced emission properties were observed for 1e-1h. Electrochemical measurements revealed that the replacement of the pyridine moiety in 1a with azine moieties reduced electrochemical gaps mainly due to a decrease in the LUMO levels. The effects of azine moieties on electronic structures were also discussed based on theoretical calculations.

Site-selective radical reactions of kinetically stable open-shell singlet diradicaloid difluorenoheteroles with tributyltin hydride and azo-based radical initiators

We have demonstrated site-selective radical reactions of the kinetically stable open-shell singlet diradicaloids difluoreno[3,4-b:4',3'-d]thiophene (DFTh) and difluoreno[3,4-b:4',3'-d]furan (DFFu) with tributyltin hydride (HSn(n-Bu)₃) and azo-based radical initiators. Treatment of these diradicaloids with HSn(n-Bu)₃ induces hydrogenation at the ipso-carbon in the five-membered rings, while treatment with 2,2'-azobis(isobutyronitrile) (AIBN) induces substitution at the carbon atoms in the peripheral six-membered rings. We have also developed one-pot substitution/hydrogenation reactions of DFTh/DFFu with various azo-based radical initiators and HSn(n-Bu)₃. The resulting products can be converted into substituted DFTh/DFFu derivatives via dehydrogenation. Theoretical calculations unveiled a detailed mechanism of the radical reactions of DFTh/DFFu with HSn(n-Bu)₃ and with AIBN, and that the site-selectivity of these radical reactions is controlled by the balance of the spin density and the steric hindrance in DFTh/DFFu.

Characterization of hydantoin-5-propionic acid amidohydrolase involved in ergothioneine utilization in Burkholderia sp. HME13

In our previous study, ertABC genes encoding ergothionase, thiourocanate hydratase, and 3-(5-oxo-2-thioxoimidazolidin-4-yl) propionic acid desulfhydrase were identified, all of which may be involved in ergothioneine utilization of Burkholderia sp. HME13. In this study, we identify the ertD gene encoding metal-dependent hydantoin-5-propionic acid amidohydrolase in this strain. Mn2+-containing ErtD showed maximum activity at 45 °C and pH 8.5 and was stable at temperatures up to 45 °C. The Km and Vmax values of Mn2+-containing ErtD for hydantoin-5-propionic acid were 2.8 m m and 16 U/mg, respectively. Real-time polymerase chain reaction (PCR) revealed that ertD expression levels in Burkholderia sp. HME13 cells cultivated in ergothioneine medium were 3.3-fold higher than those in cells cultivated in Luria-Bertani (LB) medium. ErtD activity in the crude extract from Burkholderia sp. HME13 cells cultured in ergothioneine medium was 0.018 U/mg, whereas that in LB medium was not detected. Accordingly, we suggest that ErtD is involved in ergothioneine utilization in this strain.

A double-helical S,C-bridged tetraphenyl-para-phenylenediamine and its persistent radical cation

A structurally constrained, double-helical S,C-bridged tetraphenyl-para-phenylenediamine (TPPD) has been synthesized. The stable radical cation of the S,C-bridged TPPD was generated by chemical oxidation, and the electron spin was found to be delocalized over the entire π-conjugated framework. The excellent conformational stability of the neutral molecule facilitated the separation of its enantiomers.

Phylogenic analysis of new viral cluster of large phages with unusual DNA genomes containing uracil in place of thymine in gene-sharing network, using phages S6 and PBS1 and relevant uncultured phages derived from sewage metagenomics

Bacteriophages (phages) are the most diverse and abundant life-form on Earth. Jumbophages are phages with double-stranded DNA genomes longer than 200 kbp. Among these, some jumbophages with uracil in place of thymine as a nucleic acid base, which we have tentatively termed "dU jumbophages" in this study, have been reported. Because the dU jumbophages are considered to be a living fossil from the RNA world, the evolutionary traits of dU jumbophages are of interest. In this study, we examined the phylogeny of dU jumbophages. First, tBLASTx analysis of newly sequenced dU jumbophages such as Bacillus phage PBS1 and previously isolated Staphylococcus phage S6 showed similarity to the other dU jumbophages. Second, we detected the two partial genome sequences of uncultured phages possibly relevant to dU jumbophages, scaffold_002 and scaffold_007, from wastewater metagenomics. Third, according to the gene-sharing network analysis, the dU jumbophages, including phages PBS1 and S6, and uncultured phage scaffold_002 formed a cluster, which suggested a new viral subfamily/family. Finally, analyses of the phylogenetic relationship with other phages showed that the dU jumbophage cluster, which had two clades of phages infecting Gram-negative and Gram-positive bacteria, diverged from the single ancestral phage. These findings together with previous reports may imply that dU jumbophages evolved from the same origin before divergence of Gram-negative and Gram-positive bacteria.

Medium Diradical Character, Small Hole and Electron Reorganization Energies and Ambipolar Transistors in Difluorenoheteroles

Four difluorenoheteroles having a central quinoidal core with the heteroring varying as furan, thiophene, its dioxide derivative and pyrrole have shown to be medium character diradicals. Solid-state structures, optical, photophysical, magnetic, and electrochemical properties have been discussed in terms of diradical character, variation of aromatic character and captodative effects (electron affinity). Organic field-effect transistors (OFETs) have been prepared, showing balanced hole and electron mobilities of the order of 10^-3  cm²  V^-1  s^-1 or ambipolar charge transport which is first inferred from their redox amphoterism. Quantum chemical calculations show that the electrical behavior is originated from the medium diradical character which produces similar reorganization energies for hole and electron transports. The vision of a diradical as simultaneously bearing pseudo-hole and pseudo-electron defects might justify the reduced values of reorganization energies for both regimes. Structure-function relationships between diradical and ambipolar electrical behavior are revealed.

Augmented Self-Association by Electrostatic Forces in Thienopyrrole-Fused Thiadiazoles that Contain an Ester instead of an Ether Linker

During the self-assembly of π-conjugated molecules, linkers and substituents can potentially add supportive noncovalent intermolecular interactions to π-stacking interactions. Here, we report the self-assembly behavior of thienopyrrole-fused thiadiazole (TPT) fluorescent dyes that possess ester or ether linkers and dodecyloxy side chains in solution and the condensed phase. A comparison of the self-association behavior of the ester- and ether-bridged compounds in solution using detailed UV-vis, fluorescence, and NMR spectroscopic studies revealed that the subtle replacement of the ether linkers by ester linkers leads to a distinct increase in the association constant (ca. 3-4 fold) and the enthalpic contribution (ca. 3 kcal mol-1). Theoretical calculations suggest that the ester linkers, which are in close proximity to one another due to the π-stacking interactions, induce attractive electrostatic forces and augment self-association. The self-assembly of TPT dyes into well-defined 1D clusters with high aspect ratios was observed, and their morphologies and crystallinity were investigated using SEM and X-ray diffraction analyses. TPTs with ester linkers exhibit a columnar liquid crystalline mesophase in the condensed phase.

S,C,C- and O,C,C-Bridged Triarylamines and Their Persistent Radical Cations

This work reports the synthesis, crystal structures, and electronic properties of structurally constrained S,C,C- and O,C,C-bridged triarylamine derivatives and their persistent radical cations. O,C,C-Bridged triphenylamines and a dinaphthylphenylamine were obtained through a straightforward synthetic protocol. Similar to a previously reported S,C,C-bridged triphenylamine, the O,C,C-bridged triarylamines were easily oxidized to afford the corresponding radical cations, which were obtained as hexachloroantimonate salts. X-ray crystallographic analyses showed almost planar structures for these O,C,C-bridged triarylamine radical cations, which represent new members of the family of planar triarylamine radical cations without substituents on the aryl rings. Detailed investigations of the electronic properties of the S,C,C- and O,C,C-bridged triarylamine radical cations demonstrated that the spin and positive charge are sufficiently delocalized over the planar triarylamine scaffolds. The results provide the following insights into the effects of the bridging unit (sulfur vs oxygen) and the dibenzo-annulation on the spin delocalization in the bridged triarylamine radical cations: (1) An effective decrease of the spin density on the nitrogen atom is observed for the sulfur bridge relative to the oxygen bridge; and (2) a moderate decrease of the spin density on the oxygen atom rather than the nitrogen atom is induced by the dibenzo-annulation.

Arylene-hexaynylene and -octaynylene macrocycles: extending the polyyne chains drives self-association by enhanced dispersion force

Tetraalkoxyphenanthrylene-hexaynylene and -octaynylene macrocycles, which represent the first examples of isolable arylene-alkynylene macrocycles (AAMs) that contain polyyne chains longer than tetrayne, were synthesized and their self-association behavior was examined. Extending the polyyne chain from diyne to tetrayne, hexayne, and octayne exponentially increased the self-association constant of the macrocycles.

Monoradicals and Diradicals of Dibenzofluoreno[3,2-b]fluorene Isomers: Mechanisms of Electronic Delocalization

The preparation of a series of dibenzo- and tetrabenzo-fused fluoreno[3,2-b]fluorenes is disclosed, and the diradicaloid properties of these molecules are compared with those of a similar, previously reported series of anthracene-based diradicaloids. Insights on the diradical mode of delocalization tuning by constitutional isomerism of the external naphthalenes has been explored by means of the physical approach (dissection of the electronic properties in terms of electronic repulsion and transfer integral) of diradicals. This study has also been extended to the redox species of the two series of compounds and found that the radical cations have the same stabilization mode by delocalization that the neutral diradicals while the radical anions, contrarily, are stabilized by aromatization of the central core. The synthesis of the fluorenofluorene series and their characterization by electronic absorption and vibrational Raman spectroscopies, X-ray diffraction, SQUID measurements, electrochemistry, in situ UV-vis-NIR absorption spectroelectrochemistry, and theoretical calculations are presented. This work attempts to unify the properties of different series of diradicaloids in a common argument as well as the properties of the carbocations and carbanions derived from them.

Chemical transformations of push-pull fluorenones: push-pull dibenzodicyanofulvenes as well as fluorenone- and dibenzodicyanofulvene-tetracyanobutadiene conjugates

Push-pull fluorenones (FOs) were synthesized by treating a benzopentalenequinone (BPO) derivative with alkynes that bear an electron-rich aniline moiety via a regioselective [4 + 2] cycloaddition (CA) followed by a [4 + 1] retrocycloaddition (RCA). The resulting FOs were readily converted into dibenzodicyanofulvenes (DBDCFs) by treatment with malononitrile in the presence of TiCl4 and pyridine. The FOs and DBDCFs exhibit intramolecular charge-transfer (ICT) that manifests in absorptions at 350-650 nm and amphoteric electrochemical behavior. Furthermore, FOs and DBDCFs that contain a C[triple bond, length as m-dash]C bond react with tetracyanoethylene in a formal [2 + 2] CA followed by a retro-electrocyclization to afford sterically congested tetracyanobutadiene (TCBD) conjugates. The substituent (H or Me) on the aromatic ring adjacent to the butadiene moiety thereby determines whether the butadiene adopts an s-cis or s-trans conformation, and thus controls the physicochemical properties of the resulting TCBDs. The TCBD conjugates exhibit ICT absorptions (≤800 nm) together with up to four reversible reduction steps.

White-light emission from a pyrimidine-carbazole conjugate with tunable phosphorescence-fluorescence dual emission and multicolor emission switching

A metal-free organic carbazole-pyrimidine dye exhibiting phosphorescence-fluorescence dual emission was developed into a white-light emission-switching system. The two crystal polymorphs obtained by breaking the molecular symmetry responded to the external stimuli of heating, vapor-fuming, and mechanical grinding, resulting in a tricolor switching system that includes white-light emission.

Visualization of Lipid Droplets in Living Cells and Fatty Livers of Mice Based on the Fluorescence of π-Extended Coumarin Using Fluorescence Lifetime Imaging Microscopy

Lipid droplets (LDs) are closely related to lipid metabolism in living cells and are highly associated with diverse diseases such as fatty liver, diabetes, and cancer. Herein we describe a π-extended fluorescent coumarin (PC6S) for visualizing LDs in living cells and in the tissues of living mice using confocal fluorescence lifetime imaging microscopy (FLIM). PC6S showed a large positive solvatochromic shift and high fluorescence quantum yield (>0.80) in both nonpolar and polar solvents. Additionally, the fluorescence lifetimes of PC6S were largely dependent on solvent polarity. The excellent spectral and photophysical properties of PC6S allowed its selective staining of LDs in living and fixed cells, and multicolor imaging. Fluorescence lifetime measurements of PC6S allowed estimation of the apparent polarity of LDs. The high photostability and long intracellular retention of PC6S supported in situ visualization of the formation processes of LDs resulting from the accumulation of fatty acid. Furthermore, intravenous administration of PC6S and use of the FLIM system allowed the imaging of LDs in hepatocytes in living normal mice and the growth of LDs resulting from the excess accumulation of lipids in high-fat-diet-fed mice (fatty liver model mice). Taking advantage of the high selectivity and sensitivity of PC6S for LDs in liver, we could visualize the adipocytes of lipid-rich tissues and LDs in kidney peritubular cells by PC6S fluorescence. These results demonstrated that PC6S combined with a FLIM system can be useful for monitoring and tracking the formation of LDs in both cultured cells and specific tissues and organs.

Gene cloning and characterization of thiourocanate hydratase from Burkholderia sp. HME13

A novel enzyme, thiourocanate hydratase, which catalyses the conversion of thiourocanic acid to 3-(5-oxo-2-thioxoimidazolidin-4-yl) propionic acid, was isolated from the ergothioneine-utilizing strain, Burkholderia sp. HME13. When the HME13 cells were cultured in medium containing ergothioneine as the sole nitrogen source, thiourocanate-metabolizing activity was detected in the crude extract from the cells. However, activity was not detected in the crude extract from HME13 cells that were cultured in Luria-Bertani medium. The gene encoding thiourocanate hydratase was cloned and expressed in Escherichia coli, and the recombinant enzyme was purified to homogeneity. The enzyme showed maximum activity at pH 7.5 and 55°C and was stable between pH 5.0 and 10.5, and at temperatures up to 45°C. The Km and Vmax values of thiourocanate hydratase towards thiourocanic acid were 30 μM and 7.1 μmol/min/mg, respectively. The enzyme was strongly inhibited by CuCl2 and HgCl2. The amino acid sequence of the enzyme showed 46% identity to urocanase from Pseudomonas putida, but thiourocanate hydratase had no urocanase activity.

2,4,5,7,9,10-Hexaethynylpyrenes: Synthesis, Properties, and Self-Assembly

A series of 2,4,5,7,9,10-hexaethynylpyrenes was synthesized using 2,7,9,10-tetrabromopyrene-4,5-dione as the key intermediate. The effects of the position and number of the ethynyl groups on the physicochemical properties of the corresponding pyrenes were clarified by comparison with 4,5,9,10-tetraethynylpyrene and 2,7-diethynylpyrene derivatives. The prepared hexaethynylpyrenes that bear benzene moieties self-assemble via π-π stacking in solution and/or the condensed phase.

A member of cation diffusion facilitator family, MTP11, is required for manganese tolerance and high fertility in rice

Rice MTP11 is the trans-Golgi-localized transporter that is involved in Mn tolerance with MTP8.1, and it is required for normal fertility. Rice (Oryza sativa L.) is one of the most manganese (Mn)-tolerant species, and it is able to accumulate high levels of this metal in the leaves without showing toxic symptoms. The metal tolerance protein 8.1 (MTP8.1), a member of the Mn-cation diffusion facilitator (CDF) family, has been shown to play a central role in high Mn tolerance by sequestering Mn into vacuoles. Recently, rice MTP11 was identified as an Mn transporter that is localized to Golgi-associated compartments, but its exact role in Mn tolerance in planta has not yet been understood. Here, we investigated the role of MTP11 in rice Mn tolerance using knockout lines. Old leaves presented higher levels of constitutively expressed MTP11 than other tissues and MTP11 expression was also found in reproductive organs. Fused MTP11:green fluorescent protein was co-localized to trans-Golgi markers and differentiated from other Golgi-associated markers. Knockout of MTP11 in wild-type rice did not affect tolerance and accumulation of Mn and other heavy metals, but knockout in the mtp8.1 mutant showed exacerbated Mn sensitivity at the vegetative growth stage. Knockout of MTP11 alone resulted in decreased grain yield and fertility at the reproductive stage. Thus, MTP11 is a trans-Golgi localized transporter for Mn, which plays a role in Mn tolerance through intracellular Mn compartmentalization. It is also required for maintaining high fertility in rice.

Genome Sequences of 12 Mycobacteriophages Recovered from Archival Stocks in Japan

Using Mycobacterium smegmatis mc2155, 12 siphoviruses were recovered from long-term archival stocks stored in Japan. Their genome sequences were 46.0 to 61.3 kbp with 63 to 68% G+C contents, which allowed them to be categorized within cluster W and subclusters A1, A2, B3, A7, I1, and K4.

10-Mesityl-1,8-diphenylanthracene Dimer: Synthesis, Structure, and Properties

Macrocyclic 10-mesityl-1,8-diphenylanthracene dimer 4 was synthesized by using the electron-transfer oxidation of Lipshutz cuprate derived from 1,8-bis(4-bromophenyl)-10-mesityl-anthracene 7 in moderate yield. This dimer 4 is a considerably fluorescent molecule (Φ_F 0.40) with high thermal, photo, and air stability. The X-ray analysis of 4 revealed a unique structure with a small inner cavity which can incorporate a small molecule or atom. ¹H NMR spectra in solution and emission spectra of 4 in the solid state showed that copper(I) ion was incorporated to form a 1:1 complex 4·CuOTf, whereas silver(I) ion only weakly interacted with 4 under similar conditions.

Characterization of an Alteromonas long-type ulvan lyase involved in the degradation of ulvan extracted from Ulva ohnoi

Ulvan is a sulfated polysaccharide found in the cell wall of the green algae Ulva. We first isolated several ulvan-utilizing Alteromonas sp. from the feces of small marine animals. The strain with the highest ulvan-degrading activity, KUL17, was analyzed further. We identified a 55-kDa ulvan-degrading protein secreted by this strain and cloned the gene encoding for it. The deduced amino acid sequence indicated that the enzyme belongs to polysaccharide lyase family 24 and thus the protein was named ulvan lyase. The predicted molecular mass of this enzyme is 110 kDa, which is different from that of the identified protein. By deletion analysis, the catalytic domain was proven to be located on the N-terminal half of the protein. KUL17 contains two ulvan lyases, one long and one short, but the secreted and cleaved long ulvan lyase was demonstrated to be the major enzyme for ulvan degradation.

Blue Fluorescence from BF2 Complexes of N,O-Benzamide Ligands: Synthesis, Structure, and Photophysical Properties

Small molecules having intense luminescence properties are required to promote biological and organic material applications. We prepared five types of benzamides having pyridine, pyridazine, pyrazine, and pyrimidine rings and successfully converted them into three types of the difluoroboronated complexes, Py@BAs, as novel blue fluorophores. Py@BA having a pyridine moiety (2-Py@BA) showed no fluorescence in solution, whereas Py@BAs of pyridazine and pyrazine moieties (2,3-Py@BA and 2,5-Py@BA, respectively) emitted blue fluorescence with quantum yields of ca. 0.1. Transient absorption measurements using laser flash photolysis of the Py@BAs revealed the triplet formation of 2,3- and 2,5-Py@BAs, while little transient signal was observed for 2-Py@BA. Therefore, the deactivation processes from the lowest excited singlet state of fluorescent 2,3- and 2,5-Py@BAs consist of fluorescence and intersystem crossing to the triplet state while that of the nonfluorescent Py@BA is governed almost entirely by internal conversion to the ground state. Conversely, in the solid state, 2-Py@BA emitted intense fluorescence with a fluorescence quantum yield as high as 0.66, whereas 2,3- and 2,5-Py@BAs showed fluorescence with quantum yields of ca. 0.2. The crystal structure of 2-Py@BA took a herringbone packing motif, whereas those for 2,3- and 2,5-Py@BAs were two-dimensional sheetlike. On the basis of the difference in crystal structures, the emission mechanism in the solid state was discussed.

The Tonoplast-Localized Transporter MTP8.2 Contributes to Manganese Detoxification in the Shoots and Roots of Oryza sativa L

Manganese (Mn) cation diffusion facilitators (Mn-CDFs) play important roles in the Mn homeostasis of plants. In rice, the tonoplast-localized Mn-CDF metal tolerance protein 8.1 (MTP8.1) is involved in Mn detoxification in the shoots. This study functionally characterized the Mn-CDF MTP8.2 and determined its contribution to Mn tolerance. MTP8.2 was found to share 68% identity with MTP8.1 and was expressed in both the shoots and roots, but its transcription level was lower than that of MTP8.1. Transient expression of the MTP8.2:green fluorescent protein (GFP) fusion protein and immunoblotting studies indicated that MTP8.2 was also localized to the tonoplast. MTP8.2 expression in yeast conferred tolerance to Mn but not to Fe, Zn, Co, Ni or Cd. MTP8.2 knockdown caused further growth reduction of shoots and roots in the mtp8.1 mutant, which already exhibits stunted growth under conditions of excess Mn. In the presence of high Mn, the MTP8.2 knockdown lines of the mtp8.1 mutant showed lower root Mn concentrations, as well as lower root:total Mn ratios, than those of wild-type rice and the mtp8.1 mutant. These findings indicate that MTP8.2 mediates Mn tolerance along with MTP8.1 through the sequestration of Mn into the shoot and root vacuoles.

Tetraalkoxyphenanthrene-Fused Thiadiazoloquinoxalines: Synthesis, Electronic, Optical, and Electrochemical Properties, and Self-Assembly

π-Extended thiadiazoloquinoxaline (TQ) derivatives 1a,b-3a,b, in which a tetraalkoxyphenanthrene moiety is annulated with the TQ core and benzene rings are incorporated via the ethynylene spacer, were synthesized. They display absorption bands reaching into 750 nm and possess the electron-affinity comparable to [60]fullerene. The CF₃- and OMe-substituents on the benzene rings have moderate effects on modulation of the HOMO and LUMO levels. Tetraalkoxyphenanthrene-fused TQs 1a,b-3a,b aggregate in the solid state and assemble in solution through π-π stacking interactions. The self-assembly of 1a,b-3a,b into 1D superstructures was confirmed, and the difference in the alkoxy groups and the solvents for self-assembly proved to change their morphology. Comparison of the properties of 1a and those of reference compounds 4 and 5 clarified the effects of both the fusion of the phenanthrene moiety and the introduction of ethynylene spacers on the properties.

Characterization of Pseudomonas aeruginosa phage KPP21 belonging to family Podoviridae genus N4-like viruses isolated in Japan

Bacteriophages (phages) belonging to the family Podoviridae genus N4-like viruses have been used as therapeutic agent in phage therapy against Pseudomonas aeruginosa infections. P. aeruginosa phage KPP21 was isolated in Japan, and phylogenetically investigated the phages belonging to this viral genus. Morphological and genetic analyses confirmed that phage KPP21 belongs to the family Podoviridae genus N4-like viruses. Moreover, phylogenetic analyses based on putative DNA polymerase and major virion protein showed that P. aeruginosa phages belonging to the genus N4-like viruses are separated into two lineages and that phage KPP21 is in the same clade as phage LUZ7.

Benzo- and Naphthopentalenes: Syntheses, Structures, and Properties

Benzo- and naphthopentalene derivatives were synthesized, and the effects of structural variations on their antiaromaticity and optoelectronic and electrochemical properties were examined experimentally and theoretically in detail. The results unveiled that with increasing the bond order of the carbon-carbon bond ([5,6] junction) shared by the pentalene and aromatic moieties, the 8π antiaromatic character of pentalene is enhanced and the HOMO-LUMO gap is decreased, which accompanies both the elevation of the HOMO level and the lowering of the LUMO level. The ethynylene units between the pentalene skeleton and the phenyl groups proved to extend π-conjugation sufficiently.

Screening of KHP30-like prophages among Japanese Helicobacter pylori strains, and genetic analysis of a defective KHP30-like prophage sequence integrated in the genome of the H. pylori strain NY40

We have recently reported the active Helicobacter pylori bacteriophages (phages), KHP30 and KHP40, the genomic DNAs of which exist as episomes in host bacterial strains isolated in Japan (i.e. pseudolysogeny). In this study, we examined the possibility of the lysogeny of active KHP30-like phages in Japanese H. pylori strains, because their genomes contain a putative integrase gene. Only the NY40 strain yielded partial detection of a KHP30-like prophage sequence in PCR among 174 Japanese H. pylori isolates, except for strains producing the above active phages. Next, according to the genomic analysis of the NY40 strain, the KHP30-like prophage sequence was found to be located from ca. 524 to 549 kb in the host chromosome. The attachment sites, attL and attR, in the NY40 genome showed almost the same genomic location and sequence as those detected in a French isolate B38, suggesting that an active parental KHP30-like phage had integrated into the ancestral NY40 genome in a site-specific manner. The prophage found in the NY40 genome was assumed to have been genetically modified, after site-specific integration. These, together with the data in the KHP30-like prophages of other H. pylori genomes, suggest that the lysogenic state of the KHP30-like phages is generally unstable.

Identification, Cloning, and Characterization of l-Phenylserine Dehydrogenase from Pseudomonas syringae NK-15

The gene encoding d-phenylserine dehydrogenase from Pseudomonas syringae NK-15 was identified, and a 9,246-bp nucleotide sequence containing the gene was sequenced. Six ORFs were confirmed in the sequenced region, four of which were predicted to form an operon. A homology search of each ORF predicted that orf3 encoded l-phenylserine dehydrogenase. Hence, orf3 was cloned and overexpressed in Escherichia coli cells and recombinant ORF3 was purified to homogeneity and characterized. The purified ORF3 enzyme showed l-phenylserine dehydrogenase activity. The enzymological properties and primary structure of l-phenylserine dehydrogenase (ORF3) were quite different from those of d-phenylserine dehydrogenase previously reported. l-Phenylserine dehydrogenase catalyzed the NAD⁺-dependent oxidation of the β-hydroxyl group of l-β-phenylserine. l-Phenylserine and l-threo-(2-thienyl)serine were good substrates for l-phenylserine dehydrogenase. The genes encoding l-phenylserine dehydrogenase and d-phenylserine dehydrogenase, which is induced by phenylserine, are located in a single operon. The reaction products of both enzymatic reactions were 2-aminoacetophenone and CO₂.

Characterization of a NifS-like chloroplast protein from Arabidopsis. Implications for its role in sulfur and selenium metabolism

NifS-like proteins catalyze the formation of elemental sulfur (S) and alanine from cysteine (Cys) or of elemental selenium (Se) and alanine from seleno-Cys. Cys desulfurase activity is required to produce the S of iron (Fe)-S clusters, whereas seleno-Cys lyase activity is needed for the incorporation of Se in selenoproteins. In plants, the chloroplast is the location of (seleno) Cys formation and a location of Fe-S cluster formation. The goal of these studies was to identify and characterize chloroplast NifS-like proteins. Using seleno-Cys as a substrate, it was found that 25% to 30% of the NifS activity in green tissue in Arabidopsis is present in chloroplasts. A cDNA encoding a putative chloroplast NifS-like protein, AtCpNifS, was cloned, and its chloroplast localization was confirmed using immunoblot analysis and in vitro import. AtCpNIFS is expressed in all major tissue types. The protein was expressed in Escherichia coli and purified. The enzyme contains a pyridoxal 5' phosphate cofactor and is a dimer. It is a type II NifS-like protein, more similar to bacterial seleno-Cys lyases than to Cys desulfurases. The enzyme is active on both seleno-Cys and Cys but has a much higher activity toward the Se substrate. The possible role of AtCpNifS in plastidic Fe-S cluster formation or in Se metabolism is discussed.

Characterization of a NifS-like chloroplast protein from Arabidopsis. Implications for its role in sulfur and selenium metabolism

NifS-like proteins catalyze the formation of elemental sulfur (S) and alanine from cysteine (Cys) or of elemental selenium (Se) and alanine from seleno-Cys. Cys desulfurase activity is required to produce the S of iron (Fe)-S clusters, whereas seleno-Cys lyase activity is needed for the incorporation of Se in selenoproteins. In plants, the chloroplast is the location of (seleno) Cys formation and a location of Fe-S cluster formation. The goal of these studies was to identify and characterize chloroplast NifS-like proteins. Using seleno-Cys as a substrate, it was found that 25% to 30% of the NifS activity in green tissue in Arabidopsis is present in chloroplasts. A cDNA encoding a putative chloroplast NifS-like protein, AtCpNifS, was cloned, and its chloroplast localization was confirmed using immunoblot analysis and in vitro import. AtCpNIFS is expressed in all major tissue types. The protein was expressed in Escherichia coli and purified. The enzyme contains a pyridoxal 5' phosphate cofactor and is a dimer. It is a type II NifS-like protein, more similar to bacterial seleno-Cys lyases than to Cys desulfurases. The enzyme is active on both seleno-Cys and Cys but has a much higher activity toward the Se substrate. The possible role of AtCpNifS in plastidic Fe-S cluster formation or in Se metabolism is discussed.

Network of protein-protein interactions among iron-sulfur cluster assembly proteins in Escherichia coli

The assembly of iron-sulfur (Fe-S) clusters is mediated by complex machinery which, in Escherichia coli, is encoded by the iscRSUA-hscBA-fdx-ORF3 gene cluster. Here, we demonstrate the network of protein-protein interactions among the components involved in the machinery. We have constructed (His)(6)-tagged versions of the components and identified their interacting partners that were co-purified from E. coli extracts with a Ni-affinity column. Direct associations of the defined pair of proteins were further examined in yeast cells using the two-hybrid system. In accord with the previous in vitro binding and kinetic experiments, interactions were observed for the combinations of IscS and IscU, IscU and HscB, IscU and HscA, and HscB and HscA. In addition, we have identified previously unreported interactions between IscS and Fdx, IscS and ORF3, IscA and HscA, and HscA and Fdx. We also found, by site-directed mutational analysis combined with the two-hybrid system, that two cysteine residues in IscU are essential for binding with HscB but not with IscS. Despite the complex network of interactions in various combinations of components, heteromultimeric complexes were not observed in our experiments except for the putative oligomeric form of IscU-IscS-ORF3. Thus, the sequential association and dissociation among the IscS, IscU, IscA, HscB, HscA, Fdx, and ORF3 proteins may be a critical process in the assembly of Fe-S clusters.

Structure of external aldimine of Escherichia coli CsdB, an IscS/NifS homolog: implications for its specificity toward selenocysteine

Escherichia coli CsdB is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes both cysteine desulfuration and selenocysteine deselenation. The enzyme has a high specific activity for L-selenocysteine relative to L-cysteine. On the other hand, its paralog, IscS, exhibits higher activity for L-cysteine, which acts as a sulfur donor during the biosynthesis of the iron-sulfur cluster and 4-thiouridine. The structure of CsdB complexed with L-propargylglycine was determined by X-ray crystallography at 2.8 A resolution. The overall polypeptide fold of the complex is similar to that of the uncomplexed enzyme, indicating that no significant structural change occurs upon formation of the complex. In the complex, propargylglycine forms a Schiff base with PLP, providing the features of the external aldimine formed in the active site. The Cys364 residue, which is essential for the activity of CsdB toward L-cysteine but not toward L-selenocysteine, is clearly visible on a loop of the extended lobe (Thr362-Arg375) in all enzyme forms studied, in contrast to the corresponding disordered loop (Ser321-Arg332) of the Thermotoga maritima NifS-like protein, which is closely related to IscS. The extended lobe of CsdB has an 11-residue deletion compared with that of the NifS-like protein. These facts suggest that the restricted flexibility of the Cys364-anchoring extended lobe in CsdB may be responsible for the ability of the enzyme to discriminate between selenium and sulfur.