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Development and characterization of a new enzyme reaction benefit modern biotechnologies. Here, we report a novel CIS (clamping-mediated incorporation of single-stranded DNA with concomitant DNA synthesis) reaction catalyzed by Taq polymerase. In the reaction, a single-stranded DNA (ssDNA) with 3′ Cs is attached with a preformed 3′ G-tail of double-stranded DNA (dsDNA); DNA syntheses starting from both 3′ ends result in the incorporation of ssDNA. A 3′ G-tail length of 3 nucleotides adequately supports this reaction, indicating that Taq polymerase can clump short Watson-Crick base pairs as short as three pairs and use them to initiate DNA polymerization. The reverse transcriptase from Molony murine leukemia virus catalyzes strand displacement synthesis and produces flapped-end DNA, whereas the reaction by Taq polymerase involves the nick translation. These new reaction properties may be beneficial for the development of new molecular tools applicable in various fields. Apart from its CIS reaction activity, we also report that Taq polymerase has the undesirable characteristic of removing 5' fluorescent labels from dsDNA. This characteristic may have compromised various experiments involving the preparation of fluorescently-labeled dsDNA by PCR for a long time.

In these days, for bacterial genome sequence determination, ultralong reads with homopolymeric troubles are used in combinations with short reads, resulting in genomic sequences with possible incorrect uniformity of repeat sequences. We have been determining complete bacterial genomic sequences based on NGS short reads and Newbler assemblage by utilizing functions implemented in 3 software GenoFinisher, AceFileViewer, and ShortReadManager without conducting additional experiments for gap closing, proving the concept that NGS short reads enclose enough information to determine complete genome sequences. Although some manual in silico tasks are to be conducted, they will ultimately be solved in a single pipeline. In this review, we describe the tools and implemented ideas that have enabled complete sequence determination solely based on short reads, which would be useful for establishing the basis for the future development of a short-read-based assembler that enables complete and accurate genome sequence determination at a lower cost.

γ-Hexachlorocyclohexane (γ-HCH)-degrading strain, Sphingobium sp. TA15, was newly isolated from an experimental field soil from which the archetypal γ-HCH-degrading strain, S. japonicum UT26, was isolated previously. Comparison of the complete genome sequences of these 2 strains revealed that TA15 shares the same basic genome backbone with UT26, but also has the variable regions that are presumed to have changed either from UT26 or from a putative common ancestor. Organization and localization of lin genes of TA15 were different from those of UT26. It was inferred that transposition of IS6100 had played a crucial role in these genome rearrangements. The accumulation of toxic dead-end products in TA15 was lower than in UT26, suggesting that TA15 utilizes γ-HCH more effectively than UT26. These results suggested that genome evolution related to the γ-HCH metabolic function in the soil microbial population is ongoing.

Sphingobium japonicum strain UT26, whose γ-hexachlorocyclohexane-degrading ability has been studied in detail, is a typical aerobic and heterotrophic bacterium that needs organic carbon sources for its growth, and cannot grow on a minimal salt agar medium prepared without adding any organic carbon sources. Here, we isolated a mutant of UT26 with the ability to grow to visible state on such an oligotrophic medium from a transposon-induced mutant library. This high-yield growth under oligotrophic conditions (HYGO) phenotype was CO2-dependent and accompanied with CO2 incorporation. In the HYGO mutant, a transposon was inserted just upstream of the putative Zn-dependent alcohol dehydrogenase (ADH) gene (adhX) so that the adhX gene was constitutively expressed, probably by the transposon-derived promoter. The adhX-deletion mutant (UT26DAX) harbouring a plasmid carrying the adhX gene under the control of a constitutive promoter exhibited the HYGO phenotype. Moreover, the HYGO mutants spontaneously emerged among the UT26-derived hypermutator strain cells, and adhX was highly expressed in these HYGO mutants, while no HYGO mutant appeared among UT26DAX-derived hypermutator strain cells, indicating the necessity of adhX for the HYGO phenotype. His-tagged AdhX that was expressed in Escherichia coli and purified to homogeneity showed ADH activity towards methanol and other alcohols. Mutagenesis analysis of the adhX gene indicated a correlation between the ADH activity and the HYGO phenotype. These results demonstrated that the constitutive expression of an adhX-encoding protein with ADH activity in UT26 leads to the CO2-dependent HYGO phenotype. Identical or nearly identical adhX orthologues were found in other sphingomonad strains, and most of them were located on plasmids, suggesting that the adhX-mediated HYGO phenotype may be an important adaptation strategy to oligotrophic environments among sphingomonads.

The electronic structure changes of SmS surfaces under potassium (K) doping are elucidated using synchrotron-based core-level photoelectron spectroscopy and angle-resolved photoelectron spectroscopy (ARPES). The Sm core-level and ARPES spectra indicate that the Sm mean valence of the surface increased from the nearly divalent to trivalent states, with increasing K deposition. Carrier-induced valence transition (CIVT) from Sm$^{2+}$ to Sm$^{3+}$ exhibits a behavior opposite to that under conventional electron doping. Excess electrons are trapped by isolated excitons, which is inconsistent with the phase transition from the black insulator with Sm$^{2+}$ to the gold metal with Sm$^{3+}$ under pressure. This CIVT helps to clarify the pressure-induced black-to-golden phase transition in this material, which originates from the Mott transition of excitons., Comment: 7 pages, 6 figures

Repairing of DNA termini is a crucial step in a variety of DNA handling techniques. In this study, we investigated mechanically-sheared DNA 3’-ends (MSD3Es) to establish an efficient repair method. As opposed to the canonical view of DNA terminus generated by sonication, we showed that approximately 47% and 20% of MSD3Es carried a phosphate group and a hydroxyl group, respectively. The others had unidentified abnormal terminal structures. Notably, a fraction of the abnormal 3’ termini (about 20% of the total) was not repaired after the removal of 3’ phosphates and T4 DNA polymerase (T4DP) treatment. To overcome this limitation, we devised a reaction, in which the 3’− > 5’ exonuclease activity of exonuclease III (3’− > 5’ exonuclease, insensitive to the 3’ phosphate group) was counterbalanced by the 5’− > 3’ polymerase activity of T4DP. This combined reaction, termed “SB-repairing” (for scrap-and-build repairing), will serve as a useful tool for the efficient repair of MSD3Es., Ohtsubo et al. show that mechanically sheared DNA 3’ terminus has 47% phosphate group, 20% hydroxyl group with remaining as abnormal termini, half of which is not repaired with T4 DNA polymerase treatment. They devise a method, scrap and build or SB-repairing, to efficiently repair 3’ DNA ends by combining phosphatase and exonuclease (scrap) followed by T4 DNA polymerase (build) reactions.

The beamline for angle-resolved photoemission spectroscopy (ARPES) with a nano-focused beam (nano-ARPES) is planned as one of the public beamlines in NanoTerasu, the 3-GeV next-generation synchrotron radiation facility at Tohoku, Japan, which is scheduled to start operation in 2024. A 4 m long APPLE-II type undulator provides brilliant soft X-rays with various polarizations (linear horizontal and vertical, and left and right circular) in the energy range of 50-1,000 eV. A collimated plane grating monochromator is adopted as a soft X-ray monochromator because we can select the demagnification factor of grating cf f = cosα/cosβ between the high energy-resolution (HR) mode for HR-ARPES experiments and the low divergence mode for high-flux nano-ARPES measurements. This beamline aims to produce the high flux nano-focused beam by using ultrahigh precision reflective mirror optics, not a Fresnel zone plate used as a focusing optics in the previous nano-ARPES station at other synchrotron facilities.

A synchrotron radiation beamline in the soft- and tender-X ray energy range of 180-3000 eV with versatile polarization control has been designed for NanoTerasu, the 3-GeV next-generation synchrotron radiation facility at Tohoku, Japan. A series of four APPLE-II type undulators is adopted as a photon source to realize the required beam properties with high-speed polarization switching. The beamline optics is designed for a highly efficient and precise use of x-ray magnetic circular/linear dichroism (XMCD/XMLD) technique balancing high photon flux and energy resolution. The simulated performance of the segmented undulator together with the monochromator optics achieved the sufficiently high flux and energy resolution (E/ΔE) in whole target energy range. Two endstations with the different re-focus optics, one for marginal spot size with high flux and the other for ultimate focus down to ∼10 nm are also designed. The simulated performance of the beamline encourages the future researches of high-throughput and nm-focused spintronic measurements.

The optical design of the ultrahigh-resolution RIXS beamline, which is currently developed at NanoTerasu in Japan, is described. The main goal of this beamline is to perform ultrahigh-resolution RIXS measurements with a total energy resolution of E/ΔE>150,000 for both beamline and RIXS spectrometer. To achieve the ultra-high resolution, a 2D-RIXS spectrometer using energy-dispersive X-ray is employed to compensate for lower throughput at higher energy resolution, and the optics of the beamline is optimized for the 2D-RIXS spectrometer. A vertically dispersing in-focus variable-included-angle varied-line-spacing plane grating monochromator is employed for the beamline, with an entrance slit to ensure the ultrahigh resolution. First and second mirrors focus X-ray on entrance slits vertically and horizontally, respectively, and the divergent X-ray is irradiated onto the grating. For the 2D-RIXS spectrometer, there is no exit slit, and the vertically energy-dispersed X-ray is irradiated directly onto a sample. In front of the sample, X-ray is horizontally refocused by a Wolter type-I mirror. The expected horizontal focus size at the sample is ~0.7 μm. The expected photon flux is ~1×1011 photons/s at 500–1000 eV with a virtual slit width of 2 μm required for E/ΔE>150,000. The height of the dispersed X-ray available in the 2D-RIXS spectrometer is ~120 μm, which allows the use of a remarkably high flux of ~6×1012 photons/s, and the beamline will serve as an ultrahigh-resolution and high-efficiency RIXS facility.

Cyanobacteria are a diverse group of Gram-negative prokaryotes that perform oxygenic photosynthesis. Cyanobacteria have been used for research on photosynthesis and have attracted attention as a platform for biomaterial/biofuel production. Cyanobacteria are also present in almost all habitats on Earth and have extensive impacts on global ecosystems. Given their biological, economical, and ecological importance, the number of high-quality genome sequences for Cyanobacteria strains is limited. Here, we performed genome sequencing of Cyanobacteria strains in the National Institute for Environmental Studies microbial culture collection in Japan. We sequenced 28 strains that can form a heterocyst, a morphologically distinct cell that is specialized for fixing nitrogen, and 3 non-heterocystous strains. Using Illumina sequencing of paired-end and mate-pair libraries with in silico finishing, we constructed highly contiguous assemblies. We determined the phylogenetic relationship of the sequenced genome assemblies and found potential difficulties in the classification of certain heterocystous clades based on morphological observation. We also revealed a bias on the sequenced strains by the phylogenetic analysis of the 16S rRNA gene including unsequenced strains. Genome sequencing of Cyanobacteria strains deposited in worldwide culture collections will contribute to understanding the enormous genetic and phenotypic diversity within the phylum Cyanobacteria.

We have developed a spin-resolved resonant electron energy-loss spectroscopy (SR-rEELS) in the primary energy of 0.3--1.5 keV, which corresponds to the core excitations of $2p$-$3d$ absorption of transition metals and $3d$-$4f$ absorption of rare-earths, with the energy resolution of about 100~meV using a spin-polarized electron source as a GaAs/GaAsP strained superlattice photocathode. Element- and spin-selective carrier and valence plasmons can be observed using the resonance enhancement of core absorptions and electron spin polarization. Furthermore, bulk-sensitive EELS spectra can be obtained because the primary energy corresponds to the mean free path of 1--10~nm. The methodology is expected to provide us novel information of elementary excitations by resonant inelastic x-ray scattering and resonant photoelectron spectroscopy., Comment: 9 pages, 7 figures

Bacterial iron-sulfur (Fe-S) clusters are essential cofactors for many metabolic pathways, and Fe-S cluster-containing proteins (Fe-S proteins) regulate the expression of various important genes. However, biosynthesis of such clusters has remained unknown in genus Burkholderia. Here, we clarified that Burkholderia multivorans ATCC 17616 relies on the ISC system for the biosynthesis of Fe-S clusters, and that the biosynthetic genes are organized as an isc operon, whose first gene encodes IscR, a transcriptional regulatory Fe-S protein. Transcription of the isc operon was repressed and activated under iron-rich and -limiting conditions, respectively, and Fur, an iron-responsive global transcriptional regulator, was indicated to indirectly regulate the expression of isc operon. Further analysis using a ΔiscR mutant in combination with a constitutive expression system of IscR and its derivatives indicated transcriptional repression and activation of isc operon by holo- and apo-forms of IscR, respectively, through their binding to the sequences within an isc promoter-containing (Pisc) fragment. Biochemical analysis using the Pisc fragment suggested that the apo-IscR binding sequence differs from the holo-IscR binding sequence. The results obtained in this study revealed a unique regulatory system for the expression of the ATCC 17616 isc operon that has not been observed in other genera.

Surface electronic structure and its one-dimensionality above and below the Fermi level ($E_{\rm F}$) were surveyed on the Bi/GaSb(110)-(2$\times$1) surface hosting quasi-one-dimensional (Q1D) Bi chains, using conventional (one-photon) and two-photon angle-resolved photoelectron spectroscopy (ARPES) and theoretical calculations. ARPES results reveal that the Q1D electronic states are within the projected bulk bandgap. Circular dichroism of two-photon ARPES and density-functional-theory calculation indicate clear spin and orbital polarization of the surface states consistent with the giant sizes of Rashba-type SOI, derived from the strong contribution of heavy Bi atoms. The surface conduction band above $E_{\rm F}$ forms a nearly straight constant-energy contour, suggesting its suitability for application in further studies of one-dimensional electronic systems with strong SOI. A tight-binding model calculation based on the obtained surface electronic structure successfully reproduces the surface band dispersions and predicts possible one- to two-dimensional crossover in the temperature range of 60--100~K., Comment: 18 pages, 6 figures and 2 tables

We fabricated spin-polarized surface electronic states with tunable Fermi levels from a semiconductor to low-dimensional metal in the Bi/GaSb(110)-$(2\ifmmode\times\else\texttimes\fi{}1)$ surface using angle-resolved photoelectron spectroscopy (ARPES) and spin-resolved ARPES. The spin-polarized surface band of Bi/GaSb(110) exhibits quasi-one-dimensional character with the Rashba parameter ${\ensuremath{\alpha}}_{\mathrm{R}}$ of 4.1 and 2.6 eV\AA{} at the $\overline{\mathrm{\ensuremath{\Gamma}}}$ and $\overline{\mathrm{Y}}$ points of the surface Brillouin zone, respectively. The Fermi level of the surface electronic state is tuned in situ by element-selective Ar-ion sputtering on the GaSb substrate. The giant Rashba-type spin splitting with switchable metallic/semiconducting character on a semiconductor substrate makes this system a promising candidate for future research in low-dimensional spintronic phenomena.

Conjugative transfer of bacterial plasmids to recipient cells is often mediated by type IV secretion machinery. Experimental investigations into the minimal gene sets required for efficient conjugative transfer suggest that such gene sets are variable, depending on plasmids. We have been analyzing the conjugative transfer of Pseudomonas-derived and IncP-9 plasmids, NAH7 and pWW0, whose conjugation systems belong to the MPFT type. Our deletion analysis and synthetic biology analysis in this study showed that these plasmids require previously uncharacterized genes, mpfK (formerly orf34) and its functional homolog, kikA, respectively, for their efficient conjugative transfer. MpfK was localized in periplasm and had four cysteine residues whose intramolecular or intermolecular disulfide bond formation was suggested to be important for efficient conjugative transfer. The mpfK homologs were specifically carried by many MPFT-type plasmids, including non-IncP-9 plasmids, such as R388 and R751. Intriguingly, the mpfK homologs from the two non-IncP-9 plasmids were not required for conjugation of their plasmids, but were able to complement efficiently the transfer defect of the NAH7 mpfK mutant. Our results suggested the importance of the mpfK homologs for conjugative transfer of MPFT-type plasmids.IMPORTANCE IncP-9 plasmids are important mobile genetic elements for the degradation of various aromatic hydrocarbons. Elucidation of conjugative transfer of such plasmids is expected to greatly contribute to our understanding of its role in the bioremediation of polluted environments. The present study mainly focused on the conjugation system of NAH7, a well-studied and naphthalene-catabolic IncP-9 plasmid. Our analysis showed that the NAH7 conjugation system uniquely requires, in addition to the conserved components of the type IV secretion system (T4SS), a previously uncharacterized periplasmic protein, MpfK, for successful conjugation. Our findings collectively revealed a unique type of T4SS-associated conjugation system in the IncP-9 plasmids.

Electronic states of the Bi/InAs(110)-$(2\ifmmode\times\else\texttimes\fi{}1)$ surface and its spin-polarized structure are revealed by angle-resolved photoelectron spectroscopy (ARPES), spin-resolved ARPES, and density-functional-theory calculation. The surface electronic state showed quasi-one-dimensional (Q1D) dispersion curves and a nearly metallic character; the top of the holelike band is just below the Fermi level. The size of the Rashba parameter ${\ensuremath{\alpha}}_{\mathrm{R}}$ reached a much larger value ($\ensuremath{\sim}5.5$ eV\AA{}) than for previously reported 1D systems. The present result will provide a fertile playground for further studies of the exotic electronic phenomena in 1D or Q1D systems with the spin-split electronic states as well as for advanced spintronic devices.

In this study, we investigated CIS reaction (clamping-mediated incorporation of single-stranded DNA with concomitant DNA syntheses) of Moloney murine leukaemia virus reverse transcriptase (MMLV-RT), and established a set of conditions with which single-stranded DNA is ligated to a G-tailed model substrate DNA at efficiencies close to 100%. Prior to the CIS reaction, a target blunt-end DNA was 3′ G-tailed by MMLV-RT in the presence of a tailing enhancer, deoxycytidine. In the CIS reaction, the G-tail reacted with a single-stranded DNA carrying a stretch of Cs on its 3′ end (termed as GAO for guide adaptor oligonucleotide), and MMLV-RT performed DNA polymerization, starting from the 3′ overhang, using the GAO as a template. We could append a given nucleotide sequence of as long as 72 nucleotides, which would be sufficient for various NGS-sequencing platforms. The high efficiency and the unique features of this MMLV-RT activity that enables the labelling of each DNA molecule with a unique degenerate sequence as a molecular identifier has many potential uses in biotechnology.

The anisotropic changes in the electronic structure of a metal-to-insulator transition (MIT) material, RuAs, with two-step phase transition are reported by using polarized optical conductivity [$\sigma(\omega)$] spectra, angle-integrated photoelectron (PE) spectra, and band calculations based on local density approximation (LDA). Both the PE and $\sigma(\omega)$ spectra not only in the high-temperature (HT) phase but also in the low-temperature (LT) phase as well as the energy gap formation owing to the MIT were almost consistent with those derived from the LDA band calculations, so the fundamental electronic structure in the HT and LT phases can be explained without electron correlations. However, the electronic structure in the middle phase between the HT and LT phases has not been clarified. The polarized $\sigma(\omega)$ spectra revealed not only the anisotropic energy gap formation but also the anisotropic gap-opening temperature, i.e., the energy gap along the $c$ axis in the HT phase starts to open near the higher transition temperature, but that along the $b$ axis opens below the lower transition temperature. The finding suggests that the two-step MIT originates from the anisotropic energy gap formation., Comment: 7 pages, 7 figures

Conjugative transfer of bacterial plasmids to recipient cells is often mediated by type IV secretion machinery. Experimental investigations into the minimal gene sets required for efficient conjugative transfer suggest that such gene sets are variable, depending on plasmids. We have been analyzing the conjugative transfer of Pseudomonas-derived and IncP-9 plasmids, NAH7 and pWW0, whose conjugation systems belong to the MPF(T) type. Our deletion analysis and synthetic biology analysis in this study showed that these plasmids require previously uncharacterized genes, mpfK (formerly orf34) and its functional homolog, kikA, respectively, for their efficient conjugative transfer. MpfK was localized in periplasm and had four cysteine residues whose intramolecular or intermolecular disulfide bond formation was suggested to be important for efficient conjugative transfer. The mpfK homologs were specifically carried by many MPF(T)-type plasmids, including non-IncP-9 plasmids, such as R388 and R751. Intriguingly, the mpfK homologs from the two non-IncP-9 plasmids were not required for conjugation of their plasmids, but were able to complement efficiently the transfer defect of the NAH7 mpfK mutant. Our results suggested the importance of the mpfK homologs for conjugative transfer of MPF(T)-type plasmids. IMPORTANCE IncP-9 plasmids are important mobile genetic elements for the degradation of various aromatic hydrocarbons. Elucidation of conjugative transfer of such plasmids is expected to greatly contribute to our understanding of its role in the bioremediation of polluted environments. The present study mainly focused on the conjugation system of NAH7, a well-studied and naphthalene-catabolic IncP-9 plasmid. Our analysis showed that the NAH7 conjugation system uniquely requires, in addition to the conserved components of the type IV secretion system (T4SS), a previously uncharacterized periplasmic protein, MpfK, for successful conjugation. Our findings collectively revealed a unique type of T4SS-associated conjugation system in the IncP-9 plasmids.

We determined the complete genome sequence of Thalassococcus sp. strain S3, a marine carbazole degrader isolated from Tokyo Bay in Japan that carries genes for aerobic anoxygenic phototrophy. Strain S3 has a 4.7-Mb chromosome that harbors the carbazole-degradative gene cluster and three (96-, 63-, and 46-kb) plasmids.

We study the one-electron spectral properties of one-dimensional interacting electron systems in which the interactions have finite range. We employ a mobile quantum impurity scheme that describes the interactions of the fractionalized excitations at energies above the standard Tomonga-Luttinger liquid limit and show that the phase shifts induced by the impurity describe universal properties of the one-particle spectral function. We find the explicit forms in terms of these phase shifts for the momentum dependent exponents that control the behavior of the spectral function near and at the (k,omega)-plane singularities where most of the spectral weight is located. The universality arises because the line shape near the singularities is independent of the short-distance part of the interaction potentials. For the class of potentials considered here, the charge fractionalized particles have screened Coulomb interactions that decay with a power-law exponent l>5. We apply the theory to the angle-resolved photo-electron spectroscopy (ARPES) in the highly one-dimensional bismuth-induced anisotropic structure on indium antimonide Bi/InSb(001). Our theoretical predictions agree quantitatively with both (i) the experimental value found in Bi/InSb(001) for the exponent alpha that controls the suppression of the density of states at very small excitation energy omega and (ii) the location in the (k,omega) plane of the experimentally observed high-energy peaks in the ARPES momentum and energy distributions. We conclude with a discussion of experimental properties beyond the range of our present theoretical framework and further open questions regarding the one-electron spectral properties of Bi/InSb(001)., 23 pages, 6 figures

In natural environments contaminated by recalcitrant organic pollutants, efficient biodegradation of such pollutants has been suggested to occur through the cooperation of different bacterial species. A phenanthrene-degrading bacterial consortium, MixEPa4, from polluted soil was previously shown to include a phenanthrene-degrading strain, Mycobacterium sp. EPa45, and a non-polycyclic aromatic hydrocarbon (PAH)-degrading strain, Burkholderia sp. Bcrs1W. In this study, we show that addition of phenanthrene to rich liquid medium resulted in the transient growth arrest of EPa45 during its degradation of phenanthrene. RNA-sequencing analysis of the growth-arrested cells showed the phenanthrene-dependent induction of genes that were predicted to be involved in the catabolism of this compound, and many other cell systems, such as a ferric iron-uptake, were up-regulated, implying iron deficiency of the cells. This negative effect of phenanthrene became much more apparent when using phenanthrene-containing minimal agar medium; colony formation of EPa45 on such agar was significantly inhibited in the presence of phenanthrene and its intermediate degradation products. However, growth inhibition was suppressed by the co-residence of viable Bcrs1W cells. Various Gram-negative bacterial strains, including the three other strains from MixEPa4, also exhibited varying degrees of suppression of the growth inhibition effect on EPa45, strongly suggesting that this effect is not strain-specific. Growth inhibition of EPa45 was also observed by other PAHs, biphenyl and naphthalene, and these two compounds and phenanthrene also inhibited the growth of another mycobacterial strain, M. vanbaalenii PYR-1, that can use them as carbon sources. These phenomena of growth inhibition were also suppressed by Bcrs1W. Our findings suggest that, in natural environments, various non-PAH-degrading bacterial strains play potentially important roles in the facilitation of PAH degradation by the co-residing mycobacteria.

Single crystalline bismuth (Bi) is known to have a peculiar electronic structure which is very close to the topological phase transition. The modification of the surface states of Bi depending on the temperature are revealed by angle-resolved photoelectron spectroscopy (ARPES). At low temperature, the upper branch of the surface state merged to the projected bulk conduction bands around the $\bar{M}$ point of the surface Brillouin zone (SBZ). In contrast, the same branch merged to the projected bulk valence bands at high temperature (400 K). Such behavior could be interpreted as a topological phase transition driven by the temperature, which might be applicable for future spin-thermoelectric devices. We discuss the possible mechanisms to cause such transition, such as the thermal lattice distortion and electron-phonon coupling., 15 pages with 6 figures (single column)

Bacterial strains capable of degrading man‐made xenobiotic compounds are good materials to study bacterial evolution towards new metabolic functions. Lindane (γ‐hexachlorocyclohexane, γ‐HCH, or γ‐BHC) is an especially good target compound for the purpose, because it is relatively recalcitrant but can be degraded by a limited range of bacterial strains. A comparison of the complete genome sequences of lindane‐degrading sphingomonad strains clearly demonstrated that (i) lindane‐degrading strains emerged from a number of different ancestral hosts that have recruited lin genes encoding enzymes that are able to channel lindane to central metabolites, (ii) in sphingomonads lin genes have been acquired by horizontal gene transfer mediated by different plasmids and in which IS6100 plays a role in recruitment and distribution of genes, and (iii) IS6100 plays a role in dynamic genome rearrangements providing genetic diversity to different strains and ability to evolve to other states. Lindane‐degrading bacteria whose genomes change so easily and quickly are also fascinating starting materials for tracing the bacterial evolution process experimentally in a relatively short time period. As the origin of the specific lin genes remains a mystery, such genes will be useful probes for exploring the cryptic ‘gene pool’ available to bacteria.

γ-Hexachlorocyclohexane (γ-HCH) is a recalcitrant man-made chlorinated pesticide. Here, the complete genome sequences of four γ-HCH-degrading sphingomonad strains, which are most unlikely to have been derived from one ancestral γ-HCH degrader, were compared. Together with several experimental data, we showed that (i) all the four strains carry almost identical linA to linE genes for the conversion of γ-HCH to maleylacetate (designated “specific” lin genes), (ii) considerably different genes are used for the metabolism of maleylacetate in one of the four strains, and (iii) the linKLMN genes for the putative ABC transporter necessary for γ-HCH utilization exhibit structural divergence, which reflects the phylogenetic relationship of their hosts. Replicon organization and location of the lin genes in the four genomes are significantly different with one another, and that most of the specific lin genes are located on multiple sphingomonad-unique plasmids. Copies of IS6100, the most abundant insertion sequence in the four strains, are often located in close proximity to the specific lin genes. Analysis of the footprints of target duplication upon IS6100 transposition and the experimental detection of IS6100 transposition strongly suggested that the IS6100 transposition has caused dynamic genome rearrangements and the diversification of lin-flanking regions in the four strains.

A synergistic effect between strong electron correlation and spin-orbit interaction (SOI) has been theoretically predicted to result in a new topological state of quantum matter on Kondo insulators (KIs), so-called topological Kondo insulators (TKIs). One TKI candidate has been experimentally observed on the KI SmB6(001), and the origin of the surface states (SS) and the topological order of SmB6 has been actively discussed. Here, we show a metallic SS on the clean surface of another TKI candidate YbB12(001), using angle-resolved photoelectron spectroscopy. The SS showed temperature-dependent reconstruction corresponding with the Kondo effect observed for bulk states. Despite the low-temperature insulating bulk, the reconstructed SS with c-f hybridization was metallic, forming a closed Fermi contour surrounding $\bar{\Gamma}$ on the surface Brillouin zone and agreeing with the theoretically expected behavior for SS on TKIs. These results demonstrate the temperature-dependent holistic reconstruction of two-dimensional states localized on KIs surface driven by the Kondo effect., Comment: 15 pages, 4 figures

rRNA is essential for life because of its functional importance in protein synthesis. The rRNA (rrn) operon encoding 16S, 23S, and 5S rRNAs is located on the "main" chromosome in all bacteria documented to date and is frequently used as a marker of chromosomes. Here, our genome analysis of a plant-associated alphaproteobacterium, Aureimonas sp. AU20, indicates that this strain has its sole rrn operon on a small (9.4 kb), high-copy-number replicon. We designated this unusual replicon carrying the rrn operon on the background of an rrn-lacking chromosome (RLC) as the rrn-plasmid. Four of 12 strains close to AU20 also had this RLC/rrn-plasmid organization. Phylogenetic analysis showed that those strains having the RLC/rrn-plasmid organization represented one clade within the genus Aureimonas. Our finding introduces a previously unaddressed viewpoint into studies of genetics, genomics, and evolution in microbiology and biology in general.

We determined the complete genome sequence of Erythrobacter sp. strain KY5, a bacterium isolated from Tokyo Bay and capable of degrading carbazole., We determined the complete genome sequence of Erythrobacter sp. strain KY5, a bacterium isolated from Tokyo Bay and capable of degrading carbazole. The genome consists of a 3.3-Mb circular chromosome that carries the gene clusters involved in carbazole degradation and biosynthesis of the photosynthetic apparatus of aerobic anoxygenic phototrophic bacteria.

The peculiar metallic electronic states observed in the Kondo insulator, samarium hexaboride (SmB$_6$), has stimulated considerable attention among those studying non-trivial electronic phenomena. However, experimental studies of these states have led to controversial conclusions mainly to the difficulty and inhomogeneity of the SmB$_6$ crystal surface. Here, we show the detailed electronic structure of SmB$_6$ with angle-resolved photoelectron spectroscopy measurements of the three-fold (111) surface where only two inequivalent time-reversal-invariant momenta (TRIM) exist. We observe the metallic two-dimensional state was dispersed across the bulk Kondo gap. Its helical in-plane spin polarisation around the surface TRIM suggests that SmB$_6$ is topologically non-trivial, according to the topological classification theory for weakly correlated systems. Based on these results, we propose a simple picture of the controversial topological classification of SmB$_6$., 34 pages, 4 figures for main text; 9 figures for supplementary material

Plasmid vector and allelic exchange mutagenesis systems were established for the genetic analysis of a phenanthrene-degrading mycobacterial strain, Mycobacterium sp. EPa45. Successful application of these systems revealed the necessity of the EPa45 phdI gene for the degradation of 1-hydroxy-2-naphthoate, which has been proposed to be an intermediate product in the degradation pathway of phenanthrene.

We report the complete genome sequence of Bradyrhizobium diazoefficiens USDA 122, a nitrogen-fixing soybean symbiont. The genome consists of a 9.1 Mb circular chromosome, and 8,551 coding sequences (CDSs) were predicted on the genome. The sequence will provide insight into the evolution of rhizobial genome, and the symbiotic compatibility with host plants.

Iron and heme play very important roles in various metabolic functions in bacteria, and their intracellular homeostasis is maintained because high concentrations of free forms of these molecules greatly facilitate the Fenton reaction-mediated production of large amounts of reactive oxygen species that severely damage various biomolecules. The ferric uptake regulator (Fur) from Burkholderia multivorans ATCC 17616 is an iron-responsive global transcriptional regulator, and its fur deletant exhibits pleiotropic phenotypes. In this study, we found that the phenotypes of the fur deletant were suppressed by an additional mutation in hemP . The transcription of hemP was negatively regulated by Fur under iron-replete conditions and was constitutive in the fur deletant. Growth of a hemP deletant was severely impaired in a medium containing hemin as the sole iron source, demonstrating the important role of HemP in hemin utilization. HemP was required as a transcriptional activator that specifically binds the promoter-containing region upstream of a Fur-repressive hmuRSTUV operon, which encodes the proteins for hemin uptake. A hmuR deletant was still able to grow using hemin as the sole iron source, albeit at a rate clearly lower than that of the wild-type strain. These results strongly suggested (i) the involvement of HmuR in hemin uptake and (ii) the presence in ATCC 17616 of at least part of other unknown hemin uptake systems whose expression depends on the HemP function. Our in vitro analysis also indicated high-affinity binding of HemP to hemin, and such a property might modulate transcriptional activation of the hmu operon. IMPORTANCE Although the hmuRSTUV genes for the utilization of hemin as a sole iron source have been identified in a few Burkholderia strains, the regulatory expression of these genes has remained unknown. Our analysis in this study using B. multivorans ATCC 17616 showed that its HemP protein is required for expression of the hmuRSTUV operon, and the role of HemP in betaproteobacterial species was elucidated for the first time, to our knowledge, in this study. The HemP protein was also found to have two additional properties that have not been reported for functional homologues in other species; one is that HemP is able to bind to the promoter-containing region of the hmu operon to directly activate its transcription, and the other is that HemP is also required for the expression of an unknown hemin uptake system.

In a previous study, we showed that MMLV-RT has a strong terminal transferase activity, and that the C-, G-, and T-tailing activities are enhanced by dGMP, dCMP, and dAMP, respectively. In this study, to achieve faster reaction and higher tailing efficiency, we screened other compounds for the ability to enhance the tailing activities of MMLV-RT, and determined the corresponding optimal concentrations. The C-, G-, and T-tailing activities were enhanced by guanine, cytosine, and adenine, respectively, and by derivatives thereof, suggesting a transient Watson-Click base pairing between an enhancer molecule and the nucleotide to be incorporated. In the presence of some additives (GMP and GDP for C-tailing and CMP for G-tailing), the tail length increased continuously, resulting in tail lengths of 7 to 15 (GMP and GDP) or 13 to 22 (CMP) nucleotides. Among the compounds that do not induce continuous addition, adenosine, deoxycytidine, and deoxyguanosine mostly enhanced T-, G-, and C-tailings, respectively. The enhancing chemicals described here will improve the feasibility of N-tailing by MMLV-RT in various biotechnological applications.

NAH7 and pWW0 from gammaproteobacterial Pseudomonas putida strains are IncP-9 conjugative plasmids that carry the genes for degradation of naphthalene and toluene, respectively. Although such genes on these plasmids are well-characterized, experimental investigation of their conjugation systems remains at a primitive level. To clarify these conjugation systems, in this study, we investigated the NAH7-encoded conjugation system by (i) analyzing the origin of its conjugative transfer ( oriT )-containing region and its relaxase, which specifically nicks within the oriT region for initiation of transfer, and (ii) comparing the conjugation systems between NAH7 and pWW0. The NAH7 oriT ( oriT N ) region was located within a 430-bp fragment, and the strand-specific nicking ( nic ) site and its upstream sequences that were important for efficient conjugation in the oriT N region were identified. Unlike many other relaxases, the NAH7 relaxase exhibited unique features in its ability to catalyze, in a conjugation-independent manner, the site-specific intramolecular recombination between two copies of the oriT N region, between two copies of the pWW0 oriT ( oriT W ) region (which is clearly different from the oriT N region), and between the oriT N and oriT W regions. The pWW0 relaxase, which is also clearly different from the NAH7 relaxase, was strongly suggested to have the ability to conjugatively and efficiently mobilize the oriT N -containing plasmid. Such a plasmid was, in the presence of the NAH7Δ nic derivative, conjugatively transferable to alphaproteobacterial and betaproteobacterial strains in which the NAH7 replication machinery is nonfunctional, indicating that the NAH7 conjugation system has a broader host range than its replication system. IMPORTANCE Various studies have strongly suggested an important contribution of conjugative transfer of catabolic plasmids to the rapid and wide dissemination of the plasmid-loaded degradation genes to microbial populations. Degradation genes on such plasmids are often loaded on transposons, which can be inserted into the genomes of the recipient bacterial strains where the transferred plasmids cannot replicate. The aim was to advance detailed molecular knowledge of the determinants of host range for plasmids. This aim is expected to be easily and comprehensively achieved using an experimental strategy in which the oriT region is connected with a plasmid that has a broad host range of replication. Using such a strategy in this study, we showed that (i) the NAH7 oriT -relaxase system has unique properties that are significantly different from other well-studied systems and (ii) the host range of the NAH7 conjugation system is broader than previously thought.

To identify bacterial genetic determinants for fitness in a soil environment, signature-tagged mutagenesis (STM) was applied to a soil bacterium, Burkholderia multivorans ATCC 17616. This strain was randomly mutagenized by each of 36 different signature-tagged plasposons, and 36 mutants with different tags were grouped as a set. A total of 192 sets consisting of 6912 independent mutants were each inoculated into soil and incubated. Two-step STM screening based on quantitative real-time PCR of total DNAs extracted from the resulting soil samples using the tag-specific primers led to the selection of 39 mutant candidates that exhibited a reduction in relative competitive fitness during incubation in the soil, and 32 plasposon-insertion sites were determined. Among them, mutants having plasposon insertion in fur, deaD or hrpA exhibited reduced fitness during incubation in soil when compared with the control strain. The deficiency in the soil fitness of the fur mutant was recovered by the introduction of the wild-type fur gene, indicating that the fur gene is one of the genetic determinants for fitness in the soil.

Moloney murine leukemia virus reverse transcriptase (MMLV-RT) is a widely used enzyme for cDNA synthesis. Here we show that MMLV-RT has a strong template-independent polymerase activity using blunt DNA ends as substrate that generates 3′ overhangs of A, C, G, or T. Nucleotides were appended efficiently in the order A > G > T > C, and tail lengths varied from 4 to 5, 2 to 7, 2 to 4, and 2 to 3 for A, C, G, and T, respectively. The activity was so strong that nearly all our test DNA ends were appended with at least one A, C, G, or T. The N-tailing activity of MMLV-RT was enhanced in the presence of Mn2+, and the G-, C-, and T-tailing activities were further enhanced by dCMP, dGMP, and dAMP, respectively. This is the first report of an enzymatic activity that almost thoroughly appends two or more As, or one or more Cs, Gs, or Ts to the 3′ end of double-stranded DNA, which would enable exhaustive analysis of DNA samples. The N-tailing activity of MMLV-RT is potentially useful in many biotechnological applications.

We determined the complete genome sequence of Thalassococcus sp. strain S3, a marine carbazole degrader isolated from Tokyo Bay in Japan that carries genes for aerobic anoxygenic phototrophy. Strain S3 has a 4.7-Mb chromosome that harbors the carbazole-degradative gene cluster and three (96-, 63-, and 46-kb) plasmids.