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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.

次世代放射光施設で建設中の RIXS ビームラインの光学設計について発表 する。, 14th International Conference on Synchrotron Radiation Instrumentation

次世代放射光施設で QST が第 1 期に整備される 3 本の共用ビームラインのうち、BL06U では軟 X 線ナノ光電子分光ビームラインとして、ナノ集光ビームを用いたスピン分解角度分解光電子分光（ARPES）を実現することを計画している。次世代放射光施設利用研究検討委員会ビームラインワーキンググループによって纏められた要求仕様に基づいて現在設計を進めているビームライン光学系について報告する。, 14th International Conference on Synchrotron Radiation Instrumentation

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.

次世代放射光施設で建設中のRIXSビームライン、エンドステーションの検討状況について発表する。, 第35回日本放射光学会年会・放射光科学合同シンポジウム

軟X線ナノ光電子分光（ARPES）ビームラインは、50–1,000 eVの軟X線を高精度ミラーを用いてナノ集光化し、高効率かつ多自由度のナノ集光ARPES計測を実現することを目指している。本ビームラインでは、高エネルギー分解能と極限集光を両立するためにcPGMを採用し、M1で平行化した放射光をM3振り分け鏡で再度集光して各ブランチビームラインに導く構成となっている。A/Bブランチではナノ集光ARPESステーションとマイクロ集光ARPESステーションを排他的に利用する計画である。講演ではエンドステーションの仕様も含めた最新の検討状況について報告する。, 第35回日本放射光学会年会・放射光科学合同シンポジウム

顕微スピントロニクスビームラインは、2024年から供用開始を予定している次世代放射光施設において、QSTが初期に整備する３本のビームラインのうちの１本として計画されている。伝統的な磁性材料のみならず、近年の原子層薄膜やトポロジカル物質等の発見・開発や、電流に限らないスピンを介した多様なエネルギー変換機構の構想などにより、磁性・スピントロニクス分野の研究は近年一層の活況を呈している。本ビームラインはこれらの新奇スピン物性の研究をさらに加速発展させるために、次世代放射光施設の低エミッタンス光源を活かした顕微スピン分光(X線磁気円・線二色性分光)測定を実現して、広範な試料に対して提供することを目標としている。光源には分割型APPLE-IIアンジュレータを採用して軟XからテンダーX線までの広い波長範囲と自由度の高い偏光制御を両立し、モノリシックウォルター鏡を利用したサブミクロン集光系やフレネルゾーンプレートを用いたナノ集光系等の目的に応じた空間分解能を持つ複数の顕微スピン分光エンドステーションに放射光を提供する光学系およびエンドステーション自体の設計を進めている。 講演ではエンドステーションの仕様も含めた最新の検討状況について報告する。, 第35回日本放射光学会年会・放射光科学合同シンポジウム

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

The peculiar metallic electronic states proposed and observed in Kondo insulators (KIs), whose bandgap opens at low temperature derived from the Kondo effect between itinerant and localized electrons, have attracted considerable attention in this decade, because it suggests the coexistence of strong electron correlation and non-trivial topological order (TO) in such KIs, namely topological Kondo insulators (TKIs). However, experimental studies of these states have led to controversial conclusions mainly owing to the difficulty and inhomogeneity of the single crystal surfaces of the TKI candidates, samarium hexaboride (SmB6) and ytterbium dodecaboride (YbB12). In this article, we review studies focused on the surface atomic and electronic structures of TKI candidates and recent progress to form homogeneous, well-defined clean surfaces of them. Due to the homogeneous surface formation, the surface electronic states and their non-trivial TO are elucidated well in SmB6 and YbB12, by using spin- and angle-resolved photoelectron spectroscopy.

軟X線ナノ光電⼦分光（ARPES）ビームラインは、2024年から供⽤開始を予定している次世代放射光施設において、QSTが初期に整備する3本の共⽤ビームラインのうちの1本として計画されている。本ビームラインの⽬標は、軟X線ナノ集光素⼦としてWolterミラーを採⽤して⾼フラックスのナノ集光ビームを⽣成すると共に、多チャンネルのスピン検出器を採⽤して⾼効率化を達成し、世界に先駆けてナノ集光スピン分解ARPES計測を実現することにある。ビームラインの仕様については、これまで に次世代放射光施設利⽤研究検討委員会ビームラインワーキンググループの中で議論された。ここで要求されたスペックを満たすためのビームライン光学系の検討を現在進めており、講演ではその検討状況について報告する。, 第34回日本放射光学会年会・放射光科学合同シンポジウム

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 electronic structure of a Bi 0.91 Sb 0.09 single crystal was elucidated at a bisectrix ( 11 2 ¯ ) surface by angle-resolved photoemission spectroscopy using microbeam synchrotron radiation. A Dirac-cone-like dispersion of the surface state was observed at the Γ ¯ point. The detected surface-state band likely corresponds to the one observed in previous quantum transport research (Taskin and Ando, 2009) [14].

Samarium hexaboride (SmB6) is the most extensively studied candidate of topological Kondo insulators. To clarify the topological origin of metallic surface states observed on the SmB6(001) surfaces, we studied the surface electronic structure of SmB6 on the other surface orientation, SmB6(111). Although the SmB6(111) surface cannot be obtained by cleaving, we successfully obtained the well-defined clean surface by high-temperature annealing of the mechanically polished single crystal of SmB6(111) in an ultra-high vacuum. The valence band spectra obtained by photoelectron spectroscopy with the bulk and surface-sensitive incident photon energies imply that the surface is covered with B 6 cluster without Sm atoms.

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.

Bacterial strains capable of degrading man-made xenobiotic compounds are thought to have evolved to degrade such compounds within only several decades. Various sphingomonad strains belonging to Alphaproteobacteria were isolated that degrade highly recalcitrant compounds including man-made xenobiotics, indicating the versatility of this bacterial group. However, each strain degrades only a limited set of compounds, and specific genes for the degradation of a specific compound are found only in the genomes of its degraders, suggesting the plasticity of genomes of sphingomonads. Comparison of the complete genome sequences of four γ-hexachlorocyclohexane (γ-HCH)-degrading sphingomonad strains, Sphingobium japonicum UT26, Sphingomonas sp. MM-1, Sphingobium sp. MI1205, and Sphingobium sp. TKS, strongly suggested that the γ-HCH-degrading strains emerged through the recruitment of specific lin genes for the γ-HCH degradation into ancestral strains that had core functions of sphingomonads. Plasmids, most of which are specialized for sphingomonads, and IS6100, the most abundant insertion sequence in the four strains, seem to be involved in the recruitment of the lin genes and the diversification of the lin-flanking regions in the four strains. Here, we show concrete examples and discuss the important roles of such mobile genetic elements for the emergence and evolution of the bacterial strains degrading highly recalcitrant compounds.

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.