A deeply branching thermophilic bacterium with an ancient acetyl-CoA pathway dominates a subsurface ecosystem

<div><p>A nearly complete genome sequence of <em>Candidatus</em> ‘Acetothermum autotrophicum’, a presently uncultivated bacterium in candidate division OP1, was revealed by metagenomic analysis of a subsurface thermophilic microbial mat community. Phylogenetic analysis based on the concatenated sequences of proteins common among 367 prokaryotes suggests that <em>Ca.</em> ‘A. autotrophicum’ is one of the earliest diverging bacterial lineages. It possesses a folate-dependent Wood-Ljungdahl (acetyl-CoA) pathway of CO₂ fixation, is predicted to have an acetogenic lifestyle, and possesses the newly discovered archaeal-autotrophic type of bifunctional fructose 1,6-bisphosphate aldolase/phosphatase. A phylogenetic analysis of the core gene cluster of the acethyl-CoA pathway, shared by acetogens, methanogens, some sulfur- and iron-reducers and dechlorinators, supports the hypothesis that the core gene cluster of <em>Ca.</em> ‘A. autotrophicum’ is a particularly ancient bacterial pathway. The habitat, physiology and phylogenetic position of <em>Ca.</em> ‘A. autotrophicum’ support the view that the first bacterial and archaeal lineages were H₂-dependent acetogens and methanogenes living in hydrothermal environments.</p> </div

Resolving stepping rotation in Thermus thermophilus H+-ATPase/synthase with an essentially drag-free probe

Vacuole-type ATPases (VoV1) and FoF1 ATP synthases couple ATP hydrolysis/synthesis in the soluble V1 or F1 portion with proton (or Na+) flow in the membrane-embedded Vo or Fo portion through rotation of one common shaft. Here we show at submillisecond resolutions the ATP-driven rotation of isolated V1 and the whole VoV1 from Thermus thermophilus, by attaching a 40-nm gold bead for which viscous drag is almost negligible. V1 made 120° steps, commensurate with the presence of three catalytic sites. Dwells between the steps involved at least two events other than ATP binding, one likely to be ATP hydrolysis. VoV1 exhibited 12 dwell positions per revolution, consistent with the 12-fold symmetry of the Vo rotor in T. thermophilus. Unlike F1 that undergoes 80°–40° substepping, chemo-mechanical checkpoints in isolated V1 are all at the ATP-waiting position, and Vo adds further bumps through stator–rotor interactions outside and remote from V1

Mitochondrial ATP synthase: architecture, function and pathology

Human mitochondrial (mt) ATP synthase, or complex V consists of two functional domains: F1, situated in the mitochondrial matrix, and Fo, located in the inner mitochondrial membrane. Complex V uses the energy created by the proton electrochemical gradient to phosphorylate ADP to ATP. This review covers the architecture, function and assembly of complex V. The role of complex V di-and oligomerization and its relation with mitochondrial morphology is discussed. Finally, pathology related to complex V deficiency and current therapeutic strategies are highlighted. Despite the huge progress in this research field over the past decades, questions remain to be answered regarding the structure of subunits, the function of the rotary nanomotor at a molecular level, and the human complex V assembly process. The elucidation of more nuclear genetic defects will guide physio(patho)logical studies, paving the way for future therapeutic interventions

Highly sensitive determination of boron with 1,8-dihydroxynaphthalene-3,6-disulfonic acid in ultrapurified water by fluorescence detection/flow-injection analysis

超純水中の極微量ホウ素を定量するために，クロモトロープ酸を用いるホウ素の蛍光検出/フローインジェクション（FIA）法の諸条件を再検討し，検出限界を10分の1の5×10(－10) Mに下げることに成功し，大幅な感度向上を達成した．クロモトロープ酸とホウ酸との反応生成物の蛍光を利用するホウ素のFIA法における残存クロモトロープ酸の蛍光強度を低下させるために，アンモニア水を加え，アルカリ性にした．緩衝液としてエチレンジアミン四酢酸を含む酢酸緩衝液を用い，金属のマスキングを兼ねたpH調整を行うことにより，非常に安定なベースラインを得ることに成功した．流量，反応コイル長，試料注入量，試薬濃度等のFIAパラメーターについて感度向上の観点から最適化を行い，ホウ素錯体の蛍光測定（励起波長λ(ex)＝313 nm，蛍光波長λ(em)＝360 nm）により，前処理なしでホウ素10(－9) Mの定量が可能となった．S/N＝3での検出限界は5×10(－10) M（5 ppt）で，現在最も高感度な定量法である．ホウ素6×10(－9) Mの10回繰り返し実験の相対標準偏差（RSD）は3.6％（n＝10）であり，1時間に40試料の分析が可能であった．河川水，蒸留水，イオン交換水などに存在する程度の金属イオン及び陰イオンは定量を妨害しない．本法により，イオン交換水，蒸留水中に存在するホウ素は直接定量できた．超純水中に存在する微量のホウ素（10(－10) Mレベル）は，加熱濃縮操作法を併用することにより，定量可能となった．Boron as boric acid was determined as a complex with chromotropic acid at pH 6.0 in an aqueous medium by fluorescence detection/flow-injection analysis. The complex was detected by measuring the fluorescence intensities (λ(ex) = 313 nm, λ(em) = 360 nm). EDTA was used as a buffer component with the role of a masking agent to metal ions. The background fluorescence of chromotropic acid could be decreased by mixing with 0.1 M ammonia water after complex formation, resulting in a stable baseline. The calibration graph was rectilinear over 10(−9)∼10(−6) mol dm(−3) (M), and the detection limit was 5×10(−10) M (S/N = 3). The reproducibility was 3.61% (n = 10, with the peak height) at 6×10(−9) M of boron and sample throughput was 40 h(−1). Applications to river water, ion-exchanged water and distilled water could be achived without any pretreatments. For the analysis of ultrapurified water, an evaporation/preconcentration procedure was carried out, because the concentration was under the LOD and no reference water which could be used for the carrier solution or preparation of the reagent solutions