Crystallographic studies of the Escherichia coli quinol-fumarate reductase with inhibitors bound to the quinol-binding site

The quinol-fumarate reductase (QFR) respiratory complex of Escherichia coli is a four-subunit integral-membrane complex that catalyzes the final step of anaerobic respiration when fumarate is the terminal electron acceptor. The membrane-soluble redox-active molecule menaquinol (MQH(2)) transfers electrons to QFR by binding directly to the membrane-spanning region. The crystal structure of QFR contains two quinone species, presumably MQH(2), bound to the transmembrane-spanning region. The binding sites for the two quinone molecules are termed Q(P) and Q(D), indicating their positions proximal (Q(P)) or distal (Q(D)) to the site of fumarate reduction in the hydrophilic flavoprotein and iron-sulfur protein subunits. It has not been established whether both of these sites are mechanistically significant. Co-crystallization studies of the E. coli QFR with the known quinol-binding site inhibitors 2-heptyl-4-hydroxyquinoline-N-oxide and 2-[1-(p-chlorophenyl)ethyl] 4,6-dinitrophenol establish that both inhibitors block the binding of MQH(2) at the Q(P) site. In the structures with the inhibitor bound at Q(P), no density is observed at Q(D), which suggests that the occupancy of this site can vary and argues against a structurally obligatory role for quinol binding to Q(D). A comparison of the Q(P) site of the E. coli enzyme with quinone-binding sites in other respiratory enzymes shows that an acidic residue is structurally conserved. This acidic residue, Glu-C29, in the E. coli enzyme may act as a proton shuttle from the quinol during enzyme turnover.     

A fluorescent GTP analog as a specific, high-precision label of microtubules

Fluorescent imaging of cytoskeletal structures permits studies of both organization within the cell and dynamic reorganization of the cytoskeleton itself. Traditional fluorescent labels of microtubules, part of the cytoskeleton, have been used to study microtubule localization, structure, and dynamics, both in vivo and in vitro. However, shortcomings of existing labels make imaging of microtubules with high precision light microscopy difficult. In this paper, we report a new fluorescent labeling technique for microtubules, which involves a GTP analog modified with a bright, organic fluorophore (TAMRA, Cy3, or Cy5). This fluorescent GTP binds to a specific site, the exchangeable site, on tubulin in solution with a dissociation constant of 1.0±0.4 μM. Furthermore, the label becomes permanently incorporated into the microtubule lattice once tubulin polymerizes. We show that this label is usable as a single molecule fluorescence probe with nanometer precision and expect it to be useful for modern subdiffraction optical microscopy of microtubules and the cytoskeleton.     

WNT5A signaling affects pituitary gland shape

Wnt signaling is important in organogenesis, and aberrant signaling in mature cells is associated with tumorigenesis. Several members of the Wnt family of signaling molecules are expressed in the developing pituitary gland. Wnt5a is expressed in the neuroectoderm that induces pituitary gland development and has been proposed to influence pituitary cell specification. We discovered that mice deficient in Wnt5a display abnormal morphology in the dorsal part of the developing pituitary. The expression of downstream effectors of the canonical Wnt pathway is not altered, and expression of genes in other signaling pathways such as Shh, Fgf8, Fgf10 and Fgfr2b is intact. Prop1 and Hesx1 are also important for normal shape of the pituitary primordium, but their expression is unaltered in the Wnt5a mutants. Specification of the hormone-producing cell types of the mature anterior pituitary gland occurs appropriately. This study suggests that the primary role of Wnt5a in the developing pituitary gland is in establishment of the shape of the gland.     

Biosynthesis of the beta-lactam antibiotic, thienamycin, by Streptomyces cattleya

Radioactive- and stable isotope-containing substrates were used to identify the biosynthetic precursors of the beta-lactam antibiotic, thienamycin, in Streptomyces cattleya. Acetate is utilized by the organism to form C(6) and C(7) of the beta-lactam ring. The two carbons of the hydroxyethyl group attached to C(6) are both derived from the methyl of methionine. The cysteaminyl side chain attached to C(2) is derived from cysteine. Selective inhibition of thienamycin and cephamycin C biosynthesis has been achieved either through the addition of metabolic inhibitors or through manipulation of the growth medium. These results suggest that the two beta-lactam antibiotics, thienamycin and cephamycin C, are formed by different biosynthetic pathways.     

Is the epithelium-derived inhibitory factor in guinea-pig trachea a prostanoid?

To examine further the possible prostanoid involvement in the influence of the epithelium on guinea-pig tracheal smooth muscle responsiveness, we have analyzed the effects of LTD₄, methacholine and histamine on the level of airway smooth muscle tone and on the amounts of PGE_2α and PGI₂ (determined by radioimmunoassay) in the presence and absence of the epithelium. Removal of the epithelium increased the sensitivity of guinea-pig trachea to the contractile effects of LTD₄, methacholine and histamine. LTD₄ (3–100 nM), methacoline (0.1–10 μM) or histamine (0.3–30 μM) did not increase prostanoid release above control values in either the presence or absence of the epithelium. The unstimulated release of PGE₂ and PGF_2α but not PGI₂, was decreased in tissues lacking epithelium. Indomethacin (1 μM) reduced the baseline tone to a smaller extent in the absence of epithelium. In the presence but not the absence of the epithelium, indomethacin increased the sensitivity of preparations to the contractile effect of methacholine. The results support the postulate of an epithelium-derived inhibitory factor modulating guinea-pig tracheal smooth muscle responsiveness. The identity of this factor is not known but is not PGI₂ and is unlikely to be PGF_2α or PGE₂. However, the possibility remains that the basal release of PGE₂ and/or PGF_2α derived from the epithelium may markedly affect the responsiveness of guinea-pig tracheal smooth muscle. Furthermore, the epithelium is a significant source of PGE₂ and PGF_2α which may be involved in the maintenance of baseline tone.     

Intact Flagellar Motor of Borrelia burgdorferi Revealed by Cryo-Electron Tomography: Evidence for Stator Ring Curvature and Rotor/C-Ring Assembly Flexion

The bacterial flagellar motor is a remarkable nanomachine that provides motility through flagellar rotation. Prior structural studies have revealed the stunning complexity of the purified rotor and C-ring assemblies from flagellar motors. In this study, we used high-throughput cryo-electron tomography and image analysis of intact Borrelia burgdorferi to produce a three-dimensional (3-D) model of the in situ flagellar motor without imposing rotational symmetry. Structural details of B. burgdorferi, including a layer of outer surface proteins, were clearly visible in the resulting 3-D reconstructions. By averaging the 3-D images of ∼1,280 flagellar motors, a ∼3.5-nm-resolution model of the stator and rotor structures was obtained. flgI transposon mutants lacked a torus-shaped structure attached to the flagellar rod, establishing the structural location of the spirochetal P ring. Treatment of intact organisms with the nonionic detergent NP-40 resulted in dissolution of the outermost portion of the motor structure and the C ring, providing insight into the in situ arrangement of the stator and rotor structures. Structural elements associated with the stator followed the curvature of the cytoplasmic membrane. The rotor and the C ring also exhibited angular flexion, resulting in a slight narrowing of both structures in the direction perpendicular to the cell axis. These results indicate an inherent flexibility in the rotor-stator interaction. The FliG switching and energizing component likely provides much of the flexibility needed to maintain the interaction between the curved stator and the relatively symmetrical rotor/C-ring assembly during flagellar rotation.Flagellum-based motility plays a critical role in the biology and pathogenesis of many bacteria (3, 6, 17, 31). The well-conserved flagellum is commonly divided into three physical parts: the flagellar motor, the helically shaped flagellar filament, and the hook which provides a universal joint between the motor and the filament. In most bacteria, counterclockwise rotation of the flagella results in bundling of the helical flagella and propulsion of the cell through liquid or viscous environments. Clockwise rotation of the flagellar motor results in random turning of the cell with little translational motion (“tumbling”). Bacterial motility is thus a zigzag pattern of runs and tumbles, in which chemotactic signals favor running toward attractants and away from repellents (3).Borrelia burgdorferi and other closely related spirochetes are the causative agents of Lyme disease, which is transmitted to humans via infected Ixodes ticks (40). Spirochetes have a distinctive morphology in that the flagella are enclosed within the outer membrane sheath and are thus called periplasmic flagella (6). The flagellar motors are located at both ends of the cell and are coordinated to rotate in opposite directions during translational motion and in the same direction (i.e., both clockwise or both counterclockwise) during the spirochete equivalent of tumbling, called “flexing” (6, 15). Spirochetes are also capable of reversing translational motion by coordinated reversal of the direction of motor rotation at both ends of the cell. Rotation of the flagella causes a serpentine movement of the entire cell body, allowing B. burgdorferi to efficiently bore its way through tissue and disseminate throughout the mammalian host, resulting in manifestations in the joints, nervous system, and heart (40).The flagellar motor is an extraordinary nanomachine powered by the electrochemical potential of specific ions across the cytoplasmic membrane (3). Current knowledge of the flagellar motor structure and rotational mechanisms is based primarily on studies of Escherichia coli and Salmonella enterica and is summarized in several recent comprehensive reviews (3, 22, 31, 39, 42). The flagellar motor is constructed from at least 20 different kinds of proteins. The approximate location of these flagellar proteins has been determined by a variety of approaches and appears to be relatively consistent in a wide variety of bacteria. It can be divided into several morphological domains: the MS ring (FliF, the base for the flagellar motor); the C ring (FliG, FliM, and FliN, the switch complex regulating motor rotation); the export apparatus (multiple-protein complex located at the cytoplasmic side of the MS ring); the rod (connecting the MS ring and the hook); the L and P rings on the rod (thought to serve as bushings at the outer membrane and at the peptidoglycan layer, respectively); and the stator, which is the motor force generator embedded in the cytoplasmic membrane. Electron microscopy studies of the purified flagellar motor have provided a detailed view of the rotor/C-ring assembly (11, 44). However, there is no structural information on the stator and the export apparatus in these reconstructions, because these membrane-associated structures are not retained following detergent extraction during the extensive basal body purification process. The stator and the export apparatus were visualized by using freeze fracture preparations of cytoplasmic membranes. It appears that 10 to 16 stator units form circular arrays in the membrane (9, 20). Part of the export apparatus is located in the central space of the C ring (18). Recently a 7-nm-resolution structure of the intact flagellar motor in situ was revealed by averaging 20 structures obtained using cryo-electron tomography (cryo-ET) of Treponema primitia cells (32). Further analysis of the intact flagellar motor structure would lead to a better understanding of the motor protein distribution, the rotor-stator interaction, and the mechanism of bacterial motility.Cryo-ET has emerged as a three-dimensional (3-D) imaging technique to bridge the information gap between X-ray crystallographic and optical microscopic methods (24, 30). This process involves rapidly freezing viable cells, collecting a series of electron micrographs at different angles, and computationally combining the resulting images into a 3-D density map. Cryo-ET allows investigation of the structure-function relationship of molecular complexes and supramolecular assemblies in their cellular environments without fixation, dehydration, embedding, or sectioning artifacts. Spirochetes are well suited for cryo-ET analysis because of their narrow cell diameter (typically 0.2 to 0.3 μm). Recently the cellular architecture of Treponema primitia, Treponema denticola, and B. burgdorferi, as well as the configuration of the B. burgdorferi periplasmic flagella, were revealed by cryo-ET (7, 16, 26, 33). In combination with advanced computational methods, cryo-ET is currently the most promising approach for determining the cellular architecture in situ at molecular resolution (30). We have developed novel strategies for capturing and averaging thousands of 3-D images of large macromolecular assemblies to obtain ∼2.0-nm-resolution structures (28, 29).In this study, we present the molecular structures of infectious wild-type (WT) and mutant B. burgdorferi organisms and their flagellar motors in situ using high-throughput cryo-ET and 3-D image analysis. By averaging subvolumes of 1,280 flagellar motors from 322 cells, we obtained a ∼3.5-nm-resolution model of the intact flagellar motor, providing a detailed view of rotor-stator interactions. In addition, detergent treatment of intact cells provided a preliminary identification of the rotor and stator structures. Through the comparison of WT and mutant cells, we have also determined the location of the flgI gene product in the B. burgdorferi flagellar motor.     

Decreased CSF pH at ventral brain stem induces widespread c-Fos immunoreactivity in rat brain neurons.

Physiological evidence has indicated that central respiratory chemosensitivity may be ascribed to neurons located at the ventral medullary surface (VMS); however, in recent years, multiple sites have been proposed. Because c-Fos immunoreactivity is presumed to identify primary cells as well as second- and third-order cells that are activated by a particular stimulus, we hypothesized that activation of VMS cells using a known adequate respiratory stimulus, H(+), would induce production of c-Fos in cells that participate in the central pH-sensitive respiratory chemoreflex loop. In this study, stimulation of rostral and caudal VMS respiratory chemosensitive sites in chloralose-urethane-anesthetized rats with acidic (pH 7.2) mock cerebrospinal fluid induced c-Fos protein immunoreactivity in widespread brain sites, such as VMS, ventral pontine surface, retrotrapezoid, medial and lateral parabrachial, lateral reticular nuclei, cranial nerves VII and X nuclei, A(1) and C(1) areas, area postrema, locus coeruleus, and paragigantocellular nuclei. At the hypothalamus, the c-Fos reaction product was seen in the dorsomedial, lateral hypothalamic, supraoptic, and periventricular nuclei. These results suggest that 1) multiple c-Fos-positive brain stem and hypothalamic structures may represent part of a neuronal network responsive to cerebrospinal fluid pH changes at the VMS, and 2) VMS pH-sensitive neurons project to widespread regions in the brain stem and hypothalamus that include respiratory and cardiovascular control sites.     

Mechanism of transient nocturnal hypoxemia in hypoxic chronic bronchitis and emphysema

In five patients with hypoxic chronic bronchitis and emphysema we measured ear O2 saturation (SaO2), chest movement, oronasal airflow, arterial and mixed venous gas tensions, and cardiac output during nine hypoxemic episodes (HE; SaO2 falls greater than 10%) in rapid-eye-movement (REM) sleep and during preceding periods of stable oxygenation in non-REM sleep. All nine HE occurred with recurrent short episodes of reduced chest movement, none with sleep apnea. The arterial PO2 (PaO2) fell by 6.0 +/- 1.9 (SD) Torr during the HE (P less than 0.01), but mean arterial PCO2 (PaCO2) rose by only 1.4 +/- 2.4 Torr (P greater than 0.4). The arteriovenous O2 content difference fell by 0.64 +/- 0.43 ml/100 ml of blood during the HE (P less than 0.05), but there was no significant change in cardiac output. Changes observed in PaO2 and PaCO2 during HE were similar to those in four normal subjects during 90 s of voluntary hypoventilation, when PaO2 fell by 12.3 +/- 5.6 Torr (P less than 0.05), but mean PaCO2 rose by only 2.8 +/- 2.1 Torr (P greater than 0.4). We suggest that the transient hypoxemia which occurs during REM sleep in patients with chronic bronchitis and emphysema could be explained by hypoventilation during REM sleep but that the importance of changes in distribution of ventilation-perfusion ratios cannot be assessed by presently available techniques.