Complete genome sequencing and analysis of Saprospira grandis str. Lewin, a predatory marine bacterium

Saprospira grandis is a coastal marine bacterium that can capture and prey upon other marine bacteria using a mechanism known as 'ixotrophy'. Here, we present the complete genome sequence of Saprospira grandis str. Lewin isolated from La Jolla beach in San Diego, California. The complete genome sequence comprises a chromosome of 4.35 Mbp and a plasmid of 54.9 Kbp. Genome analysis revealed incomplete pathways for the biosynthesis of nine essential amino acids but presence of a large number of peptidases. The genome encodes multiple copies of sensor globin-coupled rsbR genes thought to be essential for stress response and the presence of such sensor globins in Bacteroidetes is unprecedented. A total of 429 spacer sequences within the three CRISPR repeat regions were identified in the genome and this number is the largest among all the Bacteroidetes sequenced to date.     

Photoregulation of Respiratory Activity in the Cyanophyte Synechocystis PCC 6714: the Possibility of the Simultaneous Regulation of the Amount of PS I Complex and the Activity of Respiratory Terminal Oxidase in Thylakoids

Respiration of the cyanophyte Synechocystis PCC 6714 was studiedin relation to conditions for cell growth. Under our experimentalconditions, the KCN-sensitive O₂-uptake observed with intactcells was found to be limited at the step catalyzed by the terminaloxidase in thylakoids, indicating that the activity of O₂-uptakeby intact cells corresponds to that of the terminal oxidasein thylakoids. The activity was found to be variable dependingon the growth conditions; it was higher under conditions wherethe level of PS I, another terminal component of the thylakoidelectron transport system (ETS) was elevated, whereas it waslower under conditions where the level of PS I was reduced.Changes in the activity did not occur when protein synthesiswas suppressed by chloramphenicol. The results suggest that,similarly to the regulation of levels of PS I, the activityor the amount of terminal oxidase in thylakoids is regulatedin response to the redox steady-state of intermediate component(s)of ETS, in order to maintain a balance between the efflux ofelectrons from the ETS and the influx to the ETS. ¹Present address: P.G. Department of Botany, Utkal University,Bhubaneswar-751004, Orissa, Keonjhar, India (Received September 27, 1989; Accepted March 22, 1990)     

Permanent draft genome sequence of the gliding predator Saprospira grandis strain Sa g1 (= HR1)

Saprospira grandis Gross 1911 is a member of the Saprospiraceae, a family in the class 'Sphingobacteria' that remains poorly characterized at the genomic level. The species is known for preying on other marine bacteria via 'ixotrophy'. S. grandis strain Sa g1 was isolated from decaying crab carapace in France and was selected for genome sequencing because of its isolated location in the tree of life. Only one type strain genome has been published so far from the Saprospiraceae, while the sequence of strain Sa g1 represents the second genome to be published from a non-type strain of S. grandis. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,495,250 bp long Improved-High-Quality draft of the genome with its 3,536 protein-coding and 62 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.     

Respiratory Mechanisms in the Aroid Spadix

The flowers of Skunk-cabbage (Symplocarpus foetidus), like thespadix tissues of other Aroids, have a rapid, carbon monoxideand cyanide (HCN) resistant respiration; oxygen uptake is independentof the oxygen partial pressure over a wide range. Cell fractionswere isolated by differential centrifugation and their oxidativeactivities studied. Oxidation of succinate and citrate by mitochondriacan be inhibited 50 to 60 per cent. by 1 X 10^–3 M. HCN,and antimycin A (AA) causes partial inhibitions. An active mitochondrialcytochrome-c oxidase is present, and it shows a typical sensitivityto cyanide. The mitochondria possess an active reduced diphosphopyridine-nucleotide(DPNH) oxidase system, which is inhibited roughly 80 per cent.by 1 X 10^–3 M. HCN and 1.7 µg./ml. AA. The microsomalDPNH oxidase, which is less sensitive to inhibitors, is lessactive per gramme of tissue than that on the mitochondria. Thefinal supernatant shows little DPNH oxidase. With all fractions,reduced triphosphopyridine nucleotide (TPNH) is oxidized muchmore slowly than DPNH. DPNH-cyto-chrome-c reductase activitywas measured; the mitochondrial system is partially blockedby AA, whereas the microsomal activity is AA-insensitive. Spectro-photometricexamination of a preparation of solubilized mitochondria showedthat cytochromes a, b, and c are present. The results are discussedwith reference to the pathway and localization of hydrogen andelectron transport in the Aroid spadix.     

The Terminal Oxidase in the Marine Bacterium Pseudomonas nautica 617

The molecular properties of a novel membrane quinol oxidase from the marine bacterium Pseudomonas nautica 617 are presented. The protein contains 2b hemes/mole which may be distinguished by EPR spectroscopy but not by optical spectroscopy and electrochemistry. Respiration, though being cyanide insensitive, is not inhibited by carbon monoxide and oxygen reduction is carried out only half-way with production of hydrogen peroxide. The terminal oxidase represents, therefore, a unique example in the large family of terminal oxidases known up to date.     

Quantitation of the Tetramethyl-p-Phenylenediamine Oxidase Reaction in Neisseria Species

The tetramethyl-p-phenylenediamine oxidase reaction commonly used in the Kovacs oxidase test was quantitatively estimated for various Neisseria species employing standardized resting cell suspensions. This genus of microorganisms exhibited very high tetramethyl-p-phenylenediamine oxidase rates comparable to that of Azotobacter and Pseudomonas, and this reaction was found to be a valid measurement for the respiratory capability possessed by this group of organisms.     

Respiratory Chain of Plant Mitochondria: XVIII. Point of Interaction of the Alternate Oxidase with the Respiratory Chain

Oxidation of the respiratory chain carriers of anaerobic, CO-saturated skunk cabbage (Symplocarpus foetidus) mitochondria, by means of an O₂ pulse, proceeds primarily through the cyanide-insensitive alternate oxidase, since the oxidation of cytochromes a and a₃ takes place with a half-time of 3 seconds, corresponding to the rate of dissociation of CO from reduced cytochrome a₃. Ubiquinone and part of the flavoprotein are oxidized within 1 second under these conditions, and this rapid rate of oxidation is strongly inhibited by m-chlorobenzhydroxamic acid (mCLAM), a specific inhibitor of the alternate oxidase of plant mitochondria. The rate of ubiquinone oxidation under these conditions in white potato (Solanum tuberosum) mitochondria, which have no alternate oxidase, is the same as that in skunk cabbage mitochondria treated with mCLAM. Ubiquinone, thus identified as the carrier common to both the cytochrome and alternate oxidase pathways, is linked to the alternate oxidase by a flavoprotein of midpoint potential 50 millivolts more negative with which it is in equilibrium. This arrangement provides a switch for diverting electron transport primarily through the cytochrome pathway under state 3 conditions and primarily through the alternate oxidase pathway under state 4 conditions.     

The Respiratory Arsenite Oxidase: Structure and the Role of Residues Surrounding the Rieske Cluster

The arsenite oxidase (Aio) from the facultative autotrophic Alphaproteobacterium Rhizobium sp. NT-26 is a bioenergetic enzyme involved in the oxidation of arsenite to arsenate. The enzyme from the distantly related heterotroph, Alcaligenes faecalis, which is thought to oxidise arsenite for detoxification, consists of a large α subunit (AioA) with bis-molybdopterin guanine dinucleotide at its active site and a 3Fe-4S cluster, and a small β subunit (AioB) which contains a Rieske 2Fe-2S cluster. The successful heterologous expression of the NT-26 Aio in Escherichia coli has resulted in the solution of its crystal structure. The NT-26 Aio, a heterotetramer, shares high overall similarity to the heterodimeric arsenite oxidase from A. faecalis but there are striking differences in the structure surrounding the Rieske 2Fe-2S cluster which we demonstrate explains the difference in the observed redox potentials (+225 mV vs. +130/160 mV, respectively). A combination of site-directed mutagenesis and electron paramagnetic resonance was used to explore the differences observed in the structure and redox properties of the Rieske cluster. In the NT-26 AioB the substitution of a serine (S126 in NT-26) for a threonine as in the A. faecalis AioB explains a −20 mV decrease in redox potential. The disulphide bridge in the A. faecalis AioB which is conserved in other betaproteobacterial AioB subunits and the Rieske subunit of the cytochrome bc ₁ complex is absent in the NT-26 AioB subunit. The introduction of a disulphide bridge had no effect on Aio activity or protein stability but resulted in a decrease in the redox potential of the cluster. These results are in conflict with previous data on the betaproteobacterial AioB subunit and the Rieske of the bc ₁ complex where removal of the disulphide bridge had no effect on the redox potential of the former but a decrease in cluster stability was observed in the latter.     

Lack of relationship between gliding cyanobacteria and filamentous gliding heterotrophic eubacteria: comparison of 16S rRNA catalogues of Spirulina,Saprospira, Vitreoscilla,Leucothrix, and Herpetosiphon

Spirulina platensis and Spirulina maxima were characterized by 16S ribosomal RNA oligonucleotide cataloguing. Both species are highly related. They fall into the main group of the cyanobacteria, showing a remote relationship to Nostoc, Fischerella, Aphanocapsa, and also to Prochloron. Low similarity coefficients were found between the Spirulina species and certain organotrophic and sulfide oxidizing bacteria, viz. Saprospira grandis, Vitreoscilla stercoraria, Leucothrix mucor, Herpetosiphon aurantiacus, and Beggiatoa leptomitiformis, respectively. This result does not support the classical hypothesis that certain filamentous gliding bacteria are apochlorotic cyanobacteria.     

Existence of aa 3-Type Ubiquinol Oxidase as a Terminal Oxidase in Sulfite Oxidation of Acidithiobacillus thiooxidans

It was found that Acidithiobacillus thiooxidans has sulfite:ubiquinone oxidoreductase and ubiquinol oxidase activities in the cells. Ubiquinol oxidase was purified from plasma membranes of strain NB1-3 in a nearly homogeneous state. A purified enzyme showed absorption peaks at 419 and 595 nm in the oxidized form and at 442 and 605 nm in the reduced form. Pyridine ferrohaemochrome prepared from the enzyme showed an α-peak characteristic of haem a at 587 nm, indicating that the enzyme contains haem a as a component. The CO difference spectrum of ubiquinol oxidase showed two peaks at 428 nm and 595 nm, and a trough at 446 nm, suggesting the existence of an aa ₃-type cytochrome in the enzyme. Ubiquinol oxidase was composed of three subunits with apparent molecular masses of 57 kDa, 34 kDa, and 23 kDa. The optimum pH and temperature for ubiquinol oxidation were pH 6.0 and 30 °C. The activity was completely inhibited by sodium cyanide at 1.0 mM. In contrast, the activity was inhibited weakly by antimycin A₁ and myxothiazol, which are inhibitors of mitochondrial bc ₁ complex. Quinone analog 2-heptyl-4-hydoroxyquinoline N-oxide (HOQNO) strongly inhibited ubiquinol oxidase activity. Nickel and tungstate (0.1 mM), which are used as a bacteriostatic agent for A. thiooxidans-dependent concrete corrosion, inhibited ubiquinol oxidase activity 100 and 70% respectively.     

Enhancement of Biodesulfurization in Two-Liquid Systems by Heterogeneous Expression of Vitreoscilla Hemoglobin

The vgb gene, encoding Vitreoscilla hemoglobin (VHb), was introduced into a specific desulfurization bacterium, Rhodococcus erythropolis LSSE8-1. The VHb-specific spectrum was observed for the recombinant. Compared to the wild type, the strain bearing vgb showed a higher biomass yield and desulfurizing activity.     

Differences in the Thermostability and Subunit Species of Cytochrome c Oxidase among Tissues

Cytochrome c oxidase associated with the mitochondrial innermembrane of the overground or underground organs of mung beanwas more stable at 40–55?C than that of the correspondingorgans of pea. In both plants, the enzyme in the overgroundorgans was more resistant to heat inactivation than that inthe underground organs. When the enzyme was solubilized andpartially purified from mung bean hypocotyls or roots, the enzymebecame more labile and was stabilized by exogenous phospholipid.The enzyme partially purified from mung bean hypocotyls wasmore resistant to inactivation than that from its roots eitherin the presence or absence of phospholipid. A subunit (subunitVa) of cytochrome c oxidase in mung bean hypocotyls differedimmunologically from that in the roots. We propose that at leastin mung bean, a nuclear-encoded subunit of cytochrome c oxidaseis synthesized tissue-specifically, which may cause the differencein the thermostability of the enzyme. (Received August 7, 1988; Accepted August 22, 1988)     

Arabidopsis Species Hybrids-EmergingModel Systems for the Analysis of Species Differences

   apd: 9 March 2001     

Role of Glutamate and GABA in Mechanisms Underlying Respiratory Control

This review deals with modern concepts on the mechanisms of involvement of main central excitatory and inhibitory neurotransmitters, glutamate and GABA, in the control of the respiratory function.     

Physiological Mechanisms of Respiratory Phenomena in Anxiety and Depressive Disorders

An analysis is presented of the current views on the functional respiratory disorders associated with depressive and panic disorders. The following subjects are discussed: the phenomenology of the problem, modern diagnostic methods, the role of hypocapnia in the symptomatological development of panic disorders, the relative contributions of psychogenic and biological factors in developing respiratory disorders, and the distinctions between dyspnea and the hyperventilation syndrome.