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R K Poole

Publications and source records attributed to R K Poole.

At least 73 records · Page 4Linked to original sources
PubMed1993

Reactions of the membrane-bound cytochrome bo terminal oxidase of Escherichia coli with carbon monoxide and oxygen.

The cytochrome 'bo' quinol oxidase of Escherichia coli contains 2 mol of haem, one or both of which are 'haem O'. One of the haems forms, with the single copper present, a binuclear site for ligand binding and oxygen reduction. Cytoplasmic membranes from a strain of E. coli lacking the alternative cytochrome bd quinol oxidase, and having amplified levels of cytochrome bo, were used to study oxygen and carbon monoxide reactivity with this oxidase. The high-spin ligand-binding haem was identified from its contribution to the Soret region and the shift in midpoint potential from +211 to +477 mV in the presence of CO. Oxidative titration of a CO-liganded sample was accompanied by a decrease in the contribution from a photodissociable CO-binding haem. The photodissociation spectrum was typical of a high-spin haem. Photolysis of CO-liganded, reduced membranes in the presence of O2 at sub-zero temperatures revealed O2 binding and cytochrome oxidation characterized by differential absorbance changes in the alpha-spectral region. Monitoring by epr spectroscopy of the same reaction sequence at -80 degrees C revealed a slight increase in g = 6 signal intensity immediately after photolysis attributable to cytochrome o oxidation prior to Cu oxidation. Subsequent decline in the g = 6 signal and appearance of a g = 3 signal indicated sequential electron flow from low-spin to high-spin haems and copper oxidation, suggesting that a second haem carries electrons from ubiquinol to the binuclear centre.

Carbon Monoxide↗
PubMed1993

Mutants of Escherichia coli affected in respiration: the cloning and nucleotide sequence of ubiA, encoding the membrane-bound p-hydroxybenzoate:octaprenyltransferase.

A mutant of Escherichia coli has been isolated that is unable to grow aerobically on non-fermentable substrates, but able to grow anaerobically on glycerol with alternative electron acceptors such as fumarate. Nitrate as electron acceptor supports anaerobic growth on glycerol, but not on succinate or lactate. Oxygen consumption rates by cell-free extracts with succinate, lactate or glycerol 3-phosphate as substrates were low relative to activities in an isogenic control strain but were restored in vitro by adding ubiquinone-1. Transformation of the mutant with a cloned 2.6 kb ClaI-PvuII fragment of chromosomal DNA restored cellular quinone levels and growth on succinate. The plasmid also complemented a previously isolated ubiA mutant for aerobic growth on non-fermentable substrates. The nucleotide sequence of the cloned fragment revealed a fragment of plsB (91.7 min on the E. coli chromosome map) and three open reading frames (ORFs), one of which (ORF3) encodes a protein with a predicted molecular mass of 32511 Da. The hydrophobicity profile of the ORF3 protein is characteristic of a membrane protein with five hydrophobic regions and is very similar to that of the Saccharomyces cerevisiae COQ2 gene product (p-hydroxybenzoate:polyprenyltransferase, required for the second step of ubiquinone biosynthesis) and to the product of the E. coli cyoE gene. Complementation of ubi mutants with various deletion derivatives of the cloned DNA fragment confirms that ORF3 is ubiA. ORF3 is closely linked to ubiC (ORF2), which encodes chorismate lyase.

Alkyl and Aryl Transferases↗
PubMed1993

Cytochrome bd biosynthesis in Escherichia coli: the sequences of the cydC and cydD genes suggest that they encode the components of an ABC membrane transporter.

At least four genes are known to affect formation of the cytochrome bd-type terminal oxidase of Escherichia coli. In addition to the genes (cydA and cydB) encoding the two constituent subunits of this complex, a further two genes (cydC and cydD) map near 19 min on the E. coli chromosome. We report here the cloning of both genes on a 5.3 kb ClaI-HindIII restriction fragment, which, when used to transform either a cydC or cydD mutant, restored the ability of these mutants to grow on a selective medium containing azide and zinc ions and also restored the spectral signals associated with the cytochrome components of the oxidase complex. A subcloned 1.8 kb DdeI fragment similarly restored growth and cytochrome content of a cydD mutant, but not a cydC mutant. The complete nucleotide sequence of the ClaI-HindIII fragment reveals three open reading frames, one being trxB (19.3 min on the E. coli chromosome map, encoding thioredoxin reductase), confirming the mapping position of cydD previously established by P1-mediated transduction. Two ORFs identified by complementation experiments as cydD and cydC encode proteins with predicted molecular masses, respectively, of 65,103 and 62,946 Da. The hydropathy profile of each protein reveals an N-terminal hydrophobic domain and a C-terminal hydrophilic domain containing a putative nucleotide-binding site. The gene products probably constitute an ABC (ATP-binding cassette) family membrane transporter, the function of which is necessary for the formation of the cytochrome bd quinol oxidase. The CydDC system appears to be the first prokaryotic example of a heterodimeric ABC transport system in which each polypeptide contains both hydrophobic and ATP-binding domains.

ATP-Binding Cassette Transporters↗
PubMed1992

Spectroscopic studies on an oxygen-binding haemoglobin-like flavohaemoprotein from Escherichia coli.

The Escherichia coli haemoglobin-like flavohaemoprotein (Hmp) has been purified to near homogeneity using two chromatographic steps. The prosthetic groups are identified as FAD and protohaem IX. SDS/PAGE has indicated a molecular mass of 44 kDa for the monomeric protein consistent with the amino-acid sequence deduced from the hmp+ gene. The protein, as isolated, is in the Fe(III) state, exhibiting absorbance maxima at 403.5, 540 (shoulder) and 627 nm. The ferrous and carbonmonoxyferrous states resemble those of haemoglobin, showing maxima at 431.5 and 558 nm, and 421, 542 and 566 nm respectively. Upon aerobic addition of NAD(P)H, the ferric state is reduced to the oxygenated Fe(II) state, characterized by maxima at 413, 544 and 580 nm. This oxy form is not stable and slowly decays to the ferric state. Addition of dithionite and nitrite to the ferric protein results in the formation of a nitrosyl complex, whose e.p.r. characteristics indicate that the b-type haem is attached to the protein through a nitrogenous ligand, probably originating from a histidine residue.

Bacterial Proteins↗
PubMed1992

Metal ion-catalysed hydrolysis of ampicillin in microbiological growth media.

Anodic stripping voltammetry of bacterial growth medium containing copper(II) and ampicillin shows that Cu(II) is complexed by the antibiotic and that this complex decomposes to give Cu(II) complexes with ligands derived from ampicillin. At pH 7, substantial decomposition of ampicillin occurs over a few minutes, and even the very low levels of Cu(II) in Chelex-extracted medium are able effectively to catalyse the decomposition. The significance of this observation was shown during the screening of an Escherichia coli cosmid library for clones exhibiting increased resistance to Zn(II), Co(II) or Cd(II); the unexpected growth of the ampicillin-sensitive host E. coli strain on Luria-Bertani plates containing ampicillin and any of these metals was attributed to metal ion-catalysed decomposition of ampicillin. The instability of ampicillin (and other beta-lactam antibiotics) to metal ion-catalysed hydrolysis means that great care must be taken to ensure that such reactions do not occur in growth media. Furthermore, it is clear that double selection for resistance to ampicillin and metals such as Cu(II), Zn(II), Co(II) and Cd(II) is impossible.

Ampicillin↗
PubMed1992

The oxygenated flavohaemoglobin from Escherichia coli: evidence from photodissociation and rapid-scan studies for two kinetic and spectral forms.

The kinetics of dissociation and reassociation of the oxygenated species of Escherichia coli flavohaemoglobin (Hmp) were studied using stopped-flow rapid-scan and flash photolysis spectrophotometry at 25 degrees C. The oxygenated compound(s) form rapidly on mixing oxygen with the NADH-reduced flavohaemoglobin. On exhaustion of NADH, with residual oxygen, decay occurs in two phases to give a form in which haem b and flavin are oxidized. Spectral changes during this process suggest a direct release of O2- from the oxy form. Photodissociation of the oxygenated species generates the unliganded protein, which recombines with oxygen to give two spectrally and kinetically distinct forms. The reversibility of the oxygen reaction and the rapid reassociation kinetics after photodissociation confirm the haemoglobin-like features of this protein.

Bacterial Proteins↗
PubMed1992

Carbon monoxide-binding properties of the cytochrome bo quinol oxidase complex in Escherichia coli are changed by copper deficiency in continuous culture.

A strain of Escherichia coli having elevated levels of cytochrome bo and lacking the cytochrome bd quinol oxidase was grown in chemostat culture at low copper levels. Such cells had lowered levels of copper and of total cytochrome b. Cytochrome o concentration was unchanged when assayed by conventional CO difference spectroscopy, but apparently diminished by 80% in copper-deficient cells as determined by photodissociation of bound CO at 193 K. This is attributed to depletion of copper in the oxidase of copper-deficient cells, causing rapid recombination of photodissociated CO to haem O. CO recombination was also more sensitive to low intensities of actinic light in copper-depleted oxidase. The results illustrate a further similarity between the active sites of o- and aa3-type terminal oxidases.

Carbon Monoxide↗
PubMed1992

The cytochrome composition of the meat spoilage bacterium Brochothrix thermosphacta: identification of cytochrome a3-and d-type terminal oxidases under various conditions.

Brochothrix thermosphacta, grown in batch culture in a yeast-dextrose broth, at temperatures from 30 degrees C to 10 degrees C, contained diverse membrane-bound respiratory cytochromes. Under conditions of moderate aeration, cytochromes of the a-, b- and d-type were detected at all growth temperatures, but the proportions changed as a function of temperature, with the spectra of cells grown at 10 or 15 degrees C being dominated by a-type cytochrome(s). Cytochrome a3 was detected by its reactions with CO and cyanide in cells from all growth conditions. An additional cytochrome a, which was not cyanide-reactive, was also detected, suggesting the presence of an aa3 oxidase complex. Cytochrome d was cyanide- and CO-reactive, but not detectable in photodissociation spectra, presumably because of the very rapid recombination of CO at the sub-zero temperatures used. Decreasing the oxygen transfer rates to batch cultures resulted in enhanced expression of cytochrome d and changed the proportion of the aa3-type oxidase that could be attributed to ligand-binding cytochrome a3; at the lowest oxygen transfer rates, no cytochrome a was detected, suggesting the presence of a cytochrome ba3 terminal oxidase complex. Intact cells showed no evidence of a c-type cytochrome and no haem C was detected in membrane preparations. After growth at 10 degrees C, the cytochrome composition of B. campestris was essentially identical to that of B. thermosphacta. The multiplicity of putative terminal oxidases in B. thermosphacta is discussed.

Carbon Monoxide↗
PubMed1992

Change of speciation of Cu(II) in growth medium due to uptake of ammonia by Pseudomonas testosteroni during growth.

Growth of Pseudomonas testosteroni in a medium containing 1 mM Cu(II) causes a color change from blue to green. The spectrum of the supernatant solution from the blue culture shows an absorption at 660 nm, identical to that of 1 mM [Cu(II)] in the medium. The green supernatant solution shows a UV absorption, which tails into the visible and so is responsible for the green color, and a d-d absorption at 720 nm. The absorption at 660 nm for the blue supernatant solution is probably due to [Cu(NH3)3(H2O)3]2+. Growth of the organism causes loss of ammonia and a speciation change to [CU(NH3)2(H2O)4]2+, with a shift in absorption maximum from 660 to 720 nm. These conclusions are based upon the spectra of known aquaammine complexes of Cu(II) and calculations of the speciation of Cu(II) before and after growth. Change in metal speciation owing to nutrient uptake by an organism does not appear to have been recognized previously.

Ammonia↗
PubMed1992

Isolation and characterization of Escherichia coli mutants affected in aerobic respiration: the cloning and nucleotide sequence of ubiG. Identification of an S-adenosylmethionine-binding motif in protein, RNA, and small-molecule methyltransferases.

We report the isolation and characterization of a mutant of Escherichia coli unable to grow aerobically on non-fermentable substrates, except for very slow growth on glycerol. The mutant contains cytochrome oxidases o and d, and grows anaerobically with alternative electron acceptors. Oxygen consumption rates of cell-free extracts were low relative to activities in an isogenic control strain, but were restored in vitro by adding ubiquinone-1 to cell-free extracts. Transformation with a cloned 2.8 kb ClaI-EcoRV fragment of chromosomal DNA restored the ability of this mutant (AN2571) to grow on succinate and also restored cellular quinone levels in this strain. The plasmid also complemented a previously isolated ubiG mutant (AN151) for aerobic growth on succinate. The nucleotide sequence revealed a 0.7 kb portion of gyrA. Unidirectional nested deletions from this fragment and complementation analysis identified an open reading frame encoding a protein with a predicted molecular mass of 26.5 kDa. This gene (ubiG) encodes the enzyme 2-octaprenyl-3-methyl-5-hydroxy-6-methoxy-1,4-benzoquinone methyltransferase, which catalyses the terminal step in the biosynthesis of ubiquinone. The open reading frame is preceded by a putative Shine-Dalgarno sequence and followed by three palindromic unit sequences. Comparison of the inferred amino acid sequence of UbiG with the sequence of other S-adenosylmethionine (AdoMet)-dependent methyltransferases reveals a highly conserved AdoMet-binding region. The cloned 2.8 kb fragment also contains a sequence encoding the C-terminus of a protein with 42-44% identity to fungal acetyl-CoA synthetases.

Aerobiosis↗
PubMed1992

Effect of haemin limitation on the cytochrome complement and glucose metabolism of non-typable Haemophilus influenzae.

Haemophilus influenzae grown to exponential phase or stationary phase in medium with a low initial concentration of haemin (0.25 microgram/ml) was virtually devoid of cytochromes. Compared with bacteria grown in the presence of excess haemin (10 micrograms/ml), the haemin-limited organisms failed to respire formate and succinate and, generally, the respiratory rates with other substrates were reduced. However, growth rates were not affected by the haemin supply. Haemin-limited growth was associated with a reduced efficiency of glucose utilisation, in terms of glucose growth yields, and affected the net levels of excreted organic acids. Haemin limitation resulted in reduced acetate and increased succinate accumulation in the culture medium and the novel presence of D-lactate. These results indicate that, in contrast to the phenotype expressed in vitro during conventional cultivation of H. influenzae, the haemin-limited phenotype, which may be expressed in vivo, is characterised by a lack of cytochromes and a shift towards a more anaerobic type of metabolism.

Bronchiectasis↗
PubMed1991

Redox analysis of the cytochrome o-type quinol oxidase complex of Escherichia coli reveals three redox components.

Potentiometric analyses of the cytochrome o-type oxidase of Escherichia coli, using membranes from a strain containing amplified levels of the cytochrome bo complex, were conducted to resolve the redox centres of the oxidase. The cytochrome o-type oxidase of E. coli, a quinol oxidase, contains 2 mol of b-type haem per mol of complex and copper. Detailed analysis of potentiometric titrations, based on the absorbance of the Soret band, suggests that there are three contributions with midpoint potentials (Em,7) around +55 mV, +211 mV and +408 mV, all with maxima at 426-430 nm in the reduced state. In the alpha region of the spectra, a component with Em,6.85 = +58 mV has a maximal peak at 557 nm, and twin peaks at 556 and 564 nm nitrate with Em,6.85 = +227 mV. A feature corresponding to the highest potential Soret contribution was not observed. These data can be explained either by a model incorporating haem-haem interaction or by attributing the shorter-wavelength band (557 nm) to haem b and a split alpha-band (556, 564 nm) to the haem o (oxygen-binding haem b). Absolute spectra of oxidized membranes show continuous absorbance from 460 to 530 nm and suggest the presence of a high-spin haem component in the membranes. Monitoring absorbance at 635 minus 672 nm, contributions with midpoints (Em,7) around +52 mV, +234 mV and +371 mV are observed. This latter contribution is possibly the highest-potential component which titrates with Em greater than +400 mV in the Soret region and may represent copper-haem coupling in the cytochrome o complex.

Electrochemistry↗
PubMed1991

Characterization of a soluble catalase-peroxidase hemoprotein b-590, previously identified as 'cytochrome alpha 1' from Bradyrhizobium japonicum bacteroids.

The cytochrome "a1" or P-428, previously proposed to be a high affinity terminal oxidase in nitrogen-fixing bacteroids of Bradyrhizobium japonicum has been purified. The water-soluble native hemoprotein has an Mr of 136,000, lacks heme a and is a high-spin ferric protohemoprotein: It is slowly reduced with dithionite to give a species with an optical spectrum like that of hemoprotein b-590 (Escherichia coli; peak at 555 nm, shoulder at 590 nm), and which reacts slowly with CO. It has catalase and peroxidase activities, again resembling the E. coli b-590. Neither hemoprotein forms a stable oxy complex under conditions in which dithionite-reduced horseradish peroxidase reacts with oxygen to form such a complex. The hemoprotein, which we name hemoprotein b-590 (Bradyrhizobium japonicum), may play a role in removal of peroxides generated during respiration in the bacteroids of several Rhizobium and Bradyrhizobium species. The high-affinity terminal oxidase under nitrogen-fixing conditions remains to be identified.

Catalase↗
PubMed1991

Kinetics of the reactions of trioxodinitrate and nitrite ions with cytochrome d in Escherichia coli.

The rate of reaction of trioxodinitrate with reduced cytochrome oxidase d in membrane particles from Escherichia coli at pH 7 and 25 degrees C depends linearly upon [HN2O3-] over the concentration range studied (up to 0.05 mM) and is also first-order in cytochrome d. The known rate of decomposition of trioxodinitrate to give NO- and NO2- is about 4.5-times faster than the rate of reaction of reduced cytochrome d with trioxodinitrate, implying that cytochrome d reacts directly with NO-, with a trapping ratio of between 0.20 and 0.25, rather than with trioxodinitrate. The implications of the facile formation of the NO(-)-nitrosyl complex of cytochrome d for the mechanism of denitrification are discussed with particular reference to the mechanism of N-N bond formation. The reaction of reduced cytochrome d with nitrite (a decomposition product of trioxodinitrate) under these conditions is much slower than that with trioxodinitrate. The kinetics show a biphasic dependence of initial rate upon nitrite concentration. The rate data at low [NO2-] are consistent with saturation of a high affinity site for nitrite, having Vmax = 4.29.10(-9) M s-1 and Km = 0.034 mM. The existence of two binding sites for nitrite is consistent with the suggestion that the cytochrome bd complex contains two cytochrome d haems.

Cytochrome d Group↗
PubMed1991

Aluminium toxicity and binding to Escherichia coli.

The toxicity and binding of aluminium to Escherichia coli has been studied. Inhibition of growth by aluminium nitrate was markedly dependent on pH; growth in medium buffered to pH 5.4 was more sensitive to 0.9 mM or 2.25 mM aluminium than was growth at pH 6.6-6.8. In medium buffered with 2-(N-morpholino)ethanesulphonic acid (MES), aluminium toxicity was enhanced by omission of iron from the medium or by use of exponential phase starter cultures. Analysis of bound aluminium by atomic absorption spectroscopy showed that aluminium was bound intracellularly at one type of site with a Km of 0.4 mM and a capacity of 0.13 mol (g dry wt)-1. In contrast, binding of aluminium at the cell surface occurred at two or more sites with evidence of cooperativity. Addition of aluminium nitrate to a weakly buffered cell suspension caused acidification of the medium attributable to displacement of protons from cell surfaces by metal cations. It is concluded that aluminium toxicity is related to pH-dependent speciation [with Al(H2O)6(3+) probably being the active species] and chelation of aluminium in the medium. Aluminium transport to intracellular binding sites may involve Fe(III) transport pathways.

Aluminum↗
PubMed1991

Isolation and nucleotide sequence of the hmp gene that encodes a haemoglobin-like protein in Escherichia coli K-12.

In the course of an attempt to identify genes that encode Escherichia coli dihydropteridine reductase (DHPR) activities, a chromosomal DNA fragment that directs synthesis of two soluble polypeptides of Mr 44000 and 46000 was isolated. These proteins were partially purified and were identified by determination of their N-terminal amino acid sequences. The larger was serine hydroxymethyltransferase, encoded by the glyA gene, while the smaller was the previously described product of an unnamed gene closely linked to glyA, and transcribed in the opposite direction. Soluble extracts of E. coli cells that overproduced the 44 kDa protein had elevated DHPR activity, and were yellow in colour. Their visible absorption spectra were indicative of a CO-binding b-type haemoprotein that is high-spin in the reduced state. The sequence of the N-terminal 139 residues of the protein, deduced from the complete nucleotide sequence of the gene, had extensive homology to almost all of Vitreoscilla haemoglobin. We conclude that E. coli produces a soluble haemoglobin-like protein, the product of the hmp gene (for haemoprotein). Although the protein has DHPR activity, it is distinct from the previously purified E. coli DHPR.

Amino Acid Sequence↗