Bacterial Respiratory Chain Research Articles

The Rieske protein from Paracoccus denitrificans is inserted into the cytoplasmic membrane by the twin‐arginine translocase

The Rieske [2Fe-2S] protein (ISP) is an essential subunit of cytochrome bc(1) complexes in mitochondrial and bacterial respiratory chains. Based on the presence of two consecutive arginines, it was argued that the ISP of Paracoccus denitrificans, a Gram-negative soil bacterium, is inserted into the cytoplasmic membrane via the twin-arginine translocation (Tat) pathway. Here, we provide experimental evidence that membrane integration of the bacterial ISP indeed relies on the Tat translocon. We show that targeting of the ISP depends on the twin-arginine motif. A strict requirement is established particularly for the second arginine residue (R16); conservative replacement of the first arginine (R15K) still permits substantial ISP transport. Comparative sequence analysis reveals characteristics common to Tat signal peptides in several bacterial ISPs; however, there are distinctive features relating to the fact that the presumed ISP Tat signal simultaneously serves as a membrane anchor. These differences include an elevated hydrophobicity of the h-region compared with generic Tat signals and the absence of an otherwise well-conserved '+5'-consensus motif lysine residue. Substitution of the +5 lysine (Y20K) compromises ISP export and/or cytochrome bc(1) stability to some extent and points to a specific role for this deviation from the canonical Tat motif. EPR spectroscopy confirms cytosolic insertion of the [2Fe-2S] cofactor. Mutation of an essential cofactor binding residue (C152S) decreases the ISP membrane levels, possibly indicating that cofactor insertion is a prerequisite for efficient translocation along the Tat pathway.

Regulation of the Ubiquinone (Coenzyme Q) Biosynthetic Genes ubiCA in Escherichia coli

Ubiquinone (Coenzyme Q) is an essential component of bacterial respiratory chains. The first committed step in the biosynthetic pathway is the formation of 4-hydroxybenzoate from chorismate by the enzyme chorismate pyruvate-lyase encoded by the ubiC gene. The 4-hydroxybenzoate is prenylated by 4-hydroxybenzoate octaprenyltransferase encoded by the ubiA gene. The two genes are linked at 91.5 min in the Escherichia coli chromosome. To study the regulation, operon fusions were constructed between these two genes and the lacZ gene. The fusions were introduced into the chromosome as a single copy at the lambda attachment site. Expression of beta-galactosidase was determined in strains carrying the operon fusions ubiC'-lacZ(+) ubiCA'-lacZ(+), and ubiA'-lacZ(+). In glycerol media, the highest level of expression was observed with the operon fusion ubiC'-lacZ(+). Compared with the ubiC'-lacZ(+), the ubiCA'-lacZ(+) operon fusion showed 26% of the activity while the ubiA'-lacZ(+) operon fusion had an activity of 1%. Thus, the ubiC gene is regulated by the upstream promoter while the ubiA gene lacks its own promoter. The effect of fermentable and oxidizable carbon sources on the expression of ubiC'-lacZ(+) was determined. The expression was low in the case of a fermentable carbon source, glucose, while in the presence of oxidizable carbon sources the expression increased 2- to 3-fold. When the expression of ubiC'-lacZ(+) and ubiCA'-lacZ(+) operon fusions were compared under a wide variety of conditions, the levels of beta-galactosidase varied coordinately, suggesting that the ubiCA genes are organized into an operon. The variations in transcription of the operon under different nutritional conditions and in the regulatory mutants, arcA, fnr, and narXL are presented.

Effect of 13-epi-Sclareol on the Bacterial Respiratory Chain

13-epi-sclareol is a labdane-type diterpene isolated from the resinous exudates of the medicinal plant species Pseudognaphalium cheiranthifolium (Lam.) Hilliard et Burtt. and P. heterotrichium (Phil.) A. Anderb. This compound has antibacterial activity only against Gram-positive bacteria, showing a bactericidal and lytic action. The interaction of 13- epi-sclareol with the bacterial respiratory chain was analyzed. The compound inhibited oxygen consumption of intact Gram-positive cells, but not with Gram-negative bacteria. The compound inhibited NADH oxidase and cytochrome c reductase activities, while coenzyme Q reductase and the cytochrome c oxidase activities were not affected. These results suggest that the target site of 13-epi-sclareol is located between coenzyme Q and cytochrome c. Using cytoplasmic membrane fractions, the results of the analysis of the enzyme activities associated with the respiratory chain complexes were the same for both Gram-positive and Gram-negative bacteria, indicating that the compound has no access to the cytoplasmic membrane of intact Gram-negative bacteria. Thus, the Gram-negative envelope may act as a physical barrier that prevents the access of this compound to the site of action.

A New Type of NADH Dehydrogenase Specific for Nitrate Respiration in the Extreme Thermophile Thermus thermophilus

A four-gene operon (nrcDEFN) was identified within a conjugative element that allows Thermus thermophilus to use nitrate as an electron acceptor. Three of them encode homologues to components of bacterial respiratory chains: NrcD to ferredoxins; NrcF to iron-sulfur-containing subunits of succinate-quinone oxidoreductase (SQR); and NrcN to type-II NADH dehydrogenases (NDHs). The fourth gene, nrcE, encodes a membrane protein with no homologues in the protein data bank. Nitrate reduction with NADH was catalyzed by membrane fractions of the wild type strain, but was severely impaired in nrc::kat insertion mutants. A fusion to a thermophilic reporter gene was used for the first time in Thermus spp. to show that expression of nrc required the presence of nitrate and anoxic conditions. Therefore, a role for the nrc products as a new type of membrane NDH specific for nitrate respiration was deduced. Consistent with this, nrc::kat mutants grew more slowly than the wild type strain under anaerobic conditions, but not in the presence of oxygen. The oligomeric structure of this Nrc-NDH was deduced from the analysis of insertion mutants and a two-hybrid bacterial system. Attachment to the membrane of NrcD, NrcF, and NrcN was dependent on NrcE, whose cytoplasmic C terminus interacts with the three proteins. Interactions were also detected between NrcN and NrcF. Inactivation of nrcF produced solubilization of NrcN, but not of NrcD. These data lead us to conclude that the Nrc proteins form a distinct third type of bacterial respiratory NDH.

Chlorobenzene biodegradation under consecutive aerobic–anaerobic conditions

The biodegradation of monochlorobenzene, the main contaminant in a quaternary aquifer at Bitterfeld, Central Germany, was studied in microcosm experiments employing either original groundwater or defined mineral media together with the indigenous microbial community from the polluted site. The impact of consecutive aerobic–anaerobic–aerobic incubations on monochlorobenzene biodegradation, microbial diversity, and pH development was examined. The related changes in microbial community composition were analyzed by 16S rRNA gene-based single-strand conformation polymorphism (SSCP) fingerprints and sequencing of dominant bands and by quantitative analysis of bacterial respiratory chain quinones as biomarkers. Under aerobic conditions, the indigenous microbial community of the groundwater degraded monochlorobenzene mainly via the modified ortho-pathway. Respiratory chain quinones and SSCP analysis suggested dominance of the genera Acidovorax and Pseudomonas. A shift to anoxic conditions resulted in monochlorobenzene biotransformation but no dechlorination. The ability to degrade monochlorobenzene aerobically remained preserved throughout a fortnightly anoxic period at sufficiently high buffer capacity. Acidification, caused by monochlorobenzene biodegradation, was alkalinity-controlled. At low initial alkalinity a substantial decrease in pH, monochlorobenzene degradation, and total counts of live cells, accompanied by a change of the microbial community composition, was observed.

The cytochrome bc1 complex: function in the context of structure.

The bc1 complexes are intrinsic membrane proteins that catalyze the oxidation of ubihydroquinone and the reduction of cytochrome c in mitochondrial respiratory chains and bacterial photosynthetic and respiratory chains. The bc1 complex operates through a Q-cycle mechanism that couples electron transfer to generation of the proton gradient that drives ATP synthesis. Genetic defects leading to mutations in proteins of the respiratory chain, including the subunits of the bc1 complex, result in mitochondrial myopathies, many of which are a direct result of dysfunction at catalytic sites. Some myopathies, especially those in the cytochrome b subunit, exacerbate free-radical damage by enhancing superoxide production at the ubihydroquinone oxidation site. This bypass reaction appears to be an unavoidable feature of the reaction mechanism. Cellular aging is largely attributable to damage to DNA and proteins from the reactive oxygen species arising from superoxide and is a major contributing factor in many diseases of old age. An understanding of the mechanism of the bc1 complex is therefore central to our understanding of the aging process. In addition, a wide range of inhibitors that mimic the quinone substrates are finding important applications in clinical therapy and agronomy. Recent structural studies have shown how many of these inhibitors bind, and have provided important clues to the mechanism of action and the basis of resistance through mutation. This paper reviews recent advances in our understanding of the mechanism of the bc1 complex and their relation to these physiologically important issues in the context of the structural information available.

Assembly of Respiratory Complexes I, III, and IV into NADH Oxidase Supercomplex Stabilizes Complex I in Paracoccus denitrificans

Stable supercomplexes of bacterial respiratory chain complexes III (ubiquinol:cytochrome c oxidoreductase) and IV (cytochrome c oxidase) have been isolated as early as 1985 (Berry, E. A., and Trumpower, B. L. (1985) J. Biol. Chem. 260, 2458-2467). However, these assemblies did not comprise complex I (NADH:ubiquinone oxidoreductase). Using the mild detergent digitonin for solubilization of Paracoccus denitrificans membranes we could isolate NADH oxidase, assembled from complexes I, III, and IV in a 1:4:4 stoichiometry. This is the first chromatographic isolation of a complete "respirasome." Inactivation of the gene for tightly bound cytochrome c552 did not prevent formation of this supercomplex, indicating that this electron carrier protein is not essential for structurally linking complexes III and IV. Complex I activity was also found in the membranes of mutant strains lacking complexes III or IV. However, no assembled complex I but only dissociated subunits were observed following the same protocols used for electrophoretic separation or chromatographic isolation of the supercomplex from the wild-type strain. This indicates that the P. denitrificans complex I is stabilized by assembly into the NADH oxidase supercomplex. In addition to substrate channeling, structural stabilization of a membrane protein complex thus appears as one of the major functions of respiratory chain supercomplexes.

The quaternary structure of the Saccharomyces cerevisiae succinate dehydrogenase. Homology modeling, cofactor docking, and molecular dynamics simulation studies.

Succinate dehydrogenases and fumarate reductases are complex mitochondrial or bacterial respiratory chain proteins with remarkably similar structures and functions. Succinate dehydrogenase oxidizes succinate and reduces ubiquinone using a flavin adenine dinucleotide cofactor and iron-sulfur clusters to transport electrons. A model of the quaternary structure of the tetrameric Saccharomyces cerevisiae succinate dehydrogenase was constructed based on the crystal structures of the Escherichia coli succinate dehydrogenase, the E. coli fumarate reductase, and the Wolinella succinogenes fumarate reductase. One FAD and three iron-sulfur clusters were docked into the Sdh1p and Sdh2p catalytic dimer. One b-type heme and two ubiquinone or inhibitor analog molecules were docked into the Sdh3p and Sdh4p membrane dimer. The model is consistent with numerous experimental observations. The calculated free energies of inhibitor binding are in excellent agreement with the experimentally determined inhibitory constants. Functionally important residues identified by mutagenesis of the SDH3 and SDH4 genes are located near the two proposed quinone-binding sites, which are separated by the heme. The proximal quinone-binding site, located nearest the catalytic dimer, has a considerably more polar environment than the distal site. Alternative low energy conformations of the membrane subunits were explored in a molecular dynamics simulation of the dimer embedded in a phospholipid bilayer. The simulation offers insight into why Sdh4p Cys-78 may be serving as the second axial ligand for the heme instead of a histidine residue. We discuss the possible roles of heme and of the two quinone-binding sites in electron transport.

MCLA-dependent chemiluminescence suggests that singlet oxygen plays a pivotal role in myeloperoxidase-catalysed bactericidal action in neutrophil phagosomes.

Bacteria ingested by a neutrophil are located in phagosomes in which H(2)O(2) is produced through the NADPH oxidase-dependent respiratory burst. Myeloperoxidase (MPO) plays important role in the bactericidal action of phagosomes. MPO catalyses the reaction of H(2)O(2) and Cl(-) to produce HClO. The chemical mechanism behind the bactericidal action of the MPO-H(2)O(2)-Cl(-) system is unclear. Bactericidal action may result from (a) the direct reactions of HOCl with biological components (through amine chlorination) or (b) (1)O(2), formed non-enzymatically from HOCl and H(2)O(2), that mainly works to kill microorganisms through bacterial respiratory chain injury. To answer this question, we developed a Cypridina luciferin analogue (MCLA)-dependent chemiluminescence method to determine the rate of formation of (1)O(2) from a (1)O(2) source at pH 4.5-9.0. Using the MCLA-dependent chemiluminescence method, we found that the rate of formation of (1)O(2) from the MPO-H(2)O(2)-Cl(-) system peaked at pH 7.0. Segal et al. (28) reported that almost all Staphylococcus aureus is killed 2 min after phagocytosis by neutrophils where the phagosomal pH is 7.4-7.75. However, amine chlorination by HOCl did not proceed at pH > 7.0. Moreover, the bactericidal activities of the MPO-H(2)O(2)-Cl(-) system with Escherichia coli at pH 4.5 and 8.0 were paralleled by the rate of formation of (1)O(2). Combining these observations and the results reported by Segal et al., we concluded that (1)O(2) is a major chemical species in the killing of bacteria in neutrophil phagosomes.

Respiratory chain supercomplexes.

Respiratory chain supercomplexes have been isolated from mammalian and yeast mitochondria, and bacterial membranes. Functional roles of respiratory chain supercomplexes are catalytic enhancement, substrate channelling, and stabilization of complex I by complex III in mammalian cells. Bacterial supercomplexes are characterized by their relatively high detergent-stability compared to yeast or mammalian supercomplexes that are stable to sonication. The mobility of substrate cytochrome c increases in the order bacterial, yeast, and mammalian respiratory chain. In bacterial supercomplexes, the electron transfer between complexes III and IV involves movement of the mobile head of a tightly bound cytochrome c, whereas the yeast S. cerevisiae seems to use substrate channelling of a mobile cytochrome c, and mammalian respiratory chains have been described to use a cytochrome c pool. Dimeric ATP synthase seems to be specific for mitochondrial OXPHOS systems. Monomeric complex V was found in Acetobacterium woodii and Paracoccus denitrificans.

Inhibition of Escherichia coli respiratory enzymes by the lactoperoxidase-hydrogen peroxide-thiocyanate antimicrobial system.

The lactoperoxidase-hydrogen peroxide-thiocyanate antimicrobial system (LPAS) is known to inhibit bacterial respiration. In the present study, several respiratory enzymes of Escherichia coli were compared in terms of their susceptibility to the LPAS. Exposure of E. coli to the LPAS, upon which 99.6% of the bacteria were killed, resulted in the following percentage of inactivation of substrate-specific membrane oxidases: succinate (94.2%) > NADH (84.6%) > glycerol-3-phosphate (67.8%) > DL-lactate (64.1%). With the same treatment, substrate-specific membrane dehydrogenases were inactivated as follows: succinate (99.1%) > DL-lactate (53.8%) > glycerol-3-phosphate (45.0%) > NADH (36.8%). Terminal oxidase, however, measured using a ubiquinone analogue (2,3-dimethoxy-5-methyl-6-decyl-1,4-benzoquinone) after reduction, was only 21.4% inactivated by the LPAS. These data suggest that dehydrogenases are the primary targets of the LPAS in the respiratory chain of E. coli. This study has determined for the first time the primary targets of LPAS in the bacterial respiratory chain.

Impact of either elevated or decreased levels of cytochrome bd expression on Shigella flexneri virulence.

Shigella spp. are the major cause of bacillary dysentery worldwide. The pathogenic process involves bacterial invasion and lysis of the phagocytic vacuole, followed by replication and movement within the cell cytoplasm and, ultimately, spread directly into adjacent cells. This study demonstrates that S. flexneri cytochrome bd expression is necessary for normal intracellular survival and virulence. Cytochrome bd is one of two terminal oxidases in the bacterial respiratory chain that reduce molecular oxygen to water, utilizing intermediates shuttled through the electron transport chain. S. flexneri mutants that contain a disruption in the cydC locus, which leads to defective cytochrome bd expression, or in the riboflavin (ribE) or ubiquinol-8 (ubiH) biosynthetic pathway, which leads to elevated cytochrome bd expression, were evaluated in intracellular survival and virulence assays. The cydC mutant formed significantly smaller plaques, had significantly decreased intracellular survival, and had a 100-fold increase in lethal dose for mice compared with the wild type. The ribE and ubiH mutants each formed significantly larger plaques and had a 10-fold decrease in lethal dose for mice compared with the wild type. The data indicate that expression of cytochrome bd is required for S. flexneri intracellular survival and virulence.

Inactivation of bacterial respiratory chain enzymes by singlet oxygen

To distinguish the bactericidal action of singlet oxygen ( 1O 2) from hypohalous acids, wild-type and lycopene transformant E. coli strains were exposed to each of the oxidants and then bacterial viability was investigated. 1O 2 was generated by chemical and enzymatic systems at pH 4.5. Exposure of wild-type E. coli to 1O 2 caused a significant loss of E. coli viability due to inactivation of membrane respiratory chain enzymes by 1O 2. This action of 1O 2 could be attenuated by lycopene in the bacterial cell membrane. In the lycopene transformant strain of E. coli, inactivation of NADH oxidase and succinate oxidase by hypohalous acids were significantly suppressed, but E. coli viability was unaffected. Based on these findings, we suggest that phagocytic leukocytes produce 1O 2 as a major bactericidal oxidant in the phagosome.

Mode of antibacterial action of retrochalcones from Glycyrrhiza inflata

The antibacterial mechanism of retrochalcones isolated from the roots of Glycyrrhiza inflata was studied. Licochalcone A and C inhibited electron transport in the bacterial respiratory chain. Licochalcone A-D and echinatin, retrochalcones isolated from the roots of Glycyrrhiza inflata, showed antimicrobial activity. Among them, licochalcone A and C had potent activity against some Grampositive bacteria. These retrochalcones inhibited oxygen consumption in susceptible bacterial cells. The oxidation of NADH in bacterial membrane preparations was also inhibited by them. NADH-cytochrome c reductase was inhibited by licochalcones, while cytochrome c oxidase was not. NADH-CoQ reductase and NADH-FMN oxidoreductase were not inhibited. The site of respiratory inhibition of licochalcones was thought to be between CoQ and cytochrome c in the bacterial respiratory electron transport chain.

On the use of diethyldithiocarbamate for detection of electron-transferring copper proteins in bacterial respiratory chains

In a previous study on the anaerobic electron transport in the wild-type and a mutant strain of Paracoccus denitrificans, the differences in sensitivity towards the copper-chelating agent diethyldithiocarbamate have been interpreted to arise from a substitution of a soluble copper protein for the absent cytochrome c 550. Here it is shown that two factors complicate this interpretation: (i) diethyldithiocarbamate can also inhibit through interaction with (a) site(s) located in the cytoplasmic membrane and (ii) it has the potential of being a good electron donor for c-type cytochromes. The participation of a copper protein in the denitrification pathway thus needs to be verified by independent means.

On the use of diethyldithiocarbamate for detection of electron-transferring copper proteins in bacterial respiratory chains

In a previous study on the anaerobic electron transport in the wild-type and a mutant strain of Paracoccus denitrificans, the differences in sensitivity towards the copper-chelating agent diethyldithiocarbamate have been interpreted to arise from a substitution of a soluble copper protein for the absent cytochrome c550. Here it is shown that two factors complicate this interpretation: (i) diethyldithiocarbamate can also inhibit through interaction with (a) site(s) located in the cytoplasmic membrane and (ii) it has the potential of being a good electron donor for c-type cytochromes. The participation of a copper protein in the denitrification pathway thus needs to be verified by independent means.

Bacterial Respiratory Chains

Bacterial Respiratory Chains

On the Relationship between Bacterial Cell Integrity and Respiratory Chain Activity: A Fluorescence Anisotropy Study

The fluorescence anisotropy (r) of intracellular NADH was used as a parameter responsive to changes in the intracellular structure and cell integrity of bacteria. When Micrococcus luteus cells were subjected to gentle lysis with lysozyme in the presence of saturating concentrations of respiratory substrates, the respiratory rate was stimulated transiently followed by the decrease in respiratory chain activity correlated with r value reduction. It is concluded that immediately following lysozyme treatment, the respiratory chain in situ then exists in a state characterized by a maximal activity, until such time as cell integrity is disturbed. The preservation of a high respiratory activity in lysed bacterial cells pretreated with glutaraldehyde confirms this.

Molecular recognition: design of a biosensor with genetically engineered azurin as redox mediator

The development of a second generation biosensor that uses azurin as mediator for electron transport at the electrode surface is reported. Azurin is a small (14.6 kDa) bacterial protein that is relatively stable and that can be expressed in high yield in a heterologous system ( E. coli) making it an ideal candidate for protein engineering studies and biosensor development. This protein has a role as a natural electron transfer carrier in the bacterial anaerobic respiratory chain and is able to transfer electrons from cytochrome c 551 to nitrate reductase. The active centre of azurin is a type-1 copper centre. The copper ligand His 117 protrudes through the protein surface, and it has been mutated by site-directed mutagenesis into a glycine (His 117Gly). The absence of the side-chain of the glycine residue creates an aperture on the protein surface that makes the copper centre accessible to external ligands. In this way the azurin His 117Gly mutant can accept external ligands, such as 4-methylimidazole, that can be bound to the electrode surface. Attempts to establish fully reversible redox chemistry with the mutated azurin are underway. In principle, this allows the immobilization of azurin on an electrode surface for the construction of a biosensor. In this way azurin can be used as mediator in transferring electrons between the enzymatic system present in solution and the electrode. The combination of protein engineering with electrode surface modification allows further advances in biosensor technology.

Mediated electrocatalysis at a biocatalyst electrode based on a bacterium, Gluconobacter industrius

Mediated amperometr ic enzyme electrodes use oxidoreductases as catalysts to oxidize or reduce the substrates bioelectrocatalytically in the presence of redox molecules serving as mediators [1-3]. We are interested in the use of microorganisms in place of enzymes. It was reported in early 1966 [4] that Fe(CN)63acted as an electron acceptor for the metabolic oxidation of o-glucose by Escherichia coli (E. coli). This means that in principle, Fe(CN) 3can be used as a mediator to couple the oxidation reaction of o-glucose by E. coli to the electrode reaction of Fe(CN)63-. At tempts to use mediators to shuttle electrons from a bacterial respiratory chain to an electrode were made in biofuel cell configurations [5,6]. In a few whole cell-based biosensors, mediators have been employed to divert electrons from the micro-organisms to the electrode for monitoring photosynthetic activity [7] or eubacterial respiration [8]. However, the details of the electrocatalytic reaction have not been investigated, and the redox compounds taking part in the catalytic reaction are not clear. There is no report on studies of whole cell-based electrodes from a bioelectrocatalysis point of view. A number of micro-organisms have oxidoreductases in their cytoplasmic membranes. The oxidoreductase reaction may be linked to an electrode reaction by the use of an appropriate mediator as illustrated schematically in Fig. 1. We have tested several kinds of bacteria as catalysts and observed small currents resulting