Structure and function of proton-translocating adenosine triphosphatase (F0F1): biochemical and molecular biological approaches

The lysine 2-hydroxyisobutyrylome of Helicobacter pylori: Indicating potential roles of lysine 2-hydroxyisobutyrylation in the bacterial metabolism

Helicobacter pylori (H. pylori) is a pathogen which colonizes the stomach, causing ulcers, chronic gastritis and other related diseases. Protein post-translational modifications (PTMs) in bacteria mainly include glycosylation, ubiquitination, nitrosylation, methylation, phosphorylation and acetylation, all of which have divergent functions in the physiology and pathology of the bacterium. Lysine 2-hydroxyisobutyrylation (Khib) is a newly discovered type of PTM in recent years in some kinds of organisms, and this PTM is involved in the regulation of a variety of metabolic process, such as bacterial glucose metabolism, lipid metabolism and protein synthesis. This study performed the first qualitative lysine 2-hydroxyisobutyrylome in H. pylori, and a total of 4419 Khib sites in 812 proteins were identified. The results show that Khib sites are mainly located in the key functional regions or active domains of proteins involved in nickel-trafficking, energy production, virulence factors, anti-oxidation, metal resistance, and ribosome biosynthesis in H. pylori. The study presented here provides new hints in the metabolism and pathology of H. pylori and the proteins with Khib modification may be potentially promising targets for the further development of antibiotics, especially considering the high occurrence of treatment failure of H. pylori failure due to development of antibiotics-resistance.

Assessing the Safety and Probiotic Characteristics of Lacticaseibacillus rhamnosus X253 via Complete Genome and Phenotype Analysis

Lacticaseibacillus rhamnosus is a generalist that can adapt to different ecological niches, serving as a valuable source of probiotics. The genome of L. rhamnosus X253 contains one chromosome and no plasmids, with a size of 2.99 Mb. Both single-copy orthologous gene-based phylogenetic analysis and average nucleotide identity indicated that dairy-derived L. rhamnosus X253 was most closely related to the human-intestine-derived strain L. rhamnosus LOCK908, rather than other dairy strains. The adaptation of L. rhamnosus X253 and the human-intestine-derived strain L. rhamnosus GG to different ecological niches was explained by structural variation analysis and COG annotation. Hemolytic assays, API ZYM assays, and antimicrobial susceptibility tests were performed to validate risk-related sequences such as virulence factors, toxin-encoding genes, and antibiotic-resistance genes in the genomes of L. rhamnosus X253 and GG. The results showed that L. rhamnosus GG was able to use L-fucose, had a higher tolerance to bile salt, and adhered better to CaCo-2 cells. In contrast, L. rhamnosus X253 was capable of utilizing D-lactose, withstood larger quantities of hydrogen peroxide, and possessed excellent antioxidant properties. This study confirmed the safety and probiotic properties of L. rhamnosus X253 via complete genome and phenotype analysis, suggesting its potential as a probiotic.

Antibacterial and antibiotic-potentiation activity of the constituents from aerial part of Donella welwitshii (Sapotaceae) against multidrug resistant phenotypes

Background

The rise of multidrug-resistant (MDR) bacteria is a real public health problem worldwide and is responsible for the increase in hospital infections. Donella welwitschii is a liana or shrub belonging to the family Sapotaceae and traditionally used to cure coughs.

Objective

This study was conducted with the objective to validate the medicinal properties of this plant, the aerial part was studied for its phytochemical composition using column and PTLC chromatography and exploring its antibacterial and antibiotic-modifying activity as well as those of its phytochemicals.

Methods

The structures of the compounds were elucidated from their physical and spectroscopic data in conjunction with literature. The antibacterial activity of the isolated metabolites was performed toward a panel of MDR Gram negative and Gram-positive bacteria. The broth micro-dilution method was used to determine antibacterial activities, efflux pump effect using the efflux pump inhibitor (EPI) (phenylalanine-arginine-ß-naphthylamide (PAβN)), as well as the modulating activity of antibiotics. Monitoring the acidification of the bacterial growth medium was used to study the effects of the samples on the bacterial proton-ATPase pumps and cellular ATP production.

Results

Eleven compounds were isolated including pentacyclic triterpenes, C-glucosyl benzophenones. With a MIC value < 10 μg/mL, diospyric acid (7) significantly inhibited the growth of Escherichia coli AG102, Enterobacter aerogenes ATCC13048, Klebsiella pneumoniae KP55, Providencia stuartii NEA16 and Staphylococcus aureus MRSA3. 28-hydroxy-β-amyrin (8) significantly impaired the growth of Enterobacter aerogenes EA27, Klebsiella pneumoniae ATCC11296 and Staphylococcus aureus MRSA6; and oleanolic acid (9) strongly impaired the growth of Escherichia coli AG 102, Enterobacter aerogenes EA27 and Providencia stuartii PS2636. Diospyric acid (7) and 28-hydroxy-β-amyrin (8) induced perturbation of H⁺-ATPase pump and inhibition of the cellular ATP production. Moreover, at MIC/2 and MIC/4, compounds 7, 8, and 9 strongly improved the antibacterial activity of norfloxacin, ciprofloxacin and doxycycline with antibiotic-modulating factors ranging between 2 and 64.

Conclusion

The overall results of the current work demonstrate that diospyric acid (7), 28-hydroxy-β-amyrin (8) and oleanolic acid (9) are the major bioactive constituents of Donella welwitschia towards Gram-negative bacteria expressing MDR phenotypes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12906-022-03673-3.

Antibacterial and antibiotic-potentiation activities of the hydro-ethanolic extract and protoberberine alkaloids from the stem bark of Enantia chlorantha against multidrug-resistant bacteria expressing active efflux pumps

ETHNOPHARMACOLOGICAL RELEVANCE

Enantia chlorantha is traditionally used to treat various ailments including rickettsia fever, cough and wounds, typhoid fever, infective hepatitis, jaundice, and urinary tract infections.

AIM OF THE STUDY

To isolate the antibacterial constituents of the hydro-ethanolic extract of the stem bark of E. chlorantha (ECB) and to evaluate the antibacterial and antibiotic-modifying activities of ECB and its constituents against the multidrug-resistant (MDR) phenotypes.

MATERIALS AND METHODS

Chromatographic methods were used to isolate the constituents of ECB and Spectroscopic methods were used to elucidate the chemical structures of the isolated compounds. The antibacterial activity of samples was determined by the broth microdilution method while spectrophotometric methods were used to evaluate the effects of ECB and its most active constituent on bacterial growth. Their effects on bacterial proton-ATPase pumps was assessed through the acidification of the bacterial culture medium.

RESULTS

Six protoberberine alkaloids were isolated and identified as columbamine (1), pseudocolumbamine (2), jathrorrhizine (3), palmitine (4), 4,13-dihydroxy-3,9,10-trimethoxyprotoberberine (5), and 13-hydroxy-2,3,9,10-tetramethoxyprotoberberine (6). The crude extract (ECB) inhibited the growth of all the tested MDR bacteria, with the minimal inhibitory concentration (MIC) values below 100 μg/mL obtained against Escherichia coli ATCC 10536, AG 102, Enterobacter aerogenes EA 27, Klebsiella pneumoniae ATCC 11296 and KP 55, Providencia stuartii NEA 16, and Staphylococcus aureus MRSA3 and MRSA6. Compound 1 had the best antibacterial effects with MIC values ranging from 16 to 64 μg/mL. The efflux pump inhibitor (EPI), phenylalanine-arginine-β naphthylamide (PAβN) significantly improved the activity of compounds 1-6. Compounds 1-3 significantly potentiated the antibacterial activity of antibiotics such norfloxacin (NOR), ciprofloxacin (CIP), and doxycycline (DOX) against the tested MDR bacteria.

CONCLUSION

The crude extract (ECB) and its isolated compounds 1-6 are potential antibacterial products from Enantia chlorantha. They could be explored more to develop the antibacterial agents that could be used alone or in combination with antibiotics to overcome MDR phenotypes.

Bioenergetic consequences of FoF1-ATP synthase/ATPase deficiency in two life cycle stages of Trypanosoma brucei

Mitochondrial ATP synthase is a reversible nanomotor synthesizing or hydrolyzing ATP depending on the potential across the membrane in which it is embedded. In the unicellular parasite Trypanosoma brucei, the direction of the complex depends on the life cycle stage of this digenetic parasite: in the midgut of the tsetse fly vector (procyclic form), the F_oF₁–ATP synthase generates ATP by oxidative phosphorylation, whereas in the mammalian bloodstream form, this complex hydrolyzes ATP and maintains mitochondrial membrane potential (ΔΨm). The trypanosome F_oF₁–ATP synthase contains numerous lineage-specific subunits whose roles remain unknown. Here, we seek to elucidate the function of the lineage-specific protein Tb1, the largest membrane-bound subunit. In procyclic form cells, Tb1 silencing resulted in a decrease of F_oF₁–ATP synthase monomers and dimers, rerouting of mitochondrial electron transfer to the alternative oxidase, reduced growth rate and cellular ATP levels, and elevated ΔΨm and total cellular reactive oxygen species levels. In bloodstream form parasites, RNAi silencing of Tb1 by ∼90% resulted in decreased F_oF₁–ATPase monomers and dimers, but it had no apparent effect on growth. The same findings were obtained by silencing of the oligomycin sensitivity-conferring protein, a conserved subunit in T. brucei F_oF₁–ATP synthase. However, as expected, nearly complete Tb1 or oligomycin sensitivity-conferring protein suppression was lethal because of the inability to sustain ΔΨm. The diminishment of F_oF₁–ATPase complexes was further accompanied by a decreased ADP/ATP ratio and reduced oxygen consumption via the alternative oxidase. Our data illuminate the often diametrically opposed bioenergetic consequences of F_oF₁–ATP synthase loss in insect versus mammalian forms of the parasite.

Mechanism of the αβ conformational change in F1-ATPase after ATP hydrolysis: free-energy simulations

One of the motive forces for F1-ATPase rotation is the conformational change of the catalytically active β subunit due to closing and opening motions caused by ATP binding and hydrolysis, respectively. The closing motion is accomplished in two steps: the hydrogen-bond network around ATP changes and then the entire structure changes via B-helix sliding, as shown in our previous study. Here, we investigated the opening motion induced by ATP hydrolysis using all-atom free-energy simulations, combining the nudged elastic band method and umbrella sampling molecular-dynamics simulations. Because hydrolysis requires residues in the α subunit, the simulations were performed with the αβ dimer. The results indicate that the large-scale opening motion is also achieved by the B-helix sliding (in the reverse direction). However, the sliding mechanism is different from that of ATP binding because sliding is triggered by separation of the hydrolysis products ADP and Pi. We also addressed several important issues: 1), the timing of the product Pi release; 2), the unresolved half-closed β structure; and 3), the ADP release mechanism. These issues are fundamental for motor function; thus, the rotational mechanism of the entire F1-ATPase is also elucidated through this αβ study. During the conformational change, conserved residues among the ATPase proteins play important roles, suggesting that the obtained mechanism may be shared with other ATPase proteins. When combined with our previous studies, these results provide a comprehensive view of the β-subunit conformational change that drives the ATPase.

General and condition-specific essential functions of Pseudomonas aeruginosa

The essential functions of a bacterial pathogen reflect the most basic processes required for its viability and growth, and represent potential therapeutic targets. Most screens for essential genes have assayed a single condition--growth in a rich undefined medium--and thus have not distinguished genes that are generally essential from those that are specific to this particular condition. To help define these classes for Pseudomonas aeruginosa, we identified genes required for growth on six different media, including a medium made from cystic fibrosis patient sputum. The analysis used the Tn-seq circle method to achieve high genome coverage and analyzed more than 1,000,000 unique insertion positions (an average of one insertion every 6.0 bp). We identified 352 general and 199 condition-specific essential genes. A subset of assignments was verified in individual strains with regulated expression alleles. The profile of essential genes revealed that, compared with Escherichia coli, P. aeruginosa is highly vulnerable to mutations disrupting central carbon-energy metabolism and reactive oxygen defenses. These vulnerabilities may arise from the stripped-down architecture of the organism's carbohydrate utilization pathways and its reliance on respiration for energy generation. The essential function profile thus provides fundamental insights into P. aeruginosa physiology as well as identifying candidate targets for new antibacterial agents.

Molecular dynamics simulations of yeast F1-ATPase before and after 16° rotation of the γ subunit

We have recently proposed the "packing exchange mechanism" for F1-ATPase, wherein the perturbation by a substrate binding/release or an ATP hydrolysis is followed by the reorganization of the asymmetric packing structure of the α3β3 complex, accompanying the γ subunit rotation. As part of a further investigation of this rotational mechanism, we performed all-atom molecular dynamics simulations for yeast F1-ATPase both before and after a 16° rotation of the γ subunit triggered by a Pi release. We analyzed the structural fluctuations, the subunit interface interactions, and the dynamics of the relative subunit arrangements before and after the rotation. We found that with the Pi release the αEβE subunit interface becomes looser, which also allosterically makes the αDPβDP subunit interface looser. This structural communication between these interfaces takes place through a tightening of the αTPβTP subunit interface. The γ subunit interacts less strongly with αDP and βDP and more strongly with αTP and βTP. After the Pi release, the tightly packed interfaces are reorganized from the interfaces around βDP to those around βTP, inducing the 16° rotation. These results, which are consistent with the packing exchange mechanism, allow us to deduce a view of the structural change during the 40° rotation.

Mechanism of the conformational change of the F1-ATPase β subunit revealed by free energy simulations

F(1)-ATPase is an ATP-driven rotary motor enzyme. The β subunit changes its conformation from an open to a closed form upon ATP binding. The motion in the β subunit is regarded as a major driving force for rotation of the central stalk. In this Article, we explore the conformational change of the β subunit using all-atom free energy simulations with explicit solvent and propose a detailed mechanism for the conformational change. The β subunit conformational change is accomplished roughly in two characteristic steps: changing of the hydrogen-bond network around ATP and the dynamic movement of the C-terminal domain via sliding of the B-helix. The details of the former step agree well with experimental data. In the latter step, sliding of the B-helix enhances the hydrophobic stabilization due to the exclusion of water molecules from the interface and improved packing in the hydrophobic core. This step contributes to a decrease in free energy, leading to the generation of torque in the F(1)-ATPase upon ATP binding.

Stochastic rotational catalysis of proton pumping F-ATPase

F-ATPases synthesize ATP from ADP and phosphate coupled with an electrochemical proton gradient in bacterial or mitochondrial membranes and can hydrolyse ATP to form the gradient. F-ATPases consist of a catalytic F1 and proton channel F0 formed from the alpha3beta3gammadelta and ab2c10 subunit complexes, respectively. The rotation of gammaepsilonc10 couples catalyses and proton transport. Consistent with the threefold symmetry of the alpha3beta3 catalytic hexamer, 120 degrees stepped revolution has been observed, each step being divided into two substeps. The ATP-dependent revolution exhibited stochastic fluctuation and was driven by conformation transmission of the beta subunit (phosphate-binding P-loop/alpha-helix B/loop/beta-sheet4). Recent results regarding mechanically driven ATP synthesis finally proved the role of rotation in energy coupling.

Our research on proton pumping ATPases over three decades: their biochemistry, molecular biology and cell biology

ATP is synthesized by F-type proton-translocating ATPases (F-ATPases) coupled with an electrochemical proton gradient established by an electron transfer chain. This mechanism is ubiquitously found in mitochondria, chloroplasts and bacteria. Vacuolar-type ATPases (V-ATPases) are found in endomembrane organelles, including lysosomes, endosomes, synaptic vesicles, etc., of animal and plant cells. These two physiologically different proton pumps exhibit similarities in subunit assembly, catalysis and the coupling mechanism from chemistry to proton transport through subunit rotation. We mostly discuss our own studies on the two proton pumps over the last three decades, including ones on purification, kinetic analysis, rotational catalysis and the diverse roles of acidic luminal organelles. The diversity of organellar proton pumps and their stochastic fluctuation are the important concepts derived recently from our studies.

Biochemical and molecular characterization of a Na+-translocating F1Fo-ATPase from the thermoalkaliphilic bacterium Clostridium paradoxum

Clostridium paradoxum is an anaerobic thermoalkaliphilic bacterium that grows rapidly at pH 9.8 and 56 degrees C. Under these conditions, growth is sensitive to the F-type ATP synthase inhibitor N,N'-dicyclohexylcarbodiimide (DCCD), suggesting an important role for this enzyme in the physiology of C. paradoxum. The ATP synthase was characterized at the biochemical and molecular levels. The purified enzyme (30-fold purification) displayed the typical subunit pattern for an F1Fo-ATP synthase but also included the presence of a stable oligomeric c-ring that could be dissociated by trichloroacetic acid treatment into its monomeric c subunits. The purified ATPase was stimulated by sodium ions, and sodium provided protection against inhibition by DCCD that was pH dependent. ATP synthesis in inverted membrane vesicles was driven by an artificially imposed chemical gradient of sodium ions in the presence of a transmembrane electrical potential that was sensitive to monensin. Cloning and sequencing of the atp operon revealed the presence of a sodium-binding motif in the membrane-bound c subunit (viz., Q28, E61, and S62). On the basis of these properties, the F1Fo-ATP synthase of C. paradoxum is a sodium-translocating ATPase that is used to generate an electrochemical gradient of + that could be used to drive other membrane-bound bioenergetic processes (e.g., solute transport or flagellar rotation). In support of this proposal are the low rates of ATP synthesis catalyzed by the enzyme and the lack of the C-terminal region of the epsilon subunit that has been shown to be essential for coupled ATP synthesis.

The F1-ATP synthase complex in bloodstream stage trypanosomes has an unusual and essential function

Survival of bloodstream form Trypanosoma brucei, the agent of African sleeping sickness, normally requires mitochondrial gene expression, despite the absence of oxidative phosphorylation in this stage of the parasite's life cycle. Here we report that silencing expression of the alpha subunit of the mitochondrial F(1)-ATP synthase complex is lethal for bloodstream stage T. brucei as well as for T. evansi, a closely related species that lacks mitochondrial protein coding genes (i.e. is dyskinetoplastic). Our results suggest that the lethal effect is due to collapse of the mitochondrial membrane potential, which is required for mitochondrial function and biogenesis. We also identified a mutation in the gamma subunit of F(1) that is likely to be involved in circumventing the requirement for mitochondrial gene expression in another dyskinetoplastic form. Our data reveal that the mitochondrial ATP synthase complex functions in the bloodstream stage opposite to that in the insect stage and in most other eukaryotes, namely using ATP hydrolysis to generate the mitochondrial membrane potential.

Three copies of the ATP2 gene are arranged in tandem on chromosome X in the yeast Saccharomyces cerevisiae

We previously reported that there were three copies of ATP1 coding for F1-alpha and two copies of ATP3 coding for F1-gamma on the left and right arm of chromosome II, respectively. In this study, we present evidence that there are three closely linked copies of ATP2 encoding the beta subunit of the F1F0-ATPase complex on the right arm of chromosome X in several laboratory strains, including Saccharomyces cerevisiae strain S288C, although it was reported by the yeast genome project that ATP2 is a single-copy gene. Chromosome X fragmentation, long-PCR, chromosome-walking and ATP2-disruption analysis using haploid wild-type strains and prime clone 70645 showed that the three copies of ATP2 are present on the right arm of chromosome X, like those of ATP1 on chromosome II. Each was estimated to be approximately 4 kb apart. We designated the ATP2 proximal to the centromere as ATP2a, the middle one as ATP2b and the distal one as ATP2c. The region containing the three ATP2s is composed of two repeated units of approximately 7 kb; that is, both ends (ATP2a, ATP2c) accompanying the ATP2-neighboring ORFs are the same. A part of YJR119c, YJR120w, YJR122w (CAF17) and YJR123w (RP55), which were reported by the yeast genome project, are contained in the ATP2 repeated units; and the middle ATP2 of the three ATP2s, ATP2b, is located between the two repeated units. Expression of all three copies of ATP2 (ATP2a, ATP2b, ATP2c) was confirmed because a single or double ATP2-disruptant could grow on glycerol, but a triple ATP2-disruptant could not. In addition, of the three copies of ATP1 and ATP2, even if only one copy of the ATP1 and ATP2 genes remained, the cells grew on glycerol.

Studies on the ATP3 gene of Saccharomyces cerevisiae: presence of two closely linked copies, ATP3a and ATP3b, on the right arm of chromosome II

In this paper, we present evidence that there are two closely linked copies of the ATP3 gene coding for the gamma subunit of the F(1)F(0)-ATPase complex (EC3.6.1.34) in four laboratory strains of Saccharomyces cerevisiae, even though the yeast genome project has reported that ATP3 is a single-copy gene on chromosome II. We previously reported that the gene dosage (three copies) of ATP1 and ATP2 is coincident with the subunit number of F(1)-alpha and F(1)-beta, but that the gene dosage of ATP3 was not consistent with the subunit stoichiometry of F(1)F(0)-ATPase. By applying long PCR and gene walking analyses, we estimated that the two copies of ATP3 were approximately 20 kb apart, and we designated that which is proximal to the centromere ATP3a, while we named that which is distal ATP3b. The nucleotide sequences of the two copies of ATP3 were identical to the reported sequence in the W303-1A, W303-1B and LL20 strains, while only the DC5 strain had a single base substitution in its ATP3a. With the exception of this substitution, the other nucleotide sequences were identical to the upstream 860 bp and the downstream 150 bp. The differences between ATP3 with the single base substitution (Ser(308) to Phe) and ATP3 without the substitution on the complementation of the ATP3 disruptant and on the maintenance of the mitochondrial DNA were observed, suggesting that Atp3ap and Atp3bp in the DC5 strain might have different functions. However, it should not always be necessary for yeast cells to carry different types of ATP3 because the other three strains carry the same type of ATP3. It was also demonstrated that the disruption of the ATP3 genes basically leads to a loss of wild-type mtDNA, but the stability of the mtDNA is not dependent on the ATP3 alone.

Hemin reconstitutes proton extrusion in an H(+)-ATPase-negative mutant of Lactococcus lactis

H(+)-ATPase is considered essential for growth of Lactococcus lactis. However, media containing hemin restored the aerobic growth of an H(+)-ATPase-negative mutant, suggesting that hemin complements proton extrusion. We show that inverted membrane vesicles prepared from hemin-grown L. lactis cells are capable of coupling NADH oxidation to proton translocation.

Stoichiometry of subunit e in rat liver mitochondrial H(+)-ATP synthase and membrane topology of its putative Ca(2+)-dependent regulatory region

Previous studies have revealed that residues 34-65 of subunit e of mitochondrial H(+)-ATP synthase are homologous with the Ca(2+)-dependent tropomysin-binding region for troponin T and have suggested that subunit e could be involved in the Ca(2+)-dependent regulation of H(+)-ATP synthase activity. In this study, we determined the content of subunit e in H(+)-ATP synthase purified from rat liver mitochondria, and we also investigated the membrane topology of a putative Ca(2+)-dependent regulatory region of subunit e using an antibody against peptide corresponding to residues 34-65 of subunit e. Quantitative immunoblot analysis of subunit e in the purified H(+)-ATP synthase revealed that 1 mol of H(+)-ATP synthase contained 2 mol of subunit e. The ATPase activity of mitoplasts, in which the C-side of F(0) is present on the outer surface of the inner membrane, was significantly stimulated by the addition of the antibody, while the ATPase activity of submitochondrial particles and purified H(+)-ATP synthase was not stimulated. The antibody bound to mitoplasts but not to submitochondrial particles. These results suggest that the putative Ca(2+)-dependent regulatory region of subunit e is exposed on the surface of the C-side of F(0) and that subunit e is involved in the regulation of mitochondrial H(+)-ATP synthase activity probably via its putative Ca(2+)-dependent regulatory region.

Inverse regulation of F1-ATPase activity by a mutation at the regulatory region on the gamma subunit of chloroplast ATP synthase

Chloroplast ATP synthase is a thiol-modulated enzyme whose DeltamuH(+)-linked activation is strongly influenced by reduction and the formation of a disulphide bridge between Cys(199) and Cys(205) on the gamma subunit. In solubilized chloroplast coupling factor 1 (CF(1)), reduction of the disulphide bond elicits the latent ATP-hydrolysing activity. To assess the regulatory importance of the amino acid residues around these cysteine residues, we focused on the three negatively charged residues Glu(210)-Asp-Glu(212) close to the two cysteine residues and also on the following region from Leu(213) to Ile(230), and investigated the modulation of ATPase activity by chloroplast thioredoxins. The mutant gamma subunits were reconstituted with the alpha and beta subunits from F(1) of the thermophilic bacterium Bacillus PS3; the active ATPase complexes obtained were purified by gel-filtration chromatography. The complex formed with a mutant gamma subunit in which Glu(210) to Glu(212) had been deleted was inactivated rather than activated by reduction of the disulphide bridge by reduced thioredoxin, indicating inverse regulation. This complex was insensitive to the inhibitory CF(1)-epsilon subunit when the mutant gamma subunit was oxidized. In contrast, the deletion of Glu(212) to Ile(230) converted the complex from a modulated state into a highly active state.

Analysis of the role of the Listeria monocytogenes F0F1 -AtPase operon in the acid tolerance response

As little is known about the genes involved in the induction of an acid tolerance response in Listeria monocytogenes, the role of the F0F1-ATPase was analyzed as a consequence of its role in the acid tolerance of a number of other bacteria and its conserved nature. It was found that acid adapted cells treated with N,N'-dicyclohexylcarbodiimide (DCCD) exhibited greatly enhanced sensitivity to low pH stress. Degenerate primers were designed to amplify and sequence a portion of the atpD gene. Subsequently, a PCR product from atpA to atpD was identified. While we were unable to create a deletion in the atpA gene, the plasmid pORI19 was inserted in a region between atpA and atpG to reduce, rather than eliminate, expression of the downstream genes. As expected this mutant displayed enhanced resistance to neomycin and exhibited slower growth than the wild type strain. This mutant could still induce an acid tolerance response and remained susceptible to DCCD treatment, but its relative acid sensitivity was difficult to assess as a consequence of its slow growth.

The membrane-bound H(+)-ATPase complex is essential for growth of Lactococcus lactis

The eight genes which encode the (F(1)F(o)) H(+)-ATPase in Lactococcus lactis subsp. cremoris MG1363 were cloned and sequenced. The genes were organized in an operon with the gene order atpEBFHAGDC; i.e., the order of atpE and atpB is reversed with respect to the more typical bacterial organization. The deduced amino acid sequences of the corresponding H(+)-ATPase subunits showed significant homology with the subunits from other organisms. Results of Northern blot analysis showed a transcript at approximately 7 kb, which corresponds to the size of the atp operon. The transcription initiation site was mapped by primer extension and coincided with a standard promoter sequence. In order to analyze the importance of the H(+)-ATPase for L. lactis physiology, a mutant strain was constructed in which the original atp promoter on the chromosome was replaced with an inducible nisin promoter. When grown on GM17 plates the resulting strain was completely dependent on the presence of nisin for growth. These data demonstrate that the H(+)-ATPase is essential for growth of L. lactis under these conditions.

Identification of Pasteurella multocida virulence genes in a septicemic mouse model using signature-tagged mutagenesis

P. multocida is the causative agent of several economically significant veterinary diseases occurring in numerous species worldwide. Signature-tagged mutagenesis (STM) is a powerful genetic technique used to simultaneously screen multiple transposon mutants of a pathogen for their inability to survive in vivo. We have designed an STM system based on a mini-Tn10 transposon, chemiluminescent detection and semi-quantitative analysis and have identified transposon insertions into genes of Pasteurella multocida that attenuate virulence in a septicemic mouse model. A bank of 96 transposons containing strongly-hybridizing tags was used to create 19 pools of P. multocida transposon mutants containing approximately 70-90 mutants/pool. A total of 62 mutants were attenuated when checked individually, and 25 unique single transposon insertion mutations were identified from this group. The sequence of the disrupted ORF for each attenuated mutant was determined by either cloning or PCR-amplifying and sequencing the flanking regions. The attenuated mutants contained transposon insertions in genes encoding biosynthetic enzymes, virulence factors, regulatory components and unknown functions. This study should contribute to an understanding of the pathogenic mechanisms by which P. multocida and other pathogens in the Pasteurellaceae family cause disease and identify novel live vaccine candidates and new potential antibiotic targets.

THECHLOROPLASTATP SYNTHASE: A Rotary Enzyme?

The chloroplast adenosine triphosphate (ATP) synthase is located in the thylakoid membrane and synthesizes ATP from adenosine diphosphate and inorganic phosphate at the expense of the electrochemical proton gradient formed by light-dependent electron flow. The structure, activities, and mechanism of the chloroplast ATP synthase are discussed. Emphasis is given to the inherent structural asymmetry of the ATP synthase and to the implication of this asymmetry to the mechanism of ATP synthesis and hydrolysis. A critical evaluation of the evidence in support of and against the notion that one part of the enzyme rotates with respect to other parts during catalytic turnover is presented. It is concluded that although rotation can occur, whether it is required for activity of the ATP synthase has not been established unequivocally.

ATPase activity of a highly stable alpha(3)beta(3)gamma subcomplex of thermophilic F(1) can be regulated by the introduced regulatory region of gamma subunit of chloroplast F(1)

A mutant F(1)-ATPase alpha(3)beta(3)gamma subcomplex from the thermophilic Bacillus PS3 was constructed, in which 111 amino acid residues (Val(92) to Phe(202)) from the central region of the gamma subunit were replaced by the 148 amino acid residues of the homologous region from spinach chloroplast F(1)-ATPase gamma subunit, including the regulatory stretch, and were designated as alpha(3)beta(3)gamma((TCT)) (Thermophilic-Chloroplast-Thermophilic). By the insertion of this regulatory region into the gamma subunit of thermophilic F(1), we could confer the thiol modulation property to the thermophilic alpha(3)beta(3)gamma subcomplex. The overexpressed alpha(3)beta(3)gamma((TCT)) was easily purified in large scale, and the ATP hydrolyzing activity of the obtained complex was shown to increase up to 3-fold upon treatment with chloroplast thioredoxin-f and dithiothreitol. No loss of thermostability compared with the wild type subcomplex was found, and activation by dithiothreitol was functional at temperatures up to 80 degrees C. alpha(3)beta(3)gamma((TCT)) was inhibited by the epsilon subunit from chloroplast F(1)-ATPase but not by the one from the thermophilic F(1)-ATPase, indicating that the introduced amino acid residues from chloroplast F(1)-gamma subunit are important for functional interaction with the epsilon subunit.

The gamma subunit in chloroplast F(1)-ATPase can rotate in a unidirectional and counter-clockwise manner

Rotation of the gamma subunit in chloroplast F(1)-ATPase (CF(1)) was investigated by using a single molecule observation technique, which is developed by Noji et al. to observe the rotation of a central gamma subunit portion in the alpha(3)beta(3)gamma sub-complex of F(1)-ATPase from thermophilic Bacillus PS3 (TF(1)) during ATP hydrolysis [Noji, H. et al. (1997) Nature 386, 299-302]. We used two cysteines of the gamma subunit (Cys-199 and Cys-205) of CF(1)-ATPase, which are involved in the regulation of this enzyme, to fix the fluorochrome-labeled actin filament. Then we successfully observed a unidirectional, counter-clockwise rotation of the actin filament with the fluorescent microscope indicating the rotation of the gamma subunit in CF(1)-ATPase. We conclude that the rotation of the gamma subunit in the F(1)-motor is a ubiquitous phenomenon in all F(1)-ATPases in prokaryotes as well as in eukaryotes.

Inorganic cation transport and energy transduction in Enterococcus hirae and other streptococci

Energy metabolism by bacteria is well understood from the chemiosmotic viewpoint. We know that bacteria extrude protons across the plasma membrane, establishing an electrochemical potential that provides the driving force for various kinds of physiological work. Among these are the uptake of sugars, amino acids, and other nutrients with the aid of secondary porters and the regulation of the cytoplasmic pH and of the cytoplasmic concentration of potassium and other ions. Bacteria live in diverse habitats and are often exposed to severe conditions. In some circumstances, a proton circulation cannot satisfy their requirements and must be supplemented with a complement of primary transport systems. This review is concerned with cation transport in the fermentative streptococci, particularly Enterococcus hirae. Streptococci lack respiratory chains, relying on glycolysis or arginine fermentation for the production of ATP. One of the major findings with E. hirae and other streptococci is that ATP plays a much more important role in transmembrane transport than it does in nonfermentative organisms, probably due to the inability of this organism to generate a large proton potential. The movements of cations in streptococci illustrate the interplay between a variety of primary and secondary modes of transport.

atp Mutants of Escherichia coli fail to grow on succinate due to a transport deficiency

Escherichia coli atp mutants, which lack a functional H+-ATPase complex, are capable of growth on glucose but not on succinate or other C4-dicarboxylates (Suc- phenotype). Suc+ revertants of an atp deletion strain were isolated which were capable of growth on succinate even though they lack the entire H+-ATPase complex. Complementation in trans with the yhiF gene suppressed the growth of the Suc+ mutants on succinate, which implicates the yhiF gene product in the regulation of C4-dicarboxylate metabolism. Indeed, when the E. coli C4-dicarboxylate transporter (encoded by the dctA gene) was expressed in trans, the Suc- phenotype of the atp deletion strain reverted to Suc+, which shows that the reason why the E. coli atp mutant is unable to grow aerobically on C4-dicarboxylates is insufficient transport capacity for these substrates.

The formation or the reduction of a disulfide bridge on the gamma subunit of chloroplast ATP synthase affects the inhibitory effect of the epsilon subunit

We have studied the change of the catalytic activity of chimeric complexes that were formed by chloroplast coupling factor 1 (CF1) -gamma, alpha and beta subunits of thermophilic bacterial F1 after formation or reduction of the disulfide bridge of different gamma subunits modified by oligonucleotide-directed mutagenesis techniques. For this purpose, three mutant gamma subunits were produced: gamma Delta194-230, here 37 amino acids from Pro-194 to Ile-230 are deleted, gammaC199A, Cys-199 is changed to Ala, and gamma Delta200-204, amino acids from Asp-200 to Lys-204 are deleted. All of the chimeric subunit complexes produced from each of these mutant CF1-gamma subunits and alpha and beta subunits from thermophilic bacterial F1 lost the sensitivity against thiol reagents when compared with the complex containing wild-type CF1-gamma. The pH optimum (pH 8.5-9.0) and the concentration of methanol to stimulate ATPase activities were not affected by these mutations. These indicate that the introduction of the mutations did not change the main features of ATPase activity of the chimeric complex. However, the interaction between gamma subunit and epsilon subunit was strongly influenced by the type of gamma subunit itself. Although the ATPase activity of the chimeric complex that contained gamma Delta200-204 or gammaC199A was inhibited by the addition of recombinant epsilon subunit from CF1 similarly to complexes containing the reduced wild-type gamma subunit, the recombinant epsilon subunit did not inhibit the ATPase of the complex, which contained the oxidized form of gamma subunit. Therefore the affinity of the epsilon subunit to the gamma subunit may be dependent on the state of the gamma subunit or the epsilon subunit may bind to the oxidized form of gamma subunit in a mode that does not inhibit the activity. The ATPase activity of the complex that contains gamma Delta194-230 was not efficiently inhibited by epsilon subunit. These results show that the formation or reduction of the disulfide bond on the gamma subunit may induce a conformational change in the region that directly affects the interaction of this subunit with the adjacent epsilon subunit.

Reconstitution of F1-ATPase activity from Escherichia coli subunits alpha, beta and subunit gamma tagged with six histidine residues at the C-terminus

An engineered gamma subunit of Escherichia coli F1-ATPase with extra 14 and 20 amino acid residues at the N- and C-termini (His-tag gamma), respectively, was overproduced in E. coli and purified. Six histidines are included in the C-terminal extension. The reconstituted F1 containing alpha, beta, and His-tagged gamma exhibited sixty percent of the wild-type ATPase activity. The reconstituted alphabeta His-tag gamma complex was subjected to affinity chromatography with nickel-nitrilotriacetic acid (Ni-NTA) agarose resin. ATPase activity was eluted specifically with imidazole. These results implied that the tag sequence protruded to the surface of the complex and did not seriously impair the activity. The reconstituted alphabeta His-tag gamma complex, even after its binding to the resin, exhibited ATPase activity suggesting that the gamma subunit, when fixed to a solid phase, may rotate the alphabeta complex. This system may provide a new approach for analysis of the rotation mechanisms in F1-ATPase.

Subunit interactions of Escherichia coli F1-ATPase: mutants of the gamma subunits defective in interaction with the epsilon subunit isolated by the yeast two-hybrid system

Previously, we established a method to detect subunit interactions of F1-ATPase by the yeast two-hybrid system (Moritani, C., et al. Biochim. Biophys. Acta 1274, 67-72, 1996). Here, we isolated mutants of the gamma subunits defective in interaction with the epsilon subunit by this new procedure to study the molecular basis of coupling mechanisms of the F1F0-ATPase. Based on the intensities of the reporter gene expression in this system, five mutants of the gamma subunit with different levels of gamma-epsilon interactions were isolated and their single base substitutions were determined. Mutants with a substitution of Pro-55 for Leu, Thr-102 for Met, Val-141 for Asp, or Gln-235 for Leu exhibited decreased reporter gene expression, suggesting decreased levels of interaction, while Asp-85 for Gly mutation caused a higher level of expression, suggesting increased interaction. Among these point mutations, G85D, M102T, or D141V mutations were introduced into the gamma subunit gene in the plasmid carrying whole unc operon. Transformants carrying a deletion mutant of the whole unc operon with these expression plasmids were analyzed. Mutations M102T and D141V with decreased gamma-epsilon interaction caused increases of membrane-bound F1-ATPase activity and proton pumping activity, while G85D with increased gamma-epsilon interaction exhibited lower levels of F1-ATPase activity in the membranes. Molecular assembly of the F1 subunits on the mutant membranes detected by Western blotting exhibited no defect for all three mutants. These results suggested that the correlation between the ATPase activity and gamma-epsilon interaction is reciprocal and this interaction may regulate the ATPase activity. The topological and functional importance of Gly-85, Met-102, and Asp-141 together with Leu-55 and Leu-235 in gamma-epsilon interaction is discussed.

Interaction of the delta and b subunits contributes to F1 and F0 interaction in the Escherichia coli F1F0-ATPase

Interactions of the F1F0-ATPase subunits between the cytoplasmic domain of the b subunit (residues 26-156, bcyt) and other membrane peripheral subunits including alpha, beta, gamma, delta, epsilon, and putative cytoplasmic domains of the a subunit were analyzed with the yeast two-hybrid system and in vitro reconstitution of ATPase from the purified subunits as well. Only the combination of bcyt fused to the activation domain of the yeast GAL-4, and delta subunit fused to the DNA binding domain resulted in the strong expression of the beta-galactosidase reporter gene, suggesting a specific interaction of these subunits. Expression of bcyt fused to glutathione S-transferase (GST) together with the delta subunit in Escherichia coli resulted in the overproduction of these subunits in soluble form, whereas expression of the GST-bcyt fusion alone had no such effect, indicating that GST-bcyt was protected by the co-expressed delta subunit from proteolytic attack in the cell. These results indicated that the membrane peripheral domain of b subunit stably interacted with the delta subunit in the cell. The affinity purified GST-bcyt did not contain significant amounts of delta, suggesting that the interaction of these subunits was relatively weak. Binding of these subunits observed in a direct binding assay significantly supported the capability of binding of the subunits. The ATPase activity was reconstituted from the purified bcyt together with alpha, beta, gamma, delta, and epsilon, or with the same combination except epsilon. Specific elution of the ATPase activity from glutathione affinity column with the addition of glutathione after reconstitution demonstrated that the reconstituted ATPase formed a complex. The result indicated that interaction of b and delta was stabilized by F1 subunits other than epsilon and also suggested that b-delta interaction was important for F1-F0 interaction.

Analysis of F1F0-ATPase from Helicobacter pylori

The adaptive mechanisms that permit Helicobacter species to survive within the gastric mucosa are not well understood. The proton-translocating F1F0-ATPase is an important enzyme for regulating intracellular pH or synthesizing ATP in many other enteric bacteria; therefore, we used degenerate primers derived from conserved bacterial F1F0-ATPase sequences to PCR amplify and clone the gene (atpD) encoding the H. pylori F1F0-ATPase beta subunit. The deduced amino acid sequences of the F1F0-ATPase beta subunits from H. pylori and Wolinella succinogenes were 85% identical (91% similar). To characterize a potential functional role of F1F0-ATPase in H. pylori, H. pylori or Escherichia coli cells were incubated for 60 min in buffered solutions at pH 7, 6, 5, or 4, with or without 100 microM N,N'-dicyclohexylcarbodiimide (DCCD), a specific inhibitor of F1F0-ATPase. At pH 5 and 4, there was no significant decrease in survival of H. pylori in the presence of DCCD compared to its absence, whereas incubation with DCCD at pH 7 and 6 significantly decreased H. pylori survival. E. coli survival was unaffected by DCCD at any pH value tested. We next disrupted the cloned beta-subunit sequence in E. coli by insertion of a kanamycin resistance cassette and sought to construct an isogenic F1F0-ATPase H. pylori mutant by natural transformation and allelic exchange. In multiple transformations of H. pylori cells grown at pH 6 or 7, no kanamycin-resistant F1F0 mutants were isolated, despite consistently successful mutagenesis of other H. pylori genes by using a similar approach and PCR experiments providing evidence for integration of the kanamycin resistance cassette into atpD. The sensitivity of H. pylori to DCCD at pH 7 and 6, and failure to recover F1F0 H. pylori mutants under similar conditions, suggests that the function of this enzyme is required for survival of H. pylori at these pHs.

Composition and primary structure of the F1F0 ATP synthase from the obligately anaerobic bacterium Clostridium thermoaceticum

The subunit composition and primary structure of the proton-translocating F1F0 ATP synthase have been determined in Clostridium thermoaceticum. The isolated enzyme has a subunit composition identical to that of the F1F0 ATP synthase purified from Clostridium thermoautotrophicum (A. Das, D. M. Ivey, and L. G. Ljungdahl, J. Bacteriol. 179:1714-1720, 1997), both having six different polypeptides. The molecular masses of the six subunits were 60, 50, 32, 17, 19, and 8 kDa, and they were identified as alpha, beta, gamma, delta, epsilon, and c, respectively, based on their reactivity with antibodies against the F1 ATPase purified from C. thermoautotrophicum and by comparing their N-terminal amino acid sequences with that deduced from the cloned genes of the C. thermoaceticum atp operon. The subunits a and b found in many bacterial ATP synthases could not be detected either in the purified ATP synthase or crude membranes of C. thermoaceticum. The C. thermoaceticum atp operon contained nine genes arranged in the order atpI (i), atpB (a), atpE (c), atpF (b), atpH (delta), atpA (alpha), atpG (gamma), atpD (beta), and atpC (epsilon). The deduced protein sequences of the C. thermoaceticum ATP synthase subunits were comparable with those of the corresponding subunits from Escherichia coli, thermophilic Bacillus strain PS3, Rhodospirillum rubrum, spinach chloroplasts, and the cyanobacterium Synechococcus strain PCC 6716. The analysis of total RNA by Northern hybridization experiments reveals the presence of transcripts (mRNA) of the genes i, a, and b subunits not found in the isolated enzyme. Analysis of the nucleotide sequence of the atp genes reveals overlap of the structural genes for the i and a subunits and the presence of secondary structures (in the b gene) which could influence the posttranscriptional regulation of the corresponding genes.

Escherichia coli F1-ATPase subunit interactions: beta and gamma subunit peptides inhibit in vitro reconstitution of the active alpha beta gamma complex

For biochemical analysis of subunit interactions in the proton-translocating ATPase, a new approach with in vitro reconstitution of the Escherichia coli alpha beta gamma complex and the peptides derived from the subunits was established. Various portions of the beta or gamma subunits were used for in vitro reconstitution of the alpha beta gamma complex from the purified subunits. For the beta subunits, peptides corresponding to residues 226-459, 254-459, and 226-365 inhibited reconstitution, while those corresponding to residues 1-105, 1-146, and 295-459 did not. For the gamma subunits, peptides corresponding to residues 1-192 and 74-286 exhibited inhibitory effect on reconstitution, but the peptide containing residues 191-286 did not. Only inhibitory peptides blocked the assembly of the alpha beta gamma complex which was detected by nondenaturing polyacrylamide gel electrophoresis. These inhibitory peptides bound to the alpha or beta subunit on the filter, but the noninhibitory peptides did not. These results suggested that regions beta 254-294 and gamma 74-190 have sequences important for subunit interactions which interfered with those in the reconstitution mixtures. Based on comparison between X-ray crystallographic data of bovine alpha beta gamma complex and the present results, we discussed here the significance of the biochemical approach adopted in this study.

Purification and reconstitution into proteoliposomes of the F1F0 ATP synthase from the obligately anaerobic gram-positive bacterium Clostridium thermoautotrophicum

The proton-translocating F1F0 ATP synthase from Clostridium thermoautotrophicum was solubilized from cholate-washed membranes with Zwittergent 3-14 at 58 degrees C and purified in the presence of octylglucoside by sucrose gradient centrifugation and ion-exchange chromatography on a DEAE-5PW column. The purified enzyme hydrolyzed ATP at a rate of 12.6 micromol min(-1) mg(-1) at 58 degrees C and pH 8.5. It was composed of six different polypeptides with molecular masses of 60, 50, 32, 19, 17, and 8 kDa. These were identified as alpha, beta, gamma, delta, epsilon, and c subunits, respectively, as their N-terminal amino acid sequences matched the deduced N-terminal amino acid sequences of the corresponding genes of the atp operon sequenced from Clostridium thermoaceticum (GenBank accession no. U64318), demonstrating the close similarity of the F1F0 complexes from C. thermoaceticum and C. thermoautotrophicum. Four of these subunits, alpha, beta, gamma, and epsilon, constituted the F1-ATPase purified from the latter bacterium. The delta subunit could not be found in the purified F1 although it was present in the F1F0 complex, indicating that the F0 moiety consisted of the delta and the c subunits and lacked the a and b subunits found in many aerobic bacteria. The c subunit was characterized as N,N'-dicyclohexylcarbodiimide reactive. The F1F0 complex of C. thermoautotrophicum consisting of subunits alpha, beta, gamma, delta, epsilon, and c was reconstituted with phospholipids into proteoliposomes which had ATP-Pi exchange, carbonylcyanide p-trifluoromethoxy-phenylhydrazone-stimulated ATPase, and ATP-dependent proton-pumping activities. Immunoblot analyses of the subunits of ATP synthases from C. thermoautotrophicum, C. thermoaceticum, and Escherichia coli revealed antigenic similarities among the F1 subunits from both clostridia and the beta subunit of F1 from E. coli.

Catalytic and structural importance of Gly-454, Tyr-455, and Leu-456 in the carboxy-terminal region of Escherichia coli F1-ATPase alpha subunit

Monoclonal antibody alpha110 recognizes Leu-456 in the alpha subunit of the Escherichia coli F1-ATPase. Binding of this antibody to the alpha subunit or mutation of this residue to Pro caused enhancement of the ATPase activity, suggesting that this residue is involved in the catalytic mechanism of this molecule (H. Kanazawa et al. (1995) Arch. Biochem. Biophys. 317, 348-356). Leu-456 together with Gly-454 and Tyr-455 are the only residues in the carboxy-terminal 75 amino acids conserved among various species, suggesting that these three residues play important roles in catalysis by the ATPase. Here, we introduced site-directed mutations into these residues. Not only L456P but also G454L, Y455K, Y455L, and L456N mutations caused enhancement of the ATPase activity. Surprisingly, Y455V, L456H, and L456S caused assembly defects of F1 subunits on the membrane. Reconstitution of the alpha betagamma complex from the wild-type beta and gamma subunits with the mutant alpha subunit (L4gamma6P) exhibited enhanced ATPase activity. Addition of delta or epsilon fused to glutathione S-transferase which are functionally similar to the delta and epsilon subunits, respectively, to the reconstituted F1-ATPase did not cause significant enhancement of its activity. Decreased interaction between alpha and beta subunits with the L456P mutation was detected by the yeast two-hybrid system. According to the deduced three-dimensional structure of the bovine a subunit, Leu-456, Gly-454, and Tyr-455 are included in a small alpha helix. These results suggest that this alpha helix affects interaction of the alpha subunit with the beta subunit but not with delta or epsilon, which may be important for the catalytic mechanism and F1 assembly.

Bioenergetics of the archaebacterium Sulfolobus

Archaea are forming one of the three kingdoms defining the universal phylogenetic tree of living organisms. Within itself this kingdom is heterogenous regarding the mechanisms for deriving energy from the environment for support of cellular functions. These comprise fermentative and chemolithotrophic pathways as well as light driven and respiratory energy conservation. Due to their extreme growth conditions access to the molecular machineries of energy transduction in archaea can be experimentally limited. Among the aerobic, extreme thermoacidophilic archaea, the genus Sulfolobus has been studied in greater detail than many others and provides a comprehensive picture of bioenergetics on the level of substrate metabolism, formation and utilization of high energy phosphate bonds, and primary energy conservation in respiratory electron transport. A number of novel metabolic reactions as well as unusual structures of respiratory enzyme complexes have been detected. Since their genomic organization and many other primary structures could be determined, these studies shed light on the evolution of various bioenergetic modules. It is the aim of this comprehensive review to bring the different aspects of Sulfolobus bioenergetics into focus as a representative example of, and point of comparison for closely related, aerobic archaea.

The mitochondrial genome integrity gene, MGI1, of Kluyveromyces lactis encodes the beta-subunit of F1-ATPase

In a previous report, we found that mutations at the mitochondrial genome integrity locus, MGI1, can convert Kluyveromyces lactis into a petite-positive yeast. In this report, we describe the isolation of the MGI1 gene and show that it encodes the beta-subunit of the mitochondrial F1-ATPase. The site of mutation in four independently isolated mgi1 alleles is at Arg435, which has changed to Gly in three cases and Ile in the fourth isolate. Disruption of MGI1 does not lead to the production of mitochondrial genome deletion mutants, indicating that an assembled F1 complex is needed for the "gain-of-function" phenotype found in mgi1 point mutants. The location of Arg435 in the beta-subunit, as deduced from the three-dimensional structure of the bovine F1-ATPase, together with mutational sites in the previously identified mgi2 and mgi5 alleles, suggests that interaction of the beta- and alpha- (MGI2) subunits with the gamma-subunit (MGI5) is likely to be affected by the mutations.

Characterization of mutations in the beta subunit of the mitochondrial F1-ATPase that produce defects in enzyme catalysis and assembly

The ATP2 gene, coding for the beta subunit of the mitochondrial F1-ATPase, was cloned from nine independent isolates of chemically mutagenized yeast. Seven different mutant alleles were identified. In one case the mutation occurs in the mitochondrial targeting sequence (M1I). The remaining six mutations map to the mature part of the beta subunit protein and alter amino acids that are conserved in the bovine heart mitochondrial and Escherichia coli beta subunit proteins. Biochemical analysis of the yeast atp2 mutants identified two different phenotypes. The G133D, P179L, and G227D mutations correlate with an assembly-defective phenotype that is characterized by the accumulation of the F1 alpha and beta subunits in large protein aggregates. Strains harboring the A192V, E222K, or R293K mutations assemble an F1 of normal size that is none-the-less catalytically inactive. The effect of the atp2 mutations was also analyzed in diploids formed by crossing the mutants to wild type yeast. Hybrid enzymes formed with beta subunits containing either the G133D, E222K, or R293K mutations are compromised for steady-state ATPase activity. The display of partial dominance confirms the importance of Gly133 for structural stability and of Glu222 and Arg293 for catalytic cooperativity.

Interactions of the F1-ATPase subunits from Escherichia coli detected by the yeast two-hybrid system

Subunit interactions among the F1-ATPase subunits were studied by the yeast two-hybrid system. Various pairwise combinations of genes encoding alpha, beta, gamma, delta and epsilon subunits of Escherichia coli H+-ATPase fused to the DNA-binding or activation domain of the yeast GAL4 gene were introduced into yeast and expression of a reporter gene encoding beta-galactosidase was detected. Combinations of the alpha and beta subunit genes, and of the epsilon and gamma subunit genes showed high levels of reporter gene expression, while those of alpha and delta, beta and delta, gamma and delta, and delta and epsilon demonstrated weak but significant reporter gene expression. However, combinations of alpha and gamma, beta and gamma, alpha and epsilon, and beta and epsilon did not induce reporter expression. None of the fused genes alone induced reporter gene expression. These results suggested that specific and strong interactions between the alpha and beta, gamma and epsilon, and weak interactions between the alpha and delta, beta and delta, and gamma and delta subunits occurred in yeast cells in the two-hybrid system. Effects of previously identified mutant beta subunits with Leu-40 to Pro. Glu-41 to Lys or Pro-332 to Gln substitutions which caused defects in molecular assembly of F1-ATPase were analyzed with regard to alpha-beta interactions. No interaction of the alpha and beta subunits was observed in this system using the beta subunit with mutation of Pro-332 to Gln. However, for the other two mutations, alpha-beta interactions were observed. This system may be useful for isolating mutants which have defects in interaction of F1-ATPase subunits.

ATP-dependent H+ -pump activity in inverted vesicles of Methanosarcina mazei Gö1 and characterization of membrane ATPase

ATP-dependent H+ -pump activity was found in inverted vesicles of Methanosarcina mazei Gö1 by using acridine orange as a fluorescent probe. The H+ -pump activity specifically required both Mg and sulfite ions, but azide, an inhibitor of F0F1-ATPase, did not inhibit the activity. The membranes prepared from M. mazei also had an Mg-ATPase activity, and at least the presence of vacuolar-type ATPase was detected.

Reconstitution of the F1-ATPase activity from purified alpha, beta, gamma and delta or epsilon subunits with glutathione S-transferase fused at their amino termini

Systems for overexpression and purification of active alpha, beta and gamma subunits of Escherichia coli H(+)-ATPase were established. The alpha and beta subunits recovered as soluble form were purified by hydroxyapatite column chromatography. Since the gamma subunit was overexpressed as the insoluble form, this subunit was purified by polyacrylamide gel-electrophoresis containing sodium dodecyl sulfate. By subsequent denaturation of this subunit with guanidine hydrochloride and renaturation, the active gamma subunit for reconstitution of the F1-ATPase activity with the purified alpha and beta subunit was obtained. The delta and epsilon subunits which were fused to the carboxy terminus of glutathione S-transferase (GST) were overproduced and purified by affinity chromatography. These fused proteins (delta-GST and epsilon-GST) were incubated with the purified alpha, beta and gamma subunits and applied to affinity chromatography. The alpha beta gamma delta-GST and alpha beta gamma epsilon-GST complex were eluted specifically by addition of glutathione and exhibited high and low ATPase activity, respectively, with a subunit stoichiometry similar to that in the native F1-ATPase, indicating that active complexes could be reconstituted with the fused proteins. These results suggested that the amino-terminal ends of the delta and epsilon subunits are not involved in formation of the active complex. The fused epsilon-GST bound the gamma subunit strongly, and the alpha subunit weakly. The delta-GST bound the gamma subunit significantly, and the alpha and beta subunits very weakly.

Experimental determination of control by the H(+)-ATPase in Escherichia coli

Strains carrying deletions in the atp genes, encoding the H(+)-ATPase, were unable to grow on nonfermentable substrates such as succinate, whereas with glucose as the substrate the growth rate of an atp deletion mutant was surprisingly high (some 75-80% of wild-type growth rate). The rate of glucose and oxygen consumption of these mutants was increased compared to the wild-type rates. In order to analyze the importance of the H(+)-ATPase at its physiological level, the cellular concentration of H(+)-ATPase was modulated around the wild-type level, using genetically manipulated strains. The control coefficient by the H(+)-ATPase with respect to growth rate and catabolic fluxes was measured. Control on growth rate was absent at the wild-type concentration of H(+)-ATPase, independent of whether the substrate for growth was glucose or succinate. Control by the H(+)-ATPase on the catabolic fluxes, including respiration, was negative at the wild-type H(+)-ATPase level. Moreover, the turnover number of the individual H(+)-ATPase enzymes increased as the H(+)-ATPase concentration was lowered. The negative control by the H(+)-ATPase on catabolism may thus be involved in a homeostatic control of ATP synthesis and, to some extent, explain the zero control by the H(+)-ATPase on E. coli growth rate.

Asymmetry of Escherichia coli F1-ATPase as a function of the interaction of alpha-beta subunit pairs with the gamma and epsilon subunits

The asymmetry of Escherichia coli F1-ATPase (ECF1) has been explored in chemical modification experiments involving two mutant enzyme preparations. One mutant contains a cysteine (Cys) at position 149 of the beta subunit, along with conversion of a Val to Ala at residue 198 to suppress the deleterious effect of the Cys for Gly at 149 mutation (mutant beta G149C:V198A). The second mutant has these mutations and also Cys residues at positions 381 of beta and 108 of the epsilon subunit (mutant beta G149C:V198A:E381C/epsilon S108C). On CuCl2 treatment of this second mutant, there is cross-linking of one copy of the beta subunit to gamma via the Cys at 381, a second to the epsilon subunit (between beta Cys381 and epsilon Cys108), while the third beta subunit in the ECF1 complex is mostly free (some cross-linking to delta); thereby distinguishing the three beta subunits as beta gamma, beta epsilon, and beta free, respectively. Both mutants have ATPase activities similar to wild-type enzyme. Under all nucleotide conditions, including with essentially nucleotide-free enzyme, the three different beta subunits were found to react differently with N-ethylmaleimide (NEM) which reacts with Cys149, dicyclohexyl carbodiimide (DCCD) which reacts with Glu192, and 7-chloro-4-nitrobenzofurazan (NbfCl) which reacts with Tyr297. Thus, beta gamma reacted with DCCD but not NEM or NbfCl; beta free was reactive with all three reagents; beta epsilon reacted with NEM, but was poorly reactive to DCCD or NbfCl. There was a strong nucleotide dependence of the reaction of Cys149 in beta epsilon (but not in beta free) with NEM, indicative of the important role that the epsilon subunit plays in functioning of the enzyme.

Use of an ATP bioluminescent assay to evaluate viability of Pneumocystis carinii from rats

A bioluminescent assay which employs the luciferin-luciferase ATP-dependent reaction was used to evaluate the viability of populations of Pneumocystis carinii derived from infected rat lungs. Contamination with host cells was reduced by a purification method which involved a combination of low- and high-speed centrifugations resulting in a 1,000-fold reduction of the rat cells while enriching for the trophic form of P. carinii. A linear correlation for the number of P. carinii nuclei versus the amount of ATP was observed. The ATP content of the organism populations could be maintained at inoculum levels for one week, although the number of organisms did not increase. Addition of respiratory chain inhibitors dramatically decreased the ATP content of the P. carinii after 24 h of incubation, with the exception of the antibiotic oligomycin B. Low concentrations of trimethoprim-sulfamethoxazole and pentamidine isethionate reduced the organism ATP content by over 50% after 24 h of exposure, while no effect was observed with 100-fold greater concentrations of ampicillin. The bioluminescent assay was found to be a more sensitive indicator of viability than a dual fluorescent staining technique. This assay does not require replication of P. carinii and should be a useful method for in vitro drug screening and viability assessment of P. carinii populations.

Intergenic suppression in a beta subunit mutant with defective assembly in Escherichia coli F1ATPase. Second-site mutation in the alpha subunit

Substitution of Leu-40 by Pro in the beta subunit (beta L40P) of Escherichia coli F1-ATPase caused a decrease in the amount of the alpha and beta subunits on the membranes. A revertant strain, Re50, carrying no suppression mutations in the uncD gene encoding the beta subunit, was isolated from the beta L40P mutant. The uncA gene from this revertant was amplified by PCR, and cloned into an expression plasmid. The expression plasmid carrying the uncA gene from the revertant was used for genetic suppression assays. The suppression mutation in Re50 was in the alpha subunit, and it recovered the assembly of the alpha and beta subunits into the F1F0 complex and the ATPase activity to 50% that of the wild type. In Re50, Leu-111 was substituted by Gln in the alpha subunit. These results suggest that the regions including Leu-40 in the beta subunit and Leu-111 in the alpha subunit are located close together and interact with each other, either directly or indirectly.