A glycine-rich sequence in the catalytic site of F-type ATPase

Comparative analysis of the P-type ATPase gene family in seven Rosaceae species and an expression analysis in pear (Pyrus bretschneideri Rehd.)

P-type ATPases are integral membrane transporters that play important roles in transmembrane transport in plants. However, a comprehensive analysis of the P-type ATPase gene family has not been conducted in Chinese white pear (Pyrus bretschneideri) or other Rosaceae species. Here, we identified 419 P-type ATPase genes from seven Rosaceae species (Pyrus bretschneideri, Malus domestica, Prunus persica, Fragaria vesca, Prunus mume, Pyrus communis and Pyrus betulifolia). Structural and phylogenetic analyses revealed that P-type ATPase genes can be divided into five subfamilies. Different subfamilies have different conserved motifs and cis-acting elements, which may lead to functional divergence within one gene family. Dispersed duplication and whole-genome duplication may play critical roles in the expansion of the P-type ATPase family. Purifying selection was the primary force driving the evolution of P-type ATPase family genes. Based on the dynamic transcriptome analysis and transient transformation of Chinese white pear fruit, Pbr029767.1 in the P_3A subfamily were found to be associated with malate accumulation during pear fruit development. Using a co-expression network, we identified several transcription factors that may have regulatory relationships with the P-type ATPase gene family. Overall, this study lays a solid foundation for understanding the evolution and functions of P-type ATPase genes in Chinese white pear and six other Rosaceae species.

The vacuolar ATPase from Entamoeba histolytica: molecular cloning of the gene encoding for the B subunit and subcellular localization of the protein

Background

Entamoeba histolytica is a professional phagocytic cell where the vacuolar ATPase plays a key role. This enzyme is a multisubunit complex that regulates pH in many subcellular compartments, even in those that are not measurably acidic. It participates in a wide variety of cellular processes such as endocytosis, intracellular transport and membrane fusion. The presence of a vacuolar type H⁺-ATPase in E. histolytica trophozoites has been inferred previously from inhibition assays of its activity, the isolation of the Ehvma1 and Ehvma3 genes, and by proteomic analysis of purified phagosomes.

Results

We report the isolation and characterization of the Ehvma2 gene, which encodes for the subunit B of the vacuolar ATPase. This polypeptide is a 55.3 kDa highly conserved protein with 34 to 80% identity to orthologous proteins from other species. Particularly, in silico studies showed that EhV-ATPase subunit B displays 78% identity and 90% similarity to its Dictyostelium ortholog. A 462 bp DNA fragment of the Ehvma2 gene was expressed in bacteria and recombinant polypeptide was used to raise mouse polyclonal antibodies. EhV-ATPase subunit B antibodies detected a 55 kDa band in whole cell extracts and in an enriched fraction of DNA-containing organelles named EhkOs. The V-ATPase subunit B was located by immunofluorescence and confocal microscopy in many vesicles, in phagosomes, plasma membrane and in EhkOs. We also identified the genes encoding for the majority of the V-ATPase subunits in the E. histolytica genome, and proposed a putative model for this proton pump.

Conclusion

We have isolated the Ehvma2 gene which encodes for the V-ATPase subunit B from the E. histolytica clone A. This gene has a 154 bp intron and encodes for a highly conserved polypeptide. Specific antibodies localized EhV-ATPase subunit B in many vesicles, phagosomes, plasma membrane and in EhkOs. Most of the orthologous genes encoding for the EhV-ATPase subunits were found in the E. histolytica genome, indicating the conserved nature of V-ATPase in this parasite.

Identification of nucleotide binding sites in V-type Na+-ATPase from Enterococcus hirae

A and B subunits of the V-type Na+-ATPase from Enterococcus hirae were suggested to possess nucleotide binding sites (Murata, T. et al., J. Biochem., 132, 789-794 (2002)), although the B subunit did not have the consensus sequence for nucleotide binding. To further characterize the binding sites in the V-ATPase, we did the photoaffinity labeling study using 8-azido-[alpha-32P]ATP. A and B subunits were labeled with 8-azido-[alpha-32P]ATP when analysed with SDS polyacrylamide gel electrophoresis. The peptide fragment of A subunit obtained by lysyl endopeptidase digestion after labeling showed a molecular size of 9 kDa and its amino acid sequencing revealed that it corresponded to residues Arg423-Lys494. The peptide fragment from B subunit after photoaffinity labeling and lysyl endopeptidase digestion showed the size of 5 kDa and corresponded to residues Phe404-Lys443. In our structure model, these peptides were close to the adenine ring of ATP. We suggest that non-catalytic B subunit of E. hirae V-ATPase has a nucleotide binding site, similarly to eukaryotic V-ATPases and F-ATPases.

Sulfite stimulates the ATP hydrolysis activity of but not proton translocation by the ATP synthase of Rhodobacter capsulatus and interferes with its activation by delta muH+

Sulfite stimulates the rate of ATP hydrolysis by the ATP synthase in chromatophores of Rhodobacter capsulatus. The stimulated activity is inhibited by oligomycin. The activation takes place also in uncoupled chromatophores. The activation consists in an increase of about 12-15-fold of the Vmax for the ATP hydrolysis reaction, while the Km for MgATP is unaffected at 0.16+/-0.03 mM. The dependence of Vmax on the sulfite concentration follows a hyperbolic pattern with half maximum effect at 12 mM. Sulfite affects the ability of the enzyme in translocating protons. Concomitant measurements of the rate of ATP hydrolysis and of ATP-induced protonic flows demonstrate that at sulfite concentrations of greater than 10 mM the hydrolytic reaction becomes progressively uncoupled from the process of proton translocation. This is accompanied by an inhibition of ATP synthesis, either driven by light or by artificially induced ionic gradients. ATP synthesis is totally inhibited at concentrations of at least 80 mM. Sulfite interferes with the mechanism of activation by delta muH+. Low concentrations of this anion (< or = 2 mM) prevent the activation by delta muH+. At higher concentrations a marked stimulation of the activity prevails, regardless of the occurrence of a delta muH+ across the membrane. Phosphate at millimolar concentrations can reverse the inhibition by sulfite. These experimental results can be simulated by a model assuming multiple and competitive equilibria for phosphate or sulfite binding with two binding sites for the two ligands (for sulfite K1S = 0.26 and K2S = 37 mM, and for phosphate K1P = 0.06 and K2P = 4.22 mM), and in which the state bound only to one sulfite molecule is totally inactive in hydrolysis. The competition between phosphate and sulfite is consistent with the molecular structures of the two ligands and of the enzyme.

Modification of domains of alpha and beta subunits of F1-ATPase from the thermophylic bacterium PS3, in their isolated and associated forms, by 3'-O-(4-benzoyl)benzoyl adenosine 5'-triphosphate (BzATP)

Photoaffinity labeling by 3'-O-(4-benzoyl)benzoyl adenosine 5'-triphosphate (BzATP) of the adenine nucleotide binding site(s) on isolated and complexed alpha and beta subunits of F1-ATPase from the thermophilic bacterium PS3 (TF1) is described. BzATP binds to both isolated alpha and beta subunits, to complexed beta subunit but not to complexed alpha subunit. Amino acid sequence determination of radiolabeled peptides obtained by proteolytic digestion of [gamma-32P]BzATP-labeled alpha subunit indicates that residues on both the amino-terminal (residues A41-E67) and carboxy-terminal (residues Q422-Q476) were modified by BzATP. One of the residues in the carboxy-terminal modified by BzATP is most probably alpha Q422. Although the binding stoichiometry of 1 mol of BzATP incorporated by either isolated or complexed beta subunit was maintained, the spatial conformation of the polypeptide determines which amino acid residue(s) is more accessible to the reactive radical. CNBr derived fragments beta G10-M64, beta E75-M233, and beta D390-M469 were labeled with the isolated beta subunit. With complexed beta subunit the label was found only in CNBr fragments: beta E75-M233 and beta G339-M389. The locations where the covalently bound BzATP was found, in the soluble and assembled subunits, indicate that different conformational states exist. In the isolated form of the alpha and beta subunits the amino- and carboxy-termini can fold and reach the central domain of the polypeptide, the domain containing the adenine nucleotide binding site. When alpha combines with beta to form the alpha 3 beta 3 core complex the new conformation of the subunits is such that covalent labeling by BzATP of alpha and of the amino terminal of beta subunit is excluded.

3'-O-(4-Benzoyl)benzoyladenosine 5'-triphosphate inhibits activity of the vacuolar (H+)-ATPase from bovine brain clathrin-coated vesicles by modification of a rapidly exchangeable, noncatalytic nucleotide binding site on the B subunit

It was previously observed that the B subunit of the tonoplast V-ATPase is modified by the photoactivated nucleotide analog 3'-O-(4-benzoyl)benzoyladenosine 5'-triphosphate (BzATP) (Manolson, M. F., Rea, P. A., and Poole, R. J. (1985) J. Biol. Chem. 260, 12273-12279). We have further characterized the nucleotide binding sites on the V-ATPase and the interaction between BzATP and the B subunit. We observe that the V-ATPase isolated from bovine clathrin-coated vesicles possesses approximately 1 mol of endogenous, tightly bound ATP/mol of V-ATPase complex. BzATP is not a substrate for the V-ATPase, but does act as a noncovalent inhibitor in the absence of irradiation, changing the kinetic characteristics of ATP hydrolysis. Irradiation of the V-ATPase in the presence of [3H]BzATP results primarily in modification of the 58-kDa B subunit, with complete inhibition of V-ATPase activity occurring upon modification of one B subunit per V-ATPase complex. Inhibition occurs as the result of modification of a rapidly (t1/2 < 2 min) exchangeable site, and yet this site does not correspond to a catalytic site, as indicated by the effects of cysteine-modifying reagents which react with Cys254 located at the catalytic sites on the A subunit. Thus, the noncatalytic nucleotide binding site modified by BzATP appears to be rapidly exchangeable. The site of [3H]BzATP modification of the B subunit was localized to the region Ile164 to Gln171, which from the x-ray crystal structure of the homologous F-ATPase alpha subunit, is within 10 A of the ribose ring of ATP bound to the noncatalytic nucleotide binding site. Thus, despite the absence of a glycine-rich loop region in the B subunit, these data are consistent with a similar overall folding pattern for the V-ATPase B subunit and the F-ATPase alpha subunit.

Intragenic suppressors of P-loop mutations in the beta-subunit of the mitochondrial ATPase in the yeast Saccharomyces cerevisiae

Three intragenic second-site suppressors, P353L, T237I, and L390F, were identified that suppressed two mutations in, and one adjacent to, the P-loop in the beta-subunit of the yeast F1-ATPase. The crystal structure of bovine F1-ATPase (Abrahams, J. P., Leslie, A. G. W., Lutter, R., and Walker, J. E. (1994) Nature 370, 621-628) shows that these suppressor residues are located in the nucleotide-binding domain. Specific hypotheses have been formulated that suggest the conformational coupling of the P-loop with the suppressor sites. P353L is in a "catch" region, which forms unique interactions with the gamma-subunit in the three different conformational states of the catalytic site. The identification of this suppressor mutation demonstrates genetically that the catch region is conformationally coupled to the P-loop. T237I is shown to interact with Lys-209, which occurs just after the P-loop. This suggests that this interaction changes the conformation of the P-loop to suppress the initial mutation. L390F interacts with Ala-181, which is adjacent to the P-loop. The mechanism of this suppression is suggested to occur through the interactions of L390F with Ala-181. These results identify critical interactions that modulate the structure of the P-loop and thus the biochemistry of the enzyme.

Inhibition and labeling of the coated vesicle V-ATPase by 2-azido-[32P]ATP

Previous studies have indicated that the 73-kDa A subunit of the coated vesicle V-ATPase possesses a nucleotide-binding site essential for activity (Arai, H., Berne, M., Terres, G., Terres, H., Puopolo, K., and Forgac, M. (1987) Biochemistry 26, 6632-6638) and have identified a cysteine residue (Cys254) whose modification leads to complete loss of activity (Feng, Y., and Forgac, M. (1992) J. Biol. Chem. 267, 5817-5822). To further characterize the structure of the nucleotide-binding sites of the V-ATPase, labeling studies using the photoactivated analog 2-azido-[32P]ATP have been carried out. We have observed that 2-azido-[32P]ATP is hydrolyzed by the V-ATPase at a rate (at 1 mM) approximately 4-fold lower than observed for ATP, indicating that 2-azido-[32P]ATP is a good substrate for the V-ATPase. Irradiation of the V-ATPase in the presence of 0.5 mM 2-azido-[32P]ATP leads to inactivation of V-ATPase activity with a t1/2 of 3-5 min. The 73-kDa A subunit, the 58-kDa B subunit, and the 50-kDa subunit of the AP-2 adaptin complex (Myers, M., and Forgac, M. (1993) J. Biol. Chem. 268, 9184-9186) are all labeled in an ATP-protectable manner on irradiation of the purified V-ATPase with 2-azido-[32P]ATP. The time course for inactivation most closely correlates with labeling of the A subunit. Measurement of the stoichiometry of 2-azido-[32P]ATP incorporation into the A subunit as a function of inactivation indicates that complete loss of activity is obtained on incorporation of 1.2 mol of 2-azido-[32P]ATP/mol V-ATPase complex. 2-Azido-[32P]ATP labeling indicates that the V-ATPase possesses both rapidly (t1/2 < 2 min) and slowly (t1/2 > 2 min) exchangeable nucleotide-binding sites. The A subunit is labeled upon modification of both rapidly and slowly exchangeable sites whereas the B subunit is labeled upon modification of only rapidly exchangeable sites. Inhibition of V-ATPase activity correlates with labeling of the rapidly exchangeable sites. Amino acid sequence analysis of peptides derived from the 2-azido-[32P]ATP-labeled A subunit indicates labeling of two peptides: a 12-kDa fragment which begins at residue 511 and contains Cys532 and a 3-kDa fragment which begins at residue 233 and contains the glycine-rich loop and Cys254. Only the 12-kDa fragment is labeled upon modification of the rapidly exchangeable sites.(ABSTRACT TRUNCATED AT 400 WORDS)

Arrangement of the epsilon subunit in the Escherichia coli ATP synthase from the reactivity of cysteine residues introduced at different positions in this subunit

ECF1F0 has been purified from three mutants in which a Cys has been incorporated by site-directed mutagenesis in the epsilon subunit: these mutants are epsilon S10C, epsilon H38C and epsilon S108C, respectively. ECF1F0 from the mutant epsilon S10C had a 2-fold higher activity than wild-type enzyme, due to altered association of the epsilon subunit with the rest of the complex, and yet showed normal proton pumping function. The other two mutants had ATPase activities similar to wild-type enzyme. The introduced Cys was exposed for reaction with maleimides in epsilon S10C and epsilon S108C. In epsilon H38C, the introduced Cys reacted readily with N-ethylmaleimide in isolated ECF1, but was unavailable for reaction with this or other maleimides in ECF1F0. When this Cys at position 38 in the epsilon subunit was reacted with various maleimides in isolated ECF1 and then the ECF1 bound back to F0, the interaction between the two parts was perturbed. While ECF1F0 reconstituted with unmodified ECF1 functioned normally, enzyme with maleimide-reacted Cys-38 showed much reduced proton pumping, had only around 50% of the DCCD inhibition of unmodified or wild-type enzyme, and had a much higher LDAO activation (as much as 8.3-fold, c.f. 4-fold for wild type). Nucleotide-dependent conformational changes have been observed previously, in studies of ECF1 from the mutants epsilon S10C and epsilon S108C. Identical nucleotide-dependent structural changes were observed in cross-linking experiments with tetrafluorophenylazide maleimides when the intact ECF1F0 from these mutants was examined. Taken together, the Cys reactivity data and cross-linking results provide the orientation of the epsilon subunit in the enzyme complex.

N-ethylmaleimide-sensitive mutant (beta Val-153-->Cys) Escherichia coli F1-ATPase: cross-linking of the mutant beta subunit with the alpha subunit

A beta subunit mutation, beta Val-153-->Cys, in the glycine-rich sequence (phosphate-binding loop) of Escherichia coli F1 was constructed. Like vacuolar-type ATPase, the mutant enzyme was inhibited by N-ethylmaleimide (NEM) and labeled with [14C]NEM. The inhibition and labeling were prevented by ATP. m-Maleimidobenzoyl-N-hydroxysuccinimide (MBS) (3 microM) almost completely inhibited the mutant enzyme, and cross-linked one pair of alpha and beta subunits. These results suggest that the interaction of the domain near beta Val-153 with the alpha subunit is essential for catalytic cooperativity of the enzyme and that beta Val-153 is within 10 A of the alpha subunit.

Structural model of the ATP-binding domain of the F1-beta subunit based on analogy to the RecA protein

In contrast to the previous topological model of the ATP binding domain of the F1-ATPase beta subunit based on analogies to those of ras p21 and adenylate kinase, a more consistent model can be constructed with the known structure of the recA protein as a reference. The secondary structure of the F1-ATPase beta subunit predicted from the primary structure agrees well with that of the recA protein. The topology includes a repetitive beta alpha c beta alpha beta alpha beta alpha beta structure where all beta strands are parallel and surround the central alpha c helix above which bound ATP is located. Several residues thought to be located at catalytic site as reported in genetic and chemical labeling work can be consistently positioned in this model.

Coupling between catalytic sites and the proton channel in F1F0-type ATPases

F1F0-type ATPases catalyse both ATP-driven proton translocation and proton-gradient-driven ATP synthesis. Recent cryoelectronmicroscopy and low-resolution X-ray studies provide a first glimpse at the structure of this complicated membrane-bound enzyme. The F1 part is roughly globular and linked to the membrane-intercalated F0 part by a narrow stalk domain, which contains the gamma-, delta- and epsilon-subunits along with domains of the b-subunit of the F0 part. Here, we review evidence that conformational and positional changes in the gamma- and epsilon-subunits provide the coupling between catalytic sites and proton translocation within the F1F0 complex.

ATPase kinetics for wild-type Saccharomyces cerevisiae F1-ATPase and F1-ATPase with the beta-subunit Thr197-->Ser mutation

Unisite ATPase kinetic constants were measured for wild-type yeast Saccharomyces cerevisiae F1-ATPase and F1-ATPase with the Thr197-->Ser mutation in the beta subunit. Under unisite conditions, the concentration of ATP is greater than that of the enzyme, ATP hydrolysis is slow and the affinity of the enzyme for ATP and ADP is high. The Thr197-->Ser mutation in the yeast F1-ATPase increases the specific activity of ATP hydrolysis threefold and makes the enzyme much less sensitive to azide and oxyanions [Mueller, D. M. (1989) J. Biol. Chem. 264, 16552-16556]. A unifying hypothesis is that the affinity of F1-ATPase for ADP is altered by azide, oxyanions and the Thr197-->Ser mutation. To address this hypothesis, kinetic and thermodynamic constants were measured for the wild-type and mutant enzymes in the absence and presence of azide and oxyanions. The results indicate that sulfite and azide do not significantly alter unisite thermodynamic binding constants of either enzyme for ADP at the catalytic site. The mutation Thr197-->Ser has little effect on the binding constant for ADP, or on other unisite kinetic constants of the enzyme, in the presence or absence of azide or oxyanions. However, the binding of ADP to the enzyme was affected by oxyanions and the Thr197-->Ser mutation as measured by determining the KiADP values for multisite ATPase activity (saturating ATP). The Ki for ADP on ATPase activity was measured for the wild-type and mutant enzymes in the presence and absence of sulfite under multisite conditions. Sulfite increases the KiADP values for ATP hydrolysis under multisite conditions approximately threefold for the wild-type and mutant enzymes and the Thr197-->Ser mutation increases KiADP ninefold. The effect of sulfite on KiADP is additive to the effect of the Thr197-->Ser mutation, suggesting that these are distinct effects. These results indicate that the effects of azide, oxyanions, and the Thr197-->Ser mutation on the biochemistry of F1-ATPase are limited primarily to multisite conditions. Both sulfite and the Thr197-->Ser mutation decrease the affinity of the enzyme for ADP, as measured by the increase in the Ki values. Furthermore, the mechanisms of activation by sulfite and the Thr197-->Ser mutations are different. This difference occurs despite their common biochemical consequences on the apparent affinity for ADP.