Archaebacterial ATPases Research Articles

Function and Subunit Interactions of the N-terminal Domain of Subunit a (Vph1p) of the Yeast V-ATPase

The vacuolar (H+)-ATPases (V-ATPases) are ATP-dependent proton pumps that operate by a rotary mechanism in which ATP hydrolysis drives rotation of a ring of proteolipid subunits relative to subunit a within the integral V(0) domain. In vivo dissociation of the V-ATPase (an important regulatory mechanism) generates a V(0) domain that does not passively conduct protons. EM analysis indicates that the N-terminal domain of subunit a approaches the rotary subunits in free V(0), suggesting a possible mechanism of silencing passive proton transport. To test the hypothesis that the N-terminal domain inhibits passive proton flux by preventing rotation of the proteolipid ring in free V(0), factor Xa cleavage sites were introduced between the N- and C-terminal domains of subunit a (the Vph1p isoform in yeast) to allow its removal in vitro after isolation of vacuolar membranes. The mutant Vph1p gave rise to a partially uncoupled V-ATPase complex. Cleavage with factor Xa led to further loss of coupling of proton transport and ATP hydrolysis. Removal of the N-terminal domain by cleavage with factor Xa and treatment with KNO3 and MgATP did not, however, lead to an increase in passive proton conductance by free V(0), suggesting that removal of the N-terminal domain is not sufficient to facilitate passive proton conductance through V(0). Photoactivated cross-linking using the cysteine reagent maleimido benzophenone and single cysteine mutants of subunit a demonstrated the proximity of specific sites within the N-terminal domain and subunits E and G of the peripheral stalk. These results suggest that a localized region of the N-terminal domain (residues 347-369) is important in anchoring the peripheral stator in V1V0.

The 1.9 Å Structure of a Proteasome-11S Activator Complex and Implications for Proteasome-PAN/PA700 Interactions

Proteasomes are cylindrical structures that function in multiple cellular processes by degrading a wide variety of cytosolic and nuclear proteins. Substrate access and product release from the enclosed catalytic chamber occurs through axial pores that are opened by activator complexes. Here, we report high-resolution structures of wild-type and mutant archaeal proteasomes bound to the activator PA26. These structures support the proposal that an ordered open conformation is required for proteolysis and that its formation can be triggered by outward displacement of surrounding residues. The structures and associated biochemical assays reveal the mechanism of binding, which involves an interaction between the PA26 C terminus and a conserved lysine. Surprisingly, biochemical observations implicate an equivalent interaction for the unrelated ATP-dependent activators PAN and PA700.

Disruption of vma-1, the Gene Encoding the Catalytic Subunit of the Vacuolar H+-ATPase, Causes Severe Morphological Changes in Neurospora crassa

By using the process of Repeat-induced Point mutation (Selker, E. U., and Garrett, P. W. (1988) Proc. Natl. Acad. Sci. U. S. A. 85, 6870-6874), we inactivated vma-1, the gene encoding subunit A of the V-ATPase of Neurospora crassa. Two vma-1 mutant strains were characterized. One was mutated at multiple sites, did not make a protein product, and produced spores that only rarely germinated. The other had four point mutations, made a protein product, and produced viable spores. Neither strain had detectable V-ATPase activity. The vma-1 mutant strains did not grow in medium buffered to pH 7.0 or above or in medium supplemented with the cation Zn(2+). They were completely resistant to inhibition by concanamycin C, supporting our hypothesis that the V-ATPase is the in vivo target of this antibiotic. Inactivation of the vma-1 gene had a pronounced effect on morphology and development of the organism. In the mutants tip growth was inhibited, and multiple branching was induced. The vma-1 mutant strains could not differentiate conidia or perithecia. They could grow slowly as mycelia and could donate nuclei in a sexual cross. A mutation in the plasma membrane ATPase, which suppressed the sensitivity of wild type N. crassa to concanamycin, also proved effective in suppressing the sensitivity of a vma-1 null mutant to basic pH but did not correct the morphological defects.

An Archaebacterial ATPase, Homologous to ATPases in the Eukaryotic 26 S Proteasome, Activates Protein Breakdown by 20 S Proteasomes

In eukaryotes, the 20 S proteasome is the proteolytic core of the 26 S proteasome, which degrades ubiquitinated proteins in an ATP-dependent process. Archaebacteria lack ubiquitin and 26 S proteasomes but do contain 20 S proteasomes. Many archaebacteria, such as Methanococcus jannaschii, also contain a gene (S4) that is highly homologous to the six ATPases in the 19 S (PA700) component of the eukaryotic 26 S proteasome. To test if this putative ATPase may regulate proteasome function, we expressed it in Escherichia coli and purified the 50-kDa product as a 650-kDa complex with ATPase activity. When mixed with the well characterized 20 S proteasomes from Thermoplasma acidophilum and ATP, this complex stimulated degradation of several unfolded proteins 8-25-fold. It also stimulated proteolysis by 20 S proteasomes from another archaebacterium and mammals. This effect required ATP hydrolysis since ADP and the nonhydrolyzable analog, 5'-adenylyl beta, gamma-imidophosphate, were ineffective. CTP and to a lesser extent GTP and UTP were also hydrolyzed and also stimulated proteolysis. We therefore named this complex PAN for proteasome-activating nucleotidase. However, PAN did not promote the degradation of small peptides, which, unlike proteins, should readily diffuse into the proteasome. This ATPase complex appears to have been the evolutionary precursor of the eukaryotic 19 S complex, before the coupling of proteasome function to ubiquitination.

Mutagenesis and Reversion Analysis of Residue Met-209 of the β-Subunit ofEscherichia coliATP Synthase

Residue β-Met-209 is conserved in all known F1- ATPase sequences, and the mutation βM209I inEscherichia colicauses profound inhibition of ATP synthesis and hydrolysis. Based on the properties of this mutant it had previously been proposed that residue β-209 lies close to the site of catalysis. Two approaches were used to study this residue further. First, revertants were sought. Only wild-type and β-Ser-209 were found; the Ser revertants involved a two-base change. Significantly, Ser is found at the equivalent position in the homologous vacuolar and archaebacterial ATPases. Second, all 20 natural amino acids were placed at position β-209 by mutagenesis, and catalytic properties of the mutants were analyzed. The results showed that only a limited set of residues supported significant growth or ATPase activity, and that many of the mutations impacted severely on catalysis. X-ray structure analysis of the bovine enzyme has revealed that residue β-Met-209 lies only 3.1 Å from residue β-Glu-181, which has been proposed to act as catalytic base. The results reported here emphasize that, in this discrete region of the catalytic site, specific stereochemical constraints on structure are critical for catalysis.

The V-ATPase A subunit gene ( vma-1 from Giardia lamblia

The sequence of the gene encoding the A subunit of the vacuolar type ATPase from Giardia lamblia is reported. Comparison of the encoded protein with the homologous subunits of eukaryotic and archaebacterial ATPases reveals high levels of similarity throughout the sequence (e.g., overall 49.1 and 44.6% identity to the homologous subunit from carrot and Halobacterium, respectively). An exception are three regions which are unique to the Giardia subunit. The largest of these regions contains motifs characteristic for eukaryotic spliceosomal introns; however, comparison to the cDNA shows that this region is also present in the mRNA.

Sulfite both stimulates and inhibits the yeast vacuolar H(+)-ATPase.

The yeast vacuolar H(+)-ATPase (V-ATPase) exhibits nonlinear hydrolysis kinetics, i.e. an initial rapid rate followed by a slower, steadily declining rate. Sulfite (50-100 mM) stimulates the yeast V-ATPase specifically during the latter period. Sulfite activation has been observed for the F-ATPases and archaebacterial ATPases and is thought to be caused by the release of tightly bound nucleotide at the catalytic site. However, turnover-dependent inactivation of the yeast V-ATPase, and sulfite stimulation, were only observed at MgATP concentrations > 1.0 mM. Below 1.0 mM MgATP, the hydrolysis time course was linear, and sulfite was inhibitory. The inhibition during the initial phase and the stimulation during the later phase of the time course could be accounted for by a 5.5-fold sulfite-induced increase in the apparent Km, and a small increase in the apparent Vmax. Sulfite also protected the enzyme against inhibition by cold inactivation and by dicyclohexylcarbodiimide but not by bafilomycin. Sulfite stimulation during the later phase was antagonized by delta mu H+, particularly by delta pH. In contrast to its effects on hydrolysis, sulfite inhibited the formation of a pH gradient at all times and failed to enhance the membrane potential even when delta pH was collapsed by nigericin. These results indicate that sulfite partially uncouples hydrolysis from proton transport in a way that preserves regulation by delta mu H+.

Properties Of The Plasma Membrane Atpases Of The Halophilic Archaebacteria Haloferax Mediterranei And Haloferax Volcanii

Both, Haloferax mediterranei and Haloferax volcanii membranes contain ATPases which are capable of hydrolyzing ATP in presence of Mg2+ or Mn2+. The ATPases require high concentrations of NaCl, a pH value of 9, and high temperatures up to 60 °C. Free manganese ions inhibited the enzyme activity of either ATPase. The ATPases of Hf. mediterranei and Hf. volcanii, respectively, show different sensitivities to inhibitors of ATP hydrolysis. ATP hydrolysis of isolated Hf. mediterranei ATPase was inhibited by NaN3, which was reported to be specific for F-ATPases, by nitrate and N-ethylmaleimide (NEM), which are specific inhibitors of V-ATPases. ATP hydrolysis of Haloferax mediterranei membranes was not inhibited by DCCD , but [14C]DCCD was bound to a 14 kDa peptide of the isolated, partially purified enzyme. Furthermore, the ATPase was inactivated by preincubation with 7-chloro-4-nitrobenzofurazan (NBD-Cl). The ATPase activity of Hf. volcanii membranes was inhibited by NEM but not by nitrate and NaN3. SDS gel electrophoresis of the partially purified enzyme of Haloferax mediterranei showed putative ATPase subunits of 53.5, 49, 42, 22, 21, 14, 12, and 7.5 kDa. Immunoblots showed cross reactivity between a 53 kDa peptide and anti-β (chloroplast F1), as well as between 53, 50 and 47 kDa peptides and an ATPase antibody of Methanosarcina barkeri. The results will be discussed in context with the placement of the archaebacterial ATPases (A-ATPases) between F- and V-ATPases

Primary structure of V-ATPase subunit B from Manduca sexta midgut

The amino acid sequence of a vacuolar-type ATPase (V-ATPase) subunit B has been deduced from a cDNA clone isolated from a Manduca sexta larval midgut library. The library was screened by hybridization with a labeled cDNA encoding subunit B of Arabidopsis thaliana tonoplast V-ATPase. The M. sexta V-ATPase subunit B consists of 494 amino acids with a calculated M r of 54902. The amino acid sequence deduced for V-ATPase subunit B of M. sexta is between 98% and 76% identical with that of seven other V-ATPase subunits B and > 52% identical with three archaebacterial ATPase subunits B.

Nucleotide-protectable labeling of sulfhydryl groups in subunit I of the ATPase from Halobacterium saccharovorum

A membrane-bound ATPase from the archaebacterium Halobacterium saccharovorum is inhibited by N-ethyl-maleimide in a nucleotide-protectable manner (Stan-Lotter et al., 1991, Arch. Biochem. Biophys. 284, 116–119). When the enzyme was incubated with N-[ 14C]ethylmaleimide, the bulk of radioactivity was associated with the 87,000-Da subunit (subunit I). ATP, ADP, or AMP reduced incorporation of the inhibitor. No charge shift of subunit I was detected following labeling with N-ethylmaleimide, indicating an electroneutral reaction. The results are consistent with the selective modification of sulfhydryl groups in subunit I at or near the catalytic site and are further evidence of a resemblance between this archaebacterial ATPase and the vacuolartype ATPases.

F-type or V-type? The chimeric nature of the archaebacterial ATP synthase

Archaebacterial plasma membranes contain an ATPase acting in vivo as aΔμH+-driven ATP synthase. While functional features and their general structural design are resembling F-type ATPases, primary sequences of the two large polypeptides from the catalytic part are closely related to V-type ATPases from eucaryotic vacuolar membranes. The chimeric nature of archaebacterial ATPase fromSulfolobus was investigated in terms of nucleotide interactions and related to specific sequence parameters in a comparison to well known F- and V-type ATPases. The study disclosed a general difference of F- and V-type ATPases at one class of the nucleotide binding sites.

Archaebacterial ATPases: Relationship to Other Ion-Translocating ATPase Families Examined in Terms of Immunological Cross-Reactivity1

Immunological cross-reactivity among three types of H(+)-ATPases, that is, three archaebacterial ATPases, the F1-ATPase from thermophilic bacterium PS3 (TF1) and the vacuolar membrane ATPase from Saccharomyces cerevisiae, was examined by means of immunoblot analyses. The three archaebacterial ATPases were very similar in immunological cross-reactivity, suggesting that they belong to the same family of ATPases. Cross-reaction was also observed between the ATPase from Sulfolobus acidocaldarius, one of the three archaebacteria, and TF1. S. cerevisiae vacuolar ATPase reacted with the antibodies prepared against each of the three archaebacterial ATPases, but did not react with the antibody against TF1. Electron microscopic examination revealed that the oligomeric structure of Sulfolobus ATPase was very similar to that of F1-ATPase. These results, taken together, suggest that the archaebacterial ATPases share close structural similarities with the vacuolar ATPases, and, to a lesser degree, with the F0F1-ATPases.

Electron transport and energy conservation in the archaebacteriumSulfolobus acidocaldarius

The bioenergetic properties of the thermoacidophilic archaebacterium Sulfolobus acidocaldarius are reviewed and discussed under the aspect whether this archaebacterium conserved energy by oxidative phosphorylation and how the involved catalysts are related to those from eubacteria and eukaryotes. The thermodynamic parameters contributing to the proton-motive force and the efficiency of proton pumping are presented. The major components of the electron transport system are identified and a novel type of heme-aa3 containing terminal oxidase is described, oxidizing reduced caldariella quinone. The properties of an F1-analogous ATPase and of a DCCD-binding proteolipid from the plasmamembrane of Sulfolobus are discussed as likely components of an F0F1-analogous ATP-synthase. The structural and functional properties of this and other archaebacterial ATPases are compared to each other and with respect to evolutionary relations.

Electron transport and energy conservation in the archaebacterium Sulfolobus acidocaldarius

The bioenergetic properties of the thermoacidophilic archaebacterium Sulfolobus acidocaldarius are reviewed and discussed under the aspect whether this archaebacterium conserved energy by oxidative phosphorylation and how the involved catalysts are related to those from eubacteria and eukaryotes. The thermodynamic parameters contributing to the proton-motive force and the efficiency of proton pumping are presented. The major components of the electron transport system are identified and a novel type of heme- aa 3 containing terminal oxidase is described, oxidizing reduced caldariella quinone. The properties of an F 1-analogous ATPase and of a DCCD-binding proteolipid from the plasmamembrane of Sulfolobus are discussed as likely components of an F 0 F 1-analogous ATP-synthase. The structural and functional properties of this and other archaebacterial ATPases are compared to each other and with respect to evolutionary relations.

Hysteretic behavior of an ATPase from the archaebacterium, Halobacterium saccharovorum

The membrane-bound detergent-activated ATPase from Halobacterium saccharovorum was purified at a physiological salt concentration (4 M NaCl) in the presence of nonionic detergents. The preparation contains putative subunits of 110, 71, 31, 22, and 14 kDa. The enzyme activity required high salt concentration but was not dependent on any one specific monovalent cation or any anion. The hydrolysis of ATP was nonlinear with time; the data are consistent with a kinetic model where the enzyme is irreversibly converted from an initial into a final stable form during the first few minutes of the reaction. The model thus contains a rate constant (k) for the transition and hydrolytic rates, v1 and v2, for the two forms of the enzyme. We found that this hysteretic behavior was influenced differently by various conditions and inhibitors. The constant k was smaller with Mn2+ than with Mg2+ as the divalent cation, showed negative temperature dependence, and a distinct pH optimum between 7.5 and 8.5. Thiols decreased k, but nitrate, a specific inhibitor of archaebacterial ATPases, increased it. ADP showed competitive inhibition against both the initial and the final form of the enzyme. Nitrate reversibly inhibited only the latter and in a manner dependent on whether Mn2+ or Mg2+ was used. The kinetic data suggest that all agents tested, with effects on the hydrolytic activity, seem to act at or near the catalytic site of the enzyme.

Molecular cloning of the beta-subunit of a possible non-F0F1 type ATP synthase from the acidothermophilic archaebacterium, Sulfolobus acidocaldarius.

The gene which encodes the beta subunit of the novel membrane-associated ATPase has been identified and characterized. The beta subunit, which is most likely the soluble part of the non-F0F1 type H+-ATPase, was obtained from the archaebacterium, Sulfolobus acidocaldarius. In terms of its location, it follows just after the gene for its alpha subunit. It is comprised of 1398 nucleotides, corresponding to a protein of 465 amino acids, and the consensus sequence in the nucleotide binding proteins is poorly conserved. Together with previously described results, the distant homology of the S. acidocaldarius ATPase alpha and beta subunits when compared to those of F0F1-ATPases indicates that this archaebacterial ATPase belongs to an ion-translocating ATPase family uniquely different than F0F1-ATPases even if S. acidocaldarius ATPase and F0F1-ATPases have been derived from a common ancestral ATPase.

The membrane-associated ATPase from Sulfolobus acidocaldarius is distantly related to F1-ATPase as assessed from the primary structure of its alpha-subunit.

Isolation of novel membrane-associated ATPases, presumably soluble parts of the H+-ATPases, from archaebacteria has been recently reported, and their properties were found to be significantly different from the usual F1-ATPase. In order to assess the relationship of the archaebacterial ATPases to the F1-ATPases and other known ATPases, the amino acid sequence of the alpha subunit of the ATPase from Sulfolobus acidocaldarius, an acidothermophilic archaebacterium, was compared with the sequences of other ATPases. The gene encoding its alpha subunit was cloned from the genomic library of S. acidocaldarius, and the nucleotide sequence was determined. The 591-amino acid sequence deduced from the nucleotide sequence contains a small number of short stretches that shows sequence similarity to the alpha and beta subunits of F1-ATPase. However, the overall similarity is too weak to consider it to be a typical member of the F1-ATPase family when the highly conserved sequences of the F1-ATPase subunits among various organisms are taken into account. Moreover, most of these stretches overlap the consensus sequences that are commonly found in some nucleotide-binding proteins. There is no significant sequence similarity to the ion-translocating ATPases, which form phosphorylated intermediates, such as animal Na+,K+-ATPases. Thus, the S. acidocaldarius ATPase and probably other archaebacterial ATPases also appear to belong to a new group of ion-translocating ATPases that has only a distant relationship to F1-ATPase.

The halobacterial H +-translocating ATP synthase relates to the eukaryotic anion-sensitive H +-ATPase

The H +-translocating ATP synthase of Halobacterium halobium ( Y. Mukohata and M. Yoshida (1987) J. Biochem. 102, 797–802 ) includes a catalytic moiety of 320 kDa which is isolated as an azide-insensitive ATPase ( T. Nanba and Y. Mukohata (1987) J. Biochem. 102, 591–598 ). The polyclonal antibody against this archaebacterial ATPase cross-reacts with the anion-sensitive H +-ATPase of red beet, Beta vulgaris, tonoplast as well as with another archaebacterial ATPase from Sulfolobus acidocaldarius. The affinity is much higher than to F 1−ATPase from spinach chloroplasts or to Ca 2+-ATPase from sarcoplasmic reticulum of rabbit skeletal muscle.