Characterization and solubilization of the membrane-bound ATPase of Mycoplasma gallisepticum

Semi-automated curation of metabolic models via flux balance analysis: a case study with Mycoplasma gallisepticum

Primarily used for metabolic engineering and synthetic biology, genome-scale metabolic modeling shows tremendous potential as a tool for fundamental research and curation of metabolism. Through a novel integration of flux balance analysis and genetic algorithms, a strategy to curate metabolic networks and facilitate identification of metabolic pathways that may not be directly inferable solely from genome annotation was developed. Specifically, metabolites involved in unknown reactions can be determined, and potentially erroneous pathways can be identified. The procedure developed allows for new fundamental insight into metabolism, as well as acting as a semi-automated curation methodology for genome-scale metabolic modeling. To validate the methodology, a genome-scale metabolic model for the bacterium Mycoplasma gallisepticum was created. Several reactions not predicted by the genome annotation were postulated and validated via the literature. The model predicted an average growth rate of 0.358±0.12, closely matching the experimentally determined growth rate of M. gallisepticum of 0.244±0.03. This work presents a powerful algorithm for facilitating the identification and curation of previously known and new metabolic pathways, as well as presenting the first genome-scale reconstruction of M. gallisepticum.

Flux balance analysis (FBA) is a powerful approach for genome-scale metabolic modeling. It provides metabolic engineers with a tool for manipulating, predicting, and optimizing metabolism for biotechnological and biomedical purposes. However, we posit that it can also be used as tool for fundamental research in understanding and curating metabolic networks. Specifically, by using a genetic algorithm integrated with FBA, we developed a curation approach to identify missing reactions, incomplete reactions, and erroneous reactions. Additionally, it was possible to take advantage of the ensemble information from the genetic algorithm to identify the most critical reactions for curation. We tested our strategy using Mycoplasma gallisepticum as our model organism. Using the genome annotation as the basis, the preliminary genome-scale metabolic model consisted of 446 metabolites involved in 380 reactions. Carrying out our analysis, we found over 80 incorrect reactions and 16 missing reactions. Based upon the guidance of the algorithm, we were able to curate and resolve all discrepancies. The model predicted an average bacterial growth rate of 0.358±0.12 h⁻¹ compared to the experimentally observed 0.244±0.03 h⁻¹. Thus, our approach facilitated the curation of a genome-scale metabolic network and generated a high quality metabolic model.

The comparative metabolism of the mollicutes (Mycoplasmas): the utility for taxonomic classification and the relationship of putative gene annotation and phylogeny to enzymatic function in the smallest free-living cells

Mollicutes or mycoplasmas are a class of wall-less bacteria descended from low G + C% Gram-positive bacteria. Some are exceedingly small, about 0.2 micron in diameter, and are examples of the smallest free-living cells known. Their genomes are equally small; the smallest in Mycoplasma genitalium is sequenced and is 0.58 mb with 475 ORFs, compared with 4.639 mb and 4288 ORFs for Escherichia coli. Because of their size and apparently limited metabolic potential, Mollicutes are models for describing the minimal metabolism necessary to sustain independent life. Mollicutes have no cytochromes or the TCA cycle except for malate dehydrogenase activity. Some uniquely require cholesterol for growth, some require urea and some are anaerobic. They fix CO2 in anaplerotic or replenishing reactions. Some require pyrophosphate not ATP as an energy source for reactions, including the rate-limiting step of glycolysis: 6-phosphofructokinase. They scavenge for nucleic acid precursors and apparently do not synthesize pyrimidines or purines de novo. Some genera uniquely lack dUTPase activity and some species also lack uracil-DNA glycosylase. The absence of the latter two reactions that limit the incorporation of uracil or remove it from DNA may be related to the marked mutability of the Mollicutes and their tachytelic or rapid evolution. Approximately 150 cytoplasmic activities have been identified in these organisms, 225 to 250 are presumed to be present. About 100 of the core reactions are graphically linked in a metabolic map, including glycolysis, pentose phosphate pathway, arginine dihydrolase pathway, transamination, and purine, pyrimidine, and lipid metabolism. Reaction sequences or loci of particular importance are also described: phosphofructokinases, NADH oxidase, thioredoxin complex, deoxyribose-5-phosphate aldolase, and lactate, malate, and glutamate dehydrogenases. Enzymatic activities of the Mollicutes are grouped according to metabolic similarities that are taxonomically discriminating. The arrangements attempt to follow phylogenetic relationships. The relationships of putative gene assignments and enzymatic function in My. genitalium, My. pneumoniae, and My. capricolum subsp. capricolum are specially analyzed. The data are arranged in four tables. One associates gene annotations with congruent reports of the enzymatic activity in these same Mollicutes, and hence confirms the annotations. Another associates putative annotations with reports of the enzyme activity but from different Mollicutes. A third identifies the discrepancies represented by those enzymatic activities found in Mollicutes with sequenced genomes but without any similarly annotated ORF. This suggests that the gene sequence is significantly different from those already deposited in the databanks and putatively annotated with the same function. Another comparison lists those enzymatic activities that are both undetected in Mollicutes and not associated with any ORF. Evidence is presented supporting the theory that there are relatively small gene sequences that code for functional centers of multiple enzymatic activity. This property is seemingly advantageous for an organism with a small genome and perhaps under some coding restraint. The data suggest that a concept of "remnant" or "useless genes" or "useless enzymes" should be considered when examining the relationship of gene annotation and enzymatic function. It also suggests that genes in addition to representing what cells are doing or what they may do, may also identify what they once might have done and may never do again.

Participation of a proton-translocating plasma membrane ATPase, acid phosphatase and alkaline phosphatase in ATP degradation by Aspergillus niger extracts

Extracts of A. niger could catalyze sequential hydrolysis of the three phosphate moieties of the ATP molecule optimally at pH 2 and at pH 8. At pH 2 the hydrolysis was effected by an ATPase followed by acid phosphatase while at pH 8 alkaline phosphatase was the only involved enzyme. Separation of these three phosphate-hydrolyzing enzymes was achieved by Sephadex G-100 column chromatography. The A. niger ATPase seems to have two unique features. First, it was easily solubilized in distilled water and second it had optimum activity at pH 2. The activity of this enzyme was not affected on addition of Na+, K+ or Ca2+ to the assay reaction mixture. It was neither inhibited by sodium azide nor by potassium nitrate but inhibited by orthovanadate, DES, DCCD, Mg2+ and Pi. The substrate concentration-activity relationship was of the hyperbolic type. The enzyme had high specificity for ATP, was inert with ADP and its activity with GTP represented about 6% only of that obtained with equimolar amount of ATP.

Biochemical and immunochemical characterization of a P-type ATPase from Leishmania donovani promastigote plasma membrane

An ATPase on the plasma membrane of Leishmania donovani has been characterized. An antiserum, generated against ATPase active bands from native gels, was specific for a 105 kDa protein in promastigotes. However, in plasma membrane preparations a 70 kDa protein is also recognized, suggesting proteolysis of the intact 105 kDa protein or the presence of a second similar ATPase. [gamma-32P]ATP phosphorylates two proteins (105 kDa and 70 kDa) in promastigotes and plasma membranes. Both proteins form a transient phosphorylated intermediate, characteristic of a P-type ATPase. Immunostaining of permeabilized parasites shows diffuse staining of the surface of promastigotes and amastigotes, which is consistent with a plasma membrane protein. The antiserum immunoprecipitates a 70 kDa [14C]DCCD binding protein from whole cells and plasma membranes of promastigotes. Furthermore, the antiserum immunoprecipitates a 105 kDa and 70 kDa protein which can be subsequently phosphorylated. These results indicate the presence of a 105 kDa P-type ATPase on the L. donovani plasma membrane which is similar to the mammalian and fungal cation pumps.

Nucleotide sequence, organization and characterization of the atp genes and the encoded subunits of Mycoplasma gallisepticum ATPase

The nucleotide sequence of a 7.8 kbp DNA fragment from the genome of Mycoplasma gallisepticum has been determined. The fragment contains a cluster of nine tightly linked genes coding for the subunits of the M. gallisepticum ATPase. The gene order is I (I-subunit), B (a-subunit), E (c-subunit), F (b-subunit), H (delta-subunit), A (alpha-subunit), G (gamma-subunit), D (beta-subunit) and C (epsilon-subunit). Two open reading frames were identified in the flanking regions; one (ORFU), preceding the I gene, encodes at least 110 amino acids and the other (ORFS), following the C gene, encodes at least 90 amino acids. The deduced amino acid sequences of the various subunits are presented and discussed with regard to the structure, function and differing sensitivity of the M. gallisepticum enzyme to dicyclohexylcarbodiimide and aurovertin. The alpha- and beta-subunits of the F1 portion are well conserved (51% and 65% identity with those of Escherichia coli), whereas the gamma-, delta- and epsilon-subunits, as well as the F0-subunits, show a low percentage identity. Nonetheless, the secondary structure of the F0-subunits show a high degree of similarity to the corresponding subunits of E. coli. Two very strong potential amphipathic alpha-helices are predicted in the delta-subunit and the N-terminus of the b-subunit contains two hydrophobic helical stretches. The possible roles of these structural properties in the close association of the F1 and F0 multisubunit complexes among mycoplasmas are discussed.

Evidence for the presence of two distinct membrane ATPases in Spiroplasma citri

Triton X-100 (TX-100) extraction of Spiroplasma citri plasma membrane solubilized two types of ATPase differing in their pH of maximum activity. The activity measured at pH 8·5 was inhibited by vanadate and the activity measured at pH 6·5 was not. The vanadate-sensitive ATPase had a relatively basic isoelectric point (8·65) and therefore could be separated from the vanadate-insensitive ATPase using chromatofocusing. Elution of the TX-100 membrane extract in a pH gradient from 9 to 6 generated two peaks of ATPase activity: one in the acidic range, composed of an F0F1-type ATPase, and one in the basic range, corresponding to the vanadate-sensitive activity. Electrophoretic analysis of proteins from the latter peak revealed one major polypeptide of 37 kDa. This peptide was shown to correspond to spot A37 in a two-dimensional protein map of S. citri. Using the gene for the kdp-operon of Escherichia coli as a probe in heterologous hybridization, sequences were detected in the genomic DNA of S. citri, suggesting that a gene coding for an enzyme related to this P-type ATPase is present in the S. citri genome. We therefore postulate the presense of two distinct kinds of ATPase in S. citri: one of the F-type which is resistant to vanadate inhibition, and one, probably of the P-type, which is vanadate-sensitive.

Role of Na+ cycle in cell volume regulation of Mycoplasma gallisepticum

The mechanism for the extrusion of Na+ from Mycoplasma gallisepticum cells was examined. Na+ efflux from cells was studied by diluting 22Na+-loaded cells into an isoosmotic NaCl solution and measuring the residual 22Na+ in the cells. Uphill 22Na+ efflux was found to be glucose dependent and linear with time over a 60-s period and showed almost the same rate in the pH range of 6.5 to 8.0. 22Na+ efflux was markedly inhibited by dicyclohexylcarbodiimide (DCCD, 10 microM), but not by the proton-conducting ionophores SF6847 (0.5 microM) or carbonyl cyanide m-chlorophenylhydrazone (CCCP, 10 microM) over the entire pH range tested. An ammonium diffusion potential and a pH gradient were created by diluting intact cells or sealed membrane vesicles of M. gallisepticum loaded with NH4Cl into a choline chloride solution. The imposed H+ gradient (inside acid) was not affected by the addition of either NaCl or KCl to the medium. Dissipation of the proton motive force by CCCP had no effect on the growth of M. gallisepticum in the pH range of 7.2 to 7.8 in an Na+-rich medium. Additionally, energized M. gallisepticum cells were stable in an isoosmotic NaCl solution, even in the presence of proton conductors, whereas nonenergized cells tended to swell and lyse. These results show that in M. gallisepticum Na+ movement was neither driven nor inhibited by the collapse of the electrochemical gradient of H+, suggesting that in this organism Na+ is extruded by an electrogenic primary Na+ pump rather than by an Na+-H+ exchange system energized by the proton motive force.

Volume regulation in Mycoplasma gallisepticum: evidence that Na+ is extruded via a primary Na+ pump

The primary extrusion of Na+ from Mycoplasma gallisepticum cells was demonstrated by showing that when Na+-loaded cells were incubated with both glucose (10 mM) and the uncoupler SF6847 (0.4 microM), rapid acidification of the cell interior occurred, resulting in the quenching of acridine orange fluorescence. No acidification was obtained with Na+-depleted cells or with cells loaded with either KCl, RbCl, LiCl, or CsCl. Acidification was inhibited by dicyclohexylcarbodiimide (50 microM) and diethylstilbesterol (50 microM), but not by vanadate (100 microM). By collapsing delta chi with tetraphenylphosphonium (200 microM) or KCl (25 mM), the fluorescence was dequenched. The results are consistent with a delta chi-driven uncoupler-dependent proton gradient generated by an electrogenic ion pump specific for Na+. The ATPase activity of M. gallisepticum membranes was found to be Mg2+ dependent over the entire pH range tested (5.5 to 9.5). Na+ (greater than 10 mM) caused a threefold increase in the ATPase activity at pH 8.5, but had only a small effect at pH 5.5. In an Na+-free medium, the enzyme exhibited a pH optimum of 7.0 to 7.5, with a specific activity of 30 +/- 5 mumol of phosphate released per h per mg of membrane protein. In the presence of Na+, the optimum pH was between 8.5 and 9.0, with a specific activity of 52 +/- 6 mumol. The Na+-stimulated ATPase activity at pH 8.5 was much more stable to prolonged storage than the Na+-independent activity. Further evidence that two distinct ATPases exist was obtained by showing that M. gallisepticum membranes possess a 52-kilodalton (kDa) protein that reacts with antibodies raised against the beta-subunit of Escherichia coli ATPase as well as a 68-kDa protein that reacts with the anti-yeast plasma membrane ATPases antibodies. It is postulated that the Na+ -stimulated ATPases functions as the electrogenic Na+ pump.

Sodium ion transport decarboxylases and other aspects of sodium ion cycling in bacteria

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Cell volume regulation in Mycoplasma gallisepticum

Mycoplasma gallisepticum cells incubated in 250 mM NaCl solutions in the absence of glucose showed a progressive fall in intracellular ATP concentration over a period of 2 to 3 h. When the ATP level fell below 40 microM the cell began to swell and become progressively permeable to [14C]inulin and leak intracellular protein and nucleotides. The addition of nondiffusable substances such as MgSO4 or disaccharides prevented swelling, suggesting that NaCl (and water) entry was due to Gibbs-Donnan forces. The addition of glucose after the initiation of cell swelling increased intracellular ATP, induced cell shrinkage, and prevented the release of intracellular components. The ATPase inhibitor dicyclohexylcarbodiimide, which collapsed the chemical and electrical components of the proton motive force, caused rapid cell swelling in the presence of glucose (and high intracellular ATP levels). Extracellular impermeable solutes such as MgSO4 and disaccharides prevented swelling of dicyclohexylcarbodiimide-treated cells incubated in NaCl. It was postulated that Na+ that diffused into the cell was extruded by an electrogenic Na+-H+ exchange (antiport) energized by the proton motive force established by the dicyclohexylcarbodiimide-sensitive H+-ATPase.

Sodium and proton transport in Mycoplasma gallisepticum

When washed cells of Mycoplasma gallisepticum were incubated at 37 degrees C in 250 mM 22NaCl, the intracellular Na+ increased, and the K+ decreased. The addition of glucose to these Na+-loaded cells caused Na+ efflux and K+ uptake (both ions moving against concentration gradients). This effect of glucose was blocked by the ATPase inhibitor dicyclohexylcarbodiimide, which prevents the generation of a proton motive force in these cells. In additional experiments, Na+ extrusion was studied by diluting the 22Na+-loaded cells into Na+-free media and following the loss of 22Na+ from the cells. Glucose stimulated 22Na+ extrusion in such cells by a dicyclohexylcarbodiimide-sensitive mechanism. Proton movement was studied by measuring the pH gradient across the cell membrane with the 9-aminoacridine fluorescence technique. Glucose addition to cells preincubated with cations other than Na+ resulted in cell alkalinization (which was prevented by dicyclohexylcarbodiimide). This observation is consistent with the operation of a proton-extruding ATPase. When glucose was added to Na+-loaded cells and diluted into Na+-free media, intracellular acidification was observed, followed several minutes later by a dicyclohexylcarbodiimide-sensitive alkalinization process. The initial acidification was probably due to the operation of an Na+-H+ antiport, since Na+ exit was occurring simultaneously with H+ entry. When Na+-loaded cells were diluted into Na+-containing media, the subsequent addition of glucose resulted in a weak acidification, presumably due to H+ entry in exchange for Na+ (driven by the ATPase) plus a continuous passive influx of Na+. All of the data presented are consistent with the combined operation of an ATP-driven proton pump and an Na+ -H+ exchange reaction.