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

The role of Rnf in ion gradient formation in Desulfovibrio alaskensis

Rnf is a membrane protein complex that has been shown to be important in energy conservation. Here, Desulfovibrio alaskensis G20 and Rnf mutants of G20 were grown with different electron donor and acceptor combinations to determine the importance of Rnf in energy conservation and the type of ion gradient generated. The addition of the protonophore TCS strongly inhibited lactate-sulfate dependent growth whereas the sodium ionophore ETH2120 had no effect, indicating a role for the proton gradient during growth. Mutants in rnfA and rnfD were more sensitive to the protonophore at 5 µM than the parental strain, suggesting the importance of Rnf in the generation of a proton gradient. The electrical potential (ΔΨ), ΔpH and proton motive force were lower in the rnfA mutant than in the parental strain of D.alaskensis G20. These results provide evidence that the Rnf complex in D. alaskensis functions as a primary proton pump whose activity is important for growth.

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 Rnf complex of Clostridium ljungdahlii is a proton-translocating ferredoxin:NAD+ oxidoreductase essential for autotrophic growth

It has been predicted that the Rnf complex of Clostridium ljungdahlii is a proton-translocating ferredoxin:NAD⁺ oxidoreductase which contributes to ATP synthesis by an H⁺-translocating ATPase under both autotrophic and heterotrophic growth conditions. The recent development of methods for genetic manipulation of C. ljungdahlii made it possible to evaluate the possible role of the Rnf complex in energy conservation. Disruption of the C. ljungdahlii rnf operon inhibited autotrophic growth. ATP synthesis, proton gradient, membrane potential, and proton motive force collapsed in the Rnf-deficient mutant with H₂ as the electron source and CO₂ as the electron acceptor. Heterotrophic growth was hindered in the absence of a functional Rnf complex, as ATP synthesis, proton gradient, and proton motive force were significantly reduced with fructose as the electron donor. Growth of the Rnf-deficient mutant was also inhibited when no source of fixed nitrogen was provided. These results demonstrate that the Rnf complex of C. ljungdahlii is responsible for translocation of protons across the membrane to elicit energy conservation during acetogenesis and is a multifunctional device also implicated in nitrogen fixation.

Mechanisms for energy conservation in the acetogen Clostridium ljungdahlii are of interest because of its potential value as a chassis for the production of biocommodities with novel electron donors such as carbon monoxide, syngas, and electrons derived from electrodes. Characterizing the components implicated in the chemiosmotic ATP synthesis during acetogenesis by C. ljungdahlii is a prerequisite for the development of highly productive strains. The Rnf complex has been considered the prime candidate to be the pump responsible for the formation of an ion gradient coupled with ATP synthesis in multiple acetogens. However, experimental evidence for a proton-pumping Rnf complex has been lacking. This study establishes the C. ljungdahlii Rnf complex as a proton-translocating ferredoxin:NAD⁺ oxidoreductase and demonstrates that C. ljungdahlii has the potential of becoming a model organism to study proton translocation, electron transport, and other functions of the Rnf complex in energy conservation or other processes.

Plasminogen binding and activation by Mycoplasma fermentans

The binding of plasminogen to Mycoplasma fermentans was studied by an immunoblot analysis and by a binding assay using iodine-labeled plasminogen. The binding of 125I-labeled plasminogen was inhibited by unlabeled plasminogen, lysine, and lysine analog epsilon-aminocaproic acid. Partial inhibition was obtained by a plasminogen fragment containing kringles 1 to 3 whereas almost no inhibition was observed with a fragment containing kringle 4. Scatchard analysis revealed a dual-phase interaction, one with a dissociation constant (kd) of 0.5 microM and the second with a kd of 7.5 microM. The estimated numbers of plasminogen molecules bound were calculated to be 110 and 790 per cell, respectively. Autoradiograms of ligand blots containing M. fermentans membrane proteins incubated with 125I-labeled plasminogen identified two plasminogen-binding proteins of about 32 and 55 kDa. The binding of plasminogen to M. fermentans enhances the activation of plasminogen to plasmin by the urokinase-type plasminogen activator (uPA), as monitored by measuring the breakdown of chromogenic substrate S-2251. Enhancement was more pronounced with the low-molecular-weight and the single-chain uPA variants, known to have low plasminogen activator activities. The binding of plasminogen also promotes the invasion of HeLa cells by M. fermentans. Invasion was more pronounced in the presence of uPA, suggesting that the ability of the organism to invade host cells stems not only from its potential to bind plasminogen but also from the activation of plasminogen to plasmin.

Sequence of subunit a of the Na(+)-translocating F1F0-ATPase of Acetobacterium woodii: proposal for residues involved in Na+ binding

Na+ transport through the F0 domain of Na(+)-F1F0-ATPases involves the combined action of subunits c and a but the residues involved in Na+ liganding in subunit a are unknown. As a first step towards the identification of these residues, we have cloned and sequenced the gene encoding subunit a of the Na(+)-F1F0-ATPase of Acetobacterium woodii. This is the second sequence available now for this subunit from Na(+)-F1F0-ATPases. A comparison of subunit a from Na(+)-F1F0-ATPases with those from H(+)-translocating enzymes unraveled structural similarity in a C-terminal segment including the ultimate and penultimate transmembrane helix. Seven residues are conserved in this region and, therefore, likely to be involved in Na+ liganding.

The cell membrane of Mycoplasma penetrans: lipid composition and phospholipase A1 activity

Analysis of Mycoplasma penetrans membrane lipids revealed that, in addition to large amounts of unesterified cholesterol, M. penetrans incorporated exogenous phospholipids, preferentially sphingomyelin, from the growth medium. The major phospholipids synthesized de novo by M. penetrans were phosphatidylglycerol (PG) and diphosphatidylglycerol (DPG). In vivo labeling of PG and DPG by growing the cells with radioactive palmitate or oleate, followed by snake venom phospholipase A2 treatment, enabled us to assess the positional distribution of fatty acids in these lipids. Saturated fatty acids were found preferentially in position 2 of the glycerol backbone, and not in position 1 as found elsewhere in nature, while unsaturated fatty acids prefer position 1. M. penetrans membranes contain phospholipase activity of the A1 type, removing a fatty acid from the sn-1 ester bond of phospholipids. The activity was neither stimulated by Ca2+ nor inhibited by EGTA and had a broad pH spectrum. The substrate specificity of the enzyme was investigated with various natural lipids and with a fluorescent analog of the phosphatidylcholine. The enzyme was equally active toward phosphatidylcholine and phosphatidylglycerol, but did not hydrolyze diphosphatidylglycerol. The enzyme did not act on triacylglycerol, diacylglycerol or cholesteryl ester, but low activity was detected toward monoacylglycerol. The enzyme was heat-sensitive and detergent-sensitive, and was almost completely inhibited by p-bromophenacylbromide (50 microM), but was not affected by SH reagents. This study is the first one reporting phospholipase A1 activity in Mollicutes. A possible role of this enzyme in forming lipid mediators upon the interaction of M. penetrans cells with eukaryotic cells is suggested.

The F- or V-type Na(+)-ATPase of the thermophilic bacterium Clostridium fervidus

Clostridium fervidus is a thermophilic, anaerobic bacterium which uses solely Na+ as a coupling ion for energy transduction. Important features of the primary Na+ pump (ATPase) that generates the sodium motive force are presented. The advantage of using a sodium rather than a proton motive force at high temperatures becomes apparent from the effect of temperature on H+ and Na+ permeation in liposomes.

The laws of cell energetics

Recent progress in membrane bioenergetics studies has resulted in the important discovery that Na+ can effectively substitute for H+ as the energy coupling ion. This means that living cells can possess three convertible energy currencies, i.e. ATP, protonic and sodium potentials. Analysis of interrelations of these components in various types of living cells allows bioenergetic laws of universal applicability to be inferred.

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.

Chemiosmotic systems in bioenergetics: H(+)-cycles and Na(+)-cycles

The development of membrane bioenergetic studies during the last 25 years has clearly demonstrated the validity of the Mitchellian chemiosmotic H+ cycle concept. The circulation of H+ ions was shown to couple respiration-dependent or light-dependent energy-releasing reactions to ATP formation and performance of other types of membrane-linked work in mitochondria, chloroplasts, some bacteria, tonoplasts, secretory granules and plant and fungal outer cell membranes. A concrete version of the direct chemiosmotic mechanism, in which H+ potential formation is a simple consequence of the chemistry of the energy-releasing reaction, is already proved for the photosynthetic reaction centre complexes. Recent progress in the studies on chemiosmotic systems has made it possible to extend the coupling-ion principle to an ion other than H+. It was found that, in certain bacteria, as well as in the outer membrane of the animal cell, Na+ effectively substitutes for H+ as the coupling ion (the chemiosmotic Na+ cycle). A precedent is set when the Na+ cycle appears to be the only mechanism of energy production in the bacterial cell. In the more typical case, however, the H+ and Na+ cycles coexist in one and the same membrane (bacteria) or in two different membranes of one and the same cell (animals). The sets of delta mu H+ and delta mu Na+ generators as well as delta mu H+ and delta mu Na+ consumers found in different types of biomembranes, are listed and 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.

Transmembrane diffusion channels in Mycoplasma gallisepticum induced by tetanolysin

The permeability properties of Mycoplasma gallisepticum cells treated with a purified preparation of tetanolysin were investigated by determining the initial swelling rates of cells suspended in an isoosmotic solution of electrolytes or nonelectrolytes. The swelling, initiated by the tetanolysin, depended on the tetanolysin concentration and was markedly affected by the molecular size of the various osmotic stabilizers utilized. Thus, the initial swelling rates in an isoosmotic solution of monosaccharides were much higher than those in isoosmotic solutions of di-, tri-, or tetrasaccharides. Cell swelling induced by tetanolysin was much lower with energy-depleted M. gallisepticum cells, with arsenate-treated cells, or when the membrane potential (delta psi) was collapsed by valinomycin (10 microM) plus KCl (100 mM). Swelling was not affected by the proton-conducting ionophore carbonyl cyanide-m-chlorophenylhydrazone (1 to 10 microM) or by nigericin (5 microM). These results support the concept that the damage induced by tetanolysin is due to the formation of water-filled pores within the membranes of energized M. gallisepticum cells. Such pores allow the diffusion of hydrophilic molecules into the cells and may vary in size, depending on the tetanolysin concentration utilized.