LIPID COMPOSITION AND SYNTHESIS IN THE PLEUROPNEUMONIA-LIKE ORGANISM 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.

DEFINED MEDIUM FOR MYCOPLASMA LAIDLAWII

Tourtellotte, Mark E. (University of Connecticut, Storrs), Harold J. Morowitz, and Phil Kasimer. Defined medium for Mycoplasma laidlawii. J. Bacteriol. 88:11-15. 1964.-A defined medium for the pleuropneumonia-like organism Mycoplasma laidlawii B is described in which absolute requirements for coenzyme A and longchain fatty acids were demonstrated. This organism did not require cholesterol or macromolecules of high molecular weight, but did show a growth requirement for peptides. Optimal growth in the basal medium was obtained in the presence of two purified peptides from crystalline ribonuclease, one of which has the amino acid sequence threonine - threonine - glutamine - alanine - asparagine-lysine, and the other lysine-glutamic acid-threonine-alanine-alanine-alanine-lysine. Continuous, but suboptimal, growth was obtained with the single ribonuclease peptide: lysine-glutamic acid-threonine-alanine-alanine-alanine-lysine.

COMPARATIVE BIOSYNTHESIS OF MEVALONIC ACID BY MYCOPLASMA

Smith, Paul F. (University of South Dakota, Vermillion), and C. V. Henrikson. Comparative biosynthesis of mevalonic acid by Mycoplasma. J. Bacteriol. 89:146-153. 1965.-Three representative Mycoplasma, M. laidlawii strain B, M. gallisepticum strain J, and M. hominis strain 07, were examined for the presence or absence of enzymes associated with the biosynthetic pathway to mevalonic acid. M. laidlawii served as a control, because it synthesizes carotenoids from acetate. M. laidlawii was shown to contain a specific acetokinase and phosphotransacetylase for the synthesis of acetyl coenzyme A, and a beta-ketothiolase and coenzyme A transferase for the synthesis of acetoacetyl coenzyme A. M. gallisepticum contained a specific acetokinase, phosphotransacetylase, and possibly an aceto coenzyme A kinase forming acetyl coenzyme A; it also contained a beta-ketothiolase, a coenzyme A transferase, and a coenzyme A transphorase forming acetoacetyl coenzyme A directly or indirectly. The beta-ketothiolase of M. gallisepticum was not affected by iodoacetamide, in contrast to the other two strains. M. laidlawii exhibited beta-hydroxy-beta-methylglutaryl coenzyme A condensing enzyme, and M. hominis did not. This activity of M. gallisepticum was masked by thiolase activity. M. laidlawii and M. gallisepticum contained a nicotinamide adenine dinucleotide phosphate-linked beta-hydroxy-beta-methylglutaryl coenzyme A reductase, and M. hominis did not. C(14)-labeled acetate was incorporated into mevalonic acid only by M. laidlawii and M. gallisepticum. The lack of beta-hydroxy-beta-methylglutaryl coenzyme A condensing enzyme and reductase activities in M. hominis explains its growth requirement for sterol. The enzymatic block in M. gallisepticum must occur after mevalonic acid in the biosynthetic pathway to terpenoids.

Comparative inhibition of bacterial and microsomal 3-ketodihydrosphingosine synthetases by L-cycloserine and other inhibitors

Eleven compounds were examined for their capacity to inhibit the first enzyme of the sphingolipid pathway, 3-ketodihydrosphingosine synthetase. Of these, L-cycloserine was the most potent, affecting both bacterial and brain microsomal enzymes to a significant degree at 0.04 mM. D- and L-cycloserine irreversibly inactivated the enzyme, indicating a suicide substrate mode of action. L-Cycloserine was a more potent inhibitor of the growth of Bacteroides levii than was D-cycloserine, indicating that inhibition of sphingolipid synthesis could be a factor in the growth inhibition.

Analysis of membrane fractions from Mycoplasma gallisepticum

Membrane fractions have been isolated from Mycoplasma gallisepticum following a procedure derived from that described by Maniloff, J. and Quinlan, D.C. (J. Bacteriol. (1974) 120, 495-501). A light fraction F1 was obtained which contained structures resembling the bleb-infrableb apparatus characteristic of M. gallisepticum. It was enriched in DNA and had an electrophoretic profile different from that of unfractionated membranes. Cholesterol-to-phospholipid ratios higher than two and elevated values of the ratio of saturated to unsaturated fatty acids were other characteristics of this fraction. The two other fractions isolated (FII and FIV) also differed from intact membranes by their cholesterol and phospholipid content as well as by their saturation ratios. The membrane fluidity of FII and FIV, estimated by fluorescence polarization, was similar to that of unfractionated membranes while a slight but significant difference was recorded for the light fraction. Possible relationships between the lateral heterogeneity of the M. gallisepticum membrane and the obtainment of fractions are discussed.

Control of membrane lipids in Mycoplasma gallisepticum: effect on lipid order

Adaptation of Mycoplasma gallisepticum, a sterol-requiring Mycoplasma sp., to growth in a serum-free medium supplemented with cholesterol in decreasing concentrations and with various saturated or unsaturated fatty acids enabled us to control both the cholesterol levels and the membrane fatty acid composition. An estimate of the membrane physical state from fluorescence polarization of 1,6-diphenyl-1,3,5-hexatriene indicated that the membrane lipids of native M. gallisepticum were highly ordered. Elongation of the saturated fatty acid chains from 14 to 18 carbon atoms caused only a small increase in the membrane lipid ordering, whereas the introduction of a cis double bond reduced it significantly. Lipid-phase transitions were observed in low-cholesterol-adapted organisms, whose membrane lipids were still highly ordered at the growth temperature.

Mycoplasma growth factors in bovine serum fraction

Mycoplasma growth factors in bovine serum fraction were separated by Sephadex G150 column chromatography and density ultracentrifugation. The major growth factor of bovine serum fraction eluted from the Sephadex column in the void volume. Its growth-supporting activity was greatly enhanced by the presence of bovine serum albumin in the mycoplasma culture media. Other investigators had previously identified the major growth factor in serum as an alpha-lipoprotein. Although density ultracentrifugation revealed the presence of traces of a high-density lipoprotein in bovine serum fraction, another, less dense component, isolated by ultracentrifugation (component 3) and containing cholesterol, cholesteryl esters, free fatty acids, triglycerides, and protein, but no lipoprotein, exhibited considerably more growth-supporting activity than did the high-density lipoprotein, thus indicating that at least two mycoplasma species do not require intact serum lipoprotein for growth. Both the high-density lipoprotein and component 3 exhibited maximum activity only in the presence of bovine serum albumin. A chloroform extract containing component 3 lipids combined with bovine serum albumin to form an effective, partially defined, less complex substitute for serum in mycoplasma culture media.

Identification of the amide-linked fatty acids of Acholeplasma axanthum S743 as D(-)3-hydroxyhexadecanoate and its homologues

The amide-linked fatty acids of the sphingolipids of Acholeplasma axanthum S743 are predominantly hydroxy acids. These acids were shown by gas-liquid chromatography, mass spectrometry, and polarimetry to be the d(-)3-hydroxy fatty acids. The predominant component of the mixture was 3-hydroxyhexadecanoate (beta-hydroxypalmitate, hydroxy [h] 16:0) followed by h 20Delta (Delta = unsaturated), h14:0, h12:0, and h18Delta in decreasing order of concentration. The fatty acid profile indicates that these beta-hydroxy acids possibly arise from elongation of the fatty acids supplied in the growth medium.

Lipids of a sterol-nonrequiring Mycoplasma

The lipids of the sterol nonrequiring Mycoplasma strain S743 were found to include both ester glycerophosphatides (phosphatidylglycerol, acylphosphatidylglycerol, and diphosphatidylglycerol) and ceramide glycerophosphate compounds containing N-hydroxyacyl groups. The major phosphosphingolipid was tentatively identified as a hydroxyceramidephosphorylglycerol containing an O-acyl group. These compounds became labeled during growth in the presence of (32)P-orthophosphate, (14)C-glycerol, or (14)C-palmitate. The lipid fraction also contained free long-chain base. (14)C-palmitate was converted to labeled sphinganine. The long-chain base composition of the lipids was modified by growing the organisms in media containing different fatty acids, which were converted to bases containing two more C atoms per molecule. Ninety per cent of the long-chain base from cells grown in medium supplemented with elaidate consisted of monounsaturated C(20) base.

Lipids of Bacteroides melaninogenicus

The lipids of Bacteroides melaninogenicus were readily extractable with chloroform-methanol. Three per cent of the fatty acids were not extractable. The neutral lipids contained 4% of the extractable fatty acids, the stench characteristic of these organisms, and 0.5 mumole of vitamin K(2) isoprenologues K(2)-35, K(2)-40, and K(2)-45 per g (dry weight). This is one-fifth to one-tenth of the vitamin K(2) level found in other bacteria. Ninety-six per cent of the extractable fatty acids were associated with the phospholipids (60 mumoles of lipid phosphate/g, dry weight), which consisted of the diacyl lipids phosphatidic acid, phosphatidyl serine, and phosphatidyl ethanolamine (with phosphatidyl glycerol and cardiolipin in one strain). The unusual phosphosphingolipids ceramide phosphorylethanolamine, ceramide phosphorylglycerol, and ceramide phosphorylglycerol phosphate accounted for 50 to 70% of the lipid phosphate. In protoheme-requiring strains, the protoheme concentration in the growth medium regulated the growth rate and the amount of enzymatically reducible cytochrome c. There were no gross changes in the lipid composition in cells containing different levels of enzymatically reducible cytochrome c.

Synthesis of saturated long chain fatty acids from sodium acetate-1-C14 by Mycoplasma

Three strains of Mycoplasma, M. laidlawii A and B, and Mycoplasma sp. A60549, were grown in broth containing sodium acetate-1-C(14). The methyl esters of the phospholipid fatty acids of harvested radioactive cells were prepared and identified by comparison of their mobilities to known radioactive fatty acid methyl esters by use of a modified reversed-phase partition-thin layer chromatographic technique. No radioactive methyl oleate or methyl linoleate was detected. Compounds migrating as radioactive methyl myristate, stearate, palmitate, and, with less certainty, laurate and octanoate were detected. The qualitative findings for all three organisms appeared similar. M. laidlawii B synthesized a radioactive substance, presumably a saturated fatty acid detected as the methyl ester derivative, which migrated in a position intermediate to methyl myristate-1-C(14) and methyl palmitate-1-C(14). This work indicates that M. laidlawii A and B and Mycoplasma sp. A60549 are capable, in a complex medium containing fatty acids, of synthesizing saturated but not unsaturated fatty acids entirely or in part from acetate.

Influence of lipid components of Mycoplasma laidlawii membranes on osmotic fragility of cells

Razin, S. (University of Connecticut, Storrs), M. E. Tourtellotte, R. N. McElhaney, and J. D. Pollack. Influence of lipid components of Mycoplasma laidlawii membranes on osmotic fragility of cells. J. Bacteriol. 91:609-616. 1966.-Lipid composition of Mycoplasma laidlawii membranes could be significantly changed by variations in the growth medium. The effect of these changes on the osmotic fragility of the cells was studied. Cholesterol, incorporated into the membrane from the growth medium, had no significant effect on osmotic fragility. Carotenoids, synthesized by the cells from acetate, were likewise without effect. Unsaturated long-chain fatty acids increased markedly the resistance of M. laidlawii to osmotic lysis and promoted growth. The fatty acids of the growth medium were incorporated mainly into membrane phospholipids. The ratio between saturated and unsaturated fatty acids in membrane lipids depended on that of the growth medium.