Replacement of the aliphatic chains of Clostridium acetobutylicum by exogenous fatty acids: regulation of phospholipid and glycolipid composition

Lipid diversity in clostridia

Studies of the lipidomes of twenty-one species of clostridia have revealed considerable diversity. Even among those species now defined as Clostridium sensu stricto, which are related to Clostridium butyricum, the type species, lipid analysis has shown that a number of distinct clades have characteristic polar lipids. All species of Clostridium sensu stricto have phosphatidylethanolamine, phosphatidylglycerol and cardiolipin which are present as all acyl or alk-1'-enyl acyl (plasmalogen) species. In addition, almost every clade has specialized polar lipids. For example, the group closely related to Clostridium beijerinckii and several other solventogenic species has glycerol acetals of plasmenylethanolamine, which protects the membrane bilayer arrangement when the lipids are highly unsaturated or in the presence of solvents. The group related to Clostridium novyi has aminoacyl-phosphatidylglycerol, which protects these pathogens from cationic antimicrobial peptides (CAMPs) of innate immunity. Clostridium botulinum species, which fall into several groups, align with these clades, and have the same specific lipids. This review will present the current state of knowledge on clostridial lipids.

A division of labor between two biotin protein ligase homologs

Group I biotin protein ligases (BPLs) catalyze the covalent attachment of biotin to its cognate acceptor proteins. In contrast, Group II BPLs have an additional N-terminal DNA-binding domain and function not only in biotinylation but also in transcriptional regulation of genes of biotin biosynthesis and transport. Most bacteria contain only a single biotin protein ligase, whereas Clostridium acetobutylicum contains two biotin protein ligase homologs: BplA and BirA'. Sequence alignments showed that BplA is a typical group I BPL, whereas BirA' lacked the C-terminal domain conserved throughout extant BPL proteins. This raised the questions of why two BPL homologs are needed and why the apparently defective BirA' has been retained. We have used in vivo and in vitro assays to show that BplA is a functional BPL whereas BirA' acts as a biotin sensor involved in transcriptional regulation of biotin transport. We also successfully converted BirA' into a functional biotin protein ligase with regulatory activity by fusing it to the C-terminal domain from BplA. Finally, we provide evidence that BplA and BirA' interact in vivo.

Lipidomic Analysis of Clostridium cadaveris and Clostridium fallax

The lipidomes of Clostridium fallax and Clostridium cadaveris were studied using thin-layer chromatography (TLC) and normal phase liquid chromatography/mass spectrometry (NPLC/MS). Both species contain diradylglycerol (DRG), monohexosyldiradylglycerol (MHDRG), monohexosyl monoacylglycerol (MHMAG), phosphatidylglycerol (PtdGro), and phosphatidylethanolamine (PtdEtn). DRG, MHDRG, PtdEtn, and PtdGro are present in both diacyl and alk-1-enyl acyl (plasmalogen) forms. Both species contain cardiolipin (Ptd2 Gro), which is present in tetraacyl, monoalkenyl-triacyl, and dialkenyl-diacyl forms. Both species contain small amounts of phosphatidylcholine (PtdCho). The presence of octadecadienoic (18:2) acyl chains in some PtdCho species indicates that they arise from the medium because no 18:2 is seen in the other lipids and clostridia generally lack the capacity to synthesize polyunsaturated fatty acids. The major lipidomic differences between these two species are that C. fallax contains a glycerolacetal of plasmenylethanolamine while C. cadaveris contains an ethanolamine-phosphate-modified diacylglycerol. The significance of these lipid compositions is discussed.

Major roles for minor bacterial lipids identified by mass spectrometry

Mass spectrometry of lipids, especially those isolated from bacteria, has ballooned over the past two decades, affirming in the process the complexity of the lipidome. With this has come the identification of new and interesting lipid structures. Here is an overview of several novel lipids, from both Gram-negative and Gram-positive bacteria with roles in health and disease, whose structural identification was facilitated using mass spectrometry. This article is part of a Special Issue entitled: Bacterial Lipids edited by Russell E. Bishop.

The cellular lipids of Romboutsia

We have examined the lipids of three isolates, Romboutsia lituseburensis, Romboutsia ilealis, and Romboutsia sp. strain FRIFI, of the newly described genus Romboutsia by two-dimensional thin-layer chromatography (2D-TLC) and by liquid chromatography/mass spectrometry (LC/MS). We have found three phospholipids, phosphatidylglycerol (PG), cardiolipin and phosphatidic acid in all three species. A fourth phospholipid, lysyl-PG, was found in R. lituseburensis and strain FRIFI. Polyprenyl-phosphates were identified in the lipid extracts of all three species. Three glycolipids, mono-, di- and tri-hexosyldiacylglycerol, were common to all three species. An additional glycolipid, tetrahexosyl-diacylglycerol was identified in strain FRIFI. Acylated trihexosyldiacylglycerol and acyl-tetrahexosydiacylglycerol were also found in R. ilealis and strain FRIFI. Remarkably, no alk-1-enyl ether lipids (plasmalogens) were present in Romboutsia as distinct from bacteria of the related genus Clostridium in which these ether lipids are common. We have compared the lipidome of Romboutsia with that recently described for Clostridium difficile, which has plasmalogens, no lysyl-PG, and no tetrahexosyl-diacylglycerol. According to 16S rRNA gene sequencing, Romboutsia spp. and C. difficile are closely related (>95% sequence identity).

A curated C. difficile strain 630 metabolic network: prediction of essential targets and inhibitors

BACKGROUND

Clostridium difficile is the leading cause of hospital-borne infections occurring when the natural intestinal flora is depleted following antibiotic treatment. Current treatments for Clostridium difficile infections present high relapse rates and new hyper-virulent and multi-resistant strains are emerging, making the study of this nosocomial pathogen necessary to find novel therapeutic targets.

RESULTS

We present iMLTC806cdf, an extensively curated reconstructed metabolic network for the C. difficile pathogenic strain 630. iMLTC806cdf contains 806 genes, 703 metabolites and 769 metabolic, 117 exchange and 145 transport reactions. iMLTC806cdf is the most complete and accurate metabolic reconstruction of a gram-positive anaerobic bacteria to date. We validate the model with simulated growth assays in different media and carbon sources and use it to predict essential genes. We obtain 89.2% accuracy in the prediction of gene essentiality when compared to experimental data for B. subtilis homologs (the closest organism for which such data exists). We predict the existence of 76 essential genes and 39 essential gene pairs, a number of which are unique to C. difficile and have non-existing or predicted non-essential human homologs. For 29 of these potential therapeutic targets, we find 125 inhibitors of homologous proteins including approved drugs with the potential for drug repositioning, that when validated experimentally could serve as starting points in the development of new antibiotics.

CONCLUSIONS

We created a highly curated metabolic network model of C. difficile strain 630 and used it to predict essential genes as potential new therapeutic targets in the fight against Clostridium difficile infections.

An ethanolamine-phosphate modified glycolipid in Clostridium acetobutylicum that responds to membrane stress

Two phosphorus-containing glycolipids have previously been observed in Clostridium acetobutylicum. We had shown that the concentration of one of them increases in response to increased unsaturation of the membrane lipid hydrocarbon chains, suggesting a potential role in the regulation of lipid polymorphism in this organism. Mass spectrometry shows that these glycolipids are ethanolamine phosphate (Etn-P)-containing derivatives of a mono- and di-glycosyldiradylglycerol. The content of both diglycosyldiradylglycerol and the Etn-P-monoglycosyldiradylglycerol, which increases upon increased unsaturation of the membrane, also increases upon addition of octanol to the medium. Thus, it appears that the Etn-P-monoglycosyldiradylglycerol along with the diglycosyldiradylglycerol may serve to stabilize the membrane bilayer during membrane stress caused by the presence of the solvents produced during fermentation.

Lipid diversity among botulinum neurotoxin-producing clostridia

Clostridium botulinum has been classified into four groupings (groups I to IV) based on physiological characteristics and 16S rRNA sequencing. We have examined the lipid compositions of 11 representative strains of C. botulinum and a strain of Clostridium sporogenes by 2D-TLC and by MS. All strains contained phosphatidylglycerol (PG), cardiolipin (CL) and phosphatidylethanolamine (PE) in both the all-acyl and the alk-1'-enyl (plasmalogen) forms. Five strains in proteolytic group I, which are related to C. sporogenes, contained varying amounts of an ethanolamine-phosphate derivative of N-acetylglucosaminyl-diradylglycerol, which is also present in C. sporogenes. Three strains in group II, which are related to Clostridium butyricum, Clostridium beijerinckii and Clostridium acetobutylicum, contained lipids characteristic of these saccharolytic species: a glycerol acetal and a PG acetal of the plasmalogen form of PE. Two group III strains, which are related to Clostridium novyi, contained amino-acyl derivatives of PG, which are also found in C. novyi. A strain in group IV had PE, PG and CL, but none of the distinguishing lipids. This work shows that the lipidome of C. botulinum is consistent with its classification by other methods.

Genome-scale model for Clostridium acetobutylicum: Part I. Metabolic network resolution and analysis

A genome-scale metabolic network reconstruction for Clostridium acetobutylicum (ATCC 824) was carried out using a new semi-automated reverse engineering algorithm. The network consists of 422 intracellular metabolites involved in 552 reactions and includes 80 membrane transport reactions. The metabolic network illustrates the reliance of clostridia on the urea cycle, intracellular L-glutamate solute pools, and the acetylornithine transaminase for amino acid biosynthesis from the 2-oxoglutarate precursor. The semi-automated reverse engineering algorithm identified discrepancies in reaction network databases that are major obstacles for fully automated network-building algorithms. The proposed semi-automated approach allowed for the conservation of unique clostridial metabolic pathways, such as an incomplete TCA cycle. A thermodynamic analysis was used to determine the physiological conditions under which proposed pathways (e.g., reverse partial TCA cycle and reverse arginine biosynthesis pathway) are feasible. The reconstructed metabolic network was used to create a genome-scale model that correctly characterized the butyrate kinase knock-out and the asolventogenic M5 pSOL1 megaplasmid degenerate strains. Systematic gene knock-out simulations were performed to identify a set of genes encoding clostridial enzymes essential for growth in silico.

Integrative feedback and robustness in a lipid biosynthetic network

The homeostatic control of membrane lipid composition appears to be of central importance for cell functioning and survival. However, while lipid biosynthetic reaction networks have been mapped in detail, the underlying control architecture which underpins these networks remains elusive. A key problem in determining the control architectures of lipid biosynthetic pathways, and the mechanisms through which control is achieved, is that the compositional complexity of lipid membranes makes it difficult to determine which membrane parameter is under homeostatic control. Recently, we reported that membrane stored elastic energy provides a physical feedback signal which modulates the activity in vitro of CTP:phosphocholine cytidylyltransferase (CCT), an extrinsic membrane enzyme which catalyses a key step in the synthesis of phosphatidylcholine lipids in the Kennedy pathway (Kennedy 1953 J. Am. Chem. Soc. 75, 249-250). We postulate that stored elastic energy may be the main property of membranes that is under homeostatic control. Here we report the results of simulations based on this postulate, which reveal a possible control architecture for lipid biosynthesis networks in vivo.

New aspects on membrane lipid regulation in Acholeplasma laidlawii A and phase equilibria of monoacyldiglucosyldiacylglycerol

A new membrane lipid, monoacyldiglucosyldiacylglycerol (MADGlcDAG), was recently discovered in Acholeplasma laidlawii strain A-EF22, demanding a new study of the biosynthetic regulation, and the phase behavior, of the glucolipids in this organism. The only liquid-crystalline phase formed by MADGlcDAG is a reversed hexagonal phase. A. laidlawii A-EF22 synthesizes four lipids that have the ability to induce the formation of reversed nonlamellar phases: MADGlcDAG, monoglucosyldiacylglycerol (MGlcDAG), monoacylmonoglucosyldiacylglycerol (MAMGlcDAG), and diacylglycerol (DAG). A Cn value of approximately 16 seems to be a critical value for the fractions of these lipids in the membrane: the fractions of MADGlcDAG and MGlcDAG are largest when the Cn values are lower than 16, while the fractions of MAMGlcDAG and DAG are largest when the Cn values are higher than 16. The fraction of nonlamellar-forming lipids was 55 mol% when the Cn value was 14.8 and the degree of unsaturation was 33 mol%. This fraction was reduced to 7 mol% when the Cn value and the degree of unsaturation were increased to 17.8 and 92 mol%, respectively, i.e., at conditions that markedly favor the formation of reversed nonlamellar phases. These observations convincingly show that a balance between lamellar- and nonlamellar-forming lipids is maintained in the membrane and strongly support the validity of the lipid regulation model proposed by us. From earlier biochemical data, obtained with short acyl chains, that were difficult to reconcile with our regulation model, it could be predicted that a lipid ought to be synthesized that assists MGlcDAG to maintain the nonlamellar-forming properties with the short chains. It is shown in the present work that this lipid is MADGlcDAG and that the regulation of the balance between lamellar- and nonlamellar-forming lipids is even more complex and sophisticated in A. laidlawii A-EF22 than previously proposed.

Isolation and characterization of new phosphatidylglycerol acetals of plasmalogens. A family of ether lipids in clostridia

A new phosphatidylglycerol acetal of cardiolipin plasmalogen has been isolated from Clostridium innocuum. The structure was derived from the results of quantitative group analyses, the identification of the products of acid hydrolysis, alkaline methanolysis, hydrolysis by a cardiolipin-specific phospholipase D and by one- and two-dimensional proton NMR. Two other minor ether phospholipids: the lyso form of the phosphatidylglycerol acetal of cardiolipin plasmalogen, and the phosphatidylglycerol acetal of plasmenylglycerol have been identified in C. innocuum lipid extracts.

Regulation and phase equilibria of membrane lipids from Bacillus megaterium and Acholeplasma laidlawii strain A containing methyl-branched acyl chains

Phosphatidylethanolamine (PE) was isolated from Bacillus megaterium grown at 20 and 55 degrees C (PE-20 and PE-55). Iso and anteiso methyl-branched, saturated acyl chains are predominant in B. megaterium, and the value of the molar ratio of iso/anteiso acyl chains is more than 20-fold higher in PE-55 than in PE-20. Moreover, about 21 mol% of the acyl chains of PE-20 are monounsaturated. The phase equilibria differ between the two PE preparations: (1) PE-20 is more prone to form reversed nonlamellar phases than PE-55; (2) PE-20 forms both reversed cubic (I2) and reversed hexagonal (H(II)) phases while PE-55 forms only an HII phase; and (3) the lamellar liquid-crystalline (L alpha) phase of PE-20 takes up about 70% more water than the L alpha phase of PE-55. These differences can be explained by the differences in the acyl chain composition. When the growth temperature is raised, PE molecules with a reduced tendency to form nonlamellar phases are probably synthesized by B. megaterium in order to counteract the bilayer destabilizing effect of the temperature. The regulation of the acyl chain composition is not needed in order to regulate the temperature for the transition between gel/crystalline and L alpha phases of the membrane lipids. Acholeplasma laidlawii strain A-EF22 was grown at 37 degrees C on 15-(1,1,1(-2) H3)methylhexadecanoic acid, 14-(1,1,1(-2)H3)methylhexadecanoic acid or 13-(1,1,1(-2)H3)methylhexadecanoic acid, and these acids constituted 84-89 mol% of the acyl chains in the membrane lipids. The molar ratio between the two dominating lipids, monoglucosyldiacylglycerol (MGLcDAG) and diglucosyldiacylglycerol (DGlcDAG), decreased, and the molar fraction of the anionic lipids increased, when the methyl branch was moved from position 15 to position 13. Concomitantly, the order of the methyl branch increased in cells as well as in total lipid extracts. The phase equilibria of total lipid extracts (neutral lipids removed) were studied with 20 wt % of water, and HII and I2 phases were formed above 63-67 degrees C. These results indicate that the regulation of the polar head-group composition compensates for the difference in acyl chain packing introduced into the bilayer by the three branched-chain fatty acids. The regulation of the polar head-group composition of the A. laidlawii lipids cannot regulate the temperature for the transition between gel/crystalline and L alpha phases of the lipids, i.e. the transition to fluid acyl chains.(ABSTRACT TRUNCATED AT 400 WORDS)

Similar regulatory mechanisms despite differences in membrane lipid composition in Acholeplasma laidlawii strains A-EF22 and B-PG9. A multivariate data analysis

Mycoplasmas are small, cell wall-deficient bacteria. The metabolic regulation of the lipid composition in the membrane of the species Acholeplasma laidlawii, strains A-EF22 and B-JU, is governed mainly by the balance between the potential formation of lamellar and nonlamellar phase structures. However, the regulatory features have not been consistently observed in the B-PG9 strain. A comparison has been performed between the membrane lipid composition for strains A-EF22 and B-PG9, simultaneously changing eight experimental conditions known to affect the regulation and packing properties of the A-EF22 lipids. Multiple regression and partial least-square discriminant analyses of many variables showed: (i) quantitative differences in membrane lipid and protein composition, and in membrane protein molecular masses of the two strains; (ii) different molar fractions of the major polar lipids monoglucosyldiacylglycerol (nonlamellar) and diglucosyldiacylglycerol (lamellar), which were caused by differences in lipid acyl chain length and unsaturation inherent in the strains and by the type of growth medium used; and (iii) similar regulatory mechanisms for changes in the lipid composition under most conditions, responding to the experimentally varied bilayer and nonbilayer properties of the lipid matrix. These regulatory principles are probably valid in other bacteria as well.

Packing of a triacylglucolipid from the membrane of Acholeplasma laidlawii strain A at the air/water interface

Pressure-area curves were generated at 22 degrees C and 40 degrees C for three glucolipids isolated from Acholeplasma laidlawii strain A-EF22. The glucolipids are 1,2-diacyl-3-O-(alpha-D-glucopyranosyl)-sn-glycerol (MGlcDAG), 1,2-diacyl-3-O-[alpha-D-glucopyranosyl-(1-->2)-O-alpha-D- glucopyranosyl]-sn-glycerol (DGlcDAG), and 1,2-diacyl-3-O-[3-O-acyl-(alpha-D-glucopyranosyl)]-sn- glycerol (MAMGlc-DAG). The curves for MGlcDAG and DGlcDAG are characteristic for monolayers in a liquid phase at both temperatures. MGlcDAG has a smaller molecular area at all surface pressures compared to DGlcDAG. At 22 degrees C MAMGlcDAG shows a phase transition at 13 mN/m. However, at 40 degrees C the pressure-area curve for this lipid is characteristic for a monolayer in a liquid state. Mixed MAMGlcDAG-DGlcDAG and MGlcDAG-DGlcDAG monolayers showed no significant deviation from the additivity rule at 40 degrees C. The area per acyl chain is nearly the same for MAMGlcDAG and MGlcDAG. Our study supports our previous results that aqueous dispersions of these lipids form non-lamellar, reversed aggregates.