Membrane lipid biosynthesis in Acholeplasma laidlawii B: de novo biosynthesis of saturated fatty acids by growing cells

Draft Genome Sequence of Acholeplasma laidlawii, a Common Contaminant of Cell Cultures

Mollicutes are important cell culture contaminants which may eventually affect the results of biological assays or affect their interpretation. Acholeplasma laidlawii is one of the most frequent contaminants of cell cultures. Here, we report the complete genome sequence of A. laidlawii strain MDBK/IPV, recovered from Madin-Darby bovine kidney (MDBK) cells.

Survival of free-living Acholeplasma in aerated pig manure slurry revealed by (13)C-labeled bacterial biomass probing

Many studies have been performed on microbial community succession and/or predominant taxa during the composting process; however, the ecophysiological roles of microorganisms are not well understood because microbial community structures are highly diverse and dynamic. Bacteria are the most important contributors to the organic-waste decomposition process, while decayed bacterial cells can serve as readily digested substrates for other microbial populations. In this study, we investigated the active bacterial species responsible for the assimilation of dead bacterial cells and their components in aerated pig manure slurry by using ¹³C-labeled bacterial biomass probing. After 3 days of forced aeration, ¹³C-labeled and unlabeled dead Escherichia coli cell suspensions were added to the slurry. The suspensions contained ¹³C-labeled and unlabeled bacterial cell components, possibly including the cell wall and membrane, as well as intracellular materials. RNA extracted from each slurry sample 2 h after addition of E. coli suspension was density-resolved by isopycnic centrifugation and analyzed by terminal restriction fragment length polymorphism, followed by cloning and sequencing of bacterial 16S rRNA genes. In the heavy isotopically labeled RNA fraction, the predominant ¹³C-assimilating population was identified as belonging to the genus Acholeplasma, which was not detected in control heavy RNA. Acholeplasma spp. have limited biosynthetic capabilities and possess a wide variety of transporters, resulting in their metabolic dependence on external carbon and energy sources. The prevalence of Acholeplasma spp. was further confirmed in aerated pig manure slurry from four different pig farms by pyrosequencing of 16S rRNA genes; their relative abundance was ∼4.4%. Free-living Acholeplasma spp. had a competitive advantage for utilizing dead bacterial cells and their components more rapidly relative to other microbial populations, thus allowing the survival and prevalence of Acholeplasma spp. in pig manure slurry.

Analysis of the complete genomes of Acholeplasma brassicae, A. palmae and A. laidlawii and their comparison to the obligate parasites from 'Candidatus Phytoplasma'

Analysis of the completely determined genomes of the plant-derived Acholeplasma brassicae strain O502 and A. palmae strain J233 revealed that the circular chromosomes are 1,877,792 and 1,554,229 bp in size, have a G + C content of 36 and 29%, and encode 1,690 and 1,439 proteins, respectively. Comparative analysis of these sequences and previously published genomes of A. laidlawii strain PG-8, 'Candidatus Phytoplasma asteris' strains, 'Ca. P. australiense' and 'Ca. P. mali' show a limited shared basic genetic repertoire. The acholeplasma genomes are characterized by a low number of rearrangements, duplication and integration events. Exceptions are the unusual duplication of rRNA operons in A. brassicae and an independently introduced second gene for a single-stranded binding protein in both genera. In contrast to phytoplasmas, the acholeplasma genomes differ by encoding the cell division protein FtsZ, a wide variety of ABC transporters, the F0F1 ATP synthase, the Rnf-complex, SecG of the Sec-dependent secretion system, a richly equipped repertoire for carbohydrate metabolism, fatty acid, isoprenoid and partial amino acid metabolism. Conserved metabolic proteins encoded in phytoplasma genomes such as the malate dehydrogenase SfcA, several transporters and proteins involved in host-interaction, and virulence-associated effectors were not predicted for the acholeplasmas.

Complete genome and proteome of Acholeplasma laidlawii

We present the complete genome sequence and proteogenomic map for Acholeplasma laidlawii PG-8A (class Mollicutes, order Acholeplasmatales, family Acholeplasmataceae). The genome of A. laidlawii is represented by a single 1,496,992-bp circular chromosome with an average G+C content of 31 mol%. This is the longest genome among the Mollicutes with a known nucleotide sequence. It contains genes of polymerase type I, SOS response, and signal transduction systems, as well as RNA regulatory elements, riboswitches, and T boxes. This demonstrates a significant capability for the regulation of gene expression and mutagenic response to stress. Acholeplasma laidlawii and phytoplasmas are the only Mollicutes known to use the universal genetic code, in which UGA is a stop codon. Within the Mollicutes group, only the sterol-nonrequiring Acholeplasma has the capacity to synthesize saturated fatty acids de novo. Proteomic data were used in the primary annotation of the genome, validating expression of many predicted proteins. We also detected posttranslational modifications of A. laidlawii proteins: phosphorylation and acylation. Seventy-four candidate phosphorylated proteins were found: 16 candidates are proteins unique to A. laidlawii, and 11 of them are surface-anchored or integral membrane proteins, which implies the presence of active signaling pathways. Among 20 acylated proteins, 14 contained palmitic chains, and six contained stearic chains. No residue of linoleic or oleic acid was observed. Acylated proteins were components of mainly sugar and inorganic ion transport systems and were surface-anchored proteins with unknown functions.

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.

Chromatographic resolution of partially perdeuterated diglucosyldiacylglycerols from Acholeplasma laidlawii

Diglucosyldiacylglycerol from Acholeplasma laidlawii was isolated by adsorption chromatography and subsequently subjected to molecular species analysis by reversed-phase high-performance liquid chromatography. Twenty-three molecular species were resolved. The bacterium was grown in a medium supplemented with a mixture of oleic acid and perdeuterated palmitic acid, and incorporation of perdeuterated acyl moieties occurred in several molecular species. Short and odd-numbered acyl chains were found in combinations with palmitic acid, perdeuterated palmitic acid and oleic acid. Also, molecular species differing only by perdeuterated and protonated acyl chain content were resolved chromatographically. Separation between diglucosyldiacylglycerol and digalactosyldiacylglycerol isolated from a plant source was achieved with adsorption chromatography. The polarity of diglucosyldiacylglycerol as compared to digalactosyldiacylglycerol is discussed.

Identification and analysis of the genes coding for the putative pyruvate dehydrogenase enzyme complex in Acholeplasma laidlawii

A monospecific antibody recognizing two membrane proteins in Acholeplasma laidlawii identified a plasmid clone from a genomic library. The nucleotide sequence of the 4.6-kbp insert contained four sequential genes coding for proteins of 39 kDa (E1 alpha, N terminus not cloned), 36 kDa (E1 beta), 57 kDa (E2), and 36 kDa (E3; C terminus not cloned). The N termini of the cloned E2, E1 beta, and native A. laidlawii E2 proteins were verified by amino acid sequencing. Computer-aided searches showed that the translated DNA sequences were homologous to the four subenzymes of the pyruvate dehydrogenase complexes from gram-positive bacteria and humans. The plasmid-encoded 57-kDa (E2) protein was recognized by antibodies against the E2 subenzymes of the pyruvate and oxoglutarate dehydrogenase complexes from Bacillus subtilis. A substantial fraction of the E2 protein as well as part of the pyruvate dehydrogenase enzymatic activity was associated with the cytoplasmic membrane in A. laidlawii. In vivo complementation with three different Escherichia coli pyruvate dehydrogenase-defective mutants showed that the four plasmid-encoded proteins were able to restore pyruvate dehydrogenase enzyme activity in E. coli. Since A. laidlawii lacks oxoglutarate dehydrogenase and most likely branched-chain dehydrogenase enzyme complex activities, these results strongly suggest that the sequenced genes code for the pyruvate dehydrogenase complex.

Iso- and anteiso-fatty acids in bacteria: biosynthesis, function, and taxonomic significance

Branched-chain fatty acids of the iso and anteiso series occur in many bacteria as the major acyl constituents of membrane lipids. In addition, omega-cyclohexyl and omega-cycloheptyl fatty acids are present in several bacterial species. These two types of fatty acids are synthesized by the repeated condensation of malonyl coenzyme A with one of the branched-chain and cyclic primers by the same enzyme system. The pathway of de novo branched-chain fatty acid synthesis differs only in initial steps of synthesis from that of the common straight-chain fatty acid (palmitic acid) present in most organisms. The cell membranes composed largely of iso-, anteiso-, and omega-alicyclic acids support growth of bacteria, which inhabit normal as well as extreme environments. The occurrence of these types of fatty acids as major cellular fatty acids is an important criterion used to aid identification and classification of bacteria.

Iso- and anteiso-fatty acids in bacteria: biosynthesis, function, and taxonomic significance

Branched-chain fatty acids of the iso and anteiso series occur in many bacteria as the major acyl constituents of membrane lipids. In addition, omega-cyclohexyl and omega-cycloheptyl fatty acids are present in several bacterial species. These two types of fatty acids are synthesized by the repeated condensation of malonyl coenzyme A with one of the branched-chain and cyclic primers by the same enzyme system. The pathway of de novo branched-chain fatty acid synthesis differs only in initial steps of synthesis from that of the common straight-chain fatty acid (palmitic acid) present in most organisms. The cell membranes composed largely of iso-, anteiso-, and omega-alicyclic acids support growth of bacteria, which inhabit normal as well as extreme environments. The occurrence of these types of fatty acids as major cellular fatty acids is an important criterion used to aid identification and classification of bacteria.

Thermotropic properties of bilayers containing branched-chain phospholipids. Calorimetric, Raman, and 31P NMR studies

Diisopalmitoylphosphatidylcholine (DIPPC), -phosphatidylethanolamine (DIPPE), and -phosphatidylglycerol (DIPPG) have been synthesized, and the structures of aqueous dispersions of these lipids have been examined by high-sensitivity differential scanning calorimetry, 31P nuclear magnetic resonance, and Raman spectroscopy. DIPPC at temperatures below 23.1 degrees C readily forms a gel phase with the acyl chains packed in an orthorhombic subcell. Above this temperature, this "orthorhombic" phase converts directly to the liquid-crystalline phase. The phase diagram for the system DIPPC--dipalmitoyl-PC (DIPPC-DPPC) shows that the gel phases formed by either lipid can accommodate only limited amounts of the other species and suggests that the low-temperature orthorhombic phase of DIPPC is distinct in its structure from the "subgel" phase of DPPC. DIPPE forms a well-ordered gel phase only in samples that are equilibrated at low temperatures for long times (approximately days to weeks) or at very high lipid concentrations. However, this lipid readily forms an "intermediate" phase with a very disordered acyl chain packing upon cooling from the liquid-crystalline state. Mixtures of DIPPE with DIPPG exhibit similar thermotropic properties. Hydrated DIPPE appears to be stable in the lamellar phase up to at least 98 degrees C, while di-cis- and di-trans-9-hexadecenoyl-PE convert to the hexagonal II phase at 43.5 and 92.5 degrees C, respectively. We discuss the relevance of these results to the structure and stability of bacterial membranes containing branched-chain acyl lipids.

19F nuclear magnetic resonance studies of lipid fatty acyl chain order and dynamics in Acholeplasma laidlawii B membranes. Orientational order in the presence of a series of positional isomers of cis-octadecenoic acid

The 19F nuclear magnetic resonance (NMR) spectra of membranes of Acholeplasma laidlawii B enriched with one of a series of positional isomers of cis-octadecenoic acid plus small amounts of one of a number of isomers of monofluoropalmitic acid were interpreted in terms of an orientational order parameter (Smol). The variation of Smol with the position of the fluorine label in the liquid-crystalline state yielded an "order profile" with characteristics similar to those obtained via 2H NMR and which was relatively invariant regardless of the site of cis unsaturation. In the gel state, values of Smol approached the theoretical maximum, and the order profiles in the presence of different isomeric cis-octadecenoic acids displayed distinct dissimilarities. When the cis double bond was located proximal to the methyl terminus of the fatty acyl chain, a gradient of order across the bilayer was still evident in the gel state. When the cis double bond was located near the carbonyl head group, values of Smol were approximately equal at all chain positions. These observations were interpreted as indicating that in the gel state the stringency of packing restrictions is still subject to variation across the width of the bilayer. Relative overall orientational order among all isomers examined (specifically, 18:1c delta 4, delta 5, delta 6, delta 7, delta 8, delta 9, delta 10, delta 11, delta 12, delta 13, delta 14, and delta 15) varied directly as a function of proximity to the lipid gel to liquid-crystalline phase transition (Tm) (determined via differential scanning calorimetry) when compared at a constant temperature.(ABSTRACT TRUNCATED AT 250 WORDS)

Carotenoids acts as reinforcers of the Acholeplasma laidlawii lipid bilayer

Acholeplasma laidlawii cells grown with oleic acid produced much more colored carotenoids than did cells grown with elaidic acid. The amount of carotenoids was decreased 80 to 90% by growing the cells with 0.05 M propionate, resulting in a marked increase in the mobility of both 5-doxylstearate and 12-doxylstearate incorporated into the membranes. The fatty acid composition of the propionate-grown cells differed from that of cells grown without propionate by containing odd-numbered rather than even-numbered saturated fatty acids, but the ratios of saturated to unsaturated fatty acids were the same. To determine whether the carotenoids are the cause for the restricted mobility in the membranes, the carotenoids were selectively removed from A. laidlawii membranes by incubating the membranes with phosphatidylcholine vesicles. The carotenoid-depleted membranes showed an increase in the mobility of the hydrocarbon chains of the spin-labeled fatty acids. Furthermore, the incorporation of carotenoids into artificial membrane vesicles restricted the mobility of the hydrocarbon chain. Our results support the notion that the carotenoids in A. laidlawii act as a rigid insert reinforcing the membrane bilayer.

Differential biosynthesis of polyunsaturated fatty acids by Tetrahymena supplemented with ergosterol

Tetrahymena grown with foreign sterols such as ergosterol incorporate them into cellular membranes at the expense of the native compound, tetrahymanol. It is shown that cells grown with ergosterol have a lessened capacity to produce the polyunsaturated linoleic and gamma-linolenic acids from [14C]oleic acid. However, the same cells have normal capacities to introduce double bonds at C-6 into linoleate, alpha-linolenate, or cis-vaccenate. Thus, a presumed 12-desaturase is inhibited in the presence of ergosterol, while desaturation at C-6 is unaffected.

Analysis of corynomycolic acids and other fatty acids produced by Corynebacterium lepus grown on kerosene

The saponifiable carboxylic acids of the extracellular product of Corynebacterium lepus grown on kerosene have been isolated and characterized. About 25% of these acids were a mixture of simple, saturated fatty acids ranging from C13 to C24 and including both even and odd homologues. The distribution of these acids was bimodal, with maxima at C15 and C21. The other 75% of the acids was a mixture of corynomycolic acids [R1--CH(OH)--CH(R2)--COOH] ranging from C28 to C43. The R1 alkyl fragments varied from C16 to C25, and R2 fragments varied from C6 to C14. Both even and odd corynomycolic acid homologues were observed, and the distribution had a single pronounced maximum at C32 and C33. Bacterial utilization of the carboxylic oxidation products of the kerosene substrate is suggested to account for the wide distribution in chain length of these saturated fatty acids and for the observation of both even and odd homologues.

The mycoplasmas

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Membrane lipid biosynthesis in Acholeplasma laidlawii b: elongation of medium- and long-chain exogenous fatty acids in growing cells

The chain elongation of a wide variety of exogenous fatty acids and the subsequent incorporation of the chain elongation products into the total membrane lipids of Acholeplasma laidlawii B were systematically studied. Within each chemical class of fatty acids examined, the extent of chain elongation increased with increases in chain length, reached a maximum value, and then declined with further increases in chain length. Depending on chemical structure, exogenous fatty acids containing less than 6 to 9 carbon atoms or more than 15 to 18 carbon atoms were not substrates for the chain elongation system. The substrate specificity of this fatty acid elongation system was strikingly broad, and straight-chain, methyl isobranched, and methyl anteisobranched saturated fatty acids, as well as cis- and trans-monounsaturated, cis-cyclopropane, and cis-polyunsaturated fatty acids, underwent chain elongation in vivo. The extent of chain elongation and the average chain length of the primary elongation products correlated well with the physical properties (melting temperatures) of the exogenous fatty acid substrates. The specificity of fatty acid chain elongation in A. laidlawii B maintained the fluidity and physical state of the membrane lipids within a rather wide but definitely limited range. The fatty acid chain elongation system of this organism could be markedly influenced by the presence of a second exogenous fatty acid that was not itself a substrate for the chain elongation system but was incorporated directly into the membrane lipids. The presence of a relatively low-melting exogenous fatty acid increased both the extent of chain elongation and the average chain length of the elongation products generated, whereas the presence of a relatively high-melting fatty acid had the opposite effect. The extent of chain elongation and nature of the elongation products formed were not, however, dependent on the fluidity and physical state of the membrane lipids per se. The second exogenous fatty acid appeared instead to exert its characteristic effect by competing with the chain elongation substrate and elongation products for the stereospecific acylation of positions 1 and 2 of sn-glycerol-3-phosphate. The similar effects of alterations in environmental temperature, cholesterol content, and exposure to the antibiotic cerulenin on the fatty acid chain elongation and de novo biosynthetic activities suggested that the chain elongation system of this organism may be a component of the de novo biosynthetic system.

Membrane lipid biosynthesis in Acholeplasma laidlawii B: incorporation of exogenous fatty acids into membrane glyco- and phospholipids by growing cells

The extent of incorporation of a wide variety of exogenous saturated, unsaturated, branched-chain, and cyclopropane fatty acids into the membrane lipids of Acholeplasma laidlawii B was systematically studied. Within each fatty acid class the extent of incorporation generally increased markedly with increasing chain length, reached a maximum, and then declined progressively but less sharply with further increases above that chain length giving maximal direct incorporation. Certain shorter-chain members of each fatty acid class underwent complete or partial conversion to longer-chain homologues before utilization for complex lipid biosynthesis. The degree and extent of chain elongation and direct incorporation and the characteristic dependence of each of these processes on fatty acid chain length and structure correlated well with the physical properties (melting temperatures) of the exogenous fatty acids. The in vivo specificity of the enzyme systems responsible for the incorporation of exogenous fatty acids was such that the fluidity and physical state of the membrane lipids were maintained within a definite, albeit a relatively wide, range. We also observed that the neutral glycolipids typically have similar fatty acid compositions, which are somewhat different from those of the major phosphatides, which also exhibit similar fatty acid spectra. The phosphorylated glycolipid glycerophosphoryldiglucosyl diglyceride, however, always maintained a unique fatty acid composition quite different from that of the diglucosyl diglyceride from which it is presumably derived. These characteristic differences in fatty acid composition appear to function to minimize differences in phase transition temperatures, thus producing a more physicochemically homogeneous mixture of membrane lipids than would result from a nonspecific incorporation of fatty acids.