Improved method of determining muramic acid from environmental samples

Muramic acid is an amino sugar that forms part of the peptidoglycan in prokaryotic cell walls. Since muramic acid is found only in prokaryotes it has been used as a measure of bacterial and cyanophyte biomass. Successful application of sensitive capillary gas‐liquid chromatographic (GLC) analysis required neutralization of the acid‐hydrolysate of a biomass sample followed by centrifugation to remove humic acids. After a further fractionation on a cation exchange column followed by derivatization and GLC analysis, recoveries of 98 ±9.5 (X± S.D.) % of authentic muramic acid from estuarine sediments with sensitivities of 10^‐13 mol were achieved. The structure of the GLC derivative was established by GLC infrared analysis and GLC mass spectrometry. The improvements in reproduci‐bility and sensitivity have allowed detection of ¹³C enrichments in muramic acid from the detrital microbiota incubated with relabeled precursors.     

Muramic Acid Measurements for Bacterial Investigations in Marine Environments by High-Pressure Liquid Chromatography

Muramic acid, a constituent of procaryotic cell walls, was assayed by high-pressure liquid chromatography in samples from several marine environments (water column, surface microlayer, and sediment) and a bacterial culture. It is used as a microbial biomass indicator. The method gave a good separation of muramic acid from interfering compounds with satisfactory reproducibility. A pseudomonad culture had a muramic acid content of 4.7 × 10⁻¹⁰ to 5.3 × 10⁻¹⁰ μg per cell during growth. In natural water samples, highly significant relationships were found between muramic acid concentrations and bacterial numbers for populations of 10⁸ to 10¹¹ cells per liter. The muramic acid content in natural marine water decreased from 5.3 × 10⁻¹⁰ to 1.6 × 10⁻¹⁰ μg per cell with increasing depth. In coastal sediments exposed to sewage pollution, concentrations of muramic acid, ATP, organic carbon, and total amino acids displayed a parallel decrease with increasing distance from the sewage outlet. Advantages of muramic acid measurement by high-pressure liquid chromatography are its high sensitivity and reduction of preparation steps, allowing a short time analysis.     

Chemical Studies on the Cell Walls of Leptospira biflexa Strain Urawa and Treponema pallidum Strain Reiter

The preparation and chemical poperties of the cell walls of Leptospira biflexa Urawa and Treponema pallidum Reiter are described. Both cell walls are composed mainly of polysaccharides and peptidoglycans. The data of chemical analysis indicate that the cell wall of L. biflexa Urawa contains rhamnose, arabinose, xylose, mannose, galactose, glucose and unidentified sugars as neutral sugars, and alanine, glutamic acid, α,ε-diaminopimelic acid, glucosamine and muramic acid as major amino acids and amino sugars. As major chemical constituents of the cell wall of T. pallidum Reiter, rhamnose, arabinose, xylose, mannose, galactose, glucose, alanine, glutamic acid, ornithine, glycine, glucosamine and muramic acid have been detected. The chemical properties of protein and polysaccharide fractions prepared from the cells of T. pallidum Reiter were also partially examined.     

Lack of peptidoglycan in the cell walls of Methanosarcina barkeri

Neither muramic acid and glucosamine nor d-glutamic acid or other amino acids typical of peptidoglycan were found in cell walls of two strains of Methanosarcina barkeri. The main components are galactosamine, neutral sugars and uronic acids. Therefore, the structural component of the cell wall most likely consists of an acid heteropolysaccharide, resembling that of Halococcus morrhuae. It is, however, not sulfated.     

The Cell Wall of Rickettsia mooseri I. Morphology and Chemical Composition

Cell walls prepared by mechanically disrupting intact Rickettsia mooseri (R. typhi) were examined in an electron microscope and analyzed chemically. Electron micrographs of metal-shadowed and negatively stained rickettsial cell walls revealed no significant differences, except for smaller size, from bacterial cell walls prepared in a similar manner. The chemical composition was complex, and resembled that of gram-negative bacterial cell walls more closely than that of gram-positive bacterial cell walls. R. mooseri cell walls contained the sugars, glucose, galactose, and glucuronic acid, the amino sugars, glucosamine, and muramic acid, and at least 15 amino acids. Diaminopimelic acid, a compound hitherto found only in bacteria and blue-green algae, was demonstrated in rickettsiae for the first time. Teichoic acids were not detected. The compounds identified accounted for about 70% of the dry weight of the cell walls.     

Cell Wall Composition of Hyphomicrobium Species

Chemical analysis of cell walls obtained from Hyphomicrobium B-522 and from a morphologically and nutritionally distinct organism, Hyphomicrobium neptunium (ATCC 15444), showed that the organisms have a similar cell wall composition, which is typical of gram-negative bacteria. The walls of both strains contained many amino acids, including the characteristic mucopeptide components diaminopimelic acid and muramic acid. Isolation of the mucopeptide by use of sodium dodecyl sulfate was successful only with cell walls of H. neptunium, thus revealing a difference between the walls of the two strains. The mucopeptide preparation contained glucosamine, muramic acid, alanine, glutamic acid, diaminopimelic acid, and glycine in molar ratios of 1.05:1.21:1.84:1.0:1.04:0.31, respectively. The concentration of glycine was sufficiently high to suggest that it is a mucopeptide component rather than an impurity.     

Binding of Polysaccharide to Peptidoglycan in Cell Wall of Streptomyces roseochromogenes

The polysaccharide-peptidoglycan complex, which was prepared with lysozyme from Streptomyces roseochromogenes IAM53 cell walls, was hydrolyzed with lytic enzyme of Flavo-bacterium to separate polysaccharide. The enzymatically prepared polysaccharide (100 mg) contained 500 μmoles of hexoses, 40 μmoles of hexosamines and 31 μmoles of phosphate. Hexoses consisted of mannose and galactose in a molar ratio of 5 to 1. Hexosamines consisted of equimolar glucosamine and muramic acid, a half of which was identified as muramic acid 6-phosphate. The reducing end of the polysaccharide was muramic acid. The polysaccharide extracted with trichloroacetic acid contained no muramic acid-phosphate. So the polysaccharide moiety of S. roseochromogenes cell walls must be linked covalently to 6-position of muramic acid in peptidoglycan through phosphate,     

Cell wall constituents of Leuconostoc citrovorum and Leuconostoc mesenteroides

The cell wall constituents of Leuconostoc citrovorum 8082, L. mesenteroides 10830a, and L. mesenteroides 11449 have been ascertained. All three strains contained glycerol. Glucose and rhamnose were the major reducing sugar constituents. Alanine, glutamic acid, lysine, glucosamine, and muramic acid were the principal amino acids and amino sugars in all three strains. In addition, strain 10830a contained l-serine as a major cell wall component. Quantitative amino acid analyses indicate that glutamic acid, lysine, glucosamine, muramic acid, and serine may be present in the cell walls in equimolar amounts and that alanine is present in three to four times these quantities. The similarities and differences between the cell wall constituents of the leuconostocs and those of the lactobacilli and streptococci are discussed.     

Equivalence of microbial biomass measures based on membrane lipid and cell wall components,adenosine triphosphate,and direct counts in subsurface aquifer sediments

An uncontaminated subsurface aquifer sediment contains a sparse microbial community consisting primarily of coccobacillary bacteria of relatively uniform size which can be counted directly with appropriate staining. The morphological simplicity and the relatively decreased cell numbers, when compared with surface soils and sediments, make the subsurface an ideal natural community with which to compare the utility of chemical measures of microbial biomass to direct microscopic counts. The membrane phospholipids (estimated as the polar lipid fatty acids, the lipid phosphate, and phosopholipid glycerol phosphate), lipopolysaccharide lipid A (estimated as the LPS hydroxy fatty acids), cell walls (estimated as the muramic acid), and adenosine triphosphate all give essentially identical estimates of cell numbers and dry weight as the direct counts, using conversion factors determined on subsurface microorganism monocultures. Assays of microbial cell components are thus validated by comparison with the classical direct count in at least one soil/sediment.     

Studies on Cell Wall of Alkalophilic Bacillus

Cell walls of alkalophilic Bacillus No. C-125 and No. A-59 which grew in different pH conditions were prepared and analyzed. In the walls from cells grown at pH 10.3 (pH 10.3-cell wall) and the walls from cells grown at pH 7.5 (pH 7.5-cell wall) of the alkalophilic bacilli, the contents of neutral sugar and phosphorus were low as compared with those of Bacillus subtilis 6160, while uronic acid and amino acids were abundant. The uronic acid content of the pH 10.3-cell walls was higher than that of the pH 7.5-cell walls in both strains. The insoluble fraction (peptidoglycan) of cell walls of Bacillus No. C-125 consisted of muramic acid, glutamic acid, alanine, diaminopimelic acid and glucosamine as in neutrophilic bacilli. In the TCA soluble fraction of pH 10.3-cell walls of Bacillus No. C-125, uronic acid was a polymer of glucuronic acid containing a small amount of hexosamine, and 2/3 of the ninhydrin positive material was glutamic acid which was derived mainly from poly γ-L-glutamic acid.     

Metabolic Fate of Depsides and Alkaloid Constituents in Aqueous Extracts from Mercurialis perennis L. during Fermentation

Dog's mercury (Mercurialis perennis L.) is an old medicinal plant, nowadays used in complementary medicine. Aqueous fermented extracts of the plant are being mainly applied in remedies to treat external inflammations, but a thorough phytochemical characterization is still lacking. Therefore, the conversion of characteristic compound classes from M. perennis extracts during fermentation and storage was investigated. The microbial transformation of the two main depsides phaselic acid (=(2R)‐O‐[(E)‐caffeoyl]malic acid; 1 ) and mercurialis acid (=(2R)‐[(E)‐caffeoyloxy]glutaric acid; 2 ) was monitored by HPLC‐DAD. The degradation followed a second‐order kinetic, and the calculated half‐life periods of both constituents were 67 and 30 months, respectively. Several depside metabolites were detected by GC/MS in AcOEt extracts as ^tBuMe₂Si (TBDMS) derivatives after derivatization, mainly dihydrocinnamic acids. Moreover, numerous α‐hydroxy acids were found, allegedly as degradation products from amino acids or peptides. The microbial alteration of the main alkaloid hermidin was also examined. After three days of fermentation, three novel N‐metabolites were formed and thoroughly assigned in CH₂Cl₂ extracts as a mixture of 3‐ethylhermidin, 3‐ethylhermidin quinone, and (E/Z)‐3‐ethylidenehermidin by GC/MS and NMR methods, as well as by means of total synthesis. A mechanism for the formation of these N‐metabolites starting from dimeric hermidin oxidation products is proposed. The obtained results reveal the complex pathways plant constituents may undergo during the fermentation of the extracts.     

"Nonfibrillar" chitin associated with walls and septa of Trichophyton mentagrophytes arthrospores

Two morphologically distinct forms of chitin were found in the arthrospore walls and septa of Trichophyton mentagrophytes. Two-thirds of the total wall chitin was the microfibrillar and chitinase-sensitive form. The remaining chitin existed in a previously uncharacterized "nonfibrillar" form and was insensitive to the action of Streptomyces chitinase. Exhaustive digestion of the arthrospore walls and septa with beta (1 leads to 3)-glucanase and chitinase followed by extraction with NaOH (1 N, 100 degrees C, 3 h) resulted in a fraction which retained the original wall shape. This fraction consisted of 85% N-acetylglucosamine, 2.0% galactosamine, 2.5% glucose, and 0.4% amino acids, 74% of which were lysine. Both its infrared spectrum and its X-ray diffraction pattern were almost identical to those of authentic chitin. There was no evidence of the presence of muramic acid, hexuronic acid, phosphate, or sulfate in this fraction. Its resistance to chitinase was due neither to the presence of protective wall layers or melanin nor to its close or covalent association with beta-glucan. Aside from its nonfibrillarity, this hexosamine polymer differed from authentic chitin in that it was soluble in 6 N HCl and 7.5 N NaOH. The development of this nonfibrillar chitin layer in the cell wall during arthrosporogenesis of T. mentagrophytes may be related to the arthrospores being resistant to a variety of antifungal agents.     

Chemical Composition of the Cell Walls of Clostridium botulinum Type A

Cell walls were isolated by sonic disruption of log-phase cells of Clostridium botulinum type A strain 190L and purified by treatment with sodium dodecyl sulfate (SDS) followed by digestion with proteases. Electron microscopy revealed that the cell walls thus obtained were free of both cytoplasmic membrane and cytoplasmic fragments. The purified cell wall contained 8.7% total nitrogen, 15.0% total hexosamines, 22.4% reducing groups, 8.3% carbohydrate, and 3.1% glucose. The content of total phosphorus was very low (0.02%), and therefore it was expected that teichoic acid might be absent in the cell wall. The wall peptidoglycan contained glutamic acid, alanine, diaminopimelic acid, glucosamine and muramic acid in the molar ratios of 1.00:1.85:0:85:1.06:0.67. A low amount of galactosamine was also present, but no other amino acids were found in significant quantities. The SDS-treated cell walls were not attacked by lysozyme, but after extraction with hot formamide they were completely dissolved by the enzyme and released reducing groups. The lysozyme digest was separated into two constituents, the saccharide moiety and the peptide moiety on Sephadex G-50.     

Isolation and Chemical Structure of the Peptidoglycan of Spirillum serpens Cell Walls

The peptidoglycan layer of Spirillum serpens cell walls was isolated from intact cells after treatment with sodium dodecylsulfate and digestion with Pronase. The isolated peptidoglycan contained glucosamine, muramic acid, alanine, glutamic acid, and meso-diaminopimelic acid in the approximate molar ratio of 1:1:2:1:1. Aspartic acid and glycine were the only other amino acids found in significant quantities. N-terminal amino acid analyses of the tetrapeptide amino acids in the peptidoglycan revealed that 54% of the diaminopimelic acid molecules are involved in cross-linkage between tetrapeptides. This amount of cross-linkage is greater than that found in the peptidoglycan of previously studied cell walls of gram-negative bacteria. The polysaccharide backbone was isolated, after myxobacter AL-1 enzyme digestion of the peptidoglycan, by fractionation with ECTEOLA-cellulose and Sephadex G-100. An average length of 99 hexosamines for the polysaccharide chains was found (ratio of total hexosamines to reducing end groups).     

Macromolecular composition of Palaeozoic scolecodonts: insights into the molecular taphonomy of zoomorphs

Dutta, S., Hartkopf‐Fröder, C., Mann, U., Wilkes, H., Brocke, R. & Bertram, N. 2010: Macromolecular composition of Palaeozoic scolecodonts: insights into the molecular taphonomy of zoomorphs. Lethaia, Vol. 43, pp. 334–343. Biogeochemistry and molecular taphonomy of biopolymers of marine zoomorphs are poorly known. In order to obtain insights into this issue we report on the biogeomacromolecular composition of hand‐picked, well‐preserved scolecodonts of Ordovician, Silurian and Devonian age using micro‐Fourier transform infrared (micro‐FTIR) spectroscopy, Curie point pyrolysis‐gas chromatography‐mass spectrometry (Cupy‐GC‐MS) and tetramethylammonium hydroxide (TMAH)‐assisted thermochemolysis‐GC‐MS. The present study reveals that scolecodonts are composed of both aliphatic and aromatic moieties. The micro‐FTIR spectra of scolecodonts are characterized by aliphatic CH_x (3000–2800 and 1460–1450/cm) and CH₃ (1375/cm) absorptions and aromatic C=C (1560–1610/cm) and CH (3050/cm and 700–900/cm) absorptions. The major pyrolysis products from the scolecodonts include aromatic hydrocarbons such as alkylbenzenes, alkylnaphthalenes and alkylphenols. Aliphatic hydrocarbons are represented by a homologous series of n‐alkenes and n‐alkanes. The compounds released upon thermochemolysis with TMAH are saturated and unsaturated fatty acids (as their methyl esters), n‐alkenes/alkanes and aromatic acids (as their methyl esters). No protein/amino acid‐derived compounds have been recognized in the pyrolysates or in the thermochemolysates, and it is concluded that protein/amino acid‐related compounds, which are commonly found in the jaws of extant polychaetes, were destroyed due to diagenetic processes. Obviously, excellent morphological preservation and low thermal alteration are not paralleled by a similar degree of chemical preservation. □Biogeomacromolecules, micro‐FTIR, pyrolysis‐GC‐MS, scolecodonts, thermochemolysis‐GC‐MS.     

Total Synthesis of the Peptaibols Hypomurocin A3 and Hypomurocin A5, and Their Conformation Analysis

The total syntheses of hypomurocin A3 and hypomuricin A5 (HM A3 and HM A5, resp.) in solution phase are described. These syntheses have been successfully achieved by applying the ‘azirine/oxazolone method’ to introduce the two Aib‐Pro units into the backbone of these undecapeptaibols in one step with methyl 2,2‐dimethyl‐2H‐azirine‐3‐prolinate as the ‘Aib‐Pro synthon’. The coupling of Z‐protected (Z=(benzyloxy)carbonyl) amino acids or peptide acids with amino acid tert‐butyl esters and of peptide segments was carried out according to the TBTU (=O‐(benzotriazol‐1‐yl)‐N,N,N′,N′‐tetramethyluronium tetrafluoroborate) and HOBt (=1‐hydroxybenzotriazole) protocol. Purification by reversed‐phase HPLC gave the peptides in pure form. The products were characterized by optical rotation, NMR and IR spectroscopy, mass spectrometry, and elemental analysis. The crystal structures of HM A3 and of an octapeptide fragment of HM A5 could be obtained. An NMR analysis was also carried out with HM A3 and HM A5 to determine their conformations in solution. A global structural comparison between the three sequences of HM A1, HM A3, and HM A5 was performed, as well as the HPLC correlation of the natural HM A family and the synthetic samples.     

Characterization of the Microbial Community in Indoor Environments: a Chemical-Analytical Approach

An integrated procedure is presented whereby gas chromatography-ion trap mass spectrometry is used to determine chemical markers of gram-negative bacterial lipopolysaccharide (3-hydroxy fatty acids with 10 to 18 carbon atoms), gram-positive bacteria (branched-chain fatty acids with 15 and 17 carbon atoms), bacterial peptidoglycan (muramic acid), and fungal biomass (ergosterol) in samples of settled house dust. A hydrolysate of ¹³C-labeled cyanobacterial cells is used as an internal standard for the first three markers. These analyses require two dust samples, one for 3-OH fatty acids, branched-chain fatty acids, and muramic acid and another for ergosterol. The method may be used to characterize microbial communities in environmental samples.     

Quantification of 22 plasma amino acids combining derivatization and ion-pair LC-MS/MS

Time efficient and comprehensive quantification of amino acids continues to be a challenge. We developed a sensitive and precise method for quantitative analysis of amino acids from very small plasma and serum volumes. Ion-pair chromatography of amino acid butyl esters proved to provide an optimal combination of selectivity, sensitivity and robustness. 10 μL of plasma or serum are added to precipitation reagent containing stable isotope standards. After protein precipitation, the supernatants is dried and incubated with 3N butanolic HCl for improving chromatographic separation and ionization efficiency. Amino acid butyl esters are separated using ion-pair (heptafluorobutyric acid) reversed-phase chromatography coupled to triple quadrupole mass spectrometry. The established method enables quantitative analysis of 22 amino acids, all 20 proteinogenic amino acids, ornithine and citrulline. Cysteine is measured as cystine. The combination of precipitation, derivatization and chromatographic separation effectively avoids ion suppression and coelution. Simultaneous with quantification, analyte identity is verified in each sample using qualifier ions. The micro-method is very sensitive and accurate. The intra-assay precision for the analysis of plasma was 2.6-10.1%. Absolute accuracy as determined by comparison of external reference samples was 82-117.7%. Excellent linearity of detection response was demonstrated for all compounds in the range representative for clinical samples from infants and adults. Lower limits of quantification were in the range of 1 μmol/L for all analytes. In conclusion, the method is ideally suited for cost-effective high-throughput analysis of large numbers of samples in clinical studies and metabolomics research.     

Determination of amino acids in human serum by capillary gas chromatography

A simple and rapid method for the determination of serum amino acids by gas chromatography (GC) has been developed. Following deproteinization of serum with perchloric acid, free amino acids in the supernatant were converted into their N(O,S)-isobutoxycarbonyl methyl ester derivatives and measured by GC with flame ionization detection using a DB-17 capillary column. All the derivatives of the 22 protein amino acids were completely resolved as single peaks within 9 min by GC. The calibration curves were linear in the range 0.2–50 μg of each amino acid, and the correlation coefficients were above 0.998. By using this method, serum amino acids could be directly analysed without prior clean-up procedure such as ion-exchange column chromatography except for deproteinization of the samples, and without any interference from coexisting substances. Overall recoveries of amino acids added to serum samples were 88–108%. Analytical results for serum amino acids from normal subjects are presented.     

Studies on ultrastructure and composition of cell walls of the cyanobacterium Anacystis nidulans

The multilayered cell wall of the cyanobacterium Anacystis nidulans was studied by the freezeetching technique. A characteristic fracture face in the outer cell wall was demonstrated which is densely packed with particles of a diameter of 60–75 Å. This particle layer is comparable with layers which have been described in many cell walls of Gram-negative prokaryotes.The outer membrane of the cell wall was solubilised by extraction with phenol/water or sodium dodecyl sulfate (SDS). In the SDS-extract 31 bands were separated by polyacrylamide gel electrophoresis, among them 3–5 major proteins with molecular weights of approximately 60, 40, and 10 kdaltons, respectively. Several polypeptides of the Anacystis cell wall were comparable in their mobility with polypeptides extracted from cell walls of different Gramnegative bacteria. The analysis of the SDS-unsoluble electron dense layer (sacculi) revealed the typical components of peptidoglycan diaminopimelic acid, muramic acid, glutamic acid, glucosamine and alamine in the molar ratio of 1.0:0.9:1.1:1.5:1.9. In addition, other amino acids (molar ratio from 0.05–0.36), mannosamine (molar ratio 0.54), and lipopolysaccharide components were detected in low concentration.Abbreviations SDS sodium dodecyl sulfate - EDTA ethylene diamine tetraacetate