Sequence analysis of the agrA gene encoding beta-agarase from Pseudomonas atlantica.

The nucleotide sequence of the agrA gene encoding an extracellular beta-agarase of Pseudomonas atlantica was determined. An open reading frame of 1,515 nucleotides which corresponded to agrA was found. The nucleotide sequence predicts a primary translation product of 504 amino acids and Mr 57,486. Comparison of the deduced amino acid sequences of beta-agarase from P. atlantica and the extracellular beta-agarase from Streptomyces coelicolor A3(2) suggests that these proteins share several domains in common.     

Beta-agarases I and II from Pseudomonas atlantica. Substrate specificities

Beta-Agarase I and II were characterised by their action on agar-type polysaccharides and oligosaccharides. Beta-Agarase I, an endo-enzyme, was specific for regions containing a minimum of one unsubstituted neoagarobiose unit [3,6-anhydro-alpha-L-galactopyranosyl-(1 leads to 3)-D-galactose], hydrolysing at the reducing side of this moiety. Yaphe demonstrated that agar was degraded by this enzyme to neoagaro-oligosaccharides limited by the disaccharide but with a predominance of the tetramer [Yaphe, W. (1957) Can. J. Microbiol. 3, 987-993]. Beta-Agarase I slowly degraded neoagarohexaose but not the homologous tetrasaccharide. [1-3H]Neoagarohexaitol was cleaved to neoagarotetraose and [1-3H]neoagarobiitol. The highly substituted agar, porphyran was degraded to methylated, sulphated and unsubstituted neoagaro-oligosaccharides which were invariably terminated at the reducing end by unsubstituted neoagarobiose. The novel enzyme, beta-agarase II, was shown to be an endo-enzyme. Preliminary evidence indicated this enzyme was specific for sequences containing neoagarobiose and/or 6(1)-O-methyl-neoagarobiose. It degraded agar to neoagaro-oligosaccharides of which the disaccharide was limiting and predominant. Beta-Agarase II rapidly degraded isolated neogarotetraose and neoagarohexaose to the disaccharide. With [1-3H]neoagarohexaitol, exo-action was observed, the alditol being cleaved to neoagarobiose and [1-3H]neoagarotetraitol. Neoagarotetraitol was hydrolysed at 4% of the rate observed for the hexaitol. Porphyran was degraded to oligosaccharides, the neutral fraction comprising 24% of the starting carbohydrate. This fraction was almost exclusively disaccharides (22.4%) containing neoagarobiose (7.4%) and 6(1)-O-methyl-neoagarobiose (15%). Beta-Agarase II is probably the 'beta-neoagarotetraose hydrolase' reported by Groleau and Yaphe as an exoenzyme against neoagaro-oligosaccharides [Groleau, D. and Yaphe, W. (1977) Can. J. Microbiol. 23, 672-679].     

Study of the structure of mannans from Candida maltosa and Candida tropicalis using 13C-NMR spectroscopy

Mannans were isolated from six Candida strains and characterized. 13C-NMR spectroscopy revealed interspecific and interstrain difference of the yeasts in the structure of their mannans.     

Mobility-resolved 13C-NMR spectroscopy of primary plant cell walls

Primary plant cell walls contain highly hydrated biopolymer networks, whose major chemistry is known but whose relationship to architectural and mechanical properties is poorly understood. Nuclear magnetic resonance spectroscopy has been used to characterize segmental mobilities via relaxation and anisotropy effects in order to add a dynamic element to emerging models for cell wall architecture. For hydrated onion cell wall material, single pulse excitation revealed galactan (pectin side chains), provided that dipolar decoupling was used, and some of the pectin backbone in the additional presence of magic angle spinning. Cross-polarization excitation revealed the remaining pectin backbones, which exhibited greater mobility (contact time dependence, dipolar dephasing) than the cellulose component, whose noncrystalline and crystalline fractions showed no mobility discrimination. ¹HT₂ behavior could be quantitatively interpreted in terms of high resolution observabilities. Mobility-resolved spectroscopy of cell walls from tomato fruit, pea stem, and tobacco leaf showed similar general effects. Nuclear magnetic resonance study of the sequential chemical extraction of onion cell wall material suggests that galactans fill many of the network pores, that extractability of pectins is not dependent on segmental mobility, and that some pectic backbone (and not side chain) is strongly associated with cellulose. Analysis of the state of cellulose in four hydrated cell walls suggests a noncrystalline content of 60–80% and comparable amounts of Iα and Iβ polymorphs in the crystalline fraction. Comparison with micrographs for onion cell walls shows that noncrystalline cellulose does not equate to chains on fibril surfaces, and chemical shifts show that fully solvated cellulose is not a significant component in cell walls. © 1996 John Wiley & Sons, Inc.     

beta-agarases I and II from Pseudomonas atlantica. Purifications and some properties

The agarose-degrading system of Pseudomonas atlantica has been re-examined. In addition to the previously reported extracellular endo-beta-agarase [Yaphe, W. (1966) in Proceedings 5th International Seaweed Symposium, pp. 333-335] a second, membrane-bound endo-enzyme activity, beta-agarase II has been discovered. These two enzymes act in concert to degrade agarose to neoagarobiose [3,6-anhydro-alpha-L-galactopyranosyl-(1 leads to 3)-D-galactose] and also to degrade partially 6-O-methylated agarose to neoagarobiose and 6(1)-O-methyl-neoagarbiose. Novel assays were devised for beta-agarase II and the associated disaccharidase, neoagarobiose hydrolase. These allowed the critical purification of beta-agarase I and II. beta-Agarase I was purified 670-fold from the bacterial medium by a new method using ammonium sulphate precipitation and gel filtration on Sephadex G-100. The enzyme was resolved from the small amount of extracellular beta-agarase II. Dodecylsulphate/polyacrylamide gel electrophoresis indicated a homogeneous protein and a molecular weight of 32000. Activity was observed against agar over the pH range 3.0-9.0 and optimally at pH 7.0. The enzyme could be used indefinitely at 30 degrees C but only for up to 2 h at 40 degrees C. beta-Agarase II was partially purified (5-fold) from the soluble fraction of disrupted cells by chromatography on Sephadex G-100, hydroxyapatite and DEAE-Sepharose CL-6B. This preparation was free of beta-agarase I and disaccharidase. beta-Agarase II was stimulated by NaCl, optimally in the range 0.10-0.20 mol dm-3 (2.4-fold the activity at 0.010 mol dm-3 NaCl). Alkali earth metal (0.002 mol dm-3 CaCl2 or 0.005 mol dm-3 MgCl2) gave 1.2-fold the normal activity. Optimum activity was over pH 6.5-7.5.     

Secondary structure of calf-thymus histone H1 by means of 13C-NMR spectroscopy

¹³C-nmr spectroscopy was used to determine the location of the structured segment of the chain of histone H1 in water and NaCl solutions. The segment found (41–89) is contained in the area proposed by others on the basis of ¹H-nmr studies. The number of basic groups left in the mobile ends of the protein matches the number of bases of internucleosomal DNA.     

Identification and quantitative determination of eudesmane-type acids from the essential oil of Dittrichia viscosa sp. viscosa using 13C-NMR spectroscopy

A procedure that allows the identification and quantitative determination of eudesmane-type acids in the acidic part of the essential oil of Dittrichia viscosa sp. viscosa is described. The method involves the computer-aided analysis of the 13C-NMR spectrum of the mixture without the requirement of previous separation or derivatisation. The quantitative procedure was verified with costic acid standard and applied to three other acids which possess the same eudesmane framework.     

An investigation of the iron-sulphur proteins of benzene dioxygenase from Pseudomonas putida by electron-spin-resonance spectroscopy.

Benzene dioxygenase from Pseudomonas putida comprises three components, namely a flavoprotein (NADH:ferredoxin oxidoreductase; Mr 81000), an intermediate electron-transfer protein, or ferredoxin (Mr 12000) with a [2Fe-2S] cluster, and a terminal dioxygenase containing two [2Fe-2S] iron-sulphur clusters (Mr 215000), which requires two additional Fe2+ atoms/molecule for oxygenase activity. The ferredoxin and the dioxygenase give e.s.r. signals in the reduced state with rhombic symmetry and average g values of 1.92 and 1.896 respectively. The mid-point redox potentials were determined by e.s.r. titration at pH 7.0 to be -155 mV and -112 mV respectively. The signal from the dioxygenase shows pronounced g anisotropy and most closely resembles those of 4-methoxybenzoate mono-oxygenase from Pseudomonas putida and the [2Fe-2S] 'Rieske' proteins of the quinone-cytochrome c region of electron-transport chains of respiration and photosynthesis.     

A p-nitrophenyl alpha-galactoside hydrolase from Pseudomonas atlantica. Localization of the enzyme.

A p-nitrophenyl alpha-galactoside hydrolase is partially released when whole cells of Pseudomonas atlantica are converted to spheroplasts. The p-nitrophenyl alpha-glactoside hydrolase is completely inactivated by treatment of whole cells with diazonaphthalene -- disulfonic acid (NDS), a reagent which does not penetrate the cytoplasmic membrane. Under the conditions used no inactivation of lactic acid dehydrogenase was observed. A specific staining procedure for this enzyme for use in electron microscopy was developed. The results with this technique in conjunction with the results of spheroplasting and NDS localization suggest that p-nitrophenyl alpha-galactoside hydrolase is located in or on the double-track membranes, primarily on the outer double track.     

Triterpenes in the hexane extract of leaves of Olea europaea L.: analysis using 13C-NMR spectroscopy

Two neutral triterpenes and a triterpene acid were identified and quantified directly, in the absence of any purification steps, in a precipitate obtained during the industrial extraction of the leaves of Olea europaea L. using 13C-NMR spectroscopy (spectrometer operating at 4.7 T equipped with a 10 mm probe). The method was optimised in order to reduce the duration of analysis with a routine NMR spectrometer. Together with long-chain linear compounds, erythrodiol, uvaol and oleanolic acid accounted for 27.3, 18.3 and 12.5% of the precipitate, respectively.     

Analysis of cockroach oothecae and exuviae by solid-state 13C-NMR spectroscopy

Sclerotized oothecae from four species of cockroaches, Periplaneta americana, P. fuliginosa, Blatta orientalis and Blattella germanica, were examined by solid-state ¹³C-nuclear magnetic resonance and chemical analyses. The oothecae were composed of protein, water, calcium oxalate, diphenolic compounds, lipid, and uric acid. Calcium oxalate was the major soluble component in egg cases of P. americana, P. fuliginosa, and B. orientalis. Oothecae of B. germanica had approx. 10-fold less calcium oxalate and extractable diphenols than the other species. The major diphenolic compound extracted in cold dilute perchloric acid was 3,4-dihydroxybenzoic acid. Exuviae from P. americana, B. germanica, Gromphadorhina portentosa, Blaberus craniifer, and Leucophaea maderae also were examined by solid-state ¹³C-NMR. They contained protein, diphenols, and lipid, as well as chitin, which accounted for 30–42% of the organic content, depending upon the species.     

13C-NMR studies of acetate and methanol metabolism by methylotrophic Pseudomonas strains

The metabolism of [2-13C]acetate by Pseudomonas M27(Icl-) and Pseudomonas MA(Icl+) was studied in vivo using 13C-NMR spectroscopy. The flux of 13C-label into bicarbonate, glutamate and citrate was observed in both organisms. In addition 13C-labelled alpha, alpha-trehalose was synthesized as a major metabolite by Pseudomonas M27 but not by Pseudomonas MA. The presence of this disaccharide in cell extracts of Pseudomonas AM1(Icl-) grown with [13C]methanol was also observed. The data from analysis of the trehalose multiplet signal observed in the spectra of Pseudomonas M27 cell extracts were consistent with the absence of the glyoxylate cycle in this methylotroph.     

13C-NMR spectroscopy of human serum high density lipoprotein enriched with labelled phospholipids.

Native human serum high density lipoprotein (HDL) (d = 1.063--1.21g x cm-3) was enriched with phosphatidylcholines labelled with 13C in the polar head group ([N-13CH3]choline) and in the fatty acyl chains ([26-13C]cholesterol) and its linoleic acid ester using the previously described exchange method (Stoffel et al. 1978). The properties of the HDL particles with the exchanged lipid classes were the same as those of the native particles (Mr, CD, fluorescence, lipid and apoprotein stoichiometry, electrophoretic mobility). The T1-times were very similar to those obtained previously with recombined apolipoprotein-[13C]lipid complexes and further support our proposals concerning lipid and apoprotein interactions in the HDL particle.     

A 13C-NMR study of the structure of an acyl-linarin from Valeriana wallichii

An acylated acacetin-7-O-rutinoside of Valeriana wallichii has been shown to be a mixture of its 2?-O-and 3?-O-2-methylbutyryl esters by ¹³C-NMR, GLC, and MS.     

1H- and 13C-NMR studies of N-acetyl-L-alanine methylester and N-acetyl-L-alanine methylamide. I. Self-association

The ¹H- and ¹³C-NMR spectra of N-acetyl-L -alanine methylester and N-acetyl-L -alanine methylamide were measured to examine the modes of self-association of these molecules in solution. The different dilution shifts between these molecules seem to correspond to the difference in the associated state for each molecule. Consequently, for the former molecule, a dimer model forming the intermolecular hydrogen bond through Ala NH hydrogen atom in one molecule to Ala C?O oxygen atom in another molecule was proposed. Another dimer model, which coincides with that proposed recently by Neel and coworkers, was proposed for the latter molecule. This second dimer model forms an intermolecular hydrogen bond through the NH of the N-methylamide group in one molecule to the acetyl C?O in another molecule.     

Enzymatic hydrolysis of agar: purification and characterization of beta-neoagarotetraose hydrolase from Pseudomonas atlantica.

Agarose is degraded by a beta-agarase from Pseudomonas atlantica to neoagarooligosaccharides of degree of polymerization (DP), 4, 6, 8, and 10. A beta-neoagarotetraose hydrolase cleaves the central beta-linkage in neoagarotetraose and the beta-linkage near the nonreducing end in neoagarohexaose and -octaose to yield neoagarobiose. The beta-neoagarotetraose hydrolase was localized on or outside the cytoplasmic membrane, in the cell wall region. The enzyme was activated by NaCl, KCl, CaCl2, MnCl2, and MgSO4, has a Km of 3.4 X 10(-3) M for neoagarotetraose, was free from beta-agarase and alpha-neoagarobiose hydrolase activity, and showed no transglycosidic activity.     

The hydration response of poly (L-lysine) dynamics measured by 13C-NMR spectroscopy.

13C-nmr measurements are reported for samples of poly (L-lysine) both static and spinning at the magic angle in the beta-sheet form as a function of water content. The addition of water decreases the side-chain line widths considerably. Measurements of the cross-polarization time constants indicate that hydration by either H2O or D2O increases the time constant. Measurements of spin-lattice relaxation times in the laboratory frame and the rotating frame indicate that hydration does not change the dynamics of the backbone carbon atoms in the beta-sheet structure appreciably, but the side-chain atoms experience considerable increase in local mobility with increasing hydration. Deuteration of the exchangeable protons or the water has only small effects on the carbon relaxation times, indicating that relaxation is driven by intramolecular dipole-dipole interactions.     

Characterization of the renal epithelial cell line, PKE 5, using 31P- and 13C-NMR spectroscopy

In order to characterize intracellular pH regulation and cellular metabolism in PKE 5 cells, a mutant of the renal epithelial cell line LLC-PK1 supposed to lack Na+-H+ exchanger activity, 31P and 13C-NMR studies were conducted. The 31P studies on intact cell suspensions revealed that these cells have an ATP content and an ATP/ADP ratio similar to the parent cell line. Their intracellular pH, in the presence of 5 mM HCO3-, was 7.17 +/- 0.04 (n = 5) - identical to that of LLC-PK1 cells. After acid loading the cells with 15% CO2, the initial rate of realkalinization was 0.027 pH units/min (n = 6), 50% lower than in the parent cells. The recovery rate was not affected by the removal of extracellular sodium or by the addition of 1 mM amiloride. These results indicate that PKE 5 cells are devoid of Na+-H+ exchange activity, but are able to regulate their intracellular pH by amiloride-insensitive, sodium-independent mechanisms. Extracts prepared from PKE 5 cells incubated with [13C]lactate showed 13C spectra identical to those of the parent cell line. In particular, no synthesis of 13C-labeled D-glucose was observed.     

Elucidation of anaplerotic pathways in Corynebacterium glutamicum via 13C-NMR spectroscopy and GC-MS

We have obtained direct evidence indicating the presence of pyruvate-carboxylating activity in Corynebacterium glutamicum, a lysine-overproducing bacterium. This evidence was obtained through the use of ¹³C nuclear magnetic resonance (NMR) spectroscopy and gas chromatography/mass spectrometry (GC-MS) of secreted metabolites in a lysine fermentation. The distribution of ¹³C label after multiple turns in the tricarboxylic acid cycle was accounted for properly to obtain predictions for [¹³C] metabolite enrichments that were employed in the interpretation of ¹³C-NMR and GC-MS data. Of critical importance in arriving at the conclusions was the use of C. glutamicum mutants with deletions of the pyruvate kinase and/or phosphoenolpyruvate carboxylase enzymes. Our results demonstrate the presence of pyruvate-carboxylating pathway(s) in C.␣glutamicum operating simultaneously with phosphoenolpyruvate carboxylase, with the latter enzyme contributing approximately 10 % of the total oxaloacetate synthesis during the lysine-production phase with pyruvate and gluconate as carbon sources. These findings are important for developing strategies to increase the total carbon flux for synthesis of amino acids of the aspartate family through metabolic engineering. Received: 11 June 1996 / Received revision: 30 October 1996 / Accepted: 15 November 1996     

Quantitation of aliphatic suberin in Quercus suber L. cork by FTIR spectroscopy and solid-state (13)C-NMR spectroscopy

This work determined that the percentage of suberin in cork may be found by solid-state (13)C cross polarization/magic angle spinning (CP/MAS) NMR spectroscopy and by FTIR with photoacoustic detection (FTIR-PAS) spectroscopy. A linear relationship is found between the suberin content measured through CP/MAS spectral areas and that measured gravimetrically. Furthermore, application of a partial least squares (PLS1) regression model to the NMR and gravimetric data sets clearly correlates the two sets, enabling suberin quantification with 90% precision. Suberin quantitation by FTIR-PAS spectroscopy is also achieved by a PLS1 regression model, giving 90% accurate estimates of the percentage of suberin in cork. Therefore, (13)C-CP/MAS NMR and FTIR-PAS proved to be useful and accurate noninvasive techniques to quantify suberin in cork, thus avoiding the traditional time consuming and destructive chemical methods.