Probing alanine transaminase catalysis with hyperpolarized 13CD3-pyruvate

Hyperpolarized metabolites offer a tremendous sensitivity advantage (>10(4) fold) when measuring flux and enzyme activity in living tissues by magnetic resonance methods. These sensitivity gains can also be applied to mechanistic studies that impose time and metabolite concentration limitations. Here we explore the use of hyperpolarization by dissolution dynamic nuclear polarization (DNP) in mechanistic studies of alanine transaminase (ALT), a well-established biomarker of liver disease and cancer that converts pyruvate to alanine using glutamate as a nitrogen donor. A specific deuterated, (13)C-enriched analog of pyruvic acid, (13)C3D(3)-pyruvic acid, is demonstrated to have advantages in terms of detection by both direct (13)C observation and indirect observation through methyl protons introduced by ALT-catalyzed H-D exchange. Exchange on injecting hyperpolarized (13)C3D(3)-pyruvate into ALT dissolved in buffered (1)H(2)O, combined with an experimental approach to measure proton incorporation, provided information on mechanistic details of transaminase action on a 1.5s timescale. ALT introduced, on average, 0.8 new protons into the methyl group of the alanine produced, indicating the presence of an off-pathway enamine intermediate. The opportunities for exploiting mechanism-dependent molecular signatures as well as indirect detection of hyperpolarized (13)C3-pyruvate and products in imaging applications are discussed.

Nuclear magnetic resonance in the era of structural genomics

Current interests in structural genomics, and the associated need for high through-put structure determination methods, offer an opportunity to examine new nuclear magnetic resonance (NMR) methodology and the impact this methodology can have on structure determination of proteins. The time required for structure determination by traditional NMR methods is currently long, but improved hardware, automation of analysis, and new sources of data such as residual dipolar couplings promise to change this. Greatly improved efficiency, coupled with an ability to characterize proteins that may not produce crystals suitable for investigation by X-ray diffraction, suggests that NMR will play an important role in structural genomics programs.

N-linked oligosaccharides of cobra venom factor contain novel alpha(1-3)galactosylated Le(x) structures

Cobra venom factor (CVF), a nontoxic, complement-activating glycoprotein in cobra venom, is a functional analog of mammalian complement component C3b. The carbohydrate moiety of CVF consists exclusively of N-linked oligosaccharides with terminal alpha1-3-linked galactosyl residues, which are antigenic in human. CVF has potential for several medical applications, including targeted cell killing and complement depletion. Here, we report a detailed structural analysis of the oligosaccharides of CVF. The structures of the oligosaccharides were determined by lectin affinity chromatography, antibody affinity blotting, compositional and methylation analyses, and high-resolution (1)H-NMR spectroscopy. Approximately 80% of the oligosaccharides are diantennary complex-type, approximately 12% are tri- and tetra-antennary complex-type, and approximately 8% are oligomannose type structures. The majority of the complex-type oligosaccharides terminate in Galalpha1-3Galbeta1-4(Fucalpha1-3)GlcNAcbeta1, a unique carbohydrate structural feature abundantly present in the glycoproteins of cobra venom.

Structure elucidation of sphingolipids from the mycopathogen Sporothrix schenckii: identification of novel glycosylinositol phosphorylceramides with core manalpha1-->6Ins linkage

Acidic glycosphingolipid components were extracted from the mycelium form of the thermally dimorphic mycopathogen Sporothrix schenckii. Two fractions from the mycelium form (Ss-M1 and Ss-M2), having the highest Rf values on HPTLC analysis, were isolated and their structures elucidated by 1- and 2-D 13C- and 1H-nuclear magnetic resonance spectroscopy, and electrospray ionization mass spectrometry with lithium adduction of molecular ions. The structures of Ss-M1 and Ss-M2 were determined to be Manalpha1-->Ins1-P-1Cer and Manalpha1--> 3Manalpha1-->Ins1-P-1Cer, respectively (where Ins = myo-inositol, P = phosphodiester). The Manalpha1-->6Ins motif is found normally in diacylglycerol-based glycophosphatidylinositols of Mycobacteria, but this is the first unambiguous identification of the same linkage making up the core structure of fungal glycosylinositol phosphorylceramides (GIPCs). These results are discussed in relation to the structures of GIPCs of other mycopathogens, including Histoplasma capsulatum and Paracoccidioides brasiliensis.

Structure of a (Cys3His) zinc ribbon, a ubiquitous motif in archaeal and eucaryal transcription

Transcription factor IIB (TFIIB) is an essential component in the formation of the transcription initiation complex in eucaryal and archaeal transcription. TFIIB interacts with a promoter complex containing the TATA-binding protein (TBP) to facilitate interaction with RNA polymerase II (RNA pol II) and the associated transcription factor IIF (TFIIF). TFIIB contains a zinc-binding motif near the N-terminus that is directly involved in the interaction with RNA pol II/TFIIF and plays a crucial role in selecting the transcription initiation site. The solution structure of the N-terminal residues 2-59 of human TFIIB was determined by multidimensional NMR spectroscopy. The structure consists of a nearly tetrahedral Zn(Cys)3(His)1 site confined by type I and "rubredoxin" turns, three antiparallel beta-strands, and disordered loops. The structure is similar to the reported zinc-ribbon motifs in several transcription-related proteins from archaea and eucarya, including Pyrococcus furiosus transcription factor B (PfTFB), human and yeast transcription factor IIS (TFIIS), and Thermococcus celer RNA polymerase II subunit M (TcRPOM). The zinc-ribbon structure of TFIIB, in conjunction with the biochemical analyses, suggests that residues on the beta-sheet are involved in the interaction with RNA pol II/TFIIF, while the zinc-binding site may increase the stability of the beta-sheet.

Structural characterization of the pectic polysaccharide rhamnogalacturonan II: evidence for the backbone location of the aceric acid-containing oligoglycosyl side chain

Monomeric rhamnogalacturonan II (mRG-II) was isolated from red wine and the reducing-end galacturonic acid of the backbone converted to L-galactonic acid by treatment with NaBH4. The resulting product (mRG-II'ol) was treated with a cell-free extract from Penicillium daleae, a fungus that has been shown to produce RG-II-fragmenting glycanases. The enzymatically generated products were fractionated by size-exclusion and anion-exchange chromatographies and the quantitatively major oligosaccharide fraction isolated. This fraction contained structurally related oligosaccharides that differed only in the presence or absence of a single Kdo residue. The Kdo residue was removed by acid hydrolysis and the resulting oligosaccharide then characterized by 1- and 2D 1H NMR spectroscopy, ESMS, and by glycosyl-residue and glycosyl-linkage composition analyses. The results of these analyses provide evidence for the presence of at least two structurally related oligosaccharides in the ratio approximately 6:1. The backbone of these oligosaccharides is composed of five (1-->4)-linked alpha-D-GalpA residues and a (1-->3)-linked L-galactonate. The (1-->4)-linked GalpA residue adjacent to the terminal non-reducing GalpA residue of the backbone is substituted at O-2 with an apiosyl-containing side chain. Beta3-L-Araf-(1-->5)-beta-D-DhapA is likely to be linked to O-3 of the GalpA residue at the non-reducing end of the backbone in the quantitatively major oligosaccharide and to O-3 of a (1-->4)-linked GalpA residue in the backbone of the minor oligosaccharide. Furthermore, the results of our studies have shown that the enzymically generated aceryl acid-containing oligosaccharide contains an alpha-linked aceryl acid residue and a beta-linked galactosyl residue. Thus, the anomeric linkages of these residues in RG-II should be revised.

Characterization of sphingolipids from mycopathogens: factors correlating with expression of 2-hydroxy fatty acyl (E)-Delta 3-unsaturation in cerebrosides of Paracoccidioides brasiliensis and Aspergillus fumigatus

Significant differences exist between mammals and fungi with respect to glycosphingolipid (GSL) structure and biosynthesis. Thus, these compounds, as well as the cellular machinery regulating their expression, have considerable potential as targets for the diagnosis and treatment of fungal diseases. In this study, the major neutral GSL components extracted from both yeast and mycelium forms of the thermally dimorphic mycopathogen Paracoccidioides brasiliensis were purified and characterized by 1H and 13C NMR spectroscopy, ESI-MS and ESI-MS/CID-MS, and GC-MS. The major GSLs of both forms were identified as beta-glucopyranosylceramides (GlcCer) having (4E, 8E)-9-methyl-4,8-sphingadienine as long chain base in combination with either N-2'-hydroxyoctadecanoate or N-2'-hydroxy-(E)-3'-octadecenoate. The mycelium form GlcCer had both fatty acids in a approximately 1:1 ratio, while that of the yeast form had on average only approximately 15% of the (E)-Delta 3-unsaturated fatty acid. Cerebrosides from two strains of Aspergillus fumigatus (237 and ATCC 9197) expressing both GalCer and GlcCer were also purified and characterized by similar methods. The GalCer fractions were found to have approximately 70% and approximately 90% N-2'-hydroxy-(E)-3'-octadecenoate, respectively, in the two strains. In contrast, the GlcCer fractions had N-2'-hydroxy-(E)-3'-octadecenoate at only approximately 20 and approximately 50%, respectively. The remainder in all cases was the saturated 2-OH fatty acid, which has not been previously reported in cerebrosides from A. fumigatus. The availability of detailed structures of both glycosylinositol phosphorylceramides [Levery, S. B., Toledo, M. S., Straus, A. H., and Takahashi, H. K. (1998) Biochemistry 37, 8764-8775] and cerebrosides from P. brasiliensis revealed parallel quantitative differences in expression between yeast and mycelium forms, as well as a striking general partitioning of ceramide structure between the two classes of GSLs. These results are discussed with respect to possible functional roles for fungal sphingolipids, particularly as they relate to the morphological transitions exhibited by P. brasiliensis.

Enzymatic synthesis of natural and 13C enriched linear poly-N-acetyllactosamines as ligands for galectin-1

As part of a study of protein-carbohydrate interactions, linear N-acetyl-polyllactosamines [Galbeta1,4GlcNAcbeta1,3]nwere synthesized at the 10-100 micromol scale using enzymatic methods. The methods described also provided specifically [1-13C]-galactose-labeled tetra- and hexasaccharides ([1-13C]-Galbeta1,4GlcNAcbeta1,3Galbeta1,4Glc and Galbeta1, 4GlcNAcbeta1,3[1-13C]Galbeta1,4GlcNAcbeta1,3Galbeta 1,4Glc) suitable for NMR studies. Two series of oligosaccharides were produced, with either glucose or N-acetlyglucosamine at the reducing end. In both cases, large amounts of starting primer were available from human milk oligosaccharides (trisaccharide primer GlcNAcbeta1,3Galbeta1, 4Glc) or via transglycosylation from N-acetyllactosamine. Partially purified and immobilized glycosyltransferases, such as bovine milk beta1,4 galactosyltransferase and human serum beta1,3 N- acetylglucosaminyltransferase, were used for the synthesis. All the oligo-saccharide products were characterized by1H and13C NMR spectroscopy and MALDI-TOF mass spectrometry. The target molecules were then used to study their interactions with recombinant galectin-1, and initial1H NMR spectroscopic results are presented to illustrate this approach. These results indicate that, for oligomers containing up to eight sugars, the principal interaction of the binding site of galectin-1 is with the terminal N-acetyllactosamine residues.

The lipooligosaccharide (LOS) of Neisseria meningitidis serogroup B strain NMB contains L2, L3, and novel oligosaccharides, and lacks the lipid-A 4'-phosphate substituent

The complete structure of the lipooligosaccharide (LOS) from Neisseria meningitidis strain NMB (serotype 2b:P1.2,5), a serogroup B cerebrospinal fluid isolate, was determined. Two oligosaccharide (OS) fractions and lipid-A were obtained following mild acid hydrolysis of the LOS. The structures in these fractions were determined using glycosyl composition and linkage analyses, N spectroscopy and mass spectrometry. One oligosaccharide fraction (OS1) consists of a molecule having a glycosyl sequence identical to that previously reported for the LOS from immunotype L2 N. meningitidis [A. Gamain, M. Beurret, F. Michon, J.-R. Brisson, and H.J. Jennings, J. Biol. Chem.,267,(112) 922-925] i.e., a lacto-N-neotetraose is attached to heptose I (Hep I), with terminally linked N-acetylglucosaminosyl and glucosyl residues attached to Hep II of the inner core. Approximately 70% of this structure is acetylated at O-6 of the terminally linked alpha-N-acetyl-glucosaminosyl residue. As with the L2 structure, the NMB LOS contained phosphoethanolamine (PEA) at O-6 or O-7 of the Hep II residue. The second oligosaccharide fraction (OS2) contains a a mixture of three different molecules, all of which vary from one another in their glycosyl substitution patterns of the Hep II residue. The most abundant molecule in OS2 has a structure identical to that of OSI, i.e., it has the L2 glycosyl sequence. A second molecule (OS2a) lacks the terminal glucosyl residue at O-3 of Hep II; i.e., it has a glycosyl sequence identical to that of the mild acid released oligosaccharide of N. meningitidis immunotype L3, L4, or L7 LOSs. The third molecule (OS2b) is a novel structure that lacks the terminal N-acetylglucosaminosyl residue linked to O-2 of Hep II. Overall, 76% of OS released from NMB LOS has the L2 structure, 15% is OS2a (L3), and 9% is OS2b. A portion (20%) of the molecules in the NMB LOS preparation also contained terminally linked sialic acid attached to O-3 of the lacto-N-neotetraose galactosyl residue, which is also consistent with the L3, or L4 LOS structures. In contrast to the previously reported structure of N. meningitidis lipid-A [V. A. Kulshin, U. Zähringer, B. Linder, C.E. Frasch, C-M. Tsai, B.A. Dmitriev, and E.T Rietschel, J. Bacteriol., 174, (1992)1793-1800], only 30% of the lipid-A from NMB LOS possesses 4'-phosphate. Comparison with the lipid-A of LOS purified from an isogenic acapsulate mutant, M7, revealed that the 4'-position was almost completely occupied with phosphate. These data emphasize the structural heterogeneity of the OS and phosphate substituents of Hep II, and 4'-phosphorylation of lipid-A of meningococcal LOS.

Identification of a novel triterpenoid saponin from Pisum sativum as a specific inhibitor of the diguanylate cyclase of Acetobacter xylinum

A specific and highly potent inhibitor of diguanylate cyclase, the key regulatory enzyme of the cellulose synthesizing apparatus in the bacterium Acetobacter xylinum, was isolated from extracts of etiolated pea shoots (Pisum sativum). The inhibitor has been purified by a multistep procedure, and sufficient amounts of highly purified compound (3-8 mg) for spectral analysis were obtained. The structure of this compound was established as 3-O-alpha-L-rhamnopyranosyl-(1-->2)-beta-D-galactopyranosyl-(1--> 2)-beta-D-glucuronopyranosyl soyasapogenol B 22-O-alpha-D-glucopyranoside. The structure was elucidated on the basis of susceptibility to various enzymes, chemical and spectral methods, such as GC-MS, FAB-MS, and the following types of 2D-NMR: COSY, ROESY, TOCSEY, HMQC, HMBC analyses. An identical or a very similar compound with identical biological activity was also isolated from A. xylinum, strongly suggesting that at least certain aspects of cellulose synthesis in the bacteria and in higher plants may be regulated in a similar manner. The content of this saponin in etiolated plants was about 0.04 mumol (g fresh tissue)-1.

NodFE-dependent fatty acids that lack an alpha-beta unsaturation are subject to differential transfer, leading to novel phospholipids

In Rhizobium leguminosarum, the nodABC and nodFEL operons are involved in the production of lipo-chitin oligosaccharide signals that mediate host specificity. A nodFE-determined, highly unsaturated C18:4 fatty acid (trans-2, trans-4, trans-6, cis-11-octadecatetraenoic acid) is essential for the ability of the signals to induce nodule meristems and pre-infection thread structures on the host plant Vicia sativa. Of the nod genes, induction of only nodFE is sufficient to modify fatty acid biosynthesis to yield trans-2, trans-4, trans-6, cis-11-octadecatetraenoic acid, with an absorbance maximum of 303 nm. This unusual C18:4 fatty acid is not only found in the lipo-chitin oligosaccharides but is also associated with the phospholipids (O. Geiger, J. E. Thomas-Oates, J. Glushka, H. P. Spaink, and B. J. J. Lugtenberg, 1994, J. Biol. Chem. 269:11090-11097). Here we report that the phospholipids can contain other nodFE-derived fatty acids, a C18:3 trans-4, trans-6, cis-11-octadecatrienoic acid that has a characteristic absorption maximum at 225 nm, and a C18:2 octadecadienoic acid. Neither this C18:3 nor this C18:2 fatty acid has to date been observed attached to lipo-chitin oligosaccharides, suggesting that an as yet unknown acyl transferase (presumably NodA), responsible for the transfer of the fatty acyl chain to the glycan backbone of the lipo-chitin oligosaccharides, does not transfer all fatty acids synthesized by the action of NodFE to the lipo-chitin oligosaccharides. Rather, it must have a preference for alpha-beta unsaturated fatty acids during transfer.

A method for biotin labeling of biologically active oligogalacturonides using a chemically stable hydrazide linkage

Oligogalacturonides (oligomers of alpha-1,4-D-galacturonic acid) with degrees of polymerization (DP) between 8 and 16 were labeled with biotin using a rapid and simple two-reaction protocol that yields a stable oligogalacturonide derivative. In the first reaction biotin-x-hydrazide was coupled to the anomeric carbon of the reducing galacturonic acid residue by a hydrazone linkage. Carbohydrate-hydrazone linkages such as these have been widely used to label a variety of biomolecules. However, we show herein that the oligogalacturonide-hydrazone linkage is hydrolyzed in water. In the second reaction the hydrazone linkage was reduced with sodium cyanoborohydride to form a stable hydrazide. The stability of hydrazide-linked oligogalacturonides was confirmed using high-performance anion-exchange chromatography (HPAEC). The biotin and uronic acid content of the HPAEC fractions was determined using quantitative colorimetric microplate assays. Electrospray mass spectrometry and 1H NMR spectroscopy were used to confirm the structure of the HPAEC-purified biotin-derivatized oligogalacturonides. Biotin-derivatized oligogalacturonides will be useful in studies of the biological functions of oligogalacturonides.

Structure of the capsular polysaccharide of Clostridium perfringens Hobbs 5 as determined by NMR spectroscopy

The complete primary structure of the capsular polysaccharide of Clostridium perfringens Hobbs 5, an anaerobic bacterium implicated in food poisoning, was determined. The polysaccharide was isolated from C. perfringens Hobbs 5 cells, after deproteination, by ethanol precipitation and by ion-exchange chromatography. The polysaccharide was comprised of glucose, galactose, mannose, N-acetylglucosamine, N-acetylgalactosamine, and glucuronic acid, in equimolar ratios. Sequence and linkage assignments of the glycosyl residues were obtained by NMR spectroscopy, specifically by the combination of two-dimensional homonuclear TOCSY and NOESY experiments and heteronuclear (1H, 13C) multiple-quantum coherence (HMQC, HMQC-COSY, HMQC-TOCSY and HMBC) experiments. Thus, the envelope polysaccharide of C. perfringens Hobbs 5 was found to be a polymer composed of a hexasaccharide repeating unit with the following structure: [formula: see text] This structure is novel among bacterial cell-surface polysaccharides, and it is the first of many serotypically distinct capsular polysaccharides of C. perfringens to be described.

Synthesis and characterization of tyramine-derivatized (1-->4)-linked alpha-D-oligogalacturonides

The reducing end C-1 of (1-->4)-linked alpha-D-oligogalacturonides (oligogalacturonides), with degrees of polymerization (dp) 3 and 13, was coupled to tyramine via reductive amination in the presence of sodium cyanoborohydride. These derivatives were purified in milligram quantities and structurally characterized. Tyramination of trigalacturonic acid proceeded to completion. The yield of apparently homogeneous tyraminated trigalacturonic acid after desalting was 35%. Derivatization of tridecagalacturonide with tyramine was incomplete. The tyraminated tridecagalacturonide was purified to apparent homogeneity using semipreparative high-performance anion-exchange chromatography (HPAEC) with a yield of 30%. The structures of the derivatized oligogalacturonides were established by 1H NMR spectroscopy and electrospray mass spectrometry.

Molecular cloning of a developmentally regulated N-acetylgalactosamine alpha2,6-sialyltransferase specific for sialylated glycoconjugates

A cDNA encoding a novel sialyltransferase has been isolated employing the polymerase chain reaction using degenerate primers to conserved regions of the sialylmotif that is present in all eukaryotic members of the sialyltransferase gene family examined to date. The cDNA sequence revealed an open reading frame coding for 305 amino acids, making it the shortest sialyltransferase cloned to date. This open reading frame predicts all the characteristic structural features of other sialyltransferases including a type II membrane protein topology and both sialylmotifs, one centrally located and the second in the carboxyl-terminal portion of the cDNA. When compared with all other sialyltransferase cDNAs, the predicted amino acid sequence displays the lowest homology in the sialyltransferase gene family. Northern analysis shows this sialyltransferase to be developmentally regulated in brain with expression persisting through adulthood in spleen, kidney, and lung. Stable transfection of the full-length cDNA in the human kidney carcinoma cell line 293 produced an active sialyltransferase with marked specificity for the sialoside, Neu5Ac-alpha2,3Gal-beta1,3GalNAc and glycoconjugates carrying the same sequence such as G(M1b) and fetuin. The disialylated tetrasaccharide formed by reacting the sialyltransferase with the aforementioned sialoside was analyzed by one- and two-dimensional 1H and 13C NMR spectroscopy and was shown to be the Neu5Ac-alpha2,3Gal-beta1,3(Neu5Ac-alpha2,6)GalNAc sialoside. This indicates that the enzyme is a GalNAc alpha-2,6-sialyltransferase. Since two other ST6GalNAc sialyltransferase cDNAs have been isolated, this sialyltransferase has been designated ST6GalNAc III. Of these three, ST6GalNAc III displays the most restricted acceptor specificity and is the only sialyltransferase cloned to date capable of forming the developmentally regulated ganglioside G(D1alpha) from G(M1b).

The structure of a novel polysaccharide produced by Bradyrhizobium species within soybean nodules

Certain strains of Bradyrhizobium japonicum and B. elkanii produce a polysaccharide within the root nodules of their legume host, soybean. These nodule polysaccharides (NPSs) were isolated and characterized. The NPS produced by B. elkanii strains proved to be identical in glycosyl composition and linkages to the extracellular polysaccharide (EPS) of this species indicating that the NPS and EPS for B. elkanii have identical structures (W.F. Dudman, Carbohydr. Res., 66 (1978) 9-23), [formula: see text] However, the structure of the NPS from B. japonicum proved to be quite different from that of its EPS. Methylation analysis of this NPS showed that it consists of 3-linked Gal, 3-linked Rha, 2,4-linked Rha, 4-linked Rha, and terminal 2-O-methyl GlcA in a 1:1:1:1:1 ratio. Stereochemical configurations of the glycosyl residues were determined by the preparation and analysis of trimethylsilyl (Me3Si) (-)-2-butyl glycosides. NMR spectroscopy (both 1H and 13C) showed that the Gal residue is alpha-linked, while all the other glycosyl residues are beta-linked. Oligosaccharides produced by periodate oxidation-Smith degradation were purified, as were oligosaccharides produced by partial acid hydrolysis. Characterization of the Smith degradation products by methylation analysis. NMR spectroscopy, electrospray-mass spectrometry, and characterization of the partial acid hydrolysate oligosaccharides showed that the repeating oligosaccharide unit of the NPS has the structure, [formula: see text]

Structural identification of the lipo-chitin oligosaccharide nodulation signals of Rhizobium loti

Rhizobium loti is a fast-growing Rhizobium species that has been described as a microsymbiont of plants of the genus Lotus. Nodulation studies show that Lotus plants are nodulated by R. loti, but not by most other Rhizobium strains, indicating that R. loti produces specific lipo-chitin oligosaccharides (LCOs) which are necessary for the nodulation of Lotus plants. The LCOs produced by five different Rhizobium loti strains have been purified and were shown to be N-acetylglucosamine pentasaccharides of which the non-reducing residue is N-methylated and N-acylated with cis-vaccenic acid (C18:1) or stearic acid (C18:O) and carries a carbamoyl group. In one R. loti strain, NZP2037, an additional carbamoyl group is present on the non-reducing terminal residue. The major class of LCO molecules is substituted on the reducing terminal residue with 4-O-acetylfucose. Addition of LCOs to the roots of Lotus plants results in abundant distortion, swelling and branching of the root hairs, whereas spot inoculation leads to the formation of nodule primordia.

Branched monosialo gangliosides of the lacto-series isolated from bovine erythrocytes: characterization of a novel ganglioside, NeuGc-isooctaosylceramide

We report the isolation, purification, and structural characterization of three monosialo gangliosides (G-1, G-2, and G-3) from bovine erythrocytes. Each of the purified compounds migrates as a single band on thin-layer chromatography in three solvent systems. All three gangliosides contain ceramide (Cer) as the lipid protein, with d18:1 sphingosine as the predominant long-chain base and with C18:0, C18:1, C20:0, C20:1, and C22:1 fatty acids, as determined by gas chromatography. The structural characterization of the carbohydrate moieties of G-1, G-2, and G-3 involved glycosyl composition analysis, methylation studies, sequential exoglycosidase hydrolysis, and one-dimensional 1H NMR spectroscopy of the native gangliosides. Furthermore, the oligosaccharides were released from the sphingolipids by endoglycoceramidase and fully sequenced by one- and two-dimensional 1H NMR spectroscopy in conjunction with fast-atom-bombardment mass spectrometry and exoglycosidase treatment. The structures are as follows: [formula: see text] Gangliosides such as G-1, G-2, and G-3, with branched oligosaccharide chains comprising a number of N-acetyllactosamine (Gal-GlcNAc) moieties, are abundant in erythrocytes from various mammalian species. The simultaneous occurrence of sialic acid and alpha-galactose as terminal sugars in these gangliosides, however, is relatively rare. Specifically, G-1 represents a ganglioside with a novel structure.

Phospholipids of Rhizobium contain nodE-determined highly unsaturated fatty acid moieties

In Rhizobium leguminosarum the nodABC and nod-FEL operons are involved in the production of lipooligosaccharide signals, which mediate host specificity. A nodE-determined highly unsaturated C18:4 fatty acid (trans-2,trans-4,trans-6,cis-11-octadecatetraenoic acid) is essential for the ability of the signals to induce nodule primordia (Spaink, H. P., Sheeley, D. M., van Brussel, A. A. N., Glushka, J., York, W.S., Tak, T., Geiger, O., Kennedy, E. P., Reinhold, V. N., and Lugtenberg, B. J. J. (1991) Nature 354, 125-130) and preinfection thread structures (van Brussel, A. A. N., Bakhuizen, R., van Spronsen, P. C., Spaink, H. P., Tak, T., Lugtenberg, B. J. J., and Kijne, J. W. (1992) Science 257, 70-72) on the host plant Vicia sativa. We presently focus on the question of how these lipo-oligosaccharide signals are synthesized in Rhizobium. Here we show that after the induction of the nodFE genes, even in the absence of the nodABC genes, the trans-2,trans-4,trans-6,cis-11-octadecatetraenoic acid, which has a characteristic absorbance maximum of 303 nm, is synthesized; this shows that the biosynthesis of the unusual fatty acid is not dependent on the synthesis of the lipooligosaccharides. This finding also suggests that the biosynthesis of the unusual fatty acid is completed before it is linked to the sugar backbone of the lipooligosaccharide. In an attempt to identify the lipid fraction with which the unusual C18:4 fatty acid is associated, we found that it is linked to the sn-2 position of the phospholipids. Even when lipooligosaccharide signals are produced in a wild type Rhizobium cell, a fraction of the unusual fatty acid is still bound to all major phospholipids. These findings offer interesting possibilities. 1) The phospholipids might be biosynthetic intermediates for the synthesis of lipooligosaccharide signals, and 2) phospholipids, containing nodFE-derived fatty acids, might have a signal function of their own.

Structural characterization of the N-glycans of a humanized anti-CD18 murine immunoglobulin G

This study characterized the N-glycans of a humanized immunoglobulin G4 (IgG4) expressed in NS/O mouse myeloma cells and directed against the CD18 family of adhesion-promoting receptors on leukocytes. The N-glycans were released from the purified recombinant IgG by N-glycanase treatment, purified by Sephadex G50 chromatography, and fractionated by Bio-Gel P-4 chromatography into three oligosaccharide pools. Each pool was analyzed individually by glycosyl composition analysis, high-pH anion-exchange chromatography with pulsed amperometric detection (HPAEC-PAD), 600-MHz 1H-NMR spectroscopy, and electrospray-ionization mass spectrometry. In addition, each of the three pools was subfractionated by HPAEC and the isolated subfractions that contained sufficient material were hydrolyzed and analyzed for glycosyl composition by HPAEC-PAD. The overall results indicate the presence of five oligomannoside-type structures (containing 5 to 8 Man residues) which are not usually found in IgG, and the presence of eight diantennary (mostly truncated) N-acetyllactosamine-type structures which are typical of mouse and human IgGs. The N-acetyllactosamine-type structures were heterogeneous with regard to alpha(1-->6) fucosylation of the linkage GlcNAc, and the presence or absence of GlcNAc and/or Gal beta(1-->4)GlcNAc extending the core pentasaccharide (Man3GlcNAc2). No evidence was found for the presence of sialic acid or bisecting GlcNAc residues on the N-acetyllactosamine-type chains. The latter finding suggests that the N-glycans of this humanized IgG are of the mouse type.

The structures and biological activities of the lipo-oligosaccharide nodulation signals produced by type I and II strains of Bradyrhizobium japonicum

Bradyrhizobium japonicum produces lipo-oligosaccharide signal molecules that induce deformation of root hairs and meristematic activity on soybeans. B. japonicum USDA135 (a Type I strain) produces modified chitin pentasaccharide molecules with either a terminal N-C16:0- or N-C18:1-glucosamine with and without an O-acetyl group at C-6 and with 2-O-methylfucose linked to C-6 of the reducing N-acetylglucosamine. An additional molecule has N-C16:1-glucosamine and no O-acetyl group. All of these molecules cause root hair deformation on Vicia sativa and Glycine soja. The C18:1-containing molecules were tested and found to induce meristem formation on G. soja. USDA61 (a Type II strain) produces eight additional molecules. Five have a carbamoyl group on the terminal N-acylglucosamine. Six have chitin tetrasaccharide backbones. Three have a terminal N-acyl-N-methylglucosaminosyl residue. In four molecules, the reducing-end N-acetylglucosamine is glycosidically linked to glycerol and has a branching fucosyl, rather than a 2-O-methylfucosyl, residue. One molecule has a terminal N-acylglucosamine that has both acetyl and carbamoyl groups (one each).

Identification and structural analysis of the tetrasaccharide NeuAc alpha(2-->6)Gal beta(1-->4)GlcNAc beta(1-->3)Fuc alpha 1-->O-linked to serine 61 of human factor IX

O-Linked fucose has been found attached to Thr/Ser residues within the sequence Cys-X-X-Gly-Gly-Thr/Ser-Cys in the N-terminal EGF domains of several coagulation/fibrinolytic proteins. Carbohydrate composition and mass spectrometric analyses of tryptic and thermolytic peptides containing the corresponding site (Ser-61) in the first EGF domain of human factor IX indicated the presence of a tetrasaccharide containing one residue each of sialic acid, galactose, N-acetylglucosamine, and fucose. The Ser-61 tetrasaccharide was not susceptible to alpha-fucosidase digestion. Fragments generated during mass spectrometric analysis indicated that fucose was the attachment sugar residue. The involvement of fucose in the carbohydrate-peptide linkage was confirmed by two-dimensional 1H NMR spectroscopic analysis of the glycopeptide containing factor IX residues 57-65. The complete structure of the tetrasaccharide was obtained by methylation analysis and two-dimensional 1H TOCSY and ROESY experiments as NeuAc alpha(2-->6)Gal beta(1-->4)GlcNAc beta(1-->3)Fuc alpha 1-->O-Ser61.

Human non-secretory ribonucleases. II. Structural characterization of the N-glycans of the kidney, liver and spleen enzymes by NMR spectroscopy and electrospray mass spectrometry

The N-glycans have been removed by peptide-N-glycosidase F (PNGase F) from purified human non-secretory RNases derived from kidney, liver and spleen. The spleen RNase was purified by two procedures, one of which did not include the usual acid treatment step (0.25 M H2SO4, 45 min, 4 degrees C), to determine if acid treatment alters the carbohydrate moieties. The N-glycans of the RNases were fractionated by Bio-Gel P-4 chromatography and analysed by 600 MHz 1H-NMR spectroscopy and electrospray mass spectrometry. All four non-secretory RNase preparations contained the following structures: [formula: see text] The relative amounts of the trisaccharide, pentasaccharide and hexasaccharide appeared to vary slightly in the different tissue RNases. The overall results indicate: (i) that acid treatment during purification does not alter the N-glycans of non-secretory RNases; (ii) that the N-glycans from kidney, liver and spleen non-secretory RNases are very similar, if not identical, to one another, but different from the N-glycan structures reported for secretory RNase.

Structural characterization of novel inositol phosphosphingolipids of Tritrichomonas foetus and Trichomonas vaginalis

Two major ethanolamine phosphate-substituted inositol phosphosphingolipids have been identified in the unsaponifiable acidic lipid fractions of Tritrichomonas foetus and Trichomonas vaginalis. The compounds were radiolabelled and purified by high-performance thin-layer chromatography followed by high-performance liquid chromatography. The structures were determined by a combination of tandem mass spectrometry (MS/MS) and nuclear magnetic resonance (NMR) experiments, and gas-liquid chromatography of components obtained by degradation and derivatization. Inositol in the T. foetus component was 1-linked to the phosphosphingolipid, had the phosphoethanolamine group at the 3-position and a fucosyl residue at the 4-position. The T. vaginalis component lacked the fucosyl moiety. Both organisms also produced inositol phosphosphingolipids having the same long-chain base (sphingosine or dihydrosphingosine) and the same fatty acyl distribution as the inositol diphosphate compounds. These glycosphingolipids may represent metabolic intermediates for new types of membrane anchors for surface glycopeptides or glycolipids that mediate the host-parasite relationship of these trichomonads. The MS/MS and NMR spectroscopic data should provide reference information for structural determinations of other phosphorylated inositol derivatives.

Complete structure of the adhesin receptor polysaccharide of Streptococcus oralis ATCC 55229 (Streptococcus sanguis H1)

This report describes the determination of the complete primary structure of the adhesin receptor polysaccharide of Streptococcus oralis ATCC 55229 (previously characterized as Streptococcus sanguis H1), a Gram-positive bacteria implicated in dental plaque formation. The polysaccharide was isolated from S. oralis ATCC 55229 cells after deproteination, enzymatic hydrolysis, and ion exchange chromatography. It was shown to consist of rhamnose, galactose, glucose, glycerol, and phosphate, in molar ratios of 2:3:1:1:1. Sequence and linkage assignments of the glycosyl residues were obtained by methylation analysis followed by gas-liquid chromatography and electron-impact mass spectrometry. 31P NMR spectroscopy revealed that phosphate was present in a diester, connecting glycerol to one of the galactosyl residues. High-performance liquid chromatography of a partial acid hydrolysate of the polysaccharide confirmed this finding by showing galactose 6-phosphate and glycerol 1-phosphate. The structural determination was completed by the combination of two-dimensional homonuclear Hartmann-Hahn and NOE experiments and heteronuclear [1H,13C] and [1H,31P] multiple-quantum coherence experiments. Thus, the adhesin receptor polysaccharide of S. oralis ATCC 55229 was found to be a polymer composed of hexasaccharide repeating units that contain glycerol linked through a phosphodiester to C6 of the alpha-galactopyranosyl residue and are joined end-to-end through galactofuranosyl-beta(1-->3)-rhamnopyranosyl linkages: [formula: see text] This structure is novel among bacterial cell surface polysaccharides in general and specifically among those implicated in dental plaque formation.

Structural elucidation of a novel family of acyltrehaloses from Mycobacterium tuberculosis

Analysis of the lipids of Mycobacterium tuberculosis H37Rv, by both normal- and reverse-phase thin-layer chromatography, revealed a series of novel glycolipids based on 2,3-di-O-acyltrehalose. The structures of these acylated trehaloses were elucidated by a combination of gas chromatography-mass spectrometry, 1H, 13C, two-dimensional 1H-1H, and 1H-13C nuclear magnetic resonance spectrometry. The fatty acyl substituents were mainly of three types: saturated straight-chain C16-C19 acids; C21-C25 "mycosanoic acids"; and C24-C28 "mycolipanolic acids." Analysis of one of the major 2,3-di-O-acyltrehaloses by two-dimensional 1H-chemical shift correlated and 1H-detected heteronuclear multiple-bond correlation spectroscopy established that the C18 saturated straight-chain acyl group was located at the 2 position and that the C24 mycosanoyl substituent was at the 3 position of the same "right-hand" glucosyl residue. At least six molecular species differing only in their fatty acid content comprised this family of di-O-acylated trehaloses. We regard these acyltrehaloses as elemental forms of the multiglycosylated acyltrehaloses (the lipooligosaccharides) perhaps due to an inability of the majority of isolates of virulent tubercle bacilli to glycosylate core acyltrehaloses. The acyltrehaloses are minor but consistent components of virulent M. tuberculosis and apparently the basis of the specific serological activity long associated with its lipid fractions.

A 2-O-methylfucose moiety is present in the lipo-oligosaccharide nodulation signal of Bradyrhizobium japonicum

Bradyrhizobium japonicum is a soil bacterium that forms nitrogen-fixing nodules on the roots of the agronomically important legume soybean. Microscopic observation of plant roots showed that butanol extract of B. japonicum strain USDA110 cultures induced for nod gene expression elicited root hair deformation, an early event in the nodulation process. The metabolite produced by B. japonicum responsible for root hair deformation activity was purified. Chemical analysis of the compound revealed it to be a pentasaccharide of N-acetylglucosamine modified by a C18:1 fatty acyl chain at the nonreducing end. In these respects, the B. japonicum metabolite is similar to the lipo-oligosaccharide signals described from Rhizobium species. However, the B. japonicum compound is unique in that an additional sugar, 2-O-methylfucose, is linked to the reducing end. Comparative analysis of the B. japonicum Nod metabolite and those characterized from Rhizobium species suggests that the presence of the fucosyl residue plays an important role in the specificity of the B. japonicum-soybean symbiosis. The availability of the purified B. japonicum nodulation signal should greatly facilitate further studies of soybean nodulation.

A novel highly unsaturated fatty acid moiety of lipo-oligosaccharide signals determines host specificity of Rhizobium

In Rhizobium leguminosarum biovar viciae, the nodABC and nodFEL operons are involved in the production of lipo-oligosaccharide signals which mediate host specificity. The structure of these metabolites and those produced in nod mutants links the nodE and nodL genes to specific chemical features of the signal molecules. A nodE-determined, highly unsaturated fatty acid and a nodL-determined O-acetyl substituent are essential for the ability of the signals to induce nodule meristems on the host plant Vicia sativa.

The binding of ATP and AMP to Escherichia coli adenylate kinase investigated by 1H and 15N NMR spectroscopy

[N6 15N]ATP and [N6 15N]AMP, complexed with E.coli adenylate kinase (AKe), were observed with 15N isotope-filtered NMR pulse sequences and 1H[15N] heterocorrelated experiments to determine differences between binding sites based on chemical shifts and competition by substrate analogs. The chemical shifts of the N6 amino proton and nitrogen signals changed significantly after mixing with adenylate kinase. Differences in chemical shifts between the bound ATP and AMP signals are slight. The response of these shifts to further addition of other substrates or Mg2+ supports the view that the unchelated nucleotides can bind to both the sites, whereas the metal complexed species are restricted to the MgATP/MgADP binding site.

Observation of arginyl-deoxyoligonucleotide interactions in Taq I endonuclease by detection of specific 1H NMR signals from 140kD [N eta 1, N eta 2, 15N Arg]Taq I/oligomer complexes

Proton and nitrogen signals of the guanidinium amines in [N eta 1, N eta 2 15N Arg]Taq I endonuclease were observed using isotope filtered experiments and proton detected 1H[15N] heterocorrelated two dimensional NMR spectroscopy. These rapidly exchanging protons could be detected in the free enzyme only at pH 4.5; at pH 8.5, no signals were measured after extensive signal averaging. Addition of deoxyribonucleotide oligomers resulted in the appearance of two groups of signals at about 6.8 and 7.5 ppm. Since these signals are independent of the presence of cognate sequence or Mg2+, it is assumed they represent nonspecific arginyl-DNA interactions. This labeling/NMR approach provides a new method for investigating the role of arginine in protein-DNA interactions.