A high-resolution measurement of nucleotide sugars by using ion-pair reverse chromatography and tandem columns.

N-Linked glycosylation is a cellular process transferring sugars from glycosyl donors to proteins or lipids. Biopharmaceutical products widely produced by culturing mammalian cells such as Chinese hamster ovary (CHO) cells are typically glycosylated during biosynthesis. For some biologics, the N-linked glycan is a critical quality attribute of the drugs. Nucleotide sugars are the glycan donors and impact the intracellular glycosylation process. In current analytical methods, robust separation of nucleotide sugar isomers such as UDP glucose and UDP galactose remains a challenge because of their structural similarity. In this study, we developed a strategy to resolve the separation of major nucleotide sugars including challenging isomers based on the use of ion-pair reverse phase (IP-RP) chromatography. The strategy applies core-shell columns and connects multiple columns in tandem to increase separation power and ultimately enables high-resolution detection of nucleotide sugars from cell extracts. The key parameters in the IP-RP method, including temperature, mobile phase, and flow rates, have been systematically evaluated in this work and the theoretical mechanisms of the chromatographic behavior were proposed. Graphical abstract.

Multiplexed Capillary Electrophoresis as Analytical Tool for Fast Optimization of Multi-Enzyme Cascade Reactions - Synthesis of Nucleotide Sugars: Dedicated to Prof. Dr. Vladimir Kren on the occasion of his 60th birthday.

Nucleotide sugars are considered as bottleneck and expensive substrates for enzymatic glycan synthesis using Leloir-glycosyltransferases. Synthesis from cheap substrates such as monosaccharides is accomplished by multi-enzyme cascade reactions. Optimization of product yields in such enzyme modules is dependent on the interplay of multiple parameters of the individual enzymes and governed by a considerable time effort when convential analytic methods like capillary electrophoresis (CE) or HPLC are applied. We here demonstrate for the first time multiplexed CE (MP-CE) as fast analytical tool for the optimization of nucleotide sugar synthesis with multi-enzyme cascade reactions. We introduce a universal separation method for nucleotides and nucleotide sugars enabling us to analyze the composition of six different enzyme modules in a high-throughput format. Optimization of parameters (T, pH, inhibitors, kinetics, cofactors and enzyme amount) employing MP-CE analysis is demonstrated for enzyme modules for the synthesis of UDP-α-D-glucuronic acid (UDP-GlcA) and UDP-α-D-galactose (UDP-Gal). In this way we achieve high space-time-yields: 1.8 g/L⋆h for UDP-GlcA and 17 g/L⋆h for UDP-Gal. The presented MP-CE methodology has the impact to be used as general analytical tool for fast optimization of multi-enzyme cascade reactions.

Characterization of GDP-alpha-D-arabinopyranose, the precursor of D-Arap in Leishmania major lipophosphoglycan.

Protozoan parasites of the genus Leishmania synthesize a complex lipophosphoglycan (LPG), which is the major cell surface macromolecule. The LPG from Leishmania major contains beta-D-Arap-terminating side chains that are involved in regulating the attachment of the parasite to the midgut epithelium of its insect vector. An arabinose sugar nucleotide donor was identified in soluble extracts of L. major promastigotes. This sugar nucleotide was biosynthetically labeled with D-[2-3H]Glc and with D-[5-3H]Ara. The labeled sugar nucleotide generated [3H]Ara and GDP after mild acid hydrolysis. The absolute configuration of the arabinose was determined after reduction and acylation with a pure enantiomer of Mosher's acid chloride. The pyranose ring configuration was inferred from the ability of GDP-Ara to form borate complexes, and the anomeric configuration was deduced from the results of mild base hydrolysis experiments. Taken together these data suggest that the sugar nucleotide has the structure GDP-alpha-D-Arap. This sugar nucleotide has not been previously described from natural sources and may be unique to trypanosomatid protozoan parasites. Ara-1-PO4 and GDP-Ara were the only soluble metabolites labeled with [3H]Ara, and pulse-chase experiment data are consistent with them being precursors of the arabinosyl residues of LPG.

Proposed pathway for biosynthesis of the S-layer glycoprotein of Bacillus alvei.

The outer surface of the murein sacculus of the eubacterium Bacillus alvei is covered by a surface layer (S-layer) glycoprotein. The glycan chain of this S-layer glycoprotein consists of trisaccharide repeating units with ManNAc, Gal, and Glc as constituents. From cell extracts of B. alvei, nucleotide-activated derivatives of ManNAc, Gal, Glc, and GlcNAc were isolated. Furthermore, GDP- and dolichyl-activated oligosaccharides were obtained. On the basis of the isolated putative glycoprotein precursors, a pathway for the biosynthesis of the oligosaccharide chain is proposed.

Determination of poly(ADP-ribose) chain length distribution on polyacrylamide gels by silver staining.

Silver staining and polyacrylamide gel electrophoresis were used to visualize chain length distribution of poly(ADP-ribose) enzymatically synthesized from NAD by rat liver nuclei. The method described has the advantage that synthesis does not require radioactive-labeled NAD, and microgram quantities (greater than 5 micrograms) of poly(ADP-ribose) can be resolved and visualized as discrete bands according to chain lengths which range from 8 to 60 residues. This method can be applied to estimate size distribution of poly(ADP-ribose) chains in cells or tissues.

Characterization of poly(ADP-ribosyl)ated domains of rat pachytene chromatin.

Poly(ADP-ribosyl)ation of nuclear proteins was several-fold higher in the pachytene spermatocytes than in the premeiotic germ cells of the rat. Among the histones of the pachytene nucleus, histone subtypes H2A, H1 and H3 were poly(ADP-ribosyl)ated. Based on the immunoaffinity fractionation procedure of Malik, Miwa, Sugimara & Smulson [(1983) Proc. Natl. Acad. Sci. U.S.A. 80, 2554-2558] we have fractionated DNAase-II-solubilized chromatin into poly(ADP-ribosyl)ated chromatin (PAC) and non-poly(ADP-ribosyl)ated chromatin (non-PAC) domains on an anti-[poly(ADP-ribose)] IgG affinity matrix. Approx. 2.5% of the pachytene chromatin represented the PAC domains. A significant amount of [alpha-32P]dATP-labelled pachytene chromatin (labelled in vitro) was bound to the affinity matrix. The DNA of pachytene PAC domains had internal strand breaks, significant length of gaps and ligatable ends, namely 5'-phosphoryl and 3'-hydroxyl termini. On the other hand, the PAC domains from 18 h regenerating liver had very few gaps, if any. The presence of gaps in the pachytene PAC DNA was also evident from thermal denaturation studies. Although many of the polypeptides were common to the PAC domains of both pachytene and regenerating liver, the DNA sequences associated with these domains were quite different. A 20 kDa protein and the testis-specific histone H1t were selectively enriched in the pachytene PAC domains. The pachytene PAC domains also contained approx. 10% of the messenger coding sequences present in the DNAase-II-solubilized chromatin. The pachytene PAC domains, therefore, may represent highly enriched DNA-repair domains of the pachytene nucleus.

Comparison of the HPLC-separated species patterns of phosphatidic acid, CDP-diacylglycerol and diacylglycerol synthesized de novo in rat liver microsomes (a new method).

The species pattern of phosphatidic acid was compared with that of CDP-diacylglycerol and diacylglycerol synthesized de novo by glycerol 3-phosphate acylation in a CoA ester-generating system in liver microsomes. The similarity of the species patterns of phosphatidic acid and CDP-diacylglycerol indicated that the CTP-phosphatidyl cytidylyltransferase showed no selectivity for individual species of its phosphatidic acid substrate. Since the species pattern of diacylglycerol deviated from that of phosphatidic acid, a slight acyl selectivity of the phosphatidic acid phosphohydrolase or a slight inhomogeneity of its substrate pool might be assumed. For the determination of the molecular species of CDP-diacylglycerol, a new method was developed. By incubation of CDP-diacylglycerol with oligonucleate 5'-nucleotidohydrolase (phosphodiesterase), phosphatidic acid was produced. The CDP-diacylglycerol-derived phosphatidic acid was methylated with diazomethane and then separated by reverse-phase HPLC in 15 molecular species.

Removal of contaminating nucleoside diphosphates from commercial preparations of uridine diphosphoglucose.

Nucleoside diphosphate contamination in commercial preparations of UDP-Glc poses potential problems in activity assays for enzymes that use this substrate. For removing these contaminants, we report a simple, inexpensive, and rapid method that obviates the need for uncertain corrections in assay calculations.

High-performance liquid chromatography of in vitro synthesized poly(ADP-ribose) on ion-exchange columns, separation of oligomers of varying chain length and estimation of apparent branching.

Separated macromolecular fractions of in vitro synthesized poly(ADP-ribose) by liver nuclei were subjected to ion-exchange chromatography in a programmed high-performance liquid chromatographic elution system. The effects of ionic strength, pH and temperature on the separation of poly(ADP-ribose) chains were determined. Short chain oligomers (up to n = 11) were fractionated into individual components by baseline separation. Each fraction was analyzed for chain length. Trace amounts of Ado(P)Rib(P)Rib(P) found in phosphodiesterase digests were taken as indication of apparent branching. In phosphodiesterase digests of the shorter oligomers, besides traces of the above component, two other digestion products were also observed, presumably representing oligomer termini, one terminal fragment being dominant in short oligomers. Medium and long chain oligomers were partly resolved to individual components, and especially the long oligomers exhibited marked temperature dependent elution patterns. Apparent branching increased with increasing chain length up to about 3% for n = 44 and components presumably indicating termini diminished to mere traces. The adenine spectra of all fractions identified individual components.

Isolation of adenosine 5'-diphosphate-L-glycero-D-mannoheptose, the assumed substrate of heptose transferase(s), from Salmonella minnesota R595 and Shigella sonnei Re mutants.

From heptose transferase-less Re mutants of Salmonella minnesota and Shigella sonnei, a mixture of nucleotide-linked heptoses was isolated. After paper chromatography in different solvent systems, ADP derivatives of D-glycero-D-mannoheptose and L-glycero-D-mannoheptose could be isolated in pure form. The structure of ADP-L-glycero-D-mannoheptose was verified by analytical methods and by transformation of ADP-D-glycero-D-mannoheptose with ADP-D-glycero-D-mannoheptose-6-epimerase.

Separation of poly(ADP-ribose) by high-performance liquid chromatography.

The homopolymer of ADP-ribose, poly(ADP-ribose), was synthesized in vitro by liver nuclei from NAD. The protein-poly(ADP-ribose) adducts were isolated and, after base hydrolysis or proteolysis by proteinase K, the free polymers were separated from NAD, ADP-ribose, AMP and adenosine, and quantitatively determined by reversed-phase chromatography on an Ultrasphere ODS 5-micron column. Oxidation of the polymer by sodium periodate and labeling with 3H by borotritiation maintained the polymeric structure, but its modification was detectable by the chromatographic system employed.

Simultaneous determination of linear and branched residues in poly(ADP-ribose).

Methodology for the routine and simultaneous determination of the linear and branched residues of poly(ADP-ribose) is described. The main features of the procedure consist of the isolation of poly(ADP-ribose) by affinity chromatography; enzymatic digestion of the polymer to the unique nucleosides ribosyladenosine and diribosyladenosine which are derived from linear and branched residues, respectively; formation of fluorescent derivatives of ribosyladenosine and diribosyladenosine; and identification and quantification of these compounds by high-pressure liquid chromatography coupled with fluorescence detection. A variation on the methodology which allows the detection and quantification of ribosyladenosine and diribosyladenosine without formation of their fluorescent derivatives is also presented. Analyses of several cell lines for their capacity to synthesize poly(ADP-ribose) with a branched structure showed that the proportion of branched sites was constant (0.7-0.8%) in each of the cell lines.

Isolation of adenosine 5'-diphosphate-D-glycero-D-mannoheptose. An intermediate in lipopolysaccharide biosynthesis of Shigella sonnei.

From a Shigella sonnei R mutant which incorporates into its cell wall lipopolysaccharide D-glycero-D-mannoheptose and contains no L-glycero-D-mannoheptose, a nucleotide-linked sugar was isolated and identified as adenosine 5'-diphosphate-D-glycero-d-mannoheptose by chemical and chromatographic analysis. This intermediary compound is assumed to play a role in heptose biosynthesis of Enterobacteria.