Structural analysis of N-glycans from yellow lupin (Lupinus luteus) seed diphosphonucleotide phosphatase/phosphodiesterase

N-Glycomic and Microscopic Subcellular Localization Analyses of NPP1, 2 and 6 Strongly Indicate that trans-Golgi Compartments Participate in the Golgi to Plastid Traffic of Nucleotide Pyrophosphatase/Phosphodiesterases in Rice

Nucleotide pyrophosphatase/phosphodiesterases (NPPs) are widely distributed N-glycosylated enzymes that catalyze the hydrolytic breakdown of numerous nucleotides and nucleotide sugars. In many plant species, NPPs are encoded by a small multigene family, which in rice are referred to NPP1-NPP6 Although recent investigations showed that N-glycosylated NPP1 is transported from the endoplasmic reticulum (ER)-Golgi system to the chloroplast through the secretory pathway in rice cells, information on N-glycan composition and subcellular localization of other NPPs is still lacking. Computer-assisted analyses of the amino acid sequences deduced from different Oryza sativa NPP-encoding cDNAs predicted all NPPs to be secretory glycoproteins. Confocal fluorescence microscopy observation of cells expressing NPP2 and NPP6 fused with green fluorescent protein (GFP) revealed that NPP2 and NPP6 are plastidial proteins. Plastid targeting of NPP2-GFP and NPP6-GFP was prevented by brefeldin A and by the expression of ARF1(Q71L), a dominant negative mutant of ADP-ribosylation factor 1 that arrests the ER to Golgi traffic, indicating that NPP2 and NPP6 are transported from the ER-Golgi to the plastidial compartment. Confocal laser scanning microscopy and high-pressure frozen/freeze-substituted electron microscopy analyses of transgenic rice cells ectopically expressing the trans-Golgi marker sialyltransferase fused with GFP showed the occurrence of contact of Golgi-derived membrane vesicles with cargo and subsequent absorption into plastids. Sensitive and high-throughput glycoblotting/mass spectrometric analyses showed that complex-type and paucimannosidic-type glycans with fucose and xylose residues occupy approximately 80% of total glycans of NPP1, NPP2 and NPP6. The overall data strongly indicate that the trans-Golgi compartments participate in the Golgi to plastid trafficking and targeting mechanism of NPPs.

Comparative analysis of N-glycans in the ungerminated and germinated stages of Oryza sativa

All fundamental information such as signal transduction, metabolic control, infection, cell-to-cell signaling, and cell differentiation related to the growth of plants are preserved in germs. In preserving these information, glycans have a key role and are involved in the development and differentiation of organisms. Glycans which exist in rice germ are expected to have an important role in germination. In this study, we performed structural and correlation analysis of the N-glycans in rice germ before and after germination. Our results confirmed that the N-glycans in the ungerminated stage of the rice germ had low number of N-glycans consisting only of six kinds especially with high-mannose and paucimannose type N-glycans being 16.0% and 76.7%, respectively. On the other hand, after 48 hours germinated germ stage, there was an increase in the complex type N-glycans with the appearance of Lewis a structure, the most complex type and a decrease in paucimannose types. These results suggest that at least six kinds of N-glycans are utilized for long time preservation of rice seed, while the diversification of most complex types of N-glycans is produced an environment dependent for shoot formation of rice.

In-depth glycoproteomic characterization of γ-conglutin by high-resolution accurate mass spectrometry

The molecular characterization of bioactive food components is necessary for understanding the mechanisms of their beneficial or detrimental effects on human health. This study focused on γ-conglutin, a well-known lupin seed N-glycoprotein with health-promoting properties and controversial allergenic potential. Given the importance of N-glycosylation for the functional and structural characteristics of proteins, we studied the purified protein by a mass spectrometry-based glycoproteomic approach able to identify the structure, micro-heterogeneity and attachment site of the bound N-glycan(s), and to provide extensive coverage of the protein sequence. The peptide/N-glycopeptide mixtures generated by enzymatic digestion (with or without N-deglycosylation) were analyzed by high-resolution accurate mass liquid chromatography-multi-stage mass spectrometry. The four main micro-heterogeneous variants of the single N-glycan bound to γ-conglutin were identified as Man2(Xyl) (Fuc) GlcNAc2, Man3(Xyl) (Fuc) GlcNAc2, GlcNAcMan3(Xyl) (Fuc) GlcNAc2 and GlcNAc 2Man3(Xyl) (Fuc) GlcNAc2. These carry both core β1,2-xylose and core α1-3-fucose (well known Cross-Reactive Carbohydrate Determinants), but corresponding fucose-free variants were also identified as minor components. The N-glycan was proven to reside on Asn131, one of the two potential N-glycosylation sites. The extensive coverage of the γ-conglutin amino acid sequence suggested three alternative N-termini of the small subunit, that were later confirmed by direct-infusion Orbitrap mass spectrometry analysis of the intact subunit.

Comparative analysis of involvement of UGT1 and UGT2 splice variants of UDP-galactose transporter in glycosylation of macromolecules in MDCK and CHO cell lines

Nucleotide sugar transporters deliver nucleotide sugars into the Golgi apparatus and endoplasmic reticulum. This study aimed to further characterize mammalian UDP-galactose transporter (UGT) in MDCK and CHO cell lines. MDCK-RCA^r and CHO-Lec8 mutant cell lines are defective in UGT transporter, although they exhibit some level of galactosylation. Previously, only single forms of UGT were identified in both cell lines, UGT1 in MDCK cells and UGT2 in CHO cells. We have identified the second UGT splice variants in CHO (UGT1) and MDCK (UGT2) cells. Compared to UGT1, UGT2 is more abundant in nearly all examined mammalian tissues and cell lines, but MDCK cells exhibit different relative distribution of both splice variants. Complementation analysis demonstrated that both UGT splice variants are necessary for N- and O-glycosylation of proteins. Both mutant cell lines produce chondroitin-4-sulfate at only a slightly lower level compared to wild-type cells. This defect is corrected by overexpression of both UGT splice variants. MDCK-RCA^r mutant cells do not produce keratan sulfate and this effect is not corrected by either UGT splice variant, overexpressed either singly or in combination. Here we demonstrate that both UGT splice variants are important for glycosylation of proteins. In contrast to MDCK cells, MDCK-RCA^r mutant cells may possess an additional defect within the keratan sulfate biosynthesis pathway.

Overexpression of UDP-GlcNAc transporter partially corrects galactosylation defect caused by UDP-Gal transporter mutation

Nucleotide sugar transporters deliver substrates for glycosyltransferases into the endoplasmic reticulum and the Golgi apparatus. We demonstrated that overexpression of UDP-GlcNAc transporter (NGT) in MDCK-RCA(r) and CHO-Lec8 mutant cells defective in UDP-Gal transporter (UGT) restored galactosylation of N-glycans. NGT overexpression resulted in decreased transport of UDP-GlcNAc into the Golgi vesicles. This effect resembled the phenotype of mutant cells corrected by UGT1 overexpression. The transport of UDP-Gal was not significantly changed. Our data suggest that the biological function of UGT and NGT in galactosylation of macromolecules may be coupled.

Diphosphonucleotide phosphatase/phosphodiesterase (PPD1) from yellow lupin (Lupinus luteus L.) contains an iron-manganese center

Yellow lupin diphosphonucleotide phosphatase/phosphodiesterase (PPD1) represents a novel group of enzymes. Here we report that it possesses one iron atom and one manganese atom (1:1 molar ratio) per subunit. The enzyme exhibits visible absorption maximum at approximately 530 nm. Prolonged oxidation of PPD1 leads to loss of the charge-transfer band and catalytic activity, whereas after reduction PPD1 remains active. Replacement of conserved amino-acid residues coordinating metals results in the loss of enzymatic activity. Despite low amino-acid sequence homology of PPD1 to well-characterized approximately 55-kDa purple acid phosphatases, their overall fold, topology of active center and metal content are highly similar.

Expression and purification of active plant diphosphonucleotide phosphatase/phosphodiesterase from baculovirus-infected insect cells

We have previously purified and characterized a diphosphonucleotide phosphatase/phosphodiesterase (PPD1) from yellow lupin seeds. This report describes an efficient strategy for overexpression in baculovirus-infected Spodoptera frugiperda Sf9 cells and purification of a functional PPD1 enzyme. We tested six variants of recombinant PPD1, differing in secretion peptides, fusion tags, and promoters. The highest expression level of the active PPD1 was achieved when the native signal peptide and the C-terminal V5-6His tag were attached. This recombinant protein was secreted at very high level (18.4 mg/L) to serum-free medium. Single-step purification procedure using metal affinity chromatography resulted in the homogeneous PPD1. The overexpressed protein showed enzymatic activity comparable to the native enzyme isolated previously from plant material. We showed that PPD1, which belongs to purple acid phosphatase family, formed tetrameric structure, which is non-typical for this group of enzymes.

Purification and characterization of a β-xylosidase from potatoes (Solanum tuberosum)

Potatoes are a cheap and easily available source for the preparation of beta 1,2-xylosidase. The soluble enzyme was purified from potato tubers by ammonium sulfate precipitation, hydrophobic interaction chromatography, affinity gel blue chromatography, ion exchange and size exclusion chromatography yielding a glycoprotein with a molecular weight of 39-40 kDa, an isoelectric point of 5.1 and a typical plant N-glycosylation pattern. The enzyme releases xylose residues beta1,2-linked to the beta-mannose of an N-glycan core, if the 3-position of this mannose is not occupied. It showed an optimal enzymatic activity at pH 4.0-4.5 and at a temperature of 50 degrees C. The activity was reduced in the presence of Ni(2+) and Cu (2+) and slightly increased by the addition of Mn(2+) or Ca(2+). At 37 degrees C the cleavage of xylose from p-nitrophenyl-beta-xylopyranoside or appropriate pyridylaminated N-glycans was proportional to the time of incubation over a period of 8 h and increased with time for at least 24 h. N-Methoxycarbonylpentyl-1,5-dideoxy-1,5-iminoxylitol inhibits the enzyme effectively. Sequencing of the N-terminus showed a high homology to a number of isoforms of patatin, the main protein of potato tubers. This enzyme will be an important tool for the analysis of N-glycans and in the modification of N-glycans for immunological studies.

Processing of N-glycans of two yellow lupin phosphohydrolases during seed maturation and dormancy

Acid phosphatase (AP) and diphosphonucleoside phosphatase/phosphodiesterase (PPD1) were purified from yellow lupin (Lupinus luteus L.) immature green seeds (40 days after blooming), dry seeds (40 days later) and dry seeds stored for 160 days. Both enzymes are known to differ in the type of N-glycosylation: the first has an N-glycosylation pattern typical for a vacuolar protein, while the second enzyme has a pattern typical for an extracellular or membrane-bound protein. N-Glycans were released from each of the enzyme preparations, fluorescence labeled, separated and identified by HPLC (GlycoSep N and GlycoSep H columns). Changes in the level of each N-glycan during seed maturation and dormancy were compared. The results show that N-glycan processing in the case of AP and PPD1-two proteins residing in the same plant organ, but possibly in different compartments-is not synchronized and performed not only in metabolically active maturing seeds, but also in metabolically inactive dormant seeds.

Diphosphonucleotide phosphatase/phosphodiesterase from yellow lupin (Lupinus luteus L.) belongs to a novel group of specific metallophosphatases

A cDNA encoding previously purified and characterized diphosphonucleotide phosphatase/phosphodiesterase (PPD1) from yellow lupin (Lupinus luteus L.) was identified. The ppd1 gene encodes a protein containing a cleavable signal sequence. A functional expression of PPD1 in Saccharomyces cerevisiae confirmed the proper gene identification. A gene homologous to ppd1, encoding a putative membrane protein (PPD2), as well as fragments of two other genes encoding PPD3 and PPD4 proteins were also isolated. Amino acids composing the putative active center of PPD1 and PPD2 are similar to those present in known purple acid phosphatases, which suggests that the reported genes might encode a novel group of specific metallophosphatases. RT-PCR revealed that the corresponding PPD1 mRNA accumulates in stems and leaves, and PPD2 mRNA in stems, leaves and seedlings.