Free Sialooligosaccharides Found in the Unfertilized Eggs of a Freshwater Trout, Plecoglossus altivelis

Comprehensive Analysis of the Structure and Function of Peptide:N-Glycanase 1 and Relationship with Congenital Disorder of Deglycosylation

The cytosolic PNGase (peptide:N-glycanase), also known as peptide-N4-(N-acetyl-β-glucosaminyl)-asparagine amidase, is a well-conserved deglycosylation enzyme (EC 3.5.1.52) which catalyzes the non-lysosomal hydrolysis of an N(4)-(acetyl-β-d-glucosaminyl) asparagine residue (Asn, N) into a N-acetyl-β-d-glucosaminyl-amine and a peptide containing an aspartate residue (Asp, D). This enzyme (NGLY1) plays an essential role in the clearance of misfolded or unassembled glycoproteins through a process named ER-associated degradation (ERAD). Accumulating evidence also points out that NGLY1 deficiency can cause an autosomal recessive (AR) human genetic disorder associated with abnormal development and congenital disorder of deglycosylation. In addition, the loss of NGLY1 can affect multiple cellular pathways, including but not limited to NFE2L1 pathway, Creb1/Atf1-AQP pathway, BMP pathway, AMPK pathway, and SLC12A2 ion transporter, which might be the underlying reasons for a constellation of clinical phenotypes of NGLY1 deficiency. The current comprehensive review uncovers the NGLY1’ssdetailed structure and its important roles for participation in ERAD, involvement in CDDG and potential treatment for NGLY1 deficiency.

Characterization of O-acetylation in sialoglycans by MALDI-MS using a combination of methylamidation and permethylation

O-Acetylation of sialic acid in protein N-glycans is an important modification and can occur at either 4-, 7-, 8- or 9-position in various combinations. This modification is usually labile under alkaline reaction conditions. Consequently, a permethylation-based analytical method, which has been widely used in glycomics studies, is not suitable for profiling O-acetylation of sialic acids due to the harsh reaction conditions. Alternatively, methylamidation can be used for N-glycan analysis without affecting the base-labile modification of sialic acid. In this report, we applied both permethylation and methylamidation approaches to the analysis of O-acetylation in sialic acids. It has been demonstrated that methylamidation not only stabilizes sialic acids during MALDI processing but also allow for characterization of their O-acetylation pattern. In addition, LC-MS/MS experiments were carried out to distinguish between the O-acetylated glycans with potential isomeric structures. The repeatability of methylamidation was examined to evaluate the applicability of the approach to profiling of O-acetylation in sialic acids. In conclusion, the combination of methylamidation and permethylation methodology is a powerful MALDI-TOF MS-based tool for profiling O-acetylation in sialic acids applicable to screening of N-glycans.

Generation and degradation of free asparagine-linked glycans

Asparagine (N)-linked protein glycosylation, which takes place in the eukaryotic endoplasmic reticulum (ER), is important for protein folding, quality control and the intracellular trafficking of secretory and membrane proteins. It is known that, during N-glycosylation, considerable amounts of lipid-linked oligosaccharides (LLOs), the glycan donor substrates for N-glycosylation, are hydrolyzed to form free N-glycans (FNGs) by unidentified mechanisms. FNGs are also generated in the cytosol by the enzymatic deglycosylation of misfolded glycoproteins during ER-associated degradation. FNGs derived from LLOs and misfolded glycoproteins are eventually merged into one pool in the cytosol and the various glycan structures are processed to a near homogenous glycoform. This article summarizes the current state of our knowledge concerning the formation and catabolism of FNGs.

Building biologics by chemical synthesis: practical preparation of di- and triantennary N-linked glycoconjugates

A unified strategy for the syntheses of bi- and triantennary fully sialylated N-glycans is described. The synthesis capitalizes on a global glycosylation strategy that delivers the desired undeca- and tetradecasaccharide in excellent yields. Finally, conjugation of the glycan to PSMA oligopeptide is described.

Free glycans derived from glycoproteins present in human sera

During the course of studies on the analysis of O-glycans in biological samples, we found that significant amount of free glycans are present in normal human serum samples. The most abundant free glycan was disialo-biantennary glycan typically observed in transferrin which is one of the abundant glycoproteins found in sera. Minor glycans were also considered to be mainly due to transferrin, but some glycans were derived from mucin-type O-glycans, although the amount was quite minute. However, high mannose-type glycans could not be detected at all. Although there have been many reports on the presence of intracellular "free" N-glycans (mainly derived from high mannose-type glycans) generated either from lipid-linked oligosaccharides or from misfolded glycoproteins through endoplasmic-reticulum associated protein degradation pathway, there is little information on the presence of free glycans in extracellular matrix and biological fluids such as serum. This report is the first one which demonstrates the presence of free glycans due to glycoproteins in sera.

Solving the convergence problem in the synthesis of triantennary N-glycan relevant to prostate-specific membrane antigen (PSMA)

The first total synthesis of triantennary, fully sialylated N-glycan of complex type is described. Two strategies for installation of sialylated antennae are explored, and both approaches converge on a global glycosylation step that delivers the desired tetradecasaccharide in good yields.

Accumulation of free complex-type N-glycans in MKN7 and MKN45 stomach cancer cells

During the N-glycosylation reaction, it has been shown that ‘free’ N-glycans are generated either from lipid-linked oligosaccharides or from misfolded glycoproteins. In both cases, occurrence of high mannose-type free glycans is well-documented, and the molecular mechanism for their catabolism in the cytosol has been studied. On the other hand, little, if anything, is known with regard to the accumulation of more processed, complex-type free oligosaccharides in the cytosol of mammalian cells. During the course of comprehensive analysis of N-glycans in cancer cell membrane fractions [Naka et al. (2006) J. Proteome Res. 5, 88–97], we found that a significant amount of unusual, complex-type free N-glycans were accumulated in the stomach cancer-derived cell lines, MKN7 and MKN45. The most abundant and characteristic glycan found in these cells was determined to be NeuAcα2-6Galβ1-4GlcNAcβ1-2Manα1-3Manβ1-4GlcNAc. Biochemical analyses indicated that those glycans found were cytosolic glycans derived from lysosomes due to low integrity of the lysosomal membrane. Since the accumulation of these free N-glycans was specific to only two cell lines among the various cancer cell lines examined, these cytosolic N-glycans may serve as a specific biomarker for diagnosis of specific tumours. A cytosolic sialidase, Neu2, was shown to be involved in the degradation of these sialoglycans, indicating that the cytosol of mammalian cells might be equipped for metabolism of complex-type glycans.

Free N-linked oligosaccharide chains: formation and degradation

There is growing evidence that N-linked glycans play pivotal roles in protein folding and intra- and/or intercellular trafficking of N-glycosylated proteins. It has been shown that during the N-glycosylation of proteins, significant amounts of free oligosaccharides (free OSs) are generated in the lumen of the endoplasmic reticulum (ER) by a mechanism which remains to be clarified. Free OSs are also formed in the cytosol by enzymatic deglycosylation of misfolded glycoproteins, which are subjected to destruction by a cellular system called "ER-associated degradation (ERAD)." While the precise functions of free OSs remain obscure, biochemical studies have revealed that a novel cellular process enables them to be catabolized in a specialized manner, that involves pumping free OSs in the lumen of the ER into the cytosol where further processing occurs. This process is followed by entry into the lysosomes. In this review we summarize current knowledge about the formation, processing and degradation of free OSs in eukaryotes and also discuss the potential biological significance of this pathway. Other evidence for the occurrence of free OSs in various cellular processes is also presented.

Identification of two discrete peptide: N-glycanases in Oryzias latipes during embryogenesis

Two different types of peptide:N-glycanase (PNGase) were identified in developing embryos of medaka fish ( Oryzias latipes ). Because the optimum pH values for their activities were acidic and neutral, they were designated as acid PNGase M and neutral PNGase M, respectively. The acid PNGase M corresponded to the enzyme that had been partially purified from medaka embryos (Seko,A., Kitajima,K., Inoue,Y. and Inoue,S. (1991) J. Biol. Chem., 266, 22110-22114). The apparent molecular weight of this enzyme was 150 K, and the optimal pH was 3.5-4.0, and the K m for L-hyosophorin was 44 microM. L-Hyosophorin is a cortical alveolus-derived glycononapeptide with a large N-linked glycan chain present in the perivitelline space of the developing embryo. Acid PNGase M was competitively inhibited by a free de-N-glycosylated nonapeptide derived from L-hyosophorin. This enzyme was expressed in ovaries and embryos at all developmental stages after gastrulation, but activity was not detected in embryos at developmental stages between fertilization and gastrula. Several independent lines of evidence suggested that acid PNGase M may be responsible for the unusual accumulation of free N-glycans derived from yolk glycoproteins (Iwasaki,M., Seko,A., Kitajima,K., Inoue,Y. and Inoue,S. (1992) J. Biol. Chem., 267, 24287-24296). In contrast, the neutral PNGase M was expressed in blastoderms from the 4-8 cell stage and in cells up to early gastrula. The general significance of these findings is that they show a developmental stage-dependent expression of the two PNGase activities, and that expression of the neutral PNGase M activity occurs concomitantly with the de-N-glycosylation of L-hyosophorin. These data thus support our conclusion that the neutral PNGase M is responsible for the developmental-stage-related de-N-glycosylation of the L-hyosophorin.

Site-specific de-N-glycosylation of diglycosylated ovalbumin in hen oviduct by endogenous peptide: N-glycanase as a quality control system for newly synthesized proteins

Hen ovalbumin (OVA) is known to exist as a singly N-glycosylated form with a glycan chain on Asn-292 in egg white. Previous studies showed that di-N-glycosylated form of OVA [Di-OVA; CHO-Asn-292/CHO-Asn-311 (CHO, N-glycan chain)], which has two N-glycan chains on Asn-292 and Asn-311, was expressed only transiently in hen oviduct. Di-OVA was not found in egg white, suggesting that this form cannot be secreted normally and may possibly be converted to mono-N-glycosylated OVA (CHO-Asn-292/Asp-311) by the action of peptide:N-glycanase (PNGase) during synthesis and secretion. In this study, we have identified the putative PNGase activity in the homogenate of hen oviduct, purified 1,000-fold, and designated as PNGase HO. We examined the reactivity of Di-OVA to PNGase HO and found that this enzyme site-specifically cleaved off the glycan chain at Asn-311 to convert Di-OVA into the mono-N-glycosylated form (CHO-Asn-292/Asp-311). In contrast, this enzyme was found not to act on the mono-N-glycosylated OVA (CHO-Asn-292/Asn-311) found in egg white when it was tested as a substrate. The present findings support our view that de-N-glycosylation catalyzed by PNGase may be involved in quality control of newly synthesized proteins by converting its diglycosylated form into the mono-N-glycosylated form that can be secreted. However, the alternative possibility that de-N-glycosylation may trigger cytosolic degradation of the aberrantly glycosylated glycoprotein cannot be ruled out.

Characterization of the major core structures of the alpha2-->8-linked polysialic acid-containing glycan chains present in neural cell adhesion molecule in embryonic chick brains

To gain more insight into the possible functional significance of the core glycan chain(s) on which polysialylation takes place in polysialic acid (poly-Sia)-containing glycoproteins, the structure of the core glycans in the embryonic form of chick brain neural cell adhesion molecule (N-CAM) were examined using chemical and instrumental techniques. The following new structural features, which had not been reported by the early pioneering study by Finne (Finne, J. (1982) J. Biol. Chem. 257, 11966-11970), were revealed (Structure I). (i) Two distinct types of multiantennary N-linked glycans, i.e. tri- and tetra-antennary structures, are present; (ii) an alpha1-->6-linked fucosyl residue is attached to the proximal GlcNAc residue of the di-N-acetylchitobiosyl unit; (iii) that the action of GlcNAc-transferase V, which catalyzes the attachment of the beta-(1-->6)-linked GlcNAc residue on the (1-->6)-alpha-linked mannose (Man) arm, appears to be essential for polysialylation to occur on the core glycan chain is suggested by the fact that the Man residue alpha1-->6-linked to the beta-linked Man residue is invariably 2,6-di-O-substituted by the GlcNAc residue; (iv) both type 1 (Galbeta1-->3GlcNAc) and type 2 (Galbeta1-->4 GlcNAc) sequences are present in the peripheral portion of the core glycan structure. An extended form of the type 2 chain, i.e. Galbeta1-->4GlcNAcbeta1-->3Galbeta1-->4GlcNAc, is also expressed on the (1-->3)- and (1-->6)-alpha-linked Man arms; (v) on average about 1.4 mol of sulfate is attached to the type 2 N-acetyllactosamine chain(s), where in the extended form the sulfate group is probably substituted at the O-3 position of the outmost GlcNAc residue, i.e. Galbeta1-->4(HSO3-->3)GlcNAcbeta1-->3Galbeta1--> 4GlcNAcbeta1-->Man. It is possible that the unusual structural features identified in this study might play a role in the initiation of polysialylation and our data should facilitate future research regarding the signals that control polysialylation.

Unconjugated Man5GlcNAc occurs in vegetative tissues of tomato

Unconjugated Man alpha 1-->6(Man alpha 1-->3)Man alpha 1-->6(Man alpha 1-->3)Man beta 1-->4GlcNAc (Man5Glc NAc) delayed ripening when added exogenously at 10 ng g-1 fr. wt to both whole tomato fruit and excised pericarp tissue discs. In addition, Man5GlcNAc was one of 10 unconjugated N-glycans purified from tomato pericarp tissue. When applied exogenously at a concentration of 10 nM, Man5GlcNAc prevented the delay of ripening induced by tunicamycin, an inhibitor of its de novo synthesis. Since it was possible that this unconjugated N-glycan might be specifically related to ripening, we checked to see if it also occurred in fully expanded leaf and stem tissues using high-pH anion-exchange chromatography with pulsed amperometric detection. This method allowed us to detect 1 ng of oligosaccharide and to quantify accurately amounts in the range 60-600 ng per injection, significantly more sensitive than the amine-bonded HPLC method previously used to separate and quantify unconjugated N-glycans in tomato fruit pericarp tissue. Four high-mannosyl type unconjugated N-glycans were detected in tomato vegetative tissues, including Man5GlcNAc. These results support a potential role of Man5GlcNAc and/or other unconjugated N-glycans in plant developmental processes, in addition to its apparent role as a modulator of senescence of fruit. However, an initial experiment showed no effect of Man5GlcNAc on senescence of tomato leaf discs, as measured by chlorophyll loss.

Isolation and structures of glycoprotein-derived free oligosaccharides from the unfertilized eggs of Scyliorhinus caniculus. Characterization of the sequences galactose(alpha 1-4)galactose(beta 1-3)-N-acetylglucosamine and N-acetylneuraminic acid(alpha 2-6)galactose(beta 1-3)-N-acetylglucosamine

As previously reported [Ishii, K., Iwasaki, M., Inoue, S., Kenny, P. T. M., Komura, H. & Inoue, Y. (1989) J. Biol. Chem. 264, 1623-1630; Inoue, S., Iwasaki, M., Ishii, K., Kitajima, K. & Inoue, Y. (1989) J. Biol. Chem. 264, 18520-185261, the unfertilized eggs of two different species of fresh-water fish, Plecoglossus altivelis and Tribodolon hakonensis, contain relatively large amounts of free sialooligosaccharides. These oligosaccharides were found to derive from glycophosphoproteins, owing to the activity of a peptide - N4-(N-acetyl-beta-D-glucosaminyl)asparagine amidase [Iwasaki, M., Seko, A., Kitajima, K., Inoue, Y. & Inoue, S. (1992) J. Biol. Chem. 267, 24287-24296; Seko, A., Kitajima, K., Inoue, Y. & Inoue, S. (1991) J. Biol. Chem. 266, 22110-22114]. Here we describe a new type of free oligosaccharides, isolated from unfertilized eggs of Scyliorhinus caniculus. From the structural analysis, based upon 1H-NMR spectroscopy, the following glycan units are proposed.[Formula: see text]

Carbohydrate-binding property of peptide: N-glycanase from mouse fibroblast L-929 cells as evaluated by inhibition and binding experiments using various oligosaccharides

Carbohydrate binding to peptide: N-glycanase from mouse fibroblast L-929 cells (L-929 PNGase) and inhibition by oligosaccharides of its catalytic activity were studied. L-929 PNGase was found to bind strongly with oligosaccharides having triomannosido-N,N'-diacetyl-chitobiosyl (Man3GlcNAc2) structure (Kd = approximately 10 microM). This binding was inhibited by mannotriose (Man3; Man alpha 1-->3[Man alpha 1-->6]Man) but not by N,N'-diacetylchitobiose (GlcNAc2; GlcNAc beta 1-->4GlcNAc). Scatchard analysis indicated that there exist two binding sites for Man3 on a homodimeric form of a 105-kDa subunit. Oligosaccharides having Man3GlcNAc2 structure were also shown to be strong inhibitors for the PNGase-catalyzed reaction (Ki = approximately 10 microM). The minimum structural requirements for inhibition of the PNGase activity were Man3 and GlcNAc2. Enzyme kinetic studies showed that the mechanism of inhibition by the oligosaccharides and Man3 fits well with a model wherein two inhibitor binding sites reside on L-929 PNGase. The conformity of Kd with IC50 values may be taken as an evidence for inhibition of the catalytic activity by the oligosaccharides and Man3 through the occupation of the binding sites with these molecules. On the other hand, inhibition by GlcNAc2 followed the simple competitive mode. Since the minimum substrate for the L-929 PNGase was shown to be Man beta 1-->4GlcNAc beta 1-->4GlcNAc beta 1-->peptide, GlcNAc2 may be directly accessible to the catalytic site in competition with substrate. Interestingly, alkylation of -SH group in L-929 PNGase caused complete loss of the catalytic activity, but the carbohydrate binding activity was completely retained, indicating that the catalytic site(s) is discriminated from the carbohydrate-binding sites in the active site of this enzyme. The carbohydrate-binding property seems to be unique to soluble PNGases from mammals and may be associated not only with regulation of the enzyme activity, but also with receptor and carrier functions for glycoconjugates in certain intracellular processes.

Proton NMR study of the trimannosyl unit in a pentaantennary N-linked decasaccharide structure. Complete assignment of the proton resonances and conformational characterization

The chemical shifts of all the ring protons of the three Man residues in a pentaantennary glycan chain have been unambiguously assigned by two-dimensional proton nuclear magnetic resonance (1H-NMR) spectroscopic methods. The study, using chemical shift and J values on the conformation of the trimannosyl unit, revealed that the rotamer about the C5-C6 bond of the alpha 1-->6 linkage in the sequence of Man alpha 1-->6Man beta 1--> is predominantly confined to a gauche-gauche rotamer (omega = 180 degrees, omega = O6-C6-C5-H5) and not to a gauche-trans rotamer (omega = -60 degrees). We do not know of any previous demonstration that the dihedral angle omega (O6-C6-C5-H5) in Man alpha 1-->6Man beta 1--> is preferentially 180 degrees in complex-type N-linked glycans having no bisecting GlcNAc residue.

Identification of free glycan chain liberated by de-N-glycosylation of the cortical alveolar glycopolyprotein (hyosophorin) during early embryogenesis of the Medaka fish, Oryzias latipes

In Medaka embryos (at the stages of blastulation to organogenesis), we found the presence of free glycan of which structure is identical with the multiantennary N-linked sugar chain of L-hyosophorin molecules which were originally present in the cortical alveoli of the unfertilized eggs in their precursor high molecular form. The free glycan-enriched fraction was separated from L-hyosophorin by chromatography on DEAE-Sephadex A-25 and Sephadex G-50 after removal of the sialic acid residues with exo-sialidase. Composition analysis, 400-MHz 1H NMR spectroscopy, and pyridylamination-hydrazinolysis-nitrous acid deamination of the free glycan showed the presence of di-N-acetylchitobiosyl structure at the reducing end, suggesting that the free glycan chain was derived from L-hyosophorin by the action of a specific peptide:N-glycosidase (PNGase). When we combine the previous finding of the hyosophorin-derived unique pentaantennary free glycan chain in the flounder embryos [A. Seko et al. (1989) J. Biol. Chem. 264, 15922-15929], it is anticipated that PNGase-catalyzed de-N-glycosylation of L-hyosophorin would be required at a certain stage of embryogenesis for L-hyosophorin to play a yet undefined functional role during early development.