An in vivo approach for the identification of acceptor sites for O-glycosyltransferases: motifs for the addition of O-GlcNAc in Dictyostelium discoideum

Introduction to informatics in glycoprotein analysis

Although the field of glycome informatics has established several methods, standards and technologies for carbohydrate analysis, the analysis of glycoproteins and other glycoconjugates is still in its infancy. However, from even before the term "glycome informatics" emerged, several groups have developed methods and tools on the analysis of glycosylation sites. In particular, the Expasy server has provided such tools to aid in the prediction of glycosylation sites of N- and O-glycans, while glycosciences.de has provided tools for the analysis of the amino acid distribution around glycosylation sites in 3D space, based on data from the Protein Data Bank (PDB). In addition to these tools, databases of glycoprotein information are available that may aid in glycoprotein prediction; GlycoProtDB is a database of glycoprotein information characterized by the Japanese Consortium for Glycobiology and Glycotechnology, and UniProt includes glycosylation site information along with its protein sequence data. Furthermore, the providers of the glycosylation tools on Expasy, the Center for Biological Sequence Analysis, also provide a database of O-glycosylation called O-GlycBase. Such databases may eventually aid in the development of glycoprotein-analysis tools as more consistent data is accumulated, and some prospects on this area of research will be given.

Post-translational modification by O-GlcNAc: another way to change protein function

Modification of intracellular proteins by the beta-linkage of the monosaccharide, N-acetylglucosamine to serine or threonine hydroxyls (O-GlcNAc) is abundant and reversible. Although many proteins bear this post-translational covalent modification, the changes in function of the proteins as a result of this modification are only starting to be understood. In this article, we describe how aspects of the flux from the glucose backbone to this modification are modified and how the cellular activity and content of the GC-box binding transcription factor, Sp1, is altered by O-glycosylation. The association of the enzyme that puts on the O-GlcNAc modification with the bi-functional enzyme that removes this modification is discussed relative to the transition between transcriptional repression and activation.

Initiation of Mucin-type O-Glycosylation in Dictyostelium Is Homologous to the Corresponding Step in Animals and Is Important for Spore Coat Function

Like animal cells, many unicellular eukaryotes modify mucin-like domains of secretory proteins with multiple O-linked glycans. Unlike animal mucin-type glycans, those of some microbial eukaryotes are initiated by alpha-linked GlcNAc rather than alpha-GalNAc. Based on sequence similarity to a recently cloned soluble polypeptide hydroxyproline GlcNAc-transferase that modifies Skp1 in the cytoplasm of the social ameba Dictyostelium, we have identified an enzyme, polypeptide alpha-N-acetylglucosaminyltransferase (pp alpha-GlcNAc-T2), that attaches GlcNAc to numerous secretory proteins in this organism. Unlike the Skp1 GlcNAc-transferase, pp alpha-GlcNAc-T2 is predicted to be a type 2 transmembrane protein. A highly purified, soluble, recombinant fragment of pp alpha-GlcNAc-T2 efficiently transfers GlcNAc from UDP-GlcNAc to synthetic peptides corresponding to mucin-like domains in two proteins that traverse the secretory pathway. pp alpha-GlcNAc-T2 is required for addition of GlcNAc to peptides in cell extracts and to the proteins in vivo. Mass spectrometry and Edman degradation analyses show that pp alpha-GlcNAc-T2 attaches GlcNAc in alpha-linkage to the Thr residues of all the synthetic mucin repeats. pp alpha-GlcNAc-T2 is encoded by the previously described modB locus defined by chemical mutagenesis, based on sequence analysis and complementation studies. This finding establishes that the many phenotypes of modB mutants, including a permeability defect in the spore coat, can now be ascribed to defects in mucin-type O-glycosylation. A comparison of the sequences of pp alpha-GlcNAc-T2 and the animal pp alpha-GalNAc-transferases reveals an ancient common ancestry indicating that, despite the different N-acetylhexosamines involved, the enzymes share a common mechanism of action.

Testing the nematophagous biological control strainPaecilomyces lilacinus251 for paecilotoxin production

Paecilomyces lilacinus is a nematophagous fungus currently developed as a biological control agent. In order to evaluate potential toxin production, culture extract and concentrated culture supernatant of P. lilacinus strain 251 were tested against Gram-negative and Gram-positive bacteria. High-performance liquid chromatography analysis was carried out to compare the chromatograms of P. lilacinus strain 251 with the chromatogram of known paecilotoxin. It was found that the 251 strain of P. lilacinus did not produce detectable levels of paecilotoxin or other toxins with antimicrobial activity.

Glycan-dependent signaling: O-linked N-acetylglucosamine

The addition of O-linked N-acetylglucosamine (O-GlcNAc) to target proteins may serve as a signaling modification analogous to protein phosphorylation. Like phosphorylation, O-GlcNAc is a dynamic modification occurring in the nucleus and cytoplasm. Various analytical methods have been developed to detect O-GlcNAc and distinguish it from glycosylation in the endomembrane system. Many target molecules have been identified; these targets are typically components of supramolecular complexes such as transcription factors, nuclear pore proteins, or cytoskeletal components. The enzymes responsible for O-GlcNAc addition and removal are highly conserved molecules having molecular features consistent with a signaling role. The O-GlcNAc transferase and O-GlcNAcase are likely to act in consort with kinases and phosphatases generating various isoforms of physiological substrates. These isoforms may differ in such properties as protein-protein interactions, protein stability, and enzymatic activity. Since O-GlcNAc plays a critical role in the regulation of signaling pathways of higher plants, the glycan modification is likely to perform similar signaling functions in mammalian cells. Glucose and amino acid metabolism generates hexosamine precursors that may be key regulators of a nutrient sensing pathway involving O-GlcNAc signaling. Altered O-linked GlcNAc metabolism may also occur in human diseases including neurodegenerative disorders, diabetes mellitus and cancer.

Cellulose-binding modules from extracellular matrix proteins of Dictyostelium discoideum stalk and sheath

Cellulose-binding modules (CBMs) of two extracellular matrix proteins, St15 and ShD, from the slime mold Dictyostelium discoideum were expressed in Escherichia coli. The expressed proteins were purified to > 98% purity by extracting inclusion bodies at pH 11.5 and refolding proteins at pH 7.5. The two refolded CBMs bound tightly to amorphous phosphoric acid swollen cellulose (PASC), but had a low affinity toward xylan. Neither protein exhibited cellulase activity. St15, the stalk-specific protein, had fourfold higher binding affinity toward microcrystalline cellulose (Avicel) than the sheath-specific ShD CBM. St15 is unusual in that it consists of a solitary CBM homologous to family IIa CBMs. Sequence analysis of ShD reveals three putative domains containing: (a) a C-terminal CBM homologous to family IIb CBMs; (b) a Pro/Thr-rich linker domain; and (c) a N-terminal Cys-rich domain. The biological functions and potential role of St15 and ShD in building extracellular matrices during D. discoideum development are discussed.

Scanning the available Dictyostelium discoideum proteome for O-linked GlcNAc glycosylation sites using neural networks

Dictyostelium discoideum has been suggested as a eukaryotic model organism for glycobiology studies. Presently, the characteristics of acceptor sites for the N-acetylglucosaminyl-transferases in Dictyostelium discoideum, which link GlcNAc in an alpha linkage to hydroxyl residues, are largely unknown. This motivates the development of a species specific method for prediction of O-linked GlcNAc glycosylation sites in secreted and membrane proteins of D. discoideum. The method presented here employs a jury of artificial neural networks. These networks were trained to recognize the sequence context and protein surface accessibility in 39 experimentally determined O-alpha-GlcNAc sites found in D. discoideum glycoproteins expressed in vivo. Cross-validation of the data revealed a correlation in which 97% of the glycosylated and nonglycosylated sites were correctly identified. Based on the currently limited data set, an abundant periodicity of two (positions-3, -1, +1, +3, etc.) in Proline residues alternating with hydroxyl amino acids was observed upstream and downstream of the acceptor site. This was a consequence of the spacing of the glycosylated residues themselves which were peculiarly found to be situated only at even positions with respect to each other, indicating that these may be located within beta-strands. The method has been used for a rapid and ranked scan of the fraction of the Dictyostelium proteome available in public databases, remarkably 25-30% of which were predicted glycosylated. The scan revealed acceptor sites in several proteins known experimentally to be O-glycosylated at unmapped sites. The available proteome was classified into functional and cellular compartments to study any preferential patterns of glycosylation. A sequence based prediction server for GlcNAc O-glycosylations in D. discoideum proteins has been made available through the WWW at http://www.cbs.dtu.dk/services/DictyOGlyc/ and via E-mail to DictyOGlyc@cbs.dtu.dk.

O-linked N-acetylglucosamine levels in cerebellar neurons respond reciprocally to pertubations of phosphorylation

The novel intracellular carbohydrate O-linked N-acetylglucosamine (O-GlcNAc) is present on proteins ranging from those of viruses to those of humans and include cytosolic, nuclear and plasma-membrane proteins. In this report we have examined the effect of manipulation of phosphorylation on the levels of O-GlcNAc in cerebellar neurons from early postnatal mice. Our results indicate a reciprocal response of O-GlcNAc levels to phosphorylation. Activation of protein kinase A or C, for example, results in reduced levels of O-GlcNAc specifically in the fraction of cytoskeletal and cytoskeleton-associated proteins, while inhibition of the same kinases results in increased levels of O-GlcNAc. These data are in keeping with a reciprocal action of O-GlcNAc with respect to phosphorylation and suggest that this modification may have a role in signal transduction.

O-GLYCBASE version 4.0: a revised database of O-glycosylated proteins

O-GLYCBASE is a database of glycoproteins with O-linked glycosylation sites. Entries with at least one experimentally verified O-glycosylation site have been compiled from protein sequence databases and literature. Each entry contains information about the glycan involved, the species, sequence, a literature reference and http-linked cross-references to other databases. Version 4.0 contains 179 protein entries, an approximate 15% increase over the last version. Sequence logos representing the acceptor specificity patterns for GalNAc, GlcNAc, mannosyl and xylosyl transferases are shown. The O-GLYCBASE database is available through the WWW at http://www.cbs.dtu.dk/databases/OGLYCBASE/

Fucosebeta-1-P-Ser is a new type of glycosylation: using antibodies to identify a novel structure in Dictyostelium discoideum and study multiple types of fucosylation during growth and development

Three antibodies that recognize distinct fucose epitopes were used to study fucosylation during growth and development of Dictyostelium discoideum. mAb83.5 is known to recognize an undefined "fucose epitope" on several proteins with serine-rich domains, while mAb CAB4, and a component of anti-horse-radish peroxidase, specifically recognize Fucalpha1,6GlcNAc and Fucalpha1,3GlcNAc residues respectively in the core of N-linked oligosaccharides. We show that mAb 83.5 defines a new type of O-glycosylation. Serine-containing peptides incubated with GDPbeta[3H]Fuc and microsomes formed two fucosylated products. A neutral product accounting for 30% of the label did not react with the antibody, while the rest of the label was incorporated into a charged product which contained all the mAb83.5 reactive material. beta-Elimination of the labeled peptide or endogenous products produced [3H]Fuc-1-P, indicating phosphodiester linkage to serine. Fucbeta-1-P and GDP-betaFuc at 100 microM blocked mAb83.5 binding to endogenous and peptide products, but their alpha-linked anomers did not. Electrospray ionization mass spectra of the neutral and anionic labeled products showed major peaks of mass units corresponding to O-Fuc-Ser peptide and O-Fuc-phospho-Ser peptide, respectively. The activity of Fuc-phosphotransferase exactly paralleled the accumulation of reactive glycans during growth and development. The expressions of N-glycan core Fucalpha1,6GlcNAc and Fucalpha1,3GlcNAc and their respective fucosyl transferase activities were also synchronous, but their developmental regulation differed from one another. Fucalpha1, 6GlcNAc was expressed maximally during growth but declined during development. In contrast core Fucalpha1,3GlcNAc epitopes were expressed almost exclusively during development. These findings provide direct evidence for a novel type of O-phosphofucosylation, demonstrate the existence of an O-fucosyl transferase, and identify two different types of core fucosylation in the N-glycans of Dictyostelium.