Site-selective glycosylation of proteins: creating synthetic glycoproteins

In higher organisms, the functions of many proteins are modulated by post-translational modifications (PTMs). Glycosylation is by far the most diverse of the PTM processes. Natural protein production methods typically produce PTM or glycoform mixtures within which function is difficult to dissect or control. Chemical tagging methods allow the precise attachment of multiple glycosylation modifications to bacterially expressed (bare) protein scaffolds, allowing reconstitution of functionally effective mimics of glycoproteins in higher organisms. In this way combining chemical control of PTM with readily available protein scaffolds provides a systematic platform for creating probes of protein-PTM interactions. This protocol describes the modification of Cys residues in proteins using glycomethanethiosulfonates and glycoselenenylsulfides and the modification of azidohomoalanine residues, introduced by Met replacement using auxotrophic Met(-) Escherichia coli strains, with glycoalkynes and the combination of these techniques for the creation of dual-tagged proteins. Each glycosylation procedure outlined in this protocol can be achieved in half a day.     

Comparing the glycosylation patterns of recombinant glycoproteins.

The glycosylation profile of a recombinant glycoprotein can not only significantly affect its therapeutic profile, but is also extremely sensitive to cell-culture and purification conditions. To define glycosylation patterns and to ensure consistency of recombinant glycoproteins among different preparations requires highly sensitive and reproducible analytical methods that can be used routinely. New strategies and instrumentation are being developed which should allow such analysis to be largely automated.     

Perspectives on the significance of altered glycosylation of glycoproteins in cancer

No abstract Abbreviations: Sia, sialic acid, type unspecified; Tn antigen, GalNAcα 1-O-Ser/Thr; T antigen, Galβ1-3GalNAcα-O-Ser/Thr; Sialyl LewisX, Siaα2-3Galβ1-4(Fucα1-3)GlcNAc; Sialyl Lewisa, Siaα2-3Galβ1-3(Fucα1-4)GlcNAc; Sialyl-Tn antigen, Siaα2-6GalNAcα1-O-Ser/Thr; FucT, fucosyltransferase; ST, sialyltransferase. This revised version was published online in November 2006 with corrections to the Cover Date.     

Altered glycosylation in cancer: A promising target for biomarkers and therapeutics

Glycosylation is a well-regulated cell and microenvironment specific post-translational modification. Several glycosyltransferases and glycosidases orchestrate the addition of defined glycan structures on the proteins and lipids. Recent advances and systemic approaches in glycomics have significantly contributed to a better understanding of instrumental roles of glycans in health and diseases. Emerging research evidence recognized aberrantly glycosylated proteins as the modulators of the malignant phenotype of cancer cells. The Cancer Genome Atlas has identified alterations in the expressions of glycosylation-specific genes that are correlated with cancer progression. However, the mechanistic basis remains poorly explored. Recent researches have shown that specific changes in the glycan structures are associated with 'stemness' and epithelial-to-mesenchymal transition of cancer cells. Moreover, epigenetic changes in the glycosylation pattern make the tumor cells capable of escaping immunosurveillance mechanisms. The deciphering roles of glycans in cancer emphasize that glycans can serve as a source for the development of novel clinical biomarkers. The ability of glycans in intervening various stages of tumor progression and the biosynthetic pathways involved in glycan structures constitute a promising target for cancer therapy. Advances in the knowledge of innovative strategies for identifying the mechanisms of glycan-binding proteins are hoped to hold great potential in cancer therapy. This review discusses the fundamental role of glycans in regulating tumorigenesis and tumor progression and provides insights into the influence of glycans in the current tactics of targeted therapies in the clinical setting.     

A lectin-based gold nanoparticle assay for probing glycosylation of glycoproteins

We report a glycoanalysis method in which lectins are used to probe the glycans of therapeutic glycoproteins that are adsorbed on gold nanoparticles. A model mannose-presenting glycoprotein, ribonuclease B (RNase B), and the therapeutic monoclonal antibody (mAb) rituximab, were found to adsorb spontaneously and non-specifically to bare gold nanoparticles such that glycans were accessible for lectin binding. Addition of a multivalent binding lectin, such as concanavalin A (Con A), to a solution of the modified gold nanoparticles resulted in cross-linking of the nanoparticles. This phenomenon was evidenced within 1 min by a change in the hydrodynamic diameter, D(H), measured by dynamic light scattering (DLS) and a shift and increase in absorbance of the plasmon resonance band of the gold nanoparticles. By combining the sugar-binding specificity and the cross-linking capabilities of lectins, the non-specific adsorption of glycoproteins to gold surfaces, and the unique optical reporting properties of gold nanoparticles, a glycosylation pattern of rituximab could be generated. This assay provides advantages over currently used glycoanalysis methods in terms of short analysis time, simplicity of the conjugation method, convenience of simple spectroscopic detection, and feasibility of providing glycan characterization of the protein drug product by using a variety of binding lectins.     

A general approach for characterizing glycosylation sites of glycoproteins.

Recent advances in glycobiology have greatly stimulated carbohydrate research; however, improving techniques for identification and isolation of specific glycosylation sites in protein structure analysis remains a challenge. We report here a practical approach utilizing a membrane staining technique on Problott, a PVDF-type membrane, to screen glycoproteins and glycopeptides derived from enzymatic digests of glycoproteins. To improve the detection sensitivity, an amplified staining technique using biotinylated lectins, avidin, and biotinylated peroxidase was employed. In addition, we describe a micro-batch affinity binding procedure to isolate glycopeptides from complex glycoprotein enzymatic digests. These protocols allow us to start with a subnanomole quantity of glycoprotein and locate the glycosylation sites; isolate glycopeptides in a homogeneous form; and perform amino acid composition, amino acid sequence, and mass analyses on the isolated glycopeptides. The characterization of glycosylation site of a model glycoprotein, carboxypeptidase P, of which the structure is still largely unknown, has been investigated.     

The effect of cycloheximide on the glycosylation of lactating-rabbit mammary glycoproteins.

1. Cycloheximide inhibited immediately the incorporation of L-[4,5-3H]leucine and D-]2-3H]mannose into mammary proteins, suggesting that the mannosylation of mammary glycoproteins requires the continued supply of newly synthesized polypeptides. 2. The incorporation of radioactivity from N-acetyl-D-[1-14C] glucosamine into protein was not inhibited until approx. 30 min after cycloheximide addition. Much (greater than 90%) of this radioactivity was present as N-acetylgalactosamine. 3. N-Glycosylation appears to be inhibited immediately by cycloheximide due to a lack of newly synthesized acceptor polypeptides, whereas O-glycosylation continues for 30 min, the time taken for acceptor peptides to move from their site of synthesis to the Golgi region and for completion of glycosylation. 4. There was a transient increase in the incorporation of mannose into lipid-linked oligosaccharide in the presence of cycloheximide, followed by a decrease in the radioactivity in this fraction. 5. The major lipid-linked oligosaccharide extracted from explants incubated for 2h in the presence of cycloheximide (6-7 monosaccharide units) was smaller than that extracted from control explants (10-12 monosaccharide units).     

The impacts of treatment with biocontrol fungus (Phlebiopsis gigantea) on bacterial diversity in Norway spruce stumps

The biocontrol agent Phlebiopsis gigantea has been intensively applied to the surface of Picea abies stumps to control Heterobasidion root rot. But little is known about the possible impact of this treatment on the resident bacteria community in the stumps. High throughput DNA bar-coded pyrosequencing was used to characterize the diversity of bacteria in the stumps of P. abies at 1, 6 and 13 years after treatment with P. gigantea. The sequences were classified into 12 phyla and 160 genera, of which Proteobacteria and Acidobacteria were the most abundant groups over time. Moreover, at the initial stages of decay, Proteobacteria were the most abundant whereas Acidobacteria were the most common at advanced stages of decay. Treatment with P. gigantea led to significant increase of the genus Acidobacteria-Gp1 at 1 year after treatment. The analysis of observed and estimated operational taxonomic units (OTUs) as well as diversity indices revealed that P. gigantea treatment significantly decreased the initial bacterial richness in the stumps, but the bacterial community gradually recovered and the negative effects of P. gigantea was attenuated. These results provide additional insight on the risk assessment as well as environmental impact on the long-term use of P. gigantea in the control of Heterobasidion root rot in conifer forests.     

Effect of impaired glycosylation on the biosynthesis of Semliki forest virus glycoproteins.

The glycoproteins of Semliki Forest virus, grown in chicken embryo cells, were labeled with radioactive sugars. The data indicate a high mannose content of the nonstructural precursor glycoprotein NSP 63. This protein can also be readily labeled with 2-deoxy-D-glucose. The envelope glycoproteins E1 and E2 are relatively rich in galactose, glucosamine, and fucose. Glycosylation can be impaired by 2-deoxy-D-glucose or D-glucosamine or by omission of sugars in the culture medium. Under these conditions characteristic changes in the electrophoretic profile of the viral polypeptides are observed: in the regions of glycoproteins NSP 97, NSP 63, and E1 and E2 new protein peaks can be detected. These polypeptides seem to be aberrant forms of the glycoproteins. When compared with the normal molecules they have lower molecular weights and contain less carbohydrates, especially mannose. Pulse-chase experiments indicate that the altered glycoproteins are degraded very slowly if at all. If, however, impairment is caused by omission of sugars in the culture medium, the radioactivity is chased after addition of glucose from the region between NSP 63 and E1 + E2 into the E1 + E2 peak. This suggests a completion of the carbohydrate chains under these conditions.     

地震对山地生态系统的影响——以5.12汶川大地震为例

地震是人类面临的主要自然灾难之一,其对于自然生态系统也有着巨大的影响。地震往往会导致生态系统发生退化,尤其自身比较脆弱的山地生态系统。以5．12汶川大地震为例,系统总结了山区地震的基本特点,综述了地震对于典型山地生态系统、生物多样性、山地景观以及区域生态安伞的影响。地震对于山地生态系统可能会产生直接的影响（损毁动植物、破坏栖息地、改变水文过程）,也可能产生间接的影响（污染环境、改变动植物习性、影响生物化学循环）。无论是直接还是间接影响,都是以地震对山地生态系统地形地貌的改变为主导。山区由于地震而引发的次生灾害对于山地生态系统的影响也非常显著。建议应该加强有关地震对山地生态系统影响方面的研究,并指出了围绕此次5．12汶川大地震,应该重点开展的几个研究方向。     

Defining the N-linked glycosylation site of Hantaan virus envelope glycoproteins essential for cell fusion

The Hantaan virus (HTNV) is an enveloped virus that is capable of inducing low pH-dependent cell fusion. We molecularly cloned the viral glycoprotein (GP) and nucleocapsid (NP) cDNA of HTNV and expressed them in Vero E6 cells under the control of a CMV promoter. The viral gene expression was assessed using an indirect immunofluorescence assay and immunoprecipitation. The transfected Vero E6 cells expressing GPs, but not those expressing NP, fused and formed a syncytium following exposure to a low pH. Monoclonal antibodies (MAbs) against envelope GPs inhibited cell fusion, whereas MAbs against NP did not. We also investigated the N-linked glycosylation of HTNV GPs and its role in cell fusion. The envelope GPs of HTNV are modified by N-linked glycosylation at five sites: four sites on G1 (N134, N235, N347, and N399) and one site on G2 (N928). Site-directed mutagenesis was used to construct eight GP gene mutants, including five single N-glycosylation site mutants and three double-site mutants, which were then expressed in Vero E6 cells. The oligosaccharide chain on residue N928 of G2 was found to be crucial for cell fusion after exposure to a low pH. These results suggest that G2 is likely to be the fusion protein of HTNV.     

The relationship of N-linked glycosylation and heavy chain-binding protein association with the secretion of glycoproteins

The relationship of N-linked glycosylation and association with heavy chain binding protein (BiP) to the secretion of Factor VIII (FVIII), von Willebrand Factor (vWF), and tissue plasminogen activator (tPA) was studied in Chinese hamster ovary (CHO) cells. FVIII has a heavily glycosylated region containing 20 clustered potential N-linked glycosylation sites. A significant proportion of FVIII was detected in a stable complex with BiP and not secreted. Deletion of the heavily glycosylated region resulted in reduced association with BiP and more efficient secretion. Tunicamycin treatment of cells producing this deleted form of FVIII resulted in stable association of unglycosylated FVIII with BiP and inhibition of efficient secretion. vWF contains 17 potential N-linked glycosylation sites scattered throughout the molecule. vWF was transiently associated with BiP and efficiently secreted demonstrating that CHO cells are competent to secrete a highly glycosylated protein. tPA, which has three utilized N-linked glycosylation sites, exhibited low level association with BiP and was efficiently secreted. Disruption of N-linked glycosylation of tPA by either site-directed mutagenesis or tunicamycin treatment resulted in reduced levels of secretion and increased association with BiP. This effect was enhanced by high levels of tPA expression. The glycosylation state and extent of association with BiP could be correlated with secretion efficiency.     

Mass spectrometry investigation of glycosylation on the NXS/T sites in recombinant glycoproteins

We used a targeted proteomics approach to investigate whether introduction of new N-linked glycosylation sites in a chimeric protein influence the glycosylation of the existing glycosylation sites. To accomplish our goals, we over-expressed and purified a chimeric construct that contained the Fc region of the IgG fused to the exons 7 & 8 of mouse ZP3 (IgG-Fc-ZP3E7 protein). Immunoglobulin heavy chain (IgG-HC protein) was used as control. We then analyzed the IgG-HC and IgG-Fc-ZP3E7 proteins by liquid chromatography-tandem mass spectrometry (LC–MS/MS) and by Western blotting (WB). We concluded that in control experiments, the glycosylation site was occupied as expected. However, in the IgG-Fc-ZP3E7 protein, we concluded that only one out of three NXS/T glycosylation sites is occupied by N-linked oligosaccharides. We also concluded that in the IgG-Fc-ZP3E7 protein, upon introduction of additional potential NXS/T glycosylation sites within its sequence, the original NST/S glycosylation site from the Fc region of the IgG-Fc-ZP3E7 protein is no longer glycosylated. The biomedical significance of our findings is discussed.     

On estimating diversity in species-rich fish assemblages: an example with coral-reef fishes of eastern Indonesia

A new procedure for estimating fish species richness in open or semi-open habitats is presented with unpublished data on the coral-reef fish assemblages of Raja Ampat, eastern Indonesia, known as the centre of marine biodiversity in the western Pacific.     

Recommendations for the use of species diversity indices with reference to a recently published article as an example

There are some recommendations for the use of species diversity indices in a paper recently published in this journal by M. Ohsawa on the species richness and composition of weevils in five forest types in the middle region of Japan. Because several factors, such as small sample size, calculation of Simpson’s diversity index by the use of the original equation of Simpson’s measure of concentration D, and a weak point in the Shannon–Wiener diversity index H′, may have led to biased estimates, I recalculated these indices using combined species diversity values of the five forest types. As the general tendencies of 1−D and H′ values calculated here were similar to those in Ohsawa’s paper, there is no need to propose any change to his view. However, these recalculated diversity indices indicated that they are values which are more suitable for use. It should be noted that the characteristics and weak point associated with the diversity indices need to be taken into account in future studies.     

Sodium chloride impacts glycosylation and N- and O-glycan site occupancy of an Fc-fusion protein

Fc-fusion proteins are highly complex molecules, difficult to manufacture at scale. In this work, undesired proteoforms were detected during the manufacture of a therapeutic fusion protein produced in CHO cells. These species were characterized using gel electrophoresis, size exclusion chromatography and liquid chromatography-mass spectrometry leading to the identification of low molecular weight proteoforms presenting low N- and O-glycan site occupancy, as well as a low sialylation content. Upstream process parameters were investigated, and fusion protein quality was shown to be linked to the sodium chloride content of the medium. A mitigation strategy was developed to avoid formation of unwanted glyco-variants, resulting in an increased yield of highly glycosylated Fc-fusion protein. The effect of sodium chloride was shown to be independent of the osmolality increase and was hypothesized to be linked to a modulation of Golgi acidity, which is required for the correct localization and function of glycosyltransferases. Altogether, this study highlights the importance of the salt balance in cell culture media used to produce highly sialylated and occupied glycoproteins, helping to maximize the yield and increase robustness of processes aiming at producing biopharmaceutical complex therapeutic molecules.     

Coral-associated bacterial assemblages: current knowledge and the potential for climate-driven impacts

The importance of associations between microorganisms and their invertebrate hosts is becoming increasingly apparent. An emerging field, driven by the necessity to understand the microbial relationships that both maximize coral health and cause coral disease, is the study of coral-bacteria interactions. In this article, we review our current understanding of the diversity, specificity, development, and functions of coral-associated bacteria. We also summarize what is known regarding the role of coral microbiota in the health and disease of coral. We conduct a meta-analysis to determine whether the presence of unique taxa correlates with the state of coral health (i.e. healthy, diseased or bleached), as well as whether coral reef habitats harbor clusters of distinct taxa. We find that healthy and bleached corals harbor similar dominant taxa, although bleached corals had higher proportions of Vibrio and Acidobacteria. Diseased corals generally had more Rhodobacter, Clostridia, and Cyanobacteria sequences, and fewer Oceanospirillum sequences. We caution, however, that while 16S rRNA is useful for microbial species identification, it is a poor predictor of habitat or lifestyle, and care should be taken in interpretation of 16S rRNA surveys to identify potential pathogens amongst complex coral-microbial assemblages. Finally, we highlight evidence that coral-bacterial assemblages could be sensitive to the effects of climatic change. We suggest that the relationship between coral and their bacterial associates represents a valuable model that can be applied to the broader discipline of invertebrate-microbial interactions.