Asparagine-linked oligosaccharides of Semliki Forest virus grown in mosquito cells

The Structural Biology of Eastern Equine Encephalitis Virus, an Emerging Viral Threat

Alphaviruses are arboviruses that cause arthritis and encephalitis in humans. Eastern Equine Encephalitis Virus (EEEV) is a mosquito-transmitted alphavirus that is implicated in severe encephalitis in humans with high mortality. However, limited insights are available into the fundamental biology of EEEV and residue-level details of its interactions with host proteins. In recent years, outbreaks of EEEV have been reported mainly in the United States, raising concerns about public safety. This review article summarizes recent advances in the structural biology of EEEV based mainly on single-particle cryogenic electron microscopy (cryoEM) structures. Together with functional analyses of EEEV and related alphaviruses, these structural investigations provide clues to how EEEV interacts with host proteins, which may open avenues for the development of therapeutics.

Quantum Chemistry Meets Deep Learning for Complex Carbohydrate and Glycopeptide Species I

Carbohydrate complexes are crucial in many various biological and medicinal processes. The impacts of N-acetyl on the glycosidic linkage flexibility of methyl β-D-glucopyranose, and of the glycoamino acid β-D-glucopyranose-asparagine are poorly understood at the electronic level. Furthermore, the effect of D- and L-isomers of asparagine in the complexes of N-acetyl-β-D-glucopyranose-(L)-asparagine and N-acetyl-β-D-glucopyranose-(D)-asparagine is unknown. In this study, we performed density functional theory calculations of methyl β-D-glucopyranose, methyl N-acetyl-β-D-glucopyranose, and of glycoamino acids β-D-glucopyranose-asparagine, N-acetyl-β-D-glucopyranose-(L)-asparagine and N-acetyl-β-D-glucopyranose-(D)-asparagine for studying their linkage flexibilities, total solvated energies, thermochemical properties and intra-molecular hydrogen bond formations in an aqueous solution environment using the COnductor-like Screening MOdel (COSMO) for water. We linked these density functional theory calculations to deep learning via estimating the total solvated energy of each linkage torsional angle value. Our results show that deep learning methods accurately estimate the total solvated energies of complex carbohydrate and glycopeptide species and provide linkage flexibility trends for methyl β-D-glucopyranose, methyl N-acetyl-β-D-glucopyranose, and of glycoamino acids β-D-glucopyranose-asparagine, N-acetyl-β-D-glucopyranose-(L)-asparagine and N-acetyl-β-D-glucopyranose-(D)-asparagine in agreement with density functional theory results. To the best of our knowledge, this study represents the first application of density functional theory along with deep learning for complex carbohydrate and glycopeptide species in an aqueous solution medium. In addition, this study shows that a few thousands of optimization frames from DFT calculations are enough for accurate estimations by deep learning tools.

Structural plasticity of the Semliki Forest virus glycome upon interspecies transmission

Cross-species viral transmission subjects parent and progeny alphaviruses to differential post-translational processing of viral envelope glycoproteins. Alphavirus biogenesis has been extensively studied, and the Semliki Forest virus E1 and E2 glycoproteins have been shown to exhibit differing degrees of processing of N-linked glycans. However the composition of these glycans, including that arising from different host cells, has not been determined. Here we determined the chemical composition of the glycans from the prototypic alphavirus, Semliki Forest virus, propagated in both arthropod and rodent cell lines, by using ion-mobility mass spectrometry and collision-induced dissociation analysis. We observe that both the membrane-proximal E1 fusion glycoprotein and the protruding E2 attachment glycoprotein display heterogeneous glycosylation that contains N-linked glycans exhibiting both limited and extensive processing. However, E1 contained predominantly highly processed glycans dependent on the host cell, with rodent and mosquito-derived E1 exhibiting complex-type and paucimannose-type glycosylation, respectively. In contrast, the protruding E2 attachment glycoprotein primarily contained conserved under-processed oligomannose-type structures when produced in both rodent and mosquito cell lines. It is likely that glycan processing of E2 is structurally restricted by steric-hindrance imposed by local viral protein structure. This contrasts E1, which presents glycans characteristic of the host cell and is accessible to enzymes. We integrated our findings with previous cryo-electron microscopy and crystallographic analyses to produce a detailed model of the glycosylated mature virion surface. Taken together, these data reveal the degree to which virally encoded protein structure and cellular processing enzymes shape the virion glycome during interspecies transmission of Semliki Forest virus.

Retinal glycoprotein enrichment by concanavalin a enabled identification of novel membrane autoantigen synaptotagmin-1 in equine recurrent uveitis

Complete knowledge of autoantigen spectra is crucial for understanding pathomechanisms of autoimmune diseases like equine recurrent uveitis (ERU), a spontaneous model for human autoimmune uveitis. While several ERU autoantigens were identified previously, no membrane protein was found so far. As there is a great overlap between glycoproteins and membrane proteins, the aim of this study was to test whether pre-enrichment of retinal glycoproteins by ConA affinity is an effective tool to detect autoantigen candidates among membrane proteins. In 1D Western blots, the glycoprotein preparation allowed detection of IgG reactions to low abundant proteins in sera of ERU patients. Synaptotagmin-1, a Ca2+-sensing protein in synaptic vesicles, was identified as autoantigen candidate from the pre-enriched glycoprotein fraction by mass spectrometry and was validated as a highly prevalent autoantigen by enzyme-linked immunosorbent assay. Analysis of Syt1 expression in retinas of ERU cases showed a downregulation in the majority of ERU affected retinas to 24%. Results pointed to a dysregulation of retinal neurotransmitter release in ERU. Identification of synaptotagmin-1, the first cell membrane associated autoantigen in this spontaneous autoimmune disease, demonstrated that examination of tissue fractions can lead to the discovery of previously undetected novel autoantigens. Further experiments will address its role in ERU pathology.

Disulfide bond structure determination and biochemical analysis of glycoprotein C from herpes simplex virus

A biochemical analysis of glycoprotein C (gC of herpes simplex virus was undertaken to further characterize the structure of the glycoprotein and to determine its disulfide bond arrangement. We used three recombinant forms of gC, gC1(457t), gC1(delta33-123t), and gC2(426t), each truncated prior to the transmembrane region. The proteins were expressed and secreted by using a baculovirus expression system and have been shown to bind to monoclonal antibodies which recognize discontinuous epitopes and to complement component C3b in a dose-dependent manner. We confirmed the N-terminal residues of each mature protein by Edman degradation and confirmed the internal deletion in gC1(delta33-123t). The molecular weight and extent of glycosylation of gC1 (457t), gC1(delta33-123t), and gC2(426t) were determined by treating each protein with endoglycosidases and then subjecting it to sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and mass spectrometric analysis. The data indicate that eight to nine of the predicted N-linked oligosaccharide sites on gC1(457t) are occupied by glycans of approximately 1,000 Da. In addition, O-linked oligosaccharides are present on gC1(457t), primarily localized to the N-terminal region (amino acids [aa] 33 to 123) of the protein. gC2(426t) contains N-linked oligosaccharides, but no O-linked oligosaccharides were detected. To determine the disulfide bond arrangement of the eight cysteines of gC1(457t),the protein was cleaved with cyanogen bromide. SDS-PAGE analysis followed by Edman degradation identified three cysteine-containing fragments which are not connected by disulfide linkages. Chemical modification of cysteines combined with matrix-assisted laser desorption ionization mass spectrometry identified disulfide bonds between cysteine 1 (aa 127) and cysteine 2 (aa 144) and between cysteine 3 (aa 286) and cysteine 4 (aa 347). Further proteolysis of the cyanogen bromide-generated fragment containing cysteine 5 through cysteine 8, combined with mass spectrometry and Edman degradation, showed that disulfide bonds link cysteine 5 (aa 386) to cysteine 8 (aa 442) and cysteine 6 (aa 390) to cysteine 7 (aa 419). A similar disulfide bond arrangement is postulated to exist in gC homologs from other herpesviruses.

N-acetyl-beta-glucosaminidase accounts for differences in glycosylation of influenza virus hemagglutinin expressed in insect cells from a baculovirus vector

The hemagglutinin of fowl plague virus has been expressed in Spodoptera frugiperda (Sf9) cells and in Estigmene acrea cells by using a baculovirus vector. Structural analysis revealed that the endo-H-resistant N-glycans of HA from Sf9 cells were predominantly trimannosyl core oligosaccharides, whereas in E. acrea cells most of these cores were elongated by at least one terminal N-acetylglucosamine residue. To understand the difference in carbohydrate structures, enzymes involved in N-glycan processing have been analyzed. The results revealed that the different glycosylation patterns observed are due to an N-acetyl-beta-glucosaminidase activity that was found in Sf9 cells but not in E. acrea cells. This enzyme specifically used the GlcNAcMan(3)GlcNAc(2) oligosaccharide as a substrate. When N-acetyl-beta-glucosaminidase or alpha-mannosidase II was inhibited by specific inhibitors, the amount of terminal N-acetylglucosamine in hemagglutinin from Sf9 cells was significantly enhanced. These results demonstrate that N glycosylation in both cell lines follows the classical pathway up to the stage of GlcNAcMan(3)GlcNAc(2) oligosaccharide side chains. Whereas these structures are the end product in E. acrea cells, they are degraded in Sf9 cells to Man(3)GlcNAc(2) cores by N-acetyl-beta-glucosaminidase.

Temperature-sensitive steps in the transport of Semliki Forest virus envelope proteins in mosquito C6/36 cells

We have analysed the temperature dependence of the transport of Semliki Forest virus (SFV) envelope proteins in mosquito cells, the natural host cells of alphaviruses. These cells are cultivated at a lower temperature (28 degrees C) and have a different lipid composition as compared to mammalian cells. When the incubation temperature was reduced at early times after infection, the onset of virus shedding was delayed and the maximal titers decreased correspondingly to the temperature. No virus was shed at 12 degrees C. No evidence was observed for a block of virus release due to a shift of the sites of virus maturation. When the incubation temperature was reduced at later times after infection a critical temperature of 12 degrees C was again observed. At this temperature no transport of viral proteins took place, p62 remained uncleaved, the glycan processing of E1 did not occur and the envelope proteins accumulated in a pre-Golgi compartment. We suggest a mathematical formula which allows the extrapolation of transport data to the temperature at which intracellular protein transport becomes blocked.

Palmitoylation of Semliki Forest virus glycoproteins in insect cells (C6/36) occurs in an early compartment and is coupled to the cleavage of the precursor p62

The acylation of the envelope proteins of Semliki Forest virus by palmitic acid in infected mosquito (C6/36) cells was investigated. It is shown that in these cells palmitic acid was incorporated post-translationally via hydroxylamine-labile linkages onto cysteines in the inner domains of the viral envelope proteins. The kinetics of incorporation, however, differed considerably as compared to higher eukaryotic cells. (i) The precursor of the envelope proteins E2 and E3, p62, was weakly and incompletely palmitoylated irrespective of the duration of labeling. (ii) Under all conditions tested complete acylation of E2 was delayed as compared to E1. (iii) Heavy protein complexes were formed consisting of unacylated p62 and partially unacylated E1. From this data, we conclude that during the maturation of SFV glycoproteins in mosquito cells differently acylated intermediates of p62/E2 exist. Furthermore, acylation of p62/E2 and cleavage of p62 are coupled events, occurring in an early compartment and allowing the release of the envelope oligomers for transport.