The social amoebae (Dictyostelia) are a diverse group of Amoebozoa that achieve multicellularity by aggregation and undergo morphogenesis into fruiting bodies with terminally differentiated spores and stalk cells. There are four groups of dictyostelids, with the most derived being a group that contains the model species Dictyostelium discoideum. We have produced a draft genome sequence of another group dictyostelid, Dictyostelium purpureum, and compare it to the D. discoideum genome. The assembly (8.41 × coverage) comprises 799 scaffolds totaling 33.0 Mb, comparable to the D. discoideum genome size. Sequence comparisons suggest that these two dictyostelids shared a common ancestor approximately 400 million years ago. In spite of this divergence, most orthologs reside in small clusters of conserved synteny. Comparative analyses revealed a core set of orthologous genes that illuminate dictyostelid physiology, as well as differences in gene family content. Interesting patterns of gene conservation and divergence are also evident, suggesting function differences; some protein families, such as the histidine kinases, have undergone little functional change, whereas others, such as the polyketide synthases, have undergone extensive diversification. The abundant amino acid homopolymers encoded in both genomes are generally not found in homologous positions within proteins, so they are unlikely to derive from ancestral DNA triplet repeats. Genes involved in the social stage evolved more rapidly than others, consistent with either relaxed selection or accelerated evolution due to social conflict. The findings from this new genome sequence and comparative analysis shed light on the biology and evolution of the Dictyostelia.

/pdf/comparative-genomics-of-the-social-amoebae-dictyostelium-3079em7bgg.pdf

Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum

Although N-glycosylation was first reported in archaea almost 40 years ago, detailed insights into this process have become possible only recently, with the availability of complete genome sequences for almost 200 archaeal species and the development of appropriate molecular tools. As a result of these advances, recent efforts have not only succeeded in delineating the pathways involved in archaeal N-glycosylation, but also begun to reveal how such post-translational protein modification helps archaea to survive in some of the harshest environments on the planet.

Extreme sweetness: protein glycosylation in archaea

Helminth parasites secrete extracellular vesicles (EVs) that can be internalised by host immune cells resulting in modulation of host immunity. While the molecular cargo of EVs have been characterised in many parasites, little is known about the surface-exposed molecules that participate in ligand-receptor interactions with the host cell surface to initiate vesicle docking and subsequent internalisation. Using a membrane-impermeable biotin reagent to capture proteins displayed on the outer membrane surface of two EV sub-populations (termed 15k and 120k EVs) released by adult F. hepatica, we describe 380 surface proteins including an array of virulence factors, membrane transport proteins and molecules involved in EV biogenesis/trafficking. Proteomics and immunohistochemical analysis show that the 120k EVs have an endosomal origin and may be released from the parasite via the protonephridial (excretory) system whilst the larger 15k EVs are released from the gastrodermal epithelial cells that line the fluke gut. A parallel lectin microarray strategy was used to profile the topology of major surface oligosaccharides of intact fluorogenically-labelled EVs as they would be displayed to the host. Lectin profiles corresponding to glycoconjugates exposed on the surface of the 15 K and 120K EV sub-populations are practically identical but are distinct from those of the parasite surface tegument, although all are predominated by high mannose sugars. We found that while the F. hepatica EVs were resistant to exo- and endo-glycosidases, the glyco-amidase PNGase F drastically remodelled the surface oligosaccharides and blocked the uptake of EVs by host macrophages. In contrast, pre-treatment with antibodies obtained from infected hosts, or purified antibodies raised against the extracellular domains of specific EV surface proteins (DM9-containing protein, CD63 receptor and myoferlin), significantly enhanced their cellular internalisation. This work highlights the diversity of EV biogenesis and trafficking pathways used by F. hepatica and sheds light on the molecular interaction between parasite EVs and host cells.

https://pureadmin.qub.ac.uk/ws/files/164944731/journal.pntd.0007087.pdf

Surface molecules of extracellular vesicles secreted by the helminth pathogen Fasciola hepatica direct their internalisation by host cells.

We described the integration of the general reversibility of glycosyltransferase-catalyzed reactions, artificial glycosyl donors, and a high throughput colorimetric screen to enable the engineering of glycosyltransferases for combinatorial sugar nucleotide synthesis. The best engineered catalyst from this study, the OleD Loki variant, contained the mutations P67T/I112P/T113M/S132F/A242I compared with the OleD wild-type sequence. Evaluated against the parental sequence OleD TDP16 variant used for screening, the OleD Loki variant displayed maximum improvements in kcat/Km of >400-fold and >15-fold for formation of NDP–glucoses and UDP–sugars, respectively. This OleD Loki variant also demonstrated efficient turnover with five variant NDP acceptors and six variant 2-chloro-4-nitrophenyl glycoside donors to produce 30 distinct NDP–sugars. This study highlights a convenient strategy to rapidly optimize glycosyltransferase catalysts for the synthesis of complex sugar nucleotides and the practical synthesis of a unique set of sugar nucleotides.

https://www.pnas.org/content/pnas/110/19/7648.full.pdf

Broadening the scope of glycosyltransferase-catalyzed sugar nucleotide synthesis

This review is the fourth update of the original review, published in 1999, on the application of MALDI mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2006. The review covers fundamental studies, fragmentation of carbohydrate ions, method developments, and applications of the technique to the analysis of different types of carbohydrate. Specific compound classes that are covered include carbohydrate polymers from plants, N- and O-linked glycans from glycoproteins, glycated proteins, glycolipids from bacteria, glycosides, and various other natural products. There is a short section on the use of MALDI-TOF mass spectrometry for the study of enzymes involved in glycan processing, a section on industrial processes, particularly the development of biopharmaceuticals and a section on the use of MALDI–MS to monitor products of chemical synthesis of carbohydrates. Large carbohydrate–protein complexes and glycodendrimers are highlighted in this final section. © 2010 Wiley Periodicals, Inc., Mass Spec Rev 30:1–100, 2011

Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: an update for the period 2005-2006.

Although countless genomes have now been sequenced, the glycomes of the vast majority of eukaryotes still present a series of unmapped frontiers. However, strides are being made in a few groups of invertebrate and unicellular organisms as regards their N-glycans and N-glycosylation pathways. Thereby, the traditional classification of glycan structures inevitably approaches its boundaries. Indeed, the glycomes of these organisms are rich in surprises, including a multitude of modifications of the core regions of N-glycans and unusual antennae. From the actually rather limited glycomic information we have, it is nevertheless obvious that the biotechnological, developmental and immunological relevance of these modifications, especially in insect cell lines, model organisms and parasites means that deciphering unusual glycomes is of more than just academic interest.

/pdf/complicated-n-linked-glycans-in-simple-organisms-j0ob7kf4us.pdf

Complicated N-linked glycans in simple organisms.

The social amoeba Dictyostelium discoideum has become established as a simple model for the examination of cell–cell interactions, and early studies suggested that shifts in glycosylation profiles take place during its life cycle. In the present study, we have applied HPLC and mass spectrometric methods to show that the major N-glycans in axenic cultures of the AX3 strain are oligomannosidic forms, most of which carry core fucose and/or intersecting and bisecting N -acetylglucosamine residues, including the major structure with the composition Man8GlcNAc4Fuc1. The postulated α1,3-linkage of the core fucose correlates with the cross-reactivity of Dictyostelium glycoproteins with a horseradish peroxidase antiserum; a corresponding core α1,3-fucosyltransferase activity capable of modifying oligomannosidic N-glycans was detected in axenic Dictyostelium extracts. The presence of fucose on the N-glycans and the reactivity to the antiserum, but not the fucosyltransferase activity, are abolished in the fucose-deficient HL250 strain. In later stages of development, N-glycans at the mound and culmination stages show a reduction in both the size and the degree of modification by intersecting/bisecting residues compared with mid-exponential phase cultures, consistent with the hypothesis that glycosidase and glycosyltransferase expression levels are altered during the slime mould life cycle.

Abbreviations: EndoH, endoglycosidase H; ESI, electrospray ionization; GER, GDP-keto-6-deoxymannose 3,5-epimerase-4-reductase; GMD, GDP-mannose 4,6-dehydratase; g.u., glucose units; HRP, horseradish peroxidase; LC, liquid chromatography; MALDI, matrix-assisted laser-desorption ionization; MMF3, Manα1-6(Manα1-3)Manβ1-4GlcNAcβ1-4(Fucα1-3)GlcNAcβ1-Asn; MS/MS, tandem MS; PNGase, peptide N-glycosidase; RP, reversed-phase; TOF, time-of flight

/pdf/development-of-dictyostelium-discoideum-is-associated-with-2gphu7ba6z.pdf

Development of Dictyostelium discoideum is associated with alteration of fucosylated N-glycan structures

Exploring the Unique N-Glycome of the Opportunistic Human Pathogen Acanthamoeba

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Complicated N-linked glycans in simple organisms.

Development of Dictyostelium discoideum is associated with alteration of fucosylated N-glycan structures

Exploring the Unique N-Glycome of the Opportunistic Human Pathogen Acanthamoeba