Metalloglycobiology: The power of metals in regulating glycosylation.

The remarkable structural diversity of glycans that is exposed at the cell surface and generated along the secretory pathway is tightly regulated by several factors. The recent identification of human glycosylation diseases related to metal transporter defects opened a completely new field of investigation, referred to herein as "metalloglycobiology", on how metal changes can affect the glycosylation and hence the glycan structures that are produced. Although this field is in its infancy, this review aims to go through the different glycosylation steps/pathways that are metal dependent and that could be impacted by metal homeostasis dysregulations.

The Cellular and Chemical Biology of Endocytic Trafficking and Intracellular Delivery-The GL-Lect Hypothesis.

Lipid membranes are common to all forms of life. While being stable barriers that delimitate the cell as the fundamental organismal unit, biological membranes are highly dynamic by allowing for lateral diffusion, transbilayer passage via selective channels, and in eukaryotic cells for endocytic uptake through the formation of membrane bound vesicular or tubular carriers. Two of the most abundant fundamental fabrics of membranes-lipids and complex sugars-are produced through elaborate chains of biosynthetic enzymes, which makes it difficult to study them by conventional reverse genetics. This review illustrates how organic synthesis provides access to uncharted areas of membrane glycobiology research and its application to biomedicine. For this Special Issue on Chemical Biology Research in France, focus will be placed on synthetic approaches (i) to study endocytic functions of glycosylated proteins and lipids according to the GlycoLipid-Lectin (GL-Lect) hypothesis, notably that of Shiga toxin; (ii) to mechanistically dissect its endocytosis and intracellular trafficking with small molecule; and (iii) to devise intracellular delivery strategies for immunotherapy and tumor targeting. It will be pointed out how the chemical biologist's view on lipids, sugars, and proteins synergizes with biophysics and modeling to "look" into the membrane for atomistic scale insights on molecular rearrangements that drive the biogenesis of endocytic carriers in processes of clathrin-independent endocytosis.

Towards structure-focused glycoproteomics.

Facilitated by advances in the separation sciences, mass spectrometry and informatics, glycoproteomics, the analysis of intact glycopeptides at scale, has recently matured enabling new insights into the complex glycoproteome. While diverse quantitative glycoproteomics strategies capable of mapping monosaccharide compositions of N- and O-linked glycans to discrete sites of proteins within complex biological mixtures with considerable sensitivity, quantitative accuracy and coverage have become available, developments supporting the advancement of structure-focused glycoproteomics, a recognised frontier in the field, have emerged. Technologies capable of providing site-specific information of the glycan fine structures in a glycoproteome-wide context are indeed necessary to address many pending questions in glycobiology. In this review, we firstly survey the latest glycoproteomics studies published in 2018-2020, their approaches and their findings, and then summarise important technological innovations in structure-focused glycoproteomics. Our review illustrates that while the O-glycoproteome remains comparably under-explored despite the emergence of new O-glycan-selective mucinases and other innovative tools aiding O-glycoproteome profiling, quantitative glycoproteomics is increasingly used to profile the N-glycoproteome to tackle diverse biological questions. Excitingly, new strategies compatible with structure-focused glycoproteomics including novel chemoenzymatic labelling, enrichment, separation, and mass spectrometry-based detection methods are rapidly emerging revealing glycan fine structural details including bisecting GlcNAcylation, core and antenna fucosylation, and sialyl-linkage information with protein site resolution. Glycoproteomics has clearly become a mainstay within the glycosciences that continues to reach a broader community. It transpires that structure-focused glycoproteomics holds a considerable potential to aid our understanding of systems glycobiology and unlock secrets of the glycoproteome in the immediate future.

[New technologies to unveil the role of brain glial cells]. / De nouvelles techniques pour dévoiler le rôle des cellules gliales du cerveau.

Brain function relies on complex interactions between neurons and different types of glial cells, such as astrocytes, microglia and oligodendrocytes. The relatively young field of "gliobiology" is thriving. Thanks to various technical innovations, it is now possible to address challenging biological questions on glial cells and unravel their multiple roles in brain function and dysfunction.

TITLE: De nouvelles techniques pour dévoiler le rôle des cellules gliales du cerveau. ABSTRACT: L'exécution des fonctions cérébrales requiert des interactions optimales entre les neurones et les différents types de cellules gliales (astrocytes, microglies et oligodendrocytes). Le domaine de la gliobiologie, qui s'intéresse aux cellules gliales, est en pleine expansion. Les innovations techniques permettent désormais d'aborder des questions biologiques complexes quant aux rôles de ces cellules dans le fonctionnement physiologique et pathologique du cerveau. Dans cette synthèse, nous décrivons comment certaines de ces avancées techniques nous ont permis d'en apprendre davantage sur les origines et les rôles fonctionnels des cellules gliales. Nous illustrons également comment ces techniques et les découvertes qui en ont découlé, peuvent être transposées en clinique et pourraient, dans un futur proche, offrir des nouvelles perspectives thérapeutiques.

130 years of Plant Lectin Research.

Lectins are proteins with diverse molecular structures that share the ability to recognize and bind specifically and reversibly to carbohydrate structures without changing the carbohydrate moiety. The history of lectins started with the discovery of ricin about 130 years ago but since then our understanding of lectins has dramatically changed. Over the years the research focus was shifted from 'the characterization of carbohydrate-binding proteins' to 'understanding the biological function of lectins'. Nowadays plant lectins attract a lot of attention especially because of their potential for crop improvement and biomedical research, as well as their application as tools in glycobiology. The present review aims to give an overview of plant lectins and their applications, and how the field evolved in the last decades.

Paving the Way for Practical Use of Sugar-Binding Natural Products as Lectin Mimics in Glycobiological Research.

Pradimicins (PRMs) constitute an exceptional class of natural products that show Ca2+ -dependent recognition of d-mannose (Man). In addition to therapeutic uses as antifungal drugs, the application of PRMs as lectin mimics for glycobiological research has been attracting considerable interest, since the emerging biological roles of Man-containing glycans have been highlighted. However, only a few attempts have been made to use PRMs for glycobiological purposes. The limited use of PRMs is primarily due to the early assumption that the readily modifiable carboxyl group of PRMs is involved in Ca2+ binding, and thus, not available to prepare research tools. Recently, this assumption has been disproved by structural elucidation of the Ca2+ complex of PRMs, which paves the way for designing carboxyl group modified derivatives of PRMs for research use. This article outlines studies related to Ca2+ -mediated Man binding of PRMs and discusses their application for glycobiology.

glypy: An Open Source Glycoinformatics Library.

Glycoinformatics is a critical resource for the study of glycobiology, and glycobiology is a necessary component for understanding the complex interface between intra- and extracellular spaces. Despite this, there is limited software available to scientists studying these topics, requiring each to create fundamental data structures and representations anew for each of their applications. This leads to poor uptake of standardization and loss of focus on the real problems. We present glypy, a library written in Python for reading, writing, manipulating, and transforming glycans at several levels of precision. In addition to understanding several common formats for textual representation of glycans, the library also provides application programming interfaces (APIs) for major community databases, including GlyTouCan and UnicarbKB. The library is freely available under the Apache 2 common license with source code available at https://github.com/mobiusklein/ and documentation at https://glypy.readthedocs.io/ .

The evolution of the Glycomic Codes of extracellular matrices.

The extracellular matrices (ECMs) of living organisms are compartments responsible for maintenance of cell shape, cell adhesion, and cell communication. They are also involved in cell signaling and defense against the attack of pathogens. The plant cell walls have been recently defined as encoded structures that combine polysaccharides with other encoded structures (proteins and phenolic compounds). The term Glycomic Code has been used to define the set of mechanisms that generate cell wall architecture (the combination of polymers of different types) and biological function. Here, the composition of the extracellular matrices of archaea, bacteria, animals, fungi, algae, and plants was compared to understand how the Glycomic Code of these different organisms operate to produce polysaccharides and therefore how the Glycomic Code may have evolved in nature. It was found that the heterotrophs display EMC polysaccharides containing aminosugars (nitrogen-based polysaccharides) whereas the photosynthetic organisms have cellulose-based walls, with polymers that hardly present aminosugars in its composition. Another subgroup is of the organisms containing EMCs with sulfated polysaccharides (animals and red algae). The main hemicellulose found in plants (xyloglucan) is used as a case study along with other seed cell wall storage polysaccharides of plants to exemplify the evolution of the Glycomic Code in plants. Overall, the trends observed in this work shows for the first time how the Glycomic Code in ECMs of living organisms may have evolved and diversified in nature.

Glycosaminoglycanomics: where we are.

Glycosaminoglycans regulate numerous physiopathological processes such as development, angiogenesis, innate immunity, cancer and neurodegenerative diseases. Cell surface GAGs are involved in cell-cell and cell-matrix interactions, cell adhesion and signaling, and host-pathogen interactions. GAGs contribute to the assembly of the extracellular matrix and heparan sulfate chains are able to sequester growth factors in the ECM. Their biological activities are regulated by their interactions with proteins. The structural heterogeneity of GAGs, mostly due to chemical modifications occurring during and after their synthesis, makes the development of analytical techniques for their profiling in cells, tissues, and biological fluids, and of computational tools for mining GAG-protein interaction data very challenging. We give here an overview of the experimental approaches used in glycosaminoglycomics, of the major GAG-protein interactomes characterized so far, and of the computational tools and databases available to analyze and store GAG structures and interactions.

Fulfilling Koch's postulates in glycoscience: HCELL, GPS and translational glycobiology.

Glycoscience-based research that is performed expressly to address medical necessity and improve patient outcomes is called "translational glycobiology". In the 19th century, Robert Koch proposed a set of postulates to rigorously establish causality in microbial pathogenesis, and these postulates can be reshaped to guide knowledge into how naturally-expressed glycoconjugates direct molecular processes critical to human well-being. Studies in the 1990s indicated that E-selectin, an endothelial lectin that binds sialofucosylated carbohydrate determinants, is constitutively expressed on marrow microvessels, and investigations in my laboratory indicated that human hematopoietic stem cells (HSCs) uniquely express high levels of a specialized glycoform of CD44 called "hematopoietic cell E-/L-selectin ligand" (HCELL) that functions as a highly potent E-selectin ligand. To assess the role of HCELL in directing HSC migration to marrow, a method called "glycosyltransferase-programmed stereosubstitution" (GPS) was developed to custom-modify CD44 glycans to enforce HCELL expression on viable cell surfaces. Human mesenchymal stem cells (MSCs) are devoid of E-selectin ligands, but GPS-based glycoengineering of CD44 on MSCs licenses homing of these cells to marrow in vivo, providing direct evidence that HCELL serves as a "bone marrow homing receptor". This review will discuss the molecular basis of cell migration in historical context, will describe the discovery of HCELL and its function as the bone marrow homing receptor, and will inform on how glycoengineering of CD44 serves as a model for adapting Koch's postulates to elucidate the key roles that glycoconjugates play in human biology and for realizing the immense impact of translational glycobiology in clinical medicine.

Glycomics and glycoproteomics of membrane proteins and cell-surface receptors: Present trends and future opportunities.

Membrane proteins mediate cell-cell interactions and adhesion, the transfer of ions and metabolites, and the transmission of signals from the extracellular environment to the cell interior. The extracellular domains of most cell membrane proteins are glycosylated, often at multiple sites. There is a growing awareness that glycosylation impacts the structure, interaction, and function of membrane proteins. The application of glycoproteomics and glycomics methods to membrane proteins has great potential. However, challenges also arise from the unique physical properties of membrane proteins. Successful analytical workflows must be developed and disseminated to advance functional glycoproteomics and glycomics studies of membrane proteins. This review explores the opportunities and challenges related to glycomic and glycoproteomic analysis of membrane proteins, including discussion of sample preparation, enrichment, and MS/MS analyses, with a focus on recent successful workflows for analysis of N- and O-linked glycosylation of mammalian membrane proteins.

Recent developments on synthetic tools towards structural and functional glycodiversity.

Despite being the most abundant type of biopolymers in Nature, the biological relevance of carbohydrates has systematically been underrated for decades, associating them far less sophisticated functions (structural or energy sourcing) than those unraveled for polynucleotides and proteins. The inherently large and complex diversity of carbohydrates and glycoconjugates, together with the lack of efficient technologies to either isolate them from natural sources or produce them synthetically in useful amounts, have burdened the appreciation of their utmost importance in the most fundamental biological processes. For these reasons, carbohydrate-mediated transmission of biological information was largely unexplored. However, over the decades, it became clear that the expression of complex carbohydrates is critical in the development of living systems. Nature uses this diverse repertoire of structures as codes in fundamental biological processes such as cellular differentiation, cellular signaling, fertilization or immune response, among many others. The urgency to elucidate the glycan code in terms of structure-function relationships has fuelled chemical biology approaches uncovering new frontiers in molecular biology, for which the term glycobiology had to be coined in the early 1980s'. Novel strategies for assembling oligosaccharides, glycoproteins, glycolipids and a range of glycoconjugates have flourished ever since providing access to glycomaterials for interrogating and interfering glycan function. This account focuses on the major breakthroughs made on the strategies during the last decades to synthetically reproduce the overwhelming glycodiversity, emphasizing on the dazzling array of concepts and techniques which development was required to cope with the task. In the first place, a succinct overview of the structural and functional diversity of biologically relevant saccharides and glycoconjugates will be given. Then, a selection of the most relevant strategies that composes the complex and diversity-oriented toolbox that modern carbohydrate synthesis consists on will be dissected. Finally, a selection of the most recent applications of this synthetic toolbox to chemical biology will be captured.

Lifeomics leads the age of grand discoveries.

When our knowledge of a field accumulates to a certain level, we are bound to see the rise of one or more great scientists. They will make a series of grand discoveries/breakthroughs and push the discipline into an 'age of grand discoveries'. Mathematics, geography, physics and chemistry have all experienced their ages of grand discoveries; and in life sciences, the age of grand discoveries has appeared countless times since the 16th century. Thanks to the ever-changing development of molecular biology over the past 50 years, contemporary life science is once again approaching its breaking point and the trigger for this is most likely to be 'lifeomics'. At the end of the 20th century, genomics wrote out the 'script of life'; proteomics decoded the script; and RNAomics, glycomics and metabolomics came into bloom. These 'omics', with their unique epistemology and methodology, quickly became the thrust of life sciences, pushing the discipline to new high. Lifeomics, which encompasses all omics, has taken shape and is now signalling the dawn of a new era, the age of grand discoveries.