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Abstract The Symbol Nomenclature for Glycans (SNFG) is a community-curated standard for the depiction of monosaccharides and complex glycans using various colored-coded, geometric shapes, along with defined text additions. It is hosted by the National Center for Biotechnology Information (NCBI) at the NCBI-Glycans Page (www.ncbi.nlm.nih.gov/glycans/snfg.html). Several changes have been made to the SNFG page in the past year to update the rules for depicting glycans using the SNFG, to include more examples of use, particularly for non-mammalian organisms, and to provide guidelines for the depiction of ambiguous glycan structures. This Glycoforum article summarizes these recent changes.

Background: There are considerable differences between bacterial and mammalian glycans. In contrast to most eukaryotic carbohydrates, bacterial glycans are often composed of repeating units with diverse functions ranging from structural reinforcement to adhesion, colonization and camouflage. Since bacterial glycans are typically displayed at the cell surface, they can interact with the environment and, therefore, have significant biomedical importance.

All living systems are comprised of four fundamental classes of macromolecules--nucleic acids, proteins, lipids, and carbohydrates (glycans). Glycans play a unique role of joining three principal hierarchical levels of the living world: (1) the molecular level (pathogenic agents and vaccine recognition by the immune system, metabolic pathways involving saccharides that provide cells with energy, and energy accumulation via photosynthesis); (2) the nanoscale level (cell membrane mechanics, structural support of biomolecules, and the glycosylation of macromolecules); (3) the microscale and macroscale levels (polymeric materials, such as cellulose, starch, glycogen, and biomass). NMR spectroscopy is the most powerful research approach for getting insight into the solution structure and function of carbohydrates at all hierarchical levels, from monosaccharides to oligo- and polysaccharides. Recent progress in computational procedures has opened up novel opportunities to reveal the structural information available in the NMR spectra of saccharides and to advance our understanding of the corresponding biochemical processes. The ability to predict the molecular geometry and NMR parameters is crucial for the elucidation of carbohydrate structures. In the present paper, we review the major NMR spectrum simulation techniques with regard to chemical shifts, coupling constants, relaxation rates and nuclear Overhauser effect prediction applied to the three levels of glycomics. Outstanding development in the related fields of genomics and proteomics has clearly shown that it is the advancement of research tools (automated spectrum analysis, structure elucidation, synthesis, sequencing and amplification) that drives the large challenges in modern science. Combining NMR spectroscopy and the computational analysis of structural information encoded in the NMR spectra reveals a way to the automated elucidation of the structure of carbohydrates.

The Carbohydrate Structure Databases (CSDBs, http://csdb.glycoscience.ru) store structural, bibliographic, taxonomic, NMR spectroscopic, and other data on natural carbohydrates and their derivatives published in the scientific literature. The CSDB project was launched in 2005 for bacterial saccharides (as BCSDB). Currently, it includes two parts, the Bacterial CSDB and the Plant&Fungal CSDB. In March 2015, these databases were merged to the single CSDB. The combined CSDB includes information on bacterial and archaeal glycans and derivatives (the coverage is close to complete), as well as on plant and fungal glycans and glycoconjugates (almost all structures published up to 1998). CSDB is regularly updated via manual expert annotation of original publications. Both newly annotated data and data imported from other databases are manually curated. The CSDB data are exportable in a number of modern formats, such as GlycoRDF. CSDB provides additional services for simulation of 1H, 13C and 2D NMR spectra of saccharides, NMR-based structure prediction, glycan-based taxon clustering and other.

Staphylococcus aureus is an important human pathogen that causes life-threatening diseases including septicemia, endocarditis, toxic shock syndrome, and abscesses in organ tissues (15,25). The cell wall of the microorganism plays an important role in infectivity and pathogenicity (40). Over several decades of research, extensive knowledge has accumulated concerning epidemiology (9), virulence (25, 28), genetics (3), genomic evolution (14), the biochemistry of cell wall assembly (31), the crystal structures of ␤-lactam-resistant enzymes (24), the ultrastructure of the cell wall (4, 18), and the muropeptide composition of wild-type, methicillin-resistant (7), and vancomycinresistant strains (34). Nonetheless, the tertiary molecular structure of the cell wall, which is central for understanding cell growth and division in staphylococci, has remained elusive. As a consequence, there is no graphic illustration of the wall architecture in the literature that adequately represents known physicochemical details of staphylococcal peptidoglycan.Staphylococci are gram-positive bacteria, and their cell walls are composed of murein (32, 38, 41), teichoic acids (2), and wall-associated surface proteins (20,26,30). Stress-bearing murein represents a continuous macromolecular sacculus covering the whole cell. Murein consists of glycan strands, which are cross-linked by peptide bridges furnishing the structural integrity of the sacculus. It is a distinctive feature of staphylococci that the observed degree of murein cross-linking, which was determined as a ratio of bridged peptides to the total amount of all peptide ends in general, is extremely high, on the order of 80 to 90% (16, 35).Glycan strands in staphylococcal murein are composed of N-acetylglucosamine (GlcpNAc) and N-acetylmuramic acid (MurpNAc) residues that furnish ␤-(134)-linked disaccharide repeating units, with MurpNAc representing the reducing terminus of the chain. The carboxyl group of each MurpNAc residue is amidated by the stem pentapeptide L-Ala-D-isoGln-L-Lys-D-Ala-D-Ala, and the ε-amino group of the lysine residue is substituted with a pentaglycine appendage (37). Thus, each peptide attached to a MurpNAc residue is a branched decapeptide with an amino group on the Gly and a carboxyl group on the D-Ala terminus, and arms of the peptide side chains interact with each other to provide a high degree of murein cross-linking. Although the general principle of murein structural organization is simple, the muropeptide composition of the staphylococcal sacculi appears very complex, as a standard digestion of sacculi with muramidase (the enzyme that cleaves MurpNAc glycosidic bonds) releases more than 20 distinct components plus an unresolved material. The latter makes up about 50 to 60% of the muropeptide-containing oligomers, with up to 20 repeating units (7,38). Thus, the major part of staphylococcal murein architecture could be envisaged as being constructed of interlinked glycan and oligopeptide chains, both varying in their lengths.On electron micrographs, the ...

parallel orientation with respect to the plasma membrane. However, after integrating published experimental data on glycan chain length distribution and the degree of peptide side chain cross-linking into this computer simulation, we now report that the proposed planar network of murein appears largely dysfunctional. In contrast, a scaffold model of murein architecture, which assumes that glycan strands extend perpendicularly to the plasma membrane, was found to accommodate published experimental evidence and yield a viable stress-bearing matrix. Moreover, this model is in accordance with the wellestablished principle of murein assembly in vivo, i.e., sequential attachment of strands to the preexisting structure. For the first time, the phenomenon of division plane alternation in dividing bacteria can be reconciled with a computer model of the molecular architecture of murein.The biological role, chemical structure, physical properties, and principles of biogenesis of cell walls of both gram-positive and gram-negative bacteria have been extensively reviewed since the mid-1960s (1, 8, 17-19, 26, 29, 33, 44, 51, 53, 56, 57). The major structural component of all types of bacterial walls is murein, the terms murein and peptidoglycan being synonymous. Although its composition and fine chemical structure vary in different bacteria (52), the general principle of its structural organization holds constant. The material, regardless of the bacterial cell morphology and the wall thickness, is invariably composed of peptidoglycan strands cross-linked via peptide bridges. Other polymers that are associated with the sacculus in different bacteria (teichoic acids, lipoteichoic acids, polysaccharides, proteins, and lipoproteins) are not essential to the mechanical firmness of murein and, therefore, are not further discussed here.To date, the crucial question of how the three-dimensional organization of murein can be visualized remains unanswered. Since there is no methodology that allows investigation of the architecture of murein in intact cells, researchers have had to deduce the tertiary structure on the basis of indirect evidence, the unambiguous interpretation of which is often difficult.Currently, three models of the architecture of murein are discussed in the literature. (i) The predominant concept considers the peptidoglycan strands to run regularly and in parallel with the plasma membrane, furnishing a planar network (8,29). (ii) An analogous model assumes an irregular orientation of peptidoglycan strands in the planar network (33,34). (iii) The scaffold model proposes that peptidoglycan strands are oriented perpendicular to the plasma membrane (12, 13). The radial orientation of glycan strands within bacterial walls was hypothetically contemplated but rejected by Keleman and Rogers (32). It is important to note that the planar network models consider the thin gram-negative cell walls to consist of one major stress-bearing layer in combination with newly synthesized (innermost) and almost degraded (outermost) loosely...

Bacterial carbohydrate structure database (BCSDB) is an open-access project that collects primary publication data on carbohydrate structures originating from bacteria, their biological properties, bibliographic and taxonomic annotations, NMR spectra, etc. Almost complete coverage and outstanding data consistency are achieved. BCSDB version 3 and the principles lying behind it, including glycan description language, are reported.