Development of the ECODAB into a relational database for Escherichia coli O-antigens and other bacterial polysaccharides

Abstract

Escherichia coli O-antigen database (ECODAB) is a web-based application to support the collection of E. coli O-antigen structures, polymerase and flippase amino acid sequences, NMR chemical shift data of O-antigens as well as information on glycosyltransferases (GTs) involved in the assembly of O-antigen polysaccharides. The database content has been compiled from scientific literature. Furthermore, the system has evolved from being a repository to one that can be used for generating novel data on its own. GT specificity is suggested through sequence comparison with GTs whose function is known. The migration of ECODAB to a relational database has allowed the automation of all processes to update, retrieve and present information, thereby, endowing the system with greater flexibility and improved overall performance. ECODAB is freely available at http://www.casper.organ.su.se/ECODAB/. Currently, data on 169 E. coli unique O-antigen entries and 338 GTs is covered. Moreover, the scope of the database has been extended so that polysaccharide structure and related information from other bacteria subsequently can be added, for example, from Streptococcus pneumoniae.

Carbohydrate structure database merged from bacterial, archaeal, plant and fungal parts

“…In spite of diversity of the existing databases, most of them are dedicated to mammalian glycans, and only a few contain data on bacterial, fungal or plant carbohydrates which come mostly from CarbBank (GLYCOSCIENCES.de, EUROCarbDB) or are dedicated to specific organisms (e.g. ECODAB that covers antigens of Escherichia coli ( 25 )). Moreover, several years ago we discovered that ∼35% of CarbBank records contain errors, and these errors have been migrating between databases for decades ( 26 ).…”

Bacteriophage-mediated Glucosylation Can Modify Lipopolysaccharide O-Antigens Synthesized by an ATP-binding Cassette (ABC) Transporter-dependent Assembly Mechanism

“…Significant progress has been made in establishing their precise structures and modes of assembly. As an example, there are more than 180 chemically and serotypically distinct glycans, giving rise to LPS O-antigens in Escherichia coli, and the structures, genes, and biosynthetic enzymes have been catalogued (1)(2)(3)(4). Diversity in glycoconjugate structures results from recombination events within genetic loci responsible for the synthesis of polysaccharides to generate a new structure and by acquisition of unlinked genes whose products modify existing structures.…”

Glycoinformatics: Bridging Isolated Islands in the Sea of Data

“…Among the largest modern databases,t here are Glycosciences.de (includes CCSD data, together with NMR spectra, theoretical and empirical 3D structures,a nd data analysis tools); [2] UniCarbKB (successor of the EurocarbDB design study [8] which is focused on eukaryotic glycans,i ncluding the data from GlycoSuite, [9] as well as HPLC,M S, and NMR experimental data); [3] Japan Consortium for Glycobiology and Glycotechnology (JCGG/ACGG collection of functioncentered databases;i ncludes data on glycoproteins and glycome-associated diseases,a nd analytical data); [10] KEGG Glycan (glycan structures,b iomedical and other data from Kyoto Encyclopedia of Genes and Genomes); [4] theC arbohydrate Structure Database (CSDB;p rovides structural, taxonomic,N MR spectroscopic and other information on bacterial, fungal and plant saccharides;includes various data analysis tools); [5] the secondary database GlyTouCan (structural glycan repository created for assigning au nique id to each carbohydrate structure); [11] and some others, [12] such as the Protein Data Bank (PDB;contains 3D structures of some glycans from glycoproteins). [13] Except for rare dedicated databases (such as Escherichia coli oriented ECODAB), [14] most of these databases deposit glycans of mammalian origin. Currently,C SDB [5] (which is developed by the authors of this Viewpoint) provides the most complete coverage on carbohydrates of prokaryotes.I t should be noted that none of the projects ensures the full coverage on natural carbohydrates,and only afew of them are curated.…”

“…CAZy stores information on several hundred thousands of enzymes,b ut less than 5% of them have experimentally established activities.T he major drawback of CAZy is the absence of synthesized carbohydrate structures and bibliographic references to original research. Among the dedicated databases,t here are ECODAB (data on E. coli glycosyltransferases (GTs)); [14] Rice GT Database (data on rice GTs); [18] GlycoGene Database (GGDB) and Caenorhabditis elegans GlycoGene Database (data on CAZyrelated genes in human and C. elegans,r espectively); [19] CSDB GT (CSDB subdatabase,w hich currently provides experimentally confirmed and predicted GT activities for E. coli and Arabidopsis thaliana); [20] and some others. [21] Glycoinformatics Projects Are Isolated Islands in the Sea of Data Information support for glycomics is falling behind that for genomics and proteomics,a nd glycoscientists have al imited access to both the global data on natural carbohydrates and tools of their processing.…”