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Statistical analysis of the Bacterial Carbohydrate Structure Data Base (BCSDB): characteristics and diversity of bacterial carbohydrates in comparison with mammalian glycans.

Herget S, Toukach PV, Ranzinger R, Hull WE, Knirel YA, von der Lieth CW - BMC Struct. Biol. (2008)

Bottom Line: The sequence characteristics of glycans (monosaccharide composition, modifications, and linkage patterns) for the higher bacterial taxonomic classes have been examined and compared with the data for mammals, with both similarities and unique features becoming evident.Compared to mammalian glycans, the bacterial glycans deposited in the current databases have a more than ten-fold greater diversity at the monosaccharide level, and the disaccharide pattern space is approximately nine times larger.This study summarizes the current knowledge of bacterial glycan architecture and diversity and reveals putative targets for the rational design and development of therapeutic intervention strategies by comparing bacterial and mammalian glycans.

View Article: PubMed Central - HTML - PubMed

Affiliation: Core Facility: Molecular Structure Analysis (W160), German Cancer Research Center, Heidelberg, Germany. s.herget@dkfz.de

ABSTRACT

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.

Results: The sequence characteristics of glycans (monosaccharide composition, modifications, and linkage patterns) for the higher bacterial taxonomic classes have been examined and compared with the data for mammals, with both similarities and unique features becoming evident. Compared to mammalian glycans, the bacterial glycans deposited in the current databases have a more than ten-fold greater diversity at the monosaccharide level, and the disaccharide pattern space is approximately nine times larger. Specific bacterial subclasses exhibit characteristic glycans which can be distinguished on the basis of distinctive structural features or sequence properties.

Conclusion: For the first time a systematic database analysis of the bacterial glycome has been performed. This study summarizes the current knowledge of bacterial glycan architecture and diversity and reveals putative targets for the rational design and development of therapeutic intervention strategies by comparing bacterial and mammalian glycans.

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Related in: MedlinePlus

Distribution of monosaccharide pairs in various bacterial groups. For taxonomy Set 2 the matrix presents relative abundance data for monosaccharide residue pairs of all linkage types, involving the 20 most common residues serving as donor (children) or acceptor (parent). Each circle area reflects the relative abundance of a given donor-acceptor pair (matrix coordinates) within the corresponding taxonomic group, normalized to the total number of pairs within that group.
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Figure 10: Distribution of monosaccharide pairs in various bacterial groups. For taxonomy Set 2 the matrix presents relative abundance data for monosaccharide residue pairs of all linkage types, involving the 20 most common residues serving as donor (children) or acceptor (parent). Each circle area reflects the relative abundance of a given donor-acceptor pair (matrix coordinates) within the corresponding taxonomic group, normalized to the total number of pairs within that group.

Mentions: The topological characteristics of glycan architecture can be described by statistics which document the frequency distributions for specific neighboring pairs of monosaccharides connected either with any type of linkage (monosaccharide pair analysis) or via specific linkage positions (disaccharide pattern analysis). The matrix diagram in Fig. 10 illustrates the statistics of linked monosaccharide pairs for bacteria. Here the frequencies of any type of glycosidic linkage between the 20 most common donor and acceptor residues are shown. The areas of the circles plotted at the coordinates for a given pair represent its relative abundance within a given bacterial taxonomic group. Note that not all possible monosaccharide pairs are actually found in the natural sequences registered in the database (missing circles). Some combinations are exclusive for Gram-positive bacteria, e.g. those involving α-D-Araf or α-D-Glcp6Me in Actinobacteria while others may exhibit similar or widely differing abundances across the taxonomic groups. The high abundances found along the diagonal of the matrix stem from homopolymeric subsequences which are frequent in bacteria. Note that the results for "Kdo" (without anomeric configuration) originate from analytical artifacts. Detailed results for a total of 676 pairs in bacterial and mammalian carbohydrates are summarized in the additional material section [see Additional file 4].


Statistical analysis of the Bacterial Carbohydrate Structure Data Base (BCSDB): characteristics and diversity of bacterial carbohydrates in comparison with mammalian glycans.

Herget S, Toukach PV, Ranzinger R, Hull WE, Knirel YA, von der Lieth CW - BMC Struct. Biol. (2008)

Distribution of monosaccharide pairs in various bacterial groups. For taxonomy Set 2 the matrix presents relative abundance data for monosaccharide residue pairs of all linkage types, involving the 20 most common residues serving as donor (children) or acceptor (parent). Each circle area reflects the relative abundance of a given donor-acceptor pair (matrix coordinates) within the corresponding taxonomic group, normalized to the total number of pairs within that group.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2543016&req=5

Figure 10: Distribution of monosaccharide pairs in various bacterial groups. For taxonomy Set 2 the matrix presents relative abundance data for monosaccharide residue pairs of all linkage types, involving the 20 most common residues serving as donor (children) or acceptor (parent). Each circle area reflects the relative abundance of a given donor-acceptor pair (matrix coordinates) within the corresponding taxonomic group, normalized to the total number of pairs within that group.
Mentions: The topological characteristics of glycan architecture can be described by statistics which document the frequency distributions for specific neighboring pairs of monosaccharides connected either with any type of linkage (monosaccharide pair analysis) or via specific linkage positions (disaccharide pattern analysis). The matrix diagram in Fig. 10 illustrates the statistics of linked monosaccharide pairs for bacteria. Here the frequencies of any type of glycosidic linkage between the 20 most common donor and acceptor residues are shown. The areas of the circles plotted at the coordinates for a given pair represent its relative abundance within a given bacterial taxonomic group. Note that not all possible monosaccharide pairs are actually found in the natural sequences registered in the database (missing circles). Some combinations are exclusive for Gram-positive bacteria, e.g. those involving α-D-Araf or α-D-Glcp6Me in Actinobacteria while others may exhibit similar or widely differing abundances across the taxonomic groups. The high abundances found along the diagonal of the matrix stem from homopolymeric subsequences which are frequent in bacteria. Note that the results for "Kdo" (without anomeric configuration) originate from analytical artifacts. Detailed results for a total of 676 pairs in bacterial and mammalian carbohydrates are summarized in the additional material section [see Additional file 4].

Bottom Line: The sequence characteristics of glycans (monosaccharide composition, modifications, and linkage patterns) for the higher bacterial taxonomic classes have been examined and compared with the data for mammals, with both similarities and unique features becoming evident.Compared to mammalian glycans, the bacterial glycans deposited in the current databases have a more than ten-fold greater diversity at the monosaccharide level, and the disaccharide pattern space is approximately nine times larger.This study summarizes the current knowledge of bacterial glycan architecture and diversity and reveals putative targets for the rational design and development of therapeutic intervention strategies by comparing bacterial and mammalian glycans.

View Article: PubMed Central - HTML - PubMed

Affiliation: Core Facility: Molecular Structure Analysis (W160), German Cancer Research Center, Heidelberg, Germany. s.herget@dkfz.de

ABSTRACT

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.

Results: The sequence characteristics of glycans (monosaccharide composition, modifications, and linkage patterns) for the higher bacterial taxonomic classes have been examined and compared with the data for mammals, with both similarities and unique features becoming evident. Compared to mammalian glycans, the bacterial glycans deposited in the current databases have a more than ten-fold greater diversity at the monosaccharide level, and the disaccharide pattern space is approximately nine times larger. Specific bacterial subclasses exhibit characteristic glycans which can be distinguished on the basis of distinctive structural features or sequence properties.

Conclusion: For the first time a systematic database analysis of the bacterial glycome has been performed. This study summarizes the current knowledge of bacterial glycan architecture and diversity and reveals putative targets for the rational design and development of therapeutic intervention strategies by comparing bacterial and mammalian glycans.

Show MeSH
Related in: MedlinePlus