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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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Monosaccharide ring type distributions. The distribution of residue ring type (pyranose, furanose, linear, unknown) is shown schematically for various taxonomic groups. A. For taxonomy Set 1 the areas of the colored bars are proportional to the absolute occurrences (numbers shown) of a given ring type in each taxonomic group. The vertical scale is expanded in the inset. B. For taxonomy Set 2 two different ways of viewing the data are presented. (1) For a given ring type the area or height of each colored bar in a stack represents the relative abundance (%) of that ring type for each of the taxonomic groups, normalized to the total occurrence of that ring type across all groups (stack height = 100% for each ring type). Thus, the bar heights within a stack represent the distribution of a single ring type across all taxonomic groups. (2) The number labeled in each bar represents the frequency (in %) of residues with the corresponding ring type within the bar's taxonomic group, normalized to the total number of residues for that group. The numbers sum horizontally to 100% for each taxonomic group (color) and, therefore, represent the distribution of the different ring types within an individual group.
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Figure 8: Monosaccharide ring type distributions. The distribution of residue ring type (pyranose, furanose, linear, unknown) is shown schematically for various taxonomic groups. A. For taxonomy Set 1 the areas of the colored bars are proportional to the absolute occurrences (numbers shown) of a given ring type in each taxonomic group. The vertical scale is expanded in the inset. B. For taxonomy Set 2 two different ways of viewing the data are presented. (1) For a given ring type the area or height of each colored bar in a stack represents the relative abundance (%) of that ring type for each of the taxonomic groups, normalized to the total occurrence of that ring type across all groups (stack height = 100% for each ring type). Thus, the bar heights within a stack represent the distribution of a single ring type across all taxonomic groups. (2) The number labeled in each bar represents the frequency (in %) of residues with the corresponding ring type within the bar's taxonomic group, normalized to the total number of residues for that group. The numbers sum horizontally to 100% for each taxonomic group (color) and, therefore, represent the distribution of the different ring types within an individual group.

Mentions: Fig. 8 demonstrates that more than 70% of the monosaccharides in every taxonomic group are reported to be in the pyranose form, with most groups even reaching 90%. An interesting finding is that more than 50% of all furanose residues found in bacteria are in the 395 glycan sequences of the class Actinobacteria (cf. area of bars in Fig. 8B). Nearly 20% of all residues in Actinobacteria glycans are in the furanose form, compared to < 4% for all other bacterial groups studied. A high proportion of furanose residues has also been found for plants (data not shown). In the majority of cases where linear forms or rings of unknown size are found, they can be explained as artifacts of the structure elucidation process, especially when present at the reducing end. However, linear monosaccharides are known to occur occasionally in bacterial carbohydrate sequences and are most prevalent in Bacilli and Actinobacteria (Fig. 8B).


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)

Monosaccharide ring type distributions. The distribution of residue ring type (pyranose, furanose, linear, unknown) is shown schematically for various taxonomic groups. A. For taxonomy Set 1 the areas of the colored bars are proportional to the absolute occurrences (numbers shown) of a given ring type in each taxonomic group. The vertical scale is expanded in the inset. B. For taxonomy Set 2 two different ways of viewing the data are presented. (1) For a given ring type the area or height of each colored bar in a stack represents the relative abundance (%) of that ring type for each of the taxonomic groups, normalized to the total occurrence of that ring type across all groups (stack height = 100% for each ring type). Thus, the bar heights within a stack represent the distribution of a single ring type across all taxonomic groups. (2) The number labeled in each bar represents the frequency (in %) of residues with the corresponding ring type within the bar's taxonomic group, normalized to the total number of residues for that group. The numbers sum horizontally to 100% for each taxonomic group (color) and, therefore, represent the distribution of the different ring types within an individual group.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 8: Monosaccharide ring type distributions. The distribution of residue ring type (pyranose, furanose, linear, unknown) is shown schematically for various taxonomic groups. A. For taxonomy Set 1 the areas of the colored bars are proportional to the absolute occurrences (numbers shown) of a given ring type in each taxonomic group. The vertical scale is expanded in the inset. B. For taxonomy Set 2 two different ways of viewing the data are presented. (1) For a given ring type the area or height of each colored bar in a stack represents the relative abundance (%) of that ring type for each of the taxonomic groups, normalized to the total occurrence of that ring type across all groups (stack height = 100% for each ring type). Thus, the bar heights within a stack represent the distribution of a single ring type across all taxonomic groups. (2) The number labeled in each bar represents the frequency (in %) of residues with the corresponding ring type within the bar's taxonomic group, normalized to the total number of residues for that group. The numbers sum horizontally to 100% for each taxonomic group (color) and, therefore, represent the distribution of the different ring types within an individual group.
Mentions: Fig. 8 demonstrates that more than 70% of the monosaccharides in every taxonomic group are reported to be in the pyranose form, with most groups even reaching 90%. An interesting finding is that more than 50% of all furanose residues found in bacteria are in the 395 glycan sequences of the class Actinobacteria (cf. area of bars in Fig. 8B). Nearly 20% of all residues in Actinobacteria glycans are in the furanose form, compared to < 4% for all other bacterial groups studied. A high proportion of furanose residues has also been found for plants (data not shown). In the majority of cases where linear forms or rings of unknown size are found, they can be explained as artifacts of the structure elucidation process, especially when present at the reducing end. However, linear monosaccharides are known to occur occasionally in bacterial carbohydrate sequences and are most prevalent in Bacilli and Actinobacteria (Fig. 8B).

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