Taxonomic group: bacteria / Proteobacteria
(Phylum: Proteobacteria)
Associated disease: cystic fibrosis (CF) [ICD11:
CA25 
]
The structure was elucidated in this paperNCBI PubMed ID: 32131450Publication DOI: 10.3390/ijms21051702Journal NLM ID: 101092791Publisher: Basel, Switzerland: MDPI
Correspondence: pcescutti
units.it
Institutions: Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa, Department of Life Sciences, University of Trieste, via L. Giorgieri 1, Bdg C11, 34127 Trieste, Italy, Department of Food Science, Cornell University, Ithaca, NY 14853, USA, Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, DK-2200 Copenhagen, Denmark
Biofilms are a multicellular way of life, where bacterial cells are close together and embedded in a hydrated macromolecular matrix which offers a number of advantages to the cells. Extracellular polysaccharides play an important role in matrix setup and maintenance. A water-insoluble polysaccharide was isolated and purified from the biofilm produced by Burkholderia cenocepacia strain H111, a cystic fibrosis pathogen. Its composition and glycosidic linkages were determined using Gas-Liquid Chromatography-Mass Spectrometry (GLC-MS) on appropriate carbohydrate derivatives while its complete structure was unraveled by 1D and 2D NMR spectroscopy in deuterated sodium hydroxide (NaOD) aqueous solutions. All the collected data demonstrated the following repeating unit for the water-insoluble B. cenocepacia biofilm polysaccharide: [3)-α-d-Galp-(1→3)-α-d-Glcp-(1→3)-α-d-Galp-(1→3)-α-d-Manp-(1→]n Molecular modelling was used, coupled with NMR Nuclear Overhauser Effect (NOE) data, to obtain information about local structural motifs which could give hints about the polysaccharide insolubility. Both modelling and NMR data pointed at restricted dynamics of local conformations which were ascribed to the presence of inter-residue hydrogen bonds and to steric restrictions. In addition, the good correlation between NOE data and calculated interatomic distances by molecular dynamics simulations validated potential energy functions used for calculations.
NMR, molecular modelling, polysaccharide structure, biofilm exopolysaccharides, Burkholderia cenocepacia H111
Structure type: polymer chemical repeating unit
Location inside paper: abstract
Trivial name: water-insoluble EPS, Bep
Compound class: EPS
Contained glycoepitopes: IEDB_130701,IEDB_136906,IEDB_137472,IEDB_141794,IEDB_142488,IEDB_144983,IEDB_144998,IEDB_146664,IEDB_151528,IEDB_152206,IEDB_190606,IEDB_983930,IEDB_983931,SB_192,SB_44,SB_67,SB_7,SB_72
Methods: 13C NMR, 1H NMR, GLC-MS, NMR-2D, sugar analysis, GLC, MD simulations
Comments, role: repeating unit
3D data: molecular modeling
NCBI Taxonomy refs (TaxIDs): 1055524Reference(s) to other database(s): GTC:G54448EJ
Show glycosyltransferases
NMR conditions: in D2O / 0.3M NaOD at 323 K
[as TSV]
13C NMR data:
Linkage Residue C1 C2 C3 C4 C5 C6
3,3,3 aDGalp 101.0 68.4 74.1 66.1 72.3 62.2
3,3 aDGlcp 96.1 71.4 82.9 71.2 73.6 62.0
3 aDGalp 101.6 68.2 75.5 66.6 72.4 62.3
aDManp 96.9 71.1 80.4 67.5 73.9 62.1
1H NMR data:
Linkage Residue H1 H2 H3 H4 H5 H6
3,3,3 aDGalp 5.29 3.89 4.02 4.20 4.14 3.89
3,3 aDGlcp 5.08 3.62 3.89 3.50 3.91 3.83
3 aDGalp 5.25 3.95 3.98 4.18 4.05 3.71
aDManp 4.98 4.14 3.98 3.76 3.94 3.66
1H/13C HSQC data:
Linkage Residue C1/H1 C2/H2 C3/H3 C4/H4 C5/H5 C6/H6
3,3,3 aDGalp 101.0/5.29 68.4/3.89 74.1/4.02 66.1/4.20 72.3/4.14 62.2/3.89
3,3 aDGlcp 96.1/5.08 71.4/3.62 82.9/3.89 71.2/3.50 73.6/3.91 62.0/3.83
3 aDGalp 101.6/5.25 68.2/3.95 75.5/3.98 66.6/4.18 72.4/4.05 62.3/3.71
aDManp 96.9/4.98 71.1/4.14 80.4/3.98 67.5/3.76 73.9/3.94 62.1/3.66
1H NMR data:
| Linkage | Residue | H1 | H2 | H3 | H4 | H5 | H6 |
|---|
| 3,3,3 | aDGalp | 5.29 | 3.89 | 4.02 | 4.20 | 4.14 | 3.89 |
| 3,3 | aDGlcp | 5.08 | 3.62 | 3.89 | 3.50 | 3.91 | 3.83 |
| 3 | aDGalp | 5.25 | 3.95 | 3.98 | 4.18 | 4.05 | 3.71 |
| | aDManp | 4.98 | 4.14 | 3.98 | 3.76 | 3.94 | 3.66 |
|
13C NMR data:
| Linkage | Residue | C1 | C2 | C3 | C4 | C5 | C6 |
|---|
| 3,3,3 | aDGalp | 101.0 | 68.4 | 74.1 | 66.1 | 72.3 | 62.2 |
| 3,3 | aDGlcp | 96.1 | 71.4 | 82.9 | 71.2 | 73.6 | 62.0 |
| 3 | aDGalp | 101.6 | 68.2 | 75.5 | 66.6 | 72.4 | 62.3 |
| | aDManp | 96.9 | 71.1 | 80.4 | 67.5 | 73.9 | 62.1 |
|
There is only one chemically distinct structure:
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