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Taxonomic group: bacteria / Fusobacteria (Phylum: Fusobacteria)
Host organism: Homo sapiens
Associated disease: periodontitis [ICD11: DA0C

]; infection due to Fusobacterium nucleatum [ICD11: XN4P8

]

The structure was elucidated in this paper
NCBI PubMed ID: 33280822
Publication DOI: 10.1016/j.carres.2020.108198
Journal NLM ID: 0043535
Publisher: Elsevier
Correspondence: evguenii.vinogradov

nrc-cnrc.gc.ca
Institutions: Vaccine and Emerging Infections Research, Human Health Therapeutics Research Centre, National Research Council, Ottawa, ON, K1A 0R6, Canada

Fusobacterium nucleatum is a gram-negative bacterium, part of the normal human microflora. It is associated with various health complications, including periodontitis and colorectal cancer. Its surface is covered with lipopolysaccharide, which interacts with the immune system and can be involved in various processes in health and disease conditions. Here we present the results of structural analysis of core oligosaccharides from the lipopolysaccharides of several strains of F. nucleatum. Pure compounds were isolated using mild acid hydrolysis or alkaline deacylation of the lipopolysaccharides and analyzed by NMR spectroscopy, mass-spectrometry and chemical methods. All cores analyzed had a common octasaccharide region, including five heptose residues and a non-phosphorylated 3-deoxy-d-manno-oct-2-ulosonic acid residue. The common region is substituted with different additional components specific for each strain. By structure type the F. nucleatum core is similar to that produced by Aeromonas.

Lipopolysaccharide, NMR, structure, Fusobacterium nucleatum

Structure type: oligomer ; 2312.7
Location inside paper: table 1, Fig.1, table S3, Hex1Hep5HexN4Kdo1P3Cho1
Compound class: core oligosaccharide
Contained glycoepitopes: IEDB_115009,IEDB_116046,IEDB_136044,IEDB_137472,IEDB_140122,IEDB_140624,IEDB_141794,IEDB_141807,IEDB_151531,IEDB_190606,SB_165,SB_166,SB_187,SB_195,SB_7,SB_88

Methods: 13C NMR, 1H NMR, NMR-2D, 31P NMR, ESI-MS, mild acid hydrolysis, HPAEC, chemical methods, deamination, GPC, alkaline deacylation, fermentation
Comments, role: AcOH released core oligosaccharide. The terminal aDGlcpN6P was substituted with choline (Cho) or 2-amino-2-deoxyglycerol (GroN) in a non-stoichiometric quantity; NMR temperature: 298 or 313. Published 13C NMR sub-spectra of #5,6_aXLLmanHepp and #5,3_aXLLmanHepp that seemed erroneously interchanged in the published assignment were swapped by CSDB staff based on the Supplementary materials.

Related record ID(s): 7582, 7584, 7585, 7586, 7587, 7588, 7589, 7590, 7591, 7592, 32207
NCBI Taxonomy refs (TaxIDs): 851
Show glycosyltransferases

NMR conditions: in D2O at 306 K [as TSV]

13C NMR data:
Linkage	Residue	C1	C2	C3	C4	C5	C6	C7
5,3,2,7	aDGlcpN	96.8	55.4	71.7	70.7	73.9	61.7
5,3,2	aXLLmanHepp	103.0	72.1	72.1	67.5	73.5	69.2	71.7
5,3	aXLLmanHepp	99.7	81.4	71.3	67.6	73.0	70.4	65.0
5,4,4,4	aDGlcpN	97.1	55.4	70.8	70.3	73.4	61.1
5,4,4,6	P
5,4,4	bDGalp	104.2	71.5	72.9	77.7	73.5	63.5
5,4,6,6,6,0	xXCho	60.8	67.3	55.2
5,4,6,6,6	%xXP?
5,4,6,6	aDGlcpN	96.3	55.5	70.7	70.2	72.8	65.5
5,4,6	aXLLmanHepp	102.3	70.7	72.3	67.6	74.0	76.9	63.7
5,4	bDGlcpN	100.7	57.9	73.0	77.2	75.6	66.6
5,6	aXLLmanHepp	102.3	71.9	71.5	67.6	73.9	70.7	64.3
5,7	P
5	aXLLmanHepp	103.5	71.3	73.7	75.6	71.1	76.7	64.2
	??Sug?


1H NMR data:
Linkage	Residue	H1	H2	H3	H4	H5	H6	H7
5,3,2,7	aDGlcpN	5.10	3.47	3.89	3.66	3.74	3.87-3.92
5,3,2	aXLLmanHepp	5.20	4.01	4.01	3.84	3.85	4.34	3.54-4.01
5,3	aXLLmanHepp	5.29	4.01	3.91	3.85	3.77	4.04	3.73-3.86
5,4,4,4	aDGlcpN	5.36	3.33	3.89	3.57	4.33	3.79-3.83
5,4,4,6	P
5,4,4	bDGalp	4.53	3.63	3.91	4.20	3.83	3.90-3.98
5,4,6,6,6,0	xXCho	4.34	3.68	3.23
5,4,6,6,6	%xXP?
5,4,6,6	aDGlcpN	5.59	3.43	4.00	3.63	4.01	4.17-4.17
5,4,6	aXLLmanHepp	5.06	3.97	3.73	3.94	3.90	4.28	3.93-3.97
5,4	bDGlcpN	4.78	3.29	3.67	3.83	3.69	3.99-4.10
5,6	aXLLmanHepp	5.69	3.97	3.91	3.91	3.63	4.08	3.69-3.83
5,7	P
5	aXLLmanHepp	5.15	4.18	3.96	4.34	4.08	4.11	4.05-4.16
	??Sug?


1H/13C HSQC data:
Linkage	Residue	C1/H1	C2/H2	C3/H3	C4/H4	C5/H5	C6/H6	C7/H7
5,3,2,7	aDGlcpN	96.8/5.10	55.4/3.47	71.7/3.89	70.7/3.66	73.9/3.74	61.7/3.87-3.92
5,3,2	aXLLmanHepp	103.0/5.20	72.1/4.01	72.1/4.01	67.5/3.84	73.5/3.85	69.2/4.34	71.7/3.54-4.01
5,3	aXLLmanHepp	99.7/5.29	81.4/4.01	71.3/3.91	67.6/3.85	73.0/3.77	70.4/4.04	65.0/3.73-3.86
5,4,4,4	aDGlcpN	97.1/5.36	55.4/3.33	70.8/3.89	70.3/3.57	73.4/4.33	61.1/3.79-3.83
5,4,4,6	P
5,4,4	bDGalp	104.2/4.53	71.5/3.63	72.9/3.91	77.7/4.20	73.5/3.83	63.5/3.90-3.98
5,4,6,6,6,0	xXCho	60.8/4.34	67.3/3.68	55.2/3.23
5,4,6,6,6	%xXP?
5,4,6,6	aDGlcpN	96.3/5.59	55.5/3.43	70.7/4.00	70.2/3.63	72.8/4.01	65.5/4.17-4.17
5,4,6	aXLLmanHepp	102.3/5.06	70.7/3.97	72.3/3.73	67.6/3.94	74.0/3.90	76.9/4.28	63.7/3.93-3.97
5,4	bDGlcpN	100.7/4.78	57.9/3.29	73.0/3.67	77.2/3.83	75.6/3.69	66.6/3.99-4.10
5,6	aXLLmanHepp	102.3/5.69	71.9/3.97	71.5/3.91	67.6/3.91	73.9/3.63	70.7/4.08	64.3/3.69-3.83
5,7	P
5	aXLLmanHepp	103.5/5.15	71.3/4.18	73.7/3.96	75.6/4.34	71.1/4.08	76.7/4.11	64.2/4.05-4.16
	??Sug?

¹H NMR data:

Linkage	Residue	H1	H2	H3	H4	H5	H6	H7
5,3,2,7	aDGlcpN	5.10	3.47	3.89	3.66	3.74	3.87 3.92
5,3,2	aXLLmanHepp	5.20	4.01	4.01	3.84	3.85	4.34	3.54 4.01
5,3	aXLLmanHepp	5.29	4.01	3.91	3.85	3.77	4.04	3.73 3.86
5,4,4,4	aDGlcpN	5.36	3.33	3.89	3.57	4.33	3.79 3.83
5,4,4,6	P
5,4,4	bDGalp	4.53	3.63	3.91	4.20	3.83	3.90 3.98
5,4,6,6,6,0	xXCho	4.34	3.68	3.23
5,4,6,6,6	%xXP?
5,4,6,6	aDGlcpN	5.59	3.43	4.00	3.63	4.01	4.17 4.17
5,4,6	aXLLmanHepp	5.06	3.97	3.73	3.94	3.90	4.28	3.93 3.97
5,4	bDGlcpN	4.78	3.29	3.67	3.83	3.69	3.99 4.10
5,6	aXLLmanHepp	5.69	3.97	3.91	3.91	3.63	4.08	3.69 3.83
5,7	P
5	aXLLmanHepp	5.15	4.18	3.96	4.34	4.08	4.11	4.05 4.16
	??Sug?

¹³C NMR data:

Linkage	Residue	C1	C2	C3	C4	C5	C6	C7
5,3,2,7	aDGlcpN	96.8	55.4	71.7	70.7	73.9	61.7
5,3,2	aXLLmanHepp	103.0	72.1	72.1	67.5	73.5	69.2	71.7
5,3	aXLLmanHepp	99.7	81.4	71.3	67.6	73.0	70.4	65.0
5,4,4,4	aDGlcpN	97.1	55.4	70.8	70.3	73.4	61.1
5,4,4,6	P
5,4,4	bDGalp	104.2	71.5	72.9	77.7	73.5	63.5
5,4,6,6,6,0	xXCho	60.8	67.3	55.2
5,4,6,6,6	%xXP?
5,4,6,6	aDGlcpN	96.3	55.5	70.7	70.2	72.8	65.5
5,4,6	aXLLmanHepp	102.3	70.7	72.3	67.6	74.0	76.9	63.7
5,4	bDGlcpN	100.7	57.9	73.0	77.2	75.6	66.6
5,6	aXLLmanHepp	102.3	71.9	71.5	67.6	73.9	70.7	64.3
5,7	P
5	aXLLmanHepp	103.5	71.3	73.7	75.6	71.1	76.7	64.2
	??Sug?

There is only one chemically distinct structure:

[1*]O[C@@H]1O[C@@H]([C@H](COP(=O)(O)O)O[C@@H]2O[C@@H]([C@@H](O)CO)[C@H](O)[C@@H](O)[C@H]2O)[C@H](O[C@@H]2O[C@H](CO[C@@H]3O[C@@H]([C@H](CO)O[C@H]4O[C@H](COP(=O)(O)OCC[N+](C)(C)C)[C@@H](O)[C@H](O)[C@H]4N)[C@H](O)[C@@H](O)[C@H]3O)[C@@H](O[C@@H]3O[C@H](COP(=O)(O)O)[C@H](O[C@H]4O[C@H](CO)[C@@H](O)[C@H](O)[C@H]4N)[C@H](O)[C@H]3O)[C@H](O)[C@H]2N)[C@@H](O[C@@H]2O[C@@H]([C@@H](O)CO)[C@H](O)[C@@H](O)[C@H]2O[C@@H]2O[C@@H]([C@@H](O)CO[C@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3N)[C@H](O)[C@@H](O)[C@H]2O)[C@H]1O

SVG MW SMILES 3D mol Ionize

R1 = ??Sug?, Sug = anhKdo