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Taxonomic group: bacteria / Proteobacteria (Phylum: Proteobacteria)
Host organism: Homo sapiens
Associated disease: chronic gastritis [ICD11: DA42.Z

, ICD11: XT8W

]; peptic ulcer [ICD11: DA61

, ICD11: XN3DY

]; gastric cancer [ICD11: 2B72.Z

]; infection due to Helicobacter pylori [ICD11: XN3DY

]

The structure was elucidated in this paper
NCBI PubMed ID: 29247909
Publication DOI: 10.1016/j.carres.2017.10.024
Journal NLM ID: 0043535
Publisher: Elsevier
Correspondence: evguenii.vinogradov

nrc-cnrc.gc.ca
Institutions: Vaccines and Immunotherapeutics Program, National Research Council of Canada, Ottawa, ON K1A 0R6, Canada

Structural characterization of the lipopolysaccharide (LPS) from a nontypeable Helicobacter pylori strain PJ1 and two corresponding mutants, PJ1 HP1283:cam and PJ1 HP1284:cam, was performed using a combination of NMR and mass spectrometric techniques. It resulted in the core structure that differed significantly from the one proposed previously. Overall architecture of PJ1 LPS was found to be consistent with a structural model described for several other H. pylori strains. It contained a polymer of d-glycero-d-manno-heptose (dd-Hep) as the O-chain component, linked to α-1,6-glucan through a dd-Hep oligosaccharide. H. pylori PJ1 HP1283:cam LPS was missing dd-heptan, terminating with an α-1,6-glucan chain containing 5-13 glucose residues. LPS of strain PJ1 HP1284:cam was missing dd-Hep from the core and had β-GlcNAc attached directly to O-3 of the inner-core ld-Hep residue. To investigate the role of dd-heptan in protective immunity, delipidated LPS (dLPS) from strain PJ1 was conjugated to tetanus toxoid (TT) and immunological properties of the resultant glycoconjugate dLPS(PJ1)-TT determined. The dLPS(PJ1)-TT conjugate was immunogenic in mice and rabbits and induced specific and cross-reactive functional antibodies against homologous and heterologous strains of H. pylori. Whole cell indirect ELISA performed on a selected number of H. pylori isolates confirmed that the immune response correlated with the presence of α-1,6-glucan and was not augmented by the dd-Hep content of these strains.

Lipopolysaccharide, LPS, structure, inner core, Helicobacter pylori, D-glycero-D-manno-heptose, vaccine, conjugate

Structure type: oligomer
Location inside paper: p.20, fig.1, table 1, OS4
Compound class: core oligosaccharide
Contained glycoepitopes: IEDB_120354,IEDB_123890,IEDB_130650,IEDB_136045,IEDB_140088,IEDB_141807,IEDB_142488,IEDB_142489,IEDB_144562,IEDB_144998,IEDB_146664,IEDB_151531,IEDB_152214,IEDB_158538,IEDB_174333,IEDB_2189046,IEDB_2189047,IEDB_2346541,IEDB_983931,SB_192,SB_86

Methods: 13C NMR, 1H NMR, gel filtration, NMR-2D, de-O-acylation, ESI-MS, anion-exchange chromatography, mild acid hydrolysis, HPAEC, conjugation, delipidation
Comments, role: deacylated LPS of H. pylori PJ1 HP1284::cam mutant

Related record ID(s): 12864, 13019, 13020, 13021, 13023
NCBI Taxonomy refs (TaxIDs): 210
Show glycosyltransferases

NMR conditions: in D2O at 308 K [as TSV]

13C NMR data:
Linkage	Residue	C1	C2	C3	C4	C5	C6	C7
6,5,3,2,3,3,6,6	aDGlcp	98.8	72.5	74.5	70.7	71.3	66.6
6,5,3,2,3,3,6,6,6,3,?	Subst
6,5,3,2,3,3,6,6,6,3	aXDDmanHepp	102.2	70.9	79.4	67.8	74.1	73.8	63.5
6,5,3,2,3,3,6,6,6	aDGlcp	99.0	71.5	80.9	71.1	71.8	61.4
6,5,3,2,3,3,6	aDGlcp	99.0	72.6	74.7	70.9	71.7	66.9
6,5,3,2,3,3	aXDDmanHepp	102.9	71.1	71.5	68.9	72.8	80.0	?
6,5,3,2,3	aLFucp	103.0	69.5	77.7	72.5	69.0	16.5
6,5,3,2	bDGlcpN	97.1	57.0	83.8	69.8	77.5	61.7
6,5,3	aXLDmanHepp	102.6	68.7	78.8	68.0	74.3	?	?
6,5	aXLDmanHepp	10.3	71.2	77.8	?	?	?	?
6	aXKdop
	bDGlcpN
6,5,6,0	xXEtN
6,5,6	P
6,5,7,0	xXEtN
6,5,7	P


1H NMR data:
Linkage	Residue	H1	H2	H3	H4	H5	H6	H7
6,5,3,2,3,3,6,6	aDGlcp	4.98	3.58	3.72	3.52	3.91	3.76-3.98
6,5,3,2,3,3,6,6,6,3,?	Subst
6,5,3,2,3,3,6,6,6,3	aXDDmanHepp	5.22	4.22	3.95	3.95	4.06	4.03	3.74-3.77
6,5,3,2,3,3,6,6,6	aDGlcp	4.98	3.64	3.86	3.58	3.84	3.77-3.84
6,5,3,2,3,3,6	aDGlcp	5.16	3.61	3.75	3.52	4.12	3.76-4.00
6,5,3,2,3,3	aXDDmanHepp	5.17	4.05	3.91	3.86	3.96	4.08	?
6,5,3,2,3	aLFucp	5.06	4.04	4.03	4.02	4.29	1.21
6,5,3,2	bDGlcpN	4.98	3.39	3.82	3.66	3.56	3.80-3.85
6,5,3	aXLDmanHepp	5.26-5.29	4.28	4.25	3.92	3.77	?	?
6,5	aXLDmanHepp	5.10-5.13	4.17-4.18	4.00-4.05	?	?	?	?
6	aXKdop
	bDGlcpN
6,5,6,0	xXEtN
6,5,6	P
6,5,7,0	xXEtN
6,5,7	P


1H/13C HSQC data:
Linkage	Residue	C1/H1	C2/H2	C3/H3	C4/H4	C5/H5	C6/H6	C7/H7
6,5,3,2,3,3,6,6	aDGlcp	98.8/4.98	72.5/3.58	74.5/3.72	70.7/3.52	71.3/3.91	66.6/3.76-3.98
6,5,3,2,3,3,6,6,6,3,?	Subst
6,5,3,2,3,3,6,6,6,3	aXDDmanHepp	102.2/5.22	70.9/4.22	79.4/3.95	67.8/3.95	74.1/4.06	73.8/4.03	63.5/3.74-3.77
6,5,3,2,3,3,6,6,6	aDGlcp	99.0/4.98	71.5/3.64	80.9/3.86	71.1/3.58	71.8/3.84	61.4/3.77-3.84
6,5,3,2,3,3,6	aDGlcp	99.0/5.16	72.6/3.61	74.7/3.75	70.9/3.52	71.7/4.12	66.9/3.76-4.00
6,5,3,2,3,3	aXDDmanHepp	102.9/5.17	71.1/4.05	71.5/3.91	68.9/3.86	72.8/3.96	80.0/4.08	?/?
6,5,3,2,3	aLFucp	103.0/5.06	69.5/4.04	77.7/4.03	72.5/4.02	69.0/4.29	16.5/1.21
6,5,3,2	bDGlcpN	97.1/4.98	57.0/3.39	83.8/3.82	69.8/3.66	77.5/3.56	61.7/3.80-3.85
6,5,3	aXLDmanHepp	102.6/5.26-5.29	68.7/4.28	78.8/4.25	68.0/3.92	74.3/3.77	?/?	?/?
6,5	aXLDmanHepp	10.3/5.10-5.13	71.2/4.17-4.18	77.8/4.00-4.05	?/?	?/?	?/?	?/?
6	aXKdop
	bDGlcpN
6,5,6,0	xXEtN
6,5,6	P
6,5,7,0	xXEtN
6,5,7	P

¹H NMR data:

Linkage	Residue	H1	H2	H3	H4	H5	H6	H7
6,5,3,2,3,3,6,6	aDGlcp	4.98	3.58	3.72	3.52	3.91	3.76 3.98
6,5,3,2,3,3,6,6,6,3,?	Subst
6,5,3,2,3,3,6,6,6,3	aXDDmanHepp	5.22	4.22	3.95	3.95	4.06	4.03	3.74 3.77
6,5,3,2,3,3,6,6,6	aDGlcp	4.98	3.64	3.86	3.58	3.84	3.77 3.84
6,5,3,2,3,3,6	aDGlcp	5.16	3.61	3.75	3.52	4.12	3.76 4.00
6,5,3,2,3,3	aXDDmanHepp	5.17	4.05	3.91	3.86	3.96	4.08	?
6,5,3,2,3	aLFucp	5.06	4.04	4.03	4.02	4.29	1.21
6,5,3,2	bDGlcpN	4.98	3.39	3.82	3.66	3.56	3.80 3.85
6,5,3	aXLDmanHepp	5.26 5.29	4.28	4.25	3.92	3.77	?	?
6,5	aXLDmanHepp	5.10 5.13	4.17 4.18	4.00 4.05	?	?	?	?
6	aXKdop
	bDGlcpN
6,5,6,0	xXEtN
6,5,6	P
6,5,7,0	xXEtN
6,5,7	P

¹³C NMR data:

Linkage	Residue	C1	C2	C3	C4	C5	C6	C7
6,5,3,2,3,3,6,6	aDGlcp	98.8	72.5	74.5	70.7	71.3	66.6
6,5,3,2,3,3,6,6,6,3,?	Subst
6,5,3,2,3,3,6,6,6,3	aXDDmanHepp	102.2	70.9	79.4	67.8	74.1	73.8	63.5
6,5,3,2,3,3,6,6,6	aDGlcp	99.0	71.5	80.9	71.1	71.8	61.4
6,5,3,2,3,3,6	aDGlcp	99.0	72.6	74.7	70.9	71.7	66.9
6,5,3,2,3,3	aXDDmanHepp	102.9	71.1	71.5	68.9	72.8	80.0	?
6,5,3,2,3	aLFucp	103.0	69.5	77.7	72.5	69.0	16.5
6,5,3,2	bDGlcpN	97.1	57.0	83.8	69.8	77.5	61.7
6,5,3	aXLDmanHepp	102.6	68.7	78.8	68.0	74.3	?	?
6,5	aXLDmanHepp	10.3	71.2	77.8	?	?	?	?
6	aXKdop
	bDGlcpN
6,5,6,0	xXEtN
6,5,6	P
6,5,7,0	xXEtN
6,5,7	P

The spectrum also has 7 signals at unknown positions (not plotted).

There are 5 chemically distinct structures. Please, select:

[1*]O[C@H]1[C@@H](O)[C@H](O)[C@@H]([C@H](O)CO)O[C@@H]1O[C@@H]1[C@@H](O)[C@@H](OC[C@H]2O[C@H](OC[C@H]3O[C@H](OC[C@H]4O[C@H](OC[C@H]5O[C@H](OC[C@H]6O[C@H](OC[C@H]7O[C@H](O[C@H](CO)[C@H]8O[C@H](O[C@H]9[C@H](O)[C@H](O[C@H]%10[C@H](O)[C@@H](CO)O[C@@H](O[C@H]%11[C@@H](O)[C@H](O)[C@@H]([C@@H](O)CO)O[C@@H]%11O[C@@H]%11[C@H](O)[C@@H](O[C@@H]%12[C@H](O)C[C@](OC[C@H]%13O[C@@H](O)[C@H](N)[C@@H](O)[C@@H]%13O)(C(=O)O)O[C@@H]%12[C@H](O)CO)O[C@H]([C@H](CO)OP(=O)(O)OCCN)[C@H]%11O)[C@@H]%10N)O[C@@H](C)[C@H]9O)[C@@H](O)[C@@H](O)[C@@H]8O)[C@H](O)[C@@H](O)[C@@H]7O)[C@H](O)[C@@H](O)[C@@H]6O)[C@H](O)[C@@H](O)[C@@H]5O)[C@H](O)[C@@H](O)[C@@H]4O)[C@H](O)[C@@H](O)[C@@H]3O)[C@H](O)[C@@H](O)[C@@H]2O)O[C@H](CO)[C@H]1O

SVG MW SMILES 3D mol Ionize

R1 = OPS linker