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Taxonomic group: bacteria / Proteobacteria (Phylum: Proteobacteria)
Host organism: (Salmonidae)
Associated disease: septicemia [ICD11: MA15.Y

]; piscirickettsiosis

The structure was elucidated in this paper
NCBI PubMed ID: 23673236
Publication DOI: 10.1016/j.carres.2013.04.010
Journal NLM ID: 0043535
Publisher: Elsevier
Correspondence: R. Toman <rudolf.toman

savba.sk>
Institutions: National Research Council, Ottawa, ON, Canada K1A 0R6

Elucidation of the carbohydrate backbone structure of the lipopolysaccharide (LPS) from Piscirickettsia salmonis, the etiological agent of the salmonid rickettsial septicemia, is described. Structural information was established by a combination of monosaccharide and methylation analyses of LPS, and by NMR and mass spectrometries of oligosaccharides obtained through the use of various chemical degradations of the native polymer. The following structure of the backbone sugars was determined on the basis of the combined data from these experiments: The presence of two consecutive residues of diacetylated pseudaminic acid (Pse5,7Ac, 5,7-diacetamido-3,5,7,9-tetradeoxy-l-glycero-l-manno-non-2-ulosonic acid) in the LPS appears to be unique among polysaccharides containing this acidic sugar. Similarly, the presence of 4-aminoarabinose (Ara4N, 4-amino-4-deoxy-l-arabinopyranose) on O-4 of the α-GlcN1P of the lipid A moiety is a unique feature of this LPS.

NMR, LPS, structure, pseudaminic acid, MS, Piscirickettsia salmonis

Structure type: oligomer
Location inside paper: p.109, scheme 1, OS3
Compound class: LPS
Contained glycoepitopes: IEDB_130650,IEDB_136906,IEDB_137472,IEDB_137485,IEDB_140088,IEDB_140529,IEDB_141794,IEDB_142488,IEDB_144983,IEDB_144998,IEDB_146664,IEDB_151528,IEDB_152206,IEDB_190606,IEDB_2189047,IEDB_838988,IEDB_983930,IEDB_983931,SB_192,SB_44,SB_7,SB_72

Methods: 13C NMR, 1H NMR, methylation, NMR-2D, GC-MS, SDS-PAGE, sugar analysis, mild acid hydrolysis, CE-MS
Comments, role: mild acid hydrolysis of the LPS

Related record ID(s): 29378, 29794, 29796
NCBI Taxonomy refs (TaxIDs): 1238
Reference(s) to other database(s): GTC:G95426DX
Show glycosyltransferases

NMR conditions: in D2O at 298 K [as TSV]

13C NMR data:
Linkage	Residue	C1	C2	C3	C4	C5	C6	C7	C8	C9
5,3,2	bDGlcp	102.6	73.9	76.2	70.6	77.6	61.9
5,3,3,6,4,5	Ac	?	23.3
5,3,3,6,4,7	Ac	?	23.3
5,3,3,6,4	aXPse?	?	101.9	36.3	66.2	49.8	71.7	54.9	68.1	17.1
5,3,3,6	aDGalp	99.7	69.6	70.5	70.7	70.3	63.9
5,3,3	aDGlcp	101.0	73.1	74.2	70.1	72.3	66.4
5,3	aXLDmanHepp	100.4	78.1	75.6	68.2	72.3	?	64.3
5,4	bDManp	101.1	71.5	74.3	69.0	78.9	63.4
5,7	bLArap4N	100.5	69.3	66.8	53.0	59.3
5	aXLDmanHepp	102.1	71.4	74.3	74.5	73.0	?	72.5
	?XKdo?	?	?	34.8	66.5	?	?	70.1	64.2


1H NMR data:
Linkage	Residue	H1	H2	H3	H4	H5	H6	H7	H8	H9
5,3,2	bDGlcp	4.71	3.28	3.51	3.41	3.35	3.79-3.90
5,3,3,6,4,5	Ac	-	1.98
5,3,3,6,4,7	Ac	-	1.98
5,3,3,6,4	aXPse?	-	-	1.61-2.12	4.18	4.22	3.91	4.19	4.20	1.17
5,3,3,6	aDGalp	5.00	3.84	3.89	4.03	4.06	3.45-3.45
5,3,3	aDGlcp	5.50	3.55	4.85	3.63	4.02	3.77-4.17
5,3	aXLDmanHepp	5.37	4.19	4.11	4.10	3.70	?	3.63-3.63
5,4	bDManp	4.71	4.05	3.62	3.40	3.37	3.56-3.96
5,7	bLArap4N	5.03	3.77	4.18	3.71	3.79-4.10
5	aXLDmanHepp	5.09	4.16	4.17	4.33	4.12	?	3.71-3.91
	?XKdo?	-	-	2.10	4.14	4.11	?	3.72	3.70-3.80


1H/13C HSQC data:
Linkage	Residue	C1/H1	C2/H2	C3/H3	C4/H4	C5/H5	C6/H6	C7/H7	C8/H8	C9/H9
5,3,2	bDGlcp	102.6/4.71	73.9/3.28	76.2/3.51	70.6/3.41	77.6/3.35	61.9/3.79-3.90
5,3,3,6,4,5	Ac		23.3/1.98
5,3,3,6,4,7	Ac		23.3/1.98
5,3,3,6,4	aXPse?			36.3/1.61-2.12	66.2/4.18	49.8/4.22	71.7/3.91	54.9/4.19	68.1/4.20	17.1/1.17
5,3,3,6	aDGalp	99.7/5.00	69.6/3.84	70.5/3.89	70.7/4.03	70.3/4.06	63.9/3.45-3.45
5,3,3	aDGlcp	101.0/5.50	73.1/3.55	74.2/4.85	70.1/3.63	72.3/4.02	66.4/3.77-4.17
5,3	aXLDmanHepp	100.4/5.37	78.1/4.19	75.6/4.11	68.2/4.10	72.3/3.70	?/?	64.3/3.63-3.63
5,4	bDManp	101.1/4.71	71.5/4.05	74.3/3.62	69.0/3.40	78.9/3.37	63.4/3.56-3.96
5,7	bLArap4N	100.5/5.03	69.3/3.77	66.8/4.18	53.0/3.71	59.3/3.79-4.10
5	aXLDmanHepp	102.1/5.09	71.4/4.16	74.3/4.17	74.5/4.33	73.0/4.12	?/?	72.5/3.71-3.91
	?XKdo?			34.8/2.10	66.5/4.14	?/4.11	?/?	70.1/3.72	64.2/3.70-3.80

¹H NMR data:

Linkage	Residue	H1	H2	H3	H4	H5	H6	H7	H8	H9
5,3,2	bDGlcp	4.71	3.28	3.51	3.41	3.35	3.79 3.90
5,3,3,6,4,5	Ac		1.98
5,3,3,6,4,7	Ac		1.98
5,3,3,6,4	aXPse?			1.61 2.12	4.18	4.22	3.91	4.19	4.20	1.17
5,3,3,6	aDGalp	5.00	3.84	3.89	4.03	4.06	3.45 3.45
5,3,3	aDGlcp	5.50	3.55	4.85	3.63	4.02	3.77 4.17
5,3	aXLDmanHepp	5.37	4.19	4.11	4.10	3.70	?	3.63 3.63
5,4	bDManp	4.71	4.05	3.62	3.40	3.37	3.56 3.96
5,7	bLArap4N	5.03	3.77	4.18	3.71	3.79 4.10
5	aXLDmanHepp	5.09	4.16	4.17	4.33	4.12	?	3.71 3.91
	?XKdo?			2.10	4.14	4.11	?	3.72	3.70 3.80

¹³C NMR data:

Linkage	Residue	C1	C2	C3	C4	C5	C6	C7	C8	C9
5,3,2	bDGlcp	102.6	73.9	76.2	70.6	77.6	61.9
5,3,3,6,4,5	Ac	?	23.3
5,3,3,6,4,7	Ac	?	23.3
5,3,3,6,4	aXPse?	?	101.9	36.3	66.2	49.8	71.7	54.9	68.1	17.1
5,3,3,6	aDGalp	99.7	69.6	70.5	70.7	70.3	63.9
5,3,3	aDGlcp	101.0	73.1	74.2	70.1	72.3	66.4
5,3	aXLDmanHepp	100.4	78.1	75.6	68.2	72.3	?	64.3
5,4	bDManp	101.1	71.5	74.3	69.0	78.9	63.4
5,7	bLArap4N	100.5	69.3	66.8	53.0	59.3
5	aXLDmanHepp	102.1	71.4	74.3	74.5	73.0	?	72.5
	?XKdo?	?	?	34.8	66.5	?	?	70.1	64.2

The spectrum also has 9 signals at unknown positions (not plotted).

There are 2 chemically distinct structures. Please, select:

CC(=O)N[C@H]([C@@H]1O[C@](O[C@@H]2[C@H](O)[C@@H](O)[C@@H](OC[C@H]3O[C@H](O[C@H]4[C@H](O)[C@@H]([C@@H](O)CO)O[C@H](O[C@@H]5[C@H](O)[C@@H](O[C@H]6[C@@H]([C@H](O)CO)OC(O)(C(=O)O)C[C@H]6O)O[C@H]([C@@H](O)CO[C@H]6OC[C@H](N)[C@H](O)[C@H]6O)[C@H]5O[C@@H]5O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]5O)[C@H]4O[C@@H]4O[C@H](CO)[C@@H](O)[C@H](O)[C@H]4O)[C@H](O)[C@@H](O)[C@@H]3O)O[C@@H]2CO)(C(=O)O)C[C@H](O)[C@@H]1NC(C)=O)[C@H](C)O

SVG MW SMILES 3D mol Ionize