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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, OS1
Compound class: LPS
Contained glycoepitopes: IEDB_130650,IEDB_130659,IEDB_136906,IEDB_137472,IEDB_137485,IEDB_140088,IEDB_140529,IEDB_141794,IEDB_141807,IEDB_142488,IEDB_144983,IEDB_144998,IEDB_146664,IEDB_151528,IEDB_151531,IEDB_152206,IEDB_190606,IEDB_2189047,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: alkaline deacylation of the LPS yielded two major oligosaccharide OS1 and OS2. Published NMR assignment of aGlc C4 (79.0) is erroneous, replaced by value from OS2.

Related record ID(s): 29378, 29795, 29796
NCBI Taxonomy refs (TaxIDs): 1238
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
0,4	bLArap4N	101.3	69.7	67.1	52.2	60.6
0,6,6,4	aXKdop	?	?	35.9	68.1	68.1	73.4	72.4	64.4
0,6,6,5,3,2	bDGlcp	102.8	74.2	76.3	71.1	77.8	62.1
0,6,6,5,3,3,6,6,4	aXPse?	?	?	35.4	65.1	52.2	69.0	59.0	66.9	20.2
0,6,6,5,3,3,6,6	aXPse?	?	?	35.9	69.4	50.8	69.0	58.0	66.0	19.2
0,6,6,5,3,3,6	aDGalp	99.8	69.8	70.9	70.1	69.6	64.8
0,6,6,5,3,3	aDGlcp	101.2	73.3	74.4	70.5	72.4	66.5
0,6,6,5,3	aXLDmanHepp	101.4	78.5	75.8	68.5	72.7	69.5	64.8
0,6,6,5,4	bDManp	101.6	71.7	74.3	69.4	79.4	63.8
0,6,6,5,7	bLArap4N	101.1	69.6	67.0	53.3	59.6
0,6,6,5	aXLDmanHepp	99.7	72.0	75.0	75.0	73.3	69.6	73.2
0,6,6	aXKdop	?	?	36.1	68.0	67.0	73.7	71.0	65.2
0,6	bDGlcpN	101.1	57.0	75.7	70.6	74.3	63.7
0	aDGlcpN	92.0	55.6	71.5	79.1	72.5	70.4
	P


1H NMR data:
Linkage	Residue	H1	H2	H3	H4	H5	H6	H7	H8	H9
0,4	bLArap4N	5.38	3.83	4.18	3.75	3.87-4.14
0,6,6,4	aXKdop	-	-	1.79-2.17	4.03	4.05	3.65	4.02	3.71-3.95
0,6,6,5,3,2	bDGlcp	4.73	3.28	3.51	3.40	3.37	3.77-3.88
0,6,6,5,3,3,6,6,4	aXPse?	-	-	1.73-2.29	4.31	3.59	4.16	3.51	4.23	1.37
0,6,6,5,3,3,6,6	aXPse?	-	-	1.91-2.12	4.24	3.69	4.16	3.49	4.28	1.33
0,6,6,5,3,3,6	aDGalp	4.98	3.83	3.91	4.09	4.10	3.66-3.66
0,6,6,5,3,3	aDGlcp	5.53	3.56	3.85	3.66	4.02	3.79-4.11
0,6,6,5,3	aXLDmanHepp	5.30	4.21	4.12	4.11	3.71	4.10	3.66-3.66
0,6,6,5,4	bDManp	4.72	4.08	3.63	3.38	3.38	3.55-3.95
0,6,6,5,7	bLArap4N	5.08	3.78	4.21	3.73	3.8-4.16
0,6,6,5	aXLDmanHepp	5.24	4.13	4.24	4.34	4.34	4.06	3.78-4.26
0,6,6	aXKdop	-	-	2.00-2.23	4.04	4.21	3.62	3.86	3.56-3.92
0,6	bDGlcpN	4.98	3.12	3.65	3.64	3.64	3.55-3.58
0	aDGlcpN	5.65	3.42	4.18	3.66	4.29	3.8-4.28
	P


1H/13C HSQC data:
Linkage	Residue	C1/H1	C2/H2	C3/H3	C4/H4	C5/H5	C6/H6	C7/H7	C8/H8	C9/H9
0,4	bLArap4N	101.3/5.38	69.7/3.83	67.1/4.18	52.2/3.75	60.6/3.87-4.14
0,6,6,4	aXKdop			35.9/1.79-2.17	68.1/4.03	68.1/4.05	73.4/3.65	72.4/4.02	64.4/3.71-3.95
0,6,6,5,3,2	bDGlcp	102.8/4.73	74.2/3.28	76.3/3.51	71.1/3.40	77.8/3.37	62.1/3.77-3.88
0,6,6,5,3,3,6,6,4	aXPse?			35.4/1.73-2.29	65.1/4.31	52.2/3.59	69.0/4.16	59.0/3.51	66.9/4.23	20.2/1.37
0,6,6,5,3,3,6,6	aXPse?			35.9/1.91-2.12	69.4/4.24	50.8/3.69	69.0/4.16	58.0/3.49	66.0/4.28	19.2/1.33
0,6,6,5,3,3,6	aDGalp	99.8/4.98	69.8/3.83	70.9/3.91	70.1/4.09	69.6/4.10	64.8/3.66-3.66
0,6,6,5,3,3	aDGlcp	101.2/5.53	73.3/3.56	74.4/3.85	70.5/3.66	72.4/4.02	66.5/3.79-4.11
0,6,6,5,3	aXLDmanHepp	101.4/5.30	78.5/4.21	75.8/4.12	68.5/4.11	72.7/3.71	69.5/4.10	64.8/3.66-3.66
0,6,6,5,4	bDManp	101.6/4.72	71.7/4.08	74.3/3.63	69.4/3.38	79.4/3.38	63.8/3.55-3.95
0,6,6,5,7	bLArap4N	101.1/5.08	69.6/3.78	67.0/4.21	53.3/3.73	59.6/3.8-4.16
0,6,6,5	aXLDmanHepp	99.7/5.24	72.0/4.13	75.0/4.24	75.0/4.34	73.3/4.34	69.6/4.06	73.2/3.78-4.26
0,6,6	aXKdop			36.1/2.00-2.23	68.0/4.04	67.0/4.21	73.7/3.62	71.0/3.86	65.2/3.56-3.92
0,6	bDGlcpN	101.1/4.98	57.0/3.12	75.7/3.65	70.6/3.64	74.3/3.64	63.7/3.55-3.58
0	aDGlcpN	92.0/5.65	55.6/3.42	71.5/4.18	79.1/3.66	72.5/4.29	70.4/3.8-4.28
	P

¹H NMR data:

Linkage	Residue	H1	H2	H3	H4	H5	H6	H7	H8	H9
0,4	bLArap4N	5.38	3.83	4.18	3.75	3.87 4.14
0,6,6,4	aXKdop			1.79 2.17	4.03	4.05	3.65	4.02	3.71 3.95
0,6,6,5,3,2	bDGlcp	4.73	3.28	3.51	3.40	3.37	3.77 3.88
0,6,6,5,3,3,6,6,4	aXPse?			1.73 2.29	4.31	3.59	4.16	3.51	4.23	1.37
0,6,6,5,3,3,6,6	aXPse?			1.91 2.12	4.24	3.69	4.16	3.49	4.28	1.33
0,6,6,5,3,3,6	aDGalp	4.98	3.83	3.91	4.09	4.10	3.66 3.66
0,6,6,5,3,3	aDGlcp	5.53	3.56	3.85	3.66	4.02	3.79 4.11
0,6,6,5,3	aXLDmanHepp	5.30	4.21	4.12	4.11	3.71	4.10	3.66 3.66
0,6,6,5,4	bDManp	4.72	4.08	3.63	3.38	3.38	3.55 3.95
0,6,6,5,7	bLArap4N	5.08	3.78	4.21	3.73	3.8 4.16
0,6,6,5	aXLDmanHepp	5.24	4.13	4.24	4.34	4.34	4.06	3.78 4.26
0,6,6	aXKdop			2.00 2.23	4.04	4.21	3.62	3.86	3.56 3.92
0,6	bDGlcpN	4.98	3.12	3.65	3.64	3.64	3.55 3.58
0	aDGlcpN	5.65	3.42	4.18	3.66	4.29	3.8 4.28
	P

¹³C NMR data:

Linkage	Residue	C1	C2	C3	C4	C5	C6	C7	C8	C9
0,4	bLArap4N	101.3	69.7	67.1	52.2	60.6
0,6,6,4	aXKdop	?	?	35.9	68.1	68.1	73.4	72.4	64.4
0,6,6,5,3,2	bDGlcp	102.8	74.2	76.3	71.1	77.8	62.1
0,6,6,5,3,3,6,6,4	aXPse?	?	?	35.4	65.1	52.2	69.0	59.0	66.9	20.2
0,6,6,5,3,3,6,6	aXPse?	?	?	35.9	69.4	50.8	69.0	58.0	66.0	19.2
0,6,6,5,3,3,6	aDGalp	99.8	69.8	70.9	70.1	69.6	64.8
0,6,6,5,3,3	aDGlcp	101.2	73.3	74.4	70.5	72.4	66.5
0,6,6,5,3	aXLDmanHepp	101.4	78.5	75.8	68.5	72.7	69.5	64.8
0,6,6,5,4	bDManp	101.6	71.7	74.3	69.4	79.4	63.8
0,6,6,5,7	bLArap4N	101.1	69.6	67.0	53.3	59.6
0,6,6,5	aXLDmanHepp	99.7	72.0	75.0	75.0	73.3	69.6	73.2
0,6,6	aXKdop	?	?	36.1	68.0	67.0	73.7	71.0	65.2
0,6	bDGlcpN	101.1	57.0	75.7	70.6	74.3	63.7
0	aDGlcpN	92.0	55.6	71.5	79.1	72.5	70.4
	P

The spectrum also has 8 signals at unknown positions (not plotted).

There is only one chemically distinct structure:

C[C@H](O)[C@H](N)[C@@H]1O[C@](OC[C@H]2O[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)O[C@@](OC[C@H]7O[C@@H](OC[C@H]8O[C@H](OP(=O)(O)O)[C@H](N)[C@@H](O)[C@@H]8O[C@H]8OC[C@H](N)[C@H](O)[C@H]8O)[C@H](N)[C@@H](O)[C@@H]7O)(C(=O)O)C[C@H]6O[C@]6(C(=O)O)C[C@@H](O)[C@@H](O)[C@@H]([C@H](O)CO)O6)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)[C@H](O)[C@@H](O)[C@H]2O)(C(=O)O)C[C@H](O[C@@]2(C(=O)O)C[C@H](O)[C@H](N)[C@H]([C@@H](N)[C@H](C)O)O2)[C@@H]1N

SVG MW SMILES 3D mol Ionize