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Taxonomic group: bacteria / Bacteroidetes (Phylum: Bacteroidetes)

The structure was elucidated in this paper
NCBI PubMed ID: 32999936
Publication DOI: 10.1021/acscentsci.0c00791
Journal NLM ID: 101660035
Publisher: Washington DC: ACS
Correspondence: flaviana.dilorenzo

unina.it; molinaro

unina.it
Institutions: Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy, Task Force on Microbiome Studies, University of Naples Federico II, 80126 Naples, Italy, Department of Biology and Biotechnologies 'C. Darwin', Sapienza-University of Rome, 00185 Rome, Italy, Department of Structural and Chemical Biology, Centro de Investigaciones Biologicas, CIB-CSIC, 28040 Madrid, Spain, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw 53-114, Poland, Department of Molecular Cell Biology and Immunology, Amsterdam Infection & Immunity Institute and Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam 1081 HV, The Netherlands, Institute of Medical Microbiology and Hygiene, University of Tubingen, 72076 Tubingen, Germany

The gut microbiota guide the development of the host immune system by setting a systemic threshold for immune activation. Lipopolysaccharides (LPSs) from gut bacteria are able to trigger systemic and local proinflammatory and immunomodulatory responses, and this capability strongly relies on their fine structures. Up to now, only a few LPS structures from gut commensals have been elucidated; therefore, the molecular motifs that may be important for LPS-mammalian cell interactions at the gut level are still obscure. Here, we report on the full structure of the LPS isolated from one of the prominent species of the genus Bacteroides, Bacteroides vulgatus. The LPS turned out to consist of a particular chemical structure based on hypoacylated and mono-phosphorylated lipid A and with a galactofuranose-containing core oligosaccharide and an O-antigen built up of mannose and rhamnose. The evaluation of the immunological properties of this LPS on human in vitro models revealed a very interesting capability to produce anti-inflammatory cytokines and to induce a synergistic action of MD-2/TLR4- and TLR2-mediated signaling pathways.

human, Bacteroides, cytokines, LPS structure, immunomodulatory, gut microbiota

Structure type: oligomer
Location inside paper: p.1606, Fig.3
Compound class: LPS
Contained glycoepitopes: IEDB_130650,IEDB_136044,IEDB_136045,IEDB_136095,IEDB_136105,IEDB_137340,IEDB_137472,IEDB_137485,IEDB_137777,IEDB_141794,IEDB_141807,IEDB_142488,IEDB_142489,IEDB_144562,IEDB_144983,IEDB_146664,IEDB_150948,IEDB_151531,IEDB_152206,IEDB_152214,IEDB_153553,IEDB_174333,IEDB_189517,IEDB_190606,IEDB_225177,IEDB_461719,IEDB_885823,IEDB_983930,IEDB_983931,SB_154,SB_165,SB_166,SB_187,SB_192,SB_195,SB_44,SB_7,SB_72,SB_86,SB_88

Methods: 13C NMR, 1H NMR, NMR-2D, GLC-MS, SDS-PAGE, sugar analysis, chemical analysis, ELISA, 31P NMR, deacylation, ESI-MS, MS/MS, MALDI-TOF MS, GPC, MD simulation, measurement of cytokines activity
3D data: molecular modeling

Related record ID(s): 32091
NCBI Taxonomy refs (TaxIDs): 821
Show glycosyltransferases

There is only one chemically distinct structure:

CCCCCCCCCCCCCC(O)CC(=O)O[C@H]1[C@H](O)[C@@H](CO[C@]2(C(=O)O)C[C@@H](OP(=O)(O)O)[C@@H](O[C@@H]3O[C@@H](C)[C@H](O[C@@H]4O[C@H](CO[C@@H]5O[C@H](CO)[C@@H](O)[C@H](O[C@@H]6O[C@@H](C)[C@H](O[C@@H]7O[C@H](CO)[C@@H](O)[C@H](O[C@@H]8O[C@@H](C)[C@H](O[C@@H]9O[C@H](CO)[C@@H](O)[C@H](O[C@@H]%10O[C@@H](C)[C@H](O[C@@H]%11O[C@H](CO)[C@@H](O)[C@H](O[C@@H]%12O[C@@H](C)[C@H](O)[C@@H](O)[C@H]%12O)[C@@H]%11O)[C@@H](O)[C@H]%10O)[C@@H]9O)[C@@H](O)[C@H]8O)[C@@H]7O)[C@@H](O)[C@H]6O)[C@H]5O)[C@H](O)[C@H](O)[C@H]4O[C@@H]4O[C@@H](C)[C@@H](O)[C@@H](O)[C@@H]4O)[C@@H](O[C@@H]4O[C@@H]([C@H](O)CO)[C@H](O)[C@H]4O)[C@H]3O)[C@@H]([C@H](O)CO)O2)O[C@@H](OC[C@H]2O[C@H](OP(=O)(O)O)[C@H](NC(=O)CC(O)CCCCCCCCCCCC(C)C)[C@@H](OC(=O)CC(O)CCCCCCCCCCCCC)[C@@H]2O)[C@@H]1NC(=O)CC(CCCCCCCCCCCC(C)C)OC(=O)CCCCCCCCCCCC(C)C

SVG MW SMILES 3D mol Ionize

Warning = sub-repeat ending at bDManp: unknown unit count was assumed to be 3

unina.it; molinaro

human, Bacteroides, cytokines, LPS structure, immunomodulatory, gut microbiota

Structure type: oligomer
Location inside paper: p.1606, table 1
Compound class: LPS
Contained glycoepitopes: IEDB_130650,IEDB_136044,IEDB_136045,IEDB_136095,IEDB_136105,IEDB_137340,IEDB_137472,IEDB_137485,IEDB_137777,IEDB_141794,IEDB_141807,IEDB_142488,IEDB_142489,IEDB_144562,IEDB_144983,IEDB_146664,IEDB_150948,IEDB_151531,IEDB_152206,IEDB_152214,IEDB_153553,IEDB_174333,IEDB_189517,IEDB_190606,IEDB_225177,IEDB_461719,IEDB_885823,IEDB_983930,IEDB_983931,SB_154,SB_165,SB_166,SB_187,SB_192,SB_195,SB_44,SB_7,SB_72,SB_86,SB_88

Methods: 13C NMR, 1H NMR, NMR-2D, GLC-MS, SDS-PAGE, sugar analysis, chemical analysis, ELISA, 31P NMR, deacylation, ESI-MS, MS/MS, MALDI-TOF MS, GPC, MD simulation, measurement of cytokines activity
Comments, role: fully deacylated LPS
3D data: molecular modeling

Related record ID(s): 3349
NCBI Taxonomy refs (TaxIDs): 821
Show glycosyltransferases

NMR conditions: in D2O; pH 7 at 298 K [as TSV]

13C NMR data:
Linkage	Residue	C1	C2	C3	C4	C5	C6	C7	C8
0,6,6,5,4,6,3,4,3	aLRhap	99.7	70.3	70.3	79.4	67.5	17.09
0,6,6,5,4,6,3,4	bDManp	100.3	66.6	76.6	65.0	76.1	60.8
0,6,6,5,3	bDGalf	108.6	81.8	77.0	82.8	70.3	62.7
0,6,6,5,4,2	aLFucp	99.4	68.3	71.4	73.2	66.9	16.2
0,6,6,5,4,6,3	aLRhap	100.8	70.4	?	79.4	67.5	17.0
0,6,6,5,4,6	bDGlcp	102.5	73.5	82.4	69.9	75.6	60.8
0,6,6,5,4	bDGalp	100.2	76.8	71.4	69.7	70.6	69.0
0,6,6,5	aLRhap	101.0	70.2	78.9	73.6	68.6	16.9
0,6,6,4	P
0,6,6	aXKdop	?	?	34.5	67.2	73.3	70.5	70.2	65.6
0,6	bDGlcpN	99.6	55.6	72.3	69.8	74.5	61.3
0	aDGlcpN	90.4	54.3	69.9	70.1	73.0	68.0
	P


1H NMR data:
Linkage	Residue	H1	H2	H3	H4	H5	H6	H7	H8
0,6,6,5,4,6,3,4,3	aLRhap	4.86	3.90	3.94	3.58	3.89	1.22
0,6,6,5,4,6,3,4	bDManp	4.78	4.17	3.58	3.54	3.29	3.64-3.82
0,6,6,5,3	bDGalf	5.07	4.06	3.96	3.92	3.72	3.56
0,6,6,5,4,2	aLFucp	5.09	3.67	3.76	3.71	4.27	1.14
0,6,6,5,4,6,3	aLRhap	5.00	3.93	?	3.58	3.88	1.22
0,6,6,5,4,6	bDGlcp	4.47	3.29	3.48	3.36	3.36	3.62-3.82
0,6,6,5,4	bDGalp	4.72	3.45	3.75	3.80	3.71	3.93
0,6,6,5	aLRhap	5.11	4.16	3.96	3.85	3.85	1.23
0,6,6,4	P
0,6,6	aXKdop	-	-	1.77-2.02	4.15	4.07	3.68	3.96	3.86-3.95
0,6	bDGlcpN	4.90	2.86	3.52	3.43	3.55	3.47-3.69
0	aDGlcpN	5.50	3.22	3.81	3.27	4.07	3.80-4.12
	P


1H/13C HSQC data:
Linkage	Residue	C1/H1	C2/H2	C3/H3	C4/H4	C5/H5	C6/H6	C7/H7	C8/H8
0,6,6,5,4,6,3,4,3	aLRhap	99.7/4.86	70.3/3.90	70.3/3.94	79.4/3.58	67.5/3.89	17.09/1.22
0,6,6,5,4,6,3,4	bDManp	100.3/4.78	66.6/4.17	76.6/3.58	65.0/3.54	76.1/3.29	60.8/3.64-3.82
0,6,6,5,3	bDGalf	108.6/5.07	81.8/4.06	77.0/3.96	82.8/3.92	70.3/3.72	62.7/3.56
0,6,6,5,4,2	aLFucp	99.4/5.09	68.3/3.67	71.4/3.76	73.2/3.71	66.9/4.27	16.2/1.14
0,6,6,5,4,6,3	aLRhap	100.8/5.00	70.4/3.93	?/?	79.4/3.58	67.5/3.88	17.0/1.22
0,6,6,5,4,6	bDGlcp	102.5/4.47	73.5/3.29	82.4/3.48	69.9/3.36	75.6/3.36	60.8/3.62-3.82
0,6,6,5,4	bDGalp	100.2/4.72	76.8/3.45	71.4/3.75	69.7/3.80	70.6/3.71	69.0/3.93
0,6,6,5	aLRhap	101.0/5.11	70.2/4.16	78.9/3.96	73.6/3.85	68.6/3.85	16.9/1.23
0,6,6,4	P
0,6,6	aXKdop			34.5/1.77-2.02	67.2/4.15	73.3/4.07	70.5/3.68	70.2/3.96	65.6/3.86-3.95
0,6	bDGlcpN	99.6/4.90	55.6/2.86	72.3/3.52	69.8/3.43	74.5/3.55	61.3/3.47-3.69
0	aDGlcpN	90.4/5.50	54.3/3.22	69.9/3.81	70.1/3.27	73.0/4.07	68.0/3.80-4.12
	P

¹H NMR data:

Linkage	Residue	H1	H2	H3	H4	H5	H6	H7	H8
0,6,6,5,4,6,3,4,3	aLRhap	4.86	3.90	3.94	3.58	3.89	1.22
0,6,6,5,4,6,3,4	bDManp	4.78	4.17	3.58	3.54	3.29	3.64 3.82
0,6,6,5,3	bDGalf	5.07	4.06	3.96	3.92	3.72	3.56
0,6,6,5,4,2	aLFucp	5.09	3.67	3.76	3.71	4.27	1.14
0,6,6,5,4,6,3	aLRhap	5.00	3.93	?	3.58	3.88	1.22
0,6,6,5,4,6	bDGlcp	4.47	3.29	3.48	3.36	3.36	3.62 3.82
0,6,6,5,4	bDGalp	4.72	3.45	3.75	3.80	3.71	3.93
0,6,6,5	aLRhap	5.11	4.16	3.96	3.85	3.85	1.23
0,6,6,4	P
0,6,6	aXKdop			1.77 2.02	4.15	4.07	3.68	3.96	3.86 3.95
0,6	bDGlcpN	4.90	2.86	3.52	3.43	3.55	3.47 3.69
0	aDGlcpN	5.50	3.22	3.81	3.27	4.07	3.80 4.12
	P

¹³C NMR data:

Linkage	Residue	C1	C2	C3	C4	C5	C6	C7	C8
0,6,6,5,4,6,3,4,3	aLRhap	99.7	70.3	70.3	79.4	67.5	17.09
0,6,6,5,4,6,3,4	bDManp	100.3	66.6	76.6	65.0	76.1	60.8
0,6,6,5,3	bDGalf	108.6	81.8	77.0	82.8	70.3	62.7
0,6,6,5,4,2	aLFucp	99.4	68.3	71.4	73.2	66.9	16.2
0,6,6,5,4,6,3	aLRhap	100.8	70.4	?	79.4	67.5	17.0
0,6,6,5,4,6	bDGlcp	102.5	73.5	82.4	69.9	75.6	60.8
0,6,6,5,4	bDGalp	100.2	76.8	71.4	69.7	70.6	69.0
0,6,6,5	aLRhap	101.0	70.2	78.9	73.6	68.6	16.9
0,6,6,4	P
0,6,6	aXKdop	?	?	34.5	67.2	73.3	70.5	70.2	65.6
0,6	bDGlcpN	99.6	55.6	72.3	69.8	74.5	61.3
0	aDGlcpN	90.4	54.3	69.9	70.1	73.0	68.0
	P

The spectrum also has 3 signals at unknown positions (not plotted).

There is only one chemically distinct structure:

C[C@@H]1O[C@@H](O[C@@H]2[C@H](OP(=O)(O)O)C[C@](OC[C@H]3O[C@@H](OC[C@H]4O[C@H](OP(=O)(O)O)[C@H](N)[C@@H](O)[C@@H]4O)[C@H](N)[C@@H](O)[C@@H]3O)(C(=O)O)O[C@@H]2[C@H](O)CO)[C@H](O)[C@H](O[C@@H]2O[C@@H]([C@H](O)CO)[C@H](O)[C@H]2O)[C@H]1O[C@@H]1O[C@H](CO[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O[C@@H]3O[C@@H](C)[C@H](O[C@@H]4O[C@H](CO)[C@@H](O)[C@H](O[C@@H]5O[C@@H](C)[C@H](O[C@@H]6O[C@H](CO)[C@@H](O)[C@H](O[C@@H]7O[C@@H](C)[C@H](O[C@@H]8O[C@H](CO)[C@@H](O)[C@H](O[C@@H]9O[C@@H](C)[C@H](O)[C@@H](O)[C@H]9O)[C@@H]8O)[C@@H](O)[C@H]7O)[C@@H]6O)[C@@H](O)[C@H]5O)[C@@H]4O)[C@@H](O)[C@H]3O)[C@H]2O)[C@H](O)[C@H](O)[C@H]1O[C@@H]1O[C@@H](C)[C@@H](O)[C@@H](O)[C@@H]1O

SVG MW SMILES 3D mol Ionize

Warning = sub-repeat ending at bDManp: unknown unit count was assumed to be 3
Warning = sub-repeat ending at bDManp: unknown unit count was assumed to be 3
Warning = sub-repeat ending at bDManp: unknown unit count was assumed to be 3