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Taxonomic group: bacteria / Firmicutes (Phylum: Firmicutes)

The structure was elucidated in this paper
NCBI PubMed ID: 28653982
Publication DOI: 10.3390/md15070201
Journal NLM ID: 101213729
Publisher: Basel, Switzerland: Molecular Diversity Preservation International
Correspondence: Silipo A <silipo

unina.it>
Institutions: Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy, CNR-Istituto per i Polimeri, Compositi e Biomateriali IPCB-Unità di Catania, 95126 Catania, Italy, Department of Biology and Biotechnology ''Charles Darwin'', Sapienza-University of Rome, 00185 Rome, Italy, Marine Molecular Microbiology & Biotechnology, CNR-Institute for Coastal Marine Environment, 98122 Messina, Italy, Immanuel Kant Baltic Federal University, 236040 Kaliningrad, Russia

The structural characterization of the lipopolysaccharide (LPS) from extremophiles has important implications in several biomedical and therapeutic applications. The polyextremophile Gram-negative bacterium Halobacteroideslacunaris TB21, isolated from one of the most extreme habitats on our planet, the deep-sea hypersaline anoxic basin Thetis, represents a fascinating microorganism to investigate in terms of its LPS component. Here we report the elucidation of the full structure of the R-type LPS isolated from H. lacunaris TB21 that was attained through a multi-technique approach comprising chemical analyses, NMR spectroscopy, and Matrix-Assisted Laser Desorption Ionization (MALDI) mass spectrometry. Furthermore, cellular immunology studies were executed on the pure R-LPS revealing a very interesting effect on human innate immunity as an inhibitor of the toxic Escherichia coli LPS.

lipid A, core oligosaccharide, lipopolysaccharide (LPS), innate immunity, Halobacteroides, deep-sea hypersaline anoxic basins (DHABs), extremophiles; halophiles

Structure type: oligomer
Location inside paper: scheme 1, table 1
Compound class: core oligosaccharide
Contained glycoepitopes: IEDB_115136,IEDB_130650,IEDB_130701,IEDB_137340,IEDB_137777,IEDB_140088,IEDB_140630,IEDB_141807,IEDB_142488,IEDB_144983,IEDB_146664,IEDB_151531,IEDB_152206,IEDB_2189047,IEDB_423153,IEDB_983930,IEDB_983931,SB_192,SB_44,SB_67,SB_72

Methods: gel filtration, 13C NMR, 1H NMR, NMR-2D, methylation, GLC-MS, SDS-PAGE, ELISA, 31P NMR, acid hydrolysis, MALDI-TOF MS, de-O-acylation with hydrazine, composition analysis, enzymatic digestion, reduction with NaBD4, acetylation, SEC, immunological assays, production
Comments, role: NMR data for t)aDGlcpN residue, 1H: 5.37 3.23 3.77 3.41 3.77 3.48-3.84, 13C: 94.7 54.3 69.8 69.3 72.9 62.7.

Related record ID(s): 12437
NCBI Taxonomy refs (TaxIDs): 46470
Reference(s) to other database(s): GTC:G35968CS
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
6,6,5,2	bDGlcpA	102.3	72.4	75.2	72.4	77.3	175.8
6,6,5,3,2,3	%bDGlcp	102.8	73.2	75.8	69.8	76.2	60.6
6,6,5,3,2	aDGlcpN	98.0	54.3	74.0	71.9	73.0	62.7
6,6,5,3,3	aDManp	102.2	70.1	70.3	66.2	73.3	61.0
6,6,5,3	aXLDmanHepp	100.8	78.7	74.0	71.3	71.2	68.4	63.0
6,6,5	aXLDmanHepp	98.0	78.1	76.8	71.2	70.5	69.7	63.0
6,6,4	P
6,6	aXKdop	?	?	34.4	69.7	72.2	73.2	71.4	63.2
6,4	P
6	bDGlcpN	99.3	55.6	72.8	74.0	75.2	62.3
4	P
	aDGlcpN	90.4	54.7	69.8	69.3	72.7	69.6


1H NMR data:
Linkage	Residue	H1	H2	H3	H4	H5	H6	H7	H8
6,6,5,2	bDGlcpA	4.35	3.24	3.40	3.38	3.63	-
6,6,5,3,2,3	%bDGlcp	4.28	3.16	3.24	3.20	3.32	3.66-3.75
6,6,5,3,2	aDGlcpN	5.31	3.25	3.90	3.58	3.76	3.48-3.84
6,6,5,3,3	aDManp	5.07	4.05	4.00	3.75	3.70	3.61-3.81
6,6,5,3	aXLDmanHepp	5.15	4.14	4.13	3.71	3.63	3.87	3.61
6,6,5	aXLDmanHepp	5.10	4.18	4.19	3.73	3.88	3.83	3.62
6,6,4	P
6,6	aXKdop	-	-	1.91-2.09	4.44	4.18	3.82	3.68	3.53-3.81
6,4	P
6	bDGlcpN	4.83	2.95	3.75	3.63	3.43	3.43-3.60
4	P
	aDGlcpN	5.52	3.28	3.79	3.34	4.06	4.10-4.17


1H/13C HSQC data:
Linkage	Residue	C1/H1	C2/H2	C3/H3	C4/H4	C5/H5	C6/H6	C7/H7	C8/H8
6,6,5,2	bDGlcpA	102.3/4.35	72.4/3.24	75.2/3.40	72.4/3.38	77.3/3.63	
6,6,5,3,2,3	%bDGlcp	102.8/4.28	73.2/3.16	75.8/3.24	69.8/3.20	76.2/3.32	60.6/3.66-3.75
6,6,5,3,2	aDGlcpN	98.0/5.31	54.3/3.25	74.0/3.90	71.9/3.58	73.0/3.76	62.7/3.48-3.84
6,6,5,3,3	aDManp	102.2/5.07	70.1/4.05	70.3/4.00	66.2/3.75	73.3/3.70	61.0/3.61-3.81
6,6,5,3	aXLDmanHepp	100.8/5.15	78.7/4.14	74.0/4.13	71.3/3.71	71.2/3.63	68.4/3.87	63.0/3.61
6,6,5	aXLDmanHepp	98.0/5.10	78.1/4.18	76.8/4.19	71.2/3.73	70.5/3.88	69.7/3.83	63.0/3.62
6,6,4	P
6,6	aXKdop			34.4/1.91-2.09	69.7/4.44	72.2/4.18	73.2/3.82	71.4/3.68	63.2/3.53-3.81
6,4	P
6	bDGlcpN	99.3/4.83	55.6/2.95	72.8/3.75	74.0/3.63	75.2/3.43	62.3/3.43-3.60
4	P
	aDGlcpN	90.4/5.52	54.7/3.28	69.8/3.79	69.3/3.34	72.7/4.06	69.6/4.10-4.17

¹H NMR data:

Linkage	Residue	H1	H2	H3	H4	H5	H6	H7	H8
6,6,5,2	bDGlcpA	4.35	3.24	3.40	3.38	3.63
6,6,5,3,2,3	%bDGlcp	4.28	3.16	3.24	3.20	3.32	3.66 3.75
6,6,5,3,2	aDGlcpN	5.31	3.25	3.90	3.58	3.76	3.48 3.84
6,6,5,3,3	aDManp	5.07	4.05	4.00	3.75	3.70	3.61 3.81
6,6,5,3	aXLDmanHepp	5.15	4.14	4.13	3.71	3.63	3.87	3.61
6,6,5	aXLDmanHepp	5.10	4.18	4.19	3.73	3.88	3.83	3.62
6,6,4	P
6,6	aXKdop			1.91 2.09	4.44	4.18	3.82	3.68	3.53 3.81
6,4	P
6	bDGlcpN	4.83	2.95	3.75	3.63	3.43	3.43 3.60
4	P
	aDGlcpN	5.52	3.28	3.79	3.34	4.06	4.10 4.17

¹³C NMR data:

Linkage	Residue	C1	C2	C3	C4	C5	C6	C7	C8
6,6,5,2	bDGlcpA	102.3	72.4	75.2	72.4	77.3	175.8
6,6,5,3,2,3	%bDGlcp	102.8	73.2	75.8	69.8	76.2	60.6
6,6,5,3,2	aDGlcpN	98.0	54.3	74.0	71.9	73.0	62.7
6,6,5,3,3	aDManp	102.2	70.1	70.3	66.2	73.3	61.0
6,6,5,3	aXLDmanHepp	100.8	78.7	74.0	71.3	71.2	68.4	63.0
6,6,5	aXLDmanHepp	98.0	78.1	76.8	71.2	70.5	69.7	63.0
6,6,4	P
6,6	aXKdop	?	?	34.4	69.7	72.2	73.2	71.4	63.2
6,4	P
6	bDGlcpN	99.3	55.6	72.8	74.0	75.2	62.3
4	P
	aDGlcpN	90.4	54.7	69.8	69.3	72.7	69.6

The spectrum also has 2 signals at unknown positions (not plotted).

There is only one chemically distinct structure:

N[C@H]1[C@@H](O)O[C@H](CO[C@@H]2O[C@H](CO[C@]3(C(=O)O)C[C@@H](OP(=O)(O)O)[C@@H](O[C@H]4O[C@H]([C@@H](O)CO)[C@@H](O)[C@H](O[C@H]5O[C@H]([C@@H](O)CO)[C@@H](O)[C@H](O[C@H]6O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]6O)[C@@H]5O[C@H]5O[C@H](CO)[C@@H](O)[C@H](O[C@@H]6O[C@H](CO)[C@@H](O)[C@H](O)[C@H]6O)[C@H]5N)[C@@H]4O[C@@H]4O[C@H](C(=O)O)[C@@H](O)[C@H](O)[C@H]4O)[C@@H]([C@H](O)CO)O3)[C@@H](OP(=O)(O)O)[C@H](O)[C@H]2N)[C@@H](OP(=O)(O)O)[C@@H]1O

SVG MW SMILES 3D mol Ionize

lipid A, core oligosaccharide, lipopolysaccharide (LPS), innate immunity, Halobacteroides, deep-sea hypersaline anoxic basins (DHABs), extremophiles; halophiles

Structure type: oligomer ; 1597.9 [M-H]-
Location inside paper: fig.5
Compound class: lipid A
Contained glycoepitopes: IEDB_135394,IEDB_137340,IEDB_141807,IEDB_151531

Methods: gel filtration, 13C NMR, 1H NMR, NMR-2D, methylation, GLC-MS, SDS-PAGE, ELISA, 31P NMR, acid hydrolysis, MALDI-TOF MS, de-O-acylation with hydrazine, composition analysis, enzymatic digestion, reduction with NaBD4, acetylation, SEC, immunological assays, production
Comments, role: Hexa-acylated lipid A from H. lacunaris TB21 R-LPS. LIP = decenoic acid - C10:1{2}

Related record ID(s): 12049
NCBI Taxonomy refs (TaxIDs): 46470
Show glycosyltransferases

There is only one chemically distinct structure:

[1*]O[C@H]1[C@H](OP(=O)(O)O)[C@@H](CO)O[C@@H](OC[C@H]2O[C@H](OP(=O)(O)O)[C@H](NC(=O)CC(O)CCCCCCCCC)[C@@H](OC(=O)CC(CCCCCCCCC)OC(=O)CCCCCCCCC)[C@@H]2O)[C@@H]1NC(=O)CC(CCCCCCCCC)OC(=O)CC(O)CCCCCCCCC

SVG MW SMILES 3D mol Ionize

R1 = LIP