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Kenyon JJ, Duda KA, De Felice A, Cunneen MM, Molinaro A, Laitinen J, Skurnik M, Holst O, Reeves PR, De Castro C
Serotype O:8 isolates in the Yersinia pseudotuberculosis complex have different O-antigen gene clusters and produce various forms of rough LPS
Innate Immunity 22(3) (2016)
205-217
|
P-4)-+
|
Subst-(1-3)-+ b-D-Glcp-(1-4)-+ a-Kdop-(2-4)-+ LIP-(1-2)-+ | LIP-(1-2)-+
| | | | | |
/Variants 0/-L-gro-a-D-manHepp-(1-7)-L-gro-a-D-manHepp-(1-3)-L-gro-a-D-manHepp-(1-5)-a-Kdop-(2-6)-b-D-GlcpN-(1-6)-a-D-GlcpN-(1-P
| |
LIP-(1-3)-+ LIP-(1-3)-+
/Variants 0/ is:
b-D-Galp-(1-7)-
OR (exclusively)
D-gro-a-D-manHepp-(1-7)-
Subst = O-antigen |
Show graphically |
Yersinia pseudotuberculosis
(NCBI TaxID 633,
species name lookup)
Taxonomic group: bacteria / Proteobacteria
(Phylum: Proteobacteria)
NCBI PubMed ID: 26873504Publication DOI: 10.1177/1753425916631403Journal NLM ID: 101469670Publisher: Sage Publications
Correspondence: decastro
unina.it
Institutions: Division of Structural Biochemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Borstel, Germany, Helsinki University Central Hospital Laboratory Diagnostics, Helsinki, Finland, Department of Chemical Sciences, University of Napoli, Napoli, Italy, Department of Bacteriology and Immunology, Medicum, and Research Programs Unit, Immunobiology, University of Helsinki, Helsinki, Finland, School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia, Department of Agriculture Sciences, University of Napoli, Portici, Italy
In Yersinia pseudotuberculosis complex, the O-antigen of LPS is used for the serological characterization of strains, and 21 serotypes have been identified to date. The O-antigen biosynthesis gene cluster and corresponding O-antigen structure have been described for 18, leaving O:8, O:13 and O:14 unresolved. In this study, two O:8 isolates were examined. The O-antigen gene cluster sequence of strain 151 was near identical to serotype O:4a, though a frame-shift mutation was found in ddhD, while No. 6 was different to 151 and carried the O:1b gene cluster. Structural analysis revealed that No. 6 produced a deeply truncated LPS, suggesting a mutation within the waaF gene. Both ddhD and waaF were cloned and expressed in 151 and No. 6 strains, respectively, and it appeared that expression of ddhD gene in strain 151 restored the O-antigen on LPS, while waaF in No. 6 resulted in an LPS truncated less severely but still without the O-antigen, suggesting that other mutations occurred in this strain. Thus, both O:8 isolates were found to be spontaneous O-antigen-negative mutants derived from other validated serotypes, and we propose to remove this serotype from the O-serotyping scheme, as the O:8 serological specificity is not based on the O-antigen.
O-antigen, O-specific polysaccharide, Yersinia pseudotuberculosis, serotyping, O-antigen gene cluster, O-antigen biosynthesis, O:8 serotype
Structure type: oligomer
Location inside paper: p.207, fig.1
Compound class: LPS
Contained glycoepitopes: IEDB_130650,IEDB_130659,IEDB_130670,IEDB_135394,IEDB_135515,IEDB_136044,IEDB_137472,IEDB_140087,IEDB_140088,IEDB_140090,IEDB_141794,IEDB_141807,IEDB_142488,IEDB_146664,IEDB_150908,IEDB_151531,IEDB_190606,IEDB_2189046,IEDB_2189047,IEDB_226811,IEDB_983931,SB_165,SB_166,SB_187,SB_192,SB_195,SB_7,SB_88
Methods: 13C NMR, 1H NMR, NMR-2D, PCR, SDS-PAGE, DNA techniques, ESI-MS, DOC-PAGE, Western blotting, composition analysis, NMR-1D, genetic methods, GPC, de-N-acylation, hydrazinolysis, function analysis of gene clusters, ESI-IT-TOF-MS/MS
Comments, role: the main form of the carbohydrate backbone of the lipopolysaccharide from Y. pseudotuberculosis.
Related record ID(s): 11628, 11629, 11630
NCBI Taxonomy refs (TaxIDs): 633
Show glycosyltransferases
There is only one chemically distinct structure:
Expand this record
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Kenyon JJ, Duda KA, De Felice A, Cunneen MM, Molinaro A, Laitinen J, Skurnik M, Holst O, Reeves PR, De Castro C
Serotype O:8 isolates in the Yersinia pseudotuberculosis complex have different O-antigen gene clusters and produce various forms of rough LPS
Innate Immunity 22(3) (2016)
205-217
|
a-Kdop-(2-4)-+ P-4)-+
| |
L-gro-a-D-manHepp-(1-5)-a-Kdop-(2-6)-b-D-GlcpN-(1-6)-a-D-GlcpN-(1-P |
Show graphically |
Yersinia pseudotuberculosis O8
(Ancestor NCBI TaxID 633,
species name lookup)
Taxonomic group: bacteria / Proteobacteria
(Phylum: Proteobacteria)
The structure was elucidated in this paperNCBI PubMed ID: 26873504Publication DOI: 10.1177/1753425916631403Journal NLM ID: 101469670Publisher: Sage Publications
Correspondence: decastro
unina.it
Institutions: Division of Structural Biochemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Borstel, Germany, Helsinki University Central Hospital Laboratory Diagnostics, Helsinki, Finland, Department of Chemical Sciences, University of Napoli, Napoli, Italy, Department of Bacteriology and Immunology, Medicum, and Research Programs Unit, Immunobiology, University of Helsinki, Helsinki, Finland, School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia, Department of Agriculture Sciences, University of Napoli, Portici, Italy
In Yersinia pseudotuberculosis complex, the O-antigen of LPS is used for the serological characterization of strains, and 21 serotypes have been identified to date. The O-antigen biosynthesis gene cluster and corresponding O-antigen structure have been described for 18, leaving O:8, O:13 and O:14 unresolved. In this study, two O:8 isolates were examined. The O-antigen gene cluster sequence of strain 151 was near identical to serotype O:4a, though a frame-shift mutation was found in ddhD, while No. 6 was different to 151 and carried the O:1b gene cluster. Structural analysis revealed that No. 6 produced a deeply truncated LPS, suggesting a mutation within the waaF gene. Both ddhD and waaF were cloned and expressed in 151 and No. 6 strains, respectively, and it appeared that expression of ddhD gene in strain 151 restored the O-antigen on LPS, while waaF in No. 6 resulted in an LPS truncated less severely but still without the O-antigen, suggesting that other mutations occurred in this strain. Thus, both O:8 isolates were found to be spontaneous O-antigen-negative mutants derived from other validated serotypes, and we propose to remove this serotype from the O-serotyping scheme, as the O:8 serological specificity is not based on the O-antigen.
O-antigen, O-specific polysaccharide, Yersinia pseudotuberculosis, serotyping, O-antigen gene cluster, O-antigen biosynthesis, O:8 serotype
Structure type: oligomer
Location inside paper: p.212, table 2p.213, fig.6, structure 1
Compound class: core oligosaccharide, LPS
Contained glycoepitopes: IEDB_130650,IEDB_130659,IEDB_135394,IEDB_141807,IEDB_150908,IEDB_151531,IEDB_2189047
Methods: 13C NMR, 1H NMR, NMR-2D, PCR, SDS-PAGE, DNA techniques, ESI-MS, DOC-PAGE, Western blotting, composition analysis, NMR-1D, genetic methods, GPC, de-N-acylation, hydrazinolysis, function analysis of gene clusters, ESI-IT-TOF-MS/MS
Comments, role: Full de-lipidated LPS was isolated from Y. pseudotuberculosis O:8 isolates 151 and No. 6.
Related record ID(s): 11262, 11629, 11630
NCBI Taxonomy refs (TaxIDs): 633Reference(s) to other database(s): GlycomeDB:
37094
Show glycosyltransferases
NMR conditions: in D2O at 305 K
[as TSV]
13C NMR data:
Linkage Residue C1 C2 C3 C4 C5 C6 C7 C8
0,6,6,4 aXKdop 175.8 103.6 35.8 67.4 67.6 73.9 71.8 64.6
0,6,6,5 aXLDmanHepp 102.3 71.5 71.2 67.5 74.1 70.4 65.3
0,6,6 aXKdop 175.8 100.9 35.6 70.8 74.3 73.2 70.7 64.9
0,6,4 P
0,6 bDGlcpN 100.7 56.8 73.2 75.4 75.4 63.6
0 aDGlcpN 92.1 55.7 70.8 70.9 73.8 70.7
P
1H NMR data:
Linkage Residue H1 H2 H3 H4 H5 H6 H7 H8
0,6,6,4 aXKdop - - 1.77-2.19 4.09 4.03 3.65 3.98 3.77-4.00
0,6,6,5 aXLDmanHepp 5.35 4.05 3.98 3.84 3.84 4.03 3.74-3.74
0,6,6 aXKdop - - 1.98-2.05 4.21 4.27 3.72 3.83 3.66-3.88
0,6,4 P
0,6 bDGlcpN 4.90 3.10 3.88 3.81 3.74 3.47-3.71
0 aDGlcpN 5.67 3.42 3.92 3.58 4.16 3.77-4.29
P
1H/13C HSQC data:
Linkage Residue C1/H1 C2/H2 C3/H3 C4/H4 C5/H5 C6/H6 C7/H7 C8/H8
0,6,6,4 aXKdop 35.8/1.77-2.19 67.4/4.09 67.6/4.03 73.9/3.65 71.8/3.98 64.6/3.77-4.00
0,6,6,5 aXLDmanHepp 102.3/5.35 71.5/4.05 71.2/3.98 67.5/3.84 74.1/3.84 70.4/4.03 65.3/3.74-3.74
0,6,6 aXKdop 35.6/1.98-2.05 70.8/4.21 74.3/4.27 73.2/3.72 70.7/3.83 64.9/3.66-3.88
0,6,4 P
0,6 bDGlcpN 100.7/4.90 56.8/3.10 73.2/3.88 75.4/3.81 75.4/3.74 63.6/3.47-3.71
0 aDGlcpN 92.1/5.67 55.7/3.42 70.8/3.92 70.9/3.58 73.8/4.16 70.7/3.77-4.29
P
1H NMR data:
| Linkage | Residue | H1 | H2 | H3 | H4 | H5 | H6 | H7 | H8 |
|---|
| 0,6,6,4 | aXKdop |
|
| 1.77
2.19 | 4.09 | 4.03 | 3.65 | 3.98 | 3.77
4.00 |
| 0,6,6,5 | aXLDmanHepp | 5.35 | 4.05 | 3.98 | 3.84 | 3.84 | 4.03 | 3.74
3.74 | |
| 0,6,6 | aXKdop |
|
| 1.98
2.05 | 4.21 | 4.27 | 3.72 | 3.83 | 3.66
3.88 |
| 0,6,4 | P | |
| 0,6 | bDGlcpN | 4.90 | 3.10 | 3.88 | 3.81 | 3.74 | 3.47
3.71 | |
| 0 | aDGlcpN | 5.67 | 3.42 | 3.92 | 3.58 | 4.16 | 3.77
4.29 | |
| | P | |
|
13C NMR data:
| Linkage | Residue | C1 | C2 | C3 | C4 | C5 | C6 | C7 | C8 |
|---|
| 0,6,6,4 | aXKdop | 175.8 | 103.6 | 35.8 | 67.4 | 67.6 | 73.9 | 71.8 | 64.6 |
| 0,6,6,5 | aXLDmanHepp | 102.3 | 71.5 | 71.2 | 67.5 | 74.1 | 70.4 | 65.3 | |
| 0,6,6 | aXKdop | 175.8 | 100.9 | 35.6 | 70.8 | 74.3 | 73.2 | 70.7 | 64.9 |
| 0,6,4 | P | |
| 0,6 | bDGlcpN | 100.7 | 56.8 | 73.2 | 75.4 | 75.4 | 63.6 | |
| 0 | aDGlcpN | 92.1 | 55.7 | 70.8 | 70.9 | 73.8 | 70.7 | |
| | P | |
|
There is only one chemically distinct structure:
Expand this record
Collapse this record
Kenyon JJ, Duda KA, De Felice A, Cunneen MM, Molinaro A, Laitinen J, Skurnik M, Holst O, Reeves PR, De Castro C
Serotype O:8 isolates in the Yersinia pseudotuberculosis complex have different O-antigen gene clusters and produce various forms of rough LPS
Innate Immunity 22(3) (2016)
205-217
|
a-Kop-(2-4)-+ P-4)-+
| |
L-gro-a-D-manHepp-(1-5)-a-Kdop-(2-6)-b-D-GlcpN-(1-6)-a-D-GlcpN-(1-P |
Show graphically |
Yersinia pseudotuberculosis O8
(Ancestor NCBI TaxID 633,
species name lookup)
Taxonomic group: bacteria / Proteobacteria
(Phylum: Proteobacteria)
The structure was elucidated in this paperNCBI PubMed ID: 26873504Publication DOI: 10.1177/1753425916631403Journal NLM ID: 101469670Publisher: Sage Publications
Correspondence: decastro
unina.it
Institutions: Division of Structural Biochemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Borstel, Germany, Helsinki University Central Hospital Laboratory Diagnostics, Helsinki, Finland, Department of Chemical Sciences, University of Napoli, Napoli, Italy, Department of Bacteriology and Immunology, Medicum, and Research Programs Unit, Immunobiology, University of Helsinki, Helsinki, Finland, School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia, Department of Agriculture Sciences, University of Napoli, Portici, Italy
In Yersinia pseudotuberculosis complex, the O-antigen of LPS is used for the serological characterization of strains, and 21 serotypes have been identified to date. The O-antigen biosynthesis gene cluster and corresponding O-antigen structure have been described for 18, leaving O:8, O:13 and O:14 unresolved. In this study, two O:8 isolates were examined. The O-antigen gene cluster sequence of strain 151 was near identical to serotype O:4a, though a frame-shift mutation was found in ddhD, while No. 6 was different to 151 and carried the O:1b gene cluster. Structural analysis revealed that No. 6 produced a deeply truncated LPS, suggesting a mutation within the waaF gene. Both ddhD and waaF were cloned and expressed in 151 and No. 6 strains, respectively, and it appeared that expression of ddhD gene in strain 151 restored the O-antigen on LPS, while waaF in No. 6 resulted in an LPS truncated less severely but still without the O-antigen, suggesting that other mutations occurred in this strain. Thus, both O:8 isolates were found to be spontaneous O-antigen-negative mutants derived from other validated serotypes, and we propose to remove this serotype from the O-serotyping scheme, as the O:8 serological specificity is not based on the O-antigen.
O-antigen, O-specific polysaccharide, Yersinia pseudotuberculosis, serotyping, O-antigen gene cluster, O-antigen biosynthesis, O:8 serotype
Structure type: oligomer
Location inside paper: p.212, table 2p.213, fig.6, structure 2
Compound class: LPS
Contained glycoepitopes: IEDB_130650,IEDB_135394,IEDB_135607,IEDB_135609,IEDB_141807,IEDB_151531,IEDB_2189047
Methods: 13C NMR, 1H NMR, NMR-2D, PCR, SDS-PAGE, DNA techniques, ESI-MS, DOC-PAGE, Western blotting, composition analysis, NMR-1D, genetic methods, GPC, de-N-acylation, hydrazinolysis, function analysis of gene clusters, ESI-IT-TOF-MS/MS
Comments, role: Full de-lipidated LPS was isolated from Y. pseudotuberculosis O:8 isolates 151 and No. 6.
Related record ID(s): 11262, 11628, 11630
NCBI Taxonomy refs (TaxIDs): 633
Show glycosyltransferases
NMR conditions: in D2O at 305 K
[as TSV]
13C NMR data:
Linkage Residue C1 C2 C3 C4 C5 C6 C7 C8
0,6,6,4 aXKop ? 103.6 73.2 67.5 69.7 73.8 71.3 64.5
0,6,6,5 aXLDmanHepp 102.2 71.4 71.6 67.5 74.0 70.4 65.4
0,6,6 aXKdop 175.8 100.9 35.6 71.7 73.8 73.1 70.6 64.7
0,6,4 P
0,6 bDGlcpN 100.9 56.9 73.8 74.6 75.6 63.7
0 aDGlcpN 91.9 55.9 71.0 70.9 73.6 71.0
P
1H NMR data:
Linkage Residue H1 H2 H3 H4 H5 H6 H7 H8
0,6,6,4 aXKop - - 4.08 3.99 4.11 3.68 4.09 3.80-4.04
0,6,6,5 aXLDmanHepp 5.36 4.07 3.98 3.84 3.80 4.024 3.69-3.75
0,6,6 aXKdop - - 1.99-2.09 4.20 4.24 3.75 3.83 3.69-3.89
0,6,4 P
0,6 bDGlcpN 4.88 3.06 3.85 3.75 4.00 3.59-3.72
0 aDGlcpN 5.65 3.40 3.91 3.63 4.17 3.78-4.32
P
1H/13C HSQC data:
Linkage Residue C1/H1 C2/H2 C3/H3 C4/H4 C5/H5 C6/H6 C7/H7 C8/H8
0,6,6,4 aXKop 73.2/4.08 67.5/3.99 69.7/4.11 73.8/3.68 71.3/4.09 64.5/3.80-4.04
0,6,6,5 aXLDmanHepp 102.2/5.36 71.4/4.07 71.6/3.98 67.5/3.84 74.0/3.80 70.4/4.024 65.4/3.69-3.75
0,6,6 aXKdop 35.6/1.99-2.09 71.7/4.20 73.8/4.24 73.1/3.75 70.6/3.83 64.7/3.69-3.89
0,6,4 P
0,6 bDGlcpN 100.9/4.88 56.9/3.06 73.8/3.85 74.6/3.75 75.6/4.00 63.7/3.59-3.72
0 aDGlcpN 91.9/5.65 55.9/3.40 71.0/3.91 70.9/3.63 73.6/4.17 71.0/3.78-4.32
P
1H NMR data:
| Linkage | Residue | H1 | H2 | H3 | H4 | H5 | H6 | H7 | H8 |
|---|
| 0,6,6,4 | aXKop |
|
| 4.08 | 3.99 | 4.11 | 3.68 | 4.09 | 3.80
4.04 |
| 0,6,6,5 | aXLDmanHepp | 5.36 | 4.07 | 3.98 | 3.84 | 3.80 | 4.024 | 3.69
3.75 | |
| 0,6,6 | aXKdop |
|
| 1.99
2.09 | 4.20 | 4.24 | 3.75 | 3.83 | 3.69
3.89 |
| 0,6,4 | P | |
| 0,6 | bDGlcpN | 4.88 | 3.06 | 3.85 | 3.75 | 4.00 | 3.59
3.72 | |
| 0 | aDGlcpN | 5.65 | 3.40 | 3.91 | 3.63 | 4.17 | 3.78
4.32 | |
| | P | |
|
13C NMR data:
| Linkage | Residue | C1 | C2 | C3 | C4 | C5 | C6 | C7 | C8 |
|---|
| 0,6,6,4 | aXKop | ? | 103.6 | 73.2 | 67.5 | 69.7 | 73.8 | 71.3 | 64.5 |
| 0,6,6,5 | aXLDmanHepp | 102.2 | 71.4 | 71.6 | 67.5 | 74.0 | 70.4 | 65.4 | |
| 0,6,6 | aXKdop | 175.8 | 100.9 | 35.6 | 71.7 | 73.8 | 73.1 | 70.6 | 64.7 |
| 0,6,4 | P | |
| 0,6 | bDGlcpN | 100.9 | 56.9 | 73.8 | 74.6 | 75.6 | 63.7 | |
| 0 | aDGlcpN | 91.9 | 55.9 | 71.0 | 70.9 | 73.6 | 71.0 | |
| | P | |
|
![](nmr_drawer.py?width=750&height=130&nucleus=C&rotate_labels=false&spectrum=[{"s":103.6,"l":"2","c":[0,0,225]},{"s":73.2,"l":"3","c":[0,0,225]},{"s":67.5,"l":"4","c":[0,0,225]},{"s":69.7,"l":"5","c":[0,0,225]},{"s":73.8,"l":"6","c":[0,0,225]},{"s":71.3,"l":"7","c":[0,0,225]},{"s":64.5,"l":"8","c":[0,0,225]},{"s":102.2,"l":"1","c":[230,0,30]},{"s":71.4,"l":"2","c":[230,0,30]},{"s":71.6,"l":"3","c":[230,0,30]},{"s":67.5,"l":"4","c":[230,0,30]},{"s":74,"l":"5","c":[230,0,30]},{"s":70.4,"l":"6","c":[230,0,30]},{"s":65.4,"l":"7","c":[230,0,30]},{"s":175.8,"l":"1","c":[0,165,0]},{"s":100.9,"l":"2","c":[0,165,0]},{"s":35.6,"l":"3","c":[0,165,0]},{"s":71.7,"l":"4","c":[0,165,0]},{"s":73.8,"l":"5","c":[0,165,0]},{"s":73.1,"l":"6","c":[0,165,0]},{"s":70.6,"l":"7","c":[0,165,0]},{"s":64.7,"l":"8","c":[0,165,0]},{"s":100.9,"l":"1","c":[120,0,225]},{"s":56.9,"l":"2","c":[120,0,225]},{"s":73.8,"l":"3","c":[120,0,225]},{"s":74.6,"l":"4","c":[120,0,225]},{"s":75.6,"l":"5","c":[120,0,225]},{"s":63.7,"l":"6","c":[120,0,225]},{"s":91.9,"l":"1","c":[0,192,255]},{"s":55.9,"l":"2","c":[0,192,255]},{"s":71,"l":"3","c":[0,192,255]},{"s":70.9,"l":"4","c":[0,192,255]},{"s":73.6,"l":"5","c":[0,192,255]},{"s":71,"l":"6","c":[0,192,255]}])
The spectrum also has 1 signal at unknown position (not plotted). |
There is only one chemically distinct structure:
Expand this record
Collapse this record
Kenyon JJ, Duda KA, De Felice A, Cunneen MM, Molinaro A, Laitinen J, Skurnik M, Holst O, Reeves PR, De Castro C
Serotype O:8 isolates in the Yersinia pseudotuberculosis complex have different O-antigen gene clusters and produce various forms of rough LPS
Innate Immunity 22(3) (2016)
205-217
|
P-4)-+
|
a-Kdop-(2-4)-a-Kdop-(2-6)-b-D-GlcpN-(1-6)-a-D-GlcpN-(1-P |
Show graphically |
Yersinia pseudotuberculosis O8
(Ancestor NCBI TaxID 633,
species name lookup)
Taxonomic group: bacteria / Proteobacteria
(Phylum: Proteobacteria)
The structure was elucidated in this paperNCBI PubMed ID: 26873504Publication DOI: 10.1177/1753425916631403Journal NLM ID: 101469670Publisher: Sage Publications
Correspondence: decastro
unina.it
Institutions: Division of Structural Biochemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Borstel, Germany, Helsinki University Central Hospital Laboratory Diagnostics, Helsinki, Finland, Department of Chemical Sciences, University of Napoli, Napoli, Italy, Department of Bacteriology and Immunology, Medicum, and Research Programs Unit, Immunobiology, University of Helsinki, Helsinki, Finland, School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia, Department of Agriculture Sciences, University of Napoli, Portici, Italy
In Yersinia pseudotuberculosis complex, the O-antigen of LPS is used for the serological characterization of strains, and 21 serotypes have been identified to date. The O-antigen biosynthesis gene cluster and corresponding O-antigen structure have been described for 18, leaving O:8, O:13 and O:14 unresolved. In this study, two O:8 isolates were examined. The O-antigen gene cluster sequence of strain 151 was near identical to serotype O:4a, though a frame-shift mutation was found in ddhD, while No. 6 was different to 151 and carried the O:1b gene cluster. Structural analysis revealed that No. 6 produced a deeply truncated LPS, suggesting a mutation within the waaF gene. Both ddhD and waaF were cloned and expressed in 151 and No. 6 strains, respectively, and it appeared that expression of ddhD gene in strain 151 restored the O-antigen on LPS, while waaF in No. 6 resulted in an LPS truncated less severely but still without the O-antigen, suggesting that other mutations occurred in this strain. Thus, both O:8 isolates were found to be spontaneous O-antigen-negative mutants derived from other validated serotypes, and we propose to remove this serotype from the O-serotyping scheme, as the O:8 serological specificity is not based on the O-antigen.
O-antigen, O-specific polysaccharide, Yersinia pseudotuberculosis, serotyping, O-antigen gene cluster, O-antigen biosynthesis, O:8 serotype
Structure type: oligomer
Location inside paper: p.212, table 2p.213, fig.6, structure 3
Trivial name: core-lipid A carbohydrate backbone
Compound class: core oligosaccharide, LPS
Contained glycoepitopes: IEDB_130650,IEDB_130659,IEDB_135394,IEDB_141807,IEDB_150908,IEDB_151531
Methods: 13C NMR, 1H NMR, NMR-2D, PCR, SDS-PAGE, DNA techniques, ESI-MS, DOC-PAGE, Western blotting, composition analysis, NMR-1D, genetic methods, GPC, de-N-acylation, hydrazinolysis, function analysis of gene clusters, ESI-IT-TOF-MS/MS
Comments, role: Full de-lipidated LPS was isolated from Y. pseudotuberculosis O:8 isolates 151 and No. 6.
Related record ID(s): 11262, 11628, 11629
NCBI Taxonomy refs (TaxIDs): 633Reference(s) to other database(s): GlycomeDB:
8179, CCSD:
46733, CBank-STR:13726
Show glycosyltransferases
NMR conditions: in D2O at 298 K
[as TSV]
13C NMR data:
Linkage Residue C1 C2 C3 C4 C5 C6 C7 C8
0,6,6,4 aXKdop 177.0 100.8 35.7 67.2 67.4 74.0 71.0 64.6
0,6,6 aXKdop 176.2 101.0 34.7 69.8 65.7 72.6 70.9 64.6
0,6,4 P
0,6 bDGlcpN 100.7 56.8 73.3 75.1 75.4 63.5
0 aDGlcpN 91.9 55.7 70.9 71.1 73.9 70.7
P
1H NMR data:
Linkage Residue H1 H2 H3 H4 H5 H6 H7 H8
0,6,6,4 aXKdop - - 1.76-2.13 4.07 4.04 3.59 3.98 3.74-4.01
0,6,6 aXKdop - - 1.93-1.99 4.13 4.13 3.76 3.91 3.65-3.91
0,6,4 P
0,6 bDGlcpN 4.95 3.07 3.87 3.80 3.73 3.48-3.75
0 aDGlcpN 5.66 3.40 3.90 3.53 4.16 3.73-4.27
P
1H/13C HSQC data:
Linkage Residue C1/H1 C2/H2 C3/H3 C4/H4 C5/H5 C6/H6 C7/H7 C8/H8
0,6,6,4 aXKdop 35.7/1.76-2.13 67.2/4.07 67.4/4.04 74.0/3.59 71.0/3.98 64.6/3.74-4.01
0,6,6 aXKdop 34.7/1.93-1.99 69.8/4.13 65.7/4.13 72.6/3.76 70.9/3.91 64.6/3.65-3.91
0,6,4 P
0,6 bDGlcpN 100.7/4.95 56.8/3.07 73.3/3.87 75.1/3.80 75.4/3.73 63.5/3.48-3.75
0 aDGlcpN 91.9/5.66 55.7/3.40 70.9/3.90 71.1/3.53 73.9/4.16 70.7/3.73-4.27
P
1H NMR data:
| Linkage | Residue | H1 | H2 | H3 | H4 | H5 | H6 | H7 | H8 |
|---|
| 0,6,6,4 | aXKdop |
|
| 1.76
2.13 | 4.07 | 4.04 | 3.59 | 3.98 | 3.74
4.01 |
| 0,6,6 | aXKdop |
|
| 1.93
1.99 | 4.13 | 4.13 | 3.76 | 3.91 | 3.65
3.91 |
| 0,6,4 | P | |
| 0,6 | bDGlcpN | 4.95 | 3.07 | 3.87 | 3.80 | 3.73 | 3.48
3.75 | |
| 0 | aDGlcpN | 5.66 | 3.40 | 3.90 | 3.53 | 4.16 | 3.73
4.27 | |
| | P | |
|
13C NMR data:
| Linkage | Residue | C1 | C2 | C3 | C4 | C5 | C6 | C7 | C8 |
|---|
| 0,6,6,4 | aXKdop | 177.0 | 100.8 | 35.7 | 67.2 | 67.4 | 74.0 | 71.0 | 64.6 |
| 0,6,6 | aXKdop | 176.2 | 101.0 | 34.7 | 69.8 | 65.7 | 72.6 | 70.9 | 64.6 |
| 0,6,4 | P | |
| 0,6 | bDGlcpN | 100.7 | 56.8 | 73.3 | 75.1 | 75.4 | 63.5 | |
| 0 | aDGlcpN | 91.9 | 55.7 | 70.9 | 71.1 | 73.9 | 70.7 | |
| | P | |
|
There is only one chemically distinct structure:
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