Because CGCFinder predicted no CGC for this PUL, the gene cluster depicted below contains dbCAN2 and CGC signature predictions for all genes in the PUL, instead of a predicted CGC.


PUL ID

PUL0301

PubMed

29309918, Carbohydr Res. 2018 Mar 2;457:25-31. doi: 10.1016/j.carres.2017.12.010. Epub 2018 Jan 3.

Characterization method

sugar utilization assay,NMR

Genomic accession number

KY574599.1

Nucelotide position range

1-11426

Substrate

O-antigen

Loci

ARO73540.1-ARO73549.1

Species

Escherichia coli/562

Degradation or Biosynthesis

biosynthesis

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- - ARO73540.1 0 - 894 (+) KY574599.1:1-895 -
- - ARO73541.1 1335 - 2424 (+) KY574599.1:1336-2425 -
- - ARO73542.1 2420 - 3716 (+) KY574599.1:2421-3717 -
- - ARO73543.1 3705 - 4764 (+) KY574599.1:3706-4765 -
- - ARO73544.1 4797 - 5478 (+) KY574599.1:4798-5479 -
- - ARO73545.1 5479 - 6514 (+) KY574599.1:5480-6515 -
- - ARO73546.1 6500 - 7613 (+) KY574599.1:6501-7614 -
- - ARO73547.1 7605 - 8520 (+) KY574599.1:7606-8521 -
- - ARO73548.1 8611 - 10018 (+) KY574599.1:8612-10019 -
- - ARO73549.1 10259 - 11426 (+) KY574599.1:10260-11427 -

Cluster number

0

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 894 (+) CDS No
- 1336 - 2424 (+) CDS No
- 2421 - 3716 (+) CDS No
- 3706 - 4764 (+) CDS No
- 4798 - 5478 (+) CAZyme: GT32 No
- 5480 - 6514 (+) CAZyme: GT2_Glycos_transf_2|GT2 No
- 6501 - 7613 (+) CDS No
- 7606 - 8520 (+) CAZyme: GT2_Glycos_transf_2|GT2 No
- 8612 - 10018 (+) CDS No
- 10260 - 11426 (+) CDS No

PUL ID

PUL0301

PubMed

29309918, Carbohydr Res. 2018 Mar 2;457:25-31. doi: 10.1016/j.carres.2017.12.010. Epub 2018 Jan 3.

Title

Structure elucidation of the O-specific polysaccharide by NMR spectroscopy and selective cleavage and genetic characterization of the O-antigen of Escherichia albertii O5.

Author

Naumenko OI, Zheng H, Wang J, Senchenkova SN, Wang H, Shashkov AS, Chizhov AO, Li Q, Knirel YA, Xiong Y

Abstract

The O-specific polysaccharide (O-antigen) was obtained by mild acid degradation of the lipopolysaccharide of Escherichia albertii O5 (strain T150248) and studied by sugar analysis, selective cleavages of glycosidic linkages, and 1D and 2D (1)H and (13)C NMR spectroscopy. Partial solvolysis with anh (anhydrous) CF(3)CO(2)H and hydrolysis with 0.05 M CF(3)CO(2)H cleaved predominantly the glycosidic linkage of beta-GalpNAc or beta-Galf, respectively, whereas the linkages of alpha-GlcpNAc and beta-Galp were stable. Mixtures of the corresponding tri- and tetra-saccharides thus obtained were studied by NMR spectroscopy and high-resolution ESI MS. The following new structure was established for the tetrasaccharide repeat (O-unit) of the O-polysaccharide: -->4)-alpha-d-GlcpNAc-(1 --> 4)-beta-d-Galp6Ac-(1 --> 6)-beta-d-Galf-(1 --> 3)-beta-d-GalpNAc-(1-->where the degree of O-acetylation of d-Galp is approximately 70%. The O-polysaccharide studied has a beta-d-Galp-(1 --> 6)-beta-d-Galf-(1 --> 3)-beta-d-GalpNAc trisaccharide fragment in common with the O-polysaccharides of E. albertii O7, Escherichia coli O124 and O164, and Shigella dysenteriae type 3 studied earlier. The orf5-7 in the O-antigen gene cluster of E. albertii O5 are 47%, 78%, and 75% identical on the amino acid level to genes for predicted enzymes of E. albertii O7, including Galp-transferase wfeS, UDP-d-Galp mutase glf, and Galf-transferase wfeT, respectively, which are putatively involved with the synthesis of the shared trisaccharide fragment of the O-polysaccharides. The occurrence upstream of the O-antigen gene cluster of a 4-epimerase gene gnu for conversion of undecaprenyl diphosphate-linked d-GlcNAc (UndPP-d-GlcNAc) into UndPP-d-GalNAc indicates that d-GalNAc is the first monosaccharide of the O-unit, and hence the O-units are interlinked in the O-polysaccharide of E. albertii O5 by the beta-d-GalpNAc-(1 --> 4)-alpha-d-GlcpNAc linkage.