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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0131

PubMed

30385338, Int J Biol Macromol. 2019 Feb 1;122:555-561. doi: 10.1016/j.ijbiomac.2018.10.189. Epub 2018 Oct 29.

Characterization method

sequence homology analysis

Genomic accession number

FJ940773.1 

Nucelotide position range

107-16155

Substrate

O-antigen

Loci

manC-manB-wzm-wzt-orf5-orf6-gmd-rmd-orf9-orf10-gne-galF

Species

Acidiphilium rubrum/526

Degradation or Biosynthesis

biosynthesis

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

manC - ACV53833.1 107 - 1523 (+) FJ940773.1:214-1630 -
manB - ACV53834.1 1542 - 2916 (+) FJ940773.1:1649-3023 -
wzm - ACV53835.1 2919 - 3714 (+) FJ940773.1:3026-3821 -
wzt - ACV53836.1 3715 - 5017 (+) FJ940773.1:3822-5124 -
wejH - ACV53837.1 5038 - 7219 (+) FJ940773.1:5145-7326 -
wejI - ACV53838.1 7229 - 9725 (+) FJ940773.1:7336-9832 -
gmd - ACV53839.1 9856 - 10891 (+) FJ940773.1:9963-10998 -
rmd - ACV53840.1 10890 - 11793 (+) FJ940773.1:10997-11900 -
wejJ - ACV53841.1 11792 - 12929 (+) FJ940773.1:11899-13036 -
wejK - ACV53842.1 12934 - 14047 (+) FJ940773.1:13041-14154 -
wejL - ACV53843.1 14093 - 15254 (+) FJ940773.1:14200-15361 -
wejM - ACV53844.1 15237 - 16155 (+) FJ940773.1:15344-16262 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 108 - 1523 (+) STP: STP|AraC_binding No
- 1543 - 2916 (+) CDS No
- 2920 - 3714 (+) TC: gnl|TC-DB|Q9HTB8|3.A.1.103.6 Yes
- 3716 - 5017 (+) TC: gnl|TC-DB|Q9I3V8|3.A.1.103.6 Yes
- 5039 - 7219 (+) STP: STP|Pkinase Yes
- 7230 - 9725 (+) CAZyme: GT4 Yes
- 9857 - 10891 (+) other Yes
- 10891 - 11793 (+) other Yes
- 11793 - 12929 (+) CAZyme: GT4 Yes
- 12935 - 14047 (+) CAZyme: GT4 Yes
- 14094 - 15254 (+) CDS No
- 15238 - 16155 (+) CDS No

PUL ID

PUL0131

PubMed

30385338, Int J Biol Macromol. 2019 Feb 1;122:555-561. doi: 10.1016/j.ijbiomac.2018.10.189. Epub 2018 Oct 29.

Title

Structure and gene cluster of the O-polysaccharide of Yersinia rohdei H274-36/78.

Author

Sizova OV, Shashkov AS, Dmitrenok AS, Toukach PV, Knirel YA, Shaikhutdinova RZ, Ivanov SA, Kislichkina AA, Bogun AG, Dentovskaya SV

Abstract

A branched O-polysaccharide was obtained by mild acid degradation of the lipopolysaccharide of Yersinia rohdei H274-36/78 and found to contain d-rhamnose, d-mannose, and 3,6-dideoxy-4-C-[(S)-1-hydroxyethyl]-d-xylo-hexose called yersiniose A (Yer). Partial acid hydrolysis of the O-polysaccharide eliminated Yer residues to give a modified linear polysaccharide. Studies by sugar analysis and (1)H and (13)C NMR spectroscopy, including computational NMR analysis, enabled structure elucidation of a hexasaccharide repeating unit of the O-polysaccharide having two Yer residues attached as monosaccharide side chains. The O-antigen gene cluster of Y. rohdei H274-36/78 located between JUMPStart and galF genes contained putative genes for synthesis of precursors of two O-antigen constituents, GDP-d-Man and GDP-d-Rha, whereas genes responsible for synthesis of CDP-Yer were within the chromosome outside the O-antigen gene cluster. Glycosyltransferase genes and ABC 2 transporter genes were present in the O-antigen gene cluster, and hence the structure established is consistent with the polysaccharide synthesis gene content of the genome.