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

PUL0172

PubMed

27166227, Microbiology (Reading). 2016 Jul;162(7):1103-1113. doi: 10.1099/mic.0.000307. Epub 2016 May 10.

Characterization method

gene deletion mutant and growth assay, NMR, sugar utilization assay

Genomic accession number

KX156850.1

Nucelotide position range

117-12928

Substrate

O-antigen

Loci

rmlB-rmlA-rmlD-rmlC-orf5-wzm-wzt-orf8-orf9

Species

Franconibacter pulveris/435910

Degradation or Biosynthesis

biosynthesis

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

rmlB - ANF28848.1 117 - 1182 (+) KX156850.1:234-1299 -
rmlA - ANF28849.1 1192 - 2065 (+) KX156850.1:1309-2182 -
rmlD - ANF28850.1 2089 - 2980 (+) KX156850.1:2206-3097 -
rmlC - ANF28851.1 2984 - 3533 (+) KX156850.1:3101-3650 -
- - ANF28852.1 3540 - 4461 (+) KX156850.1:3657-4578 -
wzm - ANF28853.1 4494 - 5325 (+) KX156850.1:4611-5442 -
wzt - ANF28854.1 5314 - 6670 (+) KX156850.1:5431-6787 -
- - ANF28855.1 6701 - 11105 (+) KX156850.1:6818-11222 -
- - ANF28856.1 11110 - 12928 (+) KX156850.1:11227-13045 -

Cluster number

0

Gene name

Gene position

Gene type

Found by CGCFinder?

- 118 - 1182 (+) CDS No
- 1193 - 2065 (+) CDS No
- 2090 - 2980 (+) CDS No
- 2985 - 3533 (+) CDS No
- 3541 - 4461 (+) CAZyme: GT2_Glycos_transf_2|GT2 No
- 4495 - 5325 (+) TC: gnl|TC-DB|Q9HTB8|3.A.1.103.6 No
- 5315 - 6670 (+) TC: gnl|TC-DB|Q50864|4.D.1.3.4 No
- 6702 - 11105 (+) CDS No
- 11111 - 12928 (+) CDS No

PUL ID

PUL0172

PubMed

27166227, Microbiology (Reading). 2016 Jul;162(7):1103-1113. doi: 10.1099/mic.0.000307. Epub 2016 May 10.

Title

O antigen of FranconibacterpulverisG3872 (O1) is a 4-deoxy-d-arabino-hexose-containing polysaccharide synthesized by the ABC-transporter-dependent pathway.

Author

Wang M, Arbatsky NP, Xu L, Shashkov AS, Wang L, Knirel YA

Abstract

Franconibacter (Enterobacter, Cronobacter) pulveris bacteria share several typical characteristics with, and hence pose a challenge for the detection of, Cronobacter sakazakii, an emerging opportunistic pathogen, which can cause severe infections in neonates. A structurally variable O-specific polysaccharide (OPS) called O antigen provides the major basis for the typing of Gram-negative bacteria. We investigated the structure and genetics of the O antigen of F. pulveris G3872 (designated O1). An OPS was isolated by mild alkaline degradation of the LPS, whereas the same polysaccharide and its oligosaccharide fragments were obtained by mild acid degradation. Studies by sugar analysis and NMR spectroscopy showed that the OPS contained d-ribose, l-rhamnose (l-Rha) and a rarely occurring monosaccharide 4-deoxy-d-arabino-hexose, and the OPS structure was established. The O-antigen gene cluster of F. pulveris G3872 between JUMPStart and gnd genes includes putative genes for glycosyltransferases, ATP-binding cassette (ABC)-transporter genes wzm and wzt, and genes for the synthesis of l-Rha, but no genes for the synthesis of 4-deoxy-d-arabino-hexose. A mutation test with the wzm gene confirmed that the OPS is synthesized and exported by the ABC-transporter-dependent pathway. A trifunctional transferase was suggested to catalyse formation of two glycosidic linkages and add a methyl group to the non-reducing end of the OPS to terminate the chain elongation. A carbohydrate-binding module that presumably recognizes the terminal methyl-modified monosaccharide was found at the C-terminus of Wzt. Primers specific for F. pulveris G3872 were designed based on the wzm gene, which has potential to be used for identification and detection of the O1 serogroup.