PUL ID

PUL0502

PubMed

20829291, Microbiology (Reading). 2010 Nov;156(Pt 11):3255-3269. doi: 10.1099/mic.0.042978-0. Epub 2010 Sep 9.

Characterization method

sequence homology analysis, microscopy

Genomic accession number

CR626927.1

Nucelotide position range

2212592-2234850

Substrate

capsule polysaccharide

Loci

BF1895-BF1914

Species

Bacteroides fragilis/817

Degradation or Biosynthesis

biosynthesis

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

wcfT BF9343_1812 CAH07593.1 0 - 120 (+) CR626927.1:2212592-2212712 -
wcfU BF9343_1813 CAH07594.1 112 - 832 (+) CR626927.1:2212704-2213424 -
aepX BF9343_1814 CAH07595.1 851 - 2153 (+) CR626927.1:2213443-2214745 -
aepY BF9343_1815 CAH07596.1 2164 - 3301 (+) CR626927.1:2214756-2215893 -
aepZ BF9343_1816 CAH07597.1 3297 - 4398 (+) CR626927.1:2215889-2216990 -
wzx BF9343_1817 CAH07598.1 4417 - 5911 (+) CR626927.1:2217009-2218503 -
wcfV BF9343_1818 CAH07599.1 5914 - 7060 (+) CR626927.1:2218506-2219652 -
wcfW BF9343_1819 CAH07600.1 7056 - 7926 (+) CR626927.1:2219648-2220518 -
wcfX BF9343_1820 CAH07601.1 7933 - 8986 (+) CR626927.1:2220525-2221578 -
wcfY BF9343_1821 CAH07602.1 8988 - 10311 (+) CR626927.1:2221580-2222903 -
wcfZ BF9343_1822 CAH07603.1 10594 - 11617 (+) CR626927.1:2223186-2224209 -
wcgQ BF9343_1823 CAH07604.1 11646 - 12693 (+) CR626927.1:2224238-2225285 -
wzy BF9343_1824 CAH07605.1 12689 - 13820 (+) CR626927.1:2225281-2226412 -
wcgR BF9343_1825 CAH07606.1 13791 - 14907 (+) CR626927.1:2226383-2227499 -
wcgS BF9343_1826 CAH07607.1 14899 - 15916 (+) CR626927.1:2227491-2228508 -
wcgT BF9343_1827 CAH07608.1 15903 - 17034 (+) CR626927.1:2228495-2229626 -
wcgU BF9343_1828 CAH07609.1 17054 - 17918 (+) CR626927.1:2229646-2230510 -
wcgV BF9343_1829 CAH07610.1 17914 - 19126 (+) CR626927.1:2230506-2231718 -
wcgW BF9343_1830 CAH07611.1 19148 - 20156 (+) CR626927.1:2231740-2232748 -
wcgX BF9343_1831 CAH07612.1 20159 - 21095 (+) CR626927.1:2232751-2233687 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

wcfT 1 - 120 (+) CDS No
wcfU 113 - 832 (+) CDS No
aepX 852 - 2153 (+) CDS No
aepY 2165 - 3301 (+) CDS No
aepZ 3298 - 4398 (+) CDS No
wzx 4418 - 5911 (+) CDS No
wcfV 5915 - 7060 (+) CDS No
wcfW 7057 - 7926 (+) CAZyme: GT11 Yes
wcfX 7934 - 8986 (+) other Yes
wcfY 8989 - 10311 (+) other Yes
wcfZ 10595 - 11617 (+) CAZyme: GT2|GT2_Glycos_transf_2 Yes
wcgQ 11647 - 12693 (+) CAZyme: GT2|GT2_Glycos_transf_2 Yes
wzy 12690 - 13820 (+) other Yes
wcgR 13792 - 14907 (+) CAZyme: GT4 Yes
wcgS 14900 - 15916 (+) TC: gnl|TC-DB|Q6MMD5|9.B.18.2.1 Yes
wcgT 15904 - 17034 (+) CDS No
wcgU 17055 - 17918 (+) CDS No
wcgV 17915 - 19126 (+) CDS No
wcgW 19149 - 20156 (+) CDS No
wcgX 20160 - 21095 (+) CDS No

PUL ID

PUL0502

PubMed

20829291, Microbiology (Reading). 2010 Nov;156(Pt 11):3255-3269. doi: 10.1099/mic.0.042978-0. Epub 2010 Sep 9.

Title

Twenty-eight divergent polysaccharide loci specifying within- and amongst-strain capsule diversity in three strains of Bacteroides fragilis.

Author

Patrick S, Blakely GW, Houston S, Moore J, Abratt VR, Bertalan M, Cerdeno-Tarraga AM, Quail MA, Corton N, Corton C, Bignell A, Barron A, Clark L, Bentley SD, Parkhill J

Abstract

Comparison of the complete genome sequence of Bacteroides fragilis 638R, originally isolated in the USA, was made with two previously sequenced strains isolated in the UK (NCTC 9343) and Japan (YCH46). The presence of 10 loci containing genes associated with polysaccharide (PS) biosynthesis, each including a putative Wzx flippase and Wzy polymerase, was confirmed in all three strains, despite a lack of cross-reactivity between NCTC 9343 and 638R surface PS-specific antibodies by immunolabelling and microscopy. Genomic comparisons revealed an exceptional level of PS biosynthesis locus diversity. Of the 10 divergent PS-associated loci apparent in each strain, none is similar between NCTC 9343 and 638R. YCH46 shares one locus with NCTC 9343, confirmed by mAb labelling, and a second different locus with 638R, making a total of 28 divergent PS biosynthesis loci amongst the three strains. The lack of expression of the phase-variable large capsule (LC) in strain 638R, observed in NCTC 9343, is likely to be due to a point mutation that generates a stop codon within a putative initiating glycosyltransferase, necessary for the expression of the LC in NCTC 9343. Other major sequence differences were observed to arise from different numbers and variety of inserted extra-chromosomal elements, in particular prophages. Extensive horizontal gene transfer has occurred within these strains, despite the presence of a significant number of divergent DNA restriction and modification systems that act to prevent acquisition of foreign DNA. The level of amongst-strain diversity in PS biosynthesis loci is unprecedented.