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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0514

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

NC_006347.1

Nucelotide position range

2154906-2177179

Substrate

capsule polysaccharide

Loci

BF1830-BF1848

Species

Bacteroides fragilis/817

Degradation or Biosynthesis

biosynthesis

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- BF_RS08615 WP_005817129.1 0 - 1284 (+) NC_006347.1:2154906-2156190 -
- BF_RS08620 WP_011202609.1 1276 - 1996 (+) NC_006347.1:2156182-2156902 -
aepX BF_RS08625 WP_005817134.1 2015 - 3317 (+) NC_006347.1:2156921-2158223 5.4.2.9
aepY BF_RS08630 WP_005817136.1 3328 - 4465 (+) NC_006347.1:2158234-2159371 4.1.1.82
- BF_RS08635 WP_011202611.1 4461 - 5562 (+) NC_006347.1:2159367-2160468 2.6.1.37
- BF_RS08640 WP_011202612.1 5581 - 7075 (+) NC_006347.1:2160487-2161981 -
- BF_RS08645 WP_005817142.1 7078 - 8224 (+) NC_006347.1:2161984-2163130 -
- BF_RS08650 WP_005817145.1 8220 - 9090 (+) NC_006347.1:2163126-2163996 -
- BF_RS08655 WP_005817148.1 9097 - 10150 (+) NC_006347.1:2164003-2165056 -
- BF_RS08660 WP_005817149.1 10152 - 11475 (+) NC_006347.1:2165058-2166381 -
- BF_RS08665 WP_010992744.1 11758 - 12781 (+) NC_006347.1:2166664-2167687 -
- BF_RS08670 WP_010992745.1 12810 - 13857 (+) NC_006347.1:2167716-2168763 -
- BF_RS08675 WP_005817155.1 13853 - 14984 (+) NC_006347.1:2168759-2169890 -
- BF_RS08680 WP_011202613.1 14955 - 16071 (+) NC_006347.1:2169861-2170977 -
- BF_RS08685 WP_005817159.1 16063 - 17080 (+) NC_006347.1:2170969-2171986 -
wecB BF_RS08690 WP_005817161.1 17067 - 18198 (+) NC_006347.1:2171973-2173104 5.1.3.14
- BF_RS08695 WP_010992747.1 18218 - 19082 (+) NC_006347.1:2173124-2173988 -
- BF_RS08700 WP_005776619.1 19078 - 20290 (+) NC_006347.1:2173984-2175196 -
- BF_RS08705 WP_005786859.1 20312 - 21320 (+) NC_006347.1:2175218-2176226 -
- BF_RS08710 WP_005786860.1 21323 - 22274 (+) NC_006347.1:2176229-2177180 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 1284 (+) CDS No
- 1277 - 1996 (+) CDS No
aepX 2016 - 3317 (+) CDS No
aepY 3329 - 4465 (+) CDS No
- 4462 - 5562 (+) CDS No
- 5582 - 7075 (+) CDS No
- 7079 - 8224 (+) CDS No
- 8221 - 9090 (+) CAZyme: GT11 Yes
- 9098 - 10150 (+) other Yes
- 10153 - 11475 (+) other Yes
- 11759 - 12781 (+) CAZyme: GT2_Glycos_transf_2|GT2 Yes
- 12811 - 13857 (+) CAZyme: GT2_Glycos_transf_2|GT2 Yes
- 13854 - 14984 (+) other Yes
- 14956 - 16071 (+) CAZyme: GT4 Yes
- 16064 - 17080 (+) TC: gnl|TC-DB|Q6MMD5|9.B.18.2.1 Yes
wecB 17068 - 18198 (+) CDS No
- 18219 - 19082 (+) CDS No
- 19079 - 20290 (+) CDS No
- 20313 - 21320 (+) CDS No
- 21324 - 22274 (+) CDS No

PUL ID

PUL0514

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.