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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0494

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_016776.1

Nucelotide position range

1805684-1828904

Substrate

capsule polysaccharide

Loci

BF638R_1539-BF638R_1563

Species

Bacteroides fragilis/817

Degradation or Biosynthesis

biosynthesis

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

rfbA BF638R_RS07185 WP_014298562.1 0 - 891 (+) NC_016776.1:1805684-1806575 2.7.7.24
- BF638R_RS07195 WP_014298564.1 1581 - 2919 (+) NC_016776.1:1807265-1808603 -
- BF638R_RS07200 WP_014298565.1 2923 - 3982 (+) NC_016776.1:1808607-1809666 -
- BF638R_RS07205 WP_005795239.1 4445 - 4970 (+) NC_016776.1:1810129-1810654 -
rfbC BF638R_RS07210 WP_014298567.1 4969 - 5557 (+) NC_016776.1:1810653-1811241 5.1.3.13
- BF638R_RS07215 WP_005795234.1 5563 - 6991 (+) NC_016776.1:1811247-1812675 -
- BF638R_RS07220 WP_014298568.1 6992 - 8015 (+) NC_016776.1:1812676-1813699 -
- BF638R_RS07225 WP_014298569.1 8075 - 9206 (+) NC_016776.1:1813759-1814890 -
- BF638R_RS07230 WP_014298570.1 9417 - 10428 (+) NC_016776.1:1815101-1816112 -
- BF638R_RS07235 WP_014298571.1 10430 - 10976 (+) NC_016776.1:1816114-1816660 -
- BF638R_RS07240 WP_014298572.1 10993 - 11986 (+) NC_016776.1:1816677-1817670 -
- BF638R_RS07245 WP_014298573.1 11976 - 13125 (+) NC_016776.1:1817660-1818809 -
- BF638R_RS07250 WP_005795222.1 13133 - 14477 (+) NC_016776.1:1818817-1820161 -
- BF638R_RS07255 - 14473 - 15199 (+) NC_016776.1:1820157-1820883 -
- BF638R_RS07260 WP_014298575.1 15312 - 16008 (+) NC_016776.1:1820996-1821692 -
- BF638R_RS07265 WP_005795218.1 16020 - 16833 (+) NC_016776.1:1821704-1822517 -
- BF638R_RS07270 WP_014298576.1 16829 - 17918 (+) NC_016776.1:1822513-1823602 -
- BF638R_RS07275 WP_014298577.1 17920 - 18991 (+) NC_016776.1:1823604-1824675 -
- BF638R_RS24325 WP_100717419.1 19269 - 19452 (+) NC_016776.1:1824953-1825136 -
- BF638R_RS22750 WP_136199852.1 19482 - 19818 (+) NC_016776.1:1825166-1825502 -
- BF638R_RS22755 WP_136199853.1 19736 - 20120 (+) NC_016776.1:1825420-1825804 -
- BF638R_RS07290 WP_032564596.1 20207 - 21242 (+) NC_016776.1:1825891-1826926 -
- BF638R_RS07295 WP_014298579.1 21258 - 22155 (+) NC_016776.1:1826942-1827839 -
- BF638R_RS07300 WP_014298580.1 22273 - 23221 (+) NC_016776.1:1827957-1828905 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

rfbA 1 - 891 (+) CDS No
- 1582 - 2919 (+) CDS No
- 2924 - 3982 (+) CDS No
- 4446 - 4970 (+) CDS No
rfbC 4970 - 5557 (+) CDS No
- 5564 - 6991 (+) TC: gnl|TC-DB|O32273|2.A.66.2.6 Yes
- 6993 - 8015 (+) other Yes
- 8076 - 9206 (+) STP: STP|Aminotran_1_2 Yes
- 9418 - 10428 (+) other Yes
- 10431 - 10976 (+) other Yes
- 10994 - 11986 (+) TC: gnl|TC-DB|D0WIR7|9.B.97.1.11 Yes
- 11977 - 13125 (+) other Yes
- 13134 - 14477 (+) other Yes
- 15313 - 16008 (+) other Yes
- 16021 - 16833 (+) other Yes
- 16830 - 17918 (+) CAZyme: GT4 Yes
- 17921 - 18991 (+) CAZyme: GT4 Yes
- 19270 - 19452 (+) other Yes
- 19483 - 19818 (+) other Yes
- 19737 - 20120 (+) other Yes
- 20208 - 21242 (+) CAZyme: GT4 Yes
- 21259 - 22155 (+) other Yes
- 22274 - 23221 (+) TC: gnl|TC-DB|P0AC78|9.B.146.1.7 Yes

PUL ID

PUL0494

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.