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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0476

PubMed

19717629, Appl Environ Microbiol. 2009 Nov;75(21):6864-75. doi: 10.1128/AEM.01495-09. Epub 2009 Aug 28.

Characterization method

growth assay

Genomic accession number

NC_009441.1

Nucelotide position range

2361555-2383192

Substrate

hemicellulose,pectin

Loci

Fjoh_2019-Fjoh_2029

Species

Flavobacterium johnsoniae/986

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- FJOH_RS10520 WP_012024090.1 0 - 3951 (-) NC_009441.1:2361555-2365506 -
- FJOH_RS10525 WP_012024091.1 4341 - 7359 (+) NC_009441.1:2365896-2368914 -
- FJOH_RS10530 WP_012024092.1 7375 - 8899 (+) NC_009441.1:2368930-2370454 -
- FJOH_RS10535 WP_012024093.1 9178 - 10351 (+) NC_009441.1:2370733-2371906 -
- FJOH_RS10540 WP_012024094.1 10629 - 11658 (+) NC_009441.1:2372184-2373213 -
- FJOH_RS10545 WP_012024095.1 11856 - 13668 (+) NC_009441.1:2373411-2375223 -
- FJOH_RS10550 WP_012024096.1 13900 - 14923 (+) NC_009441.1:2375455-2376478 -
- FJOH_RS10555 WP_012024097.1 14947 - 16126 (+) NC_009441.1:2376502-2377681 -
- FJOH_RS10560 WP_012024098.1 16322 - 17300 (+) NC_009441.1:2377877-2378855 -
- FJOH_RS10565 WP_044047662.1 17484 - 19584 (+) NC_009441.1:2379039-2381139 -
nagB FJOH_RS10570 WP_012024100.1 19724 - 21638 (+) NC_009441.1:2381279-2383193 3.5.99.6

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 3951 (-) TF: DBD-Pfam|HTH_11,DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0036286,DBD-SUPERFAMILY|0035607 No
- 4342 - 7359 (+) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 7376 - 8899 (+) other Yes
- 9179 - 10351 (+) CAZyme: GH5|GH5_13 Yes
- 10630 - 11658 (+) CAZyme: GH43_18 Yes
- 11857 - 13668 (+) CAZyme: GH2 Yes
- 13901 - 14923 (+) CAZyme: GH43|GH43_26 Yes
- 14948 - 16126 (+) other Yes
- 16323 - 17300 (+) CAZyme: GH43_31 Yes
- 17485 - 19584 (+) CAZyme: GH29|CBM32 Yes
nagB 19725 - 21638 (+) STP: STP|PIG-L No

PUL ID

PUL0476

PubMed

19717629, Appl Environ Microbiol. 2009 Nov;75(21):6864-75. doi: 10.1128/AEM.01495-09. Epub 2009 Aug 28.

Title

Novel features of the polysaccharide-digesting gliding bacterium Flavobacterium johnsoniae as revealed by genome sequence analysis.

Author

McBride MJ, Xie G, Martens EC, Lapidus A, Henrissat B, Rhodes RG, Goltsman E, Wang W, Xu J, Hunnicutt DW, Staroscik AM, Hoover TR, Cheng YQ, Stein JL

Abstract

The 6.10-Mb genome sequence of the aerobic chitin-digesting gliding bacterium Flavobacterium johnsoniae (phylum Bacteroidetes) is presented. F. johnsoniae is a model organism for studies of bacteroidete gliding motility, gene regulation, and biochemistry. The mechanism of F. johnsoniae gliding is novel, and genome analysis confirms that it does not involve well-studied motility organelles, such as flagella or type IV pili. The motility machinery is composed of Gld proteins in the cell envelope that are thought to comprise the "motor" and SprB, which is thought to function as a cell surface adhesin that is propelled by the motor. Analysis of the genome identified genes related to sprB that may encode alternative adhesins used for movement over different surfaces. Comparative genome analysis revealed that some of the gld and spr genes are found in nongliding bacteroidetes and may encode components of a novel protein secretion system. F. johnsoniae digests proteins, and 125 predicted peptidases were identified. F. johnsoniae also digests numerous polysaccharides, and 138 glycoside hydrolases, 9 polysaccharide lyases, and 17 carbohydrate esterases were predicted. The unexpected ability of F. johnsoniae to digest hemicelluloses, such as xylans, mannans, and xyloglucans, was predicted based on the genome analysis and confirmed experimentally. Numerous predicted cell surface proteins related to Bacteroides thetaiotaomicron SusC and SusD, which are likely involved in binding of oligosaccharides and transport across the outer membrane, were also identified. Genes required for synthesis of the novel outer membrane flexirubin pigments were identified by a combination of genome analysis and genetic experiments. Genes predicted to encode components of a multienzyme nonribosomal peptide synthetase were identified, as were novel aspects of gene regulation. The availability of techniques for genetic manipulation allows rapid exploration of the features identified for the polysaccharide-digesting gliding bacteroidete F. johnsoniae.