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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0488

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

5974734-5995493

Substrate

beta-mannan

Loci

Fjoh_4946-Fjoh_4959

Species

Flavobacterium johnsoniae/986

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- FJOH_RS25560 WP_012026911.1 0 - 969 (-) NC_009441.1:5974734-5975703 -
- FJOH_RS25565 WP_012026912.1 979 - 2215 (-) NC_009441.1:5975713-5976949 -
- FJOH_RS25570 WP_012026913.1 2333 - 3296 (-) NC_009441.1:5977067-5978030 -
- FJOH_RS25575 WP_012026914.1 3491 - 4529 (-) NC_009441.1:5978225-5979263 -
- FJOH_RS25580 WP_012026915.1 4548 - 6147 (-) NC_009441.1:5979282-5980881 -
- FJOH_RS25585 WP_044048163.1 6160 - 9340 (-) NC_009441.1:5980894-5984074 -
- FJOH_RS25590 WP_012026917.1 9663 - 10542 (-) NC_009441.1:5984397-5985276 -
- FJOH_RS25595 WP_012026918.1 10848 - 11979 (+) NC_009441.1:5985582-5986713 -
- FJOH_RS25600 WP_012026919.1 12023 - 13415 (+) NC_009441.1:5986757-5988149 -
- FJOH_RS25605 WP_012026920.1 13446 - 14637 (+) NC_009441.1:5988180-5989371 -
- FJOH_RS25610 WP_012026921.1 14643 - 15834 (+) NC_009441.1:5989377-5990568 -
- FJOH_RS25615 WP_012026922.1 15839 - 17069 (+) NC_009441.1:5990573-5991803 3.2.1.78
- FJOH_RS25620 WP_012026923.1 17216 - 18506 (+) NC_009441.1:5991950-5993240 -
- FJOH_RS25625 WP_012026924.1 18780 - 20760 (+) NC_009441.1:5993514-5995494 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 969 (-) CAZyme: GH5|GH5_2 Yes
- 980 - 2215 (-) CAZyme: GH27 Yes
- 2334 - 3296 (-) other Yes
- 3492 - 4529 (-) other Yes
- 4549 - 6147 (-) TC: gnl|TC-DB|G0IYY9|8.A.46.1.6 Yes
- 6161 - 9340 (-) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 9664 - 10542 (-) TF: DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0036286,DBD-SUPERFAMILY|0035607 Yes
- 10849 - 11979 (+) CAZyme: GH26 Yes
- 12024 - 13415 (+) TC: gnl|TC-DB|A1S5F2|2.A.2.3.6 Yes
- 13447 - 14637 (+) CAZyme: GH130 Yes
- 14644 - 15834 (+) other Yes
- 15840 - 17069 (+) CAZyme: GH26 Yes
- 17217 - 18506 (+) CAZyme: GH5_7 Yes
- 18781 - 20760 (+) CAZyme: GH97 Yes

PUL ID

PUL0488

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.