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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0795

PubMed

39913342, ISME J. 2025 Jan 2;19(1):wraf022. doi: 10.1093/ismejo/wraf022.

Characterization method

RNA-seq,recombinant protein expression,growth assay

Genomic accession number

NC_009441.1

Nucelotide position range

850019-873685

Substrate

xyloglucan

Loci

FJOH_RS04035-FJOH_RS04090

Species

Flavobacterium johnsoniae UW101/986

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- FJOH_RS04035 WP_012022860.1 0 - 2409 (-) NC_009441.1:850019-852428 -
- FJOH_RS04040 WP_012022861.1 2605 - 4552 (-) NC_009441.1:852624-854571 -
- FJOH_RS04045 WP_012022862.1 4664 - 6173 (-) NC_009441.1:854683-856192 -
- FJOH_RS04050 WP_012022863.1 6174 - 8412 (-) NC_009441.1:856193-858431 -
- FJOH_RS04055 WP_012022864.1 8502 - 10074 (-) NC_009441.1:858521-860093 -
- FJOH_RS04060 WP_012022865.1 10141 - 11962 (-) NC_009441.1:860160-861981 3.2.1.-
- FJOH_RS27190 WP_235022995.1 11946 - 12147 (-) NC_009441.1:861965-862166 -
- FJOH_RS04070 WP_012022866.1 12399 - 14799 (-) NC_009441.1:862418-864818 -
- FJOH_RS04075 WP_012022867.1 14993 - 17477 (-) NC_009441.1:865012-867496 -
- FJOH_RS04080 WP_123875661.1 17560 - 18931 (-) NC_009441.1:867579-868950 -
- FJOH_RS04085 WP_052295218.1 18953 - 20525 (-) NC_009441.1:868972-870544 -
- FJOH_RS04090 WP_012022870.1 20535 - 23667 (-) NC_009441.1:870554-873686 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 2409 (-) CAZyme: GH95 Yes
- 2606 - 4552 (-) CAZyme: CE20|CE20 Yes
- 4665 - 6173 (-) CAZyme: GH5_4 Yes
- 6175 - 8412 (-) CAZyme: GH3 Yes
- 8503 - 10074 (-) CAZyme: GH39 Yes
- 10142 - 11962 (-) CAZyme: GH97 Yes
- 11947 - 12147 (-) other Yes
- 12400 - 14799 (-) CAZyme: GH31_3 Yes
- 14994 - 17477 (-) CAZyme: GH2 Yes
- 17561 - 18931 (-) other Yes
- 18954 - 20525 (-) other Yes
- 20536 - 23667 (-) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes

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PUL ID

PUL0795

PubMed

39913342, ISME J. 2025 Jan 2;19(1):wraf022. doi: 10.1093/ismejo/wraf022.

Title

Metabolism of hemicelluloses by root-associated Bacteroidota species.

Author

Martin H, Rogers LA, Moushtaq L, Brindley AA, Forbes P, Quinton AR, Murphy ARJ, Hipperson H, Daniell TJ, Ndeh D, Amsbury S, Hitchcock A, Lidbury IDEA

Abstract

Bacteroidota species are enriched in the plant microbiome and provide several beneficial functions for their host, including disease suppression. Determining the mechanisms that enable bacteroidota to colonise plant roots may therefore provide opportunities for enhancing crop production through microbiome engineering. By focusing on nutrient acquisition mechanisms, we discovered Bacteroidota species lack high affinity ATP-binding cassette transporters common in other plant-associated bacteria for capturing simple carbon exudates. Instead, bacteroidota possess TonB-dependent transporters predicted to import glycans produced by plant polysaccharide breakdown. Metatranscriptomics (oat rhizosphere) identified several TonB-dependent transporters genes that were highly expressed in Flavobacterium (phylum Bacteroidota). Using Flavobacterium johnsoniae as the model, we experimentally validated the function of one highly expressed TonB-dependent transporter, identifying a conserved Xyloglucan utilisation loci conferring the ability to import and degrade xyloglucan, the major hemicellulose secreted from plant roots. Xyloglucan utilisation loci harbour an endoxyloglucanase related to family 5 subfamily 4 subclade 2D glycoside hydrolases carrying a mutation that we demonstrate is required for full activity towards xyloglucan. Based on analysing 700 soil metagenomes, subclade 2D glycoside hydrolases have radiated in soil and are prevalent among plant-associated bacteroidota and certain taxa affiliated with Gammaproteobacteria. In bacteroidota, particularly Flavobacterium species, xyloglucan utilisation loci organisation was highly conserved, which may increase their competitive ability to utilise xyloglucan. Given bacteroidota lack high-affinity nutrient transporters for simple carbon, instead possessing xyloglucan utilisation loci and similar gene clusters, our data suggests hemicellulose exudates provide them with an important carbon source in the rhizosphere.