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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0705

PubMed

37121608, Environ Microbiol. 2023 Sep;25(9):1713-1727. doi: 10.1111/1462-2920.16390. Epub 2023 Apr 30.

Characterization method

fluorophore-assisted carbohydrate electrophoresis (FACE),dinitrosalicylic acid-assay (DNS-assay),HPLC,clone and expression

Genomic accession number

NZ_JPOL01000002.1

Nucelotide position range

858730-891783

Substrate

xylan

Loci

P162_RS17810-P162_RS04080

Species

Flavimarina sp. Hel_I_48/1392488

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- P162_RS17810 WP_081868372.1 0 - 2769 (-) NZ_JPOL01000002.1:858730-861499 -
- P162_RS04020 WP_031425947.1 3312 - 5274 (-) NZ_JPOL01000002.1:862042-864004 3.2.1.-
- P162_RS04025 WP_051907767.1 5305 - 7060 (-) NZ_JPOL01000002.1:864035-865790 -
- P162_RS04030 WP_081868373.1 7254 - 9939 (-) NZ_JPOL01000002.1:865984-868669 -
- P162_RS04035 WP_035916826.1 10005 - 11304 (-) NZ_JPOL01000002.1:868735-870034 -
- P162_RS04040 WP_051907768.1 11357 - 13862 (-) NZ_JPOL01000002.1:870087-872592 -
- P162_RS04045 WP_164076206.1 14479 - 18559 (+) NZ_JPOL01000002.1:873209-877289 -
- P162_RS04050 WP_035916828.1 18931 - 20071 (-) NZ_JPOL01000002.1:877661-878801 3.2.1.8
- P162_RS04055 WP_051907770.1 20268 - 21957 (-) NZ_JPOL01000002.1:878998-880687 -
- P162_RS04060 WP_031425955.1 21992 - 23027 (-) NZ_JPOL01000002.1:880722-881757 -
- P162_RS04065 WP_031425956.1 23069 - 24812 (-) NZ_JPOL01000002.1:881799-883542 -
- P162_RS04070 WP_031425957.1 24839 - 27893 (-) NZ_JPOL01000002.1:883569-886623 -
- P162_RS04075 WP_031425958.1 27955 - 29848 (-) NZ_JPOL01000002.1:886685-888578 -
- P162_RS04080 WP_035916831.1 29859 - 33054 (-) NZ_JPOL01000002.1:888589-891784 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 2769 (-) CAZyme: GH43_10|CBM91 Yes
- 3313 - 5274 (-) CAZyme: GH97 Yes
- 5306 - 7060 (-) CAZyme: GH43_12|CBM91 Yes
- 7255 - 9939 (-) CAZyme: CE6|CE1|CE1 Yes
- 10006 - 11304 (-) CAZyme: GH8 Yes
- 11358 - 13862 (-) CAZyme: GH95 Yes
- 14480 - 18559 (+) TF: DBD-Pfam|HTH_AraC,DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0035607,DBD-SUPERFAMILY|0035607 Yes
- 18932 - 20071 (-) CAZyme: GH10 Yes
- 20269 - 21957 (-) CAZyme: GH10 Yes
- 21993 - 23027 (-) other Yes
- 23070 - 24812 (-) other Yes
- 24840 - 27893 (-) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 27956 - 29848 (-) other Yes
- 29860 - 33054 (-) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes

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PUL ID

PUL0705

PubMed

37121608, Environ Microbiol. 2023 Sep;25(9):1713-1727. doi: 10.1111/1462-2920.16390. Epub 2023 Apr 30.

Title

Marine Bacteroidetes enzymatically digest xylans from terrestrial plants.

Author

Dutschei T, Beidler I, Bartosik D, Seesselberg JM, Teune M, Baumgen M, Ferreira SQ, Heldmann J, Nagel F, Krull J, Berndt L, Methling K, Hein M, Becher D, Langer P, Delcea M, Lalk M, Lammers M, Hohne M, Hehemann JH, Schweder T, Bornscheuer UT

Abstract

Marine Bacteroidetes that degrade polysaccharides contribute to carbon cycling in the ocean. Organic matter, including glycans from terrestrial plants, might enter the oceans through rivers. Whether marine bacteria degrade structurally related glycans from diverse sources including terrestrial plants and marine algae was previously unknown. We show that the marine bacterium Flavimarina sp. Hel_I_48 encodes two polysaccharide utilization loci (PULs) which degrade xylans from terrestrial plants and marine algae. Biochemical experiments revealed activity and specificity of the encoded xylanases and associated enzymes of these PULs. Proteomics indicated that these genomic regions respond to glucuronoxylans and arabinoxylans. Substrate specificities of key enzymes suggest dedicated metabolic pathways for xylan utilization. Some of the xylanases were active on different xylans with the conserved beta-1,4-linked xylose main chain. Enzyme activity was consistent with growth curves showing Flavimarina sp. Hel_I_48 uses structurally different xylans. The observed abundance of related xylan-degrading enzyme repertoires in genomes of other marine Bacteroidetes indicates similar activities are common in the ocean. The here presented data show that certain marine bacteria are genetically and biochemically variable enough to access parts of structurally diverse xylans from terrestrial plants as well as from marine algal sources.