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PlantCAZyme
Cite: NAR/gkaa742 2020

Because CGCFinder predicted no CGC for this PUL, the gene cluster depicted below contains dbCAN2 and CGC signature predictions for all genes in the PUL, instead of a predicted CGC.


PUL General Information

Literature Information

PUL ID

PUL0781

PubMed

39738071, Nat Commun. 2024 Dec 30;15(1):10906. doi: 10.1038/s41467-024-55268-w.

Characterization method

RNA-seq,differential gene expression,HPAEC-PAD,SDS-PAGE,para-hydroxybenzoic acid (PAHBAH) assay,reducing-sugar assay,Carbohydrate Polyacrylamide Gel Electrophoresis (C-PAGE),enzyme activity assay

Genomic accession number

NZ_CAWLDM010000001.1

Nucelotide position range

4971656-5000661

Substrate

fucoidan

Loci

None

Species

Neorhodopirellula lusitana/445327

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- ACI5KW_RS17950 WP_404309226.1 0 - 1656 (-) NZ_CAWLDM010000001.1:4971656-4973312 -
- ACI5KW_RS17955 WP_404309227.1 2028 - 3450 (+) NZ_CAWLDM010000001.1:4973684-4975106 -
- ACI5KW_RS17960 WP_404309228.1 3650 - 3890 (-) NZ_CAWLDM010000001.1:4975306-4975546 -
- ACI5KW_RS17965 WP_404309229.1 4369 - 4540 (-) NZ_CAWLDM010000001.1:4976025-4976196 -
- ACI5KW_RS17970 WP_404309230.1 4743 - 5988 (-) NZ_CAWLDM010000001.1:4976399-4977644 -
- ACI5KW_RS17975 WP_404309231.1 6232 - 8284 (-) NZ_CAWLDM010000001.1:4977888-4979940 2.7.11.1
- ACI5KW_RS17980 WP_404309232.1 8328 - 8949 (-) NZ_CAWLDM010000001.1:4979984-4980605 -
- ACI5KW_RS17985 WP_404309233.1 9519 - 12009 (+) NZ_CAWLDM010000001.1:4981175-4983665 -
- ACI5KW_RS17990 WP_404309234.1 12498 - 14727 (+) NZ_CAWLDM010000001.1:4984154-4986383 -
- ACI5KW_RS17995 WP_404309235.1 14810 - 18269 (+) NZ_CAWLDM010000001.1:4986466-4989925 -
- ACI5KW_RS18000 WP_404309236.1 18393 - 19785 (+) NZ_CAWLDM010000001.1:4990049-4991441 3.2.1.51
- ACI5KW_RS18005 WP_404309237.1 19852 - 21298 (+) NZ_CAWLDM010000001.1:4991508-4992954 -
- ACI5KW_RS18010 WP_404309238.1 21393 - 22809 (+) NZ_CAWLDM010000001.1:4993049-4994465 -
- ACI5KW_RS18015 WP_404309239.1 22811 - 24299 (+) NZ_CAWLDM010000001.1:4994467-4995955 -
- ACI5KW_RS18020 WP_404309240.1 24342 - 25908 (+) NZ_CAWLDM010000001.1:4995998-4997564 3.1.6.-
- ACI5KW_RS18025 WP_404309241.1 25993 - 27475 (+) NZ_CAWLDM010000001.1:4997649-4999131 3.2.1.51
- ACI5KW_RS18030 WP_404309242.1 27479 - 29006 (+) NZ_CAWLDM010000001.1:4999135-5000662 3.1.6.-

Cluster number

0

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 1656 (-) CDS No
- 2029 - 3450 (+) CDS No
- 3651 - 3890 (-) CDS No
- 4370 - 4540 (-) CDS No
- 4744 - 5988 (-) STP: STP|SBP_bac_10 No
- 6233 - 8284 (-) STP: STP|Pkinase No
- 8329 - 8949 (-) TF: DBD-Pfam|GerE No
- 9520 - 12009 (+) CAZyme: GH95 No
- 12499 - 14727 (+) CDS No
- 14811 - 18269 (+) CAZyme: GH116 No
- 18394 - 19785 (+) CAZyme: GH29 No
- 19853 - 21298 (+) CDS No
- 21394 - 22809 (+) CDS No
- 22812 - 24299 (+) CDS No
- 24343 - 25908 (+) CDS No
- 25994 - 27475 (+) CAZyme: GH29 No
- 27480 - 29006 (+) CDS No

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PUL ID

PUL0781

PubMed

39738071, Nat Commun. 2024 Dec 30;15(1):10906. doi: 10.1038/s41467-024-55268-w.

Title

Mechanisms of recalcitrant fucoidan breakdown in marine Planctomycetota.

Author

Perez-Cruz C, Moraleda-Montoya A, Liebana R, Terrones O, Arrizabalaga U, Garcia-Alija M, Lorizate M, Martinez Gascuena A, Garcia-Alvarez I, Nieto-Garai JA, Olazar-Intxausti J, Rodriguez-Colinas B, Mann E, Chiara JL, Contreras FX, Guerin ME, Trastoy B, Alonso-Saez L

Abstract

Marine brown algae produce the highly recalcitrant polysaccharide fucoidan, contributing to long-term oceanic carbon storage and climate regulation. Fucoidan is degraded by specialized heterotrophic bacteria, which promote ecosystem function and global carbon turnover using largely uncharacterized mechanisms. Here, we isolate and study two Planctomycetota strains from the microbiome associated with the alga Fucus spiralis, which grow efficiently on chemically diverse fucoidans. One of the strains appears to internalize the polymer, while the other strain degrades it extracellularly. Multi-omic approaches show that fucoidan breakdown is mediated by the expression of divergent polysaccharide utilization loci, and endo-fucanases of family GH168 are strongly upregulated during fucoidan digestion. Enzymatic assays and structural biology studies reveal how GH168 endo-fucanases degrade various fucoidan cores from brown algae, assisted by auxiliary hydrolytic enzymes. Overall, our results provide insights into fucoidan processing mechanisms in macroalgal-associated bacteria.