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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0777

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

825302-866107

Substrate

fucoidan

Loci

ACI5KW_RS03060-ACI5KW_RS03180

Species

Neorhodopirellula lusitana/445327

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- ACI5KW_RS03055 WP_404305275.1 0 - 4 (-) NZ_CAWLDM010000001.1:825302-825306 -
- ACI5KW_RS03060 WP_404305277.1 0 - 1263 (-) NZ_CAWLDM010000001.1:825302-826565 -
- ACI5KW_RS03065 WP_404305279.1 1469 - 2390 (+) NZ_CAWLDM010000001.1:826771-827692 -
- ACI5KW_RS03070 WP_404305281.1 2580 - 5292 (-) NZ_CAWLDM010000001.1:827882-830594 -
- ACI5KW_RS03075 WP_404305283.1 5322 - 6933 (-) NZ_CAWLDM010000001.1:830624-832235 -
- ACI5KW_RS03080 WP_404305284.1 8210 - 9656 (-) NZ_CAWLDM010000001.1:833512-834958 -
- ACI5KW_RS03085 WP_404305285.1 9724 - 11083 (-) NZ_CAWLDM010000001.1:835026-836385 -
- ACI5KW_RS03090 WP_404305287.1 11357 - 12836 (-) NZ_CAWLDM010000001.1:836659-838138 3.1.6.-
- ACI5KW_RS03095 WP_404305289.1 12954 - 14469 (-) NZ_CAWLDM010000001.1:838256-839771 -
- ACI5KW_RS03100 WP_404310912.1 14541 - 15891 (-) NZ_CAWLDM010000001.1:839843-841193 -
- ACI5KW_RS03105 WP_404305291.1 16253 - 17873 (-) NZ_CAWLDM010000001.1:841555-843175 -
- ACI5KW_RS03110 WP_404305293.1 18239 - 20093 (-) NZ_CAWLDM010000001.1:843541-845395 -
- ACI5KW_RS03115 WP_404305295.1 20251 - 20431 (-) NZ_CAWLDM010000001.1:845553-845733 -
- ACI5KW_RS03120 WP_404305297.1 20448 - 21828 (-) NZ_CAWLDM010000001.1:845750-847130 -
- ACI5KW_RS03125 WP_404305299.1 22087 - 24484 (-) NZ_CAWLDM010000001.1:847389-849786 -
- ACI5KW_RS03130 WP_404305301.1 24562 - 25834 (-) NZ_CAWLDM010000001.1:849864-851136 -
- ACI5KW_RS03135 WP_404305303.1 25989 - 27501 (-) NZ_CAWLDM010000001.1:851291-852803 -
- ACI5KW_RS03140 WP_283432867.1 27991 - 28153 (-) NZ_CAWLDM010000001.1:853293-853455 -
- ACI5KW_RS03145 WP_404305305.1 28233 - 29484 (-) NZ_CAWLDM010000001.1:853535-854786 -
- ACI5KW_RS03150 WP_404305307.1 29579 - 31316 (-) NZ_CAWLDM010000001.1:854881-856618 -
- ACI5KW_RS03155 WP_404305309.1 31316 - 31844 (-) NZ_CAWLDM010000001.1:856618-857146 -
- ACI5KW_RS03160 WP_404310913.1 32396 - 33944 (-) NZ_CAWLDM010000001.1:857698-859246 -
- ACI5KW_RS03165 WP_404305311.1 34041 - 35193 (-) NZ_CAWLDM010000001.1:859343-860495 -
- ACI5KW_RS03170 WP_404305313.1 35244 - 37401 (-) NZ_CAWLDM010000001.1:860546-862703 -
- ACI5KW_RS03175 WP_404305315.1 38093 - 40103 (+) NZ_CAWLDM010000001.1:863395-865405 2.7.13.3
- ACI5KW_RS03180 WP_404305317.1 40113 - 40806 (+) NZ_CAWLDM010000001.1:865415-866108 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 4 (-) CDS No
- 1 - 1263 (-) TC: gnl|TC-DB|O34691|2.A.1.82.4 Yes
- 1470 - 2390 (+) TF: DBD-Pfam|HTH_1,DBD-SUPERFAMILY|0040266 Yes
- 2581 - 5292 (-) other Yes
- 5323 - 6933 (-) other Yes
- 8211 - 9656 (-) other Yes
- 9725 - 11083 (-) other Yes
- 11358 - 12836 (-) other Yes
- 12955 - 14469 (-) other Yes
- 14542 - 15891 (-) other Yes
- 16254 - 17873 (-) other Yes
- 18240 - 20093 (-) CAZyme: GH29 Yes
- 20252 - 20431 (-) other Yes
- 20449 - 21828 (-) other Yes
- 22088 - 24484 (-) other Yes
- 24563 - 25834 (-) other Yes
- 25990 - 27501 (-) CAZyme: GH29 Yes
- 27992 - 28153 (-) other Yes
- 28234 - 29484 (-) STP: STP|SBP_bac_10 Yes
- 29580 - 31316 (-) STP: STP|FecR Yes
- 31317 - 31844 (-) STP: STP|Sigma70_r2,STP|Sigma70_r4_2 Yes
- 32397 - 33944 (-) other Yes
- 34042 - 35193 (-) other Yes
- 35245 - 37401 (-) CAZyme: GH141 Yes
- 38094 - 40103 (+) CDS No
- 40114 - 40806 (+) TF: DBD-Pfam|GerE,DBD-Pfam|GerE,DBD-SUPERFAMILY|0041905 No

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PUL ID

PUL0777

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.