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PlantCAZyme
Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0152

PubMed

30524390, Front Microbiol. 2018 Nov 22;9:2740. doi: 10.3389/fmicb.2018.02740. eCollection 2018.

Characterization method

sequence homology analysis

Genomic accession number

CP000388.1

Nucelotide position range

4406812-4416529

Substrate

alginate

Loci

PATL_RS18725-PATL_RS18760

Species

Pseudoalteromonas atlantica/288

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- Patl_3654 ABG42156.1 0 - 1386 (-) CP000388.1:4406812-4408198 -
- Patl_3655 ABG42157.1 1398 - 1680 (-) CP000388.1:4408210-4408492 -
- Patl_3656 ABG42158.1 1679 - 2849 (-) CP000388.1:4408491-4409661 -
- Patl_3657 ABG42159.1 3004 - 3928 (-) CP000388.1:4409816-4410740 2.7.1.45
- Patl_3658 ABG42160.1 3992 - 5291 (-) CP000388.1:4410804-4412103 -
- Patl_3659 ABG42161.1 5348 - 7613 (-) CP000388.1:4412160-4414425 4.2.2.3
- Patl_3660 ABG42162.1 8136 - 8874 (+) CP000388.1:4414948-4415686 -
- Patl_3661 ABG42163.1 8971 - 9718 (-) CP000388.1:4415783-4416530 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 1386 (-) TC: gnl|TC-DB|P0C188|3.D.2.2.1 Yes
- 1399 - 1680 (-) TC: gnl|TC-DB|P0C187|3.D.2.2.1 Yes
- 1680 - 2849 (-) TC: gnl|TC-DB|P0C186|3.D.2.2.1 Yes
- 3005 - 3928 (-) STP: STP|PfkB Yes
- 3993 - 5291 (-) TC: gnl|TC-DB|Q07YH1|2.A.1.14.25 Yes
- 5349 - 7613 (-) CAZyme: PL6|PL6_1 Yes
- 8137 - 8874 (+) TF: DBD-Pfam|GntR,DBD-SUPERFAMILY|0039384 No
- 8972 - 9718 (-) CDS No

PUL ID

PUL0152

PubMed

30524390, Front Microbiol. 2018 Nov 22;9:2740. doi: 10.3389/fmicb.2018.02740. eCollection 2018.

Title

Evolutionary Evidence of Algal Polysaccharide Degradation Acquisition by Pseudoalteromonas carrageenovora 9(T) to Adapt to Macroalgal Niches.

Author

Gobet A, Barbeyron T, Matard-Mann M, Magdelenat G, Vallenet D, Duchaud E, Michel G

Abstract

About half of seaweed biomass is composed of polysaccharides. Most of these complex polymers have a marked polyanionic character. For instance, the red algal cell wall is mainly composed of sulfated galactans, agars and carrageenans, while brown algae contain alginate and fucose-containing sulfated polysaccharides (FCSP) as cell wall polysaccharides. Some marine heterotrophic bacteria have developed abilities to grow on such macroalgal polysaccharides. This is the case of Pseudoalteromonas carrageenovora 9(T) (ATCC 43555(T)), a marine gammaproteobacterium isolated in 1955 and which was an early model organism for studying carrageenan catabolism. We present here the genomic analysis of P. carrageenovora. Its genome is composed of two chromosomes and of a large plasmid encompassing 109 protein-coding genes. P. carrageenovora possesses a diverse repertoire of carbohydrate-active enzymes (CAZymes), notably specific for the degradation of macroalgal polysaccharides (laminarin, alginate, FCSP, carrageenans). We confirm these predicted capacities by screening the growth of P. carrageenovora with a large collection of carbohydrates. Most of these CAZyme genes constitute clusters located either in the large chromosome or in the small one. Unexpectedly, all the carrageenan catabolism-related genes are found in the plasmid, suggesting that P. carrageenovora acquired its hallmark capacity for carrageenan degradation by horizontal gene transfer (HGT). Whereas P. carrageenovora is able to use lambda-carrageenan as a sole carbon source, genomic and physiological analyses demonstrate that its catabolic pathway for kappa- and iota-carrageenan is incomplete. This is due to the absence of the recently discovered 3,6-anhydro-D-galactosidase genes (GH127 and GH129 families). A genomic comparison with 52 Pseudoalteromonas strains confirms that carrageenan catabolism has been recently acquired only in a few species. Even though the loci for cellulose biosynthesis and alginate utilization are located on the chromosomes, they were also horizontally acquired. However, these HGTs occurred earlier in the evolution of the Pseudoalteromonas genus, the cellulose- and alginate-related loci being essentially present in one large, late-diverging clade (LDC). Altogether, the capacities to degrade cell wall polysaccharides from macroalgae are not ancestral in the Pseudoalteromonas genus. Such catabolism in P. carrageenovora resulted from a succession of HGTs, likely allowing an adaptation to the life on the macroalgal surface.