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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0149

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

FP476056.1

Nucelotide position range

2560055-2579666

Substrate

carrageenan

Loci

ZOBELLIA_2194-ZOBELLIA_2203

Species

Zobellia galactanivorans/63186

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- ZOBELLIA_2194 CAZ96350.1 0 - 1485 (-) FP476056.1:2560055-2561540 3.1.6.-
- ZOBELLIA_2195 CAZ96351.1 1772 - 4502 (+) FP476056.1:2561827-2564557 -
sgsA3 ZOBELLIA_2196 CAZ96352.1 4536 - 6027 (-) FP476056.1:2564591-2566082 3.10.1.1
- ZOBELLIA_2197 CAZ96353.1 6046 - 7387 (-) FP476056.1:2566101-2567442 3.1.6.-
- ZOBELLIA_2198 CAZ96354.1 7403 - 9530 (-) FP476056.1:2567458-2569585 3.1.6.-
- ZOBELLIA_2199 CAZ96355.1 9561 - 11454 (-) FP476056.1:2569616-2571509 3.2.1.22
- ZOBELLIA_2200 CAZ96356.1 11450 - 13256 (-) FP476056.1:2571505-2573311 3.2.1.22
sgsA4 ZOBELLIA_2201 CAZ96357.1 13283 - 14783 (-) FP476056.1:2573338-2574838 3.10.1.1
- ZOBELLIA_2202 CAZ96358.1 14937 - 16476 (-) FP476056.1:2574992-2576531 -
- ZOBELLIA_2203 CAZ96359.1 16492 - 19612 (-) FP476056.1:2576547-2579667 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 1485 (-) CDS No
- 1773 - 4502 (+) CDS No
sgsA3 4537 - 6027 (-) CDS No
- 6047 - 7387 (-) CDS No
- 7404 - 9530 (-) CDS No
- 9562 - 11454 (-) CAZyme: GH110 Yes
- 11451 - 13256 (-) CAZyme: GH110 Yes
sgsA4 13284 - 14783 (-) other Yes
- 14938 - 16476 (-) TC: gnl|TC-DB|C6Y217|8.A.46.1.3 Yes
- 16493 - 19612 (-) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes

PUL ID

PUL0149

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.