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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0148

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

3634325-3657429

Substrate

carrageenan

Loci

ZOBELLIA_3145-ZOBELLIA_3159

Species

Zobellia galactanivorans/63186

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- ZOBELLIA_3145 CAZ97284.1 0 - 1536 (-) FP476056.1:3634325-3635861 3.1.6.-
idsA3 ZOBELLIA_3146 CAZ97285.1 1535 - 3170 (-) FP476056.1:3635860-3637495 3.1.6.13
- ZOBELLIA_3147 CAZ97286.1 3211 - 5257 (-) FP476056.1:3637536-3639582 -
- ZOBELLIA_3148 CAZ97287.1 5438 - 7409 (-) FP476056.1:3639763-3641734 -
- ZOBELLIA_3149 CAZ97288.1 7445 - 9026 (-) FP476056.1:3641770-3643351 -
- ZOBELLIA_3150 CAZ97289.1 9065 - 11150 (-) FP476056.1:3643390-3645475 -
- ZOBELLIA_3151 CAZ97290.1 11465 - 13256 (-) FP476056.1:3645790-3647581 3.1.6.-
- ZOBELLIA_3152 CAZ97291.1 13297 - 15379 (-) FP476056.1:3647622-3649704 -
dgoA ZOBELLIA_3153 CAZ97292.1 15440 - 16088 (-) FP476056.1:3649765-3650413 4.1.2.21
dgoK ZOBELLIA_3154 CAZ97293.1 16077 - 17031 (-) FP476056.1:3650402-3651356 2.7.1.58
aldA ZOBELLIA_3155 CAZ97294.1 17027 - 18479 (-) FP476056.1:3651352-3652804 1.2.1.22
dgoD ZOBELLIA_3156 CAZ97295.1 18453 - 19620 (-) FP476056.1:3652778-3653945 4.2.1.6
rhaT1 ZOBELLIA_3157 CAZ97296.1 19655 - 20663 (-) FP476056.1:3653980-3654988 -
gntT3 ZOBELLIA_3158 CAZ97297.1 20798 - 22100 (-) FP476056.1:3655123-3656425 -
- ZOBELLIA_3159 CAZ97298.1 22220 - 23105 (-) FP476056.1:3656545-3657430 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 1536 (-) CDS No
idsA3 1536 - 3170 (-) CDS No
- 3212 - 5257 (-) CAZyme: GH127 Yes
- 5439 - 7409 (-) CAZyme: GH127 Yes
- 7446 - 9026 (-) TC: gnl|TC-DB|P46333|2.A.1.1.106 Yes
- 9066 - 11150 (-) CAZyme: GH127 Yes
- 11466 - 13256 (-) other Yes
- 13298 - 15379 (-) CAZyme: GH129 Yes
dgoA 15441 - 16088 (-) CDS No
dgoK 16078 - 17031 (-) CDS No
aldA 17028 - 18479 (-) CDS No
dgoD 18454 - 19620 (-) CDS No
rhaT1 19656 - 20663 (-) CDS No
gntT3 20799 - 22100 (-) CDS No
- 22221 - 23105 (-) TF: DBD-Pfam|HTH_AraC,DBD-Pfam|HTH_AraC,DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0036286,DBD-SUPERFAMILY|0035607,DBD-SUPERFAMILY|0035607 No

PUL ID

PUL0148

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.