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PlantCAZyme
Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0146

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

1036849-1074395

Substrate

carrageenan

Loci

PATL_RS04485-PATL_RS04595

Species

Pseudoalteromonas atlantica/288

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- Patl_0879 ABG39405.1 0 - 2625 (+) CP000388.1:1036849-1039474 -
- Patl_0880 ABG39406.1 2826 - 3828 (+) CP000388.1:1039675-1040677 -
- Patl_0881 ABG39407.1 3850 - 5383 (+) CP000388.1:1040699-1042232 -
- Patl_0882 ABG39408.1 5852 - 6314 (+) CP000388.1:1042701-1043163 -
- Patl_0883 ABG39409.1 6618 - 6882 (+) CP000388.1:1043467-1043731 -
- Patl_0884 ABG39410.1 7011 - 7791 (-) CP000388.1:1043860-1044640 -
- Patl_0885 ABG39411.1 7983 - 10410 (-) CP000388.1:1044832-1047259 -
- Patl_0886 ABG39412.1 10509 - 12258 (-) CP000388.1:1047358-1049107 -
- Patl_0887 ABG39413.1 12364 - 16075 (-) CP000388.1:1049213-1052924 -
- Patl_0888 ABG39414.1 17250 - 18804 (+) CP000388.1:1054099-1055653 -
- Patl_0889 ABG39415.1 18879 - 20382 (+) CP000388.1:1055728-1057231 -
- Patl_0890 ABG39416.1 20529 - 22470 (+) CP000388.1:1057378-1059319 -
- Patl_0891 ABG39417.1 22635 - 24333 (+) CP000388.1:1059484-1061182 -
- Patl_0892 ABG39418.1 24329 - 26255 (+) CP000388.1:1061178-1063104 -
- Patl_0893 ABG39419.1 26254 - 27520 (+) CP000388.1:1063103-1064369 -
- Patl_0894 ABG39420.1 27926 - 28688 (+) CP000388.1:1064775-1065537 -
- Patl_0895 ABG39421.1 28741 - 30157 (+) CP000388.1:1065590-1067006 -
- Patl_0896 ABG39422.1 30571 - 32014 (+) CP000388.1:1067420-1068863 1.2.1.16
- Patl_0897 ABG39423.1 32013 - 33177 (+) CP000388.1:1068862-1070026 -
- Patl_0898 ABG39424.1 33182 - 34244 (+) CP000388.1:1070031-1071093 2.7.1.58
- Patl_0899 ABG39425.1 34310 - 34961 (+) CP000388.1:1071159-1071810 4.1.2.21
- Patl_0900 ABG39426.1 35091 - 36648 (+) CP000388.1:1071940-1073497 -
- Patl_0901 ABG39427.1 36806 - 37547 (+) CP000388.1:1073655-1074396 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 2625 (+) CDS No
- 2827 - 3828 (+) CAZyme: GH16 Yes
- 3851 - 5383 (+) other Yes
- 5853 - 6314 (+) other Yes
- 6619 - 6882 (+) other Yes
- 7012 - 7791 (-) other Yes
- 7984 - 10410 (-) other Yes
- 10510 - 12258 (-) other Yes
- 12365 - 16075 (-) TC: gnl|TC-DB|Q9A608|1.B.14.12.1 Yes
- 17251 - 18804 (+) CDS No
- 18880 - 20382 (+) CDS No
- 20530 - 22470 (+) CDS No
- 22636 - 24333 (+) CDS No
- 24330 - 26255 (+) CDS No
- 26255 - 27520 (+) CDS No
- 27927 - 28688 (+) TF: DBD-Pfam|GntR,DBD-SUPERFAMILY|0037767 No
- 28742 - 30157 (+) CDS No
- 30572 - 32014 (+) CDS No
- 32014 - 33177 (+) CDS No
- 33183 - 34244 (+) CDS No
- 34311 - 34961 (+) CDS No
- 35092 - 36648 (+) TC: gnl|TC-DB|P96710|2.A.1.1.55 No
- 36807 - 37547 (+) TF: DBD-Pfam|GntR,DBD-SUPERFAMILY|0045032 No

PUL ID

PUL0146

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.