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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0147

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

NZ_LT965930.1

Nucelotide position range

17040-67290

Substrate

carrageenan

Loci

PCAR9_RS20140-PCAR9_RS20290

Species

Pseudoalteromonas carrageenovora/227

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- PCAR9_RS20140 WP_104644200.1 0 - 2436 (+) NZ_LT965930.1:17040-19476 -
- PCAR9_RS20145 WP_104644201.1 2651 - 3209 (+) NZ_LT965930.1:19691-20249 -
- PCAR9_RS20150 WP_104644202.1 3456 - 4980 (+) NZ_LT965930.1:20496-22020 -
- PCAR9_RS20155 WP_104644203.1 5049 - 6492 (+) NZ_LT965930.1:22089-23532 -
- PCAR9_RS20160 WP_104644283.1 6517 - 8389 (+) NZ_LT965930.1:23557-25429 -
- PCAR9_RS20165 WP_104644204.1 8483 - 9614 (+) NZ_LT965930.1:25523-26654 -
- PCAR9_RS20170 WP_104644205.1 10188 - 13899 (+) NZ_LT965930.1:27228-30939 -
- PCAR9_RS20175 WP_104644206.1 13961 - 15749 (+) NZ_LT965930.1:31001-32789 -
- PCAR9_RS20180 WP_104644207.1 15851 - 17486 (+) NZ_LT965930.1:32891-34526 -
- PCAR9_RS20185 WP_104644284.1 17646 - 18597 (+) NZ_LT965930.1:34686-35637 -
- PCAR9_RS20190 WP_158657450.1 18734 - 20528 (+) NZ_LT965930.1:35774-37568 -
- PCAR9_RS20195 WP_104644209.1 20606 - 23147 (-) NZ_LT965930.1:37646-40187 -
- PCAR9_RS20200 - 23492 - 25627 (-) NZ_LT965930.1:40532-42667 -
- PCAR9_RS20205 WP_104644210.1 25971 - 27393 (+) NZ_LT965930.1:43011-44433 -
- PCAR9_RS20210 WP_104644211.1 27413 - 28577 (+) NZ_LT965930.1:44453-45617 -
- PCAR9_RS20215 WP_104644212.1 28594 - 29470 (+) NZ_LT965930.1:45634-46510 -
- PCAR9_RS20220 WP_104644213.1 29670 - 31242 (+) NZ_LT965930.1:46710-48282 -
- PCAR9_RS20225 WP_104644214.1 31253 - 32033 (+) NZ_LT965930.1:48293-49073 -
- PCAR9_RS20230 WP_131692548.1 32079 - 33018 (+) NZ_LT965930.1:49119-50058 -
- PCAR9_RS20235 WP_104644216.1 33142 - 34570 (+) NZ_LT965930.1:50182-51610 -
- PCAR9_RS20240 WP_104644217.1 34580 - 35744 (+) NZ_LT965930.1:51620-52784 -
- PCAR9_RS20245 WP_104644218.1 35761 - 36769 (+) NZ_LT965930.1:52801-53809 -
- PCAR9_RS20250 WP_104644219.1 36759 - 37380 (+) NZ_LT965930.1:53799-54420 -
- PCAR9_RS20255 WP_104644220.1 37464 - 38157 (-) NZ_LT965930.1:54504-55197 -
- PCAR9_RS20260 WP_104644221.1 38267 - 39005 (-) NZ_LT965930.1:55307-56045 -
- PCAR9_RS20265 WP_104644222.1 39175 - 42016 (-) NZ_LT965930.1:56215-59056 -
- PCAR9_RS20270 WP_104644223.1 42276 - 43485 (+) NZ_LT965930.1:59316-60525 -
- PCAR9_RS20275 WP_104644224.1 43724 - 44918 (+) NZ_LT965930.1:60764-61958 -
- PCAR9_RS20280 WP_104644225.1 44992 - 45958 (+) NZ_LT965930.1:62032-62998 -
- PCAR9_RS20285 WP_104644285.1 46063 - 46828 (+) NZ_LT965930.1:63103-63868 -
- PCAR9_RS20290 WP_104644226.1 47422 - 50251 (+) NZ_LT965930.1:64462-67291 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 2436 (+) CDS No
- 2652 - 3209 (+) CDS No
- 3457 - 4980 (+) CDS No
- 5050 - 6492 (+) CDS No
- 6518 - 8389 (+) CDS No
- 8484 - 9614 (+) CDS No
- 10189 - 13899 (+) CDS No
- 13962 - 15749 (+) CDS No
- 15852 - 17486 (+) CDS No
- 17647 - 18597 (+) CAZyme: GH16 Yes
- 18735 - 20528 (+) other Yes
- 20607 - 23147 (-) other Yes
- 25972 - 27393 (+) other Yes
- 27414 - 28577 (+) other Yes
- 28595 - 29470 (+) other Yes
- 29671 - 31242 (+) TC: gnl|TC-DB|P96710|2.A.1.1.55 Yes
- 31254 - 32033 (+) other Yes
- 32080 - 33018 (+) other Yes
- 33143 - 34570 (+) other Yes
- 34581 - 35744 (+) other Yes
- 35762 - 36769 (+) other Yes
- 36760 - 37380 (+) other Yes
- 37465 - 38157 (-) TF: DBD-Pfam|GntR,DBD-SUPERFAMILY|0037767 Yes
- 38268 - 39005 (-) TF: DBD-Pfam|GntR,DBD-SUPERFAMILY|0045032 Yes
- 39176 - 42016 (-) TC: gnl|TC-DB|Q9AAZ6|1.B.14.12.2 Yes
- 42277 - 43485 (+) TF: DBD-Pfam|HTH_AraC,DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0036286,DBD-SUPERFAMILY|0035607 Yes
- 43725 - 44918 (+) CAZyme: GH16 Yes
- 44993 - 45958 (+) other Yes
- 46064 - 46828 (+) other Yes
- 47423 - 50251 (+) CAZyme: GH150 Yes

PUL ID

PUL0147

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.