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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0151

PubMed

30524390, Front Microbiol. 2018 Nov 22;9:2740. doi: 10.3389/fmicb.2018.02740. eCollection 2018.
32585009, Nucleic Acids Res. 2020 Aug 20;48(14):7786-7800. doi: 10.1093/nar/gkaa533.

Characterization method

sequence homology analysis,Northern Blot,RT-qPCR,electrophoretic mobility shift assay,clone and expression,gene deletion mutant and growth assay

Genomic accession number

FP476056.1

Nucelotide position range

3067454-3083329

Substrate

alginate

Loci

ZOBELLIA_2613-ZOBELLIA_2624

Species

Zobellia galactanivorans/63186

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

pfp ZOBELLIA_2613 CAZ96763.1 0 - 1227 (-) FP476056.1:3067454-3068681 2.7.1.90
kdgK1 ZOBELLIA_2614 CAZ96764.1 1245 - 2286 (-) FP476056.1:3068699-3069740 2.7.1.45
- ZOBELLIA_2615 CAZ96765.1 2340 - 3096 (-) FP476056.1:3069794-3070550 1.-.-.-
- ZOBELLIA_2616 CAZ96766.1 3132 - 4410 (-) FP476056.1:3070586-3071864 -
- ZOBELLIA_2617 CAZ96767.1 4640 - 5369 (-) FP476056.1:3072094-3072823 -
alyA2 ZOBELLIA_2618 CAZ96768.1 5610 - 6534 (-) FP476056.1:3073064-3073988 4.2.2.3
- ZOBELLIA_2619 CAZ96769.1 6542 - 7424 (-) FP476056.1:3073996-3074878 -
- ZOBELLIA_2620 CAZ96770.1 7454 - 8885 (-) FP476056.1:3074908-3076339 -
- ZOBELLIA_2621 CAZ96771.1 8918 - 12044 (-) FP476056.1:3076372-3079498 -
- ZOBELLIA_2622 CAZ96772.1 12502 - 13255 (-) FP476056.1:3079956-3080709 1.-.-.-
kdgF ZOBELLIA_2623 CAZ96773.1 13260 - 13611 (-) FP476056.1:3080714-3081065 -
alyA3 ZOBELLIA_2624 CAZ96774.1 13620 - 15876 (-) FP476056.1:3081074-3083330 4.2.2.3

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

pfp 1 - 1227 (-) CDS No
kdgK1 1246 - 2286 (-) STP: STP|PfkB No
- 2341 - 3096 (-) CDS No
- 3133 - 4410 (-) TC: gnl|TC-DB|Q07YH1|2.A.1.14.25 Yes
- 4641 - 5369 (-) TF: DBD-Pfam|GntR,DBD-SUPERFAMILY|0039384 Yes
alyA2 5611 - 6534 (-) CAZyme: PL7 Yes
- 6543 - 7424 (-) other Yes
- 7455 - 8885 (-) other Yes
- 8919 - 12044 (-) TC: gnl|TC-DB|Q93TH9|1.B.14.6.2 Yes
- 12503 - 13255 (-) other Yes
kdgF 13261 - 13611 (-) STP: STP|AraC_binding Yes
alyA3 13621 - 15876 (-) CAZyme: PL17_2|PL17 Yes

PUL ID

PUL0151

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.

PubMed

32585009, Nucleic Acids Res. 2020 Aug 20;48(14):7786-7800. doi: 10.1093/nar/gkaa533.

Title

Regulation of alginate catabolism involves a GntR family repressor in the marine flavobacterium Zobellia galactanivorans DsijT.

Author

Dudek M, Dieudonne A, Jouanneau D, Rochat T, Michel G, Sarels B, Thomas F

Abstract

Marine flavobacteria possess dedicated Polysaccharide Utilization Loci (PULs) enabling efficient degradation of a variety of algal polysaccharides. The expression of these PULs is tightly controlled by the presence of the substrate, yet details on the regulatory mechanisms are still lacking. The marine flavobacterium Zobellia galactanivorans DsijT digests many algal polysaccharides, including alginate from brown algae. Its complex Alginate Utilization System (AUS) comprises a PUL and several other loci. Here, we showed that the expression of the AUS is strongly and rapidly (<30 min) induced upon addition of alginate, leading to biphasic substrate utilization. Polymeric alginate is first degraded into smaller oligosaccharides that accumulate in the extracellular medium before being assimilated. We found that AusR, a GntR family protein encoded within the PUL, regulates alginate catabolism by repressing the transcription of most AUS genes. Based on our genetic, genomic, transcriptomic and biochemical results, we propose the first model of regulation for a PUL in marine bacteria. AusR binds to promoters of AUS genes via single, double or triple copies of operator. Upon addition of alginate, secreted enzymes expressed at a basal level catalyze the initial breakdown of the polymer. Metabolic intermediates produced during degradation act as effectors of AusR and inhibit the formation of AusR/DNA complexes, thus lifting transcriptional repression.