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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0054

PubMed

29795267, Sci Rep. 2018 May 23;8(1):8075. doi: 10.1038/s41598-018-26104-1.

Characterization method

sequence homology analysis

Genomic accession number

CP003873.1

Nucelotide position range

1019219-1032616

Substrate

alginate

Loci

AMBAS45_04385-AMBAS45_04425

Species

Alteromonas macleodii/28108

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- AMBAS45_04385 AFT94355.1 0 - 723 (-) CP003873.1:1019219-1019942 -
- AMBAS45_04390 AFT94356.1 1215 - 4170 (+) CP003873.1:1020434-1023389 -
- AMBAS45_04395 AFT94357.1 4560 - 5439 (+) CP003873.1:1023779-1024658 -
- AMBAS45_04400 AFT94358.1 5491 - 7780 (+) CP003873.1:1024710-1026999 -
- AMBAS45_04405 AFT94359.1 7786 - 9991 (+) CP003873.1:1027005-1029210 -
- AMBAS45_04410 AFT94360.1 10009 - 10354 (+) CP003873.1:1029228-1029573 -
- AMBAS45_04415 AFT94361.1 10356 - 11652 (+) CP003873.1:1029575-1030871 -
- AMBAS45_04420 AFT94362.1 11719 - 12655 (+) CP003873.1:1030938-1031874 -
- AMBAS45_04425 AFT94363.1 12780 - 13398 (+) CP003873.1:1031999-1032617 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 723 (-) CDS No
- 1216 - 4170 (+) CDS No
- 4561 - 5439 (+) CDS No
- 5492 - 7780 (+) CAZyme: PL6|PL6_1 Yes
- 7787 - 9991 (+) CAZyme: PL17_2|PL17 Yes
- 10010 - 10354 (+) STP: STP|AraC_binding Yes
- 10357 - 11652 (+) TC: gnl|TC-DB|Q07YH1|2.A.1.14.25 Yes
- 11720 - 12655 (+) STP: STP|PfkB No
- 12781 - 13398 (+) CDS No

PUL ID

PUL0054

PubMed

29795267, Sci Rep. 2018 May 23;8(1):8075. doi: 10.1038/s41598-018-26104-1.

Title

Ancient acquisition of "alginate utilization loci" by human gut microbiota.

Author

Mathieu S, Touvrey-Loiodice M, Poulet L, Drouillard S, Vincentelli R, Henrissat B, Skjak-Braek G, Helbert W

Abstract

In bacteria from the phylum Bacteroidetes, the genes coding for enzymes involved in polysaccharide degradation are often colocalized and coregulated in so-called "polysaccharide utilization loci" (PULs). PULs dedicated to the degradation of marine polysaccharides (e.g. laminaran, ulvan, alginate and porphyran) have been characterized in marine bacteria. Interestingly, the gut microbiome of Japanese individuals acquired, by lateral transfer from marine bacteria, the genes involved in the breakdown of porphyran, the cell wall polysaccharide of the red seaweed used in maki. Sequence similarity analyses predict that the human gut microbiome also encodes enzymes for the degradation of alginate, the main cell wall polysaccharide of brown algae. We undertook the functional characterization of diverse polysaccharide lyases from family PL17, frequently found in marine bacteria as well as those of human gut bacteria. We demonstrate here that this family is polyspecific. Our phylogenetic analysis of family PL17 reveals that all alginate lyases, which have all the same specificity and mode of action, cluster together in a very distinct subfamily. The alginate lyases found in human gut bacteria group together in a single clade which is rooted deeply in the PL17 tree. These enzymes were found in PULs containing PL6 enzymes, which also clustered together in the phylogenetic tree of PL6. Together, biochemical and bioinformatics analyses suggest that acquisition of this system appears ancient and, because only traces of two successful transfers were detected upon inspection of PL6 and PL17 families, the pace of acquisition of marine polysaccharide degradation system is probably very slow.