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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0053

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

AM743169.1

Nucelotide position range

2619918-2632750

Substrate

alginate

Loci

Smlt2598-Smlt2605

Species

Stenotrophomonas maltophilia/40324

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- Smlt2598 CAQ46074.1 0 - 1767 (-) AM743169.1:2619918-2621685 -
- Smlt2599 CAQ46075.1 1884 - 2628 (-) AM743169.1:2621802-2622546 -
- Smlt2600 CAQ46076.1 2730 - 5550 (-) AM743169.1:2622648-2625468 -
- Smlt2601 CAQ46077.1 5935 - 7303 (+) AM743169.1:2625853-2627221 -
- Smlt2602 CAQ46078.1 7299 - 9528 (+) AM743169.1:2627217-2629446 -
- Smlt2603 CAQ46079.1 9524 - 10829 (+) AM743169.1:2629442-2630747 -
- Smlt2604 CAQ46080.1 10871 - 11624 (+) AM743169.1:2630789-2631542 -
- Smlt2605 CAQ46081.1 11645 - 12833 (+) AM743169.1:2631563-2632751 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 1767 (-) CDS No
- 1885 - 2628 (-) TF: DBD-Pfam|GntR,DBD-SUPERFAMILY|0037767 No
- 2731 - 5550 (-) CDS No
- 5936 - 7303 (+) CAZyme: PL6_1|PL6 Yes
- 7300 - 9528 (+) CAZyme: PL17|PL17_2 Yes
- 9525 - 10829 (+) TC: gnl|TC-DB|Q07YH1|2.A.1.14.25 Yes
- 10872 - 11624 (+) CDS No
- 11646 - 12833 (+) CDS No

PUL ID

PUL0053

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.