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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0220

PubMed

25478683, ISME J. 2015 Jun;9(6):1410-22. doi: 10.1038/ismej.2014.225. Epub 2014 Dec 5.

Characterization method

mass spectrometry,target decoy database analysis

Genomic accession number

JPDI01000001.1

Nucelotide position range

2291648-2313366

Substrate

laminarin

Loci

PHEL49_2075-PHEL49_2085

Species

Polaribacter sp. Hel1_33_49/1336803

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- PHEL49_2075 KGL61177.1 0 - 1512 (-) JPDI01000001.1:2291648-2293160 -
- PHEL49_2076 KGL61178.1 1542 - 2964 (-) JPDI01000001.1:2293190-2294612 3.2.1.45
- PHEL49_2077 KGL61179.1 3049 - 4333 (-) JPDI01000001.1:2294697-2295981 -
- PHEL49_2078 KGL61180.1 4379 - 6113 (-) JPDI01000001.1:2296027-2297761 3.2.1.21
- PHEL49_2079 KGL61181.1 6187 - 9643 (-) JPDI01000001.1:2297835-2301291 -
- PHEL49_2080 KGL61182.1 9903 - 10740 (-) JPDI01000001.1:2301551-2302388 3.2.1.6
- PHEL49_2081 KGL61183.1 10763 - 12185 (-) JPDI01000001.1:2302411-2303833 -
- PHEL49_2082 KGL61184.1 12192 - 15339 (-) JPDI01000001.1:2303840-2306987 3.2.1.-
- PHEL49_2083 KGL61185.1 15731 - 17120 (-) JPDI01000001.1:2307379-2308768 -
- PHEL49_2084 KGL61186.1 17132 - 18689 (-) JPDI01000001.1:2308780-2310337 -
- PHEL49_2085 KGL61187.1 18695 - 21719 (-) JPDI01000001.1:2310343-2313367 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 1512 (-) CDS No
- 1543 - 2964 (-) CAZyme: GH30|GH30_1 Yes
- 3050 - 4333 (-) CAZyme: GH17 Yes
- 4380 - 6113 (-) CAZyme: GH3 Yes
- 6188 - 9643 (-) CAZyme: GH149 Yes
- 9904 - 10740 (-) CAZyme: GH16 Yes
- 10764 - 12185 (-) other Yes
- 12193 - 15339 (-) other Yes
- 15732 - 17120 (-) other Yes
- 17133 - 18689 (-) TC: gnl|TC-DB|F3PRQ4|8.A.46.3.2 Yes
- 18696 - 21719 (-) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes

PUL ID

PUL0220

PubMed

25478683, ISME J. 2015 Jun;9(6):1410-22. doi: 10.1038/ismej.2014.225. Epub 2014 Dec 5.

Title

Niches of two polysaccharide-degrading Polaribacter isolates from the North Sea during a spring diatom bloom.

Author

Xing P, Hahnke RL, Unfried F, Markert S, Huang S, Barbeyron T, Harder J, Becher D, Schweder T, Glockner FO, Amann RI, Teeling H

Abstract

Members of the flavobacterial genus Polaribacter thrive in response to North Sea spring phytoplankton blooms. We analyzed two respective Polaribacter species by whole genome sequencing, comparative genomics, substrate tests and proteomics. Both can degrade algal polysaccharides but occupy distinct niches. The liquid culture isolate Polaribacter sp. strain Hel1_33_49 has a 3.0-Mbp genome with an overall peptidase:CAZyme ratio of 1.37, four putative polysaccharide utilization loci (PULs) and features proteorhodopsin, whereas the agar plate isolate Polaribacter sp. strain Hel1_85 has a 3.9-Mbp genome with an even peptidase:CAZyme ratio, eight PULs, a mannitol dehydrogenase for decomposing algal mannitol-capped polysaccharides but no proteorhodopsin. Unlike other sequenced Polaribacter species, both isolates have larger sulfatase-rich PULs, supporting earlier assumptions that Polaribacter take part in the decomposition of sulfated polysaccharides. Both strains grow on algal laminarin and the sulfated polysaccharide chondroitin sulfate. For strain Hel1_33_49, we identified by proteomics (i) a laminarin-induced PUL, (ii) chondroitin sulfate-induced CAZymes and (iii) a chondroitin-induced operon that likely enables chondroitin sulfate recognition. These and other data suggest that strain Hel1_33_49 is a planktonic flavobacterium feeding on proteins and a small subset of algal polysaccharides, while the more versatile strain Hel1_85 can decompose a broader spectrum of polysaccharides and likely associates with algae.