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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0236

PubMed

24522261, ISME J. 2014 Jul;8(7):1492-502. doi: 10.1038/ismej.2014.4. Epub 2014 Feb 13.

Characterization method

proteome fractionation,mass spectrometry,target decoy database analysis

Genomic accession number

CU207366.1

Nucelotide position range

2258233-2278112

Substrate

alpha-glucan

Loci

GFO_2129-GFO_2141

Species

Gramella forsetii/411153

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- GFO_2129 CAL67094.1 0 - 861 (-) CU207366.1:2258233-2259094 -
gapA GFO_2130 CAL67095.1 939 - 1938 (-) CU207366.1:2259172-2260171 1.2.1.12
pfkA GFO_2131 CAL67096.1 1954 - 2941 (-) CU207366.1:2260187-2261174 2.7.1.11
- GFO_2132 CAL67097.1 3066 - 4512 (-) CU207366.1:2261299-2262745 3.2.1.-
- GFO_2133 CAL67098.1 4541 - 6401 (-) CU207366.1:2262774-2264634 3.2.1.-
- GFO_2134 CAL67099.1 6742 - 9049 (-) CU207366.1:2264975-2267282 3.2.1.-
pgmB GFO_2135 CAL67100.1 9048 - 9729 (-) CU207366.1:2267281-2267962 5.4.2.6
- GFO_2136 CAL67101.1 9715 - 11149 (-) CU207366.1:2267948-2269382 -
- GFO_2137 CAL67102.1 11278 - 12307 (-) CU207366.1:2269511-2270540 -
- GFO_2138 CAL67103.1 12530 - 15464 (+) CU207366.1:2270763-2273697 -
- GFO_2139 CAL67104.1 15482 - 17084 (+) CU207366.1:2273715-2275317 -
- GFO_2140 CAL67105.1 17100 - 18258 (+) CU207366.1:2275333-2276491 -
- GFO_2141 CAL67106.1 18425 - 19880 (+) CU207366.1:2276658-2278113 3.2.1.1

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 861 (-) CDS No
gapA 940 - 1938 (-) CDS No
pfkA 1955 - 2941 (-) CDS No
- 3067 - 4512 (-) CAZyme: GH13 Yes
- 4542 - 6401 (-) CAZyme: GH13|GH13_36 Yes
- 6743 - 9049 (-) CAZyme: GH65 Yes
pgmB 9049 - 9729 (-) other Yes
- 9716 - 11149 (-) TC: gnl|TC-DB|Q8EEC4|2.A.2.6.3 Yes
- 11279 - 12307 (-) TF: DBD-Pfam|LacI,DBD-SUPERFAMILY|0036955 Yes
- 12531 - 15464 (+) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 15483 - 17084 (+) other Yes
- 17101 - 18258 (+) other Yes
- 18426 - 19880 (+) CAZyme: GH13_7 Yes

PUL ID

PUL0236

PubMed

24522261, ISME J. 2014 Jul;8(7):1492-502. doi: 10.1038/ismej.2014.4. Epub 2014 Feb 13.

Title

Functional characterization of polysaccharide utilization loci in the marine Bacteroidetes 'Gramella forsetii' KT0803.

Author

Kabisch A, Otto A, Konig S, Becher D, Albrecht D, Schuler M, Teeling H, Amann RI, Schweder T

Abstract

Members of the phylum Bacteroidetes are abundant in many marine ecosystems and are known to have a pivotal role in the mineralization of complex organic substrates such as polysaccharides and proteins. We studied the decomposition of the algal glycans laminarin and alginate by 'Gramella forsetii' KT0803, a bacteroidetal isolate from North Sea surface waters. A combined application of isotope labeling, subcellular protein fractionation and quantitative proteomics revealed two large polysaccharide utilization loci (PULs) that were specifically induced, one by alginate and the other by laminarin. These regulons comprised genes of surface-exposed proteins such as oligomer transporters, substrate-binding proteins, carbohydrate-active enzymes and hypothetical proteins. Besides, several glycan-specific TonB-dependent receptors and SusD-like substrate-binding proteins were expressed also in the absence of polysaccharide substrates, suggesting an anticipatory sensing function. Genes for the utilization of the beta-1,3-glucan laminarin were found to be co-regulated with genes for glucose and alpha-1,4-glucan utilization, which was not the case for the non-glucan alginate. Strong syntenies of the PULs of 'G. forsetii' with similar loci in other Bacteroidetes indicate that the specific response mechanisms of 'G. forsetii' to changes in polysaccharide availability likely apply to other Bacteroidetes. Our results can thus contribute to an improved understanding of the ecological niches of marine Bacteroidetes and their roles in the polysaccharide decomposition part of carbon cycling in marine ecosystems.