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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0235

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

1204786-1228271

Substrate

alginate

Loci

GFO_1145-GFO_1164

Species

Gramella forsetii/411153

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- GFO_1145 CAL66119.1 0 - 1068 (-) CU207366.1:1204786-1205854 4.2.2.-
- GFO_1146 CAL66120.1 1135 - 2101 (-) CU207366.1:1205921-1206887 -
- GFO_1147 CAL66121.1 2262 - 4563 (+) CU207366.1:1207048-1209349 4.2.2.-
- GFO_1148 CAL66122.1 4569 - 5646 (+) CU207366.1:1209355-1210432 4.2.2.-
- GFO_1149 CAL66123.1 5803 - 6013 (+) CU207366.1:1210589-1210799 -
- GFO_1150 CAL66124.1 6095 - 6449 (+) CU207366.1:1210881-1211235 4.2.2.-
- GFO_1151 CAL66125.1 6551 - 8339 (+) CU207366.1:1211337-1213125 4.2.2.-
- GFO_1152 CAL66126.1 8344 - 8689 (+) CU207366.1:1213130-1213475 -
- GFO_1153 CAL66127.1 9055 - 12109 (+) CU207366.1:1213841-1216895 -
- GFO_1154 CAL66128.1 12136 - 13561 (+) CU207366.1:1216922-1218347 -
- GFO_1155 CAL66129.1 13585 - 14539 (+) CU207366.1:1218371-1219325 -
- GFO_1156 CAL66130.1 14538 - 15465 (+) CU207366.1:1219324-1220251 4.2.2.-
- GFO_1157 CAL66131.1 15442 - 16384 (+) CU207366.1:1220228-1221170 4.2.2.-
- GFO_1158 CAL66132.1 16572 - 17283 (+) CU207366.1:1221358-1222069 -
- GFO_1159 CAL66133.1 17484 - 18762 (+) CU207366.1:1222270-1223548 -
- GFO_1160 CAL66134.1 18797 - 19562 (+) CU207366.1:1223583-1224348 1.-.-.-
kdgK GFO_1161 CAL66135.1 19654 - 20674 (+) CU207366.1:1224440-1225460 2.7.1.45
kdgA GFO_1162 CAL66136.1 20681 - 21353 (+) CU207366.1:1225467-1226139 4.1.-.-
fbp GFO_1163 CAL66137.1 21411 - 22410 (+) CU207366.1:1226197-1227196 3.1.3.11
- GFO_1164 CAL66138.1 22460 - 23486 (+) CU207366.1:1227246-1228272 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 1068 (-) CAZyme: PL7|PL7_5 Yes
- 1136 - 2101 (-) other Yes
- 2263 - 4563 (+) CAZyme: PL6_1|PL6 Yes
- 4570 - 5646 (+) CAZyme: PL7|PL7_5 Yes
- 5804 - 6013 (+) other Yes
- 6096 - 6449 (+) other Yes
- 6552 - 8339 (+) CAZyme: PL17|PL17_2 Yes
- 8345 - 8689 (+) STP: STP|AraC_binding Yes
- 9056 - 12109 (+) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 12137 - 13561 (+) other Yes
- 13586 - 14539 (+) other Yes
- 14539 - 15465 (+) CAZyme: PL7 Yes
- 15443 - 16384 (+) CAZyme: PL7 Yes
- 16573 - 17283 (+) TF: DBD-Pfam|GntR,DBD-SUPERFAMILY|0039384 Yes
- 17485 - 18762 (+) TC: gnl|TC-DB|Q07YH1|2.A.1.14.25 Yes
- 18798 - 19562 (+) CDS No
kdgK 19655 - 20674 (+) STP: STP|PfkB No
kdgA 20682 - 21353 (+) CDS No
fbp 21412 - 22410 (+) CDS No
- 22461 - 23486 (+) TF: DBD-Pfam|LacI,DBD-SUPERFAMILY|0036955 No

PUL ID

PUL0235

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.