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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0199

PubMed

26458373, Mar Biotechnol (NY). 2016 Feb;18(1):15-23. doi: 10.1007/s10126-015-9667-3. Epub 2015 Oct 12.

Characterization method

enzyme activity assay,liquid chromatography and mass spectrometry

Genomic accession number

NC_007912.1

Nucelotide position range

4176251-4200317

Substrate

alginate

Loci

SDE_RS17125-SDE_RS17210

Species

Saccharophagus degradans/86304

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- SDE_RS17125 WP_011469743.1 0 - 1659 (+) NC_007912.1:4176251-4177910 -
- SDE_RS17130 WP_011469744.1 2027 - 3464 (+) NC_007912.1:4178278-4179715 -
- SDE_RS17135 WP_041325944.1 3432 - 3642 (+) NC_007912.1:4179683-4179893 -
- SDE_RS17140 WP_011469745.1 3768 - 5346 (-) NC_007912.1:4180019-4181597 4.2.2.3
- SDE_RS17145 WP_011469746.1 5464 - 8143 (-) NC_007912.1:4181715-4184394 4.2.2.3
- SDE_RS17150 WP_011469747.1 8248 - 9100 (-) NC_007912.1:4184499-4185351 -
- SDE_RS17155 WP_041325945.1 9533 - 10283 (-) NC_007912.1:4185784-4186534 5.3.1.1
- SDE_RS17160 WP_011469749.1 10307 - 12056 (-) NC_007912.1:4186558-4188307 -
fbaA SDE_RS17165 WP_011469750.1 12124 - 13222 (-) NC_007912.1:4188375-4189473 4.1.2.13
- SDE_RS17170 WP_143710915.1 13435 - 14380 (-) NC_007912.1:4189686-4190631 -
- SDE_RS17175 WP_011469752.1 14504 - 15257 (-) NC_007912.1:4190755-4191508 1.1.1.47
- SDE_RS17180 WP_011469753.1 15320 - 16595 (-) NC_007912.1:4191571-4192846 -
- SDE_RS17185 WP_011469754.1 16606 - 16951 (-) NC_007912.1:4192857-4193202 -
- SDE_RS17190 WP_011469755.1 17075 - 19286 (-) NC_007912.1:4193326-4195537 -
- SDE_RS17195 WP_011469756.1 19302 - 21585 (-) NC_007912.1:4195553-4197836 4.2.2.3
- SDE_RS17205 WP_011469757.1 22110 - 23142 (+) NC_007912.1:4198361-4199393 -
- SDE_RS17210 WP_011469758.1 23296 - 24067 (+) NC_007912.1:4199547-4200318 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 1659 (+) CAZyme: CBM16|PL18|CBM32 Yes
- 2028 - 3464 (+) other Yes
- 3433 - 3642 (+) other Yes
- 3769 - 5346 (-) CAZyme: PL6_1|PL6 Yes
- 5465 - 8143 (-) CAZyme: PL6_1|PL6 Yes
- 8249 - 9100 (-) STP: STP|SBP_bac_3 Yes
- 9534 - 10283 (-) other Yes
- 10308 - 12056 (-) other Yes
fbaA 12125 - 13222 (-) other Yes
- 13436 - 14380 (-) STP: STP|PfkB Yes
- 14505 - 15257 (-) other Yes
- 15321 - 16595 (-) TC: gnl|TC-DB|Q07YH1|2.A.1.14.25 Yes
- 16607 - 16951 (-) STP: STP|AraC_binding Yes
- 17076 - 19286 (-) CAZyme: PL17|PL17_2 Yes
- 19303 - 21585 (-) CAZyme: PL6_1|PL6 Yes
- 22111 - 23142 (+) CAZyme: PL7_5 Yes
- 23297 - 24067 (+) TF: DBD-Pfam|GntR,DBD-SUPERFAMILY|0039384 No

PUL ID

PUL0199

PubMed

26458373, Mar Biotechnol (NY). 2016 Feb;18(1):15-23. doi: 10.1007/s10126-015-9667-3. Epub 2015 Oct 12.

Title

Putative Alginate Assimilation Process of the Marine Bacterium Saccharophagus degradans 2-40 Based on Quantitative Proteomic Analysis.

Author

Takagi T, Morisaka H, Aburaya S, Tatsukami Y, Kuroda K, Ueda M

Abstract

Quantitative proteomic analysis was conducted to assess the assimilation processes of Saccharophagus degradans cultured with glucose, pectin, and alginate as carbon sources. A liquid chromatography-tandem mass spectrometry approach was used, employing our unique, long monolithic silica capillary column. In an attempt to select candidate proteins that correlated to alginate assimilation, the production of 23 alginate-specific proteins was identified by statistical analyses of the quantitative proteomic data. Based on the analysis, we propose that S. degradans has an alginate-specific gene cluster for efficient alginate utilization. The alginate-specific proteins of S. degradans were comprised of alginate lyases, enzymes related to carbohydrate metabolism, membrane transporters, and transcription factors. Among them, the short-chain dehydrogenase/reductase Sde_3281 annotated in the alginate-specific cluster showed 4-deoxy-L-erythro-5-hexoseulose uronic acid reductase (DehR) activity. Furthermore, we found two different genes (Sde_3280 and Sde_0939) encoding 2-keto-3-deoxy-D-gluconic acid (KDG) kinases (KdgK) that metabolize the KDG derived from alginate and pectin in S. degradans. S. degradans used Sde_3280 to phosphorylate the KDG derived from alginate and Sde_0939 to phosphorylate the KDG derived from pectin. The distinct selection of KdgKs provides an important clue toward the elucidation of how S. degradans recognizes and processes polysaccharides.