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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0703

PubMed

37002465, Mar Biotechnol (NY). 2023 Apr;25(2):314-327. doi: 10.1007/s10126-023-10206-7. Epub 2023 Apr 1.

Characterization method

enzyme activity assay,recombinant protein expression,thin-layer chromatography

Genomic accession number

NZ_CP098511.1

Nucelotide position range

2147167-2215680

Substrate

agarose

Loci

NBT05_RS08975-NBT05_RS09160

Species

Aquimarina sp. ERC-38/2949996

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- NBT05_RS08975 WP_265773150.1 0 - 2229 (+) NZ_CP098511.1:2147167-2149396 -
- NBT05_RS08980 WP_265773151.1 3067 - 5785 (-) NZ_CP098511.1:2150234-2152952 -
- NBT05_RS08985 WP_265773152.1 6186 - 9291 (-) NZ_CP098511.1:2153353-2156458 -
- NBT05_RS08990 WP_265773153.1 10521 - 12396 (-) NZ_CP098511.1:2157688-2159563 -
- NBT05_RS08995 WP_265773154.1 12685 - 13813 (-) NZ_CP098511.1:2159852-2160980 -
- NBT05_RS09000 WP_265773155.1 14799 - 16353 (-) NZ_CP098511.1:2161966-2163520 -
- NBT05_RS09005 WP_265773156.1 16366 - 18115 (-) NZ_CP098511.1:2163533-2165282 -
- NBT05_RS09010 WP_265773157.1 18137 - 21272 (-) NZ_CP098511.1:2165304-2168439 -
- NBT05_RS09015 WP_265773158.1 22199 - 22439 (+) NZ_CP098511.1:2169366-2169606 -
- NBT05_RS09020 WP_265773159.1 23397 - 24045 (+) NZ_CP098511.1:2170564-2171212 -
- NBT05_RS09025 WP_265773160.1 24167 - 26816 (+) NZ_CP098511.1:2171334-2173983 -
- NBT05_RS09030 WP_265773161.1 27367 - 28630 (+) NZ_CP098511.1:2174534-2175797 -
- NBT05_RS18390 WP_322874204.1 28927 - 32389 (-) NZ_CP098511.1:2176094-2179556 -
- NBT05_RS09050 WP_265773162.1 33686 - 36926 (+) NZ_CP098511.1:2180853-2184093 -
- NBT05_RS09055 WP_265773163.1 36933 - 38439 (+) NZ_CP098511.1:2184100-2185606 -
- NBT05_RS09060 WP_265773164.1 38459 - 39575 (+) NZ_CP098511.1:2185626-2186742 -
- NBT05_RS09065 WP_265773165.1 39647 - 41009 (+) NZ_CP098511.1:2186814-2188176 -
- NBT05_RS09070 WP_265773166.1 41175 - 43470 (-) NZ_CP098511.1:2188342-2190637 -
- NBT05_RS09075 WP_265773167.1 43883 - 44765 (+) NZ_CP098511.1:2191050-2191932 -
- NBT05_RS09080 WP_265773168.1 44804 - 46061 (-) NZ_CP098511.1:2191971-2193228 1.-.-.-
- NBT05_RS09085 WP_265773169.1 46111 - 46420 (-) NZ_CP098511.1:2193278-2193587 -
- NBT05_RS09090 WP_265773170.1 46480 - 47638 (-) NZ_CP098511.1:2193647-2194805 -
- NBT05_RS09095 WP_265773171.1 47725 - 48544 (-) NZ_CP098511.1:2194892-2195711 3.-.-.-
- NBT05_RS09100 WP_265773172.1 48628 - 49753 (-) NZ_CP098511.1:2195795-2196920 -
- NBT05_RS09105 WP_265773173.1 49922 - 51545 (-) NZ_CP098511.1:2197089-2198712 -
- NBT05_RS09110 WP_265773174.1 51839 - 54377 (+) NZ_CP098511.1:2199006-2201544 -
- NBT05_RS09115 WP_265773175.1 54415 - 55699 (+) NZ_CP098511.1:2201582-2202866 3.2.1.-
- NBT05_RS09120 WP_265773176.1 55713 - 56730 (+) NZ_CP098511.1:2202880-2203897 1.1.1.-
- NBT05_RS09125 WP_265773230.1 56755 - 57520 (+) NZ_CP098511.1:2203922-2204687 -
aldA NBT05_RS09130 WP_265773177.1 57550 - 59002 (+) NZ_CP098511.1:2204717-2206169 1.2.1.-
- NBT05_RS09135 WP_265773178.1 59625 - 60720 (+) NZ_CP098511.1:2206792-2207887 -
- NBT05_RS09140 WP_265773179.1 60770 - 61823 (+) NZ_CP098511.1:2207937-2208990 5.1.3.-
- NBT05_RS09145 WP_265773180.1 61871 - 62891 (+) NZ_CP098511.1:2209038-2210058 -
- NBT05_RS09150 WP_265773181.1 62974 - 64555 (+) NZ_CP098511.1:2210141-2211722 -
- NBT05_RS09155 WP_265773182.1 64885 - 66394 (-) NZ_CP098511.1:2212052-2213561 -
- NBT05_RS09160 WP_265773183.1 67323 - 68514 (+) NZ_CP098511.1:2214490-2215681 5.1.3.-

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 2229 (+) CAZyme: GH86 Yes
- 3068 - 5785 (-) CAZyme: GH16_16|CBM6 Yes
- 6187 - 9291 (-) CAZyme: GH86|GH86|CBM6 Yes
- 10522 - 12396 (-) other Yes
- 12686 - 13813 (-) CAZyme: GH16_16 Yes
- 14800 - 16353 (-) other Yes
- 16367 - 18115 (-) other Yes
- 18138 - 21272 (-) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 22200 - 22439 (+) other Yes
- 23398 - 24045 (+) other Yes
- 24168 - 26816 (+) CAZyme: GH86 Yes
- 27368 - 28630 (+) CAZyme: GH16_15 Yes
- 28928 - 32389 (-) other Yes
- 33687 - 36926 (+) TC: gnl|TC-DB|C6VV84|1.B.14.17.1 Yes
- 36934 - 38439 (+) other Yes
- 38460 - 39575 (+) other Yes
- 39648 - 41009 (+) TC: gnl|TC-DB|C6VV84|1.B.14.17.1 Yes
- 41176 - 43470 (-) other Yes
- 43884 - 44765 (+) TF: DBD-Pfam|HTH_AraC,DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0036286,DBD-SUPERFAMILY|0035607 Yes
- 44805 - 46061 (-) STP: STP|Pyr_redox_2 Yes
- 46112 - 46420 (-) other Yes
- 46481 - 47638 (-) other Yes
- 47726 - 48544 (-) CAZyme: CE1 Yes
- 48629 - 49753 (-) other Yes
- 49923 - 51545 (-) TF: DBD-Pfam|GerE Yes
- 51840 - 54377 (+) CAZyme: GH2 Yes
- 54416 - 55699 (+) CAZyme: GH117|GH117 Yes
- 55714 - 56730 (+) other Yes
- 56756 - 57520 (+) other Yes
- 57551 - 59002 (+) other Yes
- 59626 - 60720 (+) other Yes
- 60771 - 61823 (+) other Yes
- 61872 - 62891 (+) other Yes
- 62975 - 64555 (+) TC: gnl|TC-DB|P31448|2.A.21.3.21 Yes
- 64886 - 66394 (-) CAZyme: GH82 Yes
- 67324 - 68514 (+) CDS No

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PUL ID

PUL0703

PubMed

37002465, Mar Biotechnol (NY). 2023 Apr;25(2):314-327. doi: 10.1007/s10126-023-10206-7. Epub 2023 Apr 1.

Title

Agarolytic Pathway in the Newly Isolated Aquimarina sp. Bacterial Strain ERC-38 and Characterization of a Putative beta-agarase.

Author

Kang JY, Song HY, Kim JM

Abstract

Marine microbes, particularly Bacteroidetes, are a rich source of enzymes that can degrade diverse marine polysaccharides. Aquimarina sp. ERC-38, which belongs to the Bacteroidetes phylum, was isolated from seawater in South Korea. It showed agar-degrading activity and required an additional carbon source for growth on marine broth 2216. Here, the genome of the strain was sequenced to understand its agar degradation mechanism, and 3615 protein-coding sequences were predicted, which were assigned putative functions according to their annotated functional feature categories. In silico genome analysis revealed that the ERC-38 strain has several carrageenan-degrading enzymes but could not degrade carrageenan because it lacked genes encoding kappa-carrageenanase and S1_19A type sulfatase. Moreover, the strain possesses multiple genes predicted to encode enzymes involved in agarose degradation, which are located in a polysaccharide utilization locus. Among the enzymes, Aq1840, which is closest to ZgAgaC within the glycoside hydrolase 16 family, was characterized using a recombinant enzyme expressed in Escherichia coli BL21 (DE3) cells. An enzyme assay revealed that recombinant Aq1840 mainly converts agarose to NA4. Moreover, recombinant Aq1840 could weakly hydrolyze A5 into A3 and NA2. These results showed that Aq1840 is involved in at least the initial agar degradation step prior to the metabolic pathway that uses agarose as a carbon source for growth of the strain. Thus, this enzyme can be applied to development and manufacturing industry for prebiotic and antioxidant food additive. Furthermore, our genome sequence analysis revealed that the strain is a potential resource for research on marine polysaccharide degradation mechanisms and carbon cycling.