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PlantCAZyme
Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0706

PubMed

37265394, ACS Synth Biol. 2023 Jun 16;12(6):1782-1793. doi: 10.1021/acssynbio.3c00063. Epub 2023 Jun 2.

Characterization method

RNA-seq,growth assay

Genomic accession number

NC_008228.1

Nucelotide position range

929370-998729

Substrate

agar

Loci

PATL_RS04110-PATL_RS04320

Species

Pseudoalteromonas atlantica T6c/288

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- PATL_RS04110 WP_011573693.1 0 - 2577 (+) NC_008228.1:929370-931947 -
- PATL_RS04115 WP_011573694.1 2589 - 3477 (+) NC_008228.1:931959-932847 -
- PATL_RS04120 WP_011573695.1 3583 - 4252 (-) NC_008228.1:932953-933622 -
- PATL_RS04125 WP_011573696.1 4280 - 5780 (-) NC_008228.1:933650-935150 1.14.19.-
- PATL_RS04130 WP_011573697.1 5870 - 7571 (-) NC_008228.1:935240-936941 -
- PATL_RS04135 WP_011573698.1 7645 - 11302 (-) NC_008228.1:937015-940672 -
- PATL_RS04140 WP_011573699.1 11996 - 13349 (+) NC_008228.1:941366-942719 -
- PATL_RS04145 WP_011573700.1 13393 - 14308 (+) NC_008228.1:942763-943678 -
- PATL_RS04150 WP_011573701.1 14304 - 15597 (+) NC_008228.1:943674-944967 3.2.1.-
- PATL_RS04155 WP_011573702.1 15650 - 15956 (+) NC_008228.1:945020-945326 -
- PATL_RS04160 WP_011573703.1 16025 - 17444 (-) NC_008228.1:945395-946814 -
- PATL_RS04165 WP_011573704.1 17453 - 20678 (-) NC_008228.1:946823-950048 -
- PATL_RS04170 WP_041714220.1 20686 - 21928 (-) NC_008228.1:950056-951298 -
- PATL_RS04175 WP_011573706.1 21930 - 23328 (-) NC_008228.1:951300-952698 -
- PATL_RS04180 WP_011573707.1 23497 - 24379 (+) NC_008228.1:952867-953749 -
- PATL_RS04185 WP_011573708.1 24516 - 26088 (-) NC_008228.1:953886-955458 3.1.6.-
- PATL_RS04190 WP_011573709.1 26103 - 27987 (-) NC_008228.1:955473-957357 3.1.6.-
- PATL_RS04195 WP_011573710.1 27989 - 31229 (-) NC_008228.1:957359-960599 -
- PATL_RS04200 WP_011573711.1 31394 - 31751 (+) NC_008228.1:960764-961121 -
- PATL_RS04205 WP_011573712.1 31912 - 33517 (+) NC_008228.1:961282-962887 3.2.1.51
- PATL_RS04210 WP_011573713.1 33558 - 34923 (+) NC_008228.1:962928-964293 -
- PATL_RS04215 WP_011573714.1 35097 - 37299 (-) NC_008228.1:964467-966669 -
- PATL_RS04220 WP_011573715.1 37408 - 39292 (+) NC_008228.1:966778-968662 -
- PATL_RS04225 WP_011573716.1 39288 - 40167 (+) NC_008228.1:968658-969537 -
- PATL_RS04230 WP_049765849.1 40186 - 41674 (+) NC_008228.1:969556-971044 3.1.-.-
- PATL_RS04235 WP_011573718.1 41719 - 43252 (+) NC_008228.1:971089-972622 3.1.6.-
- PATL_RS04240 WP_011573719.1 43363 - 45271 (-) NC_008228.1:972733-974641 -
- PATL_RS04245 WP_041714226.1 45321 - 46914 (-) NC_008228.1:974691-976284 3.2.1.51
- PATL_RS04250 WP_011573721.1 47294 - 50234 (+) NC_008228.1:976664-979604 -
- PATL_RS04255 WP_011573722.1 50223 - 51861 (+) NC_008228.1:979593-981231 -
- PATL_RS04260 WP_011573723.1 51865 - 53344 (+) NC_008228.1:981235-982714 1.1.1.-
- PATL_RS04265 WP_011573724.1 53356 - 54925 (+) NC_008228.1:982726-984295 -
- PATL_RS04270 WP_011573725.1 54947 - 55895 (+) NC_008228.1:984317-985265 2.7.1.-
- PATL_RS04275 WP_011573726.1 55894 - 56818 (+) NC_008228.1:985264-986188 3.-.-.-
- PATL_RS04280 WP_011573727.1 56886 - 57657 (-) NC_008228.1:986256-987027 -
- PATL_RS04285 WP_011573728.1 58114 - 61066 (+) NC_008228.1:987484-990436 -
- PATL_RS04290 WP_011573729.1 61066 - 62023 (-) NC_008228.1:990436-991393 -
- PATL_RS04295 WP_157043389.1 62312 - 62528 (+) NC_008228.1:991682-991898 -
- PATL_RS04300 WP_011573731.1 63078 - 64719 (-) NC_008228.1:992448-994089 -
- PATL_RS04305 WP_011573732.1 64840 - 65695 (-) NC_008228.1:994210-995065 -
- PATL_RS04310 WP_011573733.1 66339 - 67389 (-) NC_008228.1:995709-996759 1.14.-.-
- PATL_RS04315 WP_011573734.1 67651 - 68347 (+) NC_008228.1:997021-997717 -
- PATL_RS04320 WP_011573735.1 68448 - 69360 (-) NC_008228.1:997818-998730 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 2577 (+) CAZyme: GH2 Yes
- 2590 - 3477 (+) CAZyme: GH16_14 Yes
- 3584 - 4252 (-) other Yes
- 4281 - 5780 (-) other Yes
- 5871 - 7571 (-) other Yes
- 7646 - 11302 (-) other Yes
- 11997 - 13349 (+) CAZyme: GH43_2|CBM6 Yes
- 13394 - 14308 (+) other Yes
- 14305 - 15597 (+) CAZyme: GH117|GH117 Yes
- 15651 - 15956 (+) other Yes
- 16026 - 17444 (-) other Yes
- 17454 - 20678 (-) TC: gnl|TC-DB|C6VV84|1.B.14.17.1 Yes
- 20687 - 21928 (-) other Yes
- 21931 - 23328 (-) other Yes
- 23498 - 24379 (+) TF: DBD-Pfam|HTH_AraC,DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0036286,DBD-SUPERFAMILY|0035607 Yes
- 24517 - 26088 (-) other Yes
- 26104 - 27987 (-) other Yes
- 27990 - 31229 (-) CAZyme: GH2 Yes
- 31395 - 31751 (+) other Yes
- 31913 - 33517 (+) CAZyme: GH29 Yes
- 33559 - 34923 (+) CAZyme: GH16_12 Yes
- 35098 - 37299 (-) CAZyme: GH3 Yes
- 37409 - 39292 (+) other Yes
- 39289 - 40167 (+) TF: DBD-Pfam|HTH_AraC,DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0035607,DBD-SUPERFAMILY|0035607 Yes
- 40187 - 41674 (+) other Yes
- 41720 - 43252 (+) other Yes
- 43364 - 45271 (-) CAZyme: CE20|CE20 Yes
- 45322 - 46914 (-) CAZyme: GH29 Yes
- 47295 - 50234 (+) CAZyme: GH2 Yes
- 50224 - 51861 (+) CAZyme: GH140 Yes
- 51866 - 53344 (+) other Yes
- 53357 - 54925 (+) TC: gnl|TC-DB|P96169|2.A.21.3.2 Yes
- 54948 - 55895 (+) STP: STP|PfkB Yes
- 55895 - 56818 (+) other Yes
- 56887 - 57657 (-) other Yes
- 58115 - 61066 (+) CAZyme: GH86 Yes
- 61067 - 62023 (-) other Yes
- 62313 - 62528 (+) other Yes
- 63079 - 64719 (-) CAZyme: GH43_12|CBM91 Yes
- 64841 - 65695 (-) CAZyme: GH16_14 Yes
- 66340 - 67389 (-) CDS No
- 67652 - 68347 (+) TF: DBD-Pfam|GntR,DBD-SUPERFAMILY|0039384 No
- 68449 - 69360 (-) TF: DBD-Pfam|HTH_1,DBD-SUPERFAMILY|0040517 No

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PUL ID

PUL0706

PubMed

37265394, ACS Synth Biol. 2023 Jun 16;12(6):1782-1793. doi: 10.1021/acssynbio.3c00063. Epub 2023 Jun 2.

Title

Constructing Marine Bacterial Metabolic Chassis for Potential Biorefinery of Red Algal Biomass and Agaropectin Wastes.

Author

Pathiraja D, Park B, Kim B, Stougaard P, Choi IG

Abstract

Marine red algal biomass is a promising feedstock for sustainable production of value-added chemicals. However, the major constituents of red algal biomass, such as agar and carrageenan, are not easily assimilated by most industrial metabolic chassis developed to date. Synthetic biology offers a solution by utilizing nonmodel organisms as metabolic chassis for consolidated biological processes. In this study, the marine heterotrophic bacterium Pseudoalteromonas atlantica T6c was harnessed as a metabolic chassis to produce value-added chemicals from the affordable red algal galactans or agaropectin, a byproduct of industrial agarose production. To construct a heterologous gene expression device in P. atlantica T6c, promoters related to agar metabolism were screened from the differentially expressed genes using RNA-Seq analysis. The expression device was built and tested with selected promoters fused to a reporter gene and tuned by incorporation of a cognate repressor predicted from the agar-specific polysaccharide utilization locus. The feasibility of the marine bacterial metabolic chassis was examined by introducing the biosynthetic gene clusters of beta-carotene and violacein. Our results demonstrate that the metabolic chassis platform enables direct conversion of low-cost red algal galactans or industrial waste agaropectin into valuable bioactive pigments without any pretreatment of biomass. The developed marine bacterial chassis could potentially be used in a biorefinery framework to produce value-added chemicals from marine algal galactans.