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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0796

PubMed

29774012, Front Microbiol. 2018 May 3;9:839. doi: 10.3389/fmicb.2018.00839. eCollection 2018.

Characterization method

recombinant protein expression,RT-PCR,enzyme activity assay

Genomic accession number

NZ_LSNE01000005.1

Nucelotide position range

187809-238906

Substrate

carrageenan

Loci

AX660_RS08785-AX660_RS08950

Species

Paraglaciecola hydrolytica S66/1799789

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- AX660_RS08785 WP_068376976.1 0 - 1488 (+) NZ_LSNE01000005.1:187809-189297 -
- AX660_RS08790 WP_068375678.1 1521 - 3069 (+) NZ_LSNE01000005.1:189330-190878 -
- AX660_RS08795 WP_235594702.1 3105 - 4575 (+) NZ_LSNE01000005.1:190914-192384 -
- AX660_RS08800 WP_068375680.1 4616 - 6500 (+) NZ_LSNE01000005.1:192425-194309 -
- AX660_RS08805 WP_068375683.1 6550 - 8533 (+) NZ_LSNE01000005.1:194359-196342 -
- AX660_RS08810 WP_201027429.1 8614 - 9652 (+) NZ_LSNE01000005.1:196423-197461 -
- AX660_RS08815 WP_068375685.1 9888 - 10407 (-) NZ_LSNE01000005.1:197697-198216 -
- AX660_RS23295 WP_162266411.1 10670 - 11107 (-) NZ_LSNE01000005.1:198479-198916 -
- AX660_RS08820 WP_131811777.1 11155 - 12628 (-) NZ_LSNE01000005.1:198964-200437 -
- AX660_RS08825 WP_068375690.1 13254 - 14370 (-) NZ_LSNE01000005.1:201063-202179 -
- AX660_RS08830 WP_082768866.1 14488 - 15472 (-) NZ_LSNE01000005.1:202297-203281 -
- AX660_RS08835 WP_068375692.1 15658 - 18091 (-) NZ_LSNE01000005.1:203467-205900 3.2.1.-
- AX660_RS08840 WP_068375694.1 18115 - 20467 (-) NZ_LSNE01000005.1:205924-208276 -
- AX660_RS08845 WP_068375697.1 20586 - 22263 (-) NZ_LSNE01000005.1:208395-210072 -
- AX660_RS08850 WP_068375699.1 22421 - 23138 (-) NZ_LSNE01000005.1:210230-210947 -
- AX660_RS08855 WP_068375702.1 23158 - 23890 (-) NZ_LSNE01000005.1:210967-211699 -
- AX660_RS08860 WP_162266412.1 23889 - 25281 (-) NZ_LSNE01000005.1:211698-213090 -
- AX660_RS08865 WP_068375704.1 25311 - 26280 (-) NZ_LSNE01000005.1:213120-214089 -
- AX660_RS08870 WP_068375706.1 26357 - 28118 (-) NZ_LSNE01000005.1:214166-215927 -
- AX660_RS08875 WP_068375710.1 28189 - 31855 (-) NZ_LSNE01000005.1:215998-219664 -
- AX660_RS08880 WP_068375712.1 32736 - 33822 (-) NZ_LSNE01000005.1:220545-221631 -
- AX660_RS08885 WP_068375714.1 33818 - 35399 (-) NZ_LSNE01000005.1:221627-223208 -
- AX660_RS08890 WP_068375716.1 35411 - 36698 (-) NZ_LSNE01000005.1:223220-224507 -
- AX660_RS08895 WP_068376991.1 36773 - 38900 (-) NZ_LSNE01000005.1:224582-226709 -
- AX660_RS08900 WP_068375718.1 39073 - 39574 (+) NZ_LSNE01000005.1:226882-227383 -
- AX660_RS08905 WP_068375720.1 39594 - 40059 (-) NZ_LSNE01000005.1:227403-227868 -
- AX660_RS08910 WP_068375721.1 40193 - 41267 (+) NZ_LSNE01000005.1:228002-229076 -
ctlX AX660_RS08915 WP_068375723.1 41266 - 42190 (+) NZ_LSNE01000005.1:229075-229999 -
- AX660_RS08920 WP_082768820.1 42799 - 43849 (-) NZ_LSNE01000005.1:230608-231658 -
- AX660_RS08925 WP_068375726.1 44559 - 45126 (+) NZ_LSNE01000005.1:232368-232935 -
- AX660_RS08930 WP_327082847.1 45172 - 46594 (+) NZ_LSNE01000005.1:232981-234403 -
- AX660_RS08935 WP_068375728.1 46826 - 48272 (+) NZ_LSNE01000005.1:234635-236081 1.2.1.-
- AX660_RS08940 WP_068375729.1 48268 - 49432 (+) NZ_LSNE01000005.1:236077-237241 -
- AX660_RS08945 WP_068375731.1 49469 - 50447 (+) NZ_LSNE01000005.1:237278-238256 -
- AX660_RS08950 WP_068375733.1 50456 - 51098 (+) NZ_LSNE01000005.1:238265-238907 4.1.2.21

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 1488 (+) CAZyme: GH16_13 Yes
- 1522 - 3069 (+) other Yes
- 3106 - 4575 (+) other Yes
- 4617 - 6500 (+) other Yes
- 6551 - 8533 (+) CAZyme: GH127 Yes
- 8615 - 9652 (+) other Yes
- 9889 - 10407 (-) other Yes
- 10671 - 11107 (-) other Yes
- 11156 - 12628 (-) other Yes
- 13255 - 14370 (-) other Yes
- 14489 - 15472 (-) CAZyme: GH16_13 Yes
- 15659 - 18091 (-) CAZyme: GH167 Yes
- 18116 - 20467 (-) other Yes
- 20587 - 22263 (-) CAZyme: GH82 Yes
- 22422 - 23138 (-) other Yes
- 23159 - 23890 (-) STP: STP|Y_Y_Y Yes
- 23890 - 25281 (-) CAZyme: GH16_13 Yes
- 25312 - 26280 (-) CAZyme: GH16_17 Yes
- 26358 - 28118 (-) other Yes
- 28190 - 31855 (-) other Yes
- 32737 - 33822 (-) other Yes
- 33819 - 35399 (-) other Yes
- 35412 - 36698 (-) other Yes
- 36774 - 38900 (-) TC: gnl|TC-DB|Q9LAE4|1.B.14.8.1 Yes
- 39074 - 39574 (+) TF: DBD-Pfam|MarR,DBD-SUPERFAMILY|0040517 Yes
- 39595 - 40059 (-) TF: DBD-Pfam|HTH_11,DBD-SUPERFAMILY|0044258 Yes
- 40194 - 41267 (+) other Yes
ctlX 41267 - 42190 (+) TF: DBD-Pfam|Crp Yes
- 42800 - 43849 (-) CAZyme: GH16_13 Yes
- 44560 - 45126 (+) CDS No
- 45173 - 46594 (+) CDS No
- 46827 - 48272 (+) CDS No
- 48269 - 49432 (+) CDS No
- 49470 - 50447 (+) CDS No
- 50457 - 51098 (+) CDS No

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PUL ID

PUL0796

PubMed

29774012, Front Microbiol. 2018 May 3;9:839. doi: 10.3389/fmicb.2018.00839. eCollection 2018.

Title

A Novel Enzyme Portfolio for Red Algal Polysaccharide Degradation in the Marine Bacterium Paraglaciecola hydrolytica S66(T) Encoded in a Sizeable Polysaccharide Utilization Locus.

Author

Schultz-Johansen M, Bech PK, Hennessy RC, Glaring MA, Barbeyron T, Czjzek M, Stougaard P

Abstract

Marine microbes are a rich source of enzymes for the degradation of diverse polysaccharides. Paraglaciecola hydrolytica S66(T) is a marine bacterium capable of hydrolyzing polysaccharides found in the cell wall of red macroalgae. In this study, we applied an approach combining genomic mining with functional analysis to uncover the potential of this bacterium to produce enzymes for the hydrolysis of complex marine polysaccharides. A special feature of P. hydrolytica S66(T) is the presence of a large genomic region harboring an array of carbohydrate-active enzymes (CAZymes) notably agarases and carrageenases. Based on a first functional characterization combined with a comparative sequence analysis, we confirmed the enzymatic activities of several enzymes required for red algal polysaccharide degradation by the bacterium. In particular, we report for the first time, the discovery of novel enzyme activities targeting furcellaran, a hybrid carrageenan containing both beta-carrageenan and kappa/beta-carrageenan motifs. Some of these enzymes represent a new subfamily within the CAZy classification. From the combined analyses, we propose models for the complete degradation of agar and kappa/beta-type carrageenan by P. hydrolytica S66(T). The novel enzymes described here may find value in new bio-based industries and advance our understanding of the mechanisms responsible for recycling of red algal polysaccharides in marine ecosystems.