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PlantCAZyme
Cite: NAR/gkaa742 2020

Because CGCFinder predicted no CGC for this PUL, the gene cluster depicted below contains dbCAN2 and CGC signature predictions for all genes in the PUL, instead of a predicted CGC.


PUL General Information

Literature Information

PUL ID

PUL0114

PubMed

31198441, Biotechnol Biofuels. 2019 Jun 10;12:144. doi: 10.1186/s13068-019-1483-y. eCollection 2019.

Characterization method

recombinant protein expression,enzyme activity assay

Genomic accession number

CP001348.1

Nucelotide position range

1505662-1537237

Substrate

arabinofuranose

Loci

Ccel_1229-Ccel_1242

Species

Ruminiclostridium cellulolyticum/1521

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- Ccel_1229 ACL75585.1 0 - 1608 (+) CP001348.1:1505662-1507270 -
- Ccel_1230 ACL75586.1 1713 - 3339 (+) CP001348.1:1507375-1509001 -
- Ccel_1231 ACL75587.1 3406 - 4981 (+) CP001348.1:1509068-1510643 -
- Ccel_1232 ACL75588.1 5003 - 6476 (+) CP001348.1:1510665-1512138 -
- Ccel_1233 ACL75589.1 6551 - 8792 (+) CP001348.1:1512213-1514454 -
- Ccel_1234 ACL75590.1 8875 - 10486 (+) CP001348.1:1514537-1516148 -
- Ccel_1235 ACL75591.1 10560 - 12090 (+) CP001348.1:1516222-1517752 -
- Ccel_1236 ACL75592.1 12178 - 15046 (+) CP001348.1:1517840-1520708 -
- Ccel_1237 ACL75593.1 15154 - 16969 (+) CP001348.1:1520816-1522631 -
- Ccel_1238 ACL75594.1 16998 - 20367 (+) CP001348.1:1522660-1526029 -
- Ccel_1239 ACL75595.1 20430 - 23478 (+) CP001348.1:1526092-1529140 -
- Ccel_1240 ACL75596.1 23538 - 25881 (+) CP001348.1:1529200-1531543 -
- Ccel_1241 ACL75597.1 26097 - 29592 (+) CP001348.1:1531759-1535254 -
- Ccel_1242 ACL75598.1 29686 - 31576 (+) CP001348.1:1535348-1537238 -

Cluster number

0

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 1608 (+) CAZyme: GH43|GH43_16|CBM6 No
- 1714 - 3339 (+) CAZyme: GH10|CBM6 No
- 3407 - 4981 (+) CAZyme: GH43|GH43_29|CBM6 No
- 5004 - 6476 (+) CAZyme: CE1|CBM6 No
- 6552 - 8792 (+) CAZyme: GH43_10|CBM6 No
- 8876 - 10486 (+) CAZyme: GH62|CBM6 No
- 10561 - 12090 (+) CAZyme: GH43|GH43_29|CBM6 No
- 12179 - 15046 (+) CAZyme: GH146|CBM22 No
- 15155 - 16969 (+) CAZyme: GH27|CBM6 No
- 16999 - 20367 (+) CAZyme: GH59|CBM6 No
- 20431 - 23478 (+) CAZyme: GH2|CBM6 No
- 23539 - 25881 (+) CAZyme: GH62|CE6|CBM6 No
- 26098 - 29592 (+) CAZyme: CBM32|GH95|CBM6 No
- 29687 - 31576 (+) CAZyme: GH30_8|CBM6 No

PUL ID

PUL0114

PubMed

31198441, Biotechnol Biofuels. 2019 Jun 10;12:144. doi: 10.1186/s13068-019-1483-y. eCollection 2019.

Title

The xyl-doc gene cluster of Ruminiclostridium cellulolyticum encodes GH43- and GH62-alpha-l-arabinofuranosidases with complementary modes of action.

Author

Mroueh M, Aruanno M, Borne R, de Philip P, Fierobe HP, Tardif C, Pages S

Abstract

BACKGROUND: The alpha-l-arabinofuranosidases (alpha-l-ABFs) are exoenzymes involved in the hydrolysis of alpha-l-arabinosyl linkages in plant cell wall polysaccharides. They play a crucial role in the degradation of arabinoxylan and arabinan and they are used in many biotechnological applications. Analysis of the genome of R. cellulolyticum showed that putative cellulosomal alpha-l-ABFs are exclusively encoded by the xyl-doc gene cluster, a large 32-kb gene cluster. Indeed, among the 14 Xyl-Doc enzymes encoded by this gene cluster, 6 are predicted to be alpha-l-ABFs belonging to the CAZyme families GH43 and GH62. RESULTS: The biochemical characterization of these six Xyl-Doc enzymes revealed that four of them are alpha-l-ABFs. GH43(16)-1229 (RcAbf43A) which belongs to the subfamily 16 of the GH43, encoded by the gene at locus Ccel_1229, has a low specific activity on natural substrates and can cleave off arabinose decorations located at arabinoxylan chain extremities. GH43(10)-1233 (RcAbf43A(d2,3)), the product of the gene at locus Ccel_1233, belonging to subfamily 10 of the GH43, can convert the double arabinose decorations present on arabinoxylan into single O2- or O3-linked decorations with high velocity (k (cat) = 16.6 +/- 0.6 s(-1)). This enzyme acts in synergy with GH62-1234 (RcAbf62A(m2,3)), the product of the gene at locus Ccel_1234, a GH62 alpha-l-ABF which hydrolyzes alpha-(1 --> 3) or alpha-(1 --> 2)-arabinosyl linkages present on polysaccharides and arabinoxylooligosaccharides monodecorated. Finally, a bifunctional enzyme, GH62-CE6-1240 (RcAbf62B(m2,3)Axe6), encoded by the gene at locus Ccel_1240, which contains a GH62-alpha-l-ABF module and a carbohydrate esterase (CE6) module, catalyzes deacylation of plant cell wall polymers and cleavage of arabinosyl mono-substitutions. These enzymes are also active on arabinan, a component of the type I rhamnogalacturonan, showing their involvement in pectin degradation. CONCLUSION: Arabinofuranosyl decorations on arabinoxylan and pectin strongly inhibit the action of xylan-degrading enzymes and pectinases. alpha-l-ABFs encoded by the xyl-doc gene cluster of R. cellulolyticum can remove all the decorations present in the backbone of arabinoxylan and arabinan, act synergistically, and, thus, play a crucial role in the degradation of plant cell wall polysaccharides.