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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0044

PubMed

26112186, Nat Commun. 2015 Jun 26;6:7481. doi: 10.1038/ncomms8481.
32266006, Biotechnol Biofuels. 2020 Mar 31;13:60. doi: 10.1186/s13068-020-01698-9. eCollection 2020.

Characterization method

qRT-PCR,enzyme activity assay

Genomic accession number

AAXF02000051.1

Nucelotide position range

128613-194006

Substrate

arabinoxylan

Loci

bacova_03417-bacova_03450

Species

Bacteroides ovatus/28116

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- BACOVA_03417 EDO10784.1 0 - 1605 (+) AAXF02000051.1:128613-130218 -
- BACOVA_03419 EDO10786.1 1701 - 4287 (+) AAXF02000051.1:130314-132900 -
- BACOVA_03420 EDO10787.1 4487 - 4649 (+) AAXF02000051.1:133100-133262 -
- BACOVA_03421 EDO10788.1 4719 - 6447 (+) AAXF02000051.1:133332-135060 -
- BACOVA_03422 EDO10789.1 6472 - 8917 (+) AAXF02000051.1:135085-137530 3.2.1.-
- BACOVA_03423 EDO10790.1 8913 - 10914 (+) AAXF02000051.1:137526-139527 -
- BACOVA_03424 EDO10791.1 10933 - 12265 (+) AAXF02000051.1:139546-140878 -
- BACOVA_03425 EDO10792.1 12412 - 14215 (+) AAXF02000051.1:141025-142828 -
- BACOVA_03426 EDO10793.1 14335 - 17488 (+) AAXF02000051.1:142948-146101 -
- BACOVA_03427 EDO10794.1 17504 - 19376 (+) AAXF02000051.1:146117-147989 -
- BACOVA_03428 EDO10795.1 19408 - 22228 (+) AAXF02000051.1:148021-150841 -
- BACOVA_03429 EDO10796.1 22255 - 24031 (+) AAXF02000051.1:150868-152644 -
- BACOVA_03430 EDO10797.1 24062 - 25097 (+) AAXF02000051.1:152675-153710 -
- BACOVA_03431 EDO10798.1 25129 - 27382 (+) AAXF02000051.1:153742-155995 -
- BACOVA_03432 EDO10799.1 27415 - 29059 (+) AAXF02000051.1:156028-157672 -
- BACOVA_03433 EDO10800.1 29058 - 31902 (+) AAXF02000051.1:157671-160515 -
- BACOVA_03434 EDO10801.1 31987 - 34531 (+) AAXF02000051.1:160600-163144 -
- BACOVA_03435 EDO10802.1 34557 - 36474 (+) AAXF02000051.1:163170-165087 -
- BACOVA_03436 EDO10803.1 36481 - 37870 (+) AAXF02000051.1:165094-166483 -
- BACOVA_03437 EDO10804.1 37891 - 41911 (-) AAXF02000051.1:166504-170524 -
- BACOVA_03438 EDO10805.1 42069 - 44505 (-) AAXF02000051.1:170682-173118 -
- BACOVA_03439 EDO10806.1 44501 - 44672 (-) AAXF02000051.1:173114-173285 -
- BACOVA_03440 EDO10807.1 44715 - 45183 (-) AAXF02000051.1:173328-173796 -
- BACOVA_03441 EDO10808.1 45401 - 49367 (+) AAXF02000051.1:174014-177980 -
- BACOVA_03442 EDO10809.1 49546 - 51058 (+) AAXF02000051.1:178159-179671 -
- BACOVA_03443 EDO10810.1 51262 - 54484 (+) AAXF02000051.1:179875-183097 -
- BACOVA_03444 EDO10811.1 54497 - 56354 (+) AAXF02000051.1:183110-184967 -
- BACOVA_03445 EDO10812.1 56337 - 57720 (+) AAXF02000051.1:184950-186333 -
- BACOVA_03446 EDO10813.1 57745 - 59749 (+) AAXF02000051.1:186358-188362 -
- BACOVA_03447 EDO10814.1 59770 - 60190 (+) AAXF02000051.1:188383-188803 -
- BACOVA_03448 EDO10815.1 60551 - 60677 (-) AAXF02000051.1:189164-189290 -
- BACOVA_03449 EDO10816.1 60861 - 63432 (-) AAXF02000051.1:189474-192045 -
- BACOVA_03450 EDO10817.1 63462 - 65394 (-) AAXF02000051.1:192075-194007 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 1605 (+) CAZyme: GH43|GH43_10 Yes
- 1702 - 4287 (+) CAZyme: GH3 Yes
- 4488 - 4649 (+) other Yes
- 4720 - 6447 (+) CAZyme: GH43_12|GH43 Yes
- 6473 - 8917 (+) CAZyme: GH31 Yes
- 8914 - 10914 (+) CAZyme: GH97 Yes
- 10934 - 12265 (+) CAZyme: CBM6|GH43|GH43_29 Yes
- 12413 - 14215 (+) CAZyme: GH43_12|GH43 Yes
- 14336 - 17488 (+) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 17505 - 19376 (+) other Yes
- 19409 - 22228 (+) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 22256 - 24031 (+) other Yes
- 24063 - 25097 (+) other Yes
- 25130 - 27382 (+) other Yes
- 27416 - 29059 (+) CAZyme: GH30_8 Yes
- 29059 - 31902 (+) CAZyme: CBM35|GH98 Yes
- 31988 - 34531 (+) CAZyme: GH115 Yes
- 34558 - 36474 (+) CAZyme: CE6|CE1 Yes
- 36482 - 37870 (+) CAZyme: CBM6|GH43|GH43_29 Yes
- 37892 - 41911 (-) TF: DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0036286,DBD-SUPERFAMILY|0035607 Yes
- 42070 - 44505 (-) CAZyme: GH95 Yes
- 44502 - 44672 (-) other Yes
- 44716 - 45183 (-) other Yes
- 45402 - 49367 (+) TF: DBD-Pfam|HTH_8,DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0036286,DBD-SUPERFAMILY|0035607 Yes
- 49547 - 51058 (+) CAZyme: GH30 Yes
- 51263 - 54484 (+) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 54498 - 56354 (+) other Yes
- 56338 - 57720 (+) other Yes
- 57746 - 59749 (+) other Yes
- 59771 - 60190 (+) other Yes
- 60552 - 60677 (-) other Yes
- 60862 - 63432 (-) CAZyme: GH115 Yes
- 63463 - 65394 (-) CDS No

PUL ID

PUL0044

PubMed

26112186, Nat Commun. 2015 Jun 26;6:7481. doi: 10.1038/ncomms8481.

Title

Glycan complexity dictates microbial resource allocation in the large intestine.

Author

Rogowski A, Briggs JA, Mortimer JC, Tryfona T, Terrapon N, Lowe EC, Basle A, Morland C, Day AM, Zheng H, Rogers TE, Thompson P, Hawkins AR, Yadav MP, Henrissat B, Martens EC, Dupree P, Gilbert HJ, Bolam DN

Abstract

The structure of the human gut microbiota is controlled primarily through the degradation of complex dietary carbohydrates, but the extent to which carbohydrate breakdown products are shared between members of the microbiota is unclear. We show here, using xylan as a model, that sharing the breakdown products of complex carbohydrates by key members of the microbiota, such as Bacteroides ovatus, is dependent on the complexity of the target glycan. Characterization of the extensive xylan degrading apparatus expressed by B. ovatus reveals that the breakdown of the polysaccharide by the human gut microbiota is significantly more complex than previous models suggested, which were based on the deconstruction of xylans containing limited monosaccharide side chains. Our report presents a highly complex and dynamic xylan degrading apparatus that is fine-tuned to recognize the different forms of the polysaccharide presented to the human gut microbiota.

PubMed

32266006, Biotechnol Biofuels. 2020 Mar 31;13:60. doi: 10.1186/s13068-020-01698-9. eCollection 2020.

Title

Multimodular fused acetyl-feruloyl esterases from soil and gut Bacteroidetes improve xylanase depolymerization of recalcitrant biomass.

Author

Kmezik C, Bonzom C, Olsson L, Mazurkewich S, Larsbrink J

Abstract

BACKGROUND: Plant biomass is an abundant and renewable carbon source that is recalcitrant towards both chemical and biochemical degradation. Xylan is the second most abundant polysaccharide in biomass after cellulose, and it possesses a variety of carbohydrate substitutions and non-carbohydrate decorations which can impede enzymatic degradation by glycoside hydrolases. Carbohydrate esterases are able to cleave the ester-linked decorations and thereby improve the accessibility of the xylan backbone to glycoside hydrolases, thus improving the degradation process. Enzymes comprising multiple catalytic glycoside hydrolase domains on the same polypeptide have previously been shown to exhibit intramolecular synergism during degradation of biomass. Similarly, natively fused carbohydrate esterase domains are encoded by certain bacteria, but whether these enzymes can result in similar synergistic boosts in biomass degradation has not previously been evaluated. RESULTS: Two carbohydrate esterases with similar architectures, each comprising two distinct physically linked catalytic domains from families 1 (CE1) and 6 (CE6), were selected from xylan-targeting polysaccharide utilization loci (PULs) encoded by the Bacteroidetes species Bacteroides ovatus and Flavobacterium johnsoniae. The full-length enzymes as well as the individual catalytic domains showed activity on a range of synthetic model substrates, corn cob biomass, and Japanese beechwood biomass, with predominant acetyl esterase activity for the N-terminal CE6 domains and feruloyl esterase activity for the C-terminal CE1 domains. Moreover, several of the enzyme constructs were able to substantially boost the performance of a commercially available xylanase on corn cob biomass (close to twofold) and Japanese beechwood biomass (up to 20-fold). Interestingly, a significant improvement in xylanase biomass degradation was observed following addition of the full-length multidomain enzyme from B. ovatus versus the addition of its two separated single domains, indicating an intramolecular synergy between the esterase domains. Despite high sequence similarities between the esterase domains from B. ovatus and F. johnsoniae, their addition to the xylanolytic reaction led to different degradation patterns. CONCLUSION: We demonstrated that multidomain carbohydrate esterases, targeting the non-carbohydrate decorations on different xylan polysaccharides, can considerably facilitate glycoside hydrolase-mediated hydrolysis of xylan and xylan-rich biomass. Moreover, we demonstrated for the first time a synergistic effect between the two fused catalytic domains of a multidomain carbohydrate esterase.