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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0010

PubMed

28616644, Appl Microbiol Biotechnol. 2017 Aug;101(15):6023-6037. doi: 10.1007/s00253-017-8341-2. Epub 2017 Jun 14.

Characterization method

enzyme activity assay,liquid chromatography and mass spectrometry

Genomic accession number

NC_009328.1

Nucelotide position range

1855422-1909199

Substrate

xylan

Loci

GTNG_RS09195-GTNG_RS09405

Species

Geobacillus thermodenitrificans/33940

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

xylB GTNG_RS09195 WP_011887509.1 0 - 1500 (-) NC_009328.1:1855422-1856922 2.7.1.17
xylA GTNG_RS09200 WP_008880082.1 1514 - 2852 (-) NC_009328.1:1856936-1858274 5.3.1.5
- GTNG_RS09205 WP_008880081.1 2950 - 4558 (-) NC_009328.1:1858372-1859980 -
- GTNG_RS09210 WP_008880080.1 5003 - 5666 (-) NC_009328.1:1860425-1861088 -
- GTNG_RS09215 WP_008880079.1 5688 - 6483 (-) NC_009328.1:1861110-1861905 -
- GTNG_RS09220 WP_008880078.1 6999 - 8223 (+) NC_009328.1:1862421-1863645 -
- GTNG_RS09225 WP_008880077.1 8426 - 9068 (-) NC_009328.1:1863848-1864490 -
- GTNG_RS09230 WP_011887510.1 9147 - 9993 (-) NC_009328.1:1864569-1865415 -
uxuA GTNG_RS09235 WP_008880075.1 9968 - 11084 (-) NC_009328.1:1865390-1866506 4.2.1.8
uxaC GTNG_RS09240 WP_008880074.1 11104 - 12508 (-) NC_009328.1:1866526-1867930 5.3.1.12
- GTNG_RS09245 WP_011887511.1 12549 - 13248 (-) NC_009328.1:1867971-1868670 -
- GTNG_RS09250 WP_008880072.1 13365 - 14016 (-) NC_009328.1:1868787-1869438 -
- GTNG_RS09255 WP_008880071.1 14033 - 14987 (-) NC_009328.1:1869455-1870409 -
- GTNG_RS09260 WP_008880070.1 15019 - 16540 (-) NC_009328.1:1870441-1871962 -
- GTNG_RS09265 WP_011887512.1 16556 - 18611 (-) NC_009328.1:1871978-1874033 -
- GTNG_RS09270 WP_011887513.1 18626 - 19517 (-) NC_009328.1:1874048-1874939 -
- GTNG_RS09275 WP_011887514.1 19531 - 20482 (-) NC_009328.1:1874953-1875904 -
- GTNG_RS09280 WP_011887515.1 20612 - 22256 (-) NC_009328.1:1876034-1877678 -
- GTNG_RS09285 WP_081157505.1 22804 - 23800 (-) NC_009328.1:1878226-1879222 -
- GTNG_RS09290 WP_011887517.1 23802 - 25920 (-) NC_009328.1:1879224-1881342 -
- GTNG_RS09295 WP_008880061.1 26030 - 26657 (-) NC_009328.1:1881452-1882079 -
- GTNG_RS09300 WP_008880060.1 26670 - 27720 (-) NC_009328.1:1882092-1883142 -
- GTNG_RS09305 WP_008880059.1 27935 - 28802 (-) NC_009328.1:1883357-1884224 -
- GTNG_RS09310 WP_008880058.1 28816 - 29686 (-) NC_009328.1:1884238-1885108 -
- GTNG_RS09315 WP_008880057.1 29761 - 31084 (-) NC_009328.1:1885183-1886506 -
- GTNG_RS09320 WP_008880056.1 31198 - 31990 (-) NC_009328.1:1886620-1887412 -
- GTNG_RS09325 WP_008880055.1 31989 - 33720 (-) NC_009328.1:1887411-1889142 -
- GTNG_RS09330 WP_008880054.1 34225 - 34417 (-) NC_009328.1:1889647-1889839 -
- GTNG_RS09335 - 34611 - 35946 (+) NC_009328.1:1890033-1891368 -
- GTNG_RS09340 WP_011887518.1 36251 - 37466 (-) NC_009328.1:1891673-1892888 -
- GTNG_RS09345 WP_011887519.1 37462 - 38272 (-) NC_009328.1:1892884-1893694 -
- GTNG_RS09350 WP_011887520.1 38329 - 39325 (-) NC_009328.1:1893751-1894747 -
- GTNG_RS09355 WP_011887521.1 39387 - 40896 (-) NC_009328.1:1894809-1896318 -
- GTNG_RS09360 WP_008880047.1 40935 - 41781 (-) NC_009328.1:1896357-1897203 -
- GTNG_RS09365 WP_011887522.1 41784 - 42717 (-) NC_009328.1:1897206-1898139 -
- GTNG_RS09370 WP_008880045.1 42844 - 44152 (-) NC_009328.1:1898266-1899574 -
araA GTNG_RS09375 WP_011887523.1 44652 - 46143 (-) NC_009328.1:1900074-1901565 5.3.1.4
- GTNG_RS09380 WP_011887524.1 46159 - 47854 (-) NC_009328.1:1901581-1903276 2.7.1.16
araD GTNG_RS09385 WP_011887525.1 47869 - 48556 (-) NC_009328.1:1903291-1903978 5.1.3.4
- GTNG_RS09390 WP_011887526.1 48647 - 49742 (-) NC_009328.1:1904069-1905164 -
- GTNG_RS09395 WP_011887527.1 49861 - 51085 (-) NC_009328.1:1905283-1906507 -
- GTNG_RS09400 WP_011887528.1 51086 - 52628 (-) NC_009328.1:1906508-1908050 -
- GTNG_RS09405 WP_008880038.1 52701 - 53778 (-) NC_009328.1:1908123-1909200 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

xylB 1 - 1500 (-) CDS No
xylA 1515 - 2852 (-) CDS No
- 2951 - 4558 (-) CAZyme: GH43|GH43_11 Yes
- 5004 - 5666 (-) other Yes
- 5689 - 6483 (-) other Yes
- 7000 - 8223 (+) CAZyme: GH10 Yes
- 8427 - 9068 (-) TC: gnl|TC-DB|G4PA66|9.B.28.1.5 Yes
- 9148 - 9993 (-) other Yes
uxuA 9969 - 11084 (-) other Yes
uxaC 11105 - 12508 (-) other Yes
- 12550 - 13248 (-) TF: DBD-Pfam|GntR,DBD-SUPERFAMILY|0039384 Yes
- 13366 - 14016 (-) other Yes
- 14034 - 14987 (-) STP: STP|PfkB Yes
- 15020 - 16540 (-) CAZyme: GH39 Yes
- 16557 - 18611 (-) CAZyme: GH67 Yes
- 18627 - 19517 (-) TC: gnl|TC-DB|Q09LY6|3.A.1.1.9 Yes
- 19532 - 20482 (-) TC: gnl|TC-DB|Q09LY7|3.A.1.1.9 Yes
- 20613 - 22256 (-) TC: gnl|TC-DB|C9RT46|3.A.1.1.9 Yes
- 22805 - 23800 (-) CAZyme: GH10|CBM22 Yes
- 23803 - 25920 (-) CAZyme: GH52 Yes
- 26031 - 26657 (-) CAZyme: CE4 Yes
- 26671 - 27720 (-) other Yes
- 27936 - 28802 (-) TC: gnl|TC-DB|G4FGN6|3.A.1.1.41 Yes
- 28817 - 29686 (-) TC: gnl|TC-DB|Q8RJU9|3.A.1.1.18 Yes
- 29762 - 31084 (-) STP: STP|SBP_bac_1 Yes
- 31199 - 31990 (-) TF: DBD-Pfam|HTH_AraC,DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0036286,DBD-SUPERFAMILY|0035607 Yes
- 31990 - 33720 (-) TC: gnl|TC-DB|F4LXP4|8.A.59.2.1 Yes
- 34226 - 34417 (-) other Yes
- 36252 - 37466 (-) other Yes
- 37463 - 38272 (-) other Yes
- 38330 - 39325 (-) other Yes
- 39388 - 40896 (-) CAZyme: GH51 Yes
- 40936 - 41781 (-) TC: gnl|TC-DB|P94530|3.A.1.1.34 Yes
- 41785 - 42717 (-) TC: gnl|TC-DB|P94529|3.A.1.1.34 Yes
- 42845 - 44152 (-) TC: gnl|TC-DB|P94528|3.A.1.1.34 Yes
araA 44653 - 46143 (-) other Yes
- 46160 - 47854 (-) other Yes
araD 47870 - 48556 (-) other Yes
- 48648 - 49742 (-) TF: DBD-Pfam|GntR,DBD-SUPERFAMILY|0037767 Yes
- 49862 - 51085 (-) TC: gnl|TC-DB|O05177|3.A.1.2.5 Yes
- 51087 - 52628 (-) TC: gnl|TC-DB|O05176|3.A.1.2.5 Yes
- 52702 - 53778 (-) TC: gnl|TC-DB|P25548|3.A.1.2.5 Yes

PUL ID

PUL0010

PubMed

28616644, Appl Microbiol Biotechnol. 2017 Aug;101(15):6023-6037. doi: 10.1007/s00253-017-8341-2. Epub 2017 Jun 14.

Title

Synergistic hydrolysis of xylan using novel xylanases, beta-xylosidases, and an alpha-L-arabinofuranosidase from Geobacillus thermodenitrificans NG80-2.

Author

Huang D, Liu J, Qi Y, Yang K, Xu Y, Feng L

Abstract

Lignocellulosic biomass from various types of wood has become a renewable resource for production of biofuels and biobased chemicals. Because xylan is the major component of wood hemicelluloses, highly efficient enzymes to enhance xylan hydrolysis can improve the use of lignocellulosic biomass. In this study, a xylanolytic gene cluster was identified from the crude oil-degrading thermophilic strain Geobacillus thermodenitrificans NG80-2. The enzymes involved in xylan hydrolysis, which include two xylanases (XynA1, XynA2), three beta-xylosidases (XynB1, XynB2, XynB3), and one alpha-L-arabinofuranosidase (AbfA), have many unique features, such as high pH tolerance, high thermostability, and a broad substrate range. The three beta-xylosidases were highly resistant to inhibition by product (xylose) accumulation. Moreover, the combination of xylanase, beta-xylosidase, and alpha-L-arabinofuranosidase exhibited the largest synergistic action on xylan degradation (XynA2, XynB1, and AbfA on oat spelt or beechwood xylan; XynA2, XynB3, and AbfA on birchwood xylan). We have demonstrated that the proposed enzymatic cocktail almost completely converts complex xylan to xylose and arabinofuranose and has great potential for use in the conversion of plant biomass into biofuels and biochemicals.