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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0229

PubMed

17921311, J Bacteriol. 2007 Dec;189(24):8863-70. doi: 10.1128/JB.01141-07. Epub 2007 Oct 5.

Characterization method

RT-PCR

Genomic accession number

EU024644.1

Nucelotide position range

606-12564

Substrate

aldouronate

Loci

yesN-yesM-lplA-lplB-ytcP-arguA-xynA2-xynB

Species

Paenibacillus sp. JDR-2/324057

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

yesN - ABV90480.1 14 - 1583 (+) EU024644.1:620-2189 -
yesM - ABV90481.1 1598 - 3317 (+) EU024644.1:2204-3923 -
lplA - ABV90482.2 3450 - 5163 (+) EU024644.1:4056-5769 -
lplB - ABV90483.1 5252 - 6224 (+) EU024644.1:5858-6830 -
ytcP - ABV90484.1 6263 - 7184 (+) EU024644.1:6869-7790 -
aguA - ABV90485.1 7280 - 9344 (+) EU024644.1:7886-9950 -
xynA2 - ABV90486.1 9371 - 10397 (+) EU024644.1:9977-11003 -
xynB - ABV90487.1 10393 - 11959 (+) EU024644.1:10999-12565 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 15 - 1583 (+) TF: DBD-Pfam|HTH_AraC,DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0036286,DBD-SUPERFAMILY|0035607 No
- 1599 - 3317 (+) TC: gnl|TC-DB|F4LXP4|8.A.59.2.1 Yes
- 3451 - 5163 (+) TC: gnl|TC-DB|A9QDR6|3.A.1.1.29 Yes
- 5253 - 6224 (+) TC: gnl|TC-DB|A9QDR7|3.A.1.1.29 Yes
- 6264 - 7184 (+) TC: gnl|TC-DB|A9QDR8|3.A.1.1.29 Yes
- 7281 - 9344 (+) CAZyme: GH67 Yes
- 9372 - 10397 (+) CAZyme: CBM22|GH10 Yes
- 10394 - 11959 (+) CAZyme: GH43_12|GH43 Yes

PUL ID

PUL0229

PubMed

17921311, J Bacteriol. 2007 Dec;189(24):8863-70. doi: 10.1128/JB.01141-07. Epub 2007 Oct 5.

Title

Structure, function, and regulation of the aldouronate utilization gene cluster from Paenibacillus sp. strain JDR-2.

Author

Chow V, Nong G, Preston JF

Abstract

Direct bacterial conversion of the hemicellulose fraction of hardwoods and crop residues to biobased products depends upon extracellular depolymerization of methylglucuronoxylan (MeGAX(n)), followed by assimilation and intracellular conversion of aldouronates and xylooligosaccharides to fermentable xylose. Paenibacillus sp. strain JDR-2, an aggressively xylanolytic bacterium, secretes a multimodular cell-associated GH10 endoxylanase (XynA1) that catalyzes depolymerization of MeGAX(n) and rapidly assimilates the principal products, beta-1,4-xylobiose, beta-1,4-xylotriose, and MeGAX(3), the aldotetrauronate 4-O-methylglucuronosyl-alpha-1,2-xylotriose. Genomic libraries derived from this bacterium have now allowed cloning and sequencing of a unique aldouronate utilization gene cluster comprised of genes encoding signal transduction regulatory proteins, ABC transporter proteins, and the enzymes AguA (GH67 alpha-glucuronidase), XynA2 (GH10 endoxylanase), and XynB (GH43 beta-xylosidase/alpha-arabinofuranosidase). Expression of these genes, as well as xynA1 encoding the secreted GH10 endoxylanase, is induced by growth on MeGAX(n) and repressed by glucose. Sequences in the yesN, lplA, and xynA2 genes within the cluster and in the distal xynA1 gene show significant similarity to catabolite responsive element (cre) defined in Bacillus subtilis for recognition of the catabolite control protein (CcpA) and consequential repression of catabolic regulons. The aldouronate utilization gene cluster in Paenibacillus sp. strain JDR-2 operates as a regulon, coregulated with the expression of xynA1, conferring the ability for efficient assimilation and catabolism of the aldouronate product generated by a multimodular cell surface-anchored GH10 endoxylanase. This cluster offers a desirable metabolic potential for bacterial conversion of hemicellulose fractions of hardwood and crop residues to biobased products.