Structure, Function, and Regulation of the Aldouronate Utilization Gene Cluster from
            <i>Paenibacillus</i>
            sp. Strain JDR-2

Chow, Virginia; Nong, Guangmin; Preston, James F.

doi:10.1128/jb.01141-07

Cited by 40 publications

(61 citation statements)

References 25 publications

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“…These two enzymes generated similar oligosaccharide products from laminarin and barley glucan. The preferential growth rates on both polysaccharides relative to those on cellobiose and glucose, and the coordinate expression of a cluster of genes encoding Bgl16A 1 , Bgl16A 2 , an ABC transporter, and transcriptional regulators, support the presence of a regulon for the efficient utilization of soluble glucan, similar to the xylan utilization regulon described previously (7). To the extent that 1,3-1,4-␤-glucans make up a significant portion of the grains of poaceous cereal crops, including barley, wheat, and oats, the ␤-glucanase regulon in Paenibacillus JDR-2 may serve as a model for the development of systems for the bioconversion to biofuels and chemical feedstocks of those portions of commodity crops that are in surplus relative to their current applications.…”

mentioning

confidence: 91%

“…1B). The modular composition of the Bgl16A 1 protein including 3 SLH domains suggests a similarity to the secreted Xyn10A 1 protein, which has been implicated in the efficient utilization of methylglucuronoxylans (6)(7)(8).…”

Section: Gene Neighborhood Of Gh16 Endoglucanase Genesmentioning

confidence: 99%

“…Quantitative RT-PCR (qRT-PCR) was performed as described previously (7). Quantitative RT-PCRs were set up using the iScript One-Step RT-PCR kit with SYBR green (catalog no.…”

Section: Methodsmentioning

confidence: 99%

“…The secreted xylanase includes four carbohydrate binding modules (CBM) (1 CBM9 domain, putatively binding cellulose, and 3 CBM22 domains, putatively binding xylan) and three surface layer homology (SLH) domains for anchoring to the cell surface. During growth on MeGX n or MeGAX n , the absence of accumulated neutral xylooligosaccharides or acidic aldouronic xylooligosaccharides in the medium and the coordinate expression of genes comprising a xylan utilization regulon encoding these proteins support a process in which extracellular depolymerization, import of oligosaccharides, and intracellular metabolism are thermodynamically, if not mechanistically, coupled (6)(7)(8)(9).…”

mentioning

confidence: 99%

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A 1,3-1,4-β-Glucan Utilization Regulon in Paenibacillus sp. Strain JDR-2

Chow

Kim

Rhee

et al. 2016

Appl Environ Microbiol

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bPaenibacillus sp. strain JDR-2 (Paenibacillus JDR-2) secretes a multimodular cell-associated glycoside hydrolase family 10 (GH10) endoxylanase (XynA10A 1 ) that catalyzes the depolymerization of methylglucuronoxylan (MeGX n ) and rapidly assimilates the products of depolymerization. Efficient utilization of MeGX n has been postulated to result from the coupling of the processes of exocellular depolymerization and assimilation of oligosaccharide products, followed by intracellular metabolism. Growth and substrate utilization patterns with barley glucan and laminarin similar to those observed with MeGX n as a substrate suggest similar processes for 1,3-1,4-␤-glucan and 1,3-␤-glucan depolymerization and product assimilation. The Paenibacillus JDR-2 genome includes a cluster of genes encoding a secreted multimodular GH16 ␤-glucanase (Bgl16A 1 ) containing surface layer homology (SLH) domains, a secreted GH16 ␤-glucanase with only a catalytic domain (Bgl16A 2 ), transporter proteins, and transcriptional regulators. Recombinant Bgl16A 1 and Bgl16A 2 catalyze the formation of trisaccharides, tetrasaccharides, and larger oligosaccharides from barley glucan and of mono-, di-, tri-, and tetrasaccharides and larger oligosaccharides from laminarin. The lack of accumulation of depolymerization products during growth and a marked preference for polymeric glucan over depolymerization products support a process coupling extracellular depolymerization, assimilation, and intracellular metabolism for ␤-glucans similar to that ascribed to the GH10/GH67 xylan utilization system in Paenibacillus JDR-2. Coordinate expression of genes encoding GH16 ␤-glucanases, transporters, and transcriptional regulators supports their role as a regulon for the utilization of soluble ␤-glucans. As in the case of the xylan utilization regulons, this soluble ␤-glucan regulon provides advantages in the growth rate and yields on polymeric substrates and may be exploited for the efficient conversion of plant-derived polysaccharides to targeted products.

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mentioning

confidence: 91%

Section: Gene Neighborhood Of Gh16 Endoglucanase Genesmentioning

confidence: 99%

“…Quantitative RT-PCR (qRT-PCR) was performed as described previously (7). Quantitative RT-PCRs were set up using the iScript One-Step RT-PCR kit with SYBR green (catalog no.…”

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

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A 1,3-1,4-β-Glucan Utilization Regulon in Paenibacillus sp. Strain JDR-2

Chow

Kim

Rhee

et al. 2016

Appl Environ Microbiol

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“…[25], Bacillus pumilus [26]. However, the fragments often contain the whole operon with intact regulator in the fragment [26].…”

Section: Introductionmentioning

confidence: 99%

Cloning and Over-expression of xynB Gene of Bacillus subtilis subsp. spizizenii W23 into Escherichia coli Origami Host Cells

Wahjudi

Catherina²,

Wangunhardjo³

et al. 2017

KLS

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The xynB gene of Bacillus subtilis subsp. spizizenii W23 is predicted to encode a xylan 1,4-beta-xylosidase. Application of XynB enzymes in industries is wide. Production of this enzyme in its host cells is naturally restricted by repression process. It will give certain beneficial to over-expressed the enzymes in other host-cells under inducing promoter. This study aimed to clone the xynB gene from Bacillus subtilis subsp. spizizenii W23, to pMMB67EH plasmid, and to over-express the xynB gene in Escherichia coli Origami as host cells. The xynB gene was successfully amplified by polymerase chain reaction (PCR) technique using a pair of primers flanking the gene sequence and chromosomal DNA of the W23 strain as a template. The xynB gene inserted in recombinant plasmid was confirmed by PCR detection using primers pair's specific for xynB gene and for the vector, then continued by restriction analyses. The result showed that transformants clone 9 and 10 bear the recombinant pMMB-xynB plasmid. The xylanase activity of xynB gene in Escherichia coli Origami clone 10 was detected by sodium-dodecyl-sulfate polyacrylamide gel analyses and with addition of isopropyl--D-thio-galactoside (IPTG) as an inducer. The protein seem to be overexpressed as intra-and extra-cellular protein detected on SDS-PAGE gel. Result from xylan degrading activity on Luria-Bertani-xylan-IPTG plate with addition of Congo Red, showed that the cells with pMMB-xynB recombinant plasmid have clear zone around the colonies while the transformant bearing an empty plasmid showed no clear zone. It could be concluded that the xynB gene of Bacillus subtilis subsp.spizizenii W23 has been successfully been cloned on pMMB67EH plasmid and over-expressed in the Escherichia coli Origami cells as intra-and extra-cellular protein, as observed on SDS-PAGE gel analysis. The protein has activity on xylan degradation.

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Biochemical characterization of a novel dual-function arabinofuranosidase/xylosidase isolated from a compost starter mixture

Wagschal

Heng

Lee

et al. 2009

Appl Microbiol Biotechnol

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The gene encoding a glycoside hydrolase family 43 enzyme termed deAX was isolated and subcloned from a culture seeded with a compost starter mixed bacterium population, expressed with a C-terminal His(6)-tag, and purified to apparent homogeneity. deAX was monomeric in solution and had a broad pH maximum between pH 5.5 and pH 7. A twofold greater k (cat)/K (m) for the p-nitrophenyl derivative of alpha-L: -arabinofuranose versus that for the isomeric substrate beta-D-xylopyranose was due to an appreciably lower K (m) for the arabinofuranosyl substrate. Substrate inhibition was observed for both 4-methylumbelliferryl arabinofuranoside and the xylopyranoside cogener. While no loss of activity was observed over 4 h at 40 degrees C, the observed t (1/2) value rapidly decreased from 630 min at 49 degrees C to 47 min at 53 degrees C. The enzyme exhibited end-product inhibition, with a K (i) for xylose of 145 mM, 18.5 mM for arabinose, and 750 mM for glucose. Regarding natural substrate specificity, deAX had arabinofuranosidase activity on sugar beet arabinan, 1,5-alpha-L-arabinobiose, and 1,5-alpha-L-arabinotriose, and wheat and rye arabinoxylan, while xylosidase activity was detected for the substrates xylobiose, xylotriose, xylotetraose, and arabinoxylan from beech and birch. Thus, deAX can be classified as a dual-function xylosidase/arabinofuranosidase with respect to both artificial and natural substrate specificity.

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Structure, Function, and Regulation of the Aldouronate Utilization Gene Cluster from Paenibacillus sp. Strain JDR-2

Cited by 40 publications

References 25 publications

A 1,3-1,4-β-Glucan Utilization Regulon in Paenibacillus sp. Strain JDR-2

A 1,3-1,4-β-Glucan Utilization Regulon in Paenibacillus sp. Strain JDR-2

Cloning and Over-expression of xynB Gene of Bacillus subtilis subsp. spizizenii W23 into Escherichia coli Origami Host Cells

Biochemical characterization of a novel dual-function arabinofuranosidase/xylosidase isolated from a compost starter mixture

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