Complete genome sequence of Paenibacillus sp. strain JDR-2

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b Xylans, including methylglucuronoxylans (MeGX n ) and methylglucuronoarabinoxylans (MeGAX n ), are the predominant polysaccharides in hemicellulose fractions of dicots and monocots available for conversion to biofuels and chemicals. Paenibacillus sp. strain JDR-2 (Pjdr2) efficiently depolymerizes MeGX n and MeGAX n and assimilates the generated oligosaccharides, resulting in efficient saccharification and subsequent metabolism of these polysaccharides. A xylan utilization regulon encoding a cellassociated GH10 (glycoside hydrolase family 10) endoxylanase, transcriptional regulators, ABC (ATP binding cassette) transporters, an intracellular GH67 ␣-glucuronidase, and other glycoside hydrolases contributes to complete metabolism. This GH10/GH67 system has been proposed to account for preferential utilization of xylans compared to free oligo-and monosaccharides. To identify additional genes contributing to MeGX n and MeGAX n utilization, the transcriptome of Pjdr2 has been sequenced following growth on each of these substrates as well as xylose and arabinose. Increased expression of genes with different substrates identified pathways common or unique to the utilization of MeGX n or MeGAX n . Coordinate upregulation of genes comprising the GH10/GH67 xylan utilization regulon is accompanied with upregulation of genes encoding a GH11 endoxylanase and a GH115 ␣-glucuronidase, providing evidence for a novel complementary pathway for processing xylans. Elevated expression of genes encoding a GH43 arabinoxylan arabinofuranohydrolase and an arabinose ABC transporter on MeGAX n but not on MeGX n supports a process in which arabinose may be removed extracellularly followed by its rapid assimilation. Further development of Pjdr2 for direct conversion of xylans to targeted products or introduction of these systems into fermentative strains of related bacteria may lead to biocatalysts for consolidated bioprocessing of hemicelluloses released from lignocellulose.

Section: Resultsmentioning

confidence: 99%

“…Paenibacillus sp. strain JDR-2 (Pjdr2) was previously isolated from decaying sweetgum wood in our laboratory (19,(21)(22)(23). Pjdr2 was stored, resuscitated, and cultured to prepare initial inocula as described previously (20).…”

Section: Preparation Of Xylansmentioning

confidence: 99%

Transcriptomic Analysis of Xylan Utilization Systems in Paenibacillus sp. Strain JDR-2

Sawhney

Crooks

John

et al. 2015

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“…Paenibacillus sp. JDR-2 was isolated from decaying sweetgum wood in our laboratory (11,18,21,22). A glycerol freezer stock of Paenibacillus sp.…”

Section: Methodsmentioning

confidence: 99%

“…As a xylanolytic bacterium with a fully sequenced genome, including a xylan utilization regulon, Paenibacillus sp. JDR-2 provides a system to further define and develop processes for the efficient conversion of MeGAX n as well as MeGX n to targeted products (11,18,21,22).…”

mentioning

confidence: 99%

GH51 Arabinofuranosidase and Its Role in the Methylglucuronoarabinoxylan Utilization System in Paenibacillus sp. Strain JDR-2

Sawhney

Preston

2014

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Methylglucuronoarabinoxylan (MeGAX n ) from agricultural residues and energy crops is a significant yet underutilized biomass resource for production of biofuels and chemicals. Mild thermochemical pretreatment of bagasse yields MeGAX n requiring saccharifying enzymes for conversion to fermentable sugars. A xylanolytic bacterium, Paenibacillus sp. strain JDR-2, produces an extracellular cell-associated GH10 endoxylanse (XynA 1 ) which efficiently depolymerizes methylglucuronoxylan (MeGX n ) from hardwoods coupled with assimilation of oligosaccharides for further processing by intracellular GH67 ␣-glucuronidase, GH10 endoxylanase, and GH43 ␤-xylosidase. This process has been ascribed to genes that comprise a xylan utilization regulon that encodes XynA 1 and includes a gene cluster encoding transcriptional regulators, ABC transporters, and intracellular enzymes that convert assimilated oligosaccharides to fermentable sugars. Here we show that Paenibacillus sp. JDR-2 utilized MeGAX n without accumulation of oligosaccharides in the medium. The Paenibacillus sp. JDR-2 growth rate on MeGAX n was 3.1-fold greater than that on oligosaccharides generated from MeGAX n by XynA 1 . Candidate genes encoding GH51 arabinofuranosidases with potential roles were identified. Following growth on MeGAX n , quantitative reverse transcription-PCR identified a cluster of genes encoding a GH51 arabinofuranosidase (AbfB) and transcriptional regulators which were coordinately expressed along with the genes comprising the xylan utilization regulon. The action of XynA 1 on MeGAX n generated arabinoxylobiose, arabinoxylotriose, xylobiose, xylotriose, and methylglucuronoxylotriose. Recombinant AbfB processed arabinoxylooligosaccharides to xylooligosaccharides and arabinose. MeGAX n processing by Paenibacillus sp. JDR-2 may be achieved by extracellular depolymerization by XynA 1 coupled to assimilation of oligosaccharides and further processing by intracellular enzymes, including AbfB. Paenibacillus sp. JDR-2 provides a GH10/GH67 system complemented with genes encoding intracellular GH51 arabinofuranosidases for efficient utilization of MeGAX n .

“…Recent whole-genome sequencing of Paenibacillus JDR-2 made it possible to locate resident glycoside hydrolase genes (26). In that study on glucan utilization, two adjacent GH16 endoglucanase genes, flanked by three genes that encode an ABC transporter and a pair of transcriptional regulators, were found in a cassette (Fig.…”

Section: Gene Neighborhood Of Gh16 Endoglucanase Genesmentioning

confidence: 99%

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

Chow

Kim

Rhee

et al. 2016

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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.