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

Abstract

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.

Metagenomic and metaproteomic analyses of a corn stover-adapted microbial consortium EMSD5 reveal its taxonomic and enzymatic basis for degrading lignocellulose

“…The cause for the high abundance of α-amylase was unclear. A recent transcriptomic study suggested that genes encoding amylases in Paenibacillus could be induced by xylan [51]. This was, however, unlikely in our case, because the protein abundance of the α-amylase decreased significantly over the cultivation period, as detailed below.…”

Functional diversity and properties of multiple xylanases from Penicillium oxalicum GZ-2

“…The production of multiple xylanases in microorganisms has evolved diverse enzymes with different physiological properties for more effective degradation of the complex plant biomass 20 21 . The presence of multiple xylanase isoforms in P. oxalicum GZ-2 was observed after 7 days of fermentation in previous studies using zymography 5 18 .…”

Genomic and transcriptomic analysis of carbohydrate utilization by Paenibacillus sp. JDR-2: systems for bioprocessing plant polysaccharides

“…JDR-2 (Pjdr2) originally isolated from sweetgum wood ( Liquidambar styraciflua ) disks exposed to surface soils has been shown to completely utilize the lignocellulosic polymer glucuronoxylan (GX n ). Previous studies showed that growth on minimal media supplemented with polymeric xylan was preferred to that on simple sugars such as xylose, glucose, or arabinose [ 1 , 2 ]. These studies indicated that efficient xylan utilization is attributable, in part, to a 157 kDa GH10 β-1,4-endoxylanase (Xyn10A 1 ) containing carbohydrate binding modules (CBM) for binding to polysaccharides and surface layer homology (SLH) domains for cell-association.…”

“…Genomic organization of xylan utilization genes ( a ) assigned a role in xylan utilization in Pjdr2. For a complete list see Additional file 1 [ 1 ]. Genetic organization of barley β-glucan ( b ) and starch ( c ) utilization regulons consisting of genes encoding extracellular multi-modular cell-associated or secreted glycoside hydrolases for depolymerization, ABC transporters for assimilation of the generated oligosaccharides, and intracellular glycoside hydrolases for further processing and metabolism.…”