Transcriptomic Analysis of Xylan Utilization Systems in Paenibacillus

Xylans, including methylglucuronoxylans (MeGXn) andmethylglucuronoarabinoxylans (MeGAXn), are the predominant poly-saccharides in hemicellulose fractions of dicots andmonocots available for conversion to biofuels and chemicals. Paenibacillus sp. strain JDR-2 (Pjdr2) efficiently depolymerizes MeGXn andMeGAXn and assimilates the generated oligosaccharides, resulting in efficient saccharification and subsequent metabolism of these polysaccharides. A xylan utilization regulon encoding a cell-associated GH10 (glycoside hydrolase family 10) endoxylanase, transcriptional regulators, ABC (ATP binding cassette) trans-porters, 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- andmonosaccha-rides. To identify additional genes contributing toMeGXn andMeGAXn utilization, the transcriptome of Pjdr2 has been se-quenced following growth on each of these substrates as well as xylose and arabinose. Increased expression of genes with differ-ent substrates identified pathways common or unique to the utilization of MeGXn orMeGAXn. Coordinate upregulation of genes comprising the GH10/GH67 xylan utilization regulon is accompanied with upregulation of genes encoding a GH11 en-doxylanase and a GH115-glucuronidase, providing evidence for a novel complementary pathway for processing xylans. Ele-vated expression of genes encoding a GH43 arabinoxylan arabinofuranohydrolase and an arabinose ABC transporter on MeGAXn but not onMeGXn supports a process in which arabinose may be removed extracellularly followed by its rapid assimi-lation. Further development of Pjdr2 for direct conversion of xylans to targeted products or introduction of these systems int