December 2014 – Transcriptomic Analysis of Xylan Utilization Systems in Paenibacillus sp. JDR-2

Published: January 16th, 2015

Category: Uncategorized


Xylans, including methylglucuronoxylans (MeGXn) and methylglucuronoarabinoxylans (MeGAXn), are the predominant polysaccharides in hemicellulose fractions of dicots and monocots available for conversion to biofuels and chemicals. Paenibacillus sp. JDR-2 (Pjdr2) efficiently depolymerizes MeGXn and MeGAXn 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 transporters, an intracellular GH67 α-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 MeGXn and MeGAXn 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 MeGXn or MeGAXn. Coordinate up-regulation of genes comprising the GH10/GH67 xylan-utilization regulon is accompanied with up-regulation of genes encoding a GH11 endoxylanase and a GH115 α-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 MeGAXn but not on MeGXn 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.

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Learn more about Dr. James Preston!


Department of Microbiology and Cell Science University of Florida

Ph.D.:(1967) Department of Biochemistry, University of Minnesota
Postdoctoral:(1967-1969) Department of Microbiology, Yale University School of Medicine

Contact Information


Teaching Interests

Undergraduate and graduate instruction is provided in areas relating to microbial biotechnology. Lectures and laboratory exercises are designed to provide students with experience in experimental design and the application of current techniques and instrumentation to solve problems in the areas of microbial biochemistry, genetics, and physiology.

Current instructional activity:

MCB 5458, Energy Transformations in Microorganisms. The philosophy of this course is to provide advanced undergraduate and graduate students with exposure to the experimental basis for our current concepts of metabolic potential in microorganisms.

PCB 5136L, Techniques in Microbial and Cell Biology. The philosophy of this course is to provide students with a rigorous exposure to experimental design and instrumental analysis in the general area of microbial biochemistry.

MCB 6409. Microbial Cell Structure and Function. , 3 credits, 6 to 10 students, 3 meetings per week, split with three to four other faculty. The philosophy of this course is to expose students to current approaches to solving research problems in the areas of expertise of some of the graduate faculty in the Department of Microbiology and Cell Science. This course serves first and second year students in the Department and other graduate students from other Departments, e.g. Plant Pathology, Entomology and Nematology, Animal Science, who have interest in research projects related to Microbiology.

MCB 4905. Undergraduate Research. The philosophy or teaching objective for this course is to identify and supervise a research project that is able to challenge an undergraduate student to design and execute experiments that provide credible data for interpretation. The student is expected to complete a defined research project over the course of two to four semesters, and to prepare a research paper describing the results in a format for publication.

 Description of Research

1) Selection of bacterial enzymes for the depolymerization of plant biomass and its fermentative conversion to alternative fuels and bio-based products. Cloning and expression of endoxylanases in bacterial biocatalysts for conversion of glucuronoxylan polymers of the hemicellulose fraction of hardwoods and crop residues to alternative fuels and biobased products.

2) Evolution of molecular mechanisms involved in obligate parasitic relationships of Pasteuria spp. with phytopathogenic nematodes and claderocerans. The goal of this effort is to develop protocols to apply Pasteuria spp. as alternatives to chemical nematicides for the control of root-knot and other phytopathogenic nematodes.  3) Molecular mechanisms associated with formation of bacterial biofilms.  Formation and function of Beta-1,6-poly-N-acetyl-D-glucosamine in bacteria, including plant pathogenic species of Xanthomonas, e.g. the causative agents of citrus canker (X. axonopodis pv. citri) and bacterial spot on pepper and tomato (X. vesicatoria).

Publications in Pub Med

Professional Activities

  • Undergraduate Coordinator 1978 to 1980.
  • Graduate Coordinator 1990 to 1991; 2003 to 2005. University of Florida Graduate Council 1985
  • Editorial Board. Journal of Applied and Environmental Microbiology. 1996-2001.
  • Editorial Board. Journal of Bacteriology. 2005-present.
  • Faculty Advisory Committee to the Vice President of IFAS, 2002-2004.
  • University Senate 2001-2003.
  • University of Florida Research Foundation Professor 2005-2008.

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