title: Deletion of a gene cluster encoding pectin degrading enzymes in Caldicellulosiruptor bescii reveals an important role for pectin in plant biomass recalcitrance.
abstract: BACKGROUND
  A major obstacle, and perhaps the most important economic barrier to the effective use of plant biomass for the production of fuels, chemicals, and bioproducts, is our current lack of knowledge of how to efficiently and effectively deconstruct wall polymers for their subsequent use as feedstocks. Plants represent the most desired source of renewable energy and hydrocarbons because they fix CO2, making their use carbon neutral. Their biomass structure, however, is a barrier to deconstruction, and this is often referred to as recalcitrance. Members of the bacterial genus Caldicellulosiruptor have the ability to grow on unpretreated plant biomass and thus provide an assay for plant deconstruction and biomass recalcitrance.
  
  
  RESULTS
  Using recently developed genetic tools for manipulation of these bacteria, a deletion of a gene cluster encoding enzymes for pectin degradation was constructed, and the resulting mutant was reduced in its ability to grow on both dicot and grass biomass, but not on soluble sugars. The plant biomass from three phylogenetically diverse plants, Arabidopsis (a herbaceous dicot), switchgrass (a monocot grass), and poplar (a woody dicot), was used in these analyses. These biomass types have cell walls that are significantly different from each other in both structure and composition. While pectin is a relatively minor component of the grass and woody dicot substrates, the reduced growth of the mutant on all three biomass types provides direct evidence that pectin plays an important role in biomass recalcitrance. Glycome profiling of the plant material remaining after growth of the mutant on Arabidopsis biomass compared to the wild-type revealed differences in the rhamnogalacturonan I, homogalacturonan, arabinogalactan, and xylan profiles. In contrast, only minor differences were observed in the glycome profiles of the switchgrass and poplar biomass.
  
  
  CONCLUSIONS
  The combination of microbial digestion and plant biomass analysis provides a new and important platform to identify plant wall structures whose presence reduces the ability of microbes to deconstruct plant walls and to identify enzymes that specifically deconstruct those structures.
authors.affiliation: Department of Genetics, University of Georgia, Athens, GA 30602 USA ; The BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA.
authors.forename: Daehwan
authors.initials: D
authors.lastname: Chung
authors.affiliation: Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602 USA ; The BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA.
authors.forename: Sivakumar
authors.initials: S
authors.lastname: Pattathil
authors.affiliation: Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602 USA ; The BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA.
authors.forename: Ajaya K
authors.initials: AK
authors.lastname: Biswal
authors.affiliation: The BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA ; Department of Plant Biology, University of Georgia, Athens, GA 30602 USA.
authors.forename: Michael G
authors.initials: MG
authors.lastname: Hahn
authors.affiliation: Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602 USA ; The BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA.
authors.forename: Debra
authors.initials: D
authors.lastname: Mohnen
authors.affiliation: Department of Genetics, University of Georgia, Athens, GA 30602 USA ; The BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA.
authors.forename: Janet
authors.initials: J
authors.lastname: Westpheling
keywords: Bioenergy; Biomass deconstruction; Pectin; Thermophile