C. saccharolyticus transcriptomes reveal consequences of chemical pre-treatment and genetic modification of lignocellulose

The genome of the lignocellulose-degrading, extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus encodes genes comprising clusters of glycoside hydrolases, ABC transporters and metabolic enzymes that are transcriptionally responsive to carbohydrates. Transcriptomic and biosolubilization analyses were used to determine if C. saccharolyticus could be deployed as a probe to assess the characteristics of plant biomass feedstocks and efficacy of pre-treatment methods, as these both relate to deconstruction strategies for biofuels production. Based on the response of C. saccharolyticus to plant cell wall polysaccharides, genomic loci were identified that reflected the availability of cellulose, glucomannan, pectin and xylan in biomass to microbial degradation. Furthermore, these loci were useful in assessing how various plant biomass feedstocks (genetically and chemically modified Populus sp., unpretreated Populus sp., and chemically modified switchgrass) were amenable C. saccharolyticus solubilization. Three independant 4-slide loop designs were used with a total of ten treatments. Biological repeats were harvested for each treatment. Loop #1 consists of plant model polysaccharides: crystalline cellulose (Avicel), mannan (konjac glucomannan), xylan (birchwood) and pectin. Loop #2 consists of comically pretreated and genetically modified plant biomass: Populus trichopcarpa (unpretreated), dilute acid pretreated switchgrass, dilute pretreated Populus trichocarpa x deltoides and genetically modified, lignin-reduced P. trichocarpa (as4CL1). Loop #3 consists of genetically modified P. trichocarpa: P. trichocarpa (unpretreated), and two variants of cellulose-reduced P. trichocarpa (7-1 and 7-2). Each condition was labeled with cy3 and cy5 dyes.