Caldicellulosiruptor saccharolyticus transcriptomes reveal consequences of chemical pretreatment and genetic modification of lignocellulose

Abstract

SummaryRecalcitrance of plant biomass is a major barrier for commercially feasible cellulosic biofuel production. Chemical and enzymatic assays have been developed to measure recalcitrance and carbohydrate composition; however, none of these assays can directly report which polysaccharides a candidate microbe will sense during growth on these substrates. Here, we propose using the transcriptomic response of the plant biomass‐deconstructing microbe, Caldicellulosiruptor saccharolyticus, as a direct measure of how suitable a sample of plant biomass may be for fermentation based on the bioavailability of polysaccharides. Key genes were identified using the global gene response of the microbe to model plant polysaccharides and various types of unpretreated, chemically pretreated and genetically modified plant biomass. While the majority of C. saccharolyticus genes responding were similar between plant biomasses; subtle differences were discernable, most importantly between chemically pretreated or genetically modified biomass that both exhibit similar levels of solubilization by the microbe. Furthermore, the results here present a new paradigm for assessing plant–microbe interactions that can be deployed as a biological assay to report on the complexity and recalcitrance of plant biomass.

Insights into Thermophilic Plant Biomass Hydrolysis from Caldicellulosiruptor Systems Biology

“…With the availability of genome sequences, custom oligonucleotide microarray chips were designed for C. saccharolyticus [15], C. bescii [17], and C. kronotskyensis [26]. Most studies focused on comparisons of global transcriptomes in response to various monosaccharide sugars [15,28], plant related polysaccharides [17,28,29], and plant biomass [26,29]. Despite their common ability to solubilize plant biomass, differences in the regulation of CAZymes, motility-related genes, and ABC transporters have been observed among the highly cellulolytic C. bescii, C. kronotskyensis, and moderately cellulolytic C. saccharolyticus [26] and in a proteomic comparison between C. bescii and C. obsidiansis [30].…”

Bioavailability of Carbohydrate Content in Natural and Transgenic Switchgrasses for the Extreme Thermophile Caldicellulosiruptor bescii

“…For microbially based bioprocesses, the bioavailability of the carbohydrate content of the plant cell wall is a critical factor in achieving high yields and conversion efficiencies. Carbohydrate access to microbial attack varies considerably with plant properties (6), but this issue must be addressed to develop optimal bioprocesses for generating bio-based products from renewable resources.…”

“…Thus, they offer a distinct advantage over microbes that can ferment only C 6 sugars or that are subject to carbon catabolite repression (7). When encountering plant biomass, Caldicellulosiruptor responds by upregulating carbohydrate ABC transporters and unique multidomain extracellular glycoside hydrolases (6,8), enzymes that are crucial to the degradation capacity of the microbe (13,14). The model organism in this genus, Caldicellulosiruptor bescii, not only utilizes unpretreated plant biomass (8,15,16) but has been genetically modified for improved crystalline cellulose degradation (17), xylan degradation (18), and ethanol production (19).…”

Transcriptional Regulation of Plant Biomass Degradation and Carbohydrate Utilization Genes in the Extreme Thermophile Caldicellulosiruptor bescii

“…Previous transcriptomic studies in C. bescii , C. saccharolyticus , and C. kronotskyensis identified groups of genes encoding GHs/CBMs and ABC transporters that are upregulated on plant biomass substrates cellulose and switchgrass ( 9 ). Furthermore, the transcriptional response of C. saccharolyticus to various monosaccharides ( 10 ) and polysaccharides, including cellulose, mannan, pectin, and xylan ( 11 ), revealed patterns of genes that are coordinately regulated in response to specific carbohydrates. However, the specific transcription factors (TFs) and regulatory mechanisms for the CU gene network in Caldicellulosiruptor species remain unexplored.…”