Transcriptomic and proteomic analyses of core metabolism in Clostridium termitidis CT1112 during growth on α-cellulose, xylan, cellobiose and xylose

Abstract

BackgroundClostridium termitidis CT1112 is an anaerobic, Gram-positive, mesophilic, spore-forming, cellulolytic bacterium, originally isolated from the gut of a wood feeding termite Nasusitermes lujae. It has the ability to hydrolyze both cellulose and hemicellulose, and ferment the degradation products to acetate, formate, ethanol, lactate, H2, and CO2. It is therefore ges in gene and gene product expression during growth of C. termitidis on cellobiose, xylose, xylan, and α–cellulose.ResultsCorrelation of transcriptome and proteome data with growth and fermentation profiles identified putative carbon-catabolism pathways in C. termitidis. The majority of the proteins associated with central metabolism were detected in high abundance. While major differences were not observed in gene and gene-product expression for enzymes associated with metabolic pathways under the different substrate conditions, xylulokinase and xylose isomerase of the pentose phosphate pathway were found to be highly up-regulated on five carbon sugars compared to hexoses. In addition, genes and gene-products associated with a variety of cellulosome and non-cellulosome associated CAZymes were found to be differentially expressed. Specifically, genes for cellulosomal enzymes and components were highly expressed on α–cellulose, while xylanases and glucosidases were up-regulated on 5 carbon sugars with respect to cellobiose. Chitinase and cellobiophosphorylases were the predominant CAZymes expressed on cellobiose. In addition to growth on xylan, the simultaneous consumption of two important lignocellulose constituents, cellobiose and xylose was also demonstrated.ConclusionThere are little changes in core-metabolic pathways under the different carbon sources compared. The most significant differences were found to be associated with the CAZymes, as well as specific up regulation of some key components of the pentose phosphate pathway in the presence of xylose and xylan. This study has enhanced our understanding of the physiology and metabolism of C. termitidis, and provides a foundation for future studies on metabolic engineering to optimize biofuel production from natural biomass.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-016-0711-x) contains supplementary material, which is available to authorized users.

Investigating the Central Metabolism of Clostridium thermosuccinogenes

“…Link between C 5 and C 3 /C 6 metabolism. The absence of an annotated TAL has already been discussed for several of the cellulolytic clostridia (20)(21)(22), and according to Schellenberg et al (22), 18% of clostridial genomes do not have a TAL annotated, of which at least a few, including C. thermosuccinogenes, can grow well on pentose sugars. From the transcriptomics data, no candidate genes were found, and none of the annotated genes from the nonoxidative PPP appeared to be differentially expressed during growth on xylose versus that on glucose, apart from the genes responsible for the formation of X5P (see Table S2 in the supplemental material).…”

Engineering cellulolytic bacterium Clostridium thermocellum to co‐ferment cellulose‐ and hemicellulose‐derived sugars simultaneously

“…Such conceptually desirable process configuration to yield products in one integrated step without separate addition of exogenous enzymes is referred to as consolidated bioprocessing (CBP) (Lynd, Wyman, & Gerngross, ; van Walsum & Lynd, ). Several cellulolytic microbes are under characterization and strain development (Blumer‐Schuette et al, ; Higashide, Li, Yang, & Liao, ; Kim, Chung, Himmel, Bomble, & Westpheling, ; Munir et al, ). Of these cellulolytic bacteria, Clostridium thermocellum is an anaerobe, producing an intricate multienzyme complex called the cellulosome (Bayer, Belaich, Shoham, & Lamed, ; Demain, Newcomb, & Wu, ; Doi & Kosugi, ; Schwarz, ), and displays one of the fastest growth rates on crystalline cellulose (Demain et al, ; Lynd et al, ).…”

Transcriptomic Profile of Lignocellulose Degradation from Trametes versicolor on Poplar Wood

“…Recent studies related to transcriptomic analysis of other white rot fungi were performed to evaluate the degrading mechanism of white rot fungi (Couger et al2015;Munir et al 2016). However, changes in the transcriptome of T. versicolor during growth on a wood substrate have not been studied.…”