Transcriptomics

Dataset Information

1

Contribution of cell-bound and cell-free cellulosomal versus non-cellulosomal systems in deconstruction of cellulosic biomass by Clostridium thermocellum


ABSTRACT: The high cellulose digestion capability of the anaerobic thermophilic bacterium, Clostridium thermocellum, can be attributed to its efficient glycoside hydrolase system, consisting of both a free-enzyme system and a cellulosomal system, wherein carbohydrate active enzymes (CAZymes) are organized by primary and secondary scaffoldin proteins into large protein complexes bound to the bacterial cell wall. Using an integrated series of experiments encompassing polysaccharide depolymerization assays, direct biochemical analyses and transcriptomics, we show herein that, in addition to cell-bound cellulosomes and “free” enzymes, C. thermocellum naturally employs a system of cell-free cellulosomes that are not designed to be tethered to the cell and can diffuse away to attack polysaccharide substrates at some distance from the cell. By characterizing the cells and the secretomes of a series of mutants in which genes for either individual scaffoldins or combinations thereof are deleted, we demonstrate that the cellulosome is far more important in cellulose degradation than are the free enzymes, and that the primary scaffoldin CipA is much more important for the action of the cellulosomes than is the collective contribution of the secondary scaffoldins. Extensive transcriptomics analyses confirm the above results and extend the study to the effects of scaffoldin deletions on the organism as a whole. To gain insights into the transcriptome profiles of C. thermocellum strains when various cellulosomal scaffoldin genes were deleted. High quality RNA was extracted from C. thermocellum grown on cellulose. Transcriptome profiles were obtained at one time point during actively growing fermentations, mid exponential phase when 50% of the substrate had been consumed.

ORGANISM(S): Hungateiclostridium thermocellum DSM 1313  

SUBMITTER: Qi Xu   Shihui Yang  Lee R Lynd  Edward A Bayer  Yannick J Bomble  Richard J Giannone  Michael G Resch  Kara Podkaminer  Charlotte Wilson  Dawn M Klingeman  Daniel G Olson  Bryon S Donohoe  John O Baker  Steve R Decker  Robert L Hettich  Charlotte M Wilson  Steven D Brown  Michael E Himmel 

PROVIDER: E-GEOD-63883 | ArrayExpress | 2015-02-28

SECONDARY ACCESSION(S): GSE63883PRJNA269315

REPOSITORIES: GEO, ArrayExpress

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