Systems Biology Analysis of Cellulose Degradation by Clostridium thermocellum

This is the first comprehensive examination of gene expression in C. thermocellum under defined growth conditions.

The Science

The bacterium Clostridium thermocellum is highly specialized to degrade cellulosic plant material through the use of cellulosomes, complex multi-component molecular machines tethered to the bacteria’s surface. The microbe can adjust the modular composition of its cellulosomes in response to various types of substrates and environmental conditions, but the mechanisms regulating this process remain poorly understand. Researchers at the DOE Great Lakes Bioenergy Research Center at the University of Wisconsin–Madison have completed a global analysis of gene expression in C. thermocellum during controlled growth on cellulose and cellobiose (a simpler two sugar compound). Over 350 genes involved in cellulosome assembly, cellulose chain deconstruction, product uptake, and downstream synthesis of ethanol and hydrogen were observed to be differentially expressed depending on substrate and growth rate. The most highly expressed genes from this set encode glycoside hydrolases, scaffoldins, and other proteins known to participate in cellulose utilization.  In addition, the study provided new clues on the roles of numerous C. thermocellum genes that are currently categorized as having unknown functions. These results reveal the complex control that C. thermocellum exerts over its cellulose degrading machinery and provides new routes for development of this organism for bioenergy production.

The Impact

The pattern of expression of transcriptional regulators, sigma factors, and signal transducers indicates that response to growth rate is the dominant global mechanism used for control of gene expression in C. thermocellum. Importantly, the use of the chemostat technique allowed the effects of different growth rates to be analyzed separately from the effects of different substrates.

Principal Investigator

Brian G. Fox
University of Wisconsin–Madison
[email protected]

BER Program Manager

Dawn Adin

U.S. Department of Energy, Biological and Environmental Research (SC-33)
Biological Systems Science Division
[email protected]


Riederer, A., T. E. Takasuka, S. Makino, D. M. Stevenson, Y.V. Bukhman, N. L. Elsen, and B. G. Fox. 2010. “Global Gene Expression Patterns in Clostridium thermocellum from Microarray Analysis of Chemostat Culture on Cellulose or Cellobiose,” Applied and Environmental Microbiology. DOE:10.1128/AEM.02008-10.