Article

Construction and evaluation of a Clostridium thermocellum ATCC 27405 whole-genome oligonucleotide microarray.

Microbial Ecology and Physiology Group, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
Applied biochemistry and biotechnology (Impact Factor: 1.94). 05/2007; 137-140(1-12):663-74. DOI: 10.1007/s12010-007-9087-6
Source: PubMed

ABSTRACT Clostridium thermocellum is an anaerobic, thermophilic bacterium that can directly convert cellulosic substrates into ethanol. Microarray technology is a powerful tool to gain insights into cellular processes by examining gene expression under various physiological states. Oligonucleotide microarray probes were designed for 96.7% of the 3163 C. thermocellum ATCC 27405 candidate protein-encoding genes and then a partial-genome microarray containing 70 C. thermocellum specific probes was constructed and evaluated. We detected a signal-to-noise ratio of three with as little as 1.0 ng of genomic DNA and only low signals from negative control probes (nonclostridial DNA), indicating the probes were sensitive and specific. In order to further test the specificity of the array we amplified and hybridized 10 C. thermocellum polymerase chain reaction products that represented different genes and found gene specific hybridization in each case. We also constructed a whole-genome microarray and prepared total cellular RNA from the same point in early-logarithmic growth phase from two technical replicates during cellobiose fermentation. The reliability of the microarray data was assessed by cohybridization of labeled complementary DNA from the cellobiose fermentation samples and the pattern of hybridization revealed a linear correlation. These results taken together suggest that our oligonucleotide probe set can be used for sensitive and specific C. thermocellum transcriptomic studies in the future.

0 Bookmarks
 · 
89 Views
  • [Show abstract] [Hide abstract]
    ABSTRACT: The BioEnergy Science Center, a nationally and internationally peer-reviewed center of leading scientific institutions and scientists, is organized and in operation as a U.S. Department of Energy Bioenergy Research Center. This Oak Ridge National Laboratory-led Center has members from top-tier universities, leading national labs, and private companies organized as a single project team, with each member chosen for its significant contributions in the Center’s research focus areas. The recalcitrance of cellulosic biomass is viewed as (1) the most significant obstacle to the establishment of a cellulosic biofuels industry, (2) essential to producing cost-competitive fuels, and (3) widely applicable, since nearly all biofuels and biofeedstocks would benefit from such advances. The mission of the BioEnergy Science Center is to make revolutionary advances in understanding and overcoming the recalcitrance of biomass to conversion into sugars, making it feasible to displace petroleum with ethanol and other fuels.
    In Vitro Cellular & Developmental Biology - Plant 01/2009; 45(3):193-198. · 1.14 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Thermophilic microorganisms are attractive candidates for conversion of lignocellulose to biofuels since they produce robust, effective, carbohydrate-degrading enzymes, and survive under harsh bioprocessing conditions that reflect their natural biotopes. However, no naturally occurring thermophile is known that can convert plant biomass into a liquid biofuel at rates, yields and titers that meet current bioprocessing and economic targets. Meeting those targets requires either metabolically engineering solventogenic thermophiles with additional biomass deconstruction enzymes, or engineering plant biomass degraders to produce a liquid biofuel. Thermostable enzymes from microorganisms isolated from diverse environments can serve as genetic reservoirs for both efforts. Because of the the sheer number of enzymes that are required to hydrolyze plant biomass to fermentable oligosaccharides, the latter strategy appears to be the preferred route and thus has received the most attention to date. Thermophilic plant biomass degraders fall into one of two categories: cellulosomal (i.e., multi-enzyme complexes) and non-cellulosomal (i.e., "free" enzyme systems). Plant biomass deconstructing thermophilic bacteria from the genera Clostridium (cellulosomal) and Caldicellulosiruptor (non-cellulosomal), which have potential as metabolic engineering platforms for producing biofuels, are compared and contrasted from a systems biology perspective. This article is protected by copyright. All rights reserved.
    FEMS microbiology reviews 10/2013; · 10.96 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: First isolated in 1926, Clostridium thermocellum has recently received increased attention as a high utility candidate for use in consolidated bioprocessing (CBP) applications. These applications, which seek to process lignocellulosic biomass directly into useful products such as ethanol, are gaining traction as economically feasible routes toward the production of fuel and other high value chemical compounds as the shortcomings of fossil fuels become evident. This review evaluates C. thermocellum's role in this transitory process by highlighting recent discoveries relating to its genomic, transcriptomic, proteomic, and metabolomic responses to varying biomass sources, with a special emphasis placed on providing an overview of its unique, multivariate enzyme cellulosome complex and the role that this structure performs during biomass degradation. Both naturally evolved and genetically engineered strains are examined in light of their unique attributes and responses to various biomass treatment conditions, and the genetic tools that have been employed for their creation are presented. Several future routes for potential industrial usage are presented, and it is concluded that, although there have been many advances to significantly improve C. thermocellum's amenability to industrial use, several hurdles still remain to be overcome as this unique organism enjoys increased attention within the scientific community.
    Frontiers in Chemistry 08/2014; 2:66.

Full-text

Download
5 Downloads
Available from
Oct 3, 2014