Biotechnology and Bioprocess Engineering

, Volume 10, Issue 5, pp 432–443

Design, optimization and validation of genomic DNA microarrays for examining theClostridium acetobutylicum transcriptome


  • Keith V. Alsaker
    • Department of Chemical and Biological EngineeringNorthwestern University
  • Carlos J. Paredes
    • Department of Chemical and Biological EngineeringNorthwestern University
    • Department of Chemical and Biological EngineeringNorthwestern University

DOI: 10.1007/BF02989826

Cite this article as:
Alsaker, K.V., Paredes, C.J. & Papoutsakis, E.T. Biotechnol. Bioprocess Eng. (2005) 10: 432. doi:10.1007/BF02989826


Microarray technology has contributed significantly to the understanding of bacterial genetics and transcriptional regulation. One neglected aspect of this technology has been optimization of microarray-generated signals and quality of generated information. Full genome microarrays were developed forClostridium acetobutylicum through spotting of PCR products that were designed with minimal homology with all other genes within the genome. Using statistical analyses it is demonstrated that signal quality is significantly improved by increasing the hybridization volume, possibly increasing the effective number of transcripts available to bind to a given spot, while changes in labeled probe amounts were found to be less sensitive to improving signal quality. In addition to Q-RT-PCR, array validation was tested by examining the transcriptional program of a mutant (M5) strain lacking the pSOL1 178-gene megaplasmid relative to the wildtype (WT) strain. Under optimal conditions, it is demonstrated that the fraction of false positive genes is 1% when considering differentially expressed genes and 7% when considering all genes with signal above background. To enhance genomic-scale understanding of organismal physiology, using data from these microarrays we estimated that 40–55% of theC. acetobutylicum genome is expressed at any time during batch culture, similar to estimates made forBacillus subtilis.


gram-positivesolvent-productiongene-expressionsporulationheat-shockbutanoldegenerate strainextrachromosomalnumber-of-expressed-genesSpo0AAbrBdiffusion limitationmicroarray design

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© The Korean Society for Biotechnology and Bioengineering 2005