Tuesday, April 20, 2010
11-49

C. thermocellum sigma A promoter predictions using B. subtillis

Jessica L. Linville1, Melissa Lindquist1, Jinlyung Choi2, and Chris D. Cox1. (1) Department of Civil and Environmental Engineering, University of Tennessee, 2006 McCroskey Ave, Knoxville, TN 37917, (2) Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37917

The ability to predict the locations of promoters and transcription factor binding sites within intergenic regions can provide important information for understanding gene regulation. We built a model of the sigma A promoter region of gram positive bacteria using known transcriptional start sites in B. subtlis by separate iterative alignments of the -10 and -35 promoter regions and incorporating a variable gap between the two regions. The models were based on the information content of the sequences. Models for normal and extended -10 promoter regions were developed. We tested the model’s ability to correctly identify the true promoter from a 400 bp intergenic region upstream of the translation start site. The first-generation model was able to identify 60% of the true promoters with a false positive rate of less than 15%. The sequence logos for true positive and false positive promoters were used to develop a second generation model of successfully identifying 80% of the true promoters with a false positive rate of less than 15%.

We have applied the second-generation model to the intergenic region 400bp upstream of the translational start site of predicted operons in Clostridium thermocellum. The predicted promoter locations will be compared to actual transcriptional start sites determined by large-scale pyrosequencing of cDNA reverse-transcribed from mRNA.


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