Center for Computational Molecular Biology Faculty Search Candidate
"Comparative Analyses of the Distribution of Promoter Motifs across Bacterial Genomes"
Maria Pilar Francino, Ph.D., DOE Joint Genome Institute
Wednesday, April 2, 2008 at 4:00 P.M.
Room 241 Swig Boardroom (2nd Floor CIT)
Because binding of RNA polymerase (RNAP) to misplaced sites could compromise the efficiency of transcription, natural selection for the optimization of gene expression should regulate the distribution of DNA motifs capable of RNAP-binding across the genome. We have analyzed the distribution of -10 promoter motifs recognized by the 70 subunit of RNAP in 42 bacterial genomes. We show that selection on these motifs operates across the genome, maintaining an over-representation of -10 motifs in regulatory sequences while eliminating them from the nonfunctional and, in most cases, from the protein coding regions. In some genomes, however, -10 sites are over-represented in the coding sequences; these sites could induce pauses effecting regulatory roles throughout the length of a transcriptional unit. For nonfunctional sequences, the extent of motif under-representation varies across genomes in a manner that broadly correlates with the number of tRNA genes, a good indicator of translational speed and growth rate. This suggests that minimizing the time invested in gene transcription is an important selective pressure against spurious binding. However, selection against spurious binding is also detectable in the reduced genomes of host-restricted bacteria that grow at slow rates, indicating that components of efficiency other than speed may also be important. Minimizing the number of RNAP molecules per cell required for transcription, and the corresponding energetic expense, may be most relevant in slow growers.
These results indicate that genome-level properties affecting the efficiency of transcription and translation can respond in an integrated manner to optimize gene expression. The detection of selection against promoter motifs in nonfunctional regions also indicates that no sequence may evolve free of selective constraints, at least in the relatively small and unstructured genomes of bacteria.
Host: Daniel Weinreich
| Page Owner: Webmaster | Last Modified: Mon Mar 10 15:09:14 2008 |