Szymon M. Kiełbasa (email@example.com)
Hanspeter Herzel (firstname.lastname@example.org)
Ilka M. Axmann (email@example.com)
MPI MG, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, D-14195 Berlin, Germany
ITB, Institute for Theoretical Biology, Humboldt University of Berlin, Invalidenstrasse 43, D-10115 Berlin, Germany
The free-living, oxyphototroph bacteria of the group of Prochlorococcus populate widely the oceans. Genomic information of nine marine cyanobacteria was used to predict signals essential for regulation. We implemented a pipeline that automatically calculates BLASTp alignments of query genomes, selects a representative subset of orthologs and predicts motifs conserved in their upstream sequences. Next, similar motifs are clustered into groups which could contain profiles recognized by different transcription factors. The phylogenetic footprinting pipeline revealed a minimal conserved set of putative transcription factors, binding sites and regulons for the chosen marine cyanobacterial genomes. DNA-binding motifs for NtcA and LexA were correctly identified. The relevance of transcriptional regulation of predicted cis elements was supported experimentally.