Genome-scale approach towards investigating bacterial gene regulation

We take a genome-scale approach towards tackling our questions of interest. Genomics complements the detailed findings of reductionist molecular biology and biochemistry by describing general principles and identifying exceptions. The large-scale nature and the gaining popularity of genomic studies together generate a flood of biological data, the interpretation of which requires computational tools and expertise.

Our lab is currently focusing on the evolution of transcription factors (TFs). These proteins, despite performing important roles in regulating gene expression, are not universally conserved and, in bacteria, are subject to extensive losses and lineage-specific gains by horizontal gene transfer. No comparative genomic approach has managed to identify any TF as a minimal requirement for cellular life. This is contrast to non-specific DNA binding proteins involved in, say, chromosome compaction, which would be necessary even in a hypothetical minimal cell with a couple of hundred genes. Both sequence-specific DNA binding TFs and other non-specific DNA and RNA binding proteins usually belong to the same protein superfamilies and therefore likely to be evolutionarily related. Our work at present tries to investigate these relationships for TF-containing protein families and superfamilies in Bacteria, Archaea and Eukarya.