We have addressed the distribution and abundance of 75 transcription factor (TF) 
families in complete genomes from 90 different bacterial and archaeal species. 
We found that the proportion of TFs increases with genome size. The deficit of 
TFs in some genomes might be compensated by the presence of proteins organizing 
and compacting DNA, such as histone-like proteins. Nine families are represented 
in all the bacteria and archaea we analyzed, whereas 17 families are specific to 
bacteria, providing evidence for regulon specialization at an early stage of 
evolution between the bacterial and archeal lineages. Ten of the 17 families 
identified in bacteria belong exclusively to the proteobacteria defining a 
specific signature for this taxonomical group. In bacteria, 10 families are lost 
mostly in intracellular pathogens and endosymbionts, while 9 families seem to 
have been horizontally transferred to archaea. The winged helix-turn-helix (HTH) 
is by far the most abundant structure (motif) in prokaryotes, and might have 
been the earliest HTH motif to appear as shown by its distribution and abundance 
in both bacterial and archaeal cellular domains. Horizontal gene transfer and 
lineage-specific gene losses suggest a progressive elimination of TFs in the 
course of archaeal and bacterial evolution. This analysis provides a framework 
for discussing the selective forces directing the evolution of the 
transcriptional machinery in prokaryotes.