Since the first whole-genome sequencing was completed in 1995 on
a pathogenic bacterium Haemophilus influenza ), the number of
completely sequenced prokaryotic genomes has been increasing
rapidly, with a doubling time of ~20 months for bacteria and ~34
months for archaea (15 ). Due to the abundance of publicly
available prokaryotic genomes, a large number of whole genome TF
studies have focused on these organisms. Aravind and Koonin (16
) published one of the earlier analyses on the repertoire of TF
families in four complete archaeal genomes. Using sequence
profile methods in conjunction with protein structure
information, they presented the intriguing finding that the
majority of archaeal DBDs had helix-turn-helix (HTH) structures
similar to bacterial HTH domains. This contrasts with the core
components of the archaeal transcriptional machinery, such as
basal TFs and RNA polymerases, which are more closely related to
eukaryotic systems. A more recent study by Coulson and coworkers
confirmed this finding (17