Distribution of Chromophore-Binding GAF Domains in Genome Sequence

GAF domains were first described for vertebrate cGMP-specific phosphodiesterases, a cyanobacterial adenylate cyclase and the bacterial formate hydrogen lyase transcription activator FhlA [1]. GAF domains consist of about 150 amino acids conserved in many signaling molecules. GAF domains (PF01590) can be identified in the Pfam database by their characteristic protein sequence signature. GAF domains of plant phytochromes represent the bilin-lyase-specific GAF subfamily [3]. The phytochromes form a major class of signal transducing photoreceptors in plants and the largest group of GAF containing proteins. Although, they were first discovered in higher plants, they are also widely distributed in bacteria. In this study, we surveyed the distribution of GAF domains in many organisms according to the hypothesis that chromophore-binding GAF domains (CB-GAF) evolved from the pool of original GAF domains that gained the function as a light receptor.