In recent years it has become increasingly evident that prokaryotic organisms can sense and react to light stimuli via a variety of photosensory receptors and signal transduction pathways. There are two main superfamilies of non-membrane-bound photoreceptors: the bilin-binding phytochrome-related proteins based on GAF (cGMP-specific phosphodiesterases, cyanobacterial adenylate cyclases, and transcription activator FhlA) domains (bilin-GAF proteins), and the flavin-binding proteins (FL-Blues), photoperceptive thanks to their LOV (Light, Oxygen and Voltage) and BLUF (Blue Light sensing Using Flavins) domains. In this manuscript we present a comprehensive scenario of the existence of bilin-GAF, LOV and BLUF proteins in the prokaryotic world and inspect possible phylogenetic pathways, also defining novel criteria for identifying gene (and protein) sequences based on experimentally assessed photochemical events. As a whole we have inspected almost 2000 proteins recovered in 985 bacteria and 16 archaea. For LOV and BLUF proteins, ten and, respectively, twelve superconserved amino acids have been identified, which were used as criterion for selection. A similarly strict parameter cannot be applied to the more variegate family of bilin-GAF domains. The co-presence of bilin-GAF and FL-Blues occurs in 22% of the analyzed bacteria, with emphasis on the bilin-GAF/LOV co-presence in cyanobacteria and of bilin-GAF/BLUF in the Bacteroidetes/Chlorobi group. For construction of phylogeny/distance-trees we used the neighboring-method to obtain a branching pattern, limited to photosensing domains. We observed that in many cases organisms belonging to the same phylum are neighbors, but clustering mostly occurs according to the type of functional domain associated with the photosensing modules.
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