Abstract
Organisms can respond to varying light conditions using a wide range of sensory photoreceptors. These photoreceptors can be standalone proteins or represent a module in multidomain proteins, where one or more modules sense light as an input signal which is converted into an output response via structural rearrangements in these receptors. The output signals are utilized downstream by effector proteins or multiprotein clusters to modulate their activity, which could further affect specific interactions, gene regulation or enzymatic catalysis. The blue-light using flavin (BLUF) photosensory module is an autonomous unit that is naturally distributed among functionally distinct proteins. In this study, we identified 34 BLUF photoreceptors of prokaryotic and eukaryotic origin from available bioinformatics sequence databases. Interestingly, our analysis shows diverse BLUF-effector arrangements with a functional association that was previously unknown or thought to be rare among the BLUF class of sensory proteins, such as endonucleases, tet repressor family (tetR), regulators of G-protein signaling, GAL4 transcription family and several other previously unidentified effectors, such as RhoGEF, Phosphatidyl-Ethanolamine Binding protein (PBP), ankyrin and leucine-rich repeats. Interaction studies and the indexing of BLUF domains further show the diversity of BLUF-effector combinations. These diverse modular architectures highlight how the organism’s behaviour, cellular processes, and distinct cellular outputs are regulated by integrating BLUF sensing modules in combination with a plethora of diverse signatures. Our analysis highlights the modular diversity of BLUF containing proteins and opens the possibility of creating a rational design of novel functional chimeras using a BLUF architecture with relevant cellular effectors. Thus, the BLUF domain could be a potential candidate for the development of powerful novel optogenetic tools for its application in modulating diverse cell signaling.
Highlights
Microorganisms respond to changing light conditions using an evolved repertoire of photoreceptors that perceive light and execute a light-dependent control of regulatory ‘output’domains [1]
Sci. 2019, 9, 3924 moiety of the Blue-light using flavin (BLUF) domain associated flavin chromophore absorbs blue light [10], and undergoes structural rearrangements to modulate the communion between BLUF and the effector domains [11]
The BLUF domain encoding protein sequences were retrieved from the National Center for Biotechnology Information (NCBI; https://www.ncbi.nlm.nih.gov/), and each of them was subjected to a conserved domain search using the Conserved Domain Architecture Retrieval Tool (CDART; https://www.ncbi.nlm.nih.gov/Structure/lexington/lexington.cgi) [46]
Summary
Microorganisms respond to changing light conditions using an evolved repertoire of photoreceptors that perceive light and execute a light-dependent control of regulatory ‘output’. Unlike other EAL domain proteins, YcgF acts as a transcriptional regulator and controls the YcgF/YcgE pathway, which regulates the synthesis of small regulatory proteins These small regulatory proteins are involved in the modulation of biofilm functions via the Rcs two-component pathway, necessary for E. coli to sustain the adverse environment [30]. Proteins with tandem GGDEF (diguanylate cyclase; DGC)/EAL (phosphodiesterase) domains were reported to be involved in the c-di-GMP turnover, which modulates a variety of functions ranging from the functional modification of cell surface components, the expression of extracellular signaling molecules, virulence and motility [31,32]. We have characterized the modular diversity of the BLUF domain coupled proteins that could be valuable in the development of novel synthetic photoswitches and we expand the scope of the optogenetics modulation of novel cellular signaling within a functional expression in the appropriate living system
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