Decoding Sequence-Structure-Function-Evolution of basic Leucine Zippers of Aureochromes from Heterokont Algae

Abstract

The blue light photoreceptor cum transcription factors, Aureochromes (Aureos), are present exclusively in photosynthetic stramenopiles. Co-existence of Light-Oxygen-Voltage (LOV) and basic leucine zipper (bZIP) is unique to Aureos - therefore ideal to study light-dependent DNA binding/transcriptional regulation. Further, Aureos inverse effector-sensor topology, resembling several sensory eukaryotic transcription factors, makes them prototypical optogenetic scaffolds. In absence of 3D data, this study aims for a thorough investigation of the bZIP domains from Aureos and others, and their interaction with substrate DNA using tools from sequence/structural bioinformatics, network theory, molecular dynamics simulation and in vitro experiments. An in-depth comparison of 173 Aureo/plant/opisthokont bZIPs reveals Aureos uniqueness and evolutionary significance in DNA binding specificity as well as dimer stability. An all-atom network analysis on representative bZIP-DNA co-crystal structures, especially the measurement of eigenvector centrality, further adds importance to hydrophobic interactions in the zipper region to stabilize bZIP dimer and facilitate DNA binding in Aureos and other bZIPs. Perhaps the most notable finding is the unique histidine substitution at the basic region of Aureos unlike any other bZIPs. Not only is this residue important for DNA binding, this can serve as a potential switch point in Aureo/bZIP evolution. HighlightsO_LIAureochrome is perhaps the only light-responsive transcription factor in bZIP superfamily. C_LIO_LIWe draw a comparative between aureochromes and other bZIPs via in-silico/in-vitro methods. C_LIO_LIAureochromes form a distinctly separate lineage, midway in bZIP evolution. C_LIO_LIThe unique histidine facilitates aureochromes interaction with cognate DNA substrates. C_LI