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Putative light-sensing proteins are ubiquitously encoded in the genomes of chemotrophic, non-photosynthetic bacteria. Surprisingly, these are not limited to UV-receptors: the metagenome of the chemotrophic prokaryotes encodes representatives of all known major families of photoreceptors. Insight into the mechanism of light-mediated signaling is relatively advanced, but most light-induced physiological and behavioral responses in chemotrophic bacteria are not well understood. In the current era of ‘omics’ studies, this knowledge gap could be closed rapidly. Here we review the state of the art in this field. Because light signals can be manipulated accurately, these photoreceptors might help provide a systems-level understanding of the cytology of bacteria. [Copyright &y& Elsevier]

The FixL protein of Bradyrhizobium japonicum is a dimeric oxygen sensor responsible for initiating regulation of transcription of genes encoding proteins involved in nitrogen fixation and oxidative stress. It consists of an N-terminal heme-bound PAS domain, denoted bjFixLH, and a C-terminal histidine kinase domain whose enzymatic activity depends on the ligation state of the heme. To investigate the molecular basis for this dependence and the dynamics associated with conversion between ligated and unligated states, we have conducted time-resolved Laue diffraction studies of CO recombination in bjFixLH. Time-dependent difference Fourier maps from 1 μs to 10 ms after photolysis of the heme-CO bond show movement of the side chain of Leu236 and the H and I β-strands into the ligand binding pocket formerly occupied by CO. Long-range conformational changes are evident in the protein, driven by relaxation of steric interactions between the bound ligand and amino acid side chains and/or changes in heme stereochemistry. These structural changes fully reverse as CO rebinds to the heme. Spectroscopic measurements of CO recombination kinetics in bjFixLH crystals relate the behavior of crystalline bjFixLH to solution and provide a framework for our time-resolved crystallographic experiments. Analysis of the time-dependent difference Fourier maps by singular value decomposition reveals that only one significant singular value accounts for the data. Thus only two structural states are present, the photolyzed and the CO-bound states. The first left singular vector represents the difference in density between these two states and shows features common to difference maps calculated from the static CO and deoxy states. The first right singular vector represents the time course of this difference density and agrees well with the CO recombination kinetics measured spectroscopically. We refine the structure of the photolyzed state present in the early-microsecond time range and find that it does not differ significantly in conformation from static, deoxy bjFixLH. Thus, structural relaxation from CO-bound to deoxy bjFixLH is complete in less than 1 μs. [ABSTRACT FROM AUTHOR]

NifL is a multidomain sensor protein responsible for the transcriptional regulation of genes involved in response to changes in cellular redox state and ADP concentration. Cellular redox is monitored by the N-terminal PAS domain of NifL which contains an FAD cofactor. Flavin-based PAS domains of this type have also been referred to as LOV domains. To explore the mechanism of signal recognition and transduction in NifL, we determined the crystal structure of the FAD-bound PAS domain of NifL from Azotobacter vinelandii to 1.04 Å resolution. The structure reveals a novel cavity within the PAS domain which contains two water molecules directly coordinated to the FAD. This cavity is connected to solvent by multiple access channels which may facilitate the oxidation of the FAD by molecular oxygen and the release of hydrogen peroxide. The structure contains a dimer of the NifL PAS domain that is structurally very similar to those described in other crystal structures of PAS domains and identifies a conserved dimerization motif. An N-terminal amphipathic helix constitutes part of the dimerization interface, and similar N-terminal helices are identified in other PAS domain proteins. The structure suggests a model for redox-mediated signaling in which a conformational change is initiated by redox-dependent changes in protonation at the N5 atom of FAD that lead to reorganization of hydrogen bonds within the flavin binding pocket. A structural signal is subsequently transmitted to the β-sheet interface between the monomers of the PAS domain. [ABSTRACT FROM AUTHOR]