The inner mechanics of rhodopsin guanylyl cyclase during cGMP-formation revealed by real-time FTIR spectroscopy

The Functionality of the DC Pair in a Rhodopsin Guanylyl Cyclase from Catenaria anguillulae

Rhodopsin guanylyl cyclases (RGCs) belong to the class of enzymerhodopsins catalyzing the transition from GTP into the second messenger cGMP, whereas light-regulation of enzyme activity is mediated by a membrane-bound microbial rhodopsin domain, that holds the catalytic center inactive in the dark. Structural determinants for activation of the rhodopsin moiety eventually leading to catalytic activity are largely unknown. Here, we investigate the mechanistic role of the D283-C259 (DC) pair that is hydrogen bonded via a water molecule as a crucial functional motif in the homodimeric C. anguillulae RGC. Based on a structural model of the DC pair in the retinal binding pocket obtained by MD simulation, we analyzed formation and kinetics of early and late photocycle intermediates of the rhodopsin domain wild type and specific DC pair mutants by combined UV-Vis and FTIR spectroscopy at ambient and cryo-temperatures. By assigning specific infrared bands to S-H vibrations of C259 we are able to show that the DC pair residues are tightly coupled. We show that deprotonation of D283 occurs already in the inactive L state as a prerequisite for M state formation, whereas structural changes of C259 occur in the active M state and early cryo-trapped intermediates. We propose a comprehensive molecular model for formation of the M state that activates the catalytic moiety. It involves light induced changes in bond strength and hydrogen bonding of the DC pair residues from the early J state to the active M state and explains the retarding effect of C259 mutants.

Diversity of rhodopsin cyclases in zoospore-forming fungi

Light perception for orientation in zoospore-forming fungi is linked to homo- or heterodimeric rhodopsin-guanylyl cyclases (RGCs). Heterodimeric RGCs, first identified in the chytrid Rhizoclosmatium globosum, consist of an unusual near-infrared absorbing highly fluorescent sensitizer neorhodopsin (NeoR) that is paired with a visual light-absorbing rhodopsin responsible for enzyme activation. Here, we present a comprehensive analysis of the distribution of RGC genes in early-branching fungi using currently available genetic data. Among the characterized RGCs, we identified red-sensitive homodimeric RGC variants with maximal light activation close to 600 nm, which allow for red-light control of GTP to cGMP conversion in mammalian cells. Heterodimeric RGC complexes have evolved due to a single gene duplication within the branching of Chytridiales and show a spectral range for maximal light activation between 480 to 600 nm. In contrast, the spectral sensitivity of NeoRs is reaching into the near-infrared range with maximal absorption between 641 and 721 nm, setting the low energy spectral edge of rhodopsins so far. Based on natural NeoR variants and mutational studies, we reevaluated the role of the counterion-triad proposed to cause the extreme redshift. With the help of chimera constructs, we disclose that the cyclase domain is crucial for functioning as homo- or heterodimers, which enables the adaptation of the spectral sensitivity by modular exchange of the photosensor. The extreme spectral plasticity of retinal chromophores in native photoreceptors provides broad perspectives on the achievable spectral adaptation for rhodopsin-based molecular tools ranging from UVB into the near-infrared.

Selenite reduction and biogenesis of selenium-nanoparticles by different size groups of aerobic granular sludge under aerobic conditions

Microbial transformations play a vital role in Se cycle in the environment and decrease the solubility and toxicity of Se oxyanions by converting to elemental selenium (Se⁰) nanostructures. Aerobic granular sludge (AGS) has attracted interest due to efficient reduction of selenite to biogenic Se⁰ (Bio-Se⁰) and retention in bioreactors. Here, selenite removal, biogenesis of Bio-Se⁰ and entrapment of Bio-Se⁰ by different size groups of aerobic granules were investigated to optimize biological treatment process for Se-laden wastewaters. Furthermore, a bacterial strain showing high selenite tolerance and reduction was isolated and characterized. Removal of selenite and conversion to Bio-Se⁰ were achieved by all the size groups of granules ranging from 0.12 mm to 2 mm and above. However, selenite reduction and Bio-Se⁰ formation were rapid and more efficient with large aerobic granules (≥0.5 mm). The formed Bio-Se⁰ was majorly associated with the large granules, due to better entrapment capabilities. In contrast, the Bio-Se⁰ formed by the small granules (≤0.2 mm) was distributed both in the granules and aqueous phase because of ineffective entrapment. Scanning electron microscope and energy dispersive X-ray (SEM-EDX) analysis confirmed formation of Se⁰ spheres and association with the granules. Efficient selenite reduction and entrapment of Bio-Se⁰ was related to prevalent anoxic/anaerobic zones in the large granules. A bacterial strain showing efficient SeO₃^2- reduction of up to 15 mM SeO₃^2- under aerobic conditions was identified as Microbacterium azadirachtae. SEM-EDX analysis confirmed the formation and entrapment of Se⁰ nanospheres (size: 100 ± 5 nm) in the extracellular matrix. The cells immobilized in alginate beads showed effective SeO₃^2- reduction and Bio-Se⁰ entrapment. Efficient reduction and immobilization of bio-transformed metalloids by large AGS and AGS-borne bacteria implicates prospective use in bioremediation of metal(loid) oxyanions and bio-recovery.

Rhodopsins: An Excitingly Versatile Protein Species for Research, Development and Creative Engineering

The first member and eponym of the rhodopsin family was identified in the 1930s as the visual pigment of the rod photoreceptor cell in the animal retina. It was found to be a membrane protein, owing its photosensitivity to the presence of a covalently bound chromophoric group. This group, derived from vitamin A, was appropriately dubbed retinal. In the 1970s a microbial counterpart of this species was discovered in an archaeon, being a membrane protein also harbouring retinal as a chromophore, and named bacteriorhodopsin. Since their discovery a photogenic panorama unfolded, where up to date new members and subspecies with a variety of light-driven functionality have been added to this family. The animal branch, meanwhile categorized as type-2 rhodopsins, turned out to form a large subclass in the superfamily of G protein-coupled receptors and are essential to multiple elements of light-dependent animal sensory physiology. The microbial branch, the type-1 rhodopsins, largely function as light-driven ion pumps or channels, but also contain sensory-active and enzyme-sustaining subspecies. In this review we will follow the development of this exciting membrane protein panorama in a representative number of highlights and will present a prospect of their extraordinary future potential.

Far-Red Absorbing Rhodopsins, Insights From Heterodimeric Rhodopsin-Cyclases

The recently discovered Rhodopsin-cyclases from Chytridiomycota fungi show completely unexpected properties for microbial rhodopsins. These photoreceptors function exclusively as heterodimers, with the two subunits that have very different retinal chromophores. Among them is the bimodal photoswitchable Neorhodopsin (NeoR), which exhibits a near-infrared absorbing, highly fluorescent state. These are features that have never been described for any retinal photoreceptor. Here these properties are discussed in the context of color-tuning approaches of retinal chromophores, which have been extensively studied since the discovery of the first microbial rhodopsin, bacteriorhodopsin, in 1971 (Oesterhelt et al., Nature New Biology, 1971, 233 (39), 149–152). Further a brief review about the concept of heterodimerization is given, which is widely present in class III cyclases but is unknown for rhodopsins. NIR-sensitive retinal chromophores have greatly expanded our understanding of the spectral range of natural retinal photoreceptors and provide a novel perspective for the development of optogenetic tools.

The inner mechanics of rhodopsin guanylyl cyclase during cGMP-formation revealed by real-time FTIR spectroscopy

Enzymerhodopsins represent a recently discovered class of rhodopsins which includes histidine kinase rhodopsin, rhodopsin phosphodiesterases, and rhodopsin guanylyl cyclases (RGCs). The regulatory influence of the rhodopsin domain on the enzyme activity is only partially understood and holds the key for a deeper understanding of intra-molecular signaling pathways. Here, we present a UV-Vis and FTIR study about the light-induced dynamics of a RGC from the fungus Catenaria anguillulae, which provides insights into the catalytic process. After the spectroscopic characterization of the late rhodopsin photoproducts, we analyzed truncated variants and revealed the involvement of the cytosolic N-terminus in the structural rearrangements upon photo-activation of the protein. We tracked the catalytic reaction of RGC and the free GC domain independently by UV-light induced release of GTP from the photolabile NPE-GTP substrate. Our results show substrate binding to the dark-adapted RGC and GC alike and reveal differences between the constructs attributable to the regulatory influence of the rhodopsin on the conformation of the binding pocket. By monitoring the phosphate rearrangement during cGMP and pyrophosphate formation in light-activated RGC, we were able to confirm the M state as the active state of the protein. The described setup and experimental design enable real-time monitoring of substrate turnover in light-activated enzymes on a molecular scale, thus opening the pathway to a deeper understanding of enzyme activity and protein-protein interactions.