Membrane transport proteins play vital roles in living cells by selectively transporting ions and molecules across biological membranes. Among these, microbial rhodopsins are unique in their unparalleled capacity to harness light to drive ion translocation. This distinctive feature has led to their widespread use as optogenetic tools in neuroscience, physiology, and biomed-ical applications. While not all microbial rhodopsins function as ion transporters, many ion-translocating variants have been discov-ered since the identification of the first member—a light-driven H+ pump—in the 1970s. These proteins share a compact structure composed of only seven transmembrane helices and have long been thought to specialize exclusively in transporting small inorganic ions such as H+, Cl−, and Na+. Here, we show that several anion-pumping microbial rhodopsins can also transport organic anions. In particular, a rhodopsin from cyanobacteria is capable of transporting bulky organic anions, including those containing benzene rings, with molecular volumes up to ∼120 Å[3][1]—five times that of Cl−. These organic ions bind to the dark state and are translocated upon photoactivation, following a mechanism similar to that of inorganic anion transport. Mutational analysis indicates that both classes of substrates share a common binding site. Only anions with p K a values below 2 were transported, suggesting that a retained negative charge is essential for binding to the dark state—a prerequisite for transport. This study expands the known sub-strate repertoire of microbial rhodopsins and introduces new possibilities for optogenetic strategies based on light-driven delivery of bioactive organic molecules. ### Competing Interest Statement The authors have declared no competing interest. Japan Society for the Promotion of Science, https://ror.org/00hhkn466, JP22H02579, JP22H05389 Steel Foundation for Environmental Protection Technology, C-40-56 JKA Foundation, 2025M-319 G-7 Scholarship Foundation, 7102400053 [1]: #ref-3

Microbial rhodopsins are photoactive membrane proteins known for transporting small inorganic ions such as H+, Cl-, and Na+. Their compact structure─comprising seven transmembrane helices─has long been thought to limit their substrate range to such ions. Here, we report that several anion-pumping rhodopsins can also transport organic anions. In particular, a rhodopsin from cyanobacteria transports bulky organic anions, including those with a benzene ring, with volumes up to ∼120 Å3─five times larger than Cl-. These anions bind in the dark state and are translocated upon photoactivation, via a mechanism similar to Cl-. Notably, only anions with pKa values below 2 are transported, suggesting that negative charge is essential for binding. This study provides the first evidence that naturally occurring proteins can use light to transport organic compounds across membranes. These findings broaden the functional scope of microbial rhodopsins and open new possibilities for light-driven transport of organic ions.

The continuous evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during the global pandemic challenges diagnostic technologies, underscoring the urgent need for quick adaptation and innovation to improve accuracy and efficiency against new variants. The study introduces a synthetic Lipid Nanoparticles (LNPs) model of SARS-CoV-2, utilizing advancements in LNPs vaccine technology to mimic the virus's key biochemical and genetic traits. This liposomal model encapsulates the characteristic SARS-CoV-2 mRNA and nucleocapsid (N) proteins within LNPs and further conjugates with spike (S) protein derivatives on its outer membrane, closely replicating the virus's structure and inducing accurate antigen-antibody responses in diagnostic tests. Furthermore, validation using reverse transcription-quantitative polymerase chain reaction (RT-qPCR) with commercial SARS-CoV-2 reagents confirms its effectiveness in simulating viral RNA amplification. This establishes it as an efficient tool for assessing the diagnostic efficacy of newly marketed diagnostic products. This LNPs model represents a significant advancement in diagnostic development, offering potential for therapeutic and vaccine research while ensuring safety and scalability.

AbstractLight is a significant factor for living organisms with photosystems, like microbial rhodopsin—a retinal protein that functions as an ion pump, channel, and sensory transduction. Gloeobacter violaceus PCC7421, has a proton-pumping rhodopsin gene, the Gloeobacter rhodopsin (GR). The helix-turn-helix family of transcriptional regulators has various motifs, and they regulate gene expression in the presence of various metal ions. Here, we report that active proton outward pumping rhodopsin interacted with the helix-turn-helix transcription regulator and regulated gene expression. This interaction is confirmed using ITC analysis (KD of 8 μM) and determined the charged residues required. During in vitro experiments using fluorescent and luciferase reporter systems, ATP-binding cassette (ABC) transporters and the self-regulation of G. violaceus transcriptional regulator (GvTcR) are regulated by light, and gene regulation is observed in G. violaceus using the real-time polymerase chain reaction. These results expand our understanding of the natural potential and limitations of microbial rhodopsin function.

AbstractHeliorhodopsins (HeRs) have been hypothesized to have widespread functions. Recently, the functions for few HeRs have been revealed; however, the hypothetical functions remain largely unknown. Herein, we investigate light-modulation of heterodimeric multidrug resistance ATP-binding cassette transporters (OmrDE) mediated by Omithinimicrobium cerasi HeR. In this study, we classifiy genes flanking the HeR-encoding genes and identify highly conservative residues for protein–protein interactions. Our results reveal that the interaction between OcHeR and OmrDE shows positive cooperatively sequential binding through thermodynamic parameters. Moreover, light-induced OcHeR upregulates OmrDE drug transportation. Hence, the binding may be crucial to drug resistance in O. cerasi as it survives in a drug-containing habitat. Overall, we unveil a function of HeR as regulatory rhodopsin for multidrug resistance. Our findings suggest potential applications in optogenetic technology.

Xanthorhodopsin (XR), a retinal-binding 7-transmembrane protein isolated from the eubacterium Salinibacter ruber, utilizes two chromophores (retinal and salinixanthin (SAL)) as an outward proton pump and energy-donating carotenoid. However, research on XR has been impeded owing to limitations in achieving heterogeneous expression of stable forms and high production levels of both wild-type and mutants. We successfully expressed wild-type and mutant XRs in Escherichia coli in the presence of K+. Achieving XR expression requires significant K+ and a low inducer concentration. In particular, we highlight the significance of Ser-159 in helix E located near Gly-156 (a carotenoid-binding position) as a critical site for XR expression. Our findings indicate that replacing Ser-159 with a smaller amino acid, alanine, can enhance XR expression in a manner comparable to K+, implying that Ser-159 poses a steric hindrance for pigment formation in XR. In the presence of K+, the proton pumping and photocycle of the wild-type and mutants were characterized and compared; the wild-type result suggests similar properties to the first reported XR isolation from the S. ruber membrane fraction. We propose that the K+ gradient across the cell membrane of S. ruber serves to uphold the membrane potential of the organism and plays a role in the expression of proteins, such as XR, as demonstrated in our study. Our findings deepen the understanding of adaptive protein expression, particularly in halophilic organisms. We highlight salt selection as a promising strategy for improving protein yield and functionality.

Despite the intensive research on gut microbiome-associated diseases over the past 20 years, pharmacological methods for effectively eliminating pathobionts remain unsatisfactory. This study investigated the therapeutic potential of bacteriophages against Enterococcus faecalis, in which bacterial tyrosine decarboxylase (TDC) converts orally administered levodopa (L-DOPA) to dopamine, in an MPTP mouse model of Parkinson's disease (PD). E. faecalis bacteriophages PBEF62, PBEF66, and PBEF67 (4 x 1010 PFU total/200 mu l/day), and E. faecalis cells (2 x 109 CFU/200 mu l/day) were orally administered at 2-h intervals before every MPTP (i.p.) and/or L-DOPA (p.o.) treatments for 13 days. The relative abundances of E. faecalis cells and bacteriophages in the feces peaked at 4 and 12 h after administration and gradually decreased by 12 and 48 h, respectively. While the administration of E. faecalis cells eliminated the beneficial effect of L-DOPA on MPTP-induced behavioral deficits, as assessed by cylinder and rotarod tests, the co-administration of bacteriophages with bacterial cells restored this effect. The modulating effects of L-DOPA, E. faecalis, and bacteriophages on PD behavior were closely associated with choline acetyltransferase expression levels in the striatum but not with tyrosine hydroxylase in the substantia nigra of each group. Recurrence and extinction of PD behaviors following treatment with E. faecalis and/or bacteriophages were also coincident with the dopamine levels in the blood and brain tissues of PD mice. The effectiveness of L-DOPA was restored after the three types of E. faecalis bacteriophages selectively eliminated E. faecalis cells, along with the TDC gene copies and transcripts responsible for converting L-DOPA to dopamine in the gastrointestinal tract. In conclusion, a combination of bacteriophages PBEF62, PBEF66, and PBEF67 targeting E. faecalis demonstrates potential as a valuable supplement to L-DOPA therapy for PD.

We present a CuAAC (Copper-Catalyzed Azide-Alkyne Cycloaddition) reaction protocol designed for the visualization of mRNA. To achieve this, we synthesized stable mRNA molecules incorporating the modified nucleoside analog, EU, a crucial element for fluorophore attachment. Leveraging this modified mRNA, we successfully executed the CuAAC reaction, wherein the pro-fluorophore, coumarin, was conjugated to EU on the mRNA through our meticulously designed CuAAC process. This innovative approach resulted in the emission of fluorescence, enabling both precise quantification and visual observation of mRNA. Furthermore, we demonstrated the feasibility of concurrent mRNA synthesis and visualization by seamlessly integrating the CuAAC reaction mix into the mRNA transcription process. Additionally, our novel methodology opens avenues for prospective real-time monitoring of mRNA transcription within artificial cells. These advancements hold significant promise for expanding our comprehension of fundamental cellular processes and finding applications across diverse biological contexts in the future.

Xanthorhodopsin (XR), a retinal-binding 7-transmembrane protein isolated from the eubacterium Salinibacter ruber, utilizes two chromophores (retinal and salinixanthin) as an outward proton pumps and energy-donating carotenoid. However, limited heterogeneous expression of XR has hampered research; particularly, no mutation study has been achieved. Here, we successfully expressed wild-type and mutant XRs in Escherichia coli in the presence of K+. Achieving XR expression was a slow process, requiring a significant amount of K+ and a low concentration of inducer. In particular, we report that Ser-159 in helix E—located near Gly-156 (a carotenoid-binding position)—is critical for the folding stability of XR via K+. We speculate that S. ruber employs the requisite quantity of K+ to support the functional XR and harness the K+-associated XR complex as the primary energy source. Our findings deepen our understanding of adaptive protein expression, particularly in halophilic organisms. We highlight salt selection as a promising strategy for achieving enhanced protein yields and functionality.

Abstract In this study, we specifically visualized DNA molecules at their AT base pairs after in vitro phage ejection. Our AT-specific visualization revealed that either end of the DNA molecule could be ejected first with a nearly 50% probability. This observation challenges the generally accepted theory of Last In First Out (LIFO), which states that the end of the phage λ DNA that enters the capsid last during phage packaging is the first to be ejected, and that both ends of the DNA are unable to move within the extremely condensed phage capsid. To support our observations, we conducted computer simulations that revealed that both ends of the DNA molecule are randomized, resulting in the observed near 50% probability. Additionally, we found that the length of the ejected DNA by LIFO was consistently longer than that by First In First Out (FIFO) during in vitro phage ejection. Our simulations attributed this difference in length to the stiffness difference of the remaining DNA within the phage capsid. In conclusion, this study demonstrates that a DNA molecule within an extremely dense phage capsid exhibits a degree of mobility, allowing it to switch ends during ejection.

The function of microbial as well as mammalian retinal proteins (aka rhodopsins) is associated with a photocycle initiated by light excitation of the retinal chromophore of the protein, covalently bound through a protonated Schiff base linkage. Although electrostatics controls chemical reactions of many organic molecules, attempt to understand its role in controlling excited state reactivity of rhodopsins and, thereby, their photocycle is scarce. Here, we investigate the effect of highly conserved tryptophan residues, between which the all-trans retinal chromophore of the protein is sandwiched in microbial rhodopsins, on the charge distribution along the retinal excited state, quantum yield and nature of the light-induced photocycle and absorption properties of Gloeobacter rhodopsin (GR). Replacement of these tryptophan residues by non-aromatic leucine (W222L and W122L) or phenylalanine (W222F) does not significantly affect the absorption maximum of the protein, while all the mutants showed higher sensitivity to photobleaching, compared to wild-type GR. Flash photolysis studies revealed lower quantum yield of trans-cis photoisomerization in W222L as well as W222F mutants relative to wild-type. The photocycle kinetics are also controlled by these tryptophan residues, resulting in altered accumulation and lifetime of the intermediates in the W222L and W222F mutants. We propose that protein-retinal interactions facilitated by conserved tryptophan residues are crucial for achieving high quantum yield of the light-induced retinal isomerization, and affect the thermal retinal re-isomerization to the resting state.

Microbial rhodopsin (also called retinal protein)-carotenoid conjugates represent a unique class of light-harvesting (LH) complexes, but their specific interactions and LH properties are not completely elucidated as only few rhodopsins are known to bind carotenoids. Here, we report a natural sodium-ion (Na+)-pumping Nonlabens (Donghaeana) dokdonensis rhodopsin (DDR2) binding with a carotenoid salinixanthin (Sal) to form a thermally stable rhodopsin-carotenoid complex. Different spectroscopic studies were employed to monitor the retinal-carotenoid interaction as well as the thermal stability of the protein, while size-exclusion chromatography (SEC) and homology modeling are performed to understand the protein oligomerization process. In analogy with that of another Na+-pumping protein Krokinobacter eikastus rhodopsin 2 (KR2), we propose that DDR2 (studied concentration range: 2 × 10-6 to 4 × 10-5 M) remains mainly as a pentamer at room temperature and neutral pH, while heating above 55 °C partially converted it into a thermally less stable oligomeric form of the protein. This process is affected by both the pH and concentration. At high concentrations (4 × 10-5 to 2 × 10-4 M), the protein adopts a pentamer form reflected in the excitonic circular dichroism (CD) spectrum. In the presence of Sal, the thermal stability of DDR2 is increased significantly, and the pigment is stable even at 85 °C. The results presented could have implications in designing stable rhodopsin-carotenoid antenna complexes.

Energy transfer from the 4-ketocarotenoid antenna (salinixanthin) and echinenone to xanthorhodopsin has been confirmed in Salinibacter ruber and Gloeobacter violaceus, respectively. Hundreds of carotenoids and numerous rhodopsin homologs are spreading across the life domain. Here, we found that ketocarotenoid binds to Gloeobacter rhodopsin (GR), suggesting an increased likelihood of the existence of the carotenoid-rhodopsin complex. Additionally, the recruitment of the secondary chromophore antenna is precisely controlled by rhodopsin. Therefore, comparing the binding of multiple carotenoids is of interest to GR. Particular attention was paid to the structural interaction of ligands within the protein binding pocket. While different degrees of carotenoid association are evident in the GR-carotenoid experimental data and molecular docking results, the retinal isomerization dynamics defined the relative orientation of the β-ionone ring, and structural changes in the protein acted as modest barriers for the best carotenoid for GR. Notably, the selection of carotenoid binding can be summarized in three points: (1) structural matching of a ligand molecule with the binding pocket; (2) strong binding affinity and rapid binding kinetics; (3) dynamic flexibility that is versatile to rhodopsin activation. The selected carotenoids showed significant enhancement in light-driven proton pumping as extra light-harvesting antennae and provided intrinsic protection from stress.

8-(1,3-Benzoxazol-2-yl) substituted spirobenzopyrans 1A appear as a chromogenic system susceptible of switching between positive and negative photochromism under complexation with metal ions. The thermal and photochemical reactions accompanying metal ion-induced transformation of spiropyrans 1A to the complexes formed by their photoinduced merocyanine isomers 1B were investigated. In the dark, the colorless spiropyrans interact with Mn2+, Cd2+ and Zn2+ transition metal ions to yield deeply colored 1:1 complexes possessing fluorescence, while Co2+, Ni2+, Cu2+ ions prefer to form non-fluorescent complexes with two merocyanines. Under irradiation with visible light solutions of the merocyanine-metal complexes undergo photobleaching. This effect was quantified using photokinetic method.

Photoreceptors are light-sensitive proteins found in various organisms that respond to light and relay signals into the cells. Heliorhodopsin, a retinal-binding membrane protein, has been recently discovered, however its function remains unknown. Herein, we investigated the relationship between Actinobacteria bacterium IMCC26103 heliorhodopsin (AbHeR) and an adjacent glutamine synthetase (AbGS) in the same operon. We demonstrate that AbHeR binds to AbGS and regulates AbGS activity. More specifically, the dissociation constant (Kd) value of the binding between AbHeR and AbGS is 6.06 μM. Moreover, the absence of positively charged residues within the intracellular loop of AbHeR impacted Kd value as they serve as critical binding sites for AbGS. We also confirm that AbHeR up-regulates the biosynthetic enzyme activity of AbGS both in vitro and in vivo in the presence of light. GS is a key enzyme involved in nitrogen assimilation that catalyzes the conversion of glutamate and ammonia to glutamine. Hence, the interaction between AbHeR and AbGS may be critical for nitrogen assimilation in Actinobacteria bacterium IMCC26103 as it survives in low-nutrient environments. Overall, the findings of our study describe, for the first time, to the best of our knowledge, a novel function of heliorhodopsin as a regulatory rhodopsin with the capacity to bind and regulate enzyme activity required for nitrogen assimilation.

The extracellular matrix (ECM) is a network of connective fibers that supports cells living in their surroundings. Native ECM, generated by the secretory products of each tissue's resident cells, has a unique architecture with different protein composition depending on the tissue. Therefore, it is very difficult to artificially design in vivo architecture in tissue engineering. In this study, a hybrid ECM scaffold from the basic structure of fibroblast-derived cellular ECMs is fabricated by adding major ECM components of fibronectin (FN) and collagen (COL I) externally. It is confirmed that while maintaining the basic structure of the native ECM, major protein components can be regulated. Then, decellularization is performed to prepare hybrid ECM scaffolds with various protein compositions and it is demonstrated that a liver-mimicking fibronectin (FN)-rich hybrid ECM promoted successful settling of H4IIE rat hepatoma cells. The authors believe that their method holds promise for the fabrication of scaffolds that provide a tailored cellular microenvironment for specific organs and serve as novel pathways for the replacement or regeneration of specific organ tissues.

Microbial rhodopsin is a transmembrane protein that functions with a chromophore and is regulated by light. In nature, regulation through the retinal chromophore plays an important role in physiological phenomena. However, living organisms in soil, sea, and freshwater synthesize carotenoids preferentially over retinal in the biosynthetic pathway. Evolution has extended the energy conversion photosystem with additional pigments that act as antennae. Previously, Gloeobacter rhodopsin and xanthorhodopsin have been reported to form secondary chromophores with carotenoids. In this study, we report that a thermophilic rhodopsin (TR) and Tara76 rhodopsin, the latter of which is classified as a blue light‐absorbing proteorhodopsin, can form secondary chromophores with canthaxanthin (CAN). Tara76 rhodopsin and TR were found to exhibit high thermal stabilities and photophysical properties following their interaction with CAN. Isothermal titration calorimetry analysis, spectral shift measurements, and exciton analysis were used to examine the interactions of these rhodopsins with CAN. It was found that these interactions increased the stability toward temperature and pH through highly efficient chromophore formation, in addition to rapidly recruiting the retinal at a rate approximately twice as high as that obtained in the absence of CAN.

Light quality is a significant factor for living organisms that have photosensory systems, such as rhodopsin, a seven alpha-helical transmembrane protein with the retinal chromophore. Here, we report, for the first time, the function of new rhodopsin, which is an inverted 7-transmembrane protein, isolated from Trichococcus flocculiformis. T. flocculiformis heliorhodopsin (TfHeR) works as a regulatory helper rhodopsin that binds with class 2 cyclobutane pyrimidine dimer (CPDII) photolyase to broaden the spectrum and upregulate DNA repair activity. We have confirmed their interaction through isothermal titration calorimetry (dissociation constant of 21.7 mu M) and identified the charged residues for the interaction. Based on in vivo and in vitro experiments, we showed that the binding of heliorhodopsin with photolyase improved photolyase activity by about 3-fold to repair UV-caused DNA damage. Also, the DNA repair activity of TfHeR/T. flocculiformis photolyase (TfPHR) was observed in the presence of green light. Our results suggested that heliorhodopsin directly controls the activity of photolyase and coevolves to broaden the activity spectrum by protein-protein interaction.