Mitophagy mediated by BNIP3 and NIX protects against ferroptosis by downregulating mitochondrial reactive oxygen species

Mitophagy plays an important role in the maintenance of mitochondrial homeostasis and can be categorized into two types: ubiquitin-mediated and receptor-mediated pathways. During receptor-mediated mitophagy, mitophagy receptors facilitate mitophagy by tethering the isolation membrane to mitochondria. Although at least five outer mitochondrial membrane proteins have been identified as mitophagy receptors, their individual contribution and interrelationship remain unclear. Here, we show that HeLa cells lacking BNIP3 and NIX, two of the five receptors, exhibit a complete loss of mitophagy in various conditions. Conversely, cells deficient in the other three receptors show normal mitophagy. Using BNIP3/NIX double knockout (DKO) cells as a model, we reveal that mitophagy deficiency elevates mitochondrial reactive oxygen species (mtROS), which leads to activation of the Nrf2 antioxidant pathway. Notably, BNIP3/NIX DKO cells are highly sensitive to ferroptosis when Nrf2-driven antioxidant enzymes are compromised. Moreover, the sensitivity of BNIP3/NIX DKO cells is fully rescued upon the introduction of wild-type BNIP3 and NIX, but not the mutant forms incapable of facilitating mitophagy. Consequently, our results demonstrate that BNIP3 and NIX-mediated mitophagy plays a role in regulating mtROS levels and protects cells from ferroptosis.

Chromophore-Protein Interactions Affecting the Polyene Twist and π-π* Energy Gap of the Retinal Chromophore in Schizorhodopsins

The properties of a prosthetic group are broadened by interactions with its neighboring residues in proteins. The retinal chromophore in rhodopsins absorbs light, undergoes structural changes, and drives functionally important structural changes in proteins during the photocycle. It is therefore crucial to understand how chromophore-protein interactions regulate the molecular structure and electronic state of chromophores in rhodopsins. Schizorhodopsin is a newly discovered subfamily of rhodopsins found in the genomes of Asgard archaea, which are extant prokaryotes closest to the last common ancestor of eukaryotes and of other microbial species. Here, we report the effects of a hydrogen bond between a retinal Schiff base and its counterion on the twist of the polyene chain and the color of the retinal chromophore. Correlations between spectral features revealed the unexpected fact that the twist of the polyene chain is reduced as the hydrogen bond becomes stronger, suggesting that the twist is caused by tight atomic contacts between the chromophore and nearby residues. In addition, the strength of the hydrogen bond is the primary factor affecting the color-tuning of the retinal chromophore in schizorhodopsins. The findings of this study are valuable for manipulating the molecular structure and electronic state of the chromophore by controlling chromophore-protein interactions.

Design and fabrication of a coupled high-Q photonic nanocavity system with large coupling coefficients

In a previous work, we demonstrated a coupled cavity system where photons in one storage cavity can be transferred to another storage cavity at an arbitrary time by applying a voltage pulse to a third cavity placed in a p-i-n junction. In this work, we demonstrate methods to improve the transfer efficiency and photon lifetimes of such a coupled system. Firstly, we designed a photonic-crystal structure that achieves a large coupling coefficient without reducing the radiation quality factor compared to the previously proposed structure: The photonic-crystal design was changed to a more symmetric configuration to suppress radiation losses and then optimized using an automatic structure tuning method based on the Covariance Matrix Adaptive Evolutional Strategy (CMAES). Here we added two improvements to achieve an evolution toward the desired direction in the two-dimensional target parameter space (spanned by the coupling coefficient and the inverse radiation loss). Secondly, to improve the experimental cavity quality factors, we developed a fabrication process that reduces the surface contamination associated with the fabrication of the p-i-n junction: We covered the photonic structure with a SiO2 mask to avoid the contamination and the electrode material was changed from Al to Au/Cr to enable cleaning by a weak acid. Owing to these improvements of the cavity design and the fabrication process, the obtained system provides coupling strengths that are about three times stronger and photon lifetimes that are about two times longer, compared to the previously reported system.

Multiple Roles of a Conserved Glutamate Residue for Unique Biophysical Properties in a New Group of Microbial Rhodopsins Homologous to TAT Rhodopsin

TAT rhodopsin, a microbial rhodopsin found in the marine SAR11 bacterium HIMB114, uniquely possesses a Thr-Ala-Thr (TAT) motif in the third transmembrane helix. Because of a low pKa value of the retinal Schiff base (RSB), TAT rhodopsin exhibits both a visible light-absorbing state with the protonated RSB and a UV-absorbing state with the deprotonated RSB at a neutral pH. The UV-absorbing state, in contrast to the visible light-absorbing one, converts to a long-lived photointermediate upon light absorption, implying that TAT rhodopsin functions as a pH-dependent light sensor. Despite detailed biophysical characterization and mechanistic studies on the TAT rhodopsin, it has been unknown whether other proteins with similarly unusual features exist. Here, we identified several new rhodopsin genes homologous to the TAT rhodopsin of HIMB114 (TATHIMB) from metagenomic data. Based on the absorption spectra of expressed proteins from these genes with visible and UV peaks similar to that of TATHIMB, they were classified as Twin-peaked Rhodopsin (TwR) family. TwR genes form a gene cluster with a set of 13 ORFs conserved in subclade IIIa of SAR11 bacteria. A glutamic acid in the second transmembrane helix, Glu54, is conserved in all of the TwRs. We investigated E54Q mutants of two TwRs and revealed that Glu54 plays critical roles in regulating the RSB pKa, oligomer formation, and the efficient photoreaction of the UV-absorbing state. The discovery of novel TwRs enables us to study the universality and individuality of the characteristics revealed so far in the original TATHIMB and contributes to further studies on mechanisms of unique properties of TwRs.

Cis-Trans Reisomerization Preceding Reprotonation of the Retinal Chromophore Is Common to the Schizorhodopsin Family: A Simple and Rational Mechanism for Inward Proton Pumping

The creation of unidirectional ion transporters across membranes represents one of the greatest challenges in chemistry. Proton-pumping rhodopsins are composed of seven transmembrane helices with a retinal chromophore bound to a lysine side chain via a Schiff base linkage and provide valuable insights for designing such transporters. What makes these transporters particularly intriguing is the discovery of both outward and inward proton-pumping rhodopsins. Surprisingly, despite sharing identical overall structures and membrane topologies, these proteins facilitate proton transport in opposite directions, implying an underlying rational mechanism that can transport protons in different directions within similar protein structures. In this study, we unraveled this mechanism by examining the chromophore structures of deprotonated intermediates in schizorhodopsins, a recently discovered subfamily of inward proton-pumping rhodopsins, using time-resolved resonance Raman spectroscopy. The photocycle of schizorhodopsins revealed the cis-trans thermal isomerization that precedes reprotonation at the Schiff base of the retinal chromophore. Notably, this order has not been observed in other proton-pumping rhodopsins, but here, it was observed in all seven schizorhodopsins studied across the archaeal domain, strongly suggesting that cis-trans thermal isomerization preceding reprotonation is a universal feature of the schizorhodopsin family. Based on these findings, we propose a structural basis for the remarkable order of events crucial for facilitating inward proton transport. The mechanism underlying inward proton transport by schizorhodopsins is straightforward and rational. The insights obtained from this study hold great promise for the design of transmembrane unidirectional ion transporters.

Functional characterization of four opsins and two G alpha subtypes co-expressed in the molluscan rhabdomeric photoreceptor

BACKGROUND

Rhabdomeric photoreceptors of eyes in the terrestrial slug Limax are the typical invertebrate-type but unique in that three visual opsins (Gq-coupled rhodopsin, xenopsin, Opn5A) and one retinochrome, all belonging to different groups, are co-expressed. However, molecular properties including spectral sensitivity and G protein selectivity of any of them are not determined, which prevents us from understanding an advantage of multiplicity of opsin properties in a single rhabdomeric photoreceptor. To gain insight into the functional role of the co-expression of multiple opsin species in a photoreceptor, we investigated the molecular properties of the visual opsins in the present study.

RESULTS

First, we found that the fourth member of visual opsins, Opn5B, is also co-expressed in the rhabdomere of the photoreceptor together with previously identified three opsins. The photoreceptors were also demonstrated to express Gq and Go alpha subunits. We then determined the spectral sensitivity of the four visual opsins using biochemical and spectroscopic methods. Gq-coupled rhodopsin and xenopsin exhibit maximum sensitivity at ~ 456 and 475 nm, respectively, and Opn5A and Opn5B exhibit maximum sensitivity at ~ 500 and 470 nm, respectively, with significant UV sensitivity. Notably, in vitro experiments revealed that Go alpha was activated by all four visual opsins, in contrast to the specific activation of Gq alpha by Gq-coupled rhodopsin, suggesting that the eye photoreceptor of Limax uses complex G protein signaling pathways.

CONCLUSIONS

The eye photoreceptor in Limax expresses as many as four different visual opsin species belonging to three distinct classes. The combination of opsins with different spectral sensitivities and G protein selectivities may underlie physiological properties of the ocular photoreception, such as a shift in spectral sensitivity between dark- and light-adapted states. This may be allowed by adjustment of the relative contribution of the four opsins without neural networks, enabling a simple strategy for fine-tuning of vision.

The effect of nano hydroxyapatite coating implant surfaces on gene expression and osseointegration

BACKGROUND

Hierarchical micro-nano structured topography along with surface chemistry modifications of dental implants have been suggested to positively contribute to the osseointegration process. However, the effect of such surface modifications on the molecular response as well as bone formation rate and quality are still unclear, especially in the early healing period. This study aimed to evaluate the effect of coating a double acid etched (DAE) implant surface with nano-sized (20 nm) hydroxyapatite (Nano) with respect to gene expression, histologic parameters, and nanomechanical properties when compared to DAE control at 1 and 2 weeks after implant placement in a rodent femur model.

MATERIAL AND METHODS

Expression of bone-related genes was determined by qRT-PCR (Col-I, Runx-2, Osx, Opn, Ocn, Alp). Histomorphometric evaluation of bone-to-implant contact (BIC) and bone area fraction occupancy (BAFO) within implant threads was performed using photomicrographs after histologic processing. Mechanical properties, reduced elastic modulus and hardness, were determined through nanoindentation.

RESULTS

At 1 week, the Nano group demonstrated significantly higher expression of Col-I and Ocn compared to the DAE group, indicating upregulation of osteoprogenitor and osteoblast differentiation genes. At 2 weeks, Nano surface further exhibited enhanced gene expression of Col-I and Osx in comparison to the DAE surface, suggesting an increased mineralization of the newly formed bone. Nanoindentation analysis revealed that the Nano group presented no significant difference on the ranks of reduced elastic modulus and hardness compared to DAE for both timepoints. Histomorphometric analysis yielded no significant difference in the percentage of BIC and BAFO between the Nano and DAE surfaces at 1 and 2 weeks. However, Nano implants did present a higher mean value, ~50%, of BIC compared to DAE, ~30%, after 2 weeks in vivo.

CONCLUSIONS

While no significant differences were observed in the amount and mechanical properties of newly formed bone, Nano surface positively and significantly increased the expression osteogenic genes compared to DAE surface at early healing periods.

Photochemistry of the Retinal Chromophore in Microbial Rhodopsins

Microbial rhodopsins are photoreceptive membrane proteins of microorganisms that express diverse photobiological functions. All-trans-retinylidene Schiff base, the so-called all-trans-retinal, is a chromophore of microbial rhodopsins, which captures photons. It isomerizes into the 13-cis form upon photoexcitation. Isomerization of retinal leads to sequential conformational changes in the protein, giving rise to active states that exhibit biological functions. Despite the rapidly expanding diversity of microbial rhodopsin functions, the photochemical behaviors of retinal were considered to be common among them. However, the retinal of many recently discovered rhodopsins was found to exhibit new photochemical characteristics, such as highly red-shifted absorption, isomerization to 7-cis and 11-cis forms, and energy transfer from a secondary carotenoid chromophore to the retinal, which is markedly different from that established in canonical microbial rhodopsins. Here, I review new aspects of retinal found in novel microbial rhodopsins and highlight the emerging problems that need to be addressed to understand noncanonical retinal photochemistry.

Hva22, a REEP family protein in fission yeast, promotes reticulophagy in collaboration with a receptor protein

The endoplasmic reticulum (ER) undergoes selective autophagy called reticulophagy or ER-phagy. Multiple reticulon- and receptor expression enhancing protein (REEP)-like ER-shaping proteins, including budding yeast Atg40, serve as reticulophagy receptors that stabilize the phagophore on the ER by interacting with phagophore-conjugated Atg8. Additionally, they facilitate phagophore engulfment of the ER by remodeling ER morphology. We reveal that Hva22, a REEP family protein in fission yeast, promotes reticulophagy without Atg8-binding capacity. The role of Hva22 in reticulophagy can be replaced by expressing Atg40 independently of its Atg8-binding ability. Conversely, adding an Atg8-binding sequence to Hva22 enables it to substitute for Atg40 in budding yeast. Thus, the phagophore-stabilizing and ER-shaping activities, both of which Atg40 solely contains, are divided between two separate factors, receptors and Hva22, respectively, in fission yeast.Abbreviations: AIM: Atg8-family interacting motif; Atg: autophagy related; DTT: dithiothreitol; ER: endoplasmic reticulum GFP: green fluorescent protein; NAA: 1-naphthaleneacetic acid; REEP: receptor expression enhancing protein; RFP: red fluorescent protein; UPR: unfolded protein response.

Structural basis for ion selectivity in potassium-selective channelrhodopsins

KCR channelrhodopsins (K+-selective light-gated ion channels) have received attention as potential inhibitory optogenetic tools but more broadly pose a fundamental mystery regarding how their K+ selectivity is achieved. Here, we present 2.5-2.7 Å cryo-electron microscopy structures of HcKCR1 and HcKCR2 and of a structure-guided mutant with enhanced K+ selectivity. Structural, electrophysiological, computational, spectroscopic, and biochemical analyses reveal a distinctive mechanism for K+ selectivity; rather than forming the symmetrical filter of canonical K+ channels achieving both selectivity and dehydration, instead, three extracellular-vestibule residues within each monomer form a flexible asymmetric selectivity gate, while a distinct dehydration pathway extends intracellularly. Structural comparisons reveal a retinal-binding pocket that induces retinal rotation (accounting for HcKCR1/HcKCR2 spectral differences), and design of corresponding KCR variants with increased K+ selectivity (KALI-1/KALI-2) provides key advantages for optogenetic inhibition in vitro and in vivo. Thus, discovery of a mechanism for ion-channel K+ selectivity also provides a framework for next-generation optogenetics.

Light-Driven Chloride and Sulfate Pump with Two Different Transport Modes

Ion pumps are membrane proteins that actively translocate ions by using energy. All known pumps bind ions in the resting state, and external energy allows ion transport through protein structural changes. The light-driven sodium-ion pump Krokinobacter eikastus rhodopsin 2 (KR2) is an exceptional case in which ion binding follows the energy input. In this study, we report another case of this unusual transport mode. The NTQ rhodopsin from Alteribacter aurantiacus (AaClR) is a natural light-driven chloride pump, in which the chloride ion binds to the resting state. AaClR is also able to pump sulfate ions, though the pump efficiency is much lower for sulfate ions than for chloride ions. Detailed spectroscopic analysis revealed no binding of the sulfate ion to the resting state of AaClR, indicating that binding of the substrate (sulfate ion) to the resting state is not necessary for active transport. This property of the AaClR sulfate pump is similar to that of the KR2 sodium pump. Photocycle dynamics of the AaClR sulfate pump resemble a non-functional cycle in the absence of anions. Despite this, flash photolysis and difference Fourier transform infrared spectroscopy suggest transient binding of the sulfate ion to AaClR. The molecular mechanism of this unusual active transport by AaClR is discussed.

Effects of the Unique Chromophore-Protein Interactions on the Primary Photoreaction of Schizorhodopsin

Schizorhodopsin (SzR) is a newly discovered microbial rhodopsin subfamily, functioning as an unusual inward-proton (H+) pump upon absorbing light. Two major protein structural differences around the chromophore have been found, resulting in unique chromophore-protein interactions that may be responsible for its unusual function. Therefore, it is important to elucidate how such a difference affects the primary photoreaction dynamics. We study the primary dynamics of SzR and its C75S mutant by femtosecond time-resolved absorption (TA) spectroscopy. The obtained TA data revealed that the photoisomerization in SzR proceeds more slowly and less efficiently than typical outward H+-pumping rhodopsins and that it further slows in the C75S mutant. We performed impulsive stimulated Raman measurements to clarify the effect of the cysteine residue on the retinal chromophore and found that interactions with Cys75 flatten the retinal chromophore of wild-type SzR. We discuss the effect of the unique chromophore-cysteine interaction on the retinal isomerization dynamics and structure of SzR.

Distribution of natural radionuclides in NORM samples from North Abu Rusheid area, Egypt

The North Abu Rusheid area in Egypt is a well-known high background natural radiation area (HBNRA) due to the existence of naturally occurring radioactive materials (NORMs) in mylonitic rocks. In this study, 27 rock samples were selected for dose estimation studies. ²³⁸U and ²³²Th were measured using inductively coupled plasma mass spectrometry (ICP-MS) and ⁴⁰K was measured using sodium iodide (thallium) gamma-ray spectroscopy. The ranges of activity concentrations (Bq/kg) of ²³⁸U, ²³²Th and ⁴⁰K in the samples varied from 270 ± 2 to 2120 ± 29, 350 ± 2 to 1840 ± 27 and 20 ± 2 to 1390 ± 35 with mean values of 980 ± 349, 770 ± 351, and 640 ± 402 Bq/kg, respectively. The radiological hazard parameters were estimated from activity concentrations of ²³⁸U, ²³²Th and ⁴⁰K and compared to United Nations Scientific Committee on the Effects of Atomic Radiation (UNSCEAR) values. The present study revealed that the hazard parameters were several times higher than the worldwide averages. The U/Th concentration ratio ranged from 0.7 to 3 and could be attributed to the presence of kasolite, uranothorite, zircon, and columbite in mylonitic rocks. From the radiological protection viewpoint, it is necessary to monitor natural radionuclides in these rocks prior to their use in residential and commercial construction materials.

Comparing pedigree and genomic inbreeding coefficients, and inbreeding depression of reproductive traits in Japanese Black cattle

BACKGROUND

Pedigree-based inbreeding coefficients have been generally included in statistical models for genetic evaluation of Japanese Black cattle. The use of genomic data is expected to provide precise assessment of inbreeding level and depression. Recently, many measures have been used for genome-based inbreeding coefficients; however, with no consensus on which is the most appropriate. Therefore, we compared the pedigree- ([Formula: see text]) and multiple genome-based inbreeding coefficients, which were calculated from the genomic relationship matrix with observed allele frequencies ([Formula: see text]), correlation between uniting gametes ([Formula: see text]), the observed vs expected number of homozygous genotypes ([Formula: see text]), runs of homozygosity (ROH) segments ([Formula: see text]) and heterozygosity by descent segments ([Formula: see text]). We quantified inbreeding depression from estimating regression coefficients of inbreeding coefficients on three reproductive traits: age at first calving (AFC), calving difficulty (CD) and gestation length (GL) in Japanese Black cattle.

RESULTS

The highest correlations with [Formula: see text] were for [Formula: see text] (0.86) and [Formula: see text] (0.85) whereas [Formula: see text] and [Formula: see text] provided weak correlations with [Formula: see text], with range 0.33-0.55. Except for [Formula: see text] and [Formula: see text], there were strong correlations among genome-based inbreeding coefficients ([Formula: see text] 0.94). The estimates of regression coefficients of inbreeding depression for [Formula: see text] was 2.1 for AFC, 0.63 for CD and -1.21 for GL, respectively, but [Formula: see text] had no significant effects on all traits. Genome-based inbreeding coefficients provided larger effects on all reproductive traits than [Formula: see text]. In particular, for CD, all estimated regression coefficients for genome-based inbreeding coefficients were significant, and for GL, that for [Formula: see text] had a significant.. Although there were no significant effects when using overall genome-level inbreeding coefficients for AFC and GL, [Formula: see text] provided significant effects at chromosomal level in four chromosomes for AFC, three chromosomes for CD, and two chromosomes for GL. In addition, similar results were obtained for [Formula: see text].

CONCLUSIONS

Genome-based inbreeding coefficients can capture more phenotypic variation than [Formula: see text]. In particular, [Formula: see text] and [Formula: see text] can be considered good estimators for quantifying inbreeding level and identifying inbreeding depression at the chromosome level. These findings might improve the quantification of inbreeding and breeding programs using genome-based inbreeding coefficients.

The mitochondrial intermembrane space protein mitofissin drives mitochondrial fission required for mitophagy

Mitophagy plays an important role in mitochondrial homeostasis by selective degradation of mitochondria. During mitophagy, mitochondria should be fragmented to allow engulfment within autophagosomes, whose capacity is exceeded by the typical mitochondria mass. However, the known mitochondrial fission factors, dynamin-related proteins Dnm1 in yeasts and DNM1L/Drp1 in mammals, are dispensable for mitophagy. Here, we identify Atg44 as a mitochondrial fission factor that is essential for mitophagy in yeasts, and we therefore term Atg44 and its orthologous proteins mitofissin. In mitofissin-deficient cells, a part of the mitochondria is recognized by the mitophagy machinery as cargo but cannot be enwrapped by the autophagosome precursor, the phagophore, due to a lack of mitochondrial fission. Furthermore, we show that mitofissin directly binds to lipid membranes and brings about lipid membrane fragility to facilitate membrane fission. Taken together, we propose that mitofissin acts directly on lipid membranes to drive mitochondrial fission required for mitophagy.

A light-gated cation channel with high reactivity to weak light

The cryptophyte algae, Guillardia theta, possesses 46 genes that are homologous to microbial rhodopsins. Five of them are functionally light-gated cation channelrhodopsins (GtCCR1-5) that are phylogenetically distinct from chlorophyte channelrhodopsins (ChRs) such as ChR2 from Chlamydomonas reinhardtii. In this study, we report the ion channel properties of these five CCRs and compared them with ChR2 and other ChRs widely used in optogenetics. We revealed that light sensitivity varied among GtCCR1-5, in which GtCCR1-3 exhibited an apparent EC₅₀ of 0.21-1.16 mW/mm², similar to that of ChR2, whereas GtCCR4 and GtCCR5 possess two EC50s, one of which is significantly small (0.025 and 0.032 mW/mm²). GtCCR4 is able to trigger action potentials in high temporal resolution, similar to ChR2, but requires lower light power, when expressed in cortical neurons. Moreover, a high light-sensitive response was observed when GtCCR4 was introduced into blind retina ganglion cells of rd1, a mouse model of retinitis pigmentosa. Thus, GtCCR4 provides optogenetic neuronal activation with high light sensitivity and temporal precision.

Time-resolved detection of light-induced conformational changes of heliorhodopsin

Heliorhodopsins (HeRs) are a new category of rhodopsins. They exist as a dimer and exhibit a characteristic inverted topology. HeRs bind all-trans-retinal as a chromophore in the dark, and its isomerization to the 13-cis form by light illumination leads to a photocyclic reaction involving several photo-intermediates: K, L, M, and O. In this study, the kinetics of conformational changes of HeR from Thermoplasmatales archaeon SG8-52-1 (TaHeR) were studied by the transient grating (TG) and circular dichroism (CD) methods. The TG method reveals that the diffusion coefficient (D) does not change until the O formation suggesting no significant conformation change at the surface of the protein during the early steps of the reaction. Subsequently, D decreases upon the O formation. Although two time constants (202 μs and 2.6 ms) are observed for the conversion from the M to O by the absorption detection, D decreases only at the first step (202 μs). Light-induced unfolding of helical structure is detected by the CD method. To examine the contribution of a characteristic helix in the intracellular loop 1 (ICL1 helix), Tyr93 on the ICL1 helix was replaced by Gly (Y93G), and the reaction of this mutant was also investigated. It was found that this replacement partially suppresses the D-change, although the CD-change is almost the same as that of the wild type. These results are interpreted in terms of different sensitivities of TG and CD methods, that is, D is sensitive to the structure of the solvent-exposed surface and selectively observes the conformational change in the ICL1 region. It is suggested that the structure of hydrophilic residues in the ICL1 helix is changed during this process.

Twisting and Protonation of Retinal Chromophore Regulate Channel Gating of Channelrhodopsin C1C2

Channelrhodopsins (ChRs) are light-gated ion channels and central optogenetic tools that can control neuronal activity with high temporal resolution at the single-cell level. Although their application in optogenetics has rapidly progressed, it is unsolved how their channels open and close. ChRs transport ions through a series of interlocking elementary processes that occur over a broad time scale of subpicoseconds to seconds. During these processes, the retinal chromophore functions as a channel regulatory domain and transfers the optical input as local structural changes to the channel operating domain, the helices, leading to channel gating. Thus, the core question on channel gating dynamics is how the retinal chromophore structure changes throughout the photocycle and what rate-limits the kinetics. Here, we investigated the structural changes in the retinal chromophore of canonical ChR, C1C2, in all photointermediates using time-resolved resonance Raman spectroscopy. Moreover, to reveal the rate-limiting factors of the photocycle and channel gating, we measured the kinetic isotope effect of all photoreaction processes using laser flash photolysis and laser patch clamp, respectively. Spectroscopic and electrophysiological results provided the following understanding of the channel gating: the retinal chromophore highly twists upon the retinal Schiff base (RSB) deprotonation, causing the surrounding helices to move and open the channel. The ion-conducting pathway includes the RSB, where inflowing water mediates the proton to the deprotonated RSB. The twisting of the retinal chromophore relaxes upon the RSB reprotonation, which closes the channel. The RSB reprotonation rate-limits the channel closing.

Converting a Natural-Light-Driven Outward Proton Pump Rhodopsin into an Artificial Inward Proton Pump

Microbial rhodopsins are a large family of photoreceptive membrane proteins with diverse light-regulated functions. While the most ubiquitous microbial rhodopsins are light-driven outward proton (H⁺) pumps, new subfamilies of microbial rhodopsins transporting H⁺ inwardly, i.e., light-driven inward H⁺ pumps, have been discovered recently. Although structural and spectroscopic studies provide insights into their ion transport mechanisms, the minimum key element(s) that determine the direction of H⁺ transport have not yet been clarified. Here, we conducted the first functional conversion study by substituting key amino acids in a natural outward H⁺-pumping rhodopsin (PspR) with those in inward H⁺-pumping rhodopsins. Consequently, an artificial inward H⁺ pump was constructed by mutating only three residues of PspR. This result indicates that these residues govern the key processes that discriminate between outward and inward H⁺ pumps. Spectroscopic studies revealed the presence of an inward H⁺-accepting residue in the H⁺ transport pathway and direct H⁺ uptake from the extracellular solvent. This finding of the simple element for determining H⁺ transport would provide a new basis for understanding the concept of ion transport not only by microbial rhodopsins but also by other ion-pumping proteins.

Reversible Photoreaction of a Retinal Photoisomerase, Retinal G-Protein-Coupled Receptor RGR

Retinal G-protein-coupled receptor (RGR) plays a crucial role in the visual system of vertebrates as a retinal photoisomerase, which isomerizes all-trans-retinal to 11-cis-retinal to maintain the photosensitivity of visual rhodopsins. Despite the previous characterization of bovine RGR, little is known about the spectral properties of RGR from other species. In addition, photoreactivity of the 11-cis-retinal-binding form remains unclear. In this study, we revealed that human and chicken RGRs form blue-absorbing pigments similar to bovine RGR. Furthermore, the spectroscopic and biochemical analyses revealed that bovine and chicken RGRs are bistable rhodopsins displaying a reversible photoreaction. These findings provide insight into the behavior of RGR as a retinal photoisomerase and aid in understanding its role in the visual system.

Difference FTIR Spectroscopy of Jumping Spider Rhodopsin-1 at 77 K

Animal visual rhodopsins can be classified into monostable and bistable rhodopsins, which are typically found in vertebrates and invertebrates, respectively. The former example is bovine rhodopsin (BovRh), whose structures and functions have been extensively studied. On the other hand, those of bistable rhodopsins are less known, despite their importance in optogenetics. Here, low-temperature Fourier-transform infrared (FTIR) spectroscopy was applied to jumping spider rhodopsin-1 (SpiRh1) at 77 K, and the obtained light-induced spectral changes were compared with those of squid rhodopsin (SquRh) and BovRh. Although chromophore distortion of the resting state monitored by HOOP vibrations is not distinctive between invertebrate and vertebrate rhodopsins, distortion of the all-trans chromophore after photoisomerization is unique for BovRh, and the distortion was localized at the center of the chromophore in SpiRh1 and SquRh. Highly conserved aspartate (D83 in BovRh) does not change the hydrogen-bonding environment in invertebrate rhodopsins. Thus, present FTIR analysis provides specific structural changes, leading to activation of invertebrate and vertebrate rhodopsins. On the other hand, the analysis of O-D stretching vibrations in D₂O revealed unique features of protein-bound water molecules. Numbers of water bands in SpiRh1 and SquRh were less and more than those in BovRh. The X-ray crystal structure of SpiRh1 observed a bridged water molecule between the protonated Schiff base and its counterion (E194), but strongly hydrogen-bonded water molecules were never detected in SpiRh1, as well as SquRh and BovRh. Thus, absence of strongly hydrogen-bonded water molecules is substantial for animal rhodopsins, which is distinctive from microbial rhodopsins.

Protein dynamics of a light-driven Na+ pump rhodopsin probed using a tryptophan residue near the retinal chromophore

Direct observation of protein structural changes during ion transport in ion pumps provides valuable insights into the mechanism of ion transport. In this study, we examined structural changes in the light-driven sodium ion (Na+) pump rhodopsin KR2 on the sub-millisecond time scale, corresponding with the uptake and release of Na+. We compared the ion-pumping activities and transient absorption spectra of WT and the W215F mutant, in which the Trp215 residue located near the retinal chromophore on the cytoplasmic side was replaced with a Phe residue. Our findings indicated that atomic contacts between the bulky side chain of Trp215 and the C20 methyl group of the retinal chromophore promote relaxation of the retinal chromophore from the 13-cis to the all-trans form. Since Trp215 is conserved in other ion-pumping rhodopsins, the present results suggest that this residue commonly acts as a mechanical transducer. In addition, we measured time-resolved ultraviolet resonance Raman (UVRR) spectra to show that the environment around Trp215 becomes less hydrophobic at 1 ms after photoirradiation and recovers to the unphotolyzed state with a time constant of around 10 ms. These time scales correspond to Na+ uptake and release, suggesting evolution of a transient ion channel at the cytoplasmic side for Na+ uptake, consistent with the alternating-access model of ion pumps. The time-resolved UVRR technique has potential for application to other ion-pumping rhodopsins and could provide further insights into the mechanism of ion transport.

Biophysical characterization of microbial rhodopsins with DSE motif

Microbial rhodopsins are photoreceptive transmembrane proteins that transport ions or regulate other intracellular biological processes. Recent genomic and metagenomic analyses found many microbial rhodopsins with unique sequences distinct from known ones. Functional characterization of these new types of microbial rhodopsins is expected to expand our understanding of their physiological roles. Here, we found microbial rhodopsins having a DSE motif in the third transmembrane helix from members of the Actinobacteria. Although the expressed proteins exhibited blue-green light absorption, either no or extremely small outward H+ pump activity was observed. The turnover rate of the photocycle reaction of the purified proteins was extremely slow compared to typical H+ pumps, suggesting these rhodopsins would work as photosensors or H+ pumps whose activities are enhanced by an unknown regulatory system in the hosts. The discovery of this rhodopsin group with the unique motif and functionality expands our understanding of the biological role of microbial rhodopsins.

Characterization of retinal chromophore and protonated Schiff base in Thermoplasmatales archaeon heliorhodopsin using solid-state NMR spectroscopy

Heliorhodopsin (HeR) is a seven-helical transmembrane protein with a retinal chromophore that corresponds to a new rhodopsin family. HeR from the archaebacterium Thermoplasmatales archaeon (TaHeR) exhibits unique features, such as the inverted protein orientation in the membrane compared to other rhodopsins and a long photocycle. Here, we used solid-state nuclear magnetic resonance (NMR) spectroscopy to investigate the ¹³C and ¹⁵N NMR signals of the retinal chromophore and protonated Schiff base (RPSB) in TaHeR embedded in POPE/POPG membrane. Although the 14- and 20-¹³C retinal signals indicated 13-trans/15-anti (all-trans) configurations, the 20-¹³C chemical shift value was different from that of other microbial rhodopsins, indicating weakly steric hinderance between Phe203 and the C20 methyl group. ¹⁵N RPSB/λ_max plot deviated from the linear correlation based on retinylidene-halide model compounds. Furthermore, ¹⁵N chemical shift anisotropy (CSA) suggested that Ser112 and Ser234 polar residues distinguish the electronic environment tendencies of RPSB from those of other microbial rhodopsins. Our NMR results revealed that the retinal chromophore and the RPSB in TaHeR exhibit unique electronic environments.

Phototrophy by antenna-containing rhodopsin pumps in aquatic environments

Energy transfer from light-harvesting ketocarotenoids to the light-driven proton pump xanthorhodopsins has been previously demonstrated in two unique cases: an extreme halophilic bacterium¹ and a terrestrial cyanobacterium². Attempts to find carotenoids that bind and transfer energy to abundant rhodopsin proton pumps³ from marine photoheterotrophs have thus far failed^4-6. Here we detected light energy transfer from the widespread hydroxylated carotenoids zeaxanthin and lutein to the retinal moiety of xanthorhodopsins and proteorhodopsins using functional metagenomics combined with chromophore extraction from the environment. The light-harvesting carotenoids transfer up to 42% of the harvested energy in the violet- or blue-light range to the green-light absorbing retinal chromophore. Our data suggest that these antennas may have a substantial effect on rhodopsin phototrophy in the world's lakes, seas and oceans. However, the functional implications of our findings are yet to be discovered.

Formation and evolution of carbonaceous asteroid Ryugu: Direct evidence from returned samples

Samples of the carbonaceous asteroid Ryugu were brought to Earth by the Hayabusa2 spacecraft. We analyzed 17 Ryugu samples measuring 1 to 8 millimeters. Carbon dioxide-bearing water inclusions are present within a pyrrhotite crystal, indicating that Ryugu's parent asteroid formed in the outer Solar System. The samples contain low abundances of materials that formed at high temperatures, such as chondrules and calcium- and aluminum-rich inclusions. The samples are rich in phyllosilicates and carbonates, which formed through aqueous alteration reactions at low temperature, high pH, and water/rock ratios of <1 (by mass). Less altered fragments contain olivine, pyroxene, amorphous silicates, calcite, and phosphide. Numerical simulations, based on the mineralogical and physical properties of the samples, indicate that Ryugu's parent body formed ~2 million years after the beginning of Solar System formation.

Search for the Majorana Nature of Neutrinos in the Inverted Mass Ordering Region with KamLAND-Zen

The KamLAND-Zen experiment has provided stringent constraints on the neutrinoless double-beta (0νββ) decay half-life in ^{136}Xe using a xenon-loaded liquid scintillator. We report an improved search using an upgraded detector with almost double the amount of xenon and an ultralow radioactivity container, corresponding to an exposure of 970 kg yr of ^{136}Xe. These new data provide valuable insight into backgrounds, especially from cosmic muon spallation of xenon, and have required the use of novel background rejection techniques. We obtain a lower limit for the 0νββ decay half-life of T_{1/2}^{0ν}>2.3×10^{26}  yr at 90% C.L., corresponding to upper limits on the effective Majorana neutrino mass of 36-156 meV using commonly adopted nuclear matrix element calculations.

Application of linear and machine learning models to genomic prediction of fatty acid composition in Japanese Black cattle

We collected 3180 records of oleic acid (C18:1) and monounsaturated fatty acid (MUFA) measured using gas chromatography (GC) and 6960 records of C18:1 and MUFA measured using near-infrared spectroscopy (NIRS) in intermuscular fat samples of Japanese Black cattle. We compared genomic prediction performance for four linear models (genomic best linear unbiased prediction [GBLUP], kinship-adjusted multiple loci [KAML], BayesC, and BayesLASSO) and five machine learning models (Gaussian kernel [GK], deep kernel [DK], random forest [RF], extreme gradient boost [XGB], and convolutional neural network [CNN]). For GC-based C18:1 and MUFA, KAML showed the highest accuracies, followed by BayesC, XGB, DK, GK, and BayesLASSO, with more than 6% gain of accuracy by KAML over GBLUP. Meanwhile, DK had the highest prediction accuracy for NIRS-based C18:1 and MUFA, but the difference in accuracies between DK and KAML was slight. For all traits, accuracies of RF and CNN were lower than those of GBLUP. The KAML extends GBLUP methods, of which marker effects are weighted, and involves only additive genetic effects; whereas machine learning methods capture non-additive genetic effects. Thus, KAML is the most suitable method for breeding of fatty acid composition in Japanese Black cattle.

VEGF-A165 is the predominant VEGF-A isoform in platelets, while VEGF-A121 is abundant in serum and plasma from healthy individuals

Vascular endothelial growth factor A (VEGF-A) plays pivotal roles in regulating tumor angiogenesis as well as physiological vascular function. The major VEGF-A isoforms, VEGF-A121 and VEGF-A165, in serum, plasma, and platelets have not been exactly evaluated due to the lack of the appropriate assay system. Antibodies against human VEGF-A121 and VEGF-A165 (hVEGF-A121 and hVEGF-A165) were successfully produced and Enzyme-Linked ImmunoSorbent Assay (ELISA) for hVEGF-A121 and hVEGF-A165 were separately created by these monoclonal antibodies. The measurement of recombinant hVEGF-A121 and hVEGF-A165 by the created ELISA showed no cross-reaction between hVEGF-A121 and hVEGF-A165 in conditioned media from HEK293 cells transfected with either hVEGF-A121 or hVEGF-A165 expression vector. The levels of VEGF-A121 and VEGF-A165 in serum, plasma, and platelets from 59 healthy volunteers proved that VEGF-A121 level was higher than VEGF-A165 in both plasma and serum in all the cases. VEGF-A121 or VEGF-A165 in serum represented higher level than that in plasma. In contrast, the level of VEGF-A165 was higher than VEGF-A121 in platelets. The newly developed ELISAs for hVEGF-A121 and hVEGF-A165 revealed different ratios of VEGF isoforms in serum, plasma, and platelets. Measuring these isoforms in combination provides useful information as biomarkers for diseases involving VEGF-A121 and VEGF-A165.

Evaluating the performance of genomic prediction accounting for effects of single nucleotide polymorphism markers in reproductive traits of Japanese Black cattle

We examined the prediction accuracies of genomic best linear unbiased prediction (GBLUP), various weighted GBLUP according to the degrees of marker effects (WGBLUP) and machine learning (ML) methods, and compared them with traditional BLUP for age at first calving (AFC), calving difficulty (CD), and gestation length in Japanese Black cattle. For WGBLUP, firstly, BayesC and FarmCPU were used to estimate marker effects. Then, we constructed three weighted genomic relationship matrices from information of estimated marker effects in the first step: absolute value of the estimated marker-effect WGBLUP, estimated marker-variance WGBLUP, and genomic-feature WGBLUP. For ML, we applied Gaussian kernel, random forest, extreme gradient boost, and support vector regression. We collected a total of 2583 animals having both phenotypic records and genotypes with 30,105 markers and 16,406 pedigree records. For AFC, prediction accuracies of WGBLUP methods using FarmCPU exceeded BLUP by 25.7%-39.5%. For CD, estimated marker-variance WGBLUP using BayesC achieved the highest prediction accuracy. Among ML methods, extreme gradient boost, support vector regression, and Gaussian kernel increased prediction accuracies by 28.4%, 19.0%, and 36.4% for AFC, CD, and gestation length compared with BLUP, respectively. Thus, prediction performance could be improved using suitable WGBLUP and ML methods according to target reproductive traits for the population used.

Kinetic study on the molecular mechanism of light-driven inward proton transport by schizorhodopsins

Schizorhodopsins (SzRs) are light-driven inward proton pumping membrane proteins. A H⁺ is released to the cytoplasmic solvent from the chromophore, retinal Schiff base (RSB), after light absorption, and then another H⁺ is bound to the RSB at the end of photocyclic reaction. However, the mechanistic detail of H⁺ transfers in SzR is almost unknown. Here we studied the deuterium isotope effect and the temperature dependence of the reaction rate constants of elementary steps in the photocycles of SzRs. The former indicated that deprotonation and reprotonation of RSB is mainly accomplished by H⁺ hopping between heavy atoms with similar H⁺ affinity. Furthermore, the temperature dependence of the rate constants revealed that most of H⁺ transfer events have a high entropy barrier. In contrast, the activation enthalpy and entropy of extremely thermostable SzR (MsSzR) are significantly higher than other types of SzRs (SzR1 and MtSzR) suggesting that its highly thermostable structure is optimized with at the cost of slower reaction rates at ambient temperatures.

Extensive ablation strategy for persistent atrial fibrillation impairs left atrial function but reduces recurrence rate

Background

In catheter ablation for persistent atrial fibrillation (AF), extensive ablation strategy, such as linear ablation and/or complex fractionated atrial electrogram (CFAE) ablation in addition to pulmonary vein isolation (PVI-plus), might impair left atrial function more severely than PVI-alone strategy.

Purpose

The aim of this study is to investigate the impact of extensive ablation strategy on LA function and assess the relationship between post-ablation LA function and recurrence.

Methods

This study is a post-hoc subanalysis of the EARNEST-PVI randomized controlled trial, which investigated the efficacy of the PVI-alone strategy in comparison with PVI-plus strategy for persistent AF. From the 497 participants of EARNEST-PVI trial, we enrolled 191 patients with full datasets of pre- and post-ablation cardiac computed tomography (CT) at our Hospital. Patients were divided into PVI-alone and PVI-plus groups. Within one month before and 3 months after ablation, LA volume index (LAVI) and LA emptying fraction (LAEF) were calculated by using the Comprehensive Cardiac Analysis software on the Extended Brilliance Workspace. We assessed i) post-ablation LA function, ii) AF/atrial tachycardia (AT) -free rate after single and final session, and iii) relationship between post-ablation LAEF and ablation success in each group.

Results

The indices of baseline LA remodeling were not different between PVI-alone (N=96) and PVI-plus groups (N=95) [LAVI: 71.4 (57.8, 82.0) vs. 68.7 (61.0, 78.1), P=0.92, LAEF: 13.7 (10.0, 17.4) vs. 13.0 (10.0, 16.9), PVI-alone vs. PVI-plus, P=0.78]. In overall patients, post-ablation LAEF did not differ among them [34.4 (26.1, 40.7) vs. 31.6 (26.0, 37.4), P=0.13]. In the analysis of patients showing sinus rhythm during the CT study, LAEF was significantly higher in PVI-alone (N=87) than in PVI-plus group (N=93) [35.7 (29.0, 41.0) vs. 31.7 (26.1, 37.5), P=0.011] (Figure 1A). AF/AT-free survival rate during median follow-up of 44 months was not different after first session (63.5% vs. 68.4%, P=0.33), while PVI-plus had a tendency towards higher success rate after final session (72.9% vs. 84.2%, P=0.053) (Figure 2). In receiver operating characteristics analysis for recurrence after first session, post-ablation decreased LAEF had significantly related to recurrence after PVI-alone (AUC: 0.733, P&lt;0.0001), but not after PVI-plus (AUC: 0.567, P=0.31) (Figure 1B, C).

Conclusion

Compared with PVI-alone strategy, PVI-plus strategy damaged LA function more severely, but tended to be related to higher success rate. Post-ablation LA function was related to recurrence in PVI-alone, but not in PVI-plus. Extensive ablation might have additional anti-arrhythmic effect regardless of iatrogenic myocardial damage. Myocardial injury by extensive ablation may less attribute to recurrence than intrinsic damage of LA.

Funding Acknowledgement

Type of funding sources: None.

Sex differences in terms of recurrent atrial fibrillation after catheter ablation according to the history of heart failure: insights from the Kansai Plus Atrial Fibrillation (KPAF) registry

Background

There are significant differences in the prevalence and prognosis of cardiovascular diseases between male and female. We previously reported that catheter ablation (CA) of atrial fibrillation (AF) was less effective in female than male, but whether their history of heart failure influence the recurrence after CA of AF remains still unknown.

Purpose

We sought to clarify sex differences in terms of AF recurrence after RFCA of AF according to the history of heart failure.

Methods

We conducted a large-scale, prospective, multicenter, observational study (Kansai Plus Atrial Fibrillation Registry). We enrolled 5010 consecutive patients who underwent an initial RFCA of AF at 26 centers (64±10 years; 1369 [27.3%] females; non-paroxysmal AF, 35.7%). The median follow-up duration was 2.9 years.

Results

Fourteen % of female had a history of heart failure prior to CA, while 12.8% of male had a history of heart failure at baseline (p=0.29). The 3-year cumulative incidence of AF recurrence after a single procedure was 43.3% in female and 39.0% in male (log rank P=0.0046). In patients with the history of heart failure, AF recurrence rates were 42.2% in female and 45.8% in male (log rank P=0.51). On the other hand, in patients without history of heart failure, more females experienced AF recurrence (female vs. male, 43.5% vs. 38.0%, log rank P=0.001).

The rate of AF recurrence after multiple procedures was higher in female (24.2% vs. 19.6%, log rank P&lt;0.0001). AF recurrence rates were similar between sexes in patients with history of heart failure (female vs. male, 26.0% vs. 26.7%, log rank P=0.86), while AF recurrence rates were higher in female without history of heart failure than those in male (females vs. males, 23.9% vs. 18.5%, log rank P&lt;0.0001).

Conclusion

The Kansai Plus Atrial Fibrillation Registry revealed a distinct sex difference in terms of the AF recurrence after CA of AF. Females had higher recurrence rates compared with males in patients without history of heart failure, while recurrence rates were similar between sexes in patients with history of heart failure.

Funding Acknowledgement

Type of funding sources: Foundation. Main funding source(s): Research Institute for Production Development in Kyoto, Japan.

Premature atrial contraction on Holter electrocardiogram predicts the recurrence of atrial fibrillation after catheter ablation

Introduction

It is important to detect the recurrence of atrial fibrillation (AF) after catheter ablation (CA) early, but the method of detection has not been established. The purpose of this study is to determine whether 24-h Holter electrocardiogram (ECG) can predict the recurrence of AF after CA.

Methods

We studied 336 patients of 497 patients enrolled in EARNEST-PVI trial to investigate whether the total number of premature atrial contraction (PAC) and the maximum number of PAC run by 24-h Holter ECG at 6 months after CA predicted AF recurrence after 6 months. We excluded 86 patients with recurrence by 6 months after CA and 75 patients without Holter ECG at 6 months after CA.

Results

Median age was 66 years, male were 77% and median follow-up period was 1138 days. Receiver operating characteristic curve analysis identified the total number of PAC ≥270 beats and the maximum number of PAC run ≥8 beats as the optimal cutoff for prediction of AF recurrence. Kaplan-Meier analysis showed patients with the total number of PAC ≥270 beats had more frequent AF recurrence than those without (Kaplan-Meier estimated 3-year AF recurrence rate 34% vs. 17%, Log-rank P=0.001) and patients with the maximum number of PAC run ≥8 beats had more frequent AF recurrence than those without (Kaplan-Meier estimated 3-year AF recurrence rate 33% vs. 20%, Log-rank P=0.006). Multivariate analysis revealed that the total number of PAC ≥270 beats and the maximum number of PAC run were significantly associated with AF recurrence (hazard ratio [95% confidence interval] 1.83 [1.16–2.91], P=0.01 and 1.01 [1.01–1.02], P=0.001, respectively)

Conclusion

The total number of PAC and the maximum number of PAC run on the Holter ECG may be useful in predicting AF recurrence after CA.

Funding Acknowledgement

Type of funding sources: None.

Influence of using history of immune checkpoint inhibitor therapy for neutropenia caused by combination therapy of ramucirumab and docetaxel

Recently, pretreatment with immune checkpoint inhibitors (ICIs) has been shown to enhance the therapeutic effects of the combination therapy of ramucirumab (RAM) and docetaxel (DTX); however, its influence on the drug's side effects remains unclear. This study investigated the influence of pretreatment with ICIs on the incidence of neutropenia caused by RAM + DTX therapy in patients with non-small cell lung cancer (NSCLC). Patients with NSCLC who received RAM + DTX therapy at Gifu Prefectural General Medical Center between April 2016 and December 2020 were enrolled. Retrospective data regarding age, sex, performance status and detailed treatment history, among others, at treatment initiation were collected from the patients' electronic medical records. Additionally, data on the course number of RAM + DTX therapy, supportive therapy and blood biochemical parameters, including leukocyte and neutrocyte counts, during the treatment period were collected. We identified 41 patients receiving RAM + DTX therapy. Among the more than grade 3 adverse events caused by this therapy, neutropenia was the most common (78.1%). Despite the fact that all previous risk factors influencing this incidence rate had corresponded, the only factor influencing the incidence rate of neutropenia more than grade 3 was ICI treatment history. A difference in the incidence of neutropenia more than grade 3 in the Kaplan-Meier curve was observed between patients with and without ICI pretreatment history (p = 0.037). The pretreatment history of ICI therapy affects the incidence of neutropenia caused by RAM + DTX therapy in patients with NSCLC.

Proton-transporting heliorhodopsins from marine giant viruses

Rhodopsins convert light into signals and energy in animals and microbes. Heliorhodopsins (HeRs), a recently discovered new rhodopsin family, are widely present in archaea, bacteria, unicellular eukaryotes, and giant viruses, but their function remains unknown. Here, we report that a viral HeR from Emiliania huxleyi virus 202 (V2HeR3) is a light-activated proton transporter. V2HeR3 absorbs blue-green light, and the active intermediate contains the deprotonated retinal Schiff base. Site-directed mutagenesis study revealed that E191 in TM6 constitutes the gate together with the retinal Schiff base. E205 and E215 form a PAG of the Schiff base, and mutations at these positions converted the protein into an outward proton pump. Three environmental viral HeRs from the same group as well as a more distantly related HeR exhibited similar proton-transport activity, indicating that HeR functions might be diverse similarly to type-1 microbial rhodopsins. Some strains of E. huxleyi contain one HeR that is related to the viral HeRs, while its viruses EhV-201 and EhV-202 contain two and three HeRs, respectively. Except for V2HeR3 from EhV-202, none of these proteins exhibit ion transport activity. Thus, when expressed in the E. huxleyi cell membranes, only V2HeR3 has the potential to depolarize the host cells by light, possibly to overcome the host defense mechanisms or to prevent superinfection. The neuronal activity generated by V2HeR3 suggests that it can potentially be used as an optogenetic tool, similarly to type-1 microbial rhodopsins.

Saccharibacteria harness light energy using type-1 rhodopsins that may rely on retinal sourced from microbial hosts

Microbial rhodopsins are a family of photoreceptive membrane proteins with a wide distribution across the Tree of Life. Within the candidate phyla radiation (CPR), a diverse group of putatively episymbiotic bacteria, the genetic potential to produce rhodopsins appears to be confined to a small clade of organisms from sunlit environments. Here, we characterize the metabolic context and biophysical features of Saccharibacteria Type-1 rhodopsin sequences derived from metagenomic surveys and show that these proteins function as outward proton pumps. This provides one of the only known mechanisms by which CPR can generate a proton gradient for ATP synthesis. These Saccharibacteria do not encode the genetic machinery to produce all-trans-retinal, the chromophore essential for rhodopsin function, but their rhodopsins are able to rapidly uptake this cofactor when provided in experimental assays. We found consistent evidence for the capacity to produce retinal from β-carotene in microorganisms co-occurring with Saccharibacteria, and this genetic potential was dominated by members of the Actinobacteria, which are known hosts of Saccharibacteria in other habitats. If Actinobacteria serve as hosts for Saccharibacteria in freshwater environments, exchange of retinal for use by rhodopsin may be a feature of their associations.

Rhodopsin-bestrophin fusion proteins from unicellular algae form gigantic pentameric ion channels

Many organisms sense light using rhodopsins, photoreceptive proteins containing a retinal chromophore. Here we report the discovery, structure and biophysical characterization of bestrhodopsins, a microbial rhodopsin subfamily from marine unicellular algae, in which one rhodopsin domain of eight transmembrane helices or, more often, two such domains in tandem, are C-terminally fused to a bestrophin channel. Cryo-EM analysis of a rhodopsin-rhodopsin-bestrophin fusion revealed that it forms a pentameric megacomplex (~700 kDa) with five rhodopsin pseudodimers surrounding the channel in the center. Bestrhodopsins are metastable and undergo photoconversion between red- and green-absorbing or green- and UVA-absorbing forms in the different variants. The retinal chromophore, in a unique binding pocket, photoisomerizes from all-trans to 11-cis form. Heterologously expressed bestrhodopsin behaves as a light-modulated anion channel.

AB0431 THE EFFICACY OF BELIMUMAB (BEL) AS A SPARING CORTICOSTEROID AGENCY IN PATIENTS WITH SYSTEMIC LUPUS ERYTHEMATOSUS (SLE)

Background

Patients with SLE are recommended to continue the maintenance therapy with as less glucocorticoid as possible.1) However, tapering glucocorticoid often results in the recurrence of SLE. Current reports suggested that adding BEL to the standard therapy could lead to the reduction of glucocorticoid and the recurrence of SLE.2)

Objectives

The aim of this study is to evaluate the efficacy and the safety of BEL as co-treatment in the standard therapy of SLE.

Methods

Fourteen patients receiving the maintenance therapy of SLE were enrolled in this study. Dose of prednisolone (PSL), titer of anti-DNA antibody, WBC count, serum complement and SLE disease activity index (SLEDAI) were examined retrospectively at baseline and 24 months after administration of BEL.

Results

At the baseline, the mean age of patients was 48 years old, 11 patients were female, and the mean disease duration was 8.6 years. The mean dose of PSL was significantly reduced (meansease apre-administration of BEL:6.1±1.1 mg/day, 24 months after administration of BEL: 1.2 the baseline,p=0.001). Furthermore, six patients (43 %) could withdraw PSL without the flare of the disease. There were also statistical significance about SLEDAI between baseline and after treatment by BEL(2.1patients (43 %) cp=0.03) and the titer of anti-DNA antibody (6.8 withdraw PSL without tp=0.03). There were no statistical significant in WBC count (6177out the fla7e of the dp=0.24) and serum complement (C3 87significant in WBC count (61p=0.78, C4 20erum complement (C3 87signifp=0.54).

As for adverse event, bacterial pneumonia (n=1) and pulmonary cryptococcosis (n=1) was revealed.

Conclusion

Our study is suggested that co-treatment with BEL on standard SLE therapy was enable to prevent the flare of SLE and reduce the dose of PSL with statistical significance among the patients under the maintenance treatment of SLE. In almost half of the cases, patients could withdraw PSL without the flare.

References

[1]Ann Rheum Dis 2019; 78: 736-745.

[2]Ann Rheum Dis 2018; 77: 355-745.

Disclosure of Interests

None declared

Angelica keiskei (Ashitaba) has potential as an antithrombotic health food

Angelica keiskei (Ashitaba) is a large perennial herb that is native to the Pacific coast of Japan. It has recently become popular as a healthy food in Asian countries because it might have various physiological benefits including antithrombotic properties. Most studies of the bioactive constituents from Ashitaba have focused on the activities of the major chalcones, xanthoangelol and 4-hydroxyderricin. However, other chalcones, flavanones and coumarins have also been isolated from Ashitaba, precisely characterized, and investigated in vivo. Platelets play a key role in haemostasis and wound healing processes. Dysregulated platelet activity is associated with the progression of platelet aggregation and decreased venous blood flow, which results in thrombotic diseases. A minor chalcone, xanthoangelol E, inhibits TXB2 synthesis in rabbit platelets, which seems to be the source of the belief that Ashitaba has antithrombotic properties. However, recent data showed that xanthoangelol and 4-hydroxyderricin inhibited the aggregation of rabbit platelets. Platelet aggregation stimulated by collagen was also inhibited in whole blood incubated with Xanthoangelol or 4-hydroxyderricin. Plasminogen activator inhibitor-1 is the primary physiological inhibitor of tissue type plasminogen activator, a key protease of the fibrinolytic system. An increase in plasma of this inhibitor is associated with thrombotic conditions. Ashitaba yellow exudate inhibited the elevation of plasma plasminogen activator inhibitor-1 in mice induced by obesity or chronic low-grade inflammation. These studies showed the yellow exudate from stem cuttings and chalcones isolated from Ashitaba roots and leaves might have antithrombotic activity. This article reviews the possible antithrombotic properties of Ashitaba.

Structural basis for channel conduction in the pump-like channelrhodopsin ChRmine

ChRmine, a recently discovered pump-like cation-conducting channelrhodopsin, exhibits puzzling properties (large photocurrents, red-shifted spectrum, and extreme light sensitivity) that have created new opportunities in optogenetics. ChRmine and its homologs function as ion channels but, by primary sequence, more closely resemble ion pump rhodopsins; mechanisms for passive channel conduction in this family have remained mysterious. Here, we present the 2.0 Å resolution cryo-EM structure of ChRmine, revealing architectural features atypical for channelrhodopsins: trimeric assembly, a short transmembrane-helix 3, a twisting extracellular-loop 1, large vestibules within the monomer, and an opening at the trimer interface. We applied this structure to design three proteins (rsChRmine and hsChRmine, conferring further red-shifted and high-speed properties, respectively, and frChRmine, combining faster and more red-shifted performance) suitable for fundamental neuroscience opportunities. These results illuminate the conduction and gating of pump-like channelrhodopsins and point the way toward further structure-guided creation of channelrhodopsins for applications across biology.

Impact of heart rate reduction on recurrence after catheter ablation of persistent atrial fibrillation

Funding Acknowledgements

Type of funding sources: Private company. Main funding source(s): Johnson & Johnson KK

OnBehalf

OCVC Arrhythmia Investigators

Background

Predicting heart rate (HR) after restoration of sinus rhythm (SR) remains one of the challenges when performing catheter ablation (CA) of persistent atrial fibrillation (AF).

Purpose

To evaluate the association between pre-ablation HR during AF and post-ablation HR during SR, and whether the HR reduction is associated with AF recurrence.

Methods

The analysis was performed from the EARNEST-PVI trial, a randomized controlled trial designed to assess a CA strategy for persistent AF, which was conducted in the Osaka region of Japan. After excluding patients with beta-blocker prescription, a total of 216 patients (median age, 67 years; 20% female; 23% long-standing persistent AF) with AF rhythm at baseline and SR at discharge were enrolled in this study. Baseline HR during AF and post-ablation HR during SR was measured on admission and at discharge using the 12-lead electrocardiograms, respectively.

Results

There was a mild correlation between baseline HR (median 82 [interquartile range 72-95] bpm) and post-ablation HR (78 [48-117] bpm) (r = 0.27, p &lt;0.001). Reduction in HR was positively associated with baseline HR (r = 0.79, p &lt;0.001) and was negatively associated with post-ablation HR (r = - 0.37, p &lt;0.001). During the follow-up of 1 year, 56 patients (25.9%) experienced AF recurrence. HR reduction had the higher diagnostic accuracy in predicting AF recurrence than HR at baseline and HR after CA (area under the curve, 0.625; 95% confidence interval, 0.557–0.690; p = 0.003). AF recurrence rate was significantly higher in 141 patients with smaller HR reduction (cut-off, &lt;14bpm) than those with larger HR reduction (31.9% vs. 14.7%, p = 0.009). After adjustment of age, gender, long-standing persistent AF, and CA strategy, HR reduction of &lt;14 bpm was a significant predictor of AF recurrence (hazard ratio, 2.32; 95% confidence interval, 1.20–4.51; p = 0.013).

Conclusions

There was a mild correlation between HR during AF and HR after restoration of SR in patients underwent CA of persistent AF. HR reduction after restoration of SR predicted AF recurrence.

Structural characterization of proton-pumping rhodopsin lacking a cytoplasmic proton donor residue by X-ray crystallography

DTG/DTS rhodopsin, which was named based on a three-residue motif (DTG or DTS) that is important for its function, is a light-driven proton-pumping microbial rhodopsin using a retinal chromophore. In contrast to other light-driven ion-pumping rhodopsins, DTG/DTS rhodopsin does not have a cytoplasmic proton donor residue, such as Asp, Glu, or Lys. Because of the lack of cytoplasmic proton donor residue, proton directly binds to the retinal chromophore from the cytoplasmic solvent. However, mutational experiments that showed the complicated effects of mutations were not able to clarify the roles played by each residue, and the detail of proton uptake pathway is unclear because of the lack of structural information. To understand the proton transport mechanism of DTG/DTS rhodopsin, here we report the three-dimensional structure of one of the DTG/DTS rhodopsins, PspR from Pseudomonas putida, by X-ray crystallography. We show that the structure of the cytoplasmic side of the protein is significantly different from that of bacteriorhodopsin, the best-characterized proton-pumping rhodopsin, and large cytoplasmic cavities were observed. We propose that these hydrophilic cytoplasmic cavities enable direct proton uptake from the cytoplasmic solvent without the need for a specialized cytoplasmic donor residue. The introduction of carboxylic residues homologous to the cytoplasmic donors in other proton-pumping rhodopsins resulted in higher pumping activity with less pH dependence, suggesting that DTG/DTS rhodopsins are advantageous for producing energy and avoiding intracellular alkalization in soil and plant-associated bacteria.

Diverse heliorhodopsins detected via functional metagenomics in freshwater Actinobacteria, Chloroflexi and Archaea

The recently discovered rhodopsin family of heliorhodopsins (HeRs) is abundant in diverse microbial environments. So far, the functional and biological roles of HeRs remain unknown. To tackle this issue, we combined experimental and computational screens to gain some novel insights. Here, 10 readily expressed HeR genes were found using functional metagenomics on samples from two freshwater environments. These HeRs originated from diverse prokaryotic groups: Actinobacteria, Chloroflexi and Archaea. Heterologously expressed HeRs absorbed light in the green and yellow wavelengths (543-562 nm) and their photocycles exhibited diverse kinetic characteristics. To approach the physiological function of the HeRs, we used our environmental clones along with thousands of microbial genomes to analyze genes neighbouring HeRs. The strongest association was found with the DegV family involved in activation of fatty acids, which allowed us to hypothesize that HeRs might be involved in light-induced membrane lipid modifications.

Assessment of the albumin-bilirubin grade as a prognostic factor in patients with non-small-cell lung cancer receiving anti-PD-1-based therapy

Introduction

The albumin-bilirubin (ALBI) grade is a novel indicator of the liver function. Some studies showed that the ALBI grade was a prognostic and predictive biomarker for the efficacy of chemotherapy in cancer patients. The association between the ALBI grade and outcomes in patients with non-small-cell lung cancer (NSCLC) treated with cancer immunotherapy, however, is poorly understood.

Methods

We retrospectively enrolled 452 patients with advanced or recurrent NSCLC who received anti-programmed cell death protein 1 (PD-1)-based therapy between 2016 and 2019 at three medical centers in Japan. The ALBI score was calculated from albumin and bilirubin measured at the time of treatment initiation and was stratified into three categories, ALBI grade 1-3, with reference to previous reports. We examined the clinical impact of the ALBI grade on the outcomes of NSCLC patients receiving anti-PD-1-based therapy using Kaplan–Meier survival curve analysis with log-rank test and Cox proportional hazards regression analysis.

Results

The classifications of the 452 patients were as follows: grade 1, n = 158 (35.0%); grade 2, n = 271 (60.0%); and grade 3, n = 23 (5.0%). Kaplan–Meier survival curve analysis showed that the ALBI grade was significantly associated with progression-free survival and overall survival. Moreover, Cox regression analysis revealed that the ALBI grade was an independent prognostic factor for progression-free survival and overall survival.

Conclusion

The ALBI grade was an independent prognostic factor for survival in patients with advanced or recurrent NSCLC who receive anti-PD-1-based therapy. These findings should be validated in a prospective study with a larger sample size.

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ALBI grade is calculated from albumin and bilirubin.

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We evaluated the impact of ALBI grade on survival in NSCLC patients receiving immune checkpoint inhibitors.

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ALBI grade was an independent prognostic factor for progression-free survival (PFS) and overall survival (OS).

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ALBI grade effectively stratified PFS and OS in patients with performance status 1-3.

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ALBI grade was significantly associated with PFS and OS, regardless of programmed death ligand-1.

Rhodopsins at a glance

Rhodopsins are photoreceptive membrane proteins consisting of a common heptahelical transmembrane architecture that contains a retinal chromophore. Rhodopsin was first discovered in the animal retina in 1876, but a different type of rhodopsin, bacteriorhodopsin, was reported to be present in the cell membrane of an extreme halophilic archaeon, Halobacterium salinarum, 95 years later. Although these findings were made by physiological observation of pigmented tissue and cell bodies, recent progress in genomic and metagenomic analyses has revealed that there are more than 10,000 microbial rhodopsins and 9000 animal rhodopsins with large diversity and tremendous new functionality. In this Cell Science at a Glance article and accompanying poster, we provide an overview of the diversity of functions, structures, color discrimination mechanisms and optogenetic applications of these two rhodopsin families, and will also highlight the third distinctive rhodopsin family, heliorhodopsin.

Mitophagy reporter mouse analysis reveals increased mitophagy activity in disuse-induced muscle atrophy

Muscle disuse induces atrophy through increased reactive oxygen species (ROS) released from damaged mitochondria. Mitophagy, the autophagic degradation of mitochondria, is associated with increased ROS production. However, the mitophagy activity status during disuse-induced muscle atrophy has been a subject of debate. Here, we developed a new mitophagy reporter mouse line to examine how disuse affected mitophagy activity in skeletal muscles. Mice expressing tandem mCherry-EGFP proteins on mitochondria were then used to monitor the dynamics of mitophagy activity. The reporter mice demonstrated enhanced mitophagy activity and increased ROS production in atrophic soleus muscles following a 14-day hindlimb immobilization. Results also showed an increased expression of multiple mitophagy genes, including Bnip3, Bnip3l, and Park2. Our findings thus conclude that disuse enhances mitophagy activity and ROS production in atrophic skeletal muscles and suggests that mitophagy is a potential therapeutic target for disuse-induced muscle atrophy.

Determination of physiological cardiac myosin-binging protein levels (cMyc) in healthy populations

Background

Cardiac myosin–binding protein C (cMyC) is a cardiac-restricted protein that has more abundant, rapid release and clearance kinetics than cardiac troponin. The current ESC guideline suggests the cMyC may provide value as an alternative to cardiac troponin. The 99th percentile value is universally endorsed as the reference cut off to aid in the diagnosis of acute myocardial infarction (AMI), however, none of the report of healthy population of cMyC.

Purpose

The aim of this study was to evaluate the distribution of cMyC values in healthy subjects.

Methods

We used two cohorts in this retrospective study. 1) Healthy subjects; a total of 500 subjects (250 men and 250 women) who had annual health examinations in 2012 in the area of Kamigoto, a suburb of Nagasaki city in Southern Japan were enrolled. All participants showed none of abnormal findings including cell blood counts, chemical analysis, liver function tests, general urine tests, occult blood tests of stool, barium swallow, mammography for women, abdominal ultrasound sonography, and electrocardiogram. All blood samples were obtained in a fasting state in the morning. 2) Chest pain subjects; we collected samples from 250 subjects including 50 with non-ST elevation myocardial infarction visited admitted to a university hospital for measurement of high-sensitivity troponin T and coronary artery assessment by coronary angiography. We measured cMyC level in both cohorts by HISCL™-800 system (Sysmex corporation, Japan). The assay has a limit of detection of 0.5 ng/L and a lower limit of quantification of 1.3 ng/L.

Result

In healthy subjects, median age (IQR) was 44 (20, 82) in men and 50 (23, 91) in women. The 99th percentile of cMyC was 27.3 ng/L, which was around one-third lower than that in previous report (87 ng/L). In chest pain subjects, the concentrations of cMyC at presentation were significantly higher in those with versus without AMI (median, 66 ng/L versus 10 ng/L, P&lt;0.001). Discriminatory power for AMI, as quantified by the area under the receiver-operating characteristic curve (AUC), was comparable for cMyC (AUC, 0.85 (95% CI 0.79–0.91) and hs-cTnT (AUC, 0.81 (95% CI 0.76–0.88)).

Conclusion

We defined the normal range of cMyC in healthy Japanese subjects. The level of cMyC at presentation provides discriminatory power comparable to hs-cTnT in the diagnosis of AMI. To determine the physiological value of a biomarker may be necessary to evaluate enough information about their health status.

Funding Acknowledgement

Type of funding sources: Public grant(s) – National budget only. Main funding source(s): Grant-in-Aid for Scientific Research

Association between myocardial wall thickness and left ventricular functional recovery after catheter ablation of atrial fibrillation in patients with reduced ejection fraction

Background

Catheter ablation of atrial fibrillation (AFCA) is an effective treatment to develop left ventricular (LV) functional recovery. However, the degree of recovery differs between individuals due to the different extent of myocardial fibrosis and scarring.

Purpose

To examine whether pre-ablation LV wall thickness (WT) and its regional heterogeneity predict LV functional recovery after AFCA in patients with LV systolic dysfunction.

Methods

Of 3682 consecutive patients who underwent first-time AFCA between January 2012 and September 2020 in our institution, 174 (age, 63±10 years; male, 83%; ischemic cardiomyopathy, 14%) with a baseline LV ejection fraction (LVEF) of &lt;40% were retrospectively evaluated. They were subjected to 256-slice MDCT scanning at baseline and 3 months after AFCA. Baseline WT was evaluated by 16-segment model. Mean and standard deviation (SD) of 16 regional WT were calculated in both end-systolic and end-diastolic phase.

Results

LVEF significantly improved from 30±7% to 57±17% (p&lt;0.001) after AFCA. Increase in LVEF (delta-LVEF) was positively correlated with baseline end-diastolic WT (r=0.31, p&lt;0.001) and negatively correlated with SD of end-systolic WT (r=−0.21, p=0.007). Independent of WT measurements, delta-LVEF was negatively correlated with LV end-diastolic volume (r=−0.42, p&lt;0.001). We created a scoring system to predict the degree of wall motion recovery using the median value of the 3 variables; assigned 1 point each for end-diastolic WT &gt;7.4mm, SD of end-systolic WT &lt;1.61mm, and LV end-diastolic volume &lt;125ml. The model successfully predicted improvement in LVEF after AFCA (0 point (N=13) vs. 1 point (N=72) vs. 2–3 point (N=89), 11±16% vs. 20±17% vs. 33±12%, p&lt;0.001).

Conclusion

Myocardial WT and its regional heterogeneity as well as LV end-diastolic volume predicted functional recovery after AFCA in patients with reduced LVEF.

Funding Acknowledgement

Type of funding sources: None.