Biology subjects

Kihara, A.

Publications and source records attributed to Kihara, A..

5 recordsLinked to original sources

bioRxiv2026

Discovery of dihydroxy-enone-type protein-bound ceramides as the dominant type in human stratum corneum

Protein-bound ceramides are a specialized subclass of ceramides that are essential for skin barrier function, and their defective formation leads to severe skin disorder ichthyosis. Despite their biological importance, the precise molecular structures of protein-bound ceramides have remained incompletely defined, largely due to the technical challenges arising from their unique covalent linkage between lipid and protein components with highly distinct physicochemical properties. Using mass-spectrometry-based analyses of acylceramide moieties derived from protein-bound ceramides, we investigated whether epoxy-enone (EE)-type protein-bound ceramides present in mouse epidermis are conserved in human skin. Although EE-type protein-bound ceramides were detectable in the human stratum corneum, they constituted only a minor fraction of the ceramides in this tissue. Instead, we discovered a previously unrecognized class of protein-bound ceramides, termed dihydroxy-enone (DE)-type protein-bound ceramides, as the predominant class in human skin. These DE-type ceramides are generated through hydrolytic opening of the epoxide moiety of EE-type ceramides. In contrast, DE-type protein-bound ceramides were present in mouse epidermis at much lower levels. DE-type acylceramides appeared as two chromatographically distinct peaks, which likely correspond to putative stereoisomers with (9R,10S) and (9R,10R) configurations. Age-dependent increases in the (9R,10S) form in mouse epidermis closely paralleled changes in the expression levels of the epoxide hydrolase Ephx3, suggesting a role for EPHX3 in the conversion of EE- to DE-type ceramides. Together, these findings further reveal molecular diversity in protein-bound ceramides and a fundamental difference between human and mouse epidermal lipid architectural organization.

biochemistry↗

bioRxiv2024

Fatty acyl-CoA reductase FAR1 is essential for testicular seminolipid synthesis, spermatogenesis, and male fertility

Seminolipids are testis-specific ether glycolipids that are important for spermatogenesis. The fatty alcohol (ether-linked alkyl moiety) in ether lipids is generated from an acyl-CoA by fatty acyl-CoA reductase (FAR). To date, the diversity of the alkyl and acyl moieties in seminolipids, the specific stage of spermatogenesis during which seminolipids are produced, and the FAR isozyme (FAR1 or FAR2) involved in the synthesis of the alkyl moieties have remained largely unclear. Here, we demonstrated that Far1 is expressed in the mouse testis via quantitative RT-PCR analysis, whereas Far2 was barely detectable. In situ hybridization and quantitative RT-PCR analysis of spermatogenic cells separated via FACS revealed that Far1 is expressed in spermatogonia, spermatocytes, and spermatids. We generated Far1 knockout (KO) mice and found that male Far1 KO mice were infertile. In these mice, sperms were absent in the epididymides and the testes were small, with multinucleated cells and vacuoles in the seminiferous tubules. LC-MS/MS analysis showed that the vast majority of seminolipids (> 90%) in wild-type mouse testes contained C16:0 in both the alkyl and the acyl moieties. Seminolipids were present in all subclasses of spermatogenic cells in wild-type mice, but they were absent in Far1 KO mice. Instead, the production of non-ether, diacyl-type sulfogalactosyl lipids (sulfogalactosyl diacylglycerols) was induced in Far1 KO mice. In conclusion, the alkyl and acyl moieties of seminolipids in the testis are low in diversity, and Far1 is essential for seminolipid synthesis and spermatogenesis.

biochemistry↗

bioRxiv2023

Determining the structure of protein-bound ceramides, essential lipids for skin barrier function

Protein-bound ceramides, specialized ceramides covalently bound to corneocyte surface proteins, are essential for skin permeability barrier function. However, their exact structure and target amino acid residues are unknown. Here, we found that epoxy-enone (EE) ceramides, precursors of protein-bound ceramides, as well as their synthetic analog, formed stable conjugates only with Cys among nucleophilic amino acids. NMR spectroscopy revealed that the {beta}-carbon of the enone was attached by the thiol group of Cys via a Michael addition reaction. We confirmed the presence of Cys-bound EE ceramides in mouse epidermis by mass spectrometry analysis of protease-digested epidermis samples. EE-ceramides were reversibly released from protein-bound ceramides via sulfoxide elimination. We found that protein-bound ceramides with reversible release properties accounted for approximately 60% of total protein-bound ceramides, indicating that Cys-bound EE ceramides are the predominant protein-bound ceramides. Our findings provide clues to the molecular mechanism of skin barrier formation by protein-bound ceramides. HighlightsO_LIEpoxy-enone (EE) ceramides form stable conjugates with Cys. C_LIO_LICys binds to the {beta}-carbon of the enone via a Michael addition reaction. C_LIO_LICys-bound EE ceramides exist in the mouse epidermis. C_LIO_LICys-bound EE ceramides are the predominant protein-bound ceramides. C_LI In BriefProtein-bound ceramides are specialized ceramides essential for skin permeability barrier function. In the present study, we determined the exact structure of protein-bound ceramides as Cys-bound epoxy-enone ceramides where the {beta}-carbon of the epoxy-enone ceramides is attached by Cys residues of corneocyte surface proteins via a Michael addition reaction.

cell biology↗

bioRxiv2022

An ERAD-independent role for rhomboid pseudoprotease Dfm1 in mediating sphingolipid homeostasis

Nearly one-third of nascent proteins are initially targeted to the endoplasmic reticulum (ER) where they are correctly folded and assembled before being delivered to their final cellular destinations. To prevent the accumulation of misfolded membrane proteins, ER-associated-degradation (ERAD) removes these clients from the ER membrane to the cytosol in a process known as retrotranslocation. Our recent work demonstrates that rhomboid pseudoprotease, Dfm1, is involved in the retrotranslocation of ubiquitinated integral membrane ERAD substrates. To survey for potential interaction partners of Dfm1, we performed protein-proximity labeling by BioID (proximity-dependent biotin identification) followed by mass spectrometry and identified several interacting proteins known to play a role in the sphingolipid biosynthesis pathway. Specifically, we found that Dfm1 physically interacts with the SPOTS complex, which is composed of serine palmitoyltransferase (SPT) enzymes and accessory components and is critical for catalyzing the first rate-limiting step of the sphingolipid biosynthesis pathway. We demonstrate for the first time that Dfm1 has a role in ER export, a function that is independent of Dfm1s canonical ERAD retrotranslocation function. Specifically, we show that loss of Dfm1 results in the accumulation of phosphorylated Orm2 at the ER, suggesting a novel role for Dfm1 in controlling Orm2 export from the ER and its subsequent degradation by EGAD. Moreover, recruitment of Cdc48 by Dfm1, which is critical for its role in ERAD retrotranslocation, is dispensable for Dfm1s role in ER export. Given that the accumulation of human Orm2 homologs, ORMDLs, are associated with many maladies, our study serves as a molecular foothold for understanding how dysregulation of sphingolipid metabolism leads to various diseases.

cell biology↗

bioRxiv2018

Gap junctions set the speed and nucleation rate of stage I retinal waves

Spontaneous waves in the developing retina are essential in the formation of the retinotopic mapping in the visual system. From experiments in rabbits, it is known that the earliest type of retinal waves (stage I) is nucleated spontaneously, propagates at a speed of 451{+/-}91 m/sec and relies on gap junction coupling between ganglion cells. Because gap junctions (electrical synapses) have short integration times, it has been argued that they cannot set the low speed of stage I retinal waves. Here, we present a theoretical study of a two-dimensional neural network of the ganglion cell layer with gap junction coupling and intrinsic noise. We demonstrate that this model can explain observed nucleation rates as well as the comparatively slow propagation speed of the waves. From the interaction between two coupled neurons, we estimate the wave speed in the model network. Furthermore, using simulations of small networks of neurons (N[≤]260), we estimate the nucleation rate in form of an Arrhenius escape rate. These results allow for informed simulations of a realistically sized network, yielding values of the gap junction coupling and the intrinsic noise level that are in a physiologically plausible range.\n\nAuthor summaryRetinal waves are a prominent example of spontaneous activity that is observed in neuronal systems of many different species during development. Spatio-temporally correlated bursts travel across the retina at a few hundred m/sec to facilitate the maturation of the underlying neuronal circuits. Even at the earliest stage, in which the network merely consists of ganglion cells coupled by electric synapses (gap junctions), it is unclear which mechanisms are responsible for wave nucleation and transmission speed. We propose a model of gap-junction coupled noisy neurons, in which waves emerge from rare stochastic fluctuations in single cells and the waves transmission speed is set by the latency of the burst onset in response to gap-junction currents between neighboring cells.

neuroscience↗