Biology subjects

Motomura, K.

Publications and source records attributed to Motomura, K..

7 recordsLinked to original sources

bioRxiv2026

The Lateral Protein Cluster as a Key Component of Plant Cell Polarity

Cell polarity is an ancient organizing principle across kingdoms. As in animal epithelial cells, plant cells asymmetrically distribute proteins to establish functionally distinct membrane domains. In roots, radial polarity distinguishes inner and outer cell surfaces and supports directional nutrient transport, yet its molecular basis remains poorly understood. Here, we show that the leucine-rich repeat receptor-like kinases CaMRLK and IRK occupy complementary lateral plasma membrane domains in Arabidopsis thaliana roots. Polarity-guided proximity labeling identified previously uncharacterized proteins associated with inner- and outer-lateral domains. Clade VII LRR-RLKs, protein S-acyltransferases, SICK, IRKI1, and a distinct group of NPH3/RPT2-LIKEs assemble into the Lateral Protein Cluster (LPC) through multivalent interactions. LPC components are conserved across land plants, and disruption of NRL function impairs morphogenesis in Arabidopsis and Marchantia polymorpha. Together, these findings establish the LPC as an evolutionarily conserved molecular machinery linking radial cell polarity to plant morphogenesis.

plant biology↗

bioRxiv2025

Secreted protein methyltransferase METTL9 catalyzes Nπ-histidine methylation of extracellular plasma proteins

Post-translational modifications (PTMs) of proteins alter their biophysical properties, thus affecting their activity, localization and interactions. These reactions are principally intracellular events; however, to date, only phosphorylation has been shown to occur within the extracellular space. Here, we identified METTL9 as the first secreted methyltransferase responsible for N{pi}-histidine methylation. METTL9 undergoes N-linked glycosylation, thereby forming dimers via disulfide bonds. Using a split-luciferase complementary assay, we revealed that N-glycosylated METTL9 is secreted extracellularly via the ER-Golgi pathway. Endogenous METTL9 is highly expressed in HL60 cells during neutrophil-like differentiation and secreted extracellularly. METTL9 catalyzes N{pi}-methylhistidine formation in plasma proteins, in which the thyroxine transporter transthyretin (TTR) and copper transporter ceruloplasmin are identified as substrates for methylation in vitro. Both methylations occur at the His-x-His motif, a recognition sequence for METTL9, and TTR methylation decreases its binding affinity to zinc. Our results establish that histidine methylation is the second extracellular PTM, following phosphorylation.

biochemistry↗

bioRxiv2025

Establishment of spinocerebellar ataxia type 34 model mice accompanied by early glial activation and degeneration of cerebellar neurons

Spinocerebellar ataxia type 34 (SCA34) is an autosomal dominant neurodegenerative disease primarily characterized by progressive cerebellar atrophy and ataxia, frequently accompanied by cognitive dysfunction and erythrokeratodermia variabilis. In 2014, missense mutations in the gene encoding elongation of very long chain fatty acids protein 4 (ELOVL4) were identified as the causative gene for SCA34. ELOVL4, which is involved in the synthesis of very long chain fatty acids, is highly expressed in the cerebellum compared to other brain regions, with predominant expression in neurons. We attempted to establish a mouse model of SCA34 by expressing mutant ELOVL4 in cerebellar neurons using adeno-associated virus (AAV) vectors and to elucidate the underlying pathogenic mechanisms. Expression of W246G mutant ELOVL4 successfully induced progressive motor dysfunction beginning at two weeks post-AAV vector injection. Immunohistochemical analyses revealed that the degeneration of cerebellar Purkinje cells and neurons in the deep cerebellar nuclei (DCN) paralleled the observed motor decline. Importantly, microglial activation was detected in the molecular layer of the cerebellar cortices and the DCN prior to the onset of both neurodegeneration and motor dysfunction. Furthermore, after the onset of motor symptoms, the SCA34 model mice exhibited decreased synaptic inputs from climbing fibers to Purkinje cells, as well as reduced inputs from Purkinje cells to DCN neurons. These findings suggest that early microglial activation and the resulting synaptic disturbance are critical preceding events that lead to the progressive cerebellar neurodegeneration and motor dysfunction observed in this SCA34 mouse model.

neuroscience↗

bioRxiv2025

Rare k-mers reveal centromere haplogroups underlying human diversity and cancer translocations

Centromeres are among the most diverse and dynamically evolving regions of the human genome and are commonly affected in various human cancers. However, organized into highly repetitive -satellite higher-order repeats (HORs), human centromere sequences have long resisted detailed genomic analysis. Although the development of long-read sequencing platforms has enabled the analysis of complete centromere sequences, their application to a large set of samples is still largely limited, preventing our understanding of centromere variation and haplotype structures across large human populations and the structural basis of centromere-involving translocations in cancer. Here we show that rare k-mers present in centromeric regions can serve as effective markers for dissecting the complexity of centromere structure, particularly that of active -satellite HOR arrays (aHOR arrays), across human populations and for understanding centromere-involving abnormalities in cancer. Based on rare k-mer-based clustering, centromere aHOR arrays are clustered into discrete haplogroups (aHOR-HGs) with distinct structural features. These k-mers were also used to develop a framework that enables the inference of haplogroups in a given sample based on short-read whole genome sequencing (WGS) data (ascairn). By applying ascairn to large-scale human population datasets (n > 3,300), we revealed the diversity of aHOR-HGs and their geographic histories across populations. The rare k-mer-based approach was also applied to investigate the structure of 1p/19q co-deletion, a highly recurrent centromere-involving translocation in IDH-mutated oligodendrogliomas. Analyzing short-read WGS data from 142 cases with 1p/19q co-deletion using rare k-mers, we showed that breakpoints of 1p/19q co-deletion were mapped to aHOR arrays in chromosomes 1 (D1Z7) and 19 (D19Z3), which was validated by long-read sequencing of two 1p/19q co-deletion-positive cases. Notably, the translocation preferentially involved haplogroups composed of haplotypes containing larger regions susceptible to rearrangement. These results highlight the role of rare k-mers in dissecting the complexity of centromere sequences and their evolutionary history as well as understanding centromere-involving abnormalities associated with human diseases.

genomics↗

bioRxiv2024

Microtubules ensure transport of vegetative nuclei and sperm cells by fine-tuning their home positions

The pollen tube plays a pivotal role in double fertilization by delivering sperm cells (SCs) to the ovule. In Arabidopsis thaliana, a pair of SCs tightly connects with the vegetative nucleus (VN) to form the male germ unit (MGU), which is located in the apical region during pollen-tube growth, keeping the VN ahead of the SCs. MGU transport relies on independent motility of VN and SC pairs. However, the complexity of this dual motive force has hindered our understanding of MGU behavior, including its positioning and nuclear order. We used Arabidopsis mutants or transgenic plants that produced semi-motile MGUs with aberrant VNs or SCs to analyze the positioning of VN or SCs after stochastically disconnecting the MGU. In pollen tubes with an immotile SC pair, the VN was [~]70 m away from the tip, whereas in pollen tubes with an immotile VN, the SC pair was [~]100 m away from the tip, implying that the VN and SCs have independent home positions. The position of MGU moved forward owing to the loss of the microtubule-destabilizing kinesin KINESIN-13A. Conversely, microtubule depolymerization by oryzalin treatment or introducing mutations in TUBULIN BETA 4 (TUB4) deregulated the position of the MGU and shifted its position backward. In addition, tub4 plants exhibited reduced fertility. These data indicate a significant role of microtubules in stable MGU positioning to ensure reproductive success.

plant biology↗

bioRxiv2021

Rhomboid protease RHBDL4/RHBDD1 cleaves SREBP-1c at ER monitoring and regulating fatty acids

The ER-embedded transcription factors, sterol-regulatory element-binding proteins (SREBPs), master regulators of lipid biosynthesis, are transported to Golgi for proteolytic activation to tune cellular cholesterol levels and regulate lipogenesis. However, mechanisms by which the cell responds to the levels of saturated or unsaturated fatty acids remain underexplored. Here we show that RHBDL4/RHBDD1, a rhomboid family protease, directly cleaves SREBP-1c at ER. The p97/VCP, AAA-ATPase complex then acts as an auxiliary segregase to extract the remaining ER-embedded fragment of SREBP-1c. Importantly, the enzymatic activity of RHBDL4 is enhanced by saturated fatty acids (SFAs), but inhibited by polyunsaturated fatty acids (PUFAs). Genetic deletion of RHBDL4 in mice fed on a Western diet enriched in SFAs and cholesterol prevented SREBP-1c from inducing genes for lipogenesis, particularly for synthesis and incorporation of PUFAs, and secretion of lipoproteins. The RHBDL4-SREBP-1c pathway reveals a regulatory system for monitoring fatty acid composition and maintaining cellular lipid homeostasis. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=145 SRC="FIGDIR/small/457590v2_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@591eb2org.highwire.dtl.DTLVardef@ee6361org.highwire.dtl.DTLVardef@be893eorg.highwire.dtl.DTLVardef@1247d38_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2019

No consistent evidence for microbiota in murine placental and fetal tissues

The existence of a placental microbiota and in utero colonization of the fetus has been the subject of recent debate. The objective of this study was to determine whether the placental and fetal tissues of mice harbor bacterial communities. Bacterial profiles of the placenta and fetal brain, lung, liver, and intestine were characterized through culture, qPCR, and 16S rRNA gene sequencing. These profiles were compared to those of the maternal mouth, lung, liver, uterus, cervix, vagina, and intestine, as well as to background technical controls. Positive bacterial cultures from placental and fetal tissues were rare; of the 165 total bacterial cultures of placental tissues from the 11 mice included in this study, only nine yielded at least a single colony, and five of those nine positive cultures came from a single mouse. Cultures of fetal intestinal tissues yielded just a single bacterial isolate: Staphylococcus hominis, a common skin bacterium. Bacterial loads of placental and fetal brain, lung, liver, and intestinal tissues were not higher than those of DNA contamination controls and did not yield substantive 16S rRNA gene sequencing libraries. From all placental or fetal tissues (N = 49), there was only a single bacterial isolate that came from a fetal brain sample having a bacterial load higher than that of contamination controls and that was identified in sequence-based surveys of at least one of its corresponding maternal samples. Therefore, using multiple modes of microbiologic inquiry, there was not consistent evidence of bacterial communities in the placental and fetal tissues of mice. IMPORTANCEThe prevailing paradigm in obstetrics has been the sterile womb hypothesis, which posits that fetuses are first colonized by microorganisms during the delivery process. However, some are now suggesting that fetuses are consistently colonized by microorganisms in utero by microbial communities that inhabit the placenta and intra-amniotic environment. Given the established causal role of microbial invasion of the amniotic cavity (i.e. intra-amniotic infection) in pregnancy complications, especially preterm birth, if the in utero colonization hypothesis were true, there are several aspects of current understanding that will need to be reconsidered including the magnitude of intra-amniotic microbial load required to cause disease and their potential influence on the ontogeny of the immune system. However, acceptance of the in utero colonization hypothesis is premature. Herein, we do not find consistent evidence for placental and fetal microbiota in mice using culture, qPCR, and DNA sequencing.

microbiology↗