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Maruyama, S.

Publications and source records attributed to Maruyama, S..

11 recordsLinked to original sources
bioRxiv2026

Core genome MLST reveals genetic and BafA-associated phenotypic diversities in Bartonella henselae strains

Bartonella henselae is a zoonotic pathogen associated with cat-scratch disease. Although multilocus sequence typing (MLST) has been used for strain classification, its resolution for distinguishing between B. henselae isolates remains limited. We herein developed a B. henselae-specific core genome MLST (cgMLST) scheme based on whole-genome sequencing data and examined the genetic and phenotypic diversities of 80 strains derived from cats, humans, mongooses, and masked palm civets. Using the conventional MLST scheme, the 80 strains were classified into nine sequence types (STs), while cgMLST subdivided them into 72 cgSTs, demonstrating a marked improvement in discriminatory power. The cgMLST scheme comprised 1,183 core genes and showed high applicability across the 80 strains. A phylogenetic analysis revealed that ST1, which has been associated with cat-scratch disease, was further subdivided into three major clusters and two singletons, indicating high genetic heterogeneity within this ST. We also found that the bafA subtypes clustered in a manner that was largely consistent with the cgMLST-based phylogenetic structure, suggesting a close relationship between bafA variations and the genomic background of B. henselae strains. In a human umbilical vein endothelial cell proliferation assay, strains belonging to distinct cgSTs exhibited strain-dependent differences in proliferative capacity, which were associated with the bafA subtype classification. Some strains induced focal cell fragmentation and a reduced cell density at a high multiplicity of infection, indicating strain-dependent differences in endothelial cell injury. Collectively, the present results establish a high-resolution cgMLST framework for B. henselae and demonstrate that genetically distinct strains have diverse endothelial cell phenotypes.

microbiology↗
bioRxiv2026

CRISPR/Cas9-mutagenesis reveals that varying dependence on HSF1 is associated with differences in coral heat tolerance

Coral reefs face declines due to increasing water temperatures associated with climate change. Major research efforts have focused on determining the mechanisms corals can use to adapt to heat stress and identifying molecular indicators for this adaptation. CRISPR/Cas9-based genomic editing promises a new avenue to study gene function in corals; however, these methods are limited by the annual spawning of corals in the wild. Here, we shifted spawning of the reef-building coral Galaxea fascicularis to access gametes multiple times a year in the lab. We discovered the remarkable plasticity and programmability in coral spawning, which enabled the development of a genetically tractable model coral. To investigate the molecular responses of corals to heat stress, we profiled transcriptional changes in heat-tolerant G. fascicularis and heat-sensitive Acropora millepora during acute heat stress. Comparison of the transcriptional responses to heat stress in larvae of the two species revealed that A. millepora has a stronger magnitude of the early heat stress response than G. fascicularis. This increased response in A. millepora included the upregulation of the conserved transcriptional regulator of heat stress response, Heat Shock Transcription Factor 1 (HSF1), and its predicted targets. CRISPR/Cas9 mutagenesis of HSF1 in both species showed that the heat-tolerant G. fascicularis is less dependent on HSF1 than A. millepora for survival during acute heat stress. These results suggest that differences in HSF1 expression after heat exposure contribute to variation in coral heat tolerance and may be used as biomarkers to predict heat tolerance in wild corals.

genetics↗
bioRxiv2026

Two distinct green algal symbionts cohabiting in the Japanese black salamander Hynobius nigrescens

Green algae in the genus Oophila are associated with eggs of amphibians, e.g. salamanders and frogs, and are the only known photosynthetic endosymbionts in vertebrates. However, phylogenetic placements of "Oophila" algae associated with amphibians into two distinct clades have caused significant confusion and hindered our understanding of the nature and diversity of this symbiotic system. To gain insights into this unexplored symbiotic model, we carried out a sampling of the Japanese black salamander Hynobius nigrescens eggs, an endemic species in Japan, covering five distinct locations. Egg masses from H. nigrescens all contained green algae, some of which were sampled, isolated, and cultured. In total, 32 algal isolates could grow as free-living cultures and were used for phylogenetic and morphological analyses. Our results supported the co-existence of two Oophila subgroups with H. nigrescens embryos. One is associated with the known subclades of O. amblystomatis found in North America, and the other belongs to an Oophila/Chlorococcum group in the Stephanosphaerinia. The isolates in each subgroup showed identical morphology across sampling sites, consistent with our phylogenetic findings. These new, unique cultures of amphibian-associated green algae will help to understand photosymbiosis between vertebrates and algae.

evolutionary biology↗
bioRxiv2025

Co-option of lysosomal machinery shapes the symbiosis supporting coral reefs

Intracellular photosymbiosis has evolved across life and forms the foundation of coral reef ecosystems. Using the sea anemone Aiptasia as a model, we generated a high-quality proteome of the symbiosome, the organelle that houses algal symbionts. This proteome revealed protein trafficking mechanisms and the types of biomolecules exchanged during symbiosis. Symbiosomal enrichment of lysosomal proteins, visualization of lysosomal fusion, along with reduced symbiosis following knockdown of lysosomal genes, supports its phagolysosomal identity and that extensive co-option of lysosomal proteins shapes the symbiosome. CRISPR/Cas9-induced mutations in the symbiosomal and lysosomal bicarbonate/sulfate transporter, SLC26A11, disrupted symbiosis in both Aiptasia and a reef-building coral. These findings support that anemones and corals independently evolved a carbon-concentrating and sulfate transport mechanism to fuel photosymbiosis by co-opting an orthologous lysosomal transporter.

cell biology↗
bioRxiv2025

Positive selection of a starch synthesis gene and phenotypic differentiation of starch accumulation in symbiotic and free-living coral symbiont dinoflagellate species

Symbiosis is a basis for species diversification through interactions between organisms. In tropical and subtropical oceans, dinoflagellate symbionts belonging to the family Symbiodiniaceae, including the genus Symbiodinium, support the flourishment of cnidarian hosts, including corals, and thereby the ecology of oligotrophic oceans through their photosynthate carbon transfers. Although the genus Symbiodinium includes both free-living and symbiotic species, the detailed genetic background of their lifestyle differences remains unclear. In this study, we identified candidate genes involved in the evolutionary acquisition or maintenance of symbiosis in Symbiodinium spp. by detecting genes that have undergone positive selection during symbiotic and free-living lifestyle diversification. Using multiple Symbiodinium genomes to detect positive selection, 35 genes were identified, including a gene encoding soluble starch synthase SSY1 and genes related to metabolite secretion, which may be preferred for symbiotic lifestyles. In particular, our in silico analyses revealed that the SSY1 gene family has undergone extensive gene duplications in an ancestral dinoflagellate, and that the mutations detected as positive selection have occurred in the intrinsically disordered region of one of the homologs. Consistent with molecular evolution, the phenotypes of intracellular starch synthesis/accumulation were distinct between the symbiotic and free-living species of Symbiodinium when cultured under different pH and nitrogen conditions. These results provide molecular and phenotypic insights into symbiotic Symbiodinium-coral relationships. Significance statementClarifying how coral symbiont algae of the family Symbiodiniaceae are functionally diversified is crucial for understanding the molecular mechanisms of symbiotic relationships and interactions in animal-algal symbioses. However, gene-level molecular evolution that contributes to symbiotic relationships remains unclear. Our genome-wide single-gene analyses of the genus Symbiodinium, comprising both symbiotic and free-living species, successfully detected several dozen protein-coding genes that underwent symbiont-specific positive selection after divergence from the free-living species in the genus. Furthermore, our cultivation experiments demonstrated differences in photosynthate-related phenotypes between the symbiotic and free-living species. Our findings provide a key to illuminating the molecular evolution involved in phenotypic changes that potentially contribute to symbiotic lifestyles in Symbiodinium.

evolutionary biology↗
bioRxiv2024

Experimental bleaching of photosymbiotic amoeba revealed strain-dependent differences in algal symbiosis ability.

Photosymbioses, the symbiotic relationships between photosynthetic algal symbionts and non-photosynthetic eukaryotic hosts, are sporadically found in a lot of eukaryotic lineages, but only a few taxa, such as cnidarians and ciliates hosting algal endosymbionts, have been actively studied for a long time. That has hindered understanding the universal mechanisms of the photosymbiosis establishment. Especially in Amoebozoa, only two species, Mayorella viridis and Parachaos zoochlorella, are reported as photosymbiotic in nature, and their mechanisms of establishing symbiotic relationships are still unclear. To investigate the extent to which and how photosymbiotic amoebae depend on the symbiotic relationships, M. viridis were treated with reagents that are known to induce the collapsing of photosymbiotic relationships, or bleaching, in other photosymbiotic species. As a result, we succeeded in artificially removing algal symbionts from host M. viridis cells with an herbicide, 2-amino-3-chloro-1,4-naphthoquinone. The apo-symbiotic state amoeba cells were able to survive and grow to the same extent as the symbiotic state cells when they fed microbial prey, indicating that the algal symbionts are not essential for the host growth under certain conditions. Furthermore, to see whether the photosymbiotic state is reversible, we fed two strains of algal symbionts to the apo-symbiotic amoeba host. The result showed that the apo-symbiotic hosts were able to ingest symbiont cells and re-establish the symbiotic state. The efficiencies of ingesting algal cells were significantly different depending on algal symbiont strains, indicating that different algal strains possess discrete symbiotic abilities to M. viridis. To our knowledge, we provide first insights on the establishment and collapse of photosymbiosis in Amoebozoa, which pave the way to understand the universal mechanism of photosymbiosis utilizing M. viridis as a model system.

evolutionary biology↗
bioRxiv2023

Coordinated multiple cellular processes in tongue development

Dysfunction of primary cilia leads to genetic disorder, ciliopathies, which shows various malformations in many vital organs such as brain. Multiple tongue deformities including cleft, hamartoma and ankyloglossia are also seen in ciliopathies, which yield difficulties in fundamental functions such as mastication and vocalization. Here, we found these tongue anomalies in mice with mutation of ciliary protein. Abnormal cranial neural crest-derived cells (CNCC) failed to evoke Hh signal for differentiation of mesoderm-derived cells into myoblasts, which resulted in abnormal differentiation of mesoderm-derived cells into adipocytes. The ectopic adipose subsequently arrested migration of other mesoderm-derived cells and CNCC. Some aberrant CNCC abnormally differentiated into osteoblasts due to the lack of Hh signal, which migrated into tongue to form ectopic bone. Ankyloglossia was caused by aberrant cell migration due to lack of non-canonical Wnt signaling. In addition to ciliopathies, these tongue anomalies are often observed as non-familial condition in human. We found that these tongue deformities could be reproduced in wild-type mice by simple mechanical manipulations in CNCC to disturb cellular processes which were disrupted in mutant mice. Thus, tongue development requires coordinated multiple cellular processes (cell-cell contact, migration and differentiation). Our results provide hints for possible future treatment in ciliopathies.

developmental biology↗
bioRxiv2022

Metagenomic thermometer

Various microorganisms exist in environments, and each of which has an optimal growth temperature (OGT). The relationship between genomic information and OGT of each species has long been studied, and one such study revealed that OGT of prokaryotes can be accurately predicted based on the fraction of seven amino acids (IVYWREL) among all encoded amino-acid sequences in its genome. Extending this discovery, the fraction of IVYWREL among all amino acids encoded in the metagenomic DNA in an environment may reflect the environmental temperature to which the microorganisms have adapted. In the present study, we developed a Metagenomic Thermometer as a means of predicting environmental temperature based on metagenomic sequences. Analysis of 41 metagenomic samples obtained from hot springs of varying temperature revealed that the Metagenomic Thermometer could indeed predict environmental temperature with high accuracy (R2 = 0.75). Although the taxonomic composition of microbial community was substantially affected by pH, the performance of the Metagenomic Thermometer was refractory to changes in community composition. The Metagenomic Thermometer was also applied to 616 human gut metagenomic samples, yielding a reasonably accurate value (i.e., 36.22 {+/-} 1.98{degrees}C) for human body temperature. Our results suggest that environmental temperature can be predicted based on metagenomic sequence data.

bioinformatics↗
bioRxiv2022

Environmental pH signals the release of monosaccharides from cell wall in coral symbiotic alga

Reef-building corals thrive in oligotrophic environments due to their possession of endosymbiotic algae. Confined to the low pH interior of the symbiosome within the cell, the algal symbiont provides the coral host with photosynthetically fixed carbon. However, it remains unknown how carbon is released from the algal symbiont for uptake by the host. Here we show, using cultured symbiotic dinoflagellate, Breviolum sp., that decreases in pH directly accelerates the release of monosaccharides, i.e., glucose and galactose, into the ambient environment. Under low pH conditions, the cell surface structures were deformed and genes related to cellulase were significantly upregulated in Breviolum. Importantly, the release of monosaccharides was suppressed by the cellulase inhibitor, glucopyranoside, linking the release of carbon to degradation of the agal cell wall. Our results suggest that the low pH signals the cellulase-mediated release of monosaccharides from the algal cell wall as an environmental response in coral reef ecosystems.

evolutionary biology↗
bioRxiv2017

Glutamine metabolism regulates Th2 cell differentiation via the α-ketoglutarate-dependent demethylation of histone H3K27

The acquisition of T cell functions seems to be closely linked to the reprogramming of the metabolic pathway. However, the impact of metabolic changes on the differentiation of helper T cell subsets remains unclear. We found that TCR-mediated activation of glutamine metabolism regulates Th2 cell differentiation via the supplementation of -ketogulutalate (-KG) and histone H3K27 demethylation. Deprivation of glutamine or pharmacological inhibition of glutamine metabolism blocks the induction of Th2 cell differentiation without affecting Stat6 phosphorylation. The methylation status of H3K27 at the Th2 cytokine gene locus was significantly increased in Th2 cells cultured under glutamine-deprived conditions. The inhibitory effect of glutamine-deprivation was antagonized by -KG, and the -KG-dependent induction of Th2 cell differentiation was reduced in utx- and jmjd3-deficient naive CD4 T cells. These findings show that the glutamine-a-ketoglutarate axis is crucial to regulating the epigenetic status at the Th2 cytokine gene locus and subsequent Th2 cell differentiation.

immunology↗