Biology subjects

Arita, M.

Publications and source records attributed to Arita, M..

18 recordsLinked to original sources

bioRxiv2026

Elucidation of the anti-inflammatory mechanism of isoliquiritigenin from Glycyrrhiza uralensis using activity-based protein profiling

Glycyrrhiza uralensis is a widely used medicinal plant present in more than 70% of Kampo formulations in Japan owing to its diverse pharmacological activities, including immunomodulatory, antitumor, and antioxidant effects. Isoliquiritigenin (ILG), a major chalcone constituent of G. uralensis, exhibits anti-inflammatory activity; however, its molecular mechanism remains unclear. Here, we employed an activity-based protein profiling approach to identify the molecular targets of ILG. Given that the ,{beta}-unsaturated carbonyl moiety of ILG can covalently react with reactive cysteine residues via nucleophilic addition, we used an iodoacetamide-based probe to globally profile cysteine-reactive proteomes. The comparative analysis between ILG- and vehicle-treated RAW 264.7 macrophages identified cysteine 65 (Cys65) of lipocalin-type prostaglandin D2 synthase (L-PGDS) as a potential covalent target. ILG treatment did not alter L-PGDS expression levels, indicating that reduced probe labeling reflects direct covalent competition rather than changes in expression. Consistently, ILG significantly suppressed prostaglandin D2 (PGD2) production, comparable to the selective L-PGDS inhibitor AT-56. Although both ILG and AT-56 reduced interleukin-6 expression, ILG exerted a stronger inhibitory effect. Our results demonstrate that covalent inhibition of L-PGDS and subsequent suppression of PGD2 production represent a key mechanism underlying the anti-inflammatory activity of ILG.

biochemistry↗

bioRxiv2026

Diversity and stability of the gut microbiome of naked mole-rat (Heterocephalus glaber), the longest-lived rodent

The naked mole-rat is a subterranean rodent adapted to extreme hypoxia and low metabolic demands, with an exceptionally long lifespan relative to its small body size, while maintaining reproductive capacity. Using 16S rRNA gene sequencing of 24 samples and whole-metagenome sequencing of 11 samples from individuals up to 15 years of age, we characterized the gut microbiota and showed its complexity and distinctiveness compared with that of other rodents, including mice, squirrels, and rabbits. Although all animals were born and raised in a laboratory setting, the gut microbiota remained taxonomically stable across ages and retained key taxa previously reported in wild naked mole-rats (e.g., Treponema and Desulfovibrio). Metagenome-assembled genomes revealed the presence of archaeal methanogens and termite-gut-associated bacteria (e.g., Methanobacteria within Euryarchaeota and Avelusimicrobium within Elusimicrobiota), together with genes involved in hydrogen metabolism and archaeal methanogenesis. Compared with mice, the naked mole-rat gut microbiota was enriched in carbohydrate-active enzymes targeting plant cell-wall polysaccharides, resembling those found in ruminants. We also detected evidence of flagellates, ciliates, and fungi, which may further contribute to polysaccharide degradation and fermentation, potentially within the enlarged cecum. Together, this comprehensive analysis provides distinctive gut microbial features of the naked mole-rat that may be associated with the naked mole-rats low metabolic rate and exceptional longevity.

microbiology↗

bioRxiv2025

Dual Metabolic Compensation to Dietary Choline Deficiency by the Drosophila Hologenome

Coping with an unbalanced diet is critical in animals. However, the mechanisms that mitigate deficiencies of specific nutrients, such as choline, remain poorly understood. Choline is converted to phosphatidylcholine (PC), a major phospholipid. Using genetic, nutritional, and microbiome manipulation tools in Drosophila melanogaster, we identified two independent mechanisms that ameliorate the effects of choline deficiency. First, a strain of commensal bacteria synthesizes PC via choline-independent pathway and provides it to the host. Second, a host-derived phospholipid, {beta}-methylphosphatidylcholine ({beta}mPC), is generated from carnitine, which compensates choline deficiency as a functional analog of PC. Our findings reveal microbial and host metabolic processes that modulate dietary requirement for choline. This study also provides evidence that hologenomic coordination of metabolism enables animals to adapt to a micronutrient deficiency.

physiology↗

bioRxiv2025

How The Transition of Aphid Life Cycles Affect Endosymbiotic Bacteria

How symbiotic bacteria coordinate and respond to their hosts during complex life cycle transitions is a fascinating and unresolved topic, particularly for organisms that exist solely in natural environments, where their intricate life cycles make laboratory cultivation extremely challenging. Complex life cycles are often associated with host alternation in aphids, especially in eriosomatine gall-forming aphids, which exhibit seven distinct morphs throughout their life cycle while shifting their host plants seasonally. Despite these dramatic changes, these aphids maintain the obligate symbiotic bacterium, Buchnera aphidicola, to enhance their nutritional status. The bacterial communities in our wild-derived samples were dominated by aphid symbionts, including Buchnera, Regiella inseticola, Wolbachia, Arsenophonus, and Serratia symbiotica. Buchnera and Regiella prevailed in Tetraneura akinire and Tetraneura sorini, while Buchnera and Arsenophonus were more abundant in Eriosoma harunire. Our study, utilizing 16S rRNA metagenomic sequencing on the aphid Tetraneura akinire, demonstrates that Buchnera plays significant roles during most life cycle stages but is absent during the sexual male stage, where it is replaced by Regiella. Moreover, Buchnera densities exhibit significant variability across the aphids life cycles and are notably lower in gall generations. This result contradicts the previous hypothesis that galls provide superior nutrition compared to aphids in grassroot-feeding generations. In this study, we reveal the dynamics of symbiotic bacteria across the complex life cycles of three eriosomatine aphid species that form galls on the same Japanese elm tree, Ulmus davidiana var. japonica. Within the framework of tripartite symbiosis, the seemingly passive symbiotic bacteria adjust the hosts specific life stages and influence the changing host ecology in a cascading manner.

evolutionary biology↗

bioRxiv2024

Data-independent acquisition coupled with electron-activated dissociation for in-depth structure elucidation of fatty acid ester of hydroxy fatty acids

Fatty acid esters of hydroxy fatty acid (FAHFAs) are a biologically important class of lipids known for their anti-inflammatory and anti-diabetic effects in animals. The physiological activity of FAHFAs varies depending on the length of the carbon chain, number and position of double bonds (DBs), and the position of the hydroxyl (OH) group. Moreover, gut bacteria produce FAHFAs with more diverse structures than those produced by the host, which necessitates a FAHFA-lipidomics approach grasping their diverse structures to fully understand the physiological and metabolic significance of FAHFAs. In this study, we developed a methodology for in-depth structural elucidation of FAHFAs. First, FAHFAs were enriched using a solid-phase extraction (SPE) system coated with titanium and zirconium dioxide, which separated these analytes from neutral lipids and phospholipids. The fractionated metabolites were then derivatized using N,N-dimethylethylenediamine (DMED) to facilitate FAHFA detection in the positive ion mode of a liquid chromatography-tandem mass spectrometry (LC-MS/MS) system. A data-independent acquisition technique known as sequential window acquisition of all theoretical mass spectra (SWATH-DIA) was used to collect sequential MS/MS spectra of the DMED-derivatized fatty acid metabolites. Structural elucidation was based on the fragment ions generated by electron-activated dissociation (EAD). DMED-FAHFAs were annotated using the newly updated MS-DIAL program, and FAHFA isomers were quantified using the MRMPROBS program, which quantifies lipids based on SWATH-MS/MS chromatograms. This procedure was applied to profile the FAHFAs present in mouse fecal samples, characterizing seven structures at the molecular species level, 63 structures at the OH position-resolved level, and 15 structures at both the DB and OH position-resolved levels using the MS-DIAL program. In the MRMPROBS analysis, 2OH and 3OH hydroxy fatty acids with more than 20 carbon atoms were predominantly expressed, while 5OH-13OH hydroxy fatty acids with 16 or 18 carbon atoms were the major components, abundant at positions 5, 7, 9, and 10. Furthermore, age-related changes in FAHFA isomers were also observed, where FAHFA 4:0/2O(FA 26:0) and FAHFA 16:0/10O(FA 16:0) significantly increased with age. In conclusion, our study offers a novel LC-SWATH-EAD-MS/MS technique with the updates of computational MS to facilitate in-depth structural lipidomics of FAHFAs. TOC graphics O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=101 SRC="FIGDIR/small/627939v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@1d33c09org.highwire.dtl.DTLVardef@10a97b5org.highwire.dtl.DTLVardef@6e2c35org.highwire.dtl.DTLVardef@1186da5_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2024

Dietary control of peripheral adipose storage capacity through membrane lipid remodelling

Complex genetic and dietary cues contribute to the development of obesity, but how these are integrated on a molecular level is incompletely understood. Here, we show that PPAR{gamma} supports hypertrophic expansion of adipose tissue via transcriptional control of LPCAT3, a membrane-bound O-acyltransferase that enriches diet-derived omega-6 (n-6) polyunsaturated fatty acids (PUFAs) in the phospholipidome. In high-fat diet-fed mice, lowering membrane n-6 PUFA levels by adipocyte-specific Lpcat3 knockout (Lpcat3AKO) or by dietary lipid manipulation leads to dysfunctional triglyceride (TG) storage, ectopic fat deposition and insulin resistance. Aberrant lipolysis of stored TGs in Lpcat3AKO adipose tissues instigates a non-canonical adaptive response that engages a futile lipid cycle to increase energy expenditure and limit further body weight gain. Mechanistically, we find that adipocyte LPCAT3 activity promotes TG storage by selectively enriching n-6 arachidonoyl-phosphatidylethanolamine at the ER-lipid droplet interface, which in turn favours the budding of large droplets that exhibit greater resistance to ATGL-dependent hydrolysis. Thus, our study highlights the PPAR{gamma}-LPCAT3 pathway as a molecular link between dietary n-6 PUFA intake, adipose expandability and systemic energy balance.

physiology↗

bioRxiv2024

Formation of giant ER sheets by pentadecanoic acid causes lipotoxicity in fission yeast

Excess amounts of saturated fatty acids are toxic to organisms, a condition termed lipotoxicity, which is often accompanied by pleiotropic cellular and tissue dysfunction. Here we show that pentadecanoic acid (C15:0) exerts toxicity on the fission yeast Schizosaccharomyces pombe by generating an aberrantly planar endoplasmic reticulum (ER) structure, which we named a "giant ER sheet." Untargeted lipidomics revealed that C15:0 is incorporated into complex lipids depending on an acyl-CoA ligase Lcf1 and an acyl-CoA transferase Slc1, thereby increasing the saturation level of the acyl chains. The toxicity and giant ER sheet formation were abolished by deleting Lcf1 or Slc1, indicating that the incorporation of C15:0 into glycerophospholipids causes giant ER sheet formation. The giant ER sheets disrupted the correct migration of Mid1, a protein determining the cell division site, and physically blocked septum formation, hindering correct cell separation. Our results suggest that the ER is the primary site targeted by saturated fatty acids, leading to lipotoxicity.

cell biology↗

bioRxiv2024

MS2Lipid: a lipid subclass prediction program using machine learning and curated tandem mass spectral data

Untargeted lipidomics using collision-induced dissociation-based tandem mass spectrometry (CID-MS/MS) is essential for biological and clinical applications. However, annotation confidence is still guaranteed by manual curation by analytical chemists, although various software tools have been developed for automatic spectral processing based on rule-based fragment annotations. In this study, we provide a novel machine learning model, MS2Lipid, for the prediction of lipid subclasses from MS/MS queries to provide an orthogonal decision of lipidomics software programs to determine the lipid subclass of ion features, in which a new descriptor, MCH (mode of carbon and hydrogen), was designed to increase the specificity of lipid subclasses in nominal mass resolution MS data. The model trained with 5,224 and 5,408 manually curated MS/MS spectra for the positive- and negative-ion modes mapped the query into one or several categories of 97 lipid subclasses, with an accuracy of 95.5% queries in the test set. Our program outperformed the CANOPUS ontology prediction program, providing correct annotations for 38.7% of the same test set. The program was further validated using various datasets from different machines and curators, and the average accuracy exceeded 87.4 %. Furthermore, the function of MS2Lipid was showcased by the annotation of novel esterified bile acids, whose abundance was significantly increased in obese patients in a human cohort study, suggesting that the machine learning model provides an independent criterion for lipid subclass classification, in addition to an environment for annotating lipid metabolites that have been previously unknown.

bioinformatics↗

bioRxiv2024

MS-DIAL 5 multimodal mass spectrometry data mining unveils lipidome complexities

Lipidomics and metabolomics communities comprise various informatics tools; however, software programs that can handle multimodal mass spectrometry (MS) data with structural annotations guided by the Lipidomics Standards Initiative are limited. Here, we provide MS-DIAL 5 to facilitate the in-depth structural elucidation of lipids through electron-activated dissociation (EAD)-based tandem MS, as well as determine their molecular localization through MS imaging (MSI) data using a species/tissue-specific lipidome database containing the predicted collision-cross section (CCS) values. With the optimized EAD settings using 14 eV kinetic energy conditions, the program correctly delineated the lipid structures based on EAD-MS/MS data from 96.4% of authentic standards. Our workflow was showcased by annotating the sn- and double-bond positions of eye-specific phosphatidylcholine molecules containing very-long-chain polyunsaturated fatty acids (VLC-PUFAs), characterized as PC n-3-VLC-PUFA/FA. Using MSI data from the eye and HeLa cells supplemented with n-3-VLC-PUFA, we identified glycerol 3-phosphate (G3P) acyltransferase (GPAT) as an enzyme candidate responsible for incorporating n-3 VLC-PUFAs into the sn-1 position of phospholipids in mammalian cells, which was confirmed using recombinant proteins in a cell-free system. Therefore, the MS-DIAL 5 environment, combined with optimized MS data acquisition methods, facilitates a better understanding of lipid structures and their localization, offering novel insights into lipid biology.

bioinformatics↗

bioRxiv2023

One thousand samples per day capillary-flow LC/MS/MS for high-speed, high-sensitivity and in-depth proteomics

We developed a capillary-flow LC/MS/MS system with ultrahigh speed, enabling a throughput of 1,000 samples per day while maintaining high sensitivity and depth of analysis. In targeted LC/MS mode, 36 endogenous phosphopeptides in HeLa cells, including EphA2- derived phosphopeptide isomers, were successfully quantified with high selectivity and linearity by combining ion mobility separation. When 500 ng of HeLa cell digest was measured 100 times repeatedly in data-dependent acquisition mode, the coefficient of variation of retention time, peak intensity and number of identified peptides were on average 3.4%, 19.8%, and 6.0%, respectively. In data-independent acquisition mode, this system achieved the identification and quantification of 3,139 protein groups from a 100 ng HeLa cell digest and 2,145 protein groups from a sample of only 10 ng. The coefficient of variation of protein commonly quantified in the triplicate analysis ranged from 12 to 24% for HeLa digest samples ranging from 10 to 1000 ng. Finally, we applied this high-speed system to the spatial proteomics of the mouse brain, and succeeded in capturing the proteome distribution along a 96-sectioned brain structure in 135 minutes. This is the first LC/MS/MS system to achieve both more than 500 samples per day and more than 3000 identified protein groups ID with less than 100 ng human cultured cells simultaneously.

systems biology↗

bioRxiv2023

Liquid-liquid extraction of lipidated peptides for direct identification of lipidation sites

Proteins can be modified by lipids in various ways, for example by myristoylation, palmitoylation, farnesylation, and geranylgeranylation--these processes are collectively referred to as lipidation. Current chemical proteomics using alkyne lipids has enabled the identification of lipidated protein candidates but does not identify endogenous lipidation sites and is not readily applicable to in vivo systems. Here, we introduce a proteomic methodology for global analyses of endogenous lipidation sites that combines liquid-liquid extraction of hydrophobic lipidated peptides with liquid chromatography-tandem mass spectrometry using a gradient program of acetonitrile in the high concentration range. We applied this method to explore lipidation sites in HeLa cells, and identified a total of 90 lipidation sites, including 75 protein N-terminal myristoylation sites, which is more than the number of high-confidence lipidated proteins identified by myristic acid analog-based chemical proteomics. Isolation of lipidated peptides from digests prepared with different proteases enabled the identification of different lipidated sites, extending the coverage. Moreover, our peptide-centric approach successfully identified dually modified peptides having myristoylation and palmitoylation. Finally, we analyzed in vivo myristoylation sites in mouse tissues and found that the lipidation profile is tissue-specific. This simple method (not requiring chemical labeling or affinity purification) should be a promising tool for global profiling of various protein lipidations.

biochemistry↗

bioRxiv2023

Genome and transcriptome analyses reveal genes involved in the formation of fine ridges on petal epidermal cells in Hibiscus trionum.

Hibiscus trionum, commonly known as the Flower of an Hour, is an easily cultivated plant in the Malvaceae family. The purple base part of its petal exhibits structural color due to the fine ridges on the epidermal cell surface, and the molecular mechanism of ridge formation has been actively investigated. We performed genome sequencing of H. trionum using a long-read sequencing technology with transcriptome and pathway analyses to identify candidate genes for fine structure formation. The ortholog of AtSHINE1, which is involved in the biosynthesis of cuticular wax in Arabidopsis thaliana, was significantly overexpressed in the iridescent tissue. In addition, orthologs of AtCUS2 and AtCYP77A, which contribute to cutin synthesis, were also overexpressed. Our results provide important insights into the formation of fine ridges on epidermal cells in plants using H. trionum as a model.

bioinformatics↗

bioRxiv2022

Mitochondria directly sense osmotic stress to trigger rapid metabolic remodeling via PDH regulation

A high-salt diet significantly impacts various diseases, including cancer and immune diseases. Recent studies suggest that the high-salt/hyperosmotic environment in the body may alter the chronic properties of cancer and immune cells in the disease context. However, little is known about the acute metabolic changes in hyperosmotic stress. Here, we found that hyperosmotic stress for a few minutes induces Warburg-like metabolic remodeling in HeLa and Raw264.7 cells and suppresses fatty acid oxidation. Regarding Warburg-like remodeling, the PDH phosphorylation status was altered bidirectionally (high in hyperosmolarity and low in hypoosmolarity) to osmotic stress in isolated mitochondria, suggesting that mitochondria themselves have an acute osmo-sensing mechanism. Warburg-like remodeling is required for HeLa cells to maintain ATP levels and survive under hyperosmotic conditions. Our findings suggest that cells exhibit acute metabolic remodeling under osmotic stress via the regulation of PDH phosphorylation by direct osmosensing within mitochondria.

cell biology↗

bioRxiv2022

Plastomes of Garcinia mangostana L. and comparative analysis with other Garcinia species

The two varieties of mangosteen (Garcinia mangostana L.) cultivated in Malaysia are known as Manggis and Mesta. The latter is preferred for its flavor, texture, and seedlessness. Here, we report a complete plastome (156,580 bp) of the Mesta variety which was obtained through a hybrid assembly approach using PacBio and Illumina sequencing reads. It encompasses a large single-copy (LSC) region (85,383 bp) and a small single-copy (SSC) region (17,137 bp) that are separated by 27,230 bp of inverted repeat (IR) regions at both ends. The plastome comprises 128 genes, namely 83 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The plastome of the Manggis variety (156,582 bp) obtained from reference-guided assembly of Illumina reads was found to be nearly identical to Mesta except for two indels and the presence of a single nucleotide polymorphism (SNP). Comparative analyses with other publicly available Garcinia plastomes, including G. anomala, G. gummi-gutta, G. mangostana var. Thailand, G. oblongifolia, G. paucinervis, and G. pedunculata found that the gene content, gene order, and gene orientation were highly conserved among the Garcinia species. Phylogenomic analysis divided the six Garcinia plastomes into three groups with the Mesta and Manggis varieties clustered closer to G. anomala, G. gummi-gutta, and G. oblongifolia, while the Thailand variety clustered with G. pedunculata in another group. These findings serve as future references for the identification of species or varieties and facilitate phylogenomic analysis of lineages from the Garcinia genus to better understand their evolutionary history.

plant biology↗

bioRxiv2022

Mitochondrial Genome of Garcinia mangostana L. variety Mesta

Fruits of Garcinia mangostana L. (mangosteen) are rich in nutrients with xanthones found in the pericarp having great pharmaceutical potential. Mangosteen variety Mesta is only found in Malaysia, which tastes sweeter than the common Manggis variety in Southeast Asia. In this study, we report the complete mitogenome of G. mangostana L. variety Mesta with a total sequence length of 371,235 bp of which 1.7% could be of plastid origin. The overall GC content of the mitogenome is 43.8%, comprising 29 protein-coding genes, 3 rRNA genes, and 21 tRNA genes. Repeat and tandem repeat sequences accounted for 5.8% and 0.15% of the Mesta mitogenome, respectively. There are 333 predicted RNA-editing sites in Mesta mitogenome. These include the RNA-editing events that generated the start codon of nad1 gene and the stop codon of ccmFC gene. Phylogenomic analysis with a maximum likelihood method showed that the mitogenome of mangosteen variety Mesta was grouped under Malpighiales order. This is the first complete mitogenome from the Garcinia genus for future evolutionary studies.

plant biology↗

bioRxiv2020

Requirement for proper mitochondrial RNA processing in the restrictive control of cell proliferation during early lateral root morphogenesis

Although mechanisms that activate organogenesis in plants are well established, much less is known about the subsequent fine-tuning of cell proliferation, which is crucial for creating properly structured and sized organs. Here we show, through analysis of temperature-dependent fasciation (TDF) mutants of Arabidopsis, root redifferentiation defective 1 (rrd1), rrd2, and root initiation defective 4 (rid4), that mitochondrial RNA processing is required for limiting cell division during early lateral root (LR) organogenesis. These mutants formed abnormally broadened (i.e., fasciated) LRs under high-temperature conditions due to excessive cell division. All TDF proteins localized to mitochondria, where they were found to participate in RNA processing: RRD1 in mRNA deadenylation, and RRD2 and RID4 in mRNA editing. Further analysis suggested that LR fasciation in the TDF mutants is triggered by reactive oxygen species generation caused by defective mitochondrial respiration. Our findings provide novel clues for the physiological significance of mitochondrial activities in plant organogenesis.

plant biology↗

bioRxiv2020

MS-DIAL 4: accelerating lipidomics using an MS/MS, CCS, and retention time atlas

To the EditorWe formulated mass spectral fragmentations of lipids across 117 lipid subclasses and included ion mobility tandem mass spectrometry (MS/MS) to provide a comprehensive lipidome atlas with retention time, collision cross section, and MS/MS information. The all-in-one solution from import of raw MS data to export of a common output format (mztab-M) was packaged in MS-DIAL 4 (http://prime.psc.riken.jp/) providing an enhanced standardized untargeted lipidomics procedure following lipidomics standards initiative (LSI) semi-quantitative definitions and shorthand notation system of lipid structures with a 1-2% estimated false discovery rate, which will contribute to harmonizing lipidomics data across laboratories to accelerate lipids research.

bioinformatics↗

bioRxiv2019

Trans-omic analysis reveals allosteric and gene regulation-axes for altered glucose-responsive liver metabolism associated with obesity

Impaired glucose tolerance associated with obesity causes postprandial hyperglycemia and can lead to type 2 diabetes. To study the differences in liver metabolism in the healthy and obese states, we constructed and analyzed trans-omic glucose-responsive metabolic networks with layers for metabolites, expression data for metabolic enzyme genes, transcription factors, and insulin signaling proteins from the livers of healthy and obese mice. We integrated multi-omic time-course data from wild-type (WT) and leptin-deficient obese (ob/ob) mice after orally administered glucose. In WT mice, metabolic reactions were rapidly regulated (within 10 minutes of oral glucose administration) primarily by glucose-responsive metabolites, especially ATP and NADP+, which functioned as allosteric regulators and substrates of metabolic enzymes, and by Akt-dependent glucose-responsive genes encoding metabolic enzymes. In ob/ob mice, most rapid regulation by glucose-responsive metabolites was absent; instead, glucose administration produced slow changes in the expression of metabolic enzyme-encoding genes to alter metabolic reactions in a time scale of hours. Few common regulatory events occurred in both the healthy and obese mice. Thus, our trans-omic network analysis revealed regulation of liver metabolism in response to glucose is mediated through different mechanisms in the healthy and obese states: Rapid changes in allosteric regulators and substrates and in gene expression dominate the healthy state, and slow transcriptional regulation dominates the obese state.\n\nOne Sentence SummaryRapid changes in regulatory metabolites and gene expression dominate the healthy state, and slow transcriptional regulation dominates the obese state.

systems biology↗