Biology subjects

Obata, T.

Publications and source records attributed to Obata, T..

16 recordsLinked to original sources

bioRxiv2026

Natural Variation in Maize Shikimate Dehydrogenase Alters Enzyme Activity and Kernel Homoserine Accumulation.

Metabolic diversity in maize kernels determines nutritional quality and end-use value. Therefore, understanding its genetic basis is essential for crop improvement and elucidating plant metabolic regulation. Here, we integrated metabolite profiling with metabolite-based genome-wide association studies (mGWAS), structural modeling, enzyme kinetics, and genome-scale metabolic simulations to identify genetic determinants of kernel metabolite variation in 265 maize inbred lines. Profiling of 57 metabolites revealed inter-genotypic variation, with homoserine among the most variable metabolites. mGWAS identified 62 locus-trait associations implicating 788 candidate genes, including 154 encoding metabolic enzymes. A major association for homoserine mapped to the shikimate dehydrogenase gene Sad1 on chromosome 10. Four tightly linked coding-region SNPs, including three non-synonymous variants, defined two Sad1 haplotypes associated with differential homoserine accumulation, independent of gene expression variation. Structural analysis and recombinant enzyme assays showed that these substitutions occur within catalytic and cofactor-binding domains and alter catalytic efficiency. Genome-scale metabolic modeling indicated that variation in SAD1 activity influences plastidial oxaloacetate availability for aspartate and homoserine biosynthesis through redox-coupled flux via the malate-oxaloacetate shuttle. Together, our results indicate that Sad1 allelic variation alters enzyme function and amino acid accumulation, linking the shikimate pathway, redox metabolism, and amino acid biosynthesis in maize kernels.

plant biology↗

bioRxiv2026

Epithelial Reprogramming and Transition during Pulmonary Bioengineering

Recent research has emphasized the critical role of cell state transitions in tissue homeostasis. In lung biology, transitional cells are recognized as a feature of tissue-scale processes during both normal physiology and disease. The precise way that transitional cell states emerge and are regulated remains to be determined. Engineered tissues, built in a laboratory through bioengineering approaches, allow detailed study of cellular states that are not commonly found in native biology, and allow opportunities to directly induce and manipulate cellular transitions. The following study explores and characterizes epithelial cell states that emerge via cellular reprogramming in a tissue engineering context. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=172 SRC="FIGDIR/small/701406v1_ufig1.gif" ALT="Figure 1"> View larger version (68K): org.highwire.dtl.DTLVardef@1d456f3org.highwire.dtl.DTLVardef@1989ba5org.highwire.dtl.DTLVardef@127dd7org.highwire.dtl.DTLVardef@3dd7a_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2025

Dynamic assembly of malate dehydrogenase-citrate synthase multienzyme complex in the mitochondria

The tricarboxylic acid (TCA) cycle enzymes malate dehydrogenase (MDH1) and citrate synthase (CIT1) form a multienzyme complex, referred to as a metabolon, that channels intermediate oxaloacetate between their reaction centers. Given that the MDH1-CIT1 metabolon enhances pathway reactions in vitro, its dynamic assembly is hypothesized to contribute to TCA cycle regulation in response to cellular metabolic demands. Here, we demonstrated that yeast mitochondrial MDH1 and CIT1 dissociated when aerobic respiration was suppressed by the Crabtree effect and associated when the respiratory activity was enhanced by acetate. Pharmacological TCA cycle inhibition dissociated the complex, whereas electron transport chain inhibition enhanced the interaction. The multienzyme complex assembly was related to the mitochondrial matrix acidification and oxidation, as well as cellular levels of malate, fumarate, and citrate. These factors significantly affected the MDH1-CIT1 complex affinity in vitro. Especially, variations in buffer pH within the physiological pH range between 6.0 and 7.0 in the mitochondrial matrix significantly impacted the MDH1-CIT1 affinity. These results demonstrate the dynamic association and dissociation of the MDH1-CIT1 metabolon and its relationship with respiratory activity, supporting metabolon dynamics as an integral factor in metabolic regulation governed by multiple factors such as mitochondrial pH and metabolite levels.

biochemistry↗

bioRxiv2024

Engineered Whole Lungs for Tissue Biology

End-stage lung disease and lung cancer significantly contribute to global mortality, necessitating new research strategies for studying pulmonary biology. Here, we present an engineered whole-lung tissue model used to evaluate the effects of cellular communities on tissue organization and alveolar barrier function. Engineered lungs were grown ex vivo on decellularized whole-lung matrices as structurally biomimetic, bioactive scaffolds. Histologic architecture of engineered lungs improved with the addition of alveolar macrophages, coming to resemble neonatal lung. Incorporating alveolar macrophages maximized the differentiation of native-like cellular communities, including alveolar type I-like epithelium, bronchioalveolar stem cells, microvascular endothelium, and pericytes. Cell-cell signaling in engineered lungs showed activation of developmental and inflammatory pathways, including WNT, Notch, and FGF signaling pathways. Engineered lungs containing alveolar macrophages showed a 668% improvement in measured alveolar barrier function. This work demonstrates the potential utility of engineered lung models for studying principles of tissue biology and pulmonary regeneration.

bioengineering↗

bioRxiv2024

Transcripts and genomic intervals associated with variation in metabolite abundance in maize leaves under field conditions

Plants exhibit extensive environment-dependent intraspecific metabolic variation, which likely plays a role in determining variation in whole plant phenotypes. However, much of the work seeking to use natural variation to link genes and transcripts impacts on plant metabolism has employed data from controlled environments. Here we generate and employ data on variation in the abundance of twenty-six metabolites across 660 maize inbred lines under field conditions. We employ these data and previously published transcript and whole plant phenotype data reported for the same field experiment to identify both genomic intervals (through genome-wide association studies) and transcripts (through both transcriptome-wide association studies and an explainable AI approach based on the random forest) associated with variation in metabolite abundance. Both genome-wide association and random forest-based methods identified substantial numbers of significant associations including genes with plausible links to the metabolites they are associated with. In contrast, the transcriptome-wide association identified only six significant associations. In three cases, genetic markers associated with metabolic variation in our study colocalized with markers linked to variation in non-metabolic traits scored in the same experiment. We speculate that the poor performance of transcriptome-wide association studies in identifying transcript-metabolite associations may reflect a high prevalence of non-linear interactions between transcripts and metabolites and/or a bias towards rare transcripts playing a large role in determining intraspecific metabolic variation.

genomics↗

bioRxiv2024

Genomic prediction of metabolic content in rice grain in response to warmer night conditions

It has been argued that metabolic content can be used as a selection marker to accelerate crop improvement because metabolic profiles in crops are often under genetic control. Evaluating the role of genetics in metabolic variation is a long-standing challenge. Rice, one of the worlds most important staple crops, is known to be sensitive to recent increases in nighttime temperatures. Quantification of metabolic levels can help measure rice responses to high night temperature (HNT) stress. However, the extent of metabolic variation that can be explained by regression on whole-genome molecular markers remains to be evaluated. In the current study, we generated metabolic profiles for mature grains from a subset of rice diversity panel accessions grown under optimal and HNT conditions. Metabolite accumulation was low to moderately heritable, and genomic prediction accuracies of metabolite accumulation were within the expected upper limit set by their genomic heritability estimates. Genomic heritability estimates were slightly higher in the control group than in the HNT group. Genomic correlation estimates for the same metabolite accumulation between the control and HNT conditions indicated the presence of genotype-by-environment interactions. Reproducing kernel Hilbert spaces regression and image-based deep learning improved prediction accuracy, suggesting that some metabolite levels are under non-additive genetic control. Joint analysis of multiple metabolite accumulation simultaneously was effective in improving prediction accuracy by exploiting correlations among metabolites. The current study serves as an important first step in evaluating the cumulative effect of markers in influencing metabolic variation under control and HNT conditions. Core ideasO_LIRice is sensitive to increases in nighttime and daytime temperatures C_LIO_LIMetabolite accumulation from rice grains was low to moderately heritable C_LIO_LINon-additive genomic prediction models improved prediction accuracy for some metabolites C_LIO_LIResults shed new light on the utility of genomic predictions for metabolite accumulation from rice grains C_LI

genetics↗

bioRxiv2024

A neuroimaging dataset during sequential color qualia similarity judgments with and without reports

Recent neuroscientific research has advanced our understanding of consciousness, yet the connection between specific qualitative aspects of consciousness, known as "qualia," and particular brain regions or networks remains elusive. Traditional methods that rely on verbal descriptions from participants pose challenges in neuroimaging studies. To address this, our group has introduced a novel "qualia structure" paradigm that leverages exhaustive, structural, and relational comparisons among qualia instead of verbal reports. In this study, we present the first fMRI dataset that captures relational similarity judgments among two out of nine color qualia per trial from 35 participants. This dataset also includes a "no-report" condition in half of the trials to assess the impact of overt reporting. Additionally, each participants color discriminability was evaluated with a hue test conducted outside the scanner. Our data offer valuable insights into the brain functions associated with color qualia and contribute to a deeper understanding of the neural foundations of consciousness.

neuroscience↗

bioRxiv2024

Organ Boundary Circuits Regulate Sox9+ Alveolar Tuft Cells During Post-Pneumonectomy Lung Regeneration

Tissue homeostasis is controlled by cellular circuits governing cell growth, organization, and differentation. In this study we identify previously undescribed cell-to-cell communication that mediates information flow from mechanosensitive pleural mesothelial cells to alveolar-resident stem-like tuft cells in the lung. We find mesothelial cells to express a combination of mechanotransduction genes and lineage-restricted ligands which makes them uniquely capable of responding to tissue tension and producing paracrine cues acting on parenchymal populations. In parallel, we describe a large population of stem-like alveolar tuft cells that express the endodermal stem cell markers Sox9 and Lgr5 and a receptor profile making them uniquely sensitive to cues produced by pleural Mesothelium. We hypothesized that crosstalk from mesothelial cells to alveolar tuft cells might be central to the regulation of post-penumonectomy lung regeneration. Following pneumonectomy, we find that mesothelial cells display radically altered phenotype and ligand expression, in a pattern that closely tracks with parenchymal epithelial proliferation and alveolar tissue growth. During an initial pro-inflammatory stage of tissue regeneration, Mesothelium promotes epithelial proliferation via WNT ligand secretion, orchestrates an increase in microvascular permeability, and encourages immune extravasation via chemokine secretion. This stage is followed first by a tissue remodeling period, characterized by angiogenesis and BMP pathway sensitization, and then a stable return to homeostasis. Coupled with key changes in parenchymal structure and matrix production, the cumulative effect is a now larger organ including newly-grown, fully-functional tissue parenchyma. This study paints Mesothelial cells as a key orchestrating cell type that defines the boundary of the lung and exerts critical influence over the tissue-level signaling state regulating resident stem cell populations. The cellular circuits unearthed here suggest that human lung regeneration might be inducible through well-engineered approaches targeting the induction of tissue regeneration and safe return to homeostasis.

systems biology↗

bioRxiv2022

Evaluating metabolic and genomic data for predicting grain traits under high night temperature stress in rice

The asymmetric increase in average nighttime temperatures relative to increase in average daytime temperatures due to climate change is decreasing grain yield and quality in rice. Therefore, a better understanding of the impact of higher night temperature on single grain at whole genome level is essential for future development of more resilient rice. We investigated the utility of metabolites obtained from grains to classify high night temperature conditions of genotypes, and metabolites and single nucleotide polymorphisms to predict grain length, width, and perimeter phenotypes using a rice diversity panel. We found that the metabolic profiles of rice genotypes alone could be used to classify control and high night temperature conditions with high accuracy using random forest or extreme gradient boosting. The best linear unbiased prediction and BayesC showed greater metabolic prediction performance than machine learning models for grain-size phenotypes. Metabolic prediction was most effective for grain width, resulting in the highest prediction performance. Genomic prediction performed better than metabolic prediction. Integrating metabolites and genomics simultaneously in a prediction model slightly improved prediction performance. We did not observe a difference in prediction between the control and high night temperature conditions. Several metabolites were identified as auxiliary phenotypes that could be used to enhance the multi-trait genomic prediction of grain-size phenotypes. Our results showed that, in addition to single nucleotide polymorphisms, metabolites collected from grains offer rich information to perform predictive analyses, including classification modeling of high night temperature responses and regression modeling of grain size-related phenotypes in rice.

genetics↗

bioRxiv2022

Distribution of intraperitoneally administered D2O in AQP4-knockout mouse brain after MCA occlusion

As the movement of water in the brain is known to be involved in neural activity and various brain pathologies, the ability to assess water dynamics in the brain will be important for the understanding of brain function and the diagnosis and treatment of brain diseases. Aquaporin-4 (AQP4) is a membrane channel protein that is highly expressed in brain astrocytes and is important for the movement of water molecules in the brain. In this study, we investigated the contribution of AQP4 to brain water dynamics by administering deuterium-labeled water (D2O) intraperitoneally to wild-type and AQP4 knockout (AQP4-ko) mice that had undergone surgical occlusion of the middle cerebral artery. Water dynamics in the infarct region and on either side of the anterior cerebral artery (ACA) was monitored with proton-density-weighted imaging (PDWI) performed on a 7T animal MRI. D2O caused a negative signal change quickly after administration. The AQP4-ko mice showed a delay of the time-to-minimum in both contralateral and ipsilateral ACA region compared to wild-type mice. Also, only the AQP4-ko mice showed a delay of the time-to-minimum in the ipsilateral ACA region compared to the contralateral side. In only the wild-type mice, the signal minimum in the ipsilateral ACA region was higher than that in the contralateral ACA region. In the infarct region, the signal attenuation was slower for the AQP4-ko mice in comparison to the wild-type mice. These results suggest that AQP4 loss affects water dynamics in the ACA region not only in the infarct region. Dynamic PDWI after D2O administration may be a useful tool for showing the effects of AQP4 in vivo. HighlightsO_LIThe measurement of brain water dynamics with D2O. C_LIO_LIIn vivo investigation of AQP4 loss and focal brain ischemia. C_LIO_LIAQP4 loss affects water dynamics in the ACA region not only in the infarct region. C_LI

physiology↗

bioRxiv2022

A historically balanced locus under recent directional selection in responding to changed nitrogen conditions during modern maize breeding

Understanding the patterns of selection during plant evolution and recent crop improvement processes is the central topic in plant breeding and genetics. As an essential macronutrient for plant growth and development, nitrogen (N) is a key factor in affecting plant adaptation and crop improvement. The widespread adoption of less expensive industrial N fixation has dramatically reshaped plant morphology by favoring compact maize plants to tolerant crowding stress. The associated genetic changes, however, have not been systematically studied. Here, we investigated maize inbred lines developed before and after the 1960s -- the time point when inorganic N fertilizer started to be widely used for maize production. We identified a strong selective sweep exhibiting pronounced genomic differentiation between Old-Era (pre-1960s) and New-Era (post-1960s) inbred lines. Further study revealed population genetics statistics in the sweep exhibited patterns consistent with historical balancing selection. This balanced genomic interval is associated with a number of morphological, physiological, and metabolite traits related to vegetative N responses. A cluster of three glutamate receptor-like (GLR) genes is located within the region targeted by selection. Functional characterizations suggested differences in transcriptional activity of the GLR genes between the haplotypes carried by Old-Era and New-Era inbred lines likely play an essential role in mediating distinct N responses. The identification of both targets of selection and changes in the regulation of N responsive genes between maize lines developed in different eras sheds light on the N sensing and regulation pathways and paves the way to developing N resilient crops.

genomics↗

bioRxiv2021

Quantitative Measurement of Diffusion-weighted Imaging Signal Using Expression-controlled Aquaporin-4 Cells: Comparative Study of 2-compartment and Diffusion Kurtosis Imaging Models

PurposeThe purpose of this study was to compare parameter estimates for the 2-compartment (2Comp) and diffusion kurtosis imaging (DKm) models obtained from diffusion-weighted imaging (DWI) of aquaporin-4 (AQP4) expression-controlled cells, and to look for biomarkers that indicate differences in the cell membrane water permeability. MethodsDWI was performed on AQP4-expressing and non-expressing cells and the signal was analyzed with the 2Comp and DKm models. For the 2Comp model, the diffusion coefficients (Df, Ds) and volume fractions (Ff, Fs, Ff=1-Fs) of the fast and slow compartments were estimated. For the DKm model, estimates of the diffusion kurtosis (K) and corrected diffusion coefficient (D) were obtained. ResultsFor the 2Comp model, Ds and Fs showed clear differences between AQP4-expressing and non-expressing cells. Fs was also sensitive to cell density. There was no clear relationship with the cell type for the DKm parameters. ConclusionsChanges to cell membrane water permeability due to AQP4 expression affected DWI of cell suspensions. For the 2Comp and DKm models, Ds was the parameter most sensitive to differences in AQP4 expression.

cell biology↗

bioRxiv2021

The genome of stress tolerant crop wild relativePaspalum vaginatum leads to increased biomassproductivity in the crop Zea mays

A number of crop wild relatives can tolerate extreme stressed to a degree outside the range observed in their domesticated relatives. However, it is unclear whether or how the molecular mechanisms employed by these species can be translated to domesticated crops. Paspalum Paspalum vaginatum is a self-incompatible and multiply stress-tolerant wild relative of maize and sorghum. Here we describe the sequencing and pseudomolecule level assembly of a vegetatively propagated accession of P. vaginatum. Phylogenetic analysis based on 6,151 single-copy syntenic orthologous conserved in 6 related grass species placed paspalum as an outgroup of the maize-sorghum clade demonstrating paspalum as their closest sequenced wild relative. In parallel metabolic experiments, paspalum, but neither maize nor sorghum, exhibited significant increases in trehalose when grown under nutrient-deficit conditions. Inducing trehalose accumulation in maize, imitating the metabolic phenotype of paspalum, resulting in autophagy dependent increases in biomass accumulation.

plant biology↗

bioRxiv2021

Association of the malate dehydrogenase-citrate synthase metabolon is modulated by intermediates of the Krebs tricarboxylic acid cycle

Mitochondrial malate dehydrogenase (MDH)-citrate synthase (CS) multi-enzyme complex is a part of the Krebs tricarboxylic acid (TCA) cycle metabolon which is enzyme machinery catalyzing sequential reactions without diffusion of reaction intermediates into a bulk matrix. This complex is assumed to be a dynamic structure involved in the regulation of the cycle by enhancing metabolic flux. Microscale Thermophoresis analysis of the porcine heart MDH-CS complex revealed that substrates of the MDH and CS reactions, NAD+ and acetyl-CoA, enhance complex association while products of the reactions, NADH and citrate, weaken the affinity of the complex. Oxaloacetate enhanced the interaction only when it was presented together with acetyl-CoA. Structural modeling using published CS structures suggested that the binding of these substrates can stabilize the closed format of CS which favors the MDH-CS association. Two other TCA cycle intermediates, ATP, and low pH also enhanced the association of the complex. These results suggest that dynamic formation of the MDH-CS multi-enzyme complex is modulated by metabolic factors responding to respiratory metabolism, and it may function in the feedback regulation of the cycle and adjacent metabolic pathways.

biochemistry↗

bioRxiv2019

Phytochrome light receptors control metabolic flux, and their action during seedling development sets the trajectory for biomass production

The phytochromes (phys) photoreceptors are known to be major regulators of plastic growth responses to vegetation shade. Recent reports have begun to uncover an important role for phys in carbon resource management. Our earlier work showed that phy mutants had a distinct metabolic profile with elevated levels of metabolites including TCA intermediates, amino acids and sugars. Here we show that in seedlings phy regulates the balance between glucose and starch. Multi-allele phy mutants have excess glucose and low starch levels, which is conducive to hypocotyl elongation. 13C-CO2 labelling demonstrates that metabolic flux balance in adult plants is markedly altered in phy mutants. Phytochrome reduces synthesis rates of stress metabolites, including raffinose and proline and several typical stress-induced biosynthetic genes related to these metabolites show higher expression in phy mutants.\n\nSince growth and metabolism are typically inter-connected, we investigated why phy mutants have severely reduced biomass. Quantification of carbon fixation, biomass accumulation, and 13C labelling of cell wall polysaccharides established that relative growth rate is impaired in multi allele phy mutants for the first 2.5 weeks after germination but equivalent to the WT thereafter. Mathematical modelling predicts that the altered growth dynamics and final biomass deficit can be explained by the smaller cotyledon size of the multiple phy mutants. This indicates that the established role of phy in promoting seedling establishment has enduring effects that govern adult plant biomass.

plant biology↗

bioRxiv2018

Biparental inheritance of chloroplasts is controlled by lipid biosynthesis

In most eukaryotes, organellar genomes are transmitted preferentially by the mother, but molecular mechanisms and evolutionary forces underlying this fundamental biological principle are far from understood. It is believed that biparental inheritance promotes competition between the cytoplasmic organelles and allows the spread of so-called selfish cytoplasmic elements. Those can be, for example, fast replicating or aggressive chloroplasts (plastids) that are incompatible with the hybrid nuclear genome and therefore maladaptive.\n\nHere we show that the ability of plastids to compete against each other is a metabolic phenotype determined by extremely rapidly evolving genes in the plastid genome of the evening primrose Oenothera. Repeats in the regulatory region of accD (the plastid-encoded subunit of the acetyl-CoA carboxylase, which catalyzes the first and rate limiting step of lipid biosynthesis), as well as in ycf2 (a giant reading frame of still unknown function), are responsible for the differences in competitive behavior of plastid genotypes. Polymorphisms in these genes influence lipid synthesis and most likely profiles of the plastid envelope membrane. These in turn determine plastid division and/or turn-over rates and hence competitiveness. This work uncovers cytoplasmic drive loci controlling the outcome of biparental chloroplast transmission. Here, they define the mode of chloroplast inheritance, since plastid competitiveness can result in uniparental inheritance (through elimination of the \"weak\" plastid) or biparental inheritance (when two similarly \"strong\" plastids are transmitted).\n\nSignificance statementPlastids and mitochondria are usually uniparentally inherited, typically maternally. When the DNA-containing organelles are transmitted to the progeny by both parents, evolutionary theory predicts that the maternal and paternal organelles will compete in the hybrid. As their genomes do not undergo sexual recombination, one organelle will \"try\" to outcompete the other, thus favoring the evolution and spread of aggressive cytoplasms. The investigations described here in the evening primrose, a model species for biparental plastid transmission, have discovered that chloroplast competition is a metabolic phenotype. It is conferred by rapidly evolving genes that are encoded on the chloroplast genome and control lipid biosynthesis. Due to their high mutation rate these loci can evolve and become fixed in a population very quickly.

genetics↗