Biology subjects

Wada, K.

Publications and source records attributed to Wada, K..

At least 19 recordsLinked to original sources

bioRxiv2026

Unsupervised explainable AI reveals similar oligonucleotide-usage zones matching the highest-resolution human chromosome bands

Unsupervised and explainable AI can uncover genomic features that extend beyond human expectations. Oligonucleotides such as penta- and hexanucleotides often function as core binding motifs for regulatory proteins, and their usage provides a powerful tool in functional genomics. We applied an unsupervised, explainable AI approach to odds ratio (observed/expected) profiles of all 1-Mb euchromatic fragments in the human genome. This odds-ratio analysis identified oligonucleotide features independent of mononucleotide composition, thereby highlighting functional roles of oligonucleotide motifs. AI-based clustering of all 1-Mb euchromatic fragments, using either penta- or hexanucleotide odds ratios (1,024 or 4,096 variables), unexpectedly revealed nearly 2,000 distinct zones, despite the large differences in dimensionality. If these [~]2,000 zones represent biologically meaningful segmentations, comparable structures would be expected to emerge when other oligonucleotide types are analyzed. Consistent with this expectation, CG-containing penta- and hexanucleotides (244 and 1,185 variables) produced comparable [~]2,000 zones, indicating that the underlying segmental structures reflect fundamental functional divisions within the genome. Human chromosomes exhibit well-established Giemsa-banding patterns comprising 850 bands at prometaphase and 2,000 bands at prophase. Since single-nucleotide coordinates are available for the 850 bands, we identified a diagnostic oligonucleotide set that distinguishes Giemsa-negative and -positive regions. Computational pseudo-band reconstruction based on this set generated genome segmentations that more closely paralleled the AI-derived [~]2,000 clusters than the 850 bands. These unexpected findings indicate that AI captures the characteristic features of chromosomal bands and can predict high-resolution banding from genome sequences alone, thereby bridging classical cytogenetics and modern AI-based genomics.

genomics↗

bioRxiv2024

The lysosomal membrane protein LAMP2B mediates microlipophagy to target obesity-related disorders

Lifestyle diseases, such as obesity, diabetes, and metabolic syndrome, are leading health problems, most of which are related to abnormal lipid metabolism. Lysosomes can degrade lipid droplets (LDs) via microautophagy. Here, we report the molecular mechanism and pathophysiological roles of microlipophagy, regulated by the lysosomal membrane protein LAMP2B. Our study revealed that LAMP2B interacts with phosphatidic acid, facilitating lysosomal-LD interactions and enhancing lipid hydrolysis via microlipophagy depending on endosomal sorting complexes required for transport. Correlative light and electron microscopy demonstrated direct LDs uptake into lysosomes at contact sites. Moreover, LAMP2B overexpression in mice prevents high-fat diet-induced obesity, insulin resistance, and adipose tissue inflammation; liver lipidomics analysis suggested enhanced triacylglycerol hydrolysis. Overall, the findings of this study elucidated the mechanism of microlipophagy, which could be promising for the treatment of obesity and related disorders.

cell biology↗

bioRxiv2024

Embryonic exposure to valproic acid and neonicotinoid deteriorates the developmental GABA switch and impairs long-term potentiation in the local circuit of intermediate medial mesopallium of chick telencephalon

Embryonic exposure to valproic acid (VPA) and imidacloprid (IMI, a neonicotinoid insecticide) impairs filial imprinting in hatchlings, and the deteriorating effects of VPA are mitigated by post-hatch injection of bumetanide, a blocker of the chloride intruder NKCC1. Here, we report that these exposures depolarized the reversal potential of local GABAergic transmission in the neurons of the intermediate medial mesopallium (IMM), the pallial region critical for imprinting. Furthermore, exposure increased field excitatory post-synaptic potentials in pre-tetanus recordings (fEPSPs) and impaired long-term potentiation by low-frequency tetanic stimulation (LTP). Bath-applied bumetanide rescued the impaired LTP in the VPA slices, whereas VU0463271, a blocker of the chloride extruder KCC2, suppressed LTP in the control slices, suggesting that hyperpolarizing GABA action is necessary for the potentiation of excitatory synaptic transmission. However, the transcriptional profiles of IMM slices did not support the expected increase in the NKCC1/KCC2 ratio, suggesting a potential modification of post-transcriptional processes. Instead, exposure to both VPA and IMI downregulated several transcriptional regulators (FOS, NR4A1, and NR4A2) and upregulated the RNA component of signal recognition particles (RN7SL1). As a limited set of response genes were shared, VPA and IMI could cause common neuronal malfunctions via distinct molecular cascades.

neuroscience↗

bioRxiv2024

Protonation/deprotonation-driven switch for the redox stability of low-potential ferredoxin

Ferredoxin is a small iron-sulfur protein and acts as an electron carrier. Low-potential ferredoxins harbor [4Fe-4S] cluster(s), which play(s) a crucial role as the redox center. Low-potential ferredoxins are able to cover a wide range of redox potentials (-700 to -200 mV); however, the mechanisms underlying the factors which control the redox potential are still enigmatic. Here, we determined the neutron structure of ferredoxin from Bacillus thermoproteolyticus, and experimentally revealed the exact hydrogen-bonding network involving the [4Fe-4S] cluster. The density functional theory calculations based on the hydrogen-bonding network revealed that protonation states of the sidechain of Asp64 close to the [4Fe-4S] cluster critically affected the stability of the reduced state in the cluster. These findings provide the first identification of the intrinsic control factor of redox potential for the [4Fe-4S] cluster in low-potential ferredoxins.

biochemistry↗

bioRxiv2024

The minimal SUF system can substitute for the canonical iron-sulfur cluster biosynthesis systems by using inorganic sulfide as the sulfur source.

Biosynthesis of iron-sulfur (Fe-S) clusters is indispensable for living cells. Three biosynthesis systems termed NIF, ISC and SUF have been extensively characterized in both bacteria and eukarya. For these L-cysteine is the sulfur source. A bioinformatic survey suggested the presence of a minimal SUF system composed of only two components, SufB* (a putative ancestral form of SufB and SufD) and SufC, in anaerobic archaea and bacteria. Here, we report the successful complementation of an Escherichia coli mutant devoid of the usual ISC and SUF systems upon expression of the archaeal sufB*C genes. Strikingly, this heterologous complementation occurred under anaerobic conditions only when sulfide was supplemented to the culture media. Mutational analysis and structural predictions suggest that the archaeal SufB*C most likely forms a SufB*2C2 complex and serves as the scaffold for de novo Fe-S cluster assembly using the essential Cys and Glu residues conserved between SufB* and SufB, in conjunction with a His residue shared between SufB* and SufD. We also demonstrate artificial conversion of the SufB*2C2 structure to the SufBC2D type by introducing several mutations to the two copies of sufB*. Our study thus elucidates the molecular function of this minimal SUF system and suggests that it is the evolutionary prototype of the canonical SUF system.

microbiology↗

bioRxiv2023

Auditory feedback-independent maintenance of song performance through daily singing in adult songbirds

Many songbirds learn to produce songs through vocal practice early in life and continue to sing numerous renditions of their learned songs daily throughout their lifetime. While it is well-known that adult songbirds sing as part of a mating ritual, the functions of singing behavior outside of reproductive contexts are not fully understood. Here, we demonstrate that adult singing outside of reproductive contexts serves to prevent passive changes in song performance. We suppressed the daily singing behavior of adult zebra finches produced in the solo context for two weeks using a reversible behavioral manipulation and examined the effect on song performance. Our results indicated that suppressing daily singing significantly decreased the pitch of song elements and both the amplitude and duration of song motifs. These findings suggest that adult song is not acoustically stable without singing, and that adult birds maintain their song performance by daily singing. Moreover, we found that the changes in song structure caused by singing suppression were substantially recovered within two weeks of free singing, even in deafened birds. Thus, the recovery of song performance does not necessarily require auditory feedback but is predominantly caused by singing behavior per se (i.e., the physical act of singing). Finally, unlike the auditory feedback-dependent song plasticity reported previously, the passive song changes caused by singing suppression were not significantly dependent on age. Taken together, our findings demonstrate that adult songbirds maintain song performance by preventing passive song changes through the physical act of daily singing throughout their life. Such daily singing likely functions as vocal training to maintain the neural and/or muscular system in optimal conditions for song performance in reproductive contexts, similar to how human singers and athletes practice daily to maintain their performance.

animal behavior and cognition↗

bioRxiv2022

FUS regulates RAN translation through modulating the G-quadruplex structure of GGGGCC repeat RNA in C9orf72-linked ALS/FTD

Abnormal expansions of GGGGCC repeat sequence in the noncoding region of the C9orf72 gene is the most common cause of familial amyotrophic lateral sclerosis and frontotemporal dementia (C9-ALS/FTD). The expanded repeat sequence is translated into dipeptide repeat proteins (DPRs) by noncanonical repeat-associated non-AUG (RAN) translation. Since DPRs play central roles in the pathogenesis of C9-ALS/FTD, we here investigate the regulatory mechanisms of RAN translation, focusing on the effects of RNA-binding proteins (RBPs) targeting GGGGCC repeat RNAs. Using C9-ALS/FTD model flies, we demonstrated that the ALS/FTD-linked RBP FUS suppresses RAN translation and neurodegeneration in an RNA-binding activity-dependent manner. Moreover, we found that FUS directly binds to and modulates the G-quadruplex structure of GGGGCC repeat RNA as an RNA chaperone, resulting in the suppression of RAN translation in vitro. These results reveal a previously unrecognized regulatory mechanism of RAN translation by G-quadruplex-targeting RBPs, providing therapeutic insights for C9-ALS/FTD and other repeat expansion diseases.

neuroscience↗

bioRxiv2022

Requirement of sequential hydrolysis by CD73 and ALP for uptake of vitamin B2 into cells

Extracellular hydrolysis of flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN) to riboflavin is thought to be important for cellular uptake of vitamin B2 because FAD and FMN are hydrophilic and do not pass the plasma membrane. However, it is not clear whether FAD and FMN are hydrolyzed by cell surface enzymes for vitamin B2 uptake. Here, we show that in human cells, FAD, a major form of vitamin B2 in plasma, is hydrolyzed by CD73 (also called ecto-5' nucleotidase) to FMN, then FMN is hydrolyzed by alkaline phosphatase to riboflavin, which is efficiently imported into cells. This process is impaired on the surface of glycosylphosphatidylinositol (GPI)-deficient cells due to lack of these GPI-anchored enzymes. During culture of GPI-deficient cells with FAD or FMN, hydrolysis of these forms of vitamin B2, intracellular levels of vitamin B2, vitamin B2-dependent pyridoxal 5'-phosphate formation, and mitochondrial functions were significantly decreased compared with those in GPI-restored cells. These results suggest that inefficient uptake of vitamin B2 might account for mitochondrial dysfunction seen in some cases of inherited GPI deficiency.

biochemistry↗

bioRxiv2022

Impaired Epigenesis of Imprinting Predispositions Causes Autism-like Behavioral Phenotypes in Domestic Chicks

Several environmental chemicals are suspected as risk factors for autism spectrum disorder (ASD), including valproic acid (VPA) and pesticides acting on nicotinic acetylcholine receptor (nAChR) if exposed during pregnancy. However, their target processes in fetal neuro-development are unspecified. We report that fetal injection of VPA impaired the imprinting of an artifact object in hatchlings, while the predisposed preference to biological motion (BM) remained intact. Blockade of nAChR acted oppositely, namely, spared imprinting and impaired BM in chicks. Beside ketamine and tubocurarine, significant effects of imidacloprid (a neonicotinoid insecticide) appeared at dose [≤]1ppm. Despite the distinct processes, both VPA and nAChR blockade similarly impaired imprinting of biological image composed of point-light animation. Furthermore, both impairments were rescued by post-natal bumetanide treatment, suggesting common pathology underlying the social attachment malformation. Ambient neonicotinoid could hinder adaptive socialization through impaired development of visual perception in early neonates.

animal behavior and cognition↗

bioRxiv2022

AI-based search for convergently expanding, advantageous mutations in SARS-CoV-2 by focusing on oligonucleotide frequencies

Among mutations that occur in SARS-CoV-2, efficient identification of mutations advantageous for viral replication and transmission is important to characterize and defeat this rampant virus. Mutations rapidly expanding frequency in a viral population are candidates for advantageous mutations, but neutral mutations hitchhiking with advantageous mutations are also likely to be included. To distinguish these, we focus on mutations that appear to occur independently in different lineages and expand in frequency in a convergent evolutionary manner. Batch-learning SOM (BLSOM) can separate SARS-CoV-2 genome sequences according by lineage from only providing the oligonucleotide composition. Focusing on remarkably expanding 20-mers, each of which is only represented by one copy in the viral genome, allows us to correlate the expanding 20-mers to mutations. Using visualization functions in BLSOM, we can efficiently identify mutations that have expanded remarkably both in the Omicron lineage, which is phylogenetically distinct from other lineages, and in other lineages. Most of these mutations involved changes in amino acids, but there were a few that did not, such as an intergenic mutation.

bioinformatics↗

bioRxiv2021

Unsupervised explainable AI for the collective analysis of a massive number of genome sequences: various examples from the small genome of pandemic SARS-CoV-2 to the human genome

In genetics and related fields, huge amounts of data, such as genome sequences, are accumulating, and the use of artificial intelligence (AI) suitable for big data analysis has become increasingly important. Unsupervised AI that can reveal novel knowledge from big data without prior knowledge or particular models is highly desirable for analyses of genome sequences, particularly for obtaining unexpected insights. We have developed a batch-learning self-organizing map (BLSOM) for oligonucleotide compositions that can reveal various novel genome characteristics. Here, we explain the data mining by the BLSOM: unsupervised and explainable AI. As a specific target, we first selected SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) because a large number of the viral genome sequences have been accumulated via worldwide efforts. We analyzed more than 0.6 million sequences collected primarily in the first year of the pandemic. BLSOMs for short oligonucleotides (e.g., 4~6-mers) allowed separation into known clades, but longer oligonucleotides further increased the separation ability and revealed subgrouping within known clades. In the case of 15-mers, there is mostly one copy in the genome; thus, 15-mers appeared after the epidemic start could be connected to mutations. Because BLSOM is an explainable AI, BLSOM for 15-mers revealed the mutations that contributed to separation into known clades and their subgroups. After introducing the detailed methodological strategies, we explained BLSOMs for various topics. The tetranucleotide BLSOM for over 5 million 5-kb fragment sequences derived from almost all microorganisms currently available and its use in metagenome studies. We also explained BLSOMs for various eukaryotes, such as fishes, frogs and Drosophila species, and found a high separation ability among closely related species. When analyzing the human genome, we found evident enrichments in transcription factor-binding sequences (TFBSs) in centromeric and pericentromeric heterochromatin regions. The tDNAs (tRNA genes) were separated by the corresponding amino acid.

bioinformatics↗

bioRxiv2021

Visualization of ecological successions in lakes subdivided by volcanic eruption at Akan Caldera, Hokkaido, Japan

It is not feasible to continuously observe ecological succession in lakes because of the long time-scales generally involved. Thus, the process has been inductively deduced by comparing many lakes with different succession states, or indirectly simulated by tracking studies of smaller water bodies, experiments using microcosms or mesocosms, and reconstruction of lake history by sediment analysis. However, the reality of succession processes in large lakes with slow succession is not well understood, and new approaches are needed. Theoretically, in a group of large and small lakes of similar ages and with similar initial and watershed environments, the rate of nutrient accumulation in each lake depends on the ratio of watershed area to lake size, and the lakes are predicted to evolve to different trophic levels over time. Here, we tested this hypothesis on the 10 lakes of varying sizes in Akan Caldera, Japan, which were formed thousands of years ago by fragmentation due to volcanic eruptions within the caldera. Topographic and water quality studies showed that the ratio of accumulated watershed area to lake size (area and volume), expressed logarithmically, had a positive linear regression with the total phosphorus concentration, an indicator of trophic level. The trophic levels of the lakes were diverse, including oligotrophic, mesotrophic, and eutrophic types in the traditional "lake type" classification based on total phosphorus and chlorophyll-a concentrations. Furthermore, 21 species of aquatic macrophytes were observed by a diving survey, and the plant species composition was classified into five groups corresponding to the trophic status of the lakes, indicating a conventional "hydrarch succession". The diversity of water quality and aquatic vegetation in a group of lakes with similar origins paves the way for new comparative studies of lakes, including large lakes.

ecology↗

bioRxiv2020

Structural basis of the protochromic green/red photocycle of the chromatic acclimation sensor RcaE

Cyanobacteriochromes (CBCRs) are bilin-binding photosensors of the phytochrome superfamily that show remarkable spectral diversity. The green/red CBCR subfamily is important for regulating chromatic acclimation of photosynthetic antenna in cyanobacteria and is applied for optogenetic control of gene expression in synthetic biology. They are suggested to combine the bilin C15-Z/C15-E photoisomerization with a change in the bilin protonation state to drive their absorption changes. However, structural information and direct evidence of the bilin protonation state are lacking. Here we report a high-resolution (1.63[A]) crystal structure of the bilin-binding domain of the chromatic acclimation sensor RcaE in the red-absorbing photoproduct state. The bilin is buried within a "pan" consisting of hydrophobic residues, where the bilin configuration/conformation is C5-Z,syn/C10-Z,syn/C15-E,syn with the A-C rings co-planar and the D-ring tilted. Three pyrrole nitrogens of the A-C rings are covered in the -face with a hydrophobic lid of Leu249 influencing the bilin pKa, whereas they are directly hydrogen-bonded in the {beta}-face with the carboxyl group of Glu217. Glu217 is further connected to a cluster of waters forming a hole in the pan, which are in exchange with solvent waters in molecular dynamics simulation. We propose that the "holey pan" structure functions as a proton-exit/influx pathway upon photoconversion. NMR analysis demonstrated that the four pyrrole nitrogen atoms are indeed fully protonated in the red-absorbing state, but one of them, most likely the B-ring nitrogen, is deprotonated in the green-absorbing state. These findings deepen our understanding of the diverse spectral tuning mechanisms present in CBCRs. Significance StatementGreen/red CBCRs are one of the most important CBCR subfamilies owing to their physiological roles in cyanobacteria phylum and optogenetic applications. They are known to utilize a change in the bilin protonation state to drive the marked change in green/red absorption, but the structural basis of the protochromic green/red photocycle are not well understood. Here, we have determined the crystal structure of the chromatic acclimation sensor RcaE of this subfamily in the photoproduct state, demonstrating a unique conformation of the bilin and its interacting residues. In addition, we provide direct evidence of the protonation state of the bilin via NMR analysis. These findings bring insight to our understanding of the molecular mechanisms underlying the spectral diversity of CBCRs.

biochemistry↗

bioRxiv2020

Unsupervised explainable AI for simultaneous molecular evolutionary study of forty thousand SARS-CoV-2 genomes

Unsupervised AI (artificial intelligence) can obtain novel knowledge from big data without particular models or prior knowledge and is highly desirable for unveiling hidden features in big data. SARS-CoV-2 poses a serious threat to public health and one important issue in characterizing this fast-evolving virus is to elucidate various aspects of their genome sequence changes. We previously established unsupervised AI, a BLSOM (batch-learning SOM), which can analyze five million genomic sequences simultaneously. The present study applied the BLSOM to the oligonucleotide compositions of forty thousand SARS-CoV-2 genomes. While only the oligonucleotide composition was given, the obtained clusters of genomes corresponded primarily to known main clades and internal divisions in the main clades. Since the BLSOM is explainable AI, it reveals which features of the oligonucleotide composition are responsible for clade clustering. The BLSOM has powerful image display capabilities and enables efficient knowledge discovery about viral evolutionary processes.

evolutionary biology↗

bioRxiv2020

Identifications of novel avian and mammalian deltaviruses filled the large evolutionally gaps and revealed inter-family transmission of deltaviruses

Hepatitis delta virus (HDV) is a satellite virus that requires hepadnavirus envelope proteins for its transmission. Although recent studies identified HDV-related deltaviruses in certain animals, the evolution of deltaviruses, such as the origin of HDV and the mechanism of its coevolution with its helper viruses, is unknown, mainly because of the phylogenetic gaps among deltaviruses. Here we identified novel deltaviruses of passerine birds, woodchucks, and white-tailed deer by extensive database searches and molecular surveillance. Phylogenetic and molecular epidemiological analyses suggest that HDV originated from mammalian deltaviruses and the past interspecies transmission of mammalian and passerine deltaviruses. Further, metaviromic and experimental analyses suggest that the satellite-helper relationship between HDV and hepadnavirus was established after the divergence of the HDV lineage from non-HDV mammalian deltaviruses. Our findings enhance our understanding of deltavirus evolution, diversity, and transmission, indicating the importance of further surveillance for deltaviruses.

microbiology↗

bioRxiv2020

Distinct synaptic and related transcriptional abnormalities in neonatal, childhood and mature autism model of primate: implications for early-age therapeutic intervention

Autism spectrum disorder (ASD) is a synapse-related disorder that is diagnosed at around 3 years of age. Earlier intervention is desirable for better ASD prognosis; however, there is limited biological literature regarding early-age ASD. This study aimed to assess altered cortical synapses and gene expression in the ASD model marmoset. There were distinct phenotypes in the model animals across the neonate, childhood, and mature stages in the dorsomedial prefrontal cortex (Brodmann area 8b/9). At the neonate stage, synapses were underdeveloped and modulated genes were enriched with synaptogenesis- and ASD-related genes. At the childhood stage, synaptic features and gene expressions associated with experience-dependent circuit remodeling were altered in model animals. At the mature stage, there were synapse overdevelopment and altered gene expression similar to those in human ASD. These early synaptic phenotypes and altered gene expressions could be novel targets of efficient therapy from a young age.

neuroscience↗

bioRxiv2020

Direct uptake mechanism in lysosome required for neuromuscular homeostasis

The degradation of cellular components plays an essential role in homeostasis. However, the known degradation pathways cannot account for the levels of proteolysis in cells. Here, we demonstrate that cytosolic proteins are imported into lysosomes in an ATP-dependent manner for degradation through a direct uptake mechanism distinct from any known pathway. SIDT2, a lysosomal membrane protein previously reported as an RNA transporter, translocates substrate proteins across the lysosomal membrane. Furthermore, we identify a dominant-negative mutation in SIDT2 that causes neuropathy and distal myopathy with rimmed vacuoles, a protein aggregation disease in humans. We generate Sidt2 knockout mice, recapitulating the characteristic features of this disease. Our results reveal a novel degradation pathway and illustrate its crucial role in cellular proteostasis, physiology, and pathophysiology. One Sentence SummaryDiscovery of a novel proteolytic pathway in cells, the dysfunction of which leads to protein aggregation disease in humans.

cell biology↗

bioRxiv2020

Time-series analyses of directional sequence changes in SARS-CoV-2 genomes and an efficient search method for advantageous mutations for growth in human cells

We first conducted time-series analysis of mono- and dinucleotide composition for over 10,000 SARS-CoV-2 genomes, as well as over 1500 Zaire ebolavirus genomes, and found clear time-series changes in the compositions on a monthly basis, which should reflect viral adaptations for efficient growth in human cells. We next developed a sequence alignment free method that extensively searches for advantageous mutations and rank them in an increase level for their intrapopulation frequency. Time-series analysis of occurrences of oligonucleotides of diverse lengths for SARS-CoV-2 genomes revealed seven distinctive mutations that rapidly expanded their intrapopulation frequency and are thought to be candidates of advantageous mutations for the efficient growth in human cells.

bioinformatics↗