Biology subjects

Yoshizawa, S.

Publications and source records attributed to Yoshizawa, S..

13 recordsLinked to original sources

bioRxiv2026

SAR11 Genome Atlas: a genome and gene catalog for functional profiling of the most abundant bacterial clade in the ocean

The SAR11 clade, also known as the order Candidatus Pelagibacterales, is among the most abundant bacterial lineages in the ocean and plays central roles in marine biogeochemical cycles. However, many SAR11 genes remain functionally uncharacterized, highlighting the need for a comprehensive, integrated catalog that supports genomic, functional, and ecological analyses across the clade. Here, we present the SAR11 Genome Atlas, an interactive ortholog group (OG)-centered web resource that integrates 542 SAR11 genomes, including all 132 cultured strain genomes, with functional annotations, synteny, phylogenetic distribution, metatranscriptomic expression, and predicted protein structure information. To demonstrate its utility, we used environmental expression profiles to identify OGs associated with high-latitude environments, recovering OGs known to be involved in cold adaptation and proposing a hypothesis for the function of uncharacterized protein. We further analyzed phylogenetic distribution patterns to identify mutually exclusive functional modules, including candidate alternative systems for Mn/Zn homeostasis and phosphate acquisition, and to associate these modules with distinct oceanographic environments. Together, these case studies demonstrate that the SAR11 Genome Atlas supports complementary analyses that connect environmental signals to genes of interest and use phylogenetic or functional distributions to generate hypotheses about ecological specialization. Through a user-friendly web interface, the SAR11 Genome Atlas enables researchers to explore genomic, environmental, and structural information without specialized computational expertise. All data and analysis outputs are freely accessible online at [https://stsnsn.github.io/SAR11_Atlas/]. The SAR11 Genome Atlas thus provides a scalable framework for generating and testing hypotheses that connect SAR11 genomic variation to protein function and oceanographic context, supporting advances in marine microbial ecology and biogeochemistry.

microbiology↗

bioRxiv2026

Genomic, spatial, and evolutionary insights into a dominant Mycoplasmatota symbiont colonizing the body wall of deep-sea holothurians

Subcuticular bacteria (SCB) are widespread symbionts of echinoderms and often dominate the body-wall microbiome, suggesting important roles in host physiology. However, their diversity, metabolic properties, and host associations remain poorly characterized. Here, we report a novel dominant SCB lineage associated with deep-sea holothurians, Scotoplanes spp. collected from the Northwest Pacific. We recovered two high-quality genomes, including a 649-kb complete circular genome, and propose a new genus and species, "Candidatus Abyssoplasma scotoplanesicola", within Mycoplasmatota. The two genomes showed a highly reduced metabolic repertoire, lacking central pathways including glycolysis. In contrast, acidic cell-surface-associated proteins, including large proteins exceeding 5,000 amino acids, accounted for 27.6% of the complete genome and clustered near defense islands. Localized genome plasticity in these regions, revealed by comparison between the two closely related genomes, suggests a possible mechanism for diversification of cell-surface proteins at the host-symbiont interface. "Candidatus Abyssoplasma scotoplanesicola" occupied 76.4-98.9% of the body-wall microbiome of the Scotoplanes specimens. Fluorescence in situ hybridization analysis confirmed that these bacteria formed aggregates on the epidermal side of the body wall. Overall, this study provides genome-and spatially resolved views of dominant SCB in holothurians and offers evolutionary insights into host-interface diversification in the deep-sea holothurian body wall.

microbiology↗

bioRxiv2026

AI-enabled rhodopsin design for blue-light enhanced bacterial growth

We developed an AI-guided design pipeline that generated and validated non-natural microbial rhodopsins with spectral properties not yet known in nature. The pipeline comprised a three-stage in silico design, a genetic algorithm (GA) for sequence generation, a stacked LASSO and XGBoost machine-learning (ML) regressor for spectral prediction and fitness ranking, and a Markov-based sequence plausibility filter to enforce proton pumping like characteristics. Four candidate rhodopsins (APR1, APR2, APR6, and APR7) targeting blue light absorption were designed and AlphaFold3 structural modelling predicted retinal binding pocket architecture consistent with outward proton-pumping function. Experimental characterisation confirmed that all four variants absorbed light at [~]410 nm and significantly promoted the growth of Cupriavidus necator under blue light illumination. This study demonstrates that AI-enabled design can engineer proteins with no natural precedent, generating light-harvesting rhodopsins with novel spectral properties while preserving biological function, marking a significant advance in programmable synthetic biology.

Synthetic Biology↗

bioRxiv2025

Functional Unknomics of the SAR11 clade using bioinformatics approaches

A substantial fraction of the genes in marine bacteria lack detectable sequence similarity to genes with known functions. These functionally uncharacterized genes--collectively referred to as the "unknome"--represent a largely unexplored genetic repertoire harboring insights into marine bacterial ecology. In this study, we explored the function of the unknome of SAR11 clade, the most abundant bacterial lineage in the ocean, with a particular focus on genes that provide insight into their ecology. Based on the COG classification, approximately 58% of SAR11 ortholog groups were classified as unknome. Among the SAR11 unknome, we successfully inferred the functions of 69 ortholog groups that are conserved in SAR11 clade by protein structure similarity searches and genomic context analyses. These ortholog groups include putative transporter components, supporting the current ecological understanding that SAR11 clade is specialized in substrate uptake to adapt to oligotrophic marine environments. Furthermore, structural analysis indicated that the DUF2237-containing protein, enriched in marine environments, has potential interactions with purine nucleotide-containing compounds. This may suggest the existence of unique nucleotide utilization mechanisms in marine bacteria. In addition, we found candidates of virus defense systems within the unknome, which demonstrates that diverse defense systems are present at least in one-third of the cultured SAR11 strains. The conservation of these viral defense systems, even within streamlined SAR11 genomes, suggests that they confer significant ecological advantages. Our exploration provided insights into the genetic basis of bottom-up processes (adaptation to oligotrophic environments) and top-down processes (antiviral defense strategy) contributing to ecological success of SAR11.

microbiology↗

bioRxiv2025

MitoNGS: an online platform to analyze fish metabarcoding data in high-resolution

Environmental DNA (eDNA) metabarcoding has become a powerful tool for assessing fish biodiversity in aquatic ecosystems. However, accurate species-level identification remains challenging due to incomplete and contaminated reference databases, as well as ambiguous taxa sharing identical barcode sequences. Here, we present MitoNGS, a next-generation platform that succeeds the widely used MiFish pipeline, designed for high-resolution analysis of fish metabarcoding data. MitoNGS addresses these challenges by incorporating more comprehensive references including non-fish species and detailed annotations of heterospecific regions. Additionally, it introduces the "species group" strategy in conjunction with environmental habitat and geographic occurrence data to resolve ambiguous taxa. Furthermore, MitoNGS expands the functionalities of the legacy MiFish pipeline. It can analyze data from any mitochondrial markers and from Nanopore sequencing platforms. MitoNGS demonstrated excellent performance on our testing datasets from diverse locations, markers and sequencing platforms. MitoNGS offers a user-friendly, web-based solution for fish detection, biodiversity monitoring, conservation research, and bioresource management. MitoNGS is freely available via https://mitofish.aori.u-tokyo.ac.jp/mito-ngs.

bioinformatics↗

bioRxiv2024

Carotenoid pigments enhance rhodopsin-mediated phototrophy by light-harvesting and photocycle-accelerating

Microbial rhodopsins, photoreceptor proteins widely distributed in marine microorganisms, receive large amount of light energy that sustains marine ecosystems. Although rhodopsins generally harbor retinal as their only chromophore, a recent study reported that carotenoid antennae transfer light energy to the retinal in proteorhodopsins, proton pump rhodopsins abundant in marine environments. Here, using marine bacterial isolates, we detected energy transfer from a carotenoid (myxol) to retinal not only in proteorhodopsin but also in the chloride ion-pumping rhodopsin. Carotenoid binding improved the light utilization efficiency of the proteorhodopsin by accelerating the photocycle, together with facilitating light-harvesting. The carotenoid-binding ability is conserved in rhodopsins of the phylum Bacteroidota, which are widely transcribed in the photic zone. These findings suggest that the distribution of carotenoid-binding rhodopsins is more taxon-specific than previously thought, thus underscoring the importance of carotenoid-binding rhodopsins that provide an extended light utilization strategy in the environmental adaptation of marine bacteria.

microbiology↗

bioRxiv2023

Probe capture enrichment sequencing of amoA genes discloses diverse ammonia-oxidizing archaeal and bacterial populations

The ammonia monooxygenase subunit A (amoA) gene has been used to investigate the phylogenetic diversity, spatial distribution, and activity of ammonia-oxidizing archaeal (AOA) and bacterial (AOB), which contribute significantly to the nitrogen cycle in various ecosystems. Amplicon sequencing of amoA is a widely used method; however, it produces inaccurate results owing to the lack of a universal primer set. Moreover, currently available primer sets suffer from amplification biases, which can lead to severe misinterpretation. Although shotgun metagenomic and metatranscriptomic analyses are alternative approaches without amplification bias, the low concentration of target genes in heterogeneous environmental DNA restricts a comprehensive analysis to a realizable sequencing depth. In this study, we developed a method for amoA enrichment sequencing using a hybridization capture technique. Using metagenomic mock community samples, our approach effectively enriched amoA genes with low compositional changes, outperforming amplification and meta-omics sequencing analyses. Following the analysis of metatranscriptomic marine samples, we predicted 80 operational taxonomic units (OTUs) assigned to either AOA or AOB, of which 30 OTUs were unidentified using simple metatranscriptomic or amoA gene amplicon sequencing. Mapped read ratios to all the detected OTUs were significantly higher for the capture samples (50.4 {+/-} 27.2%) than for non-capture samples (0.05 {+/-} 0.02%), demonstrating the high enrichment efficiency of the method. The analysis also revealed the spatial diversity of AOA ecotypes with high sensitivity and phylogenetic resolution, which are difficult to examine using conventional approaches.

microbiology↗

bioRxiv2022

Distribution and survival strategies of diazotrophs in the Arctic Ocean revealed by global-scale metagenomic analysis

Nitrogen fixation is the major source of reactive nitrogen in the ocean and has been considered to occur specifically in low-latitude oligotrophic oceans. Recent studies have shown that nitrogen fixation also occurs in the polar regions and thus is a global process, although the physiological and ecological characteristics of polar diazotrophs are not yet known. Here, we successfully reconstructed genomes, including that of cyanobacterium UCYN-A (Candidatus Atelocyanobacterium thalassa), from metagenome data corresponding to 111 samples isolated from the Arctic Ocean. These diazotrophs were highly abundant in the Arctic Ocean (max., 1.28% of the total microbial community), suggesting that they have important roles in the Arctic ecosystem and biogeochemical cycles. Diazotrophs in the Arctic Ocean were either Arctic-specific or universal species. Arctic-specific diazotrophs, including Arctic UCYN-A, had unique gene sets (e.g., aromatics degradation) and/or a very small cell size (<0.2 {micro}m), suggesting adaptations to Arctic-specific conditions. Universal diazotrophs were generally heterotrophs and commonly had the gene that encodes the cold-inducible RNA chaperone, which presumably makes their survival possible even in deep, cold waters and polar regions. Thus both types of diazotroph have physiological traits adaptable to their environments, which allow nitrogen fixation on a global scale.

ecology↗

bioRxiv2022

Energy transfer in ubiquitous rhodopsin pumps with xanthophyll antennas

Energy transfer from light-harvesting ketocarotenoids to light-driven proton pumps xanthorhodopsins has been previously demonstrated in two unique cases: an extreme halophilic bacterium1 and a terrestrial cyanobacterium2. Attempts to find carotenoids that bind and transfer energy to rhodopsin proton pumps from the abundant marine and freshwater photoheterotrophs have thus far failed3-5. Here, using functional metagenomics combined with chromophore extraction from the environment, we detected light energy transfer from the widespread hydroxylated carotenoids zeaxanthin and lutein to the retinal moiety of xanthorhodopsins and proteorhodopsins. The light-harvesting carotenoids transfer up to 42% of the harvested energy in the violet/blue-light range to the green-light absorbing retinal chromophore. Our data suggest that these antennas have a significant impact on rhodopsin phototrophy in the worlds lakes, seas and oceans.

microbiology↗

bioRxiv2022

Proton-pumping rhodopsins in marine diatoms

Diatoms are a major phytoplankton group responsible for about 20% of Earths primary production. They carry out photosynthesis inside the plastid, an organelle obtained through eukaryote-eukaryote endosymbiosis. Recently, microbial rhodopsin, a photoreceptor distinct from chlorophyll-based photosystems, has been identified in certain diatoms. However, the physiological function of diatom rhodopsin is not well understood. Here we show that the diatom rhodopsin acts as a light-driven proton pump and localizes to the outermost membrane of the four membrane-bound complex plastids. Heterologous expression techniques were used to investigate the protein function and subcellular localization of diatom rhodopsin. Using model simulations, we further evaluated the physiological role of the acidic pool in the plastid produced by proton-transporting rhodopsin. Our results propose that the rhodopsin-derived acidic pool may be involved in a photosynthetic CO2-concentrating mechanism and assist CO2 fixation in diatom cells.

microbiology↗

bioRxiv2021

Unidirectional ion transport mechanism of a light-driven chloride pump revealed using X-ray free electron lasers

Light-driven chloride-pumping rhodopsins actively transport anions, including various halide ions, across cell membranes. Recent studies using time-resolved serial femtosecond crystallography (TR-SFX) have uncovered the structural changes and ion transfer mechanisms in light-driven cation-pumping rhodopsins. However, the mechanism by which the conformational changes pump an anion to achieve unidirectional ion transport, from the extracellular side to the cytoplasmic side, in anion-pumping rhodopsins remains enigmatic. We have collected TR-SFX data of Nonlabens marinus rhodopsin-3 (NM-R3), derived from a marine flavobacterium, at 10 s and 1 ms time-points after photoexcitation. Our structural analysis reveals the conformational alterations during ion transfer and after ion release. Movements of the retinal chromophore initially displace a conserved tryptophan to the cytoplasmic side of NM-R3, accompanied with a slight shift of the halide ion bound to the retinal. After ion release, the inward movements of helix C and helix G and the lateral displacements of the retinal block access to the extracellular side of NM-R3. Anomalous signal data have also been obtained from NM-R3 crystals containing iodide ions. The anomalous density maps provide insight into the halide binding site for ion transfer in NM-R3. SignificanceLight-driven chloride pumps have been identified in various species, including archaea and marine flavobacteria. The function of ion transportation controllable by light is utilized for optogenetics tools in neuroscience. Chloride pumps differ among species, in terms of amino acid homology and structural similarity. Our time-resolved crystallographic studies using X-ray free electron lasers reveal the molecular mechanism of halide ion transfer in a light-driven chloride pump from a marine flavobacterium. Our data indicate a common mechanism in chloride pumping rhodopsins, as compared to previous low temperature trapping studies of chloride pumps. These findings are significant not only for further improvements of optogenetic tools but also for a general understanding of the ion pumping mechanisms of microbial rhodopsins.

molecular biology↗

bioRxiv2021

The OceanDNA MAG catalog contains over 50,000 prokaryotic genomes originated from various marine environments

Marine microorganisms are immensely diverse and play fundamental roles in global geochemical cycling. Recent metagenome-assembled genome studies, with special attention to large-scale projects such as Tara Oceans, have expanded the genomic repertoire of marine microorganisms. However, published marine metagenome data has not been fully explored yet. Here, we collected 2,057 marine metagenomes (>29 Tera bps of sequences) covering various marine environments and developed a new genome reconstruction pipeline. We reconstructed 52,325 qualified genomes composed of 8,466 prokaryotic species-level clusters spanning 59 phyla, including genomes from deep-sea deeper than 1,000 m (n=3,337), low-oxygen zones of <90 mol O2 per kg water (n=7,884), and polar regions (n=7,752). Novelty evaluation using a genome taxonomy database shows that 6,256 species (73.9%) are novel and include genomes of high taxonomic novelty such as new class candidates. These genomes collectively expanded the known phylogenetic diversity of marine prokaryotes by 34.2% and the species representatives cover 26.5 - 42.0% of prokaryote-enriched metagenomes. This genome resource, thoroughly leveraging accumulated metagenomic data, illuminates uncharacterized marine microbial dark matter lineages.

microbiology↗

bioRxiv2020

A cytosine-to-uracil change within the programmed -1 ribosomal frameshift signal of SARS-CoV-2 results in structural similarities with the MERS-CoV signal

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of the ongoing COVID-19 pandemic, like many other viruses, uses programmed ribosomal frameshifting (PRF) to enable synthesis of multiple proteins from its compact genome. In independent analyses, we evaluated the PRF regions of all SARS-CoV-2 sequences available in GenBank and from the Global Initiative on Sharing All Influenza Data for variations. Of the 5,156 and 27,153 sequences analyzed, respectively, the PRF regions were identical in 95.7% and 97.2% of isolates. The most common change from the reference sequence was from C to U at position 13,536, which lies in the three-stemmed pseudoknot known to stimulate frameshifting. With the conversion of the G13493-C13536 Watson-Crick pair to G-U, the SARS-CoV-2 PRF closely resembles its counterpart in the Middle East respiratory syndrome coronavirus. The occurrence of this change increased from 0.5 to 3% during the period of March to May 2020.

genomics↗