Biology subjects

Onishi, M.

Publications and source records attributed to Onishi, M..

At least 19 recordsLinked to original sources

bioRxiv2026

MillionTrees: A global benchmark for tree detection across geography, sensor, and annotation geometry

Airborne tree monitoring using remotely sensed data, combined with the growth of computer vision models for object detection and segmentation, can facilitate broad scale assessment of tree health, ecology and ecosystem function. However, datasets for airborne tree detection have been largely limited to a single geography, resolution, or annotation approach, making it difficult to develop general models and benchmark their utility for broad applications. We compile existing and newly published annotation datasets to create a comprehensive dataset for training and evaluating airborne tree detection in RGB imagery. The MillionTrees dataset has over a million individual trees from a broad range of forest types, tree species, and geographic locations. In addition, it has six million weakly supervised annotations from a range of sources including airborne LiDAR and photogrammetry, arborist surveys, and simulated landscapes. An evaluation standard is provided to facilitate rapid model development. We benchmark several existing tree detection algorithms and demonstrate that while current open-source models do not generalize across the diverse datasets in the benchmark, training on MillionTrees improves both within-domain and out-of-domain performance. Held-out validation datasets using ground truth derived from terrestrial LiDAR paired with overhead RGB show that overfitting to test data is common and hyperparameter tuning is an underappreciated challenge towards a global zero shot tree detection method. We discuss the limitations of the currently available data for airborne RGB tree detection, how to create more robust evaluation data and the need for better understanding of the uncertainty and utility of tree detection from airborne remote sensing.

ecology↗

bioRxiv2026

Crown-based growth strategies explain the distribution and co-occurrence of tree functional groups along environmental gradients

Elucidating interspecific variation in growth strategies across environments is critical for understanding tree diversity and distribution. However, a systematic analysis across diverse forests remains scarce due to limited large-tree crown measurements. We analysed 3,814 trees from 107 canopy species in 23 natural forests using forest census data and unmanned aerial vehicle. Relative growth rate (growth rate/biomass) was decomposed into growing space efficiency (growth rate/crown area) and crown area ratio (crown area/biomass). Relative growth rates were similar among functional groups (deciduous broadleaf, evergreen broadleaf, evergreen conifer), but their underlying components differed. Deciduous trees exhibited 34-43% higher crown area ratio but 24-27% lower growing space efficiency than evergreen broadleaf and conifer trees. Across environments, growing space efficiency correlated positively with mean annual temperature, likely from extended growing seasons while crown area ratio correlated negatively, particularly in deciduous species. Snow loading limited crown area ratio in evergreen species, while deciduous achieved higher values through avoiding snow loads. Correlation between crown area ratio and specific leaf area indicated a coordinated strategy between crowns and leaves. Different functional groups achieve comparable growth efficiency either through crown expansion or biomass production, explaining their distinct distribution as well as co-occurrence across broad environments.

ecology↗

bioRxiv2026

Dual-targeted NADK2 Links Mitochondrial Redox Homeostasis to Carbon Partitioning and Heterotrophic Growth in Chlamydomonas reinhardtii

NAD kinases (NADKs) can modulate NADP(H) levels across shifting environmental conditions. In Chlamydomonas reinhardtii, we localized CreNADK1 to the chloroplast, CreNADK3 to the cytoplasm, and CreNADK2 to both the chloroplast and mitochondria. Importantly, during mixotrophic (light + acetate) and photoautotrophic (light) growth, most CreNADK2 is chloroplast localized whereas an increased proportion resides in mitochondria when the cells are grown heterotrophically (dark + acetate). In Crenadk2 mutants, a diminished ability to synthesize mitochondrial NADP(H) inhibits the TCA cycle and markedly retards heterotrophic growth. In the light, photosynthesis becomes the primary energy source, and the presence of chloroplastic CreNADK1 enables near-normal growth in mutant cells, with inhibition of TCA cycle activity partially ameliorated via rerouting of acetate metabolism through the glyoxylate shunt, bypassing the TCA cycle and diminishing mitochondrial ROS production. These findings demonstrate spatial plasticity of NAD(H)Ks and the implementation of bypass metabolism to enable growth of Crenadk2 mutants.

cell biology↗

bioRxiv2026

Testing Reversibility of Endosymbiotic Gene Transfer between Chloroplast and Nucleus

Most proteins targeted to the organelles of endosymbiotic origin are encoded in the nuclear genome, placing them under the regulatory dominance of the nucleus. For photosynthetic eukaryotes, nuclear-encoded chloroplast proteins arise via two routes: First, genes of cyanobacterial origin were relocated to the nucleus through endosymbiotic gene transfer (EGT). Second, proteins of eukaryotic origin emerged to support chloroplast function and structure. These proteins are reimported into the chloroplast via an import machinery. Reversing the transfer of such genes from the nucleus to the chloroplast genome may offer insights into chloroplast regulation and evolution. In this study, we established a highly efficient and accessible electroporation protocol for chloroplast transformation in the green alga Chlamydomonas reinhardtii, and used it to reverse-transfer two nuclear-encoded genes encoding proteins arising via the two routes described above: the cyanobacteria-derived chloroplast division protein FtsZ1 and the Rubisco-linker EPYC1 of eukaryotic origin. Regardless of origin, both chloroplast-encoded FtsZ1 and EPYC1 showed proper localization and functionality comparable to their nuclear-encoded counterparts. Together, our study provides a robust protocol for chloroplast transformation, a platform for investigating the evolutionary drivers of EGT, and a foundation for advancing chloroplast bioengineering. SIGNIFICANCE STATEMENTO_LIEndosymbiotic gene transfer has resulted in the mass migration of genes from the chloroplast genome to the nuclear genome. Reversing the gene transfer could reveal the evolutionary significance of genome partitioning. C_LIO_LIUsing the green alga Chlamydomonas reinhardtii, this study developed an efficient, electroporation-based protocol for chloroplast transformation. Relocating the genes encoding two chloroplast-targeted proteins, FTSZ1 and EPYC1, to the chloroplast genome showed that the proteins maintained normal localization and function. C_LIO_LIThe established transformation protocol facilitates systematic testing of reverse gene transfer to elucidate the potential evolutionary advantages of genome partitioning and opens new avenues for chloroplast bioengineering. C_LI

cell biology↗

bioRxiv2026

Septin-mediated coupling of protein import and division during chloroplast evolution

Chloroplast biogenesis depends on both protein import and organelle division, yet how their coordination emerged during evolution remains unclear. Here, we show that the single septin SEP1 links these pathways in the green alga Chlamydomonas reinhardtii. SEP1 forms a filamentous network on the chloroplast envelope during interphase and reorganizes into a ring at the chloroplast division site during cytokinesis. Loss of SEP1 selectively impairs import of chloroplast-division proteins and causes mispositioning of the division ring, without impairing bulk chloroplast protein import. SEP1 physically associates with outer-envelope TOC GTPases through evolutionarily related GTPase domains. Phylogenetic analysis places TOC GTPases within an algal septin-derived clade, and heterologous expression of SEP1 in land plants, in which septins are absent, shows conservation of its chloroplast targeting and TOC binding. Together, these findings identify septins as coordinators of plastid protein import and division and suggest that this coupling emerged early in chloroplast evolution.

cell biology↗

bioRxiv2025

M1C is a druggable target for NSCLC KRAS G12C mutant tumors resistant to KRAS inhibitors

Treatment of NSCLC KRAS G12C mutant tumors with the allele-selective sotorasib inhibitor is invariably associated with acquired resistance. The MUC1-encoded oncogenic M1C protein is necessary for self-renewal of NSCLC KRAS mutant cells. We report that treatment of NSCLC KRAS G12C cells with sotorasib induces M1C expression by a STAT1-dependent pathway. In turn, M1C drives sotorasib resistance by NF-{kappa}B-mediated induction of the epithelial-mesenchymal transition (EMT). Targeting M1C(R)NF-{kappa}B signaling (i) suppresses EMT, and (ii) reverses sotorasib resistance. Of translational relevance, treatment with a M1C antibody-drug conjugate (ADC) is effective against sotorasib-resistant NSCLC KRAS G12C cell line and patient-derived tumor xenografts. Clinically, targeted treatment of patients with NSCLC KRAS G12C tumors overexpressing MUC1 associates with decreases in overall survival. These findings identify M1C as a key effector of sotorasib resistance and as a target for treatment of patients with refractory NSCLC KRAS G12C mutant tumors.

cancer biology↗

bioRxiv2025

Tubulin Acetylation Deficiency Promotes Axonemal Turnover and Increases Cytoplasmic Microtubules

Tubulin post-translational modifications regulate microtubule dynamics; among these, -tubulin acetylation has been linked to microtubule stability. We generated a Chlamydomonas mutant lacking the acetyltransferase TAT1, which completely abolished -tubulin K40 acetylation. Surprisingly, the lengths of normally acetylated structures, axonemes and rootlets, were largely unaffected. TAT1 localized to the flagellar tip, suggesting that it is the primary site of acetylation. Loss of acetylation caused an increase in axonemal tubulin turnover, as revealed by dikaryon-fusion assays. Unexpectedly, the tat1 mutant displayed an increased number of dynamic cytoplasmic microtubules and could regenerate long flagella after amputation, even when protein synthesis was inhibited. Despite these cytoskeletal changes, steady-state flagellar length, cell growth, and cell division remained essentially normal. These findings suggest that acetylation modulates microtubule behavior by regulating axonemal tubulin turnover and cytoplasmic microtubule dynamics, while cellular morphology is buffered against variations in microtubule content.

cell biology↗

bioRxiv2025

Mitotic entry is controlled by the plant-specific phosphatase BSL1 and cyclin-dependent kinase B

Cell cycle regulation is well understood in opisthokonts (fungi and metazoans) but not in plants and Apicomplexa, as some cell cycle regulators are not conserved1-3. In opisthokonts, cell cycle progression requires dephosphorylation of cyclin-dependent kinase (CDK) by the CDC25 phosphatase4. Plants have no CDC25, and thus their mechanisms of cell cycle regulation remain elusive1,5,6. Here, we show that the BSL1 phosphatase dephosphorylates CDKB1 to promote mitotic entry in Chlamydomonas. Mutations of BSL1 or CDKB1 block mitotic entry after DNA replication. BSL1 shows dynamic localization through the cell cycle at the basal bodies, spindle poles, and cleavage furrow. CDKB1 is hyperphosphorylated at T14 and Y15 residues in the bsl1 mutant and in wild-type cells treated with DNA replication inhibitors. BSL1 binds to CDKB1 and dephosphorylates CDKB1 pT14/pY15 in vitro. Phospho-mimicking mutations of T14/Y15 inactivate CDKB1 function, whereas phospho-blocking mutations cause sensitivity to DNA replication inhibitors, which delay cytokinesis in wild-type cells more than cells expressing unphosphorylatable mutant CDKB1. These results indicate that CDKB1 T14/Y15 is phosphorylated to block mitotic entry before DNA replication is complete, and BSL1 dephosphorylates CDKB1 to promote mitosis. Our study demonstrates that BSL1, a phosphatase conserved in plants and Apicomplexa but absent in fungi and animals, is a CDKB1-activating mitosis-promoting factor that has evolved additional signaling functions in receptor kinase pathways in higher plants. One-Sentence SummaryBSL1 is a mitosis-promoting phosphatase that activates CDKB1 in plants.

plant biology↗

bioRxiv2024

Imaging-based screen identifies novel natural compounds that perturb cell and chloroplast division in Chlamydomonas reinhardtii

Successful cell division requires faithful division and segregation of organelles into daughter cells. The unicellular alga Chlamydomonas reinhardtii has a single, large chloroplast whose division is spatiotemporally coordinated with furrowing. Cytoskeletal structures form in the same plane at the midzone of the dividing chloroplast (FtsZ) and the cell (microtubules), but how these structures are coordinated is not understood. Previous work showed that loss of F-actin blocks chloroplast division but not furrow ingression, suggesting that pharmacological perturbations can disorganize these events. In this study, we developed an imaging platform to screen natural compounds that perturb cell division while monitoring FtsZ and microtubules and identified 70 unique compounds. One compound, curcumin, has been proposed to bind to both FtsZ and tubulin proteins in bacteria and eukaryotes, respectively. In C. reinhardtii, where both targets coexist and are involved in cell division, curcumin at a specific dose range caused a severe disruption of the FtsZ ring in chloroplast while leaving the furrow-associated microtubule structures largely intact. Time-lapse imaging showed that loss of FtsZ and chloroplast division failure delayed the completion of furrowing but not the initiation, suggesting that the chloroplast-division checkpoint proposed in other algae requires FtsZ or is absent altogether in C. reinhardtii. SIGNIFICANCE STATEMENTO_LISuccessful cell division requires the coordination of both organelle inheritance and cytokinesis. The unicellular alga Chlamydomonas reinhardtii, which spatiotemporally coordinates the division of its chloroplast with cytokinesis, is an excellent model to study the regulation. C_LIO_LIWe screened libraries of natural compounds for perturbations of cell and/or chloroplast division, identifying 70 unique chemicals. By time-lapse microscopy using one of the hits, curcumin, we demonstrate that although chloroplast division failures delay the completion of cytokinesis, it does not impair initiation. C_LIO_LIThese findings suggest that the chloroplast-division checkpoint proposed in other algae requires FtsZ or is absent altogether in C. reinhardtii. C_LI

cell biology↗

bioRxiv2024

Species interactions and food-web context drive temperature-dependent prey evolution

Global warming is reshaping food webs globally. Rapid evolution has been proposed as a buffer against climate change, but how simultaneous shifts in biotic and abiotic environments may influence evolution is unknown. Using experimental evolution and mathematical modeling in microbial food webs of prey algae and ciliate predators, we tested 1) how temperature affects prey evolution and 2) how the food-web context--i.e., predator identity, abundance, and competition among predators-- mediates prey evolutionary dynamics. We found that temperature alone does not drive prey evolution unless predators are present, and food-web context determines ensuing evolutionary dynamics. These seemingly complex evolutionary responses are predictable from the joint effects of temperature-dependent, predator-specific predation rates, and the emergence of temperature-dependent prey plasticity. We reveal that evolutionary outcomes under warming are shaped by the broader food web context of species, suggesting that the same species may exhibit different eco-evolutionary responses in different food webs under novel climates. SIGNIFICANCEPredicting how species evolve under climate change is critical for understanding future changes in food webs. Evolutionary responses have long been known to be driven by environmental change--like temperature--but whether and how ecological interactions influence this process is unknown. Using experimental evolution and mathematical modeling, we show that temperature alone does not drive prey evolution. Instead, the broader food webs context--predator identity, abundance, and competition--mediates how species evolve under warming. Additionally, we demonstrate that prey evolution depends on temperature-dependent predator-specific predation rates and prey plasticity. Our findings highlight that the same species may evolve differently within different food webs, urging the need to integrate ecological interactions when forecasting evolutionary responses to climate change.

ecology↗

bioRxiv2024

Rapid adaptive evolution of microbial thermal performance curves

Microbial respiration is a key biotic driver of climate change. Warming boosts microbial population growth, which increases biomass and respiration. This feedback might be disrupted by adaptation in thermal performance curves (TPCs) -whose shape describes how temperature drives growth. In this study, we uncover substantial genetic variation (G) in microbial intrinsic population growth rates (r), demonstrate a causal link between G variation in r and G variation in TPC shape, and show how this variation constrains r-TPC shape evolution along specific evolutionary paths across temperatures. We also uncover Gene-by-Environment (G x E) variation in r, which results in specific signatures in TPC shape and predictable temperature-dependent rapid TPC evolution but also lower G, which could reduce future evolutionary potential. Overall, we show how temperature-dependent evolution in a linchpin of global ecosystem function--microbial TPC shape--is determined by a combination of heritable and non-heritable variation in intrinsic growth rates.

ecology↗

bioRxiv2024

ER-associated degradation by Doa10 restrains mitophagy in yeast

Degradation of defective or superfluous mitochondria via mitophagy, a specialized form of selective autophagy, is important for maintaining mitochondrial quality and quantity. In yeast, the pro-mitophagic factor Atg32 is transcriptionally upregulated upon oxidative stress and anchored to the mitochondrial surface, where it acts as a molecular signal to initiate efficient degradation of mitochondria. However, how the protein levels of Atg32 are regulated post-translationally remains enigmatic. Here we show that the endoplasmic reticulum (ER) serves as a hub to govern Atg32 protein turnover. We found that the ER-associated degradation (ERAD) E3 ligase Doa10 interacts with Atg32, leading to its degradation by the proteasome. Furthermore, we show that Atg32 is destined for the ER in a manner dependent on the GET (guided entry of tail-anchored proteins) pathway, which mediates the delivery of tail-anchored (TA) proteins to the ER where Atg32 is potentially recognized by Doa10. Notably, Doa10 deficiency increased Atg32 levels and enhanced mitophagy under respiratory conditions, thus determining that ERAD serves as a brake on mitophagy.

cell biology↗

bioRxiv2024

The Evolutionary Origins and Ancestral Features of Septins

Septins are a family of membrane-associated cytoskeletal GTPases that play crucial roles in various cellular processes, such as cell division, phagocytosis, and organelle fission. Despite their importance, the evolutionary origins and ancestral function of septins remain unclear. In opisthokonts, septins form five distinct groups of orthologs, with subunits from multiple groups assembling into heteropolymers, thus supporting their diverse molecular functions. Recent studies have revealed that septins are also conserved in algae and protists, indicating an ancient origin from the last eukaryotic common ancestor. However, the phylogenetic relationships among septins across eukaryotes remained unclear. Here, we expanded the list of non-opisthokont septins, including previously unrecognized septins from rhodophyte red algae and glaucophyte algae. Constructing a rooted phylogenetic tree of 254 total septins, we observed a bifurcation between the major non-opisthokont and opisthokont septin clades. Within the non-opisthokont septins, we identified three major subclades: Group 6 representing chlorophyte green algae (6A mostly for species with single septins, 6B for species with multiple septins), Group 7 representing algae in chlorophytes, heterokonts, haptophytes, chrysophytes, and rhodophytes, and Group 8 representing ciliates. Glaucophyte and some ciliate septins formed orphan lineages in-between all other septins and the outgroup. Combining ancestral-sequence reconstruction and AlphaFold predictions, we tracked the structural evolution of septins across eukaryotes. In the GTPase domain, we identified a conserved GAP-like arginine finger within the G-interface of at least one septin in most algal and ciliate species. This residue is required for homodimerization of the single Chlamydomonas septin, and its loss coincided with septin duplication events in various lineages. The loss of the arginine finger is often accompanied by the emergence of the 0 helix, a known NC-interface interaction motif, potentially signifying the diversification of septin-septin interaction mechanisms from homo-dimerization to hetero-oligomerization. Lastly, we found amphipathic helices in all septin groups, suggesting that curvature-sensing is an ancestral trait of septin proteins. Coiled-coil domains were also broadly distributed, while transmembrane domains were found in some septins in Group 6A and 7. In summary, this study advances our understanding of septin distribution and phylogenetic groupings, shedding light on their ancestral features, potential function, and early evolution.

cell biology↗

bioRxiv2023

Chloroplast Methyltransferase Homolog RMT2 is Involved in Photosystem I Biogenesis

Oxygen (O2), a dominant element in the atmosphere and essential for most life on Earth, is produced by the photosynthetic oxidation of water. However, metabolic activity can cause accumulation of reactive O2 species (ROS) and severe cell damage. To identify and characterize mechanisms enabling cells to cope with ROS, we performed a high-throughput O2 sensitivity screen on a genome-wide insertional mutant library of the unicellular alga Chlamydomonas reinhardtii. This screen led to identification of a gene encoding a protein designated Rubisco methyltransferase 2 (RMT2). Although homologous to methyltransferases, RMT2 has not been experimentally demonstrated to have methyltransferase activity. Furthermore, the rmt2 mutant was not compromised for Rubisco (first enzyme of Calvin-Benson Cycle) levels but did exhibit a marked decrease in accumulation/activity of photosystem I (PSI), which causes light sensitivity, with much less of an impact on other photosynthetic complexes. This mutant also shows increased accumulation of Ycf3 and Ycf4, proteins critical for PSI assembly. Rescue of the mutant phenotype with a wild-type (WT) copy of RMT2 fused to the mNeonGreen fluorophore indicates that the protein localizes to the chloroplast and appears to be enriched in/around the pyrenoid, an intrachloroplast compartment present in many algae that is packed with Rubisco and potentially hypoxic. These results indicate that RMT2 serves an important role in PSI biogenesis which, although still speculative, may be enriched around or within the pyrenoid. Significance StatementA high-throughput genetic screen was used to identify O2 sensitive mutants of Chlamydomonas reinhardtii (Chlamydomonas throughout) that experience elevated oxidative stress in the light relative to WT cells. Identification of genes altered in these mutants offers opportunities to discover activities that a) protect photosynthetic cells from oxidative damage, b) participate in rapid assembly of photosynthetic complexes, which would limit accessibility of intermediates to O2, and/or c) facilitate repair of damaged cellular complexes. A mutant from this screen disrupted for RMT2, originally described as encoding a Rubisco methyltransferase, was defective for PSI biogenesis. Additionally, RMT2 appears to be enriched in/around the pyrenoid, a chloroplast localized compartment harboring much of the Chlamydomonas Rubisco, raising the possibility that this compartment plays a role in PSI biogenesis.

plant biology↗

bioRxiv2023

A novel vaccine strategy using quick and easy conversion of bacterial pathogens to unnatural amino acid-auxotrophic suicide derivatives

We propose a novel strategy for quick and easy preparation of suicide live vaccine candidates against bacterial pathogens. This method requires only the transformation of one or more plasmids carrying genes encoding for two types of biological devices, an unnatural amino acid (uAA) incorporation system and toxin-antitoxin systems in which translation of the antitoxins requires the uAA incorporation. Escherichia coli BL21-AI laboratory strains carrying the plasmids were viable in the presence of the uAA, whereas the free toxins killed these strains after removal of the uAA. The survival time after uAA removal could be controlled by the choice of uAA incorporation system and toxin-antitoxin systems. Multilayered toxin-antitoxin systems suppressed escape frequency to less than 1 escape per 109 generations in the best case. This conditional suicide system also worked in Salmonella enterica and E. coli clinical isolates. The S. enterica vaccine strains were attenuated with a >105-fold lethal dose. Serum IgG response and protection against the parental pathogenic strain were confirmed. In addition, the live E. coli vaccine strain was significantly more immunogenic and provided greater protection than a formalin-inactivated vaccine. The live E. coli vaccine was not detected after inoculation, presumably because the uAA is not present in the host animals or in the natural environment. These results suggest that this strategy provides a novel way to rapidly produce safe and highly immunogenic live bacterial vaccine candidates. SignificanceLive vaccines are the oldest vaccines with a history of more than 200 years. Due to their strong immunogenicity, live vaccines are still an important category of vaccines today. However, the development of live vaccines has been challenging due to the difficulties in achieving a balance between safety and immunogenicity. In recent decades, the frequent emergence of various new and old pathogens at risk of causing pandemics has highlighted the need for rapid vaccine development processes. We have pioneered the use of unnatural amino acids to control gene expression and to conditionally kill host bacteria as a biological containment system. This report highlights a quick and easy conversion of bacterial pathogens into live vaccine candidates using this containment system.

microbiology↗

bioRxiv2022

Murine breast cancers disorganize the liver transcriptome in zonated manners

The spatially organized gene expression program within the liver specifies hepatocyte functions according to their relative distances to the bloodstream (i.e., zonation), contributing to liver homeostasis. Despite the knowledge that solid cancers remotely disrupt liver homeostasis, it remains unexplored whether solid cancers affect liver zonation. Here, using spatial transcriptomics, we thoroughly investigate the abundance and zonation of hepatic genes in cancer-bearing mice. We find that breast cancers affect liver zonation in various distinct manners depending on biological pathways. Aspartate metabolism and triglyceride catabolic processes retain relatively intact zonation patterns, but the zonation of xenobiotic catabolic process genes exhibits a strong disruption. The acute phase response is induced in zonated manners. Furthermore, we demonstrate that breast cancers activate innate immune cells in particular neutrophils in distinct zonated manners, rather than in a uniform fashion within the liver. Collectively, breast cancers disorganize hepatic transcriptomes in zonated manners, thereby disrupting zonated functions of the liver.

cancer biology↗

bioRxiv2022

Alternative proteoforms and proteoform-dependent assemblies in humans and plants

Variability of proteins at the sequence level creates an enormous potential for proteome complexity. Exploring the depths and limits of this complexity is an ongoing goal in biology. Here, we systematically survey human and plant high-throughput bottom-up native proteomics data for protein truncation variants, where substantial regions of the full-length protein are missing from an observed protein product. In humans, Arabidopsis, and the green alga Chlamydomonas, approximately one percent of observed proteins show a short form, which we can assign by comparison to RNA isoforms as either likely deriving from transcript-directed processes or limited proteolysis. While some detected protein fragments align with known splice forms and protein cleavage events, multiple examples are previously undescribed, such as our observation of fibrocystin proteolysis and nuclear translocation in a green alga. We find that truncations occur almost entirely between structured protein domains, even when short forms are derived from transcript variants. Intriguingly, multiple endogenous protein truncations of phase-separating translational proteins resemble cleaved proteoforms produced by enteroviruses during infection. Some truncated proteins are also observed in both humans and plants, suggesting that they date to the last eukaryotic common ancestor. Finally, we describe novel proteoform-specific protein complexes, where loss of a domain may accompany complex formation.

systems biology↗

bioRxiv2021

Intensive Single Cell Analysis Reveals Immune Cell Diversity among Healthy Individuals

It is believed that immune responses are different between individuals and at different times. In addition, personal health histories and unique environmental conditions should collectively determine the present state of immune cells. However, the cellular and molecular system mechanisms underlying such heterogeneity remain largely elusive. In this study, we conducted a systematic time-lapse single-cell analysis, using 171 single-cell libraries and 30 mass cytometry datasets intensively for seven healthy individuals. We found substantial diversity in immune cell populations and their gene expression patterns between different individuals. These patterns showed daily fluctuations even within the same individual spending a usual life. Similar diversities were also observed for the T cell receptor and B cell receptor repertoires. Detailed immune cell profiles at healthy statuses should give an essential background information to understand their immune responses, when the individual is exposed to various environmental conditions. To demonstrate this idea, we conducted the similar analysis for the same individuals on the vaccination of Influenza and SARS-CoV-2, since the date and the dose of the antigens are well-defined in these cases. In fact, we found that the distinct responses to vaccines between individuals, althougth key responses are common. Single cell immune cell profile data should make fundamental data resource to understand variable immune responses, which are unique to each individual.

genomics↗