Biology subjects

Tomita, M.

Publications and source records attributed to Tomita, M..

15 recordsLinked to original sources

bioRxiv2026

Genome-resolved ecology and evolution of the microbiome enabled by quantitative long-read metagenomics

Standard metagenomics resolves microbial communities only in relative terms and at coarse taxonomic resolution, obscuring how individual strains change in absolute abundance and evolve within a host. We present long-read quantiomics (LRQ), a quantitative metagenomics platform coupling long-read sequencing with plasmid-based internal standards to recover high-quality genomes, including from degraded or low-input stool, and measure absolute, genome-resolved strain abundances. We validate LRQ using large plasmid standards and bacterial spike-ins, then apply it to eight years of dense sampling from an individual with colonic Crohn's disease. LRQ resolves co-resident strains of the same species following opposing trajectories with inflammation. Escherichia coli, long treated as a single pathobiont, separates into two sub-populations with opposing inflammation responses; the inflammation-associated lineage carries an immune-evasion module of virulence-associated metal-acquisition, biofilm, capsule and toxin genes. We observe genome-wide adaptive sweeps on timescales matched to disease incidence. LRQ therefore converts long-read metagenomics from a genome-recovery tool into a quantitative framework providing absolute, strain-level measurement of microbial ecology and evolution.

microbiology↗

bioRxiv2025

Extremely Early Flowering and Large Grain Isogenic Japonica Rice Koshihikari Integrated with Gene e1 and GW2

The extremely early flowering/large-grain isogenic Koshihikari was developed by combining the large-grain allele, GW2, derived from Inochinoichi with the year-round flowering allele, e1, from Kanto 79. We conducted four back crosses with Koshihikari as a recurrent parent by using an extremely early flowering/large-grain e1GW2 homozygote as a non-recurrent parent, which was segregated in B1F2 between Kanto 79 and a large-grain fixed F3 plant in Koshihikari x Inochinoichi. In the BC4F2 population, the e1GW2 homozygous phenotype was selected and fixed in BC4F3 as Kshihikari e1GW2. plants were segregated according to a ratio of 1 extremely early flowering/large-grain e1GW2 : 3 extremely early maturing/small-grain e1gw2 : 3 medium-maturing/large-grain e1GW2 : 9 medium-flowering/small-grain E1gw2 and e1GW2 homozygous isogenic Koshihikari [Koshihiakri e1GW2] was fixed in BC4F3. Whole genome sequencing of Koshihiakri e1GW2 proved that already known 1 deletion in GW2 at 8,147,416 bp on chromosome 2, and an e1 isogenic-specific SNP at 9,090,618 bp, which was 35,213 bp downstream to the 3{square} side of Ghd7 on chromosome 7. RT-qPCR analyses showed that the transcription of Ghd7 was suppressed in Koshihikari e1GW2 than in Koshihikari. The Koshihikari e1GW2 flowered 14 days earlier than Koshihikari and thousand grain weight of Koshihikari e1GW2 (27.8 g) was 18% larger than Koshihikari (23.6 g). We successfully integrated GW2 with e1 for the first time, especially in the genome of a globally produced Japonica leading cultivar Koshihikari. The Koshihikari e1GW2 was registered under plant varietal protection.

genomics↗

bioRxiv2024

Rice novel useful semidwarf gene d60 on chromosome 2 causing pleiotropically gamete abortion

Rice semidwarf gene d60 is inherited according to a unique mode because it causes pleiotropically gamete abortion in the case of coexistence with the gamete lethal gene gal. Namely, F2 progenies of Koshihikari (D60D60galgal, long stem) x Hokuriku 100 (d60d60GalGal, short stem) segregated in the ratio of 1 semidwarf (1 d60d60GalGal):2 tall and quarter sterile (2 D60d60Galgal):6 tall (2 D60d60GalGal:1 D60D60GalGal:2 D60D60Galgal:1 D60D60galgal), which is skewed from the Mendelian 1 semidwarf:3 tall ratio. Firstly, genetic linkage was tested on the basis that the segregation ratios of the phenotypic marker genes linked to d60 do not fit Mendelian ratio. F2 of Koshihikari d60 line (d60d60GalGal) x lines carrying d30 or gh2 on chromosome 2, the segregation ratios of these alleles were deviated from 1:3 but well fitted to 5:4 when d30 and gh2 were closely linked to D60. We then conducted molecular fine mapping of d60 by using DNA polymorphisms in F2 of Koshihikari d60 line x line carrying the indica chromosome 2 segment in Koshihikari. As a result, d60 was tightly linked with RM12970 by a recombination value 0.0 at the region 10.3 Mb away from the distal end of the short arm of chromosome 2. Whole genome sequencing of Koshihikari d60 revealed no SNPs and Indels around the 10.3 Mb region. RT-qPCR for ent-copalyl diphosphate synthase-like gene on 10.3 Mb indicated its transcription was reduced compared to that of Koshihikari.

genetics↗

bioRxiv2024

A semidwarf and late-flowering isogenic Kosihihikari d60Hd16: development, productivity, and regional suitability revealed by correlation-based network analysis.

Breeding rice varieties that are tolerant to weather variability and optimizing cultivation methods for each developed variety are challenging issues for global food problems. In this study, the late-flowering gene Hd16 of Koganebare was introduced into Koshihikari through backcrossing to create Koshihikari Hd16. It was then crossed with Koshihikari d60 to develop an isogenic Koshihikari containing both Hd16 and d60. Productivity tests were conducted in nine prefectures in Japan for two homogeneous rice genotypes, Hd16 (late flowering) and d60Hd16 (short culm and late flowering). By analyzing the relationship between genotype, traits, and accumulation temperature, we reexamined the characteristics of each genotype and inferred the optimal growing areas. Correlation-based network analysis among yield, grain quality, and value of taste and traits showed that quality was positively correlated with panicle length and 1000-grain weight, and yield was strongly positively correlated with 1000-grain weight. d60 genotype was negatively correlated with culm length and lodging degree. These correlations were supported by partial correlation analysis and significant differences compared to the wildtype was identified. Principal component analysis of d60Hd16 revealed that Yamanashi and Ehime, which have longer panicle length and culm length, were suitable in terms of yield and quality, while Shimane, which is warmer and has shorter panicle length and culm length, was suitable in terms of eating quality. Moreover, Koshihikari d60Hd16 could express traits that are less prone to lodging degree while maintaining the same quality and yield as the wild type in cultivation of late-flowering strains. Thus, the d60 and H16 genotypes express stable traits adapted to a wide range of Japanese climatic conditions and growing environments. This study provides fundamental information for promoting new smart agriculture, in which improved varieties are deployed in different regions with different climatic conditions.

plant biology↗

bioRxiv2023

Diversification of Polynucleotide Kinase Clp1 Family Proteins and Their Possible Origins in Eukaryotic Evolution

The Clp1 family proteins, consisting of the Clp1 and Nol9/Grc3 groups, have polynucleotide kinase (PNK) activity at the 5' end of RNA strands and are important enzymes in the processing of some precursor RNAs. However, it remains unclear how this enzyme family diversified in the eukaryotes. We performed a large-scale molecular evolutionary analysis of the full-length genomes of 358 eukaryotic species and identified a group of protist proteins that we consider to be the evolutionary origin of Clp1 family proteins. First, we detected an average of 4.2 Clp1 family genes in members of in the protist phylum Euglenozoa, arising from gene duplication. For example, in Trypanosoma brucei, there are three genes of the Clp1 group and one gene of the Nol9/Grc3 group. In the Clp1 group proteins encoded by these three genes, the C-terminal domains have been replaced by unique characteristics domains, so we designated these proteins Tb-Clp1-t1, Tb-Clp1-t2, and Tb-Clp1-t3. Experimental validation showed that only Tb-Clp1-t2 has PNK activity against RNA strands. In a phylogenetic analysis of the PNK domain, Tb-Clp1-t2 mapped to the earliest position on the tree. Interestingly, Tb-Clp1-t1, for which no PNK activity was detected, was located on the phylogenetic tree near fungal Saccharomyces cerevisiae Clp1, which also lacks PNK activity. The analysis also revealed that in the higher eukaryotes, such as humans and plants, the Clp1 proteins diversified with the creation of isoforms by alternative splicing.

evolutionary biology↗

bioRxiv2022

Molecular evidence of chemical disguise by the socially parasitic spiny ant Polyrhachis lamellidens (Hymenoptera: Formicidae) when invading a host colony

While most ant species establish a colony independently, some socially parasitic ants build the foundation of their colony by invading other ant (host) colonies and utilizing their labour forces. Many socially parasitic ants disguise their cuticular hydrocarbon (CHC) profile, which is also known as nestmate discrimination pheromones, when invading the host colony. Since the strategy of chemical disguise is widespread in socially parasitic ants, elucidating the mechanism of chemical disguise will promote knowledge on the evolutionary history of social parasitism. However, detailed knowledge is still lacking, as the relevant information has only originated from circumstantial evidence, which was obtained from ecological observations. In this study, we investigated the mechanism of chemical disguise in a new queen of a temporary socially parasitic spiny ant (Polyrhachis lamellidens) by measuring its CHC profile, performing a tracing assay with labelled substances, and analysing gene expression levels. First, after rubbing behaviour was observed against the host workers, the CHC profile in P. lamellidens shifted to pronounced peaks that closely resembling that of the host workers. We also observed a reduction in aggressive behaviours by the host ant against P. lamellidens after rubbing behaviour was performed. In addition, P. lamellidens acquired artificially-applied labelling substances from host workers through their rubbing behaviours, while gene expression profiling showed the expression of CHC synthesis-related genes did not change during this behaviour. These results suggest that P. lamellidens directly obtains host CHCs through rubbing behaviour, and these host CHCs enables P. lamellidens to remain disguised during colony invasion.

ecology↗

bioRxiv2022

Features of smaller ribosomes in Candidate Phyla Radiation (CPR) bacteria revealed with a molecular evolutionary analysis

The Candidate Phyla Radiation (CPR) is a large bacterial group consisting mainly of uncultured lineages. They have small cells and small genomes, and often lack ribosomal proteins L1, L9, and/or L30, which are basically ubiquitous in ordinary (non-CPR) bacteria. Here, we comprehensively analyzed the genomic information of CPR bacteria and identified their unique properties. In the distribution of protein lengths in CPR bacteria, the peak was at around 100-150 amino acids, whereas the position of the peak varies in the range of 100-300 amino acids in free-living non-CPR bacteria, and at around 100-200 amino acids in most symbiotic non-CPR bacteria. These results show that CPR bacteria have smaller proteins on average, like symbiotic non-CPR bacteria. We found that ribosomal proteins L28, L29, L32, and L33 are also deleted in CPR bacteria, in a lineage-specific manner. Moreover, the sequences of approximately half of all ribosomal proteins in CPR differ, in part, from those of non-CPR bacteria, with missing regions or specific added region. We also found that several regions of the 16S, 23S, and 5S rRNAs are lacking in CPR bacteria and that the total predicted length of the three rRNAs in CPR bacteria is smaller than that in non-CPR bacteria. The regions missing in the CPR ribosomal proteins and rRNAs are located near the surface of the ribosome, and some are close to one another. These observations suggest that ribosomes are smaller in CPR bacteria than in free-living non-CPR bacteria, with simplified surface structures.

bioinformatics↗

bioRxiv2021

Distinct Expansion of Group II Introns Depends on the Type of Intron-encoded Protein and Genomic Signatures in Prokaryotes

Group II introns (G2Is) are self-splicing ribozymes that have retroelement characteristics in prokaryotes. Although G2Is are considered an important factor in the evolution of prokaryotes, comprehensive analyses of these introns among the tens of thousands of prokaryotic genomes currently available are still limited. Here, we developed a bioinformatic pipeline that systematically collects G2Is and applied it to prokaryotic genomes. We found that in bacteria, 25% (447 of 1,790) of the total representative species had an average of 5.3 G2Is, and in archaea, 9% (28 of 296) of the total representative species had an average of 3.0 G2Is. The greatest number of G2Is per species was 101 in Arthrospira platensis (phylum Cyanobacteriota). A comprehensive sequence analysis of the intron-encoded protein (IEP) in each G2I sequence was conducted and resulted in the addition of three new IEP classes (U1-U3) to the previous classification. This analysis suggested that about 30% of all IEPs are noncanonical IEPs. The number of G2Is per species was defined almost at the phylum level, and the type of IEP was associated as a factor in the G2I increase, i.e. there was an explosive increase in G2Is with bacterial C-type IEPs in the phylum Firmicutes and in G2Is with CL-type IEPs in the phylum Cyanobacteriota. We also systematically analyzed the relationship between genomic signatures and the mechanism of these increases in G2Is. This is the first study to systematically characterize G2Is in the prokaryotic phylogenies.

evolutionary biology↗

bioRxiv2021

Multicomponent nature underlies the extraordinary mechanical properties of spider dragline silk

Dragline silk of golden orb-weaver spiders (Nephilinae) is noted for its unsurpassed toughness, combining extraordinary extensibility and tensile strength, suggesting industrial application as a sustainable biopolymer material. To pinpoint the molecular composition of dragline silk and the roles of its constituents in achieving its mechanical properties, we report a multiomics approach combining high-quality genome sequencing and assembly, silk gland transcriptomics, and dragline silk proteomics of four Nephilinae spiders. We observed the consistent presence of the MaSp3B spidroin unique to this subfamily, as well as several non-spidroin SpiCE proteins. Artificial synthesis and combination of these components in vitro showed that the multicomponent nature of dragline silk, including MaSp3B and SpiCE, along with MaSp1 and MaSp2, is essential to realize the mechanical properties of spider dragline silk.

molecular biology↗

bioRxiv2021

Cinnamon bark extract suppresses metastatic dissemination of cancer cells through inhibition of glycolytic metabolism

Metastasis, a leading contributor to the morbidity of cancer patients, occurs through multiple steps. As each of these steps is promoted by different molecular mechanisms, blocking metastasis needs to target each of these steps. Here we report that cinnamon bark extract (CBE) has a suppressor effect on metastatic dissemination of cancer cells. Though a zebrafish embryo screen which utilizes conserved mechanisms between metastasis and zebrafish gastrulation for identifying anti-metastasis drugs, CBE was identified to interfere with gastrulation progression of zebrafish. A zebrafish xenotransplantation model of metastasis validated that CBE suppressed metastatic dissemination of human cancer cells (MDA-MB-231). Interestingly, quantitative metabolome analyses revealed that CBE-treated MDA-MB-231 cells disrupted the production of glucose 6-phosphate (G6P) and fructose 6-phosphate (F6P), which are intermediate metabolites of glycolytic metabolism. CBE decreased the expression of hexokinase 2 (HK2), which catalyzes G6P production, and pharmacological inhibition of HK2 suppressed cell invasion and migration of MDA-MB-231 cells. Taken together, CBE suppressed metastatic dissemination of human cancer cells by inhibiting glycolytic metabolism.

pharmacology and toxicology↗

bioRxiv2020

A novel Mn-dependent peroxidase contributes to tardigrade anhydrobiosis

Tardigrades are microscopic animals that are capable of tolerating extreme environments by entering a desiccated ametabolic state known as anhydrobiosis. While antioxidative stress genes, antiapoptotic pathways and tardigrade-specific intrinsically disordered proteins have been implicated in the anhydrobiotic machinery, conservation of these mechanisms is not universal within the phylum Tardigrada, suggesting the existence of overlooked components. Here, we show that a novel Mn-dependent peroxidase is an important factor in tardigrade anhydrobiosis. Through comparative time-series transcriptome analysis of Ramazzottius varieornatus specimens exposed to desiccation or ultraviolet light, we first identified several novel gene families without similarity to existing sequences that are induced rapidly after stress exposure. Among these, a single gene family with multiple orthologs that is highly conserved within the phylum Tardigrada and enhances oxidative stress tolerance when expressed in human cells was identified. Crystallographic study of this protein suggested Zn or Mn binding at the active site, and we further confirmed that this protein has Mn-dependent peroxidase activity in vitro. Our results demonstrated novel mechanisms for coping with oxidative stress that may be a fundamental mechanism of anhydrobiosis in tardigrades. Furthermore, localization of these sets of proteins in the Golgi apparatus suggests an indispensable role of the Golgi stress response in desiccation tolerance.

molecular biology↗

bioRxiv2020

Multiomics study of a heterotardigrade, Echinisicus testudo, suggests convergent evolution of anhydrobiosis-related proteins in Tardigrada

Many limno-terrestrial tardigrades can enter an ametabolic state upon desiccation, in which the animals can withstand extreme environments. To date, studies of the molecular mechanism have predominantly investigated the class Eutardigrada, and that in the Heterotardigrada, remains elusive. To this end, we report a multiomics study of the heterotardigrade Echiniscus testudo, which is one of the most desiccation-tolerant species. None of the previously identified tardigrade-specific anhydrobiosis-related genes was conserved, while the loss and expansion of existing pathways were partly shared. Furthermore, we identified two families of novel abundant heat-soluble proteins and the proteins exhibited structural changes from random coil to -helix as the water content decreased in vitro. These characteristics are analogous to those of anhydrobiosis-related protein in eutardigrades, while there is no conservation at the sequence level. Our results suggest that Heterotardigrada have partly shared but distinct anhydrobiosis machinery compared with Eutardigrada, possibly due to convergent evolution within Tardigrada.

genomics↗

bioRxiv2019

A single CRISPR base editor to induce simultaneous C-to-T and A-to-G mutations

While several Cas9-derived base editors have been developed to induce either C-to-T or A-to-G mutation at target genomic sites, the possible genome editing space when using the current base editors remains limited. Here, we present a novel base editor, Target-ACE, which integrates the abilities of both of the previously developed C-to-T and A-to-G base editors by fusing an activation-induced cytidine deaminase (AID) and an engineered tRNA adenosine deaminase (TadA) to a catalytically impaired Streptococcus pyogenes Cas9. In mammalian cells, Target-ACE enabled heterologous editing of multiple bases in a small sequence window of target sites with increased efficiency compared with a mixture of two relevant base editor enzymes, each of which may block the same target DNA molecule from the other. Furthermore, by modeling editing patterns using deep sequencing data, the editing spectra of Target-ACE and other base editors were simulated across the human genome, demonstrating the highest potency of Target-ACE to edit amino acid coding patterns. Taking these findings together, Target-ACE is a new tool that broadens the capabilities for base editing for various applications.

bioengineering↗

bioRxiv2018

Fast and global detection of periodic sequence repeats in large genomic resources

Periodically repeating DNA and protein elements are involved in various important biological events including genomic evolution, gene regulation, protein complex formation, and immunity. Notably, the currently used genome editing tools such as ZFNs, TALENs, and CRISPRs are also all associated with periodically repeating biomolecules of natural organisms. Despite the biological importance of periodically repeating sequences and the expectation that new genome editing modules could be discovered from such periodical repeats, no software that globally detects such structured elements in large genomic resources in a high-throughput and unsupervised manner has been developed. Here, we developed new software, SPADE (Search for Patterned DNA Elements), that exhaustively explores periodic DNA and protein repeats from large-scale genomic datasets based on k-mer periodicity evaluation. SPADE precisely captured reported genome-editing-associated sequences and other protein families involving repeating domains with significantly better performance than the other software designed for limited sets of repetitive biomolecular sequences.

bioinformatics↗

bioRxiv2017

Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus

Tardigrada, a phylum of meiofaunal organisms, have been at the center of discussions of the evolution of Metazoa, the biology of survival in extreme environments, and the role of horizontal gene transfer in animal evolution. Tardigrada are placed as sisters to Arthropoda and Onychophora (velvet worms) in the superphylum Ecdysozoa by morphological analyses, but many molecular phylogenies fail to recover this relationship. This tension between molecular and morphological understanding may be very revealing of the mode and patterns of evolution of major groups. Similar to bdelloid rotifers, nematodes and other animals of the water film, limno-terrestrial tardigrades display extreme cryptobiotic abilities, including anhydrobiosis and cryobiosis. These extremophile behaviors challenge understanding of normal, aqueous physiology: how does a multicellular organism avoid lethal cellular collapse in the absence of liquid water? Meiofaunal species have been reported to have elevated levels of HGT events, but how important this is in evolution, and in particular in the evolution of extremophile physiology, is unclear. To address these questions, we resequenced and reassembled the genome of Hypsibius dujardini, a limno-terrestrial tardigrade that can undergo anhydrobiosis only after extensive pre-exposure to drying conditions, and compared it to the genome of Ramazzottius varieornatus, a related species with tolerance to rapid desiccation. The two species had contrasting gene expression responses to anhydrobiosis, with major transcriptional change in H. dujardini but limited regulation in R. varieornatus. We identified few horizontally transferred genes, but some of these were shown to be involved in entry into anhydrobiosis. Whole-genome molecular phylogenies supported a Tardigrada+Nematoda relationship over Tardigrada+Arthropoda, but rare genomic changes tended to support Tardigrada+Arthropoda.

genomics↗