Updated on 2024/07/18

写真a

 
MINETA, Katsuhiko
 
Affiliation
Research Council (Research Organization), Research Organization for Nano & Life Innovation
Job title
Senior Researcher(Professor)

Research Experience

  • 2023.01
    -
    Now

    AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory   Visiting Researcher

  • 2022.09
    -
    Now

    Marine open innovation institute   Deputy director

  • 2022.07
    -
    Now

    Waseda University   Research Organization for Nano & Life Innovation   Senior Researcher/Professor

  • 2018.11
    -
    Now

    National Center for Global Health and Medicine   Adjunctive Research Fellow

  • 2014.06
    -
    2022.06

    King Abdullah University of Science and Technology   Senior Research Scientist/Principal Research Scientist

  • 2004.04
    -
    2014.05

    Hokkaido University   Graduate School of Information Science and Technology   Associate Professor

  • 2003.08
    -
    2004.03

    University of Chicago   Research Associate

  • 2002.04
    -
    2003.06

    JST   Post doctral scientist

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Education Background

  • 1999.04
    -
    2002.03

    Graduate University of Advanced Studies   School of Life Science   Department of Genetics  

  • 1997.04
    -
    1999.03

    University of Tokyo   Graduate School of Agricultural and Life Sciences   Department of Applied Agricultural Chemistry  

  • 1993.04
    -
    1997.03

    University of Tokyo   Faculty of Agriculture  

Professional Memberships

  •  
     
     

    THE MOLECULAR BIOLOGY SOCIETY OF JAPAN

  •  
     
     

    SOCIETY OF EVOLUTIONARY STUDIES, JAPAN

  •  
     
     

    THE GENETICS SOCIETY OF JAPAN

  •  
     
     

    Japanese Society for Marine Biotechnology

  •  
     
     

    Society for Biotechnology, Japan

  •  
     
     

    The Society for Molecular Biology and Evolution

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Research Areas

  • Genome biology / Genetics / Evolutionary biology

Research Interests

  • environmental genome

  • Population genomics

  • metagenome

  • 分子進化

  • 情報生物学

  • データベース

  • 感覚

  • 味覚

  • 聴覚

  • 脳・神経系

  • Marine science

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Papers

  • Comparative single-cell genomics of Atribacterota JS1 in the Japan Trench hadal sedimentary biosphere

    Kana Jitsuno, Tatsuhiko Hoshino, Yohei Nishikawa, Masato Kogawa, Katsuhiko Mineta, Michael Strasser, Ken Ikehara, Jeremy Everest, Lena Maeda, Fumio Inagaki, Haruko Takeyama, Piero Bellanova, Morgane Brunet, Zhirong Cai, Antonio Cattaneo, Katharina Hochmuth, Kanhsi Hsiung, Takashi Ishizawa, Takuya Itaki, Kana Jitsuno, Joel Johnson, Toshiya Kanamatsu, Myra Keep, Arata Kioka, Christian Maerz, Cecilia McHugh, Aaron Micallef, Luo Min, Dhananjai Pandey, Jean Noel Proust, Troy Rasbury, Natascha Riedinger, Rui Bao, Yasufumi Satoguchi, Derek Sawyer, Chloe Seibert, Maxwell Silver, Susanne Straub, Joonas Virtasalo, Yonghong Wang, Ting-Wei Wu, Sarah Zellers, Martin Kölling, Jyh-Jaan Steven Huang, Yoshitaka Nagahashi

    mSphere    2024.01  [Refereed]

     View Summary

    ABSTRACT

    Deep-sea and subseafloor sedimentary environments host heterotrophic microbial communities that contribute to Earth’s carbon cycling. However, the potential metabolic functions of individual microorganisms and their biogeographical distributions in hadal ocean sediments remain largely unexplored. In this study, we conducted single-cell genome sequencing on sediment samples collected from six sites (7,445–8,023 m water depth) along an approximately 500 km transect of the Japan Trench during the International Ocean Discovery Program Expedition 386. A total of 1,886 single-cell amplified genomes (SAGs) were obtained, offering comprehensive genetic insights into sedimentary microbial communities in surface sediments (<1 m depth) above the sulfate-methane transition zone along the Japan Trench. Our genome data set included 269 SAGs from Atribacterota JS1, the predominant bacterial clade in these hadal environments. Phylogenetic analysis classified SAGs into nine distinct phylotypes, whereas metagenome-assembled genomes were categorized into only two phylotypes, advancing JS1 diversity coverage through a single cell-based approach. Comparative genomic analysis of JS1 lineages from different habitats revealed frequent detection of genes related to organic carbon utilization, such as extracellular enzymes like clostripain and α-amylase, and ABC transporters of oligopeptide from Japan Trench members. Furthermore, specific JS1 phylotypes exhibited a strong correlation with in situ methane concentrations and contained genes involved in glycine betaine metabolism. These findings suggest that the phylogenomically diverse and novel Atribacterota JS1 is widely distributed in Japan Trench sediment, playing crucial roles in carbon cycling within the hadal sedimentary biosphere.

    IMPORTANCE

    The Japan Trench represents tectonically active hadal environments associated with Pacific plate subduction beneath the northeastern Japan arc. This study, for the first time, documented a large-scale single-cell and metagenomic survey along an approximately 500 km transect of the Japan Trench, obtaining high-quality genomic information on hadal sedimentary microbial communities. Single-cell genomics revealed the predominance of diverse JS1 lineages not recoverable through conventional metagenomic binning. Their metabolic potential includes genes related to the degradation of organic matter, which contributes to methanogenesis in the deeper layers. Our findings enhance understanding of sedimentary microbial communities at water depths exceeding 7,000 m and provide new insights into the ecological role of biogeochemical carbon cycling in the hadal sedimentary biosphere.

    DOI

  • Glutamate-Sensing Genes Are Conserved among Populations Compared to Glutamate Metabolism Genes.

    Kosuke Goto, Yoko Masuzawa, Masanori Kohmura, Asuka Takumi, Haruko Takeyama, Satoru Miyazaki, Takashi Gojobori, Katsuhiko Mineta

    Annals of nutrition & metabolism   79 ( 6 ) 502 - 510  2023.11  [Refereed]  [International journal]

    Authorship:Last author, Corresponding author

     View Summary

    INTRODUCTION: Glutamate is a representative taste molecule with an umami flavor and is a major nutrient found abundantly in nature. Furthermore, it plays a significant role in the human body as a key metabolic intermediate and neurotransmitter. Therefore, the divergence of glutamate functions among populations during their evolution is of particular interest with a hypothesis that the genetic variation can lead to understanding divergence in taste perception. To elucidate variation in glutamate applications and to deepen our understanding of taste perception, we examined the nucleotide diversity of genes associated with glutamate sensing and metabolism among human populations. METHODS: We first established 67 genes related to glutamate sensing and metabolism based on the database and literature survey. Then, for those genes, we used a population genomics approach based on ten populations over 76,156 human genomes in the gnomAD database. RESULTS: Statistical tests of means and medians of the minor allele frequencies did not show any significant difference among populations. However, we observed substantial differences between two functional groups, glutamate sensing and glutamate metabolism, in populations of Latino/admixed American, Ashkenazi Jewish, and Others. Interestingly, we could find significant differences between the African population and the East Asian population at the single nucleotide polymorphism level of glutamate metabolism genes, but no clear differences were noted in glutamate-sensing genes. These suggest that glutamate-sensing genes are under the functional constraint compared to glutamate metabolism genes. CONCLUSION: Thus, glutamate-sensing genes and metabolism genes have a contrasting mode of the evolution, and glutamate-sensing genes are conservatively evolved, indicating its functional importance.

    DOI PubMed

  • Current trends in RNA virus detection through metatranscriptome sequencing data.

    So Nakagawa, Shoichi Sakaguchi, Atsushi Ogura, Katsuhiko Mineta, Toshinori Endo, Yoshiyuki Suzuki, Takashi Gojobori

    FEBS open bio   13 ( 6 ) 992 - 1000  2023.05  [Refereed]  [International journal]

     View Summary

    With advances in sequencing technology, metatranscriptome sequencing from a variety of environmental and biological sources has revealed the existence of various previously unknown RNA viruses. This review presents recent major RNA virome studies sampled from invertebrate and vertebrate species as well as aquatic environments. In particular, we focus on severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and related RNA virus identification through metatranscriptome sequencing analyses. Recently developed bioinformatics software and databases for RNA virus identification are introduced. A relationship between newly identified RNA viruses and endogenous viral elements in host genomes is also discussed.

    DOI PubMed

  • Computational network analysis of host genetic risk variants of severe COVID-19.

    Sakhaa B Alsaedi, Katsuhiko Mineta, Xin Gao, Takashi Gojobori

    Human genomics   17 ( 1 ) 17 - 17  2023.03  [Refereed]  [International journal]

     View Summary

    BACKGROUND: Genome-wide association studies have identified numerous human host genetic risk variants that play a substantial role in the host immune response to SARS-CoV-2. Although these genetic risk variants significantly increase the severity of COVID-19, their influence on body systems is poorly understood. Therefore, we aim to interpret the biological mechanisms and pathways associated with the genetic risk factors and immune responses in severe COVID-19. We perform a deep analysis of previously identified risk variants and infer the hidden interactions between their molecular networks through disease mapping and the similarity of the molecular functions between constructed networks. RESULTS: We designed a four-stage computational workflow for systematic genetic analysis of the risk variants. We integrated the molecular profiles of the risk factors with associated diseases, then constructed protein-protein interaction networks. We identified 24 protein-protein interaction networks with 939 interactions derived from 109 filtered risk variants in 60 risk genes and 56 proteins. The majority of molecular functions, interactions and pathways are involved in immune responses; several interactions and pathways are related to the metabolic and cardiovascular systems, which could lead to multi-organ complications and dysfunction. CONCLUSIONS: This study highlights the importance of analyzing molecular interactions and pathways to understand the heterogeneous susceptibility of the host immune response to SARS-CoV-2. We propose new insights into pathogenicity analysis of infections by including genetic risk information as essential factors to predict future complications during and after infection. This approach may assist more precise clinical decisions and accurate treatment plans to reduce COVID-19 complications.

    DOI PubMed

  • Lactate-mediated neural plasticity genes emerged during the evolution of memory systems.

    Amal Bajaffer, Katsuhiko Mineta, Pierre Magistretti, Takashi Gojobori

    Scientific reports   12 ( 1 ) 19238 - 19238  2022.11  [Refereed]  [International journal]

     View Summary

    The ability to record experiences and learning is present to different degrees in several species; however, the complexity and diversity of memory processes are cognitive function features that differentiate humans from other species. Lactate has recently been discovered to act as a signaling molecule for neuronal plasticity linked to long-term memory. Because lactate is not only an energy substrate for neurons but also a signaling molecule for plasticity (Magistretti and Allaman in Nat Rev Neurosci 19:235-249, 2018. https://doi.org/10.1038/nrn.2018.19 ), it is of particular interest to understand how and when memory-related genes and lactate-mediated neural plasticity (LMNP) genes emerged and evolved in humans. To understand the evolutionary origin and processes of memory and LMNP genes, we first collected information on genes related to memory and LMNP from the literature and then conducted a comparative analysis of these genes. We found that the memory and LMNP genes have different origins, suggesting that these genes may have become established gradually in evolutionarily and functional terms and not at the same time. We also found that memory and LMNP systems have a similar evolutionary history, having been formed with the gradual participation of newly emerging genes throughout their evolution. We propose that the function of LMNP as a signaling process may be evolutionarily associated with memory systems through an unidentified system that is linked by 13 common genes between memory and LMNP gene sets. This study provides evolutionary insight into the possible relationship between memory and the LMNP systems that deepens our understanding of the evolution of memory systems.

    DOI PubMed

  • Validation of the application of gel beads-based single-cell genome sequencing platform to soil and seawater

    Yohei Nishikawa, Masato Kogawa, Masahito Hosokawa, Ryota Wagatsuma, Katsuhiko Mineta, Kai Takahashi, Keigo Ide, Kei Yura, Hayedeh Behzad, Takashi Gojobori, Haruko Takeyama

    ISME Communications   2 ( 1 )  2022.09  [Refereed]

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    Abstract

    Single-cell genomics is applied to environmental samples as a method to solve the problems of current metagenomics. However, in the fluorescence-activated cell sorting-based cell isolation and subsequent whole genome amplification, the sorting efficiency and the sequence quality are greatly affected by the type of target environment, limiting its adaptability. Here, we developed an improved single-cell genomics platform, named SAG-gel, which utilizes gel beads for single-cell isolation, lysis, and whole genome amplification. To validate the versatility of SAG-gel, single-cell genome sequencing was performed with model bacteria and microbial samples collected from eight environmental sites, including soil and seawater. Gel beads enabled multiple lysis treatments. The genome coverage with model bacteria was improved by 9.1–25%. A total of 734 single amplified genomes were collected from the diverse environmental samples, and almost full-length 16S rRNA genes were recovered from 57.8% of them. We also revealed two marine Rhodobacter strains harboring nearly identical 16S rRNA genes but having different genome contents. In addition, searching for viral sequences elucidated the virus-host linkage over the sampling sites, revealing the geographic distribution and diverse host range of viruses.

    DOI

  • Identification of lipolytic enzymes using high-throughput single-cell screening and sorting of a metagenomic library.

    Amani Alma'abadi, Hayedeh Behzad, Mohammed Alarawi, David Conchouso, Yoshimoto Saito, Masahito Hosokawa, Yohei Nishikawa, Masato Kogawa, Haruko Takeyama, Katsuhiko Mineta, Takashi Gojobori

    New biotechnology   70   102 - 108  2022.09  [Refereed]  [International journal]

    Authorship:Corresponding author

     View Summary

    The demand for novel, robust microbial biocatalysts for use in industrial and pharmaceutical applications continues to increase rapidly. As a result, there is a need to develop advanced tools and technologies to exploit the vast metabolic potential of unculturable microorganisms found in various environments. Single-cell and functional metagenomics studies can explore the enzymatic potential of entire microbial communities in a given environment without the need to culture the microorganisms. This approach has contributed substantially to the discovery of unique microbial genes for industrial and medical applications. Functional metagenomics involves the extraction of microbial DNA directly from environmental samples, constructing expression libraries comprising the entire microbial genome, and screening of the libraries for the presence of desired phenotypes. In this study, lipolytic enzymes from the Red Sea were targeted. A high-throughput single-cell microfluidic platform combined with a laser-based fluorescent screening bioassay was employed to discover new genes encoding lipolytic enzymes. Analysis of the metagenomic library led to the identification of three microbial genes encoding lipases based on their functional similarity and sequence homology to known lipases. The results demonstrated that microfluidics is a robust technology that can be used for screening in functional metagenomics. The results also indicate that the Red Sea is a promising, under-investigated source of new genes and gene products.

    DOI PubMed

  • Comprehensive evolutionary analysis and nomenclature of plant G3BPs.

    Aala A Abulfaraj, Hajime Ohyanagi, Kosuke Goto, Katsuhiko Mineta, Takashi Gojobori, Heribert Hirt, Naganand Rayapuram

    Life science alliance   5 ( 9 )  2022.09  [Refereed]  [International journal]

     View Summary

    Stress induces extensive reprogramming of mRNA metabolism, which includes the transcription and translation of stress-related genes and the formation of stress granules. RasGAP SH3 domain-binding proteins (G3BPs, also called Rasputins) form a highly conserved family of proteins found throughout eukaryotic evolution, which coordinate signal transduction and posttranscriptional gene regulation and play a key role in the formation of stress granules. G3BPs play a role in osmotic, oxidative, and biotic stress in mammals, and recent results revealed that they play similar functions in higher plants. Although simple eukaryotes such as yeast have only one G3BP gene, higher plants show a massive expansion of their G3BP genes into distinct subfamilies. However, because this family of genes has not been well-characterized in plants, functions that have evolved during this expansion remain unidentified. Therefore, we carried out a phylogenetic analysis of G3BPs in different eukaryotes, particularly focusing on the green lineage. On the basis of this evolutionary analysis of G3BPs in eukaryotes, we propose a uniform nomenclature for plant G3BPs that should help predict the evolutionary and functional diversification in this family.

    DOI PubMed

  • A cautionary signal from the Red Sea on the impact of increased dust activity on marine microbiota.

    Hayedeh Behzad, Hajime Ohyanagi, Badr Alharbi, Martin Ibarra, Mohammed Alarawi, Yoshimoto Saito, Carlos M Duarte, Vladimir Bajic, Katsuhiko Mineta, Takashi Gojobori

    BMC genomics   23 ( 1 ) 277 - 277  2022.04  [Refereed]  [International journal]

    Authorship:Corresponding author

     View Summary

    BACKGROUND: Global climate change together with growing desertification is leading to increased dust emissions to the atmosphere, drawing attention to possible impacts on marine ecosystems receiving dust deposition. Since microorganisms play important roles in maintaining marine homeostasis through nutrient cycling and carbon flow, detrimental changes in the composition of marine microbiota in response to increased dust input could negatively impact marine health, particularly so in seas located within the Global Dust Belt. Due to its strategic location between two deserts and unique characteristics, the Red Sea provides an attractive semi-enclosed "megacosm" to examine the impacts of large dust deposition on the vastly diverse microbiota in its exceptionally warm oligotrophic waters. RESULTS: We used culture-independent metagenomic approaches to assess temporal changes in the Red Sea microbiota in response to two severe sandstorms, one originated in the Nubian Desert in the summer 2016 and a second one originated in the Libyan Desert in the spring 2017. Despite differences in sandstorm origin and meteorological conditions, both sandstorms shifted bacterial and Archaeal groups in a similar mode. In particular, the relative abundance of autotrophic bacteria declined while those of heterotrophic bacteria, particularly Bacteroidetes, and Archaea increased. The changes peaked within six days from the start of sandstorms, and the community recovered the original assemblage within one month. CONCLUSION: Our results suggest that increased dust emission with expanding desertification could lead to undesirable impacts in ocean function, enhancing heterotrophic processes while reducing autotrophic ones, thereby affecting the marine food web in seas receiving dust deposition.

    DOI PubMed

  • Seawater desalination based drinking water: Microbial characterization during distribution with and without residual chlorine.

    Nadia Farhat, Lanhee Kim, Katsuhiko Mineta, Mohammed Alarawi, Takashi Gojobori, Pascal Saikaly, Johannes Vrouwenvelder

    Water research   210   117975 - 117975  2022.02  [Refereed]  [International journal]

     View Summary

    Monitoring the changes that occur to water during distribution is vital to ensure water safety. In this study, the biological stability of reverse osmosis (RO) produced drinking water, characterized by low cell concentration and low assimilable organic carbon, in combination with chlorine disinfection was investigated. Water quality at several locations throughout the existing distribution network was monitored to investigate whether microbial water quality changes can be identified. Results revealed that the water leaving the plant had an average bacterial cell concentration of 103 cells/mL. A 0.5-1.5 log increase in bacterial cell concentration was observed at locations in the network. The residual disinfectant was largely dissipated in the network from 0.5 mg/L at the treatment plant to less than 0.1 mg/L in the network locations. The simulative study involving miniature distribution networks, mimicking the dynamics of a distribution network, fed with the RO produced chlorinated and non-chlorinated drinking water revealed that distributing RO produced water without residual disinfection, especially at high water temperatures (25-30 °C), poses a higher chance for water quality change. Within six months of operation of the miniature network fed with unchlorinated RO produced water, the adenosine triphosphate (ATP) and total cell concentration (TCC) in the pipe biofilm were 4 × 102 pg ATP/cm2 and 1 × 107 cells/ cm2. The low bacterial cell concentration and organic carbon concentration in the RO-produced water did not prevent biofilm development inside the network with and without residual chlorine. The bacterial community analysis using 16S ribosomal RNA (rRNA) gene sequencing revealed that mesophilic bacteria with higher temperature tolerance and bacteria associated with oligotrophic, nutrient-poor conditions dominated the biofilm, with no indication of the existence of opportunistic pathogenic species. However, chlorination selected against most bacterial groups and the bacterial community that remained was mainly the bacteria capable of surviving disinfection regimes. Biofilms that developed in the presence of chlorine contained species classified as opportunistic pathogens. These biofilms have an impact on shaping the water quality received at the consumer tap. The presence of these bacteria on its own is not a health risk indicator; viability assessment and qPCRs targeting genes specific to the opportunistic pathogens as well as quantitative microbiological risk assessment (QMRA) should be included to assess the risk. The results from this study highlight the importance of implementing multiple barriers to ensure water safety. Changes in water quality detected even when high-quality disinfected RO-produced water is distributed highlight microbiological challenges that chlorinated systems endure, especially at high water temperatures.

    DOI PubMed

  • DeepSVP: integration of genotype and phenotype for structural variant prioritization using deep learning.

    Azza Althagafi, Lamia Alsubaie, Nagarajan Kathiresan, Katsuhiko Mineta, Taghrid Aloraini, Fuad Al Mutairi, Majid Alfadhel, Takashi Gojobori, Ahmad Alfares, Robert Hoehndorf

    Bioinformatics(Bioinform.)   38 ( 6 ) 1677 - 1684  2022  [Refereed]  [International journal]

    DOI

  • Evolution of memory system-related genes.

    Amal Bajaffer, Katsuhiko Mineta, Takashi Gojobori

    FEBS open bio   11 ( 12 ) 3201 - 3210  2021.12  [Refereed]  [International journal]

     View Summary

    Memory has an essential function in human life as it helps individuals remember and recognize their surroundings. It is also the major form of cognition that controls behavior. As memory is a function that is highly characteristic of humans, how it was established is of particular interest. Recent progress in the field of neurosciences, together with the technological advancement of genome-wide approaches, has led to the accumulation of evidence regarding the presence and similar/distinct mechanisms of memory among species. However, the understanding of the evolution of memory obtained utilizing these genome-wide approaches remains unclear. The purpose of this review was to provide an overview of the literature on the evolution of the memory system among species and the genes involved in this process. This review also discusses possible approaches to study the evolution of memory systems to guide future research.

    DOI PubMed

  • Comparative Analysis of Mitochondrial Genomes in Gryllidea (Insecta: Orthoptera): Implications for Adaptive Evolution in Ant-Loving Crickets.

    Ryuto Sanno, Kosuke Kataoka, Shota Hayakawa, Keigo Ide, Chuong N Nguyen, Thao P Nguyen, Binh T N Le, Oanh T P Kim, Katsuhiko Mineta, Haruko Takeyama, Makio Takeda, Toshiyuki Sato, Takeshi Suzuki, Kei Yura, Toru Asahi

    Genome biology and evolution   13 ( 10 )  2021.10  [Refereed]  [International journal]

     View Summary

    Species of infraorder Gryllidea, or crickets, are useful invertebrate models for studying developmental biology and neuroscience. They have also attracted attention as alternative protein sources for human food and animal feed. Mitochondrial genomic information on related invertebrates, such as katydids, and locusts, has recently become available in attempt to clarify the controversial classification schemes, although robust phylogenetic relationships with emphasis on crickets remain elusive. Here, we report newly sequenced complete mitochondrial genomes of crickets to study their phylogeny, genomic rearrangements, and adaptive evolution. First, we conducted de novo assembly of mitochondrial genomes from eight cricket species and annotated protein-coding genes and transfer and ribosomal RNAs using automatic annotations and manual curation. Next, by combining newly described protein-coding genes with public data of the complete Gryllidea genomes and gene annotations, we performed phylogenetic analysis and found gene order rearrangements in several branches. We further analyzed genetic signatures of selection in ant-loving crickets (Myrmecophilidae), which are small wingless crickets that inhabit ant nests. Three distinct approaches revealed two positively selected sites in the cox1 gene in these crickets. Protein 3D structural analyses suggested that these selected sites could influence the interaction of respiratory complex proteins, conferring benefits to ant-loving crickets with a unique ecological niche and morphology. These findings enhance our understanding of the genetic basis of cricket evolution without relying on estimates based on a limited number of molecular markers.

    DOI PubMed

  • Genome sequencing and identification of cellulase genes in Bacillus paralicheniformis strains from the Red Sea.

    Siham Fatani, Yoshimoto Saito, Mohammed Alarawi, Takashi Gojobori, Katsuhiko Mineta

    BMC microbiology   21 ( 1 ) 254 - 254  2021.09  [Refereed]  [International journal]

    Authorship:Last author, Corresponding author

     View Summary

    BACKGROUND: Cellulolytic microorganisms are considered a key player in the degradation of plant biomass in various environments. These microorganisms can be isolated from various environments, such as soils, the insect gut, the mammalian rumen and oceans. The Red Sea exhibits a unique environment in terms of presenting a high seawater temperature, high salinity, low nutrient levels and high biodiversity. However, there is little information regarding cellulase genes in the Red Sea environment. This study aimed to examine whether the Red Sea can be a resource for the bioprospecting of microbial cellulases by isolating cellulase-producing microorganisms from the Red Sea environment and characterizing cellulase genes. RESULTS: Three bacterial strains were successfully isolated from the plankton fraction and the surface of seagrass. The isolated strains were identified as Bacillus paralicheniformis and showed strong cellulase activity. These results suggested that these three isolates secreted active cellulases. By whole genome sequencing, we found 10 cellulase genes from the three isolates. We compared the expression of these cellulase genes under cellulase-inducing and non-inducing conditions and found that most of the cellulase genes were generally upregulated during cellulolysis in the isolates. Our operon structure analysis also showed that cellulase genes form operons with genes involved in various kinds of cellular reactions, such as protein metabolism, which suggests the existence of crosstalk between cellulolysis and other metabolic pathways in the bacterial isolates. These results suggest that multiple cellulases are playing important roles in cellulolysis. CONCLUSIONS: Our study reports the isolation and characterization of cellulase-producing bacteria from the Red Sea. Our whole-genome sequencing classified our three isolates as Bacillus paralicheniformis, and we revealed the presence of ten cellulase orthologues in each of three isolates' genomes. Our comparative expression analysis also identified that most of the cellulase genes were upregulated under the inducing conditions in general. Although cellulases have been roughly classified into three enzyme groups of beta-glucosidase, endo-β-1,4-glucanase and exoglucanase, these findings suggest the importance to consider microbial cellulolysis as a more complex reaction with various kinds of cellulase enzymes.

    DOI PubMed

  • Seasonal and annual changes in the microbial communities of Ofunato Bay, Japan, based on metagenomics.

    Atsushi Kobiyama, Jonaira Rashid, Md Shaheed Reza, Yuri Ikeda, Yuichiro Yamada, Toshiaki Kudo, Nanami Mizusawa, Saki Yanagisawa, Daisuke Ikeda, Shigeru Sato, Takehiko Ogata, Kazuho Ikeo, Shinnosuke Kaga, Shiho Watanabe, Kimiaki Naiki, Yoshimasa Kaga, Satoshi Segawa, Yumiko Tada, Tatsuya Musashi, Katsuhiko Mineta, Takashi Gojobori, Shugo Watabe

    Scientific reports   11 ( 1 ) 17277 - 17277  2021.08  [Refereed]  [International journal]

     View Summary

    Five years of datasets from 2015 to 2019 of whole genome shotgun sequencing for cells trapped on 0.2-µm filters of seawater collected monthly from Ofunato Bay, an enclosed bay in Japan, were analysed, which included the 2015 data that we had reported previously. Nucleotide sequences were determined for extracted DNA from three locations for both the upper (1 m) and deeper (8 or 10 m) depths. The biotic communities analysed at the domain level comprised bacteria, eukaryotes, archaea and viruses. The relative abundance of bacteria was over 60% in most months for the five years. The relative abundance of the SAR86 cluster was highest in the bacterial group, followed by Candidatus Pelagibacter and Planktomarina. The relative abundance of Ca. Pelagibacter showed no relationship with environmental factors, and those of SAR86 and Planktomarina showed positive correlations with salinity and dissolved oxygen, respectively. The bacterial community diversity showed seasonal changes, with high diversity around September and low diversity around January for all five years. Nonmetric multidimensional scaling analysis also revealed that the bacterial communities in the bay were grouped in a season-dependent manner and linked with environmental variables such as seawater temperature, salinity and dissolved oxygen.

    DOI PubMed

  • Development of a time-series shotgun metagenomics database for monitoring microbial communities at the Pacific coast of Japan.

    Kazutoshi Yoshitake, Gaku Kimura, Tomoko Sakami, Tsuyoshi Watanabe, Yukiko Taniuchi, Shigeho Kakehi, Akira Kuwata, Haruyo Yamaguchi, Takafumi Kataoka, Masanobu Kawachi, Kazuho Ikeo, Engkong Tan, Yoji Igarashi, Masafumi Ohtsubo, Shugo Watabe, Yutaka Suzuki, Shuichi Asakawa, Sonoko Ishino, Kosuke Tashiro, Yoshizumi Ishino, Takanori Kobayashi, Katsuhiko Mineta, Takashi Gojobori

    Scientific reports   11 ( 1 ) 12222 - 12222  2021.06  [Refereed]  [International journal]

     View Summary

    Although numerous metagenome, amplicon sequencing-based studies have been conducted to date to characterize marine microbial communities, relatively few have employed full metagenome shotgun sequencing to obtain a broader picture of the functional features of these marine microbial communities. Moreover, most of these studies only performed sporadic sampling, which is insufficient to understand an ecosystem comprehensively. In this study, we regularly conducted seawater sampling along the northeastern Pacific coast of Japan between March 2012 and May 2016. We collected 213 seawater samples and prepared size-based fractions to generate 454 subsets of samples for shotgun metagenome sequencing and analysis. We also determined the sequences of 16S rRNA (n = 111) and 18S rRNA (n = 47) gene amplicons from smaller sample subsets. We thereafter developed the Ocean Monitoring Database for time-series metagenomic data ( http://marine-meta.healthscience.sci.waseda.ac.jp/omd/ ), which provides a three-dimensional bird's-eye view of the data. This database includes results of digital DNA chip analysis, a novel method for estimating ocean characteristics such as water temperature from metagenomic data. Furthermore, we developed a novel classification method that includes more information about viruses than that acquired using BLAST. We further report the discovery of a large number of previously overlooked (TAG)n repeat sequences in the genomes of marine microbes. We predict that the availability of this time-series database will lead to major discoveries in marine microbiome research.

    DOI PubMed

  • A single neuron subset governs a single coactive neuron circuit in Hydra vulgaris, representing a possible ancestral feature of neural evolution.

    Yukihiko Noro, Hiroshi Shimizu, Katsuhiko Mineta, Takashi Gojobori

    Scientific reports   11 ( 1 ) 10828 - 10828  2021.05  [Refereed]  [International journal]

     View Summary

    The last common ancestor of Bilateria and Cnidaria is believed to be one of the first animals to develop a nervous system over 500 million years ago. Many of the genes involved in the neural function of the advanced nervous system in Bilateria are well conserved in Cnidaria. Thus, the cnidarian Hydra vulgaris is a good model organism for the study of the putative primitive nervous system in its last common ancestor. The diffuse nervous system of Hydra consists of several peptidergic neuron subsets. However, the specific functions of these subsets remain unclear. Using calcium imaging, here we show that the neuron subsets that express neuropeptide, Hym-176, function as motor circuits to evoke longitudinal contraction. We found that all neurons in a subset defined by the Hym-176 gene (Hym-176A) or its paralogs (Hym-176B) expression are excited simultaneously, followed by longitudinal contraction. This indicates not only that these neuron subsets have a motor function but also that a single molecularly defined neuron subset forms a single coactive circuit. This is in contrast with the bilaterian nervous system, where a single molecularly defined neuron subset harbors multiple coactive circuits, showing a mixture of neurons firing with different timings. Furthermore, we found that the two motor circuits, one expressing Hym-176B in the body column and the other expressing Hym-176A in the foot, are coordinately regulated to exert region-specific contraction. Our results demonstrate that one neuron subset is likely to form a monofunctional circuit as a minimum functional unit to build a more complex behavior in Hydra. This simple feature (one subset, one circuit, one function) found in Hydra may represent the simple ancestral condition of neural evolution.

    DOI PubMed

  • Characterization of microbiologically influenced corrosion by comprehensive metagenomic analysis of an inland oil field.

    Badoor Nasser, Yoshimoto Saito, Mohammed Alarawi, Abdulmohsen A Al-Humam, Katsuhiko Mineta, Takashi Gojobori

    Gene   774   145425 - 145425  2021.03  [Refereed]  [International journal]

    Authorship:Corresponding author

     View Summary

    Corrosion in pipelines and reservoir tanks in oil plants is a serious problem in the global energy industry because it causes substantial economic losses associated with frequent part replacement and can lead to potential damage to entire crude oil fields. Previous studies revealed that corrosion is mainly caused by microbial activities in a process currently termed microbiologically influenced corrosion or biocorrosion. Identifying the bacteria responsible for biocorrosion is crucial for its suppression. In this study, we analyzed the microbial communities present at corrosion sites in oil plant pipelines using comparative metagenomic analysis along with bioinformatics and statistics. We analyzed the microbial communities in pipelines in an oil field in which groundwater is used as injection water. We collected samples from four different facilities in the oil field. Metagenomic analysis revealed that the microbial community structures greatly differed even among samples from the same facility. Treatments such as biocide administration and demineralization at each location in the pipeline may have independently affected the microbial community structure. The results indicated that microbial inspection throughout the pipeline network is essential to prevent biocorrosion at industrial plants. By identifying the bacterial species responsible for biocorrosion, this study provides bacterial indicators to detect and classify biocorrosion. Furthermore, these species may serve as biomarkers to detect biocorrosion at an early stage. Then, appropriate management such as treatment with suitable biocides can be performed immediately and appropriately. Thus, our study will serve as a platform for obtaining microbial information related to biocorrosion to enable the development of a practical approach to prevent its occurrence.

    DOI PubMed

  • Indigenous Arabs have an intermediate frequency of a Neanderthal-derived COVID-19 risk haplotype compared with other world populations.

    Katsuhiko Mineta, Kosuke Goto, Takashi Gojobori, Fowzan S Alkuraya

    Clinical genetics   99 ( 3 ) 484 - 485  2021.03  [Refereed]  [International journal]

    Authorship:Lead author

    DOI PubMed

  • Population structure of indigenous inhabitants of Arabia.

    Katsuhiko Mineta, Kosuke Goto, Takashi Gojobori, Fowzan S Alkuraya

    PLoS genetics   17 ( 1 ) e1009210  2021.01  [Refereed]  [International journal]

    Authorship:Lead author

     View Summary

    Modern day Saudi Arabia occupies the majority of historical Arabia, which may have contributed to ancient waves of migration out of Africa. This ancient history has left a lasting imprint in the genetics of the region, including the diverse set of tribes that call Saudi Arabia their home. How these tribes relate to each other and to the world's major populations remains an unanswered question. In an attempt to improve our understanding of the population structure of Saudi Arabia, we conducted genomic profiling of 957 unrelated individuals who self-identify with 28 large tribes in Saudi Arabia. Consistent with the tradition of intra-tribal unions, the subjects showed strong clustering along tribal lines with the distance between clusters correlating with their geographical proximities in Arabia. However, these individuals form a unique cluster when compared to the world's major populations. The ancient origin of these tribal affiliations is supported by analyses that revealed little evidence of ancestral origin from within the 28 tribes. Our results disclose a granular map of population structure and have important implications for future genetic studies into Mendelian and common diseases in the region.

    DOI PubMed

  • Significant variants of type 2 diabetes in the Arabian Region through an Integration of exome databases.

    Kosuke Goto, Katsuhiko Mineta, Satoru Miyazaki, Takashi Gojobori

    PloS one   16 ( 4 ) e0249226  2021  [Refereed]  [International journal]

     View Summary

    Type 2 diabetes (T2D) is a major global health issue, and it has also become one of the major diseases in Arab countries. In addition to the exome databases that have already been established, whole exome sequencing data for the Greater Middle East are now available. To elucidate the genetic features of T2D in the Arabian Peninsula, we integrated two exome databases (gnomAD exome and the Greater Middle East Variome Project) with clinical information from the ClinVar. After the integration, we obtained 18 single nucleotide polymorphisms and found two statistically and clinically significant variants in two genes, SLC30A8 rs13266634 and KCNJ11 rs5219. Interestingly, the two genes are linked to the uptake of the metals, Zn and K respectively, which indicating the regional features of the genetic variants. The frequency of the risk allele of rs13266634 among individuals in the Arabian Peninsula was higher than among individuals in other regions. On the other hand, the frequency of the risk allele of rs5219 in the Arabian Peninsula was lower than that in other regions. We identified and characterized T2D-related variants that show unique tendencies in the Arabian Peninsula. Our analyses contribute to and provide guidance for the clinical research of T2D in the Arabian Peninsula.

    DOI PubMed

  • Integration of Droplet Microfluidic Tools for Single-Cell Functional Metagenomics: An Engineering Head Start.

    David Conchouso, Amani D. Alma'abadi, Hayedeh Behzad, Mohammed Alarawi, Masahito Hosokawa, Yohei Nishikawa, Haruko Takeyama, Katsuhiko Mineta, Takashi Gojobori

    Genomics, Proteomics & Bioinformatics   19 ( 3 ) 504 - 518  2021  [Refereed]  [International journal]

    Authorship:Corresponding author

    DOI

  • Integrated Metabolic Modeling, Culturing, and Transcriptomics Explain Enhanced Virulence of Vibrio cholerae during Coinfection with Enterotoxigenic Escherichia coli.

    Alyaa M Abdel-Haleem, Vaishnavi Ravikumar, Boyang Ji, Katsuhiko Mineta, Xin Gao, Jens Nielsen, Takashi Gojobori, Ivan Mijakovic

    mSystems   5 ( 5 )  2020.09  [Refereed]  [International journal]

     View Summary

    Gene essentiality is altered during polymicrobial infections. Nevertheless, most studies rely on single-species infections to assess pathogen gene essentiality. Here, we use genome-scale metabolic models (GEMs) to explore the effect of coinfection of the diarrheagenic pathogen Vibrio cholerae with another enteric pathogen, enterotoxigenic Escherichia coli (ETEC). Model predictions showed that V. cholerae metabolic capabilities were increased due to ample cross-feeding opportunities enabled by ETEC. This is in line with increased severity of cholera symptoms known to occur in patients with dual infections by the two pathogens. In vitro coculture systems confirmed that V. cholerae growth is enhanced in cocultures relative to single cultures. Further, expression levels of several V. cholerae metabolic genes were significantly perturbed as shown by dual RNA sequencing (RNAseq) analysis of its cocultures with different ETEC strains. A decrease in ETEC growth was also observed, probably mediated by nonmetabolic factors. Single gene essentiality analysis predicted conditionally independent genes that are essential for the pathogen's growth in both single-infection and coinfection scenarios. Our results reveal growth differences that are of relevance to drug targeting and efficiency in polymicrobial infections.IMPORTANCE Most studies proposing new strategies to manage and treat infections have been largely focused on identifying druggable targets that can inhibit a pathogen's growth when it is the single cause of infection. In vivo, however, infections can be caused by multiple species. This is important to take into account when attempting to develop or use current antibacterials since their efficacy can change significantly between single infections and coinfections. In this study, we used genome-scale metabolic models (GEMs) to interrogate the growth capabilities of Vibrio cholerae in single infections and coinfections with enterotoxigenic E. coli (ETEC), which cooccur in a large fraction of diarrheagenic patients. Coinfection model predictions showed that V. cholerae growth capabilities are enhanced in the presence of ETEC relative to V. cholerae single infection, through cross-fed metabolites made available to V. cholerae by ETEC. In vitro, cocultures of the two enteric pathogens further confirmed model predictions showing an increased growth of V. cholerae in coculture relative to V. cholerae single cultures while ETEC growth was suppressed. Dual RNAseq analysis of the cocultures also confirmed that the transcriptome of V. cholerae was distinct during coinfection compared to single-infection scenarios where processes related to metabolism were significantly perturbed. Further, in silico gene-knockout simulations uncovered discrepancies in gene essentiality for V. cholerae growth between single infections and coinfections. Integrative model-guided analysis thus identified druggable targets that would be critical for V. cholerae growth in both single infections and coinfections; thus, designing inhibitors against those targets would provide a broader spectrum of coverage against cholera infections.

    DOI PubMed

  • What is the right sequencing approach? Solo VS extended family analysis in consanguineous populations.

    Ahmed Alfares, Lamia Alsubaie, Taghrid Aloraini, Aljoharah Alaskar, Azza Althagafi, Ahmed Alahmad, Mamoon Rashid, Abdulrahman Alswaid, Ali Alothaim, Wafaa Eyaid, Faroug Ababneh, Mohammed Albalwi, Raniah Alotaibi, Mashael Almutairi, Nouf Altharawi, Alhanouf Alsamer, Marwa Abdelhakim, Senay Kafkas, Katsuhiko Mineta, Nicole Cheung, Abdallah M Abdallah, Stine Büchmann-Møller, Yoshinori Fukasawa, Xiang Zhao, Issaac Rajan, Robert Hoehndorf, Fuad Al Mutairi, Takashi Gojobori, Majid Alfadhel

    BMC medical genomics   13 ( 1 ) 103 - 103  2020.07  [Refereed]  [International journal]

     View Summary

    BACKGROUND: Testing strategies is crucial for genetics clinics and testing laboratories. In this study, we tried to compare the hit rate between solo and trio and trio plus testing and between trio and sibship testing. Finally, we studied the impact of extended family analysis, mainly in complex and unsolved cases. METHODS: Three cohorts were used for this analysis: one cohort to assess the hit rate between solo, trio and trio plus testing, another cohort to examine the impact of the testing strategy of sibship genome vs trio-based analysis, and a third cohort to test the impact of an extended family analysis of up to eight family members to lower the number of candidate variants. RESULTS: The hit rates in solo, trio and trio plus testing were 39, 40, and 41%, respectively. The total number of candidate variants in the sibship testing strategy was 117 variants compared to 59 variants in the trio-based analysis. We noticed that the average number of coding candidate variants in trio-based analysis was 1192 variants and 26,454 noncoding variants, and this number was lowered by 50-75% after adding additional family members, with up to two coding and 66 noncoding homozygous variants only, in families with eight family members. CONCLUSION: There was no difference in the hit rate between solo and extended family members. Trio-based analysis was a better approach than sibship testing, even in a consanguineous population. Finally, each additional family member helped to narrow down the number of variants by 50-75%. Our findings could help clinicians, researchers and testing laboratories select the most cost-effective and appropriate sequencing approach for their patients. Furthermore, using extended family analysis is a very useful tool for complex cases with novel genes.

    DOI PubMed

  • Massively parallel single-cell genome sequencing enables high-resolution analysis of soil and marine microbiome

    Yohei Nishikawa, Masato Kogawa, Masahito Hosokawa, Katsuhiko Mineta, Kai Takahashi, Chikako Sakanashi, Hayedeh Behzad, Takashi Gojobori, Haruko Takeyama

       2020.03

     View Summary

    <title>Abstract</title>To improve our understanding of the environmental microbiome, we developed a single-cell genome sequencing platform, named SAG-gel, which utilizes gel beads for single-cell isolation, cell lysis, and whole genome amplification (WGA) for sequencing. SAG-gel enables serial, parallel and independent reactions of &gt; 100,000 single cells in a single tube, delivering high-quality genome recovery with storable randomized single-cell genome libraries. From soil and marine environmental sources, we acquired 734 partial genomes that are recapitulated in 231 species, 35% of which were assigned as high-to-medium qualities. We found that each genome to be almost unique and 98.7% of them were newly identified, implying the complex genetic diversities across 44 phyla. The various metabolic capabilities including virulence factors and biosynthetic gene clusters were found across the lineages at single-cell resolution. This technology will accelerate the accumulation of reference genomes of uncharacterized environmental microbes and provide us new insights for their roles.

    DOI

  • Ontology-based prediction of cancer driver genes.

    Sara Althubaiti, Andreas Karwath, Ashraf Dallol, Adeeb Noor, Shadi Salem Alkhayyat, Rolina Alwassia, Katsuhiko Mineta, Takashi Gojobori, Andrew D Beggs, Paul N Schofield, Georgios V Gkoutos, Robert Hoehndorf

    Scientific reports   9 ( 1 ) 17405 - 17405  2019.11  [Refereed]  [International journal]

     View Summary

    Identifying and distinguishing cancer driver genes among thousands of candidate mutations remains a major challenge. Accurate identification of driver genes and driver mutations is critical for advancing cancer research and personalizing treatment based on accurate stratification of patients. Due to inter-tumor genetic heterogeneity many driver mutations within a gene occur at low frequencies, which make it challenging to distinguish them from non-driver mutations. We have developed a novel method for identifying cancer driver genes. Our approach utilizes multiple complementary types of information, specifically cellular phenotypes, cellular locations, functions, and whole body physiological phenotypes as features. We demonstrate that our method can accurately identify known cancer driver genes and distinguish between their role in different types of cancer. In addition to confirming known driver genes, we identify several novel candidate driver genes. We demonstrate the utility of our method by validating its predictions in nasopharyngeal cancer and colorectal cancer using whole exome and whole genome sequencing.

    DOI PubMed

  • Finding Nemo's Genes: A chromosome-scale reference assembly of the genome of the orange clownfish Amphiprion percula.

    Robert Lehmann, Damien J Lightfoot, Celia Schunter, Craig T Michell, Hajime Ohyanagi, Katsuhiko Mineta, Sylvain Foret, Michael L Berumen, David J Miller, Manuel Aranda, Takashi Gojobori, Philip L Munday, Timothy Ravasi

    Molecular ecology resources   19 ( 3 ) 570 - 585  2019.05  [Refereed]  [International journal]

     View Summary

    The iconic orange clownfish, Amphiprion percula, is a model organism for studying the ecology and evolution of reef fishes, including patterns of population connectivity, sex change, social organization, habitat selection and adaptation to climate change. Notably, the orange clownfish is the only reef fish for which a complete larval dispersal kernel has been established and was the first fish species for which it was demonstrated that antipredator responses of reef fishes could be impaired by ocean acidification. Despite its importance, molecular resources for this species remain scarce and until now it lacked a reference genome assembly. Here, we present a de novo chromosome-scale assembly of the genome of the orange clownfish Amphiprion percula. We utilized single-molecule real-time sequencing technology from Pacific Biosciences to produce an initial polished assembly comprised of 1,414 contigs, with a contig N50 length of 1.86 Mb. Using Hi-C-based chromatin contact maps, 98% of the genome assembly were placed into 24 chromosomes, resulting in a final assembly of 908.8 Mb in length with contig and scaffold N50s of 3.12 and 38.4 Mb, respectively. This makes it one of the most contiguous and complete fish genome assemblies currently available. The genome was annotated with 26,597 protein-coding genes and contains 96% of the core set of conserved actinopterygian orthologs. The availability of this reference genome assembly as a community resource will further strengthen the role of the orange clownfish as a model species for research on the ecology and evolution of reef fishes.

    DOI PubMed

  • Marine Metagenomic Sequence Counts of Reads Assigned to Taxa Consistently Proportionate to Read Counts Obtained for per g of Seawater Sample

    Toshiaki Kudo, Md Shaheed Reza, Atsushi Kobiyama, Jonaira Rashid, Yuichiro Yamada, Yuri Ikeda, Daisuke Ikeda, Nanami Mizusawa, Saki Yanagisawa, Kazuho Ikeo, Shigeru Sato, Takehiko Ogata, Shinnosuke Kaga, Shiho Watanabe, Kimiaki Naiki, Yoshimasa Kaga, Satoshi Segawa, Katsuhiko Mineta, Vladimir Bajic, Takashi Gojobori, Shugo Watabe

    Marine Metagenomics: Technological Aspects and Applications     183 - 188  2019.01

     View Summary

    Development of high-throughput DNA sequencing technologies has enabled scientists to generate vast amounts of genetic information that may provide a comprehensive understanding of key roles played by environmental microorganisms. Generally the microorganisms inhabit a particular niche and correlate well with environmental changes. It is accepted that the read counts obtained through metagenomic analyses correlate semi-quantitatively with the relative abundance of bacterial species. In our marine metagenomic study conducted on the Ofunato Bay, Iwate Prefecture, Japan, we observed such correlation which exists for bacterioplankton Candidatus Pelagibacter ubique, identified as the dominant bacterial species of the bay. Shotgun metagenomic analyses identified three strains of Ca. Pelagibacter in the bay, viz., dmdA-HTCC1062, dmdAHTCC9022, and O19-dmdA, that showed a dynamic change throughout the year particularly in the 10-m depth zone. Interestingly, the total abundances of those strains that fall in the Ca. Pelagibacter genus were found to correlate well with the read counts per g seawater samples used for analyses. It is assumed that wholegenome sequence (WGS) reads for members of the metagenome would show similar trend provided that proper precautions are taken to ensure collection of representative sample from the environment.

    DOI

  • MetagenomicMethods: From Seawater to the Database

    Md Shaheed Reza, Atsushi Kobiyama, Jonaira Rashid, Yuichiro Yamada, Yuri Ikeda, Daisuke Ikeda, Nanami Mizusawa, Saki Yanagisawa, Kazuho Ikeo, Shigeru Sato, Takehiko Ogata, Toshiaki Kudo, Shinnosuke Kaga, Shiho Watanabe, Kimiaki Naiki, Yoshimasa Kaga, Satoshi Segawa, Katsuhiko Mineta, Vladimir Bajic, Takashi Gojobori, Shugo Watabe

    Marine Metagenomics: Technological Aspects and Applications     3 - 16  2019.01

     View Summary

    In this article, methods or techniques of metagenomics including targeted 16S/18S rRNA analyses and shotgun sequencing will be discussed. It is sometimes difficult, especially for beginners, to follow the manufacturer’s recommendation as mentioned in the protocol and to go through different steps from the preparation of starting material (e.g., DNA), library preparation, and so on. We will try to explain all the steps in detail and share our experience here. It all starts with collection of samples and collection of ecological/environmental metadata followed by sample fractionation (optional), extraction of DNA, sequencing, and finally data analyses to interpret results. Sample collection has always been the most important part of a study as it requires proper planning, a good workforce to execute, permission(s) of sampling from appropriate authority, and precaution(s) about endangered species during sampling. Here, we first describe methodology for a shallow river and in the later section methodology for a deep marine bay. In either case, slight modifications can be made to succeed in sampling. Determination of physicochemical parameters as metadata simultaneously is also an important task. These samples are then processed to extract DNA which needs to be representative of all cells present in the sample. Finally, sequencing is done by a next-generation sequencer, and data analyses are completed. Through these methods, scientists are now able to overcome the unculturability problem of more than 99% of environmental microorganisms and uncovered functional gene diversity of environmental microorganisms.

    DOI

  • Regionalized nervous system in Hydra and the mechanism of its development.

    Yukihiko Noro, Seungshic Yum, Chiemi Nishimiya-Fujisawa, Christina Busse, Hiroshi Shimizu, Katsuhiko Mineta, Xiaoming Zhang, Thomas W Holstein, Charles N David, Takashi Gojobori, Toshitaka Fujisawa

    Gene expression patterns : GEP   31   42 - 59  2019.01  [Refereed]  [International journal]

     View Summary

    The last common ancestor of Bilateria and Cnidaria is considered to develop a nervous system over 500 million years ago. Despite the long course of evolution, many of the neuron-related genes, which are active in Bilateria, are also found in the cnidarian Hydra. Thus, Hydra is a good model to study the putative primitive nervous system in the last common ancestor that had the great potential to evolve to a more advanced one. Regionalization of the nervous system is one of the advanced features of bilaterian nervous system. Although a regionalized nervous system is already known to be present in Hydra, its developmental mechanisms are poorly understood. In this study we show how it is formed and maintained, focusing on the neuropeptide Hym-176 gene and its paralogs. First, we demonstrate that four axially localized neuron subsets that express different combination of the neuropeptide Hym-176 gene and its paralogs cover almost an entire body, forming a regionalized nervous system in Hydra. Second, we show that positional information governed by the Wnt signaling pathway plays a key role in determining the regional specificity of the neuron subsets as is the case in bilaterians. Finally, we demonstrated two basic mechanisms, regionally restricted new differentiation and phenotypic conversion, both of which are in part conserved in bilaterians, are involved in maintaining boundaries between the neuron subsets. Therefore, this study is the first comprehensive analysis of the anatomy and developmental regulation of the divergently evolved and axially regionalized peptidergic nervous system in Hydra, implicating an ancestral origin of neural regionalization.

    DOI PubMed

  • Comparative genome and transcriptome analysis of diatom, Skeletonema costatum, reveals evolution of genes for harmful algal bloom

    Atsushi Ogura, Yuki Akizuki, Hiroaki Imoda, Katsuhiko Mineta, Takashi Gojobori, Satoshi Nagai

    BMC Genomics   19 ( 1 )  2018.10  [Refereed]  [International journal]

     View Summary

    Background: Diatoms play a great role in carbon fixation with about 20% of the whole fixation in the world. However, harmful algal bloom as known as red tide is a major problem in environment and fishery industry. Even though intensive studies have been conducted so far, the molecular mechanism behind harmful algal bloom was not fully understood. There are two major diatoms have been sequenced, but more diatoms should be examined at the whole genome level, and evolutionary genome studies were required to understand the landscape of molecular mechanism of the harmful algal bloom. Results: Here we sequenced the genome of Skeletonema costatum, which is the dominant diatom in Japan causing a harmful algal bloom, and also performed RNA-sequencing analysis for conditions where harmful algal blooms often occur. As results, we found that both evolutionary genomic and comparative transcriptomic studies revealed genes for oxidative stress response and response to cytokinin is a key for the proliferation of the diatom. Conclusions: Diatoms causing harmful algal blooms have gained multi-copy of genes related to oxidative stress response and response to cytokinin and obtained an ability to intensive gene expression at the blooms.

    DOI PubMed

  • Vocal practice regulates singing activity-dependent genes underlying age-independent vocal learning in songbirds.

    Shin Hayase, Hongdi Wang, Eri Ohgushi, Masahiko Kobayashi, Chihiro Mori, Haruhito Horita, Katsuhiko Mineta, Wan-Chun Liu, Kazuhiro Wada

    PLoS biology   16 ( 9 ) e2006537  2018.09  [Refereed]  [International journal]

     View Summary

    The development of highly complex vocal skill, like human language and bird songs, is underlain by learning. Vocal learning, even when occurring in adulthood, is thought to largely depend on a sensitive/critical period during postnatal development, and learned vocal patterns emerge gradually as the long-term consequence of vocal practice during this critical period. In this scenario, it is presumed that the effect of vocal practice is thus mainly limited by the intrinsic timing of age-dependent maturation factors that close the critical period and reduce neural plasticity. However, an alternative, as-yet untested hypothesis is that vocal practice itself, independently of age, regulates vocal learning plasticity. Here, we explicitly discriminate between the influences of age and vocal practice using a songbird model system. We prevented zebra finches from singing during the critical period of sensorimotor learning by reversible postural manipulation. This enabled to us to separate lifelong vocal experience from the effects of age. The singing-prevented birds produced juvenile-like immature song and retained sufficient ability to acquire a tutored song even at adulthood when allowed to sing freely. Genome-wide gene expression network analysis revealed that this adult vocal plasticity was accompanied by an intense induction of singing activity-dependent genes, similar to that observed in juvenile birds, rather than of age-dependent genes. The transcriptional changes of activity-dependent genes occurred in the vocal motor robust nucleus of the arcopallium (RA) projection neurons that play a critical role in the production of song phonology. These gene expression changes were accompanied by neuroanatomical changes: dendritic spine pruning in RA projection neurons. These results show that self-motivated practice itself changes the expression dynamics of activity-dependent genes associated with vocal learning plasticity and that this process is not tightly linked to age-dependent maturational factors.

    DOI PubMed

  • Global Ramifications of Dust and Sandstorm Microbiota.

    Hayedeh Behzad, Katsuhiko Mineta, Takashi Gojobori

    Genome biology and evolution   10 ( 8 ) 1970 - 1987  2018.08  [Refereed]  [International journal]

     View Summary

    Dust and sandstorm events inject substantial quantities of foreign microorganisms into global ecosystems, with the ability to impact distant environments. The majority of these microorganisms originate from deserts and drylands where the soil is laden with highly stress-resistant microbes capable of thriving under extreme environmental conditions, and a substantial portion of them survive long journeys through the atmosphere. This large-scale transmission of highly resilient alien microbial contaminants raises concerns with regards to the invasion of sensitive and/or pristine sink environments, and to human health-concerns exacerbated by increases in the rate of desertification. Further increases in the transport of dust-associated microbiota could extend the spread of foreign microbes to new ecosystems, increase their load in present sink environments, disrupt ecosystem balance, and potentially introduce new pathogens. Our present understanding of these microorganisms, their phylogenic affiliations and functional significance, is insufficient to determine their impact. The purpose of this review is to provide an overview of available data regarding dust and sandstorm microbiota and their potential ramifications on human and ecosystem health. We conclude by discussing current gaps in dust and sandstorm microbiota research, and the need for collaborative studies involving high-resolution meta-omic approaches in conjunction with extensive ecological time-series studies to advance the field towards an improved and sufficient understanding of these invisible atmospheric travelers and their global ramifications.

    DOI PubMed

  • Basin-scale seasonal changes in marine free-living bacterioplankton community in the Ofunato Bay.

    Md Shaheed Reza, Atsushi Kobiyama, Yuichiro Yamada, Yuri Ikeda, Daisuke Ikeda, Nanami Mizusawa, Kazuho Ikeo, Shigeru Sato, Takehiko Ogata, Mitsuru Jimbo, Toshiaki Kudo, Shinnosuke Kaga, Shiho Watanabe, Kimiaki Naiki, Yoshimasa Kaga, Katsuhiko Mineta, Vladimir Bajic, Takashi Gojobori, Shugo Watabe

    Gene   665   185 - 191  2018.07  [Refereed]  [International journal]

     View Summary

    The Ofunato Bay in the northeastern Pacific Ocean area of Japan possesses the highest biodiversity of marine organisms in the world and has attracted much attention due to its economic and environmental importance. We report here a shotgun metagenomic analysis of the year-round variation in free-living bacterioplankton collected across the entire length of the bay. Phylogenetic differences among spring, summer, autumn and winter bacterioplankton suggested that members of Proteobacteria tended to decrease at high water temperatures and increase at low temperatures. It was revealed that Candidatus Pelagibacter varied seasonally, reaching as much as 60% of all sequences at the genus level in the surface waters during winter. This increase was more evident in the deeper waters, where they reached up to 75%. The relative abundance of Planktomarina also rose during winter and fell during summer. A significant component of the winter bacterioplankton community was Archaea (mainly represented by Nitrosopumilus), as their relative abundance was very low during spring and summer but high during winter. In contrast, Actinobacteria and Cyanobacteria appeared to be higher in abundance during high-temperature periods. It was also revealed that Bacteroidetes constituted a significant component of the summer bacterioplankton community, being the second largest bacterial phylum detected in the Ofunato Bay. Its members, notably Polaribacter and Flavobacterium, were found to be high in abundance during spring and summer, particularly in the surface waters. Principal component analysis and hierarchal clustering analyses showed that the bacterial communities in the Ofunato Bay changed seasonally, likely caused by the levels of organic matter, which would be deeply mixed with surface runoff in the winter.

    DOI PubMed

  • Seasonal changes in the communities of photosynthetic picoeukaryotes in Ofunato Bay as revealed by shotgun metagenomic sequencing.

    Jonaira Rashid, Atsushi Kobiyama, Md Shaheed Reza, Yuichiro Yamada, Yuri Ikeda, Daisuke Ikeda, Nanami Mizusawa, Kazuho Ikeo, Shigeru Sato, Takehiko Ogata, Toshiaki Kudo, Shinnosuke Kaga, Shiho Watanabe, Kimiaki Naiki, Yoshimasa Kaga, Katsuhiko Mineta, Vladimir Bajic, Takashi Gojobori, Shugo Watabe

    Gene   665   127 - 132  2018.07  [Refereed]  [International journal]

     View Summary

    Small photosynthetic eukaryotes play important roles in oceanic food webs in coastal regions. We investigated seasonal changes in the communities of photosynthetic picoeukaryotes (PPEs) of the class Mamiellophyceae, including the genera Bathycoccus, Micromonas and Ostreococcus, in Ofunato Bay, which is located in northeastern Japan and faces the Pacific Ocean. The abundances of PPEs were assessed over a period of one year in 2015 at three sampling stations, KSt. 1 (innermost bay area), KSt. 2 (middle bay area) and KSt. 3 (bay entrance area) at depths of 1 m (KSt. 1, KSt. 2 and KSt. 3), 8 m (KSt. 1) or 10 m (KSt. 2 and KSt. 3) by employing MiSeq shotgun metagenomic sequencing. The total abundances of Bathycoccus, Ostreococcus and Micromonas were in the ranges of 42-49%, 35-49% and 13-17%, respectively. Considering all assayed sampling stations and depths, seasonal changes revealed high abundances of PPEs during the winter and summer and low abundances during late winter to early spring and late summer to early autumn. Bathycoccus was most abundant in the winter, and Ostreococcus showed a high abundance during the summer. Another genus, Micromonas, was relatively low in abundance throughout the study period. Taken together with previously suggested blooming periods of phytoplankton, as revealed by chlorophyll a concentrations in Ofunato Bay during spring and autumn, these results for PPEs suggest that greater phytoplankton blooming has a negative influence on the seasonal occurrences of PPEs in the bay.

    DOI PubMed

  • Taxonomic profiles in metagenomic analyses of free-living microbial communities in the Ofunato Bay.

    Reza MS, Kobiyama A, Yamada Y, Ikeda Y, Ikeda D, Mizusawa N, Ikeo K, Sato S, Ogata T, Jimbo M, Kudo T, Kaga S, Watanabe S, Naiki K, Kaga Y, Mineta K, Bajic V, Gojobori T, Watabe S

    Gene   665   192 - 200  2018.07  [Refereed]  [International journal]

    DOI PubMed

  • Seasonal changes in the abundance of bacterial genes related to dimethylsulfoniopropionate catabolism in seawater from Ofunato Bay revealed by metagenomic analysis.

    Kudo T, Kobiyama A, Rashid J, Reza MS, Yamada Y, Ikeda Y, Ikeda D, Mizusawa N, Ikeo K, Sato S, Ogata T, Jimbo M, Kaga S, Watanabe S, Naiki K, Kaga Y, Segawa S, Mineta K, Bajic V, Gojobori T, Watabe S

    Gene   665   174 - 184  2018.07  [Refereed]  [International journal]

    DOI PubMed

  • Metagenome-based diversity analyses suggest a strong locality signal for bacterial communities associated with oyster aquaculture farms in Ofunato Bay.

    Kobiyama A, Ikeo K, Reza MS, Rashid J, Yamada Y, Ikeda Y, Ikeda D, Mizusawa N, Sato S, Ogata T, Jimbo M, Kudo T, Kaga S, Watanabe S, Naiki K, Kaga Y, Mineta K, Bajic V, Gojobori T, Watabe S

    Gene   665   149 - 154  2018.07  [Refereed]  [International journal]

    DOI PubMed

  • Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting.

    Alyaa M. Abdel-Haleem, Hooman Hefzi, Katsuhiko Mineta, Xin Gao 0001, Takashi Gojobori, Bernhard O. Palsson, Nathan E. Lewis, Neema Jamshidi

    PLoS Computational Biology   14 ( 1 )  2018  [Refereed]  [International journal]

    DOI

  • Coordinated regulations of mRNA synthesis and decay during cold acclimation in arabidopsis cells

    Toshihiro Arae, Shiori Isai, Akira Sakai, Katsuhiko Mineta, Masami Yokota Hirai, Yuya Suzuki, Shigehiko Kanaya, Junji Yamaguchi, Satoshi Naito, Yukako Chiba

    Plant & Cell Physiology   58 ( 6 ) 1090 - 1102  2017.07  [Refereed]  [International journal]

     View Summary

    Plants possess a cold acclimation system to acquire freezing tolerance through pre-exposure to non-freezing low temperatures. The transcriptional cascade of C-repeat-binding factors (CBFs)/dehydration response element-binding factors (DREBs) is considered a major transcriptional regulatory pathway during cold acclimation. However, little is known regarding the functional significance of mRNA stability regulation in the response of gene expression to cold stress. The actual level of individual mRNAs is determined by a balance between mRNA synthesis and degradation. Therefore, it is important to assess the regulatory steps to increase our understanding of gene regulation. Here, we analyzed temporal changes in mRNA amounts and half-lives in response to cold stress in Arabidopsis cell cultures based on genome-wide analysis. In this mRNA decay array method, mRNA half-life measurements and microarray analyses were combined. In addition, temporal changes in the integrated value of transcription rates were estimated from the above two parameters using a mathematical approach. Our results showed that several cold-responsive genes, including Cold-regulated 15a, were relatively destabilized, whereas the mRNA amounts were increased during cold treatment by accelerating the transcription rate to overcome the destabilization. Considering the kinetics of mRNA synthesis and degradation, this apparently contradictory result supports that mRNA destabilization is advantageous for the swift increase in CBF-responsive genes in response to cold stress.

    DOI PubMed

  • Corrigendum: The genome of Chenopodium quinoa.

    David E Jarvis, Yung Shwen Ho, Damien J Lightfoot, Sandra M Schmöckel, Bo Li, Theo J A Borm, Hajime Ohyanagi, Katsuhiko Mineta, Craig T Michell, Noha Saber, Najeh M Kharbatia, Ryan R Rupper, Aaron R Sharp, Nadine Dally, Berin A Boughton, Yong H Woo, Ge Gao, Elio G W M Schijlen, Xiujie Guo, Afaque A Momin, Sónia Negrão, Salim Al-Babili, Christoph Gehring, Ute Roessner, Christian Jung, Kevin Murphy, Stefan T Arold, Takashi Gojobori, C Gerard van der Linden, Eibertus N van Loo, Eric N Jellen, Peter J Maughan, Mark Tester

    Nature   545 ( 7655 ) 510 - 510  2017.05  [Refereed]  [International journal]

     View Summary

    This corrects the article DOI: 10.1038/nature21370.

    DOI PubMed

  • FARNA: knowledgebase of inferred functions of non-coding RNA transcripts

    Tanvir Alam, Mahmut Uludag, Magbubah Essack, Adil Salhi, Haitham Ashoor, John B. Hanks, Craig Kapfer, Katsuhiko Mineta, Takashi Gojobori, Vladimir B. Bajic

    NUCLEIC ACIDS RESEARCH   45 ( 5 ) 2838 - 2848  2017.03  [Refereed]  [International journal]

     View Summary

    Non-coding RNA (ncRNA) genes play a major role in control of heterogeneous cellular behavior. Yet, their functions are largely uncharacterized. Current available databases lack in-depth information of ncRNA functions across spectrum of various cells/tissues. Here, we present FARNA, a knowledgebase of inferred functions of 10,289 human ncRNA transcripts ( 2,734 microRNA and 7,555 long ncRNA) in 119 tissues and 177 primary cells of human. Since transcription factors (TFs) and TF co-factors (TcoFs) are crucial components of regulatory machinery for activation of gene transcription, cellular processes and diseases in which TFs and TcoFs are involved suggest functions of the transcripts they regulate. In FARNA, functions of a transcript are inferred from TFs and TcoFs whose genes co-express with the transcript controlled by these TFs and TcoFs in a considered cell/tissue. Transcripts were annotated using statistically enriched GO terms, pathways and diseases across cells/tissues based on guilt-by-association principle. Expression profiles across cells/tissues based on Cap Analysis of Gene Expression (CAGE) are provided. FARNA, having the most comprehensive function annotation of considered ncRNAs across widest spectrum of human cells/tissues, has a potential to greatly contribute to our understanding of ncRNA roles and their regulatory mechanisms in human. FARNA can be accessed at: http://cbrc.kaust.edu.sa/farna

    DOI

  • The genome of Chenopodium quinoa

    David E. Jarvis, Yung Shwen Ho, Damien J. Lightfoot, Sandra M. Schmockel, Bo Li, Theo J. A. Borm, Hajime Ohyanagi, Katsuhiko Mineta, Craig T. Michell, Noha Saber, Najeh M. Kharbatia, Ryan R. Rupper, Aaron R. Sharp, Nadine Dally, Berin A. Boughton, Yong H. Woo, Ge Gao, Elio G. W. M. Schijlen, Xiujie Guo, Afaque A. Momin, Sonia Negrao, Salim Al-Babili, Christoph Gehring, Ute Roessner, Christian Jung, Kevin Murphy, Stefan T. Arold, Takashi Gojobori, C. Gerard van der Linden, Eibertus N. van Loo, Eric N. Jellen, Peter J. Maughan, Mark Tester

    NATURE   542 ( 7641 ) 307 - +  2017.02  [Refereed]  [International journal]

     View Summary

    Chenopodium quinoa (quinoa) is a highly nutritious grain identified as an important crop to improve world food security. Unfortunately, few resources are available to facilitate its genetic improvement. Here we report the assembly of a high-quality, chromosome-scale reference genome sequence for quinoa, which was produced using single-molecule real-time sequencing in combination with optical, chromosome-contact and genetic maps. We also report the sequencing of two diploids from the ancestral gene pools of quinoa, which enables the identification of sub-genomes in quinoa, and reduced-coverage genome sequences for 22 other samples of the allotetraploid goosefoot complex. The genome sequence facilitated the identification of the transcription factor likely to control the production of anti-nutritional triterpenoid saponins found in quinoa seeds, including a mutation that appears to cause alternative splicing and a premature stop codon in sweet quinoa strains. These genomic resources are an important first step towards the genetic improvement of quinoa.

    DOI

  • In silico screening for candidate chassis strains of free fatty acid-producing cyanobacteria.

    Olaa Motwalli, Magbubah Essack, Boris R Jankovic, Boyang Ji, Xinyao Liu, Hifzur Rahman Ansari, Robert Hoehndorf, Xin Gao, Stefan T Arold, Katsuhiko Mineta, John A C Archer, Takashi Gojobori, Ivan Mijakovic, Vladimir B Bajic

    BMC genomics   18 ( 1 ) 33 - 33  2017.01  [Refereed]  [International journal]

     View Summary

    BACKGROUND: Finding a source from which high-energy-density biofuels can be derived at an industrial scale has become an urgent challenge for renewable energy production. Some microorganisms can produce free fatty acids (FFA) as precursors towards such high-energy-density biofuels. In particular, photosynthetic cyanobacteria are capable of directly converting carbon dioxide into FFA. However, current engineered strains need several rounds of engineering to reach the level of production of FFA to be commercially viable; thus new chassis strains that require less engineering are needed. Although more than 120 cyanobacterial genomes are sequenced, the natural potential of these strains for FFA production and excretion has not been systematically estimated. RESULTS: Here we present the FFA SC (FFASC), an in silico screening method that evaluates the potential for FFA production and excretion of cyanobacterial strains based on their proteomes. A literature search allowed for the compilation of 64 proteins, most of which influence FFA production and a few of which affect FFA excretion. The proteins are classified into 49 orthologous groups (OGs) that helped create rules used in the scoring/ranking of algorithms developed to estimate the potential for FFA production and excretion of an organism. Among 125 cyanobacterial strains, FFASC identified 20 candidate chassis strains that rank in their FFA producing and excreting potential above the specifically engineered reference strain, Synechococcus sp. PCC 7002. We further show that the top ranked cyanobacterial strains are unicellular and primarily include Prochlorococcus (order Prochlorales) and marine Synechococcus (order Chroococcales) that cluster phylogenetically. Moreover, two principal categories of enzymes were shown to influence FFA production the most: those ensuring precursor availability for the biosynthesis of lipids, and those involved in handling the oxidative stress associated to FFA synthesis. CONCLUSION: To our knowledge FFASC is the first in silico method to screen cyanobacteria proteomes for their potential to produce and excrete FFA, as well as the first attempt to parameterize the criteria derived from genetic characteristics that are favorable/non-favorable for this purpose. Thus, FFASC helps focus experimental evaluation only on the most promising cyanobacteria.

    DOI PubMed

  • The Emerging Facets of Non-Cancerous Warburg Effect.

    Alyaa M Abdel-Haleem, Nathan E Lewis, Neema Jamshidi, Katsuhiko Mineta, Xin Gao, Takashi Gojobori

    Frontiers in endocrinology   8   279 - 279  2017  [Refereed]  [International journal]

     View Summary

    The Warburg effect (WE), or aerobic glycolysis, is commonly recognized as a hallmark of cancer and has been extensively studied for potential anti-cancer therapeutics development. Beyond cancer, the WE plays an important role in many other cell types involved in immunity, angiogenesis, pluripotency, and infection by pathogens (e.g., malaria). Here, we review the WE in non-cancerous context as a "hallmark of rapid proliferation." We observe that the WE operates in rapidly dividing cells in normal and pathological states that are triggered by internal and external cues. Aerobic glycolysis is also the preferred metabolic program in the cases when robust transient responses are needed. We aim to draw attention to the potential of computational modeling approaches in systematic characterization of common metabolic features beyond the WE across physiological and pathological conditions. Identification of metabolic commonalities across various diseases may lead to successful repurposing of drugs and biomarkers.

    DOI PubMed

  • Low Concentrations of Vitamin C Reduce the Synthesis of Extracellular Polymers and Destabilize Bacterial Biofilms.

    Santosh Pandit, Vaishnavi Ravikumar, Alyaa M Abdel-Haleem, Abderahmane Derouiche, V R S S Mokkapati, Carina Sihlbom, Katsuhiko Mineta, Takashi Gojobori, Xin Gao, Fredrik Westerlund, Ivan Mijakovic

    Frontiers in microbiology   8   2599 - 2599  2017  [Refereed]  [International journal]

     View Summary

    Extracellular polymeric substances (EPS) produced by bacteria form a matrix supporting the complex three-dimensional architecture of biofilms. This EPS matrix is primarily composed of polysaccharides, proteins and extracellular DNA. In addition to supporting the community structure, the EPS matrix protects bacterial biofilms from the environment. Specifically, it shields the bacterial cells inside the biofilm, by preventing antimicrobial agents from getting in contact with them, thereby reducing their killing effect. New strategies for disrupting the formation of the EPS matrix can therefore lead to a more efficient use of existing antimicrobials. Here we examined the mechanism of the known effect of vitamin C (sodium ascorbate) on enhancing the activity of various antibacterial agents. Our quantitative proteomics analysis shows that non-lethal concentrations of vitamin C inhibit bacterial quorum sensing and other regulatory mechanisms underpinning biofilm development. As a result, the EPS biosynthesis in reduced, and especially the polysaccharide component of the matrix is depleted. Once the EPS content is reduced beyond a critical point, bacterial cells get fully exposed to the medium. At this stage, the cells are more susceptible to killing, either by vitamin C-induced oxidative stress as reported here, or by other antimicrobials or treatments.

    DOI PubMed

  • Databases of the marine metagenomics

    Katsuhiko Mineta, Takashi Gojobori

    GENE   576 ( 2 ) 724 - 728  2016.02  [Refereed]  [International journal]

    Authorship:Lead author

     View Summary

    The metagenomic data obtained from marine environments is significantly useful for understanding marine microbial communities. In comparison with the conventional amplicon-based approach of metagenomics, the recent shotgun sequencing-based approach has become a powerful tool that provides an efficient way of grasping a diversity of the entire microbial community at a sampling point in the sea. However, this approach accelerates accumulation of the metagenome data as well as increase of data complexity. Moreover, when metagenomic approach is used for monitoring a time change of marine environments at multiple locations of the seawater, accumulation of metagenomics data will become tremendous with an enormous speed. Because this kind of situation has started becoming of reality at many marine research institutions and stations all over the world, it looks obvious that the data management and analysis will be confronted by the so-called Big Data issues such as how the database can be constructed in an efficient way and how useful knowledge should be extracted from a vast amount of the data. In this review, we summarize the outline of all the major databases of marine metagenome that are currently publically available, noting that database exclusively on marine metagenome is none but the number of metagenome databases including marine metagenome data are six, unexpectedly still small. We also extend our explanation to the databases, as reference database we call, that will be useful for constructing a marine metagenome database as well as complementing important information with the database. Then, we would point out a number of challenges to be conquered in constructing the marine metagenome database. (C) 2015 Elsevier B.V. All rights reserved.

    DOI

  • Metagenomic studies of the Red Sea

    Hayedeh Behzad, Martin Augusto Ibarra, Katsuhiko Mineta, Takashi Gojobori

    GENE   576 ( 2 ) 717 - 723  2016.02  [Refereed]  [International journal]

     View Summary

    Metagenomics has significantly advanced the field of marine microbial ecology, revealing the vast diversity of previously unknown microbial life forms in different marine niches. The tremendous amount of data generated has enabled identification of a large number of microbial genes (metagenomes), their community interactions, adaptation mechanisms, and their potential applications in pharmaceutical and biotechnology-based industries. Comparative metagenomics reveals that microbial diversity is a function of the local environment, meaning that unique or unusual environments typically harbor novel microbial species with unique genes and metabolic pathways. The Red Sea has an abundance of unique characteristics; however, its microbiota is one of the least studied among marine environments. The Red Sea harbors approximately 25 hot anoxic brine pools, plus a vibrant coral reef ecosystem. Physiochemical studies describe the Red Sea as an oligotrophic environment that contains one of the warmest and saltiest waters in the world with year-round high UV radiations. These characteristics are believed to have shaped the evolution of microbial communities in the Red Sea. Over-representation of genes involved in DNA repair, high-intensity light responses, and osmoregulation were found in the Red Sea metagenomic databases suggesting acquisition of specific environmental adaptation by the Red Sea microbiota. The Red Sea brine pools harbor a diverse range of halophilic and thermophilic bacterial and archaeal communities, which are potential sources of enzymes for pharmaceutical and biotechnology-based application. Understanding the mechanisms of these adaptations and their function within the larger ecosystem could also prove useful in light of predicted global warming scenarios where global ocean temperatures are expected to rise by 1-3 degrees C in the next few decades. In this review, we provide an overview of the published metagenomic studies that were conducted in the Red Sea, and the bio-prospecting potential of the Red Sea microbiota. Furthermore, we discuss the limitations of the previous studies and the need for generating a large and representative metagenomic database of the Red Sea to help establish a dynamic model of the Red Sea microbiota. (C) 2015 Elsevier B.V. All rights reserved.

    DOI

  • DESM: portal for microbial knowledge exploration systems

    Adil Salhi, Magbubah Essack, Aleksandar Radovanovic, Benoit Marchand, Salim Bougouffa, Andre Antunes, Marta Filipa Simoes, Feras F. Lafi, Olaa A. Motwalli, Ameerah Bokhari, Tariq Malas, Soha Al Amoudi, Ghofran Othum, Intikhab Allam, Katsuhiko Mineta, Xin Gao, Robert Hoehndorf, John A. C. Archer, Takashi Gojobori, Vladimir B. Bajic

    NUCLEIC ACIDS RESEARCH   44 ( D1 ) D624 - D633  2016.01  [Refereed]  [International journal]

     View Summary

    Microorganisms produce an enormous variety of chemical compounds. It is of general interest for microbiology and biotechnology researchers to have means to explore information about molecular and genetic basis of functioning of different microorganisms and their ability for bioproduction. To enable such exploration, we compiled 45 topic-specific knowledgebases (KBs) accessible through DESM portal (www.cbrc.kaust.edu.sa/desm). The KBs contain information derived through text-mining of PubMed information and complemented by information data-mined from various other resources (e.g. ChEBI, Entrez Gene, GO, KOBAS, KEGG, UniPathways, BioGrid). All PubMed records were indexed using 4 538 278 concepts from 29 dictionaries, with 1 638 986 records utilized in KBs. Concepts used are normalized whenever possible. Most of the KBs focus on a particular type of microbial activity, such as production of biocatalysts or nutraceuticals. Others are focused on specific categories of microorganisms, e.g. streptomyces or cyanobacteria. KBs are all structured in a uniform manner and have a standardized user interface. Information exploration is enabled through various searches. Users can explore statistically most significant concepts or pairs of concepts, generate hypotheses, create interactive networks of associated concepts and export results. We believe DESM will be a useful complement to the existing resources to benefit microbiology and biotechnology research.

    DOI

  • Claudin-21 Has a Paracellular Channel Role at Tight Junctions.

    Tanaka H, Yamamoto Y, Kashihara H, Yamazaki Y, Tani K, Fujiyoshi Y, Mineta K, Takeuchi K, Tamura A, Tsukita S

    Molecular and cellular biology   36 ( 6 ) 954 - 964  2016.01  [Refereed]  [International journal]

    DOI PubMed

  • An Individual-Based Diploid Model Predicts Limited Conditions Under Which Stochastic Gene Expression Becomes Advantageous.

    Matsumoto T, Mineta K, Osada N, Araki H

    Frontiers in genetics   6 ( NOV ) 336 - 336  2015.11  [Refereed]  [International journal]

    DOI PubMed CiNii J-GLOBAL

  • Marine Metagenome as A Resource for Novel Enzymes.

    Amani D. Alma'abadi, Takashi Gojobori, Katsuhiko Mineta

    Genomics, Proteomics & Bioinformatics   13 ( 5 ) 290 - 295  2015.10  [Refereed]  [International journal]

    Authorship:Last author

     View Summary

    More than 99% of identified prokaryotes, including many from the marine environment, cannot be cultured in the laboratory. This lack of capability restricts our knowledge of microbial genetics and community ecology. Metagenomics, the culture-independent cloning of environmental DNAs that are isolated directly from an environmental sample, has already provided a wealth of information about the uncultured microbial world. It has also facilitated the discovery of novel biocatalysts by allowing researchers to probe directly into a huge diversity of enzymes within natural microbial communities. Recent advances in these studies have led to a great interest in recruiting microbial enzymes for the development of environmentally-friendly industry. Although the metagenomics approach has many limitations, it is expected to provide not only scientific insights but also economic benefits, especially in industry. This review highlights the importance of metagenomics in mining microbial lipases, as an example, by using high-throughput techniques. In addition, we discuss challenges in the metagenomics as an important part of bioinformatics analysis in big data.

    DOI

  • Population genetics of non-genetic traits: evolutionary roles of stochasticity in gene expression.

    Mineta K, Matsumoto T, Osada N, Araki H

    Gene   562 ( 1 ) 16 - 21  2015.05  [Refereed]  [International journal]

    Authorship:Lead author

    DOI PubMed J-GLOBAL

  • Challenges and Opportunities of Airborne Metagenomics

    Hayedeh Behzad, Takashi Gojobori, Katsuhiko Mineta

    GENOME BIOLOGY AND EVOLUTION   7 ( 5 ) 1216 - 1226  2015.05  [Refereed]  [International journal]

    Authorship:Last author

     View Summary

    Recent metagenomic studies of environments, such as marine and soil, have significantly enhanced our understanding of the diverse microbial communities living in these habitats and their essential roles in sustaining vast ecosystems. The increase in the number of publications related to soil and marine metagenomics is in sharp contrast to those of air, yet airborne microbes are thought to have significant impacts on many aspects of our lives from their potential roles in atmospheric events such as cloud formation, precipitation, and atmospheric chemistry to their major impact on human health. In this review, we will discuss the current progress in airborne metagenomics, with a special focus on exploring the challenges and opportunities of undertaking such studies. The main challenges of conducting metagenomic studies of airborne microbes are as follows: 1) Low density of microorganisms in the air, 2) efficient retrieval of microorganisms from the air, 3) variability in airborne microbial community composition, 4) the lack of standardized protocols and methodologies, and 5) DNA sequencing and bioinformatics-related challenges. Overcoming these challenges could provide the groundwork for comprehensive analysis of airborne microbes and their potential impact on the atmosphere, global climate, and our health. Metagenomic studies offer a unique opportunity to examine viral and bacterial diversity in the air and monitor their spread locally or across the globe, including threats from pathogenic microorganisms. Airborne metagenomic studies could also lead to discoveries of novel genes and metabolic pathways relevant to meteorological and industrial applications, environmental bioremediation, and biogeochemical cycles.

    DOI

  • Evolutionary Divergence of Plant Borate Exporters and Critical Amino Acid Residues for the Polar Localization and Boron-Dependent Vacuolar Sorting of AtBOR1.

    Wakuta S, Mineta K, Amano T, Toyoda A, Fujiwara T, Naito S, Takano J

    Plant and Cell Physiology   56 ( 5 ) 852 - 862  2015  [Refereed]  [International journal]

    DOI PubMed CiNii

  • The four-transmembrane protein IP39 of Euglena forms strands by a trimeric unit repeat

    Hiroshi Suzuki, Yasuyuki Ito, Yuji Yamazaki, Katsuhiko Mineta, Masami Uji, Kazuhiro Abe, Kazutoshi Tani, Yoshinori Fujiyoshi, Sachiko Tsukita

    NATURE COMMUNICATIONS   4   1766  2013.04  [Refereed]  [International journal]

     View Summary

    Euglenoid flagellates have striped surface structures comprising pellicles, which allow the cell shape to vary from rigid to flexible during the characteristic movement of the flagellates. In Euglena gracilis, the pellicular strip membranes are covered with paracrystalline arrays of a major integral membrane protein, IP39, a putative four-membrane-spanning protein with the conserved sequence motif of the PMP-22/EMP/MP20/Claudin superfamily. Here we report the three-dimensional structure of Euglena IP39 determined by electron crystallography. Two-dimensional crystals of IP39 appear to form a striated pattern of antiparallel double-rows in which trimeric IP39 units are longitudinally polymerised, resulting in continuously extending zigzag-shaped lines. Structural analysis revealed an asymmetric molecular arrangement in the trimer, and suggested that at least four different interactions between neighbouring protomers are involved. A combination of such multiple interactions would be important for linear strand formation of membrane proteins in a lipid bilayer.

    DOI PubMed

  • Changes in mRNA stability associated with cold stress in arabidopsis cells

    Yukako Chiba, Katsuhiko Mineta, Masami Y. Hirai, Yuya Suzuki, Shigehiko Kanaya, Hiro Takahashi, Hitoshi Onouchi, Junji Yamaguchi, Satoshi Naito

    Plant and Cell Physiology   54 ( 2 ) 181 - 194  2013  [Refereed]  [International journal]

     View Summary

    Control of mRNA half-life is a powerful strategy to adjust individual mRNA levels to various stress conditions, because the mRNA degradation rate controls not only the steady-state mRNA level but also the transition speed of mRNA levels. Here, we analyzed mRNA half-life changes in response to cold stress in Arabidopsis cells using genome-wide analysis, in which mRNA half-life measurements and transcriptome analysis were combined. Half-lives of average transcripts were determined to be elongated under cold conditions. Taking this general shift into account, we identified more than a thousand transcripts that were classified as relatively stabilized or relatively destabilized. The relatively stabilized class was predominantly observed in functional categories that included various regulators involved in transcriptional, post-transcriptional and post-translational processes. On the other hand, the relatively destabilized class was enriched in categories related to stress and hormonal response proteins, supporting the idea that rapid decay of mRNA is advantageous for swift responses to stress. In addition, pentatricopeptide repeat, cyclin-like F-box and Myb transcription factor protein families were significantly over-represented in the relatively destabilized class. The global analysis presented here demonstrates not only the importance of mRNA turnover control in the cold stress response but also several structural characteristics that might be important in the control of mRNA stability. © 2011 The Author 2012. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved.

    DOI PubMed

  • Strand formation by a trimeric unit repeat of four-transmembrane proteins in Euglena

    H. Suzuki, Y. Ito, Y. Yamazaki, K. Mineta, M. Uji, K. Abe, K. Tani, Y. Fujiyoshi, S. Tsukita

    Nat. Commun   4  2013  [Refereed]  [International journal]

    DOI J-GLOBAL

  • Exploring functionally related enzymes using radially distributed properties of active sites around the reacting points of bound ligands

    Keisuke Ueno, Katsuhiko Mineta, Kimihito Ito, Toshinori Endo

    BMC STRUCTURAL BIOLOGY   12   5  2012.04  [Refereed]  [International journal]

     View Summary

    Background: Structural genomics approaches, particularly those solving the 3D structures of many proteins with unknown functions, have increased the desire for structure-based function predictions. However, prediction of enzyme function is difficult because one member of a superfamily may catalyze a different reaction than other members, whereas members of different superfamilies can catalyze the same reaction. In addition, conformational changes, mutations or the absence of a particular catalytic residue can prevent inference of the mechanism by which catalytic residues stabilize and promote the elementary reaction. A major hurdle for alignment-based methods for prediction of function is the absence (despite its importance) of a measure of similarity of the physicochemical properties of catalytic sites. To solve this problem, the physicochemical features radially distributed around catalytic sites should be considered in addition to structural and sequence similarities.
    Results: We showed that radial distribution functions (RDFs), which are associated with the local structural and physicochemical properties of catalytic active sites, are capable of clustering oxidoreductases and transferases by function. The catalytic sites of these enzymes were also characterized using the RDFs. The RDFs provided a measure of the similarity among the catalytic sites, detecting conformational changes caused by mutation of catalytic residues. Furthermore, the RDFs reinforced the classification of enzyme functions based on conventional sequence and structural alignments.
    Conclusions: Our results demonstrate that the application of RDFs provides advantages in the functional classification of enzymes by providing information about catalytic sites.

    DOI PubMed

  • Predicted expansion of the claudin multigene family

    Katsuhiko Mineta, Yasuko Yamamoto, Yuji Yamazaki, Hiroo Tanaka, Yukiyo Tada, Kuniaki Saito, Atsushi Tamura, Michihiro Igarashi, Toshinori Endo, Kosei Takeuchi, Sachiko Tsukita

    FEBS LETTERS   585 ( 4 ) 606 - 612  2011.02  [Refereed]  [International journal]

    Authorship:Lead author, Corresponding author

     View Summary

    Claudins (Cldn) are essential membrane proteins of tight junctions (TJs), which form the paracellular permselective barrier. They are produced by a multi-gene family of 24 reported members in mouse and human. Based on a comprehensive search combined with phylogenetic analyses, we identified three novel claudins (claudin-25, -26, and -27). Quantitative RT-PCR revealed that the three novel claudins were expressed in a tissue- and/or developmental stage-dependent manner. Claudins-25 and -26, but not claudin-27, were immunofluorescently localized to TJs when exogenously expressed in cultured MDCK and Eph epithelial cell lines. These findings expand the claudin family to include at least 27 members.
    Structured summary:
    Claudin-25 and ZO-1 colocalize by fluorescence microscopy (View interaction)
    ZO-1 and Claudin-26 colocalize by fluorescence microscopy (View interaction) (C) 2011 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

    DOI PubMed

  • CIPRO 2.5: Ciona intestinalis Protein integrated database with large-scale omics data, bioinformatic analyses and curated annotation, with ability for user rating and comments

    Lixy Yamada, Mamoru Nomura, Michio Ogasawara, Junko Yaguchi, Hiroki Takahashi, Alu Konno, Ayako Nakajima, Sasakura Yasunori, Akiyasu Yoshizawa, Toshinori Endo, Hisaaki Taniguchi, Keisuke Ueno, Chisato Yamasaki, Kouki Yonezawa, Miho Sera, Katsuhiko Mineta, Tadashi Imanishi, Kazuo Inaba, Kohji Hotta, Mia Nakachi, Yutaka Satou

    Nature Precedings    2011.01

     View Summary

    Abstract

    CIPRO database is an integrated protein database for a tunicate species Ciona intestinalis that belongs to the Urochordata. Although the CIPRO database deals with proteomic and transcriptomic data of a single species, the animal is considered unique in the evolutionary tree, representing a possible origin of the vertebrates and is a good model for understanding chordate evolution, including that of humans. Furthermore, C. intestinalis has been one of the favorites of developmental biologists; there exists a huge amount of accumulated knowledge on its development and morphology, in addition to the recent genome sequence and gene expression data. The CIPRO database is aimed at not only collecting published data, but also presenting unique information, including the unpublished transcriptomic and proteomic data and human curated annotation, for the use by researchers in broad research fields of biology and bioinformatics.

    DOI

  • CIPRO 2.5

    Endo Toshinori, Ueno Keisuke, Yonezawa Kouki, Mineta Katsuhiko, Hotta Kohji, Satou Yutaka, Yamada Lixy, Ogasawara Michio, Takahashi Hiroki, Nakajima Ayako, Nakachi Mia, Nomura Mamoru, Yaguchi Junko, Sasakura Yasunori, Yamasaki Chisato, Sera Miho, Yoshizawa Akiyasu C, Imanishi Tadashi, Taniguchi Hisaaki, Inaba Kazuo

    Nucleic Acids Research   39 ( SUPPL. 1 )  2011.01

     View Summary

    &lt;p&gt;The Ciona intestinalis protein database (CIPRO) is an integrated protein database for the tunicate species C. intestinalis. The database is unique in two respects: first, because of its phylogenetic position, Ciona is suitable model for understanding vertebrate evolution; and second, the database includesoriginal large-scale transcriptomic and proteomic data. Ciona intestinalis has also been a favorite ofdevelopmental biologists. Therefore, large amounts of data exist on its development and morphology, along with a recent genome sequence and geneexpression data. The CIPRO database is aimed at collecting those published data as well as providing unique information from unpublished experimental data, such as 3D expression profiling, 2D-PAGE and mass spectrometry-based large-scale analysesat various developmental stages, curated annotation data and various bioinformatic data, to facilitate research in diverse areas, including developmental, comparative and evolutionary biology. For medical and evolutionary research, homologs in humans and major model organisms are intentionally included. The current database is based on a recently developed KH model containing 36 034 unique sequenc

    DOI

  • CIPRO 2.5: Ciona intestinalis protein database, a unique integrated repository of large-scale omics data, bioinformatic analyses and curated annotation, with user rating and reviewing functionality

    Toshinori Endo, Keisuke Ueno, Kouki Yonezawa, Katsuhiko Mineta, Kohji Hotta, Yutaka Satou, Lixy Yamada, Michio Ogasawara, Hiroki Takahashi, Ayako Nakajima, Mia Nakachi, Mamoru Nomura, Junko Yaguchi, Yasunori Sasakura, Chisato Yamasaki, Miho Sera, Akiyasu C. Yoshizawa, Tadashi Imanishi, Hisaaki Taniguchi, Kazuo Inaba

    NUCLEIC ACIDS RESEARCH   39   D807 - D814  2011.01  [Refereed]  [International journal]

     View Summary

    The Ciona intestinalis protein database (CIPRO) is an integrated protein database for the tunicate species C. intestinalis. The database is unique in two respects: first, because of its phylogenetic position, Ciona is suitable model for understanding vertebrate evolution; and second, the database includes original large-scale transcriptomic and proteomic data. Ciona intestinalis has also been a favorite of developmental biologists. Therefore, large amounts of data exist on its development and morphology, along with a recent genome sequence and gene expression data. The CIPRO database is aimed at collecting those published data as well as providing unique information from unpublished experimental data, such as 3D expression profiling, 2D-PAGE and mass spectrometry-based large-scale analyses at various developmental stages, curated annotation data and various bioinformatic data, to facilitate research in diverse areas, including developmental, comparative and evolutionary biology. For medical and evolutionary research, homologs in humans and major model organisms are intentionally included. The current database is based on a recently developed KH model containing 36 034 unique sequences, but for higher usability it covers 89 683 all known and predicted proteins from all gene models for this species. Of these sequences, more than 10 000 proteins have been manually annotated. Furthermore, to establish a community-supported protein database, these annotations are open to evaluation by users through the CIPRO website. CIPRO 2.5 is freely accessible at http://cipro.ibio.jp/2.5.

    DOI PubMed

  • Ancient genome-wide admixture extends beyond the current hybrid zone between Macaca fascicularis and M-mulatta

    Naoki Osada, Yasuhiro Uno, Katsuhiko Mineta, Yosuke Kameoka, Ichiro Takahashi, Keiji Terao

    MOLECULAR ECOLOGY   19 ( 14 ) 2884 - 2895  2010.07  [Refereed]  [International journal]

     View Summary

    Macaca fascicularis and Macaca mulatta are two of the most commonly used laboratory macaques, yet their genetic differences at a genome-wide level remain unclear. We analysed the multilocus DNA sequence data of 54 autosomal loci obtained from M. fascicularis samples from three different geographic origins and M. mulatta samples of Burmese origin. M. fascicularis shows high nucleotide diversity, four to five times higher than humans, and a strong geographic population structure between Indonesian-Malaysian and Philippine macaques. The pattern of divergence and polymorphism between M. fascicularis and M. mulatta shows a footprint of genetic exchange not only within their current hybrid zone but also across a wider range for more than 1 million years. However, genetic admixture may not be a random event in the genome. Whereas randomly selected genic and intergenic regions have the same evolutionary dynamics between the species, some cytochrome oxidase P450 (CYP) genes (major chemical metabolizing genes and potential target genes for local adaptation) have a significantly larger species divergence than other genes. By surveying CYP3A5 gene sequences of more than a hundred macaques, we identified three nonsynonymous single nucleotide polymorphisms that were highly differentiated between the macaques. The mosaic pattern of species divergence in the genomes may be a consequence of genetic differentiation under ecological adaptation and may be a salient feature in the genomes of nascent species under parapatry.

    DOI PubMed

  • Specific expression of Gsta4 in mouse cochlear melanocytes: a novel role for hearing and melanocyte differentiation

    Shigeyuki Uehara, Yoshiko Izumi, Yuko Kubo, Chi Chiu Wang, Katsuhiko Mineta, Kazuho Ikeo, Takashi Gojobori, Masayoshi Tachibana, Toshihiko Kikuchi, Toshimitsu Kobayashi, Shigeki Shibahara, Choji Taya, Hiromichi Yonekawa, Toshihiko Shiroishi, Hiroaki Yamamoto

    PIGMENT CELL & MELANOMA RESEARCH   22 ( 1 ) 111 - 119  2009.02  [Refereed]  [International journal]

     View Summary

    Mammalian pigment cells produce melanin as the main pigment. Melanocytes, one of the two types of mammalian pigment cells, differentiate from the neural crest and migrate to a variety of organs during development. Melanocytes exist not only in the skin but also in other sites such as the cochlea where they are essential for hearing. Mitf(mi-bw) is one of the known recessive alleles of the mouse microphthalmia-associated transcription factor (Mitf) locus, which is essential for the development of pigment cells. Homozygous Mitf(mi-bw)/Mitf(mi-bw) mice have a completely white coat with black eyes and are deaf due to the lack of melanocytes. By comparing gene expression profiles in cochleae of wild-type and Mitf(mi-bw)/Mitf(mi-bw) mice, we now demonstrate the specific expression of glutathione S-transferase alpha 4 (Gsta4) in the stria vascularis. Gsta4 encodes one of the cytosolic glutathione S-transferases (GSTs) which participate in detoxification processes of many tissues. This gene is specifically expressed in intermediate cells of the stria vascularis, suggesting a novel function for cochlear melanocytes. Moreover, among mammalian pigment cells, expression of Gsta4 was restricted to cochlear melanocytes, suggesting that melanocytes in various tissues differentiate from one another depending on their location.

    DOI PubMed

  • Improved genome assembly and evidence-based global gene model set for the chordate Ciona intestinalis: new insight into intron and operon populations.

    Satou Y, Mineta K, Ogasawara M, Sasakura Y, Shoguchi E, Ueno K, Yamada L, Matsumoto J, Wasserscheid J, Dewar K, Wiley GB, Macmil SL, Roe BA, Zeller RW, Hastings KE, Lemaire P, Lindquist E, Endo T, Hotta K, Inaba K

    Genome biology   9 ( 10 ) R152  2008.10  [Refereed]  [International journal]

     View Summary

    BACKGROUND: The draft genome sequence of the ascidian Ciona intestinalis, along with associated gene models, has been a valuable research resource. However, recently accumulated expressed sequence tag (EST)/cDNA data have revealed numerous inconsistencies with the gene models due in part to intrinsic limitations in gene prediction programs and in part to the fragmented nature of the assembly. RESULTS: We have prepared a less-fragmented assembly on the basis of scaffold-joining guided by paired-end EST and bacterial artificial chromosome (BAC) sequences, and BAC chromosomal in situ hybridization data. The new assembly (115.2 Mb) is similar in length to the initial assembly (116.7 Mb) but contains 1,272 (approximately 50%) fewer scaffolds. The largest scaffold in the new assembly incorporates 95 initial-assembly scaffolds. In conjunction with the new assembly, we have prepared a greatly improved global gene model set strictly correlated with the extensive currently available EST data. The total gene number (15,254) is similar to that of the initial set (15,582), but the new set includes 3,330 models at genomic sites where none were present in the initial set, and 1,779 models that represent fusions of multiple previously incomplete models. In approximately half, 5'-ends were precisely mapped using 5'-full-length ESTs, an important refinement even in otherwise unchanged models. CONCLUSION: Using these new resources, we identify a population of non-canonical (non-GT-AG) introns and also find that approximately 20% of Ciona genes reside in operons and that operons contain a high proportion of single-exon genes. Thus, the present dataset provides an opportunity to analyze the Ciona genome much more precisely than ever.

    DOI PubMed

  • Structure and function of primitive immunoglobulin superfamily neural cell adhesion molecules: a lesson from studies on planarian

    E Fusaoka, T Inoue, K Mineta, K Agata, K Takeuchi

    GENES TO CELLS   11 ( 5 ) 541 - 555  2006.05  [Refereed]  [International journal]

     View Summary

    Precise wiring and proper remodeling of the neural network are essential for its normal function. The freshwater planarian is an attractive animal in which to study the formation and maintenance of the neural network due to its high regenerative capability and developmental plasticity. Although a recent study revealed that homologs of netrin and its receptors are required for regeneration and maintenance of the planarian central nervous system (CNS), the roles of cell adhesion in the formation and maintenance of the planarian neural network remain poorly understood. In the present study, we found primitive immunoglobulin superfamily cell adhesion molecules (IgCAMs) in a planarian that are homologous to vertebrate neural IgCAMs. We identified planarian orthologs of NCAM, L1CAM, contactin and DSCAM, and designated them DjCAM, DjLCAM, DjCTCAM and DjDSCAM, respectively. We further confirmed that they function as cell adhesion molecules using cell aggregation assays. DjCAM and DjDSCAM were found to be differentially expressed in the CNS. Functional analyses using RNA interference revealed that DjCAM is partly involved in axon formation, and that DjDSCAM plays crucial roles in neuronal cell migration, axon outgrowth, fasciculation and projection.

    DOI PubMed CiNii

  • Integration of Gene Expression Profiles into the Visualized Data Management System

    Katsuhiko MINETA, Kazuho IKEO, Yuzuru TANAKA, Takashi GOJOBORI

    Journal of Japan Society of Information and Knowledge   16 ( 3 ) 50 - 55  2006  [Refereed]

    Authorship:Lead author

     View Summary

    An explosive increase of the gene expression data provides us a chance to analyze fundamental biological phenomena such as how the genes are being used in the organisms. As the data increases, however, we faced new problems how we deal with and analyze an enormously large amount of data. Moreover, the gene expression data includes information of the time, location and network of the genes that cannot be managed easily. Thus, the establishment of a novel management system for the gene expression data is one of the most essential tasks in the biological data analyses. Here, we introduce our visualizing platform of higher-dimensional biological data for the management of the gene expression data.

    DOI CiNii

  • Origin and evolutionary process of the CNS elucidated by comparative genomics analysis of planarian ESTs

    K Mineta, M Nakazawa, F Cebria, K Ikeo, K Agata, T Gojobori

    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA   100 ( 13 ) 7666 - 7671  2003.06  [Refereed]  [International journal]

    Authorship:Lead author

     View Summary

    Among the bilateral animals, a centralized nervous system is found in both the deuterostome and protostome. To address the question of whether the CNS was derived from a common ancestor of deuterostomes and protostomes, it is essential to know kinds of genes existed in the CNS of the putative common ancestor and to trace the evolutionary divergence of genes expressed in the CNS. To answer these questions, we took a comparative approach using different species, particularly focusing on one of the lower bilateral animals, the planarian (Platyhelminthes, Tricladida), which is known to possess a CNS. We determined the nucleotide sequence of ESTs from the head portion of planarians, obtaining 3,101 nonredundant EST clones. As a result of homology searches, we found that 116 clones had significant similarity to known genes related to the nervous system. Here, we compared these 116 planarian EST clones with all ORFs of the complete genome sequences of the human, fruit fly, and nematode, and showed that &gt;95% of these 116 nervous system-related genes, including genes involved in brain or neural morphogenesis, were commonly shared among these organisms, thus providing evidence at the molecular level for the existence of a common ancestral CNS. Interestingly, we found that approximate to30% of planarian nervous system-related genes had homologous sequences in Arabidopsis and yeast, which do not possess a nervous system. This implies that the origin of nervous system-related genes greatly predated the emergence of the nervous system, and that these genes might have been recruited toward the nervous system.

    DOI PubMed CiNii

  • Search for the evolutionary origin of a brain: Planarian brain characterized by microarray

    M Nakazawa, F Cebria, K Mineta, K Ikeo, K Agata, T Gojobori

    MOLECULAR BIOLOGY AND EVOLUTION   20 ( 5 ) 784 - 791  2003.05  [Refereed]  [International journal]

     View Summary

    The origin of the brain remains a challenging problem in evolutionary studies. To understand when and how the structural brain emerged, we analyzed the central nervous system (CNS) of a lower invertebrate, planarian. We conducted a large-scale screening of the head part-specific genes in the planarian by constructing a cDNA microarray. Competitive hybridization of cDNAs between a head portion and the other body portion of planarians revealed 205 genes with head part-specific spikes, including essential genes in the vertebrate nervous system. The expression patterns of the top 30 genes showing the strongest spikes implied that the planarian brain has undergone functional regionalization. We demonstrate the complex cytoarchitecture of the planarian brain, despite its simple superficiality of the morphology.

    DOI PubMed

  • FGFR-related gene nou-darake restricts brain tissues to the head region of planarians

    F Cebria, C Kobayashi, Y Umesono, M Nakazawa, K Mineta, K Ikeo, T Gojobori, M Itoh, M Taira, AS Alvarado, K Agata

    NATURE   419 ( 6907 ) 620 - 624  2002.10  [Refereed]  [International journal]

     View Summary

    The study of planarian regeneration may help us to understand how we can rebuild organs and tissues after injury, disease or ageing(1). The robust regenerative abilities of planarians are based upon a population of totipotent stem cells (neoblasts)(2-4), and among the organs regenerated by these animals is a well-organized central nervous system(5,6). In recent years, methodologies such as whole-mount in situ hybridizations and double-stranded RNA have been extended to planarians with the aim of unravelling the molecular basis of their regenerative capacities(7-11). Here we report the identification and characterization of nou-darake (ndk), a gene encoding a fibroblast growth factor receptor (FGFR)-like molecule specifically expressed in the head region of the planarian Dugesia japonica. Loss of function of ndk by RNA interference results in the induction of ectopic brain tissues throughout the body. This ectopic brain formation was suppressed by inhibition of two planarian FGFR homologues (FGFR1 and FGFR2). Additionally, ndk inhibits FGF signalling in Xenopus embryos. The data suggest that ndk may modulate FGF signalling in stem cells to restrict brain tissues to the head region of planarians.

    DOI PubMed CiNii

  • Induction of a noggin-like gene by ectopic DV interaction during planarian regeneration

    K Ogawa, S Ishihara, Y Saito, K Mineta, M Nakazawa, K Ikeo, T Gojobori, K Watanabe, K Agatat

    DEVELOPMENTAL BIOLOGY   250 ( 1 ) 59 - 70  2002.10  [Refereed]  [International journal]

     View Summary

    in previous studies, we have shown that dorsoventral (DV) interaction evokes not only blastema formation, but also morphogenetic events similar to those that occur in regeneration. However, it is still unclear what kinds of signal molecules are involved in the DV interaction. To investigate the signal systems involved in the DV interaction, we focused on a noggin-like gene (Djnlg) identified by the planarian EST project. Djnlg is the first noggin homologue isolated from an invertebrate. In DjNLG, the positions of nine cysteine residues which may be essential for dimer formation were well conserved, but overall, the amino acid sequence of DjNLG did not show high similarity to the sequences of vertebrate Noggins. Expression of Djnlg was observed only in the proximal region of the branch structures in the brain of intact planarians, suggesting that Djnlg may have a role in pattern formation in the brain. Interestingly, transient strong expression of Djnlg was observed in the amputated region of regenerating planarians. Djnlg-expressing cells were detected beneath the muscle 9 h after amputation and were then detected in the ventral subepidermal region of the blastema. The induction of Djnlg expression by amputation was not affected by X-ray irradiation, even though the stem cells were completely eliminated, implying the existence of signal-producing cells which may provide a positional cue to the stem cells. In DV reversed grafting, expression of Djnlg was strongly induced in the DV boundary between the host and donor. These results suggest that ectopic DV interaction may induce expression of Djnlg in the positional cue-producing cells, and that it might be involved in stimulation of blastema formation as well as DV patterning of the body. (C) 2002 Elsevier Science (USA).

    DOI PubMed CiNii

  • The expression of neural-specific genes reveals the structural and molecular complexity of the planarian central nervous system

    F Cebria, T Kudome, M Nakazawa, K Mineta, K Ikeo, T Gojobori, K Agata

    MECHANISMS OF DEVELOPMENT   116 ( 1月2日 ) 199 - 204  2002.08  [Refereed]  [International journal]

     View Summary

    Planarians are attractive animals in which various questions related to the central nervous system (CNS) can be addressed, such as its origin and evolution, its degree of functional conservation among different organisms, and the plasticity and regenerative capabilities of neural cells and networks. However, it is first necessary to characterize at the gene expression level how this CNS is organized in intact animals. Previous studies have shown that the planarian brain can be divided into at least three distinct domains based on the expression of otd/Otx-related genes. In order to further characterize the planarian brain, we have recently isolated a large number of planarian neural-specific genes through DNA microarrays and ESTs projects. Here, we describe new molecular domains within the brain of intact planarians by the expression of 16 planarian neural-specific genes, including the putative homologues of protein tyrosine phosphatase receptor, synaptotagmin VII, slit, G protein and glutamate and acetylcholine receptors, by in situ hybridization in both whole-mount and transverse sections. Our results indicate that planarian otd/Otx-positive domains can be further subdivided into distinct molecular regions according to the expression of different neural genes. We found differences at the gene expression level between the dorsal and ventral sides of the brain, along its antero-posterior axis and also between the proximal and distal parts of the brain lateral branches. This high level of regionalization in the planarian brain contrasts with its apparent simplicity at the morphological level. (C) 2002 Elsevier Science Ireland Ltd. All rights reserved.

    DOI

  • Dissecting planarian central nervous system regeneration by the expression of neural-specific genes

    F Cebria, M Nakazawa, K Mineta, K Ikeo, T Gojobori, K Agata

    DEVELOPMENT GROWTH & DIFFERENTIATION   44 ( 2 ) 135 - 146  2002.04  [Refereed]  [International journal]

     View Summary

    The planarian central nervous system (CNS) can be used as a model for studying neural regeneration in higher organisms. Despite its simple structure, recent studies have shown that the planarian CNS can be divided into several molecular and functional domains defined by the expression of different neural genes. Remarkably, a whole animal, including the molecularly complex CNS, can regenerate from a small piece of the planarian body. In this study, a collection of neural markers has been used to characterize at the molecular level how the planarian CNS is rebuilt. Planarian CNS is composed of an anterior brain and a pair of ventral nerve cords that are distinct and overlapping structures in the head region. During regeneration, 12 neural markers have been classified as early, mid-regeneration and late expression genes depending on when they are upregulated in the regenerative blastema. Interestingly, the results from this study show that the comparison of the expression patterns of different neural genes supports the view that at day one of regeneration, the new brain appears within the blastema, whereas the pre-existing ventral nerve cords remain in the old tissues. Three stages in planarian CNS regeneration are suggested.

    DOI PubMed CiNii

  • Localization of MT2a gene promoter expression is different from the site(s) of copper accumulation in the roots of transgenic Arabidopsis thaliana

    K Mineta, E Akahoshi, K Takahashi, T Horiguchi, H Hayashi, T Ohyama, T Ikarashi, T Fujiwara, M Chino

    SOIL SCIENCE AND PLANT NUTRITION   46 ( 1 ) 189 - 197  2000.03  [Refereed]  [International journal]

    Authorship:Lead author

     View Summary

    Accumulation of mRNA for MT2a, a metallothionein of Arabidopsis thaliana, is known to be upregulated by excess copper (Cu), We compared the localization of the promoter activity of the MT2a gene and the accumulation site(s) of Cu in the roots of transgenic A. thaliana. Open reading frame of the beta-glucuronidase (GUS) gene was fused with the MT2a gene promoter and introduced into A, thaliana, Strong GUS activity was observed in the region near or within the stele in the presence of Cu at a high concentration (high-Cu condition), Electron probe X-ray micro-analysis demonstrated that under high-Cu conditions, Cu accumulated most abundantly in the cortex, where GUS activity was not significantly induced. These results indicate that the sites showing the MT2a promoter activity and Cu accumulation did not coincide with each other, suggesting that Cu is not a direct activator of the MT2a promoter.

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Books and Other Publications

  • Marine Metagenomics: Technological Aspects and Applications

    Takashi Gojobori, Tokio Wada, Takanori Kobayashi, Katsuhiko Mineta

    Springer Singapore  2019 ISBN: 9789811381331

  • キーノートシリーズ 生命情報学キーノート

    シュプリンガーフェアラーク東京  2003

  • ゲノムからみた生物の多様性と進化

    シュプリンガーフェアラーク東京  2003

 

Syllabus

 

Sub-affiliation

  • Faculty of Science and Engineering   School of Advanced Science and Engineering