Researcher Profile and Settings

Master

Affiliation (Master)

• Research Faculty of Agriculture　Fundamental AgriScience Research　Applied Bioscience

Affiliation (Master)

• Research Faculty of Agriculture　Fundamental AgriScience Research　Applied Bioscience

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Profile and Settings

Profile and Settings

• Name (Japanese)

  Sato

• Name (Kana)

  Masanao

• Name

  201701011669372275

Achievement

Research Interests

• gene regulatory network, systems biology, host-microbe interactions   

Research Areas

• Life sciences / Virology / Baculoviruses, Potyviruses
• Life sciences / Genomics / Gene regulatory networks, Transcriptome

Research Experience

• 2022/07 - Today Hokkaido University Graduate School of Agriculture Research Faculty of Agriculture Division of Applied Bioscience Associate Professor
• 2016/04 - 2022/06 北海道大学大学院農学研究院 応用分子昆虫学 助教
• 2015/04 - 2016/03 Keio University
• 2009/08 - 2015/03 National Institute for Basic Biology Developmental Genetics Assistant professor

Published Papers

• Clinically approved chemical-controlled suppression of protein expression in BmN cells

  Toshiki Nakanishi, Shin-ichiro Asano, Hisanori Bando, Masanao Sato

  Journal of Insect Biotechnology and Sericology 93 (1) 1 - 10 2024/05/28 [Refereed]
  
• The transcription regulator ChpA affects the global transcriptome including quorum sensing-dependent genes in Ralstonia pseudosolanacearum strain OE1-1.

  Chika Takemura, Wakana Senuma, Masayuki Tsuzuki, Yuki Terazawa, Kanako Inoue, Masanao Sato, Akinori Kiba, Kouhei Ohnishi, Kenji Kai, Yasufumi Hikichi

  Molecular plant pathology 2023/07/14 

  The gram-negative plant-pathogenic β-proteobacterium Ralstonia pseudosolanacearum strain OE1-1 produces methyl 3-hydroxymyristate as a quorum sensing (QS) signal through methyltransferase PhcB and senses the chemical via the sensor histidine kinase PhcS. This leads to activation of the LysR family transcription regulator PhcA, which regulates the genes (QS-dependent genes) responsible for QS-dependent phenotypes, including virulence. The transcription regulator ChpA, which possesses a response regulator receiver domain and also a hybrid sensor histidine kinase/response regulator phosphore-acceptor domain but lacks a DNA-binding domain, is reportedly involved in QS-dependent biofilm formation and virulence of R. pseudosolanacearum strain GMI1000. To explore the function of ChpA in QS of OE1-1, we generated a chpA-deletion mutant (ΔchpA) and revealed that the chpA deletion leads to significantly altered QS-dependent phenotypes. Furthermore, ΔchpA exhibited a loss in its infectivity in xylem vessels of tomato plant roots, losing virulence on tomato plants, similar to the phcA-deletion mutant (ΔphcA). Transcriptome analysis showed that the transcript levels of phcB, phcQ, phcR, and phcA in ΔchpA were comparable to those in OE1-1. However, the transcript levels of 89.9% and 88.9% of positively and negatively QS-dependent genes, respectively, were significantly altered in ΔchpA compared with OE1-1. Furthermore, the transcript levels of these genes in ΔchpA were positively correlated with those in ΔphcA. Together, our results suggest that ChpA is involved in the regulation of these QS-dependent genes, thereby contributing to the behaviour in host plant roots and virulence of OE1-1.
• The dataset of de novo assembly and inferred functional annotation of the transcriptome of Heterosigma akashiwo, a bloom-forming, cosmopolitan raphidophyte

  Masanao Sato, Masahide Seki, Yutaka Suzuki, Shoko Ueki

  Data in Brief 48 109071 - 109071 2352-3409 2023/06 [Refereed][Not invited]
  
• Construction of gene co-expression networks in cultured silkworm cells and identification of previously uncharacterized lepidopteran-specific genes required for chromosome dynamics.

  Hiroaki Mon, Masanao Sato, Jae Man Lee, Takahiro Kusakabe

  Insect biochemistry and molecular biology 151 103875 - 103875 2022/12 

  Advances in sequencing technology and bioinformatics have accelerated gene discovery and homology-based functional annotation in many species, and numerous targeted gene studies have greatly expanded the understanding of gene functions. Nevertheless, there are still many genes that lack homology with genes in other evolutionary lineages and are left as genes with unknown functions. We constructed a gene co-expression network from the Bombyx mori ovary-derived cell line, BmN4, and attempted to infer the biological roles of uncharacterized genes based on the correlation between the function-known and unknown genes. Within this network, we focused on the co-expression modules involved in chromosome architecture, dynamics, and integrity, and selected the uncharacterized genes for subsequent RNAi-based phenotypic screening. This approach enabled the identification of 5 genes whose knockdown led to abnormalities in chromosome dynamics and spindle morphology in mitosis. One of them was a recently characterized gene, BmCenp-T, which plays a central role in building the kinetochore protein complex on the silkworm holocentric chromosomes. In this study, we suggest a method for constructing the gene co-expression network and selecting candidate genes for small-scale RNAi screening. This approach is complementary to homology-based annotation and may be useful for the analysis of lineage-specific uncharacterized genes such as orphan genes.
• Intraspecies variation of the mitochondrial genome: An evaluation for phylogenetic approaches based on the conventional choices of genes and segments on mitogenome.

  Jesús Morón-López, Karen Vergara, Masanao Sato, Gonzalo Gajardo, Shoko Ueki

  PloS one 17 (8) e0273330  2022 

  Intraspecies nucleotide sequence variation is a key to understanding the evolutionary history of a species, such as the geographic distribution and population structure. To date, numerous phylogenetic and population genetics studies have been conducted based on the sequences of a gene or an intergenic region on the mitochondrial genome (mtDNA), such as cytochrome c oxidase subunits or the D-loop. To evaluate the credibility of the usage of such 'classic' markers, we compared the phylogenetic inferences based on the analyses of the partial and entire mtDNA sequences. Importantly, the phylogenetic reconstruction based on the short marker sequences did not necessarily reproduce the tree topologies based on the analyses of the entire mtDNA. In addition, analyses on the datasets of various organisms revealed that the analyses based on the classic markers yielded phylogenetic trees with poor confidence in all tested cases compared to the results based on full-length mtDNA. These results demonstrated that phylogenetic analyses based on complete mtDNA sequences yield more insightful results compared to those based on mitochondrial genes and segments. To ameliorate the shortcomings of the classic markers, we identified a segment of mtDNA that may be used as an 'approximate marker' to closely reproduce the phylogenetic inference obtained from the entire mtDNA in the case of mammalian species, which can be utilized to design amplicon-seq-based studies. Our study demonstrates the importance of the choice of mitochondrial markers for phylogenetic analyses and proposes a novel approach to choosing appropriate markers for mammalian mtDNA that reproduces the phylogenetic inferences obtained from full-length mtDNA.
• PhcQ mainly contributes to the regulation of quorum sensing-dependent genes, in which PhcR is partially involved, in Ralstonia pseudosolanacearum strain OE1-1

  Takemura, C., Senuma, W., Hayashi, K., Minami, A., Terazawa, Y., Kaneoka, C., Sakata, M., Chen, M., Zhang, Y., Nobori, T., Sato, M., Kiba, A., Ohnishi, K., Tsuda, K., Kai, K., Hikichi, Y.

  Molecular Plant Pathology 22 (12) 1538 - 1552 1364-3703 2021/12 [Refereed][Not invited]
  
• Proliferation of Bombyx mori nucleopolyhedrovirus strain H4 in BmN cells is enhanced by exchange of the F gene sequence with type strain T3.

  Mami Sakai, Satoshi Kakutani, Shin-Ichiro Asano, Masanao Sato, Hisanori Bando

  Virus research 291 198195 - 198195 2021/01/02 [Refereed]
   

  The Bombyx mori nucleopolyhedrovirus (BmNPV)-based baculoviral expression vector system is among the most efficient expression vector systems for eukaryotic proteins especially when used in combination with silkworms as a host. We newly isolated a novel BmNPV strain (BmNPV H4) in Hokkaido, Japan that outperforms the type strain T3 in terms of both proliferation and expression of polyhedrin protein in silkworm larvae; however, it proliferates poorly in the BmN cell line. We inferred the gene responsible for the differences in proliferation between viral strains by quantifying amino acid similarity distances in protein functional domains and identifying highly divergent alleles between the H4 and T3 strains. Among proteins that differ markedly in functional domain sequence between H4 and T3, we identified the F gene, which encodes the F protein, as a putative cause of proliferative differences between the two strains. Using recombinant viruses with the F protein-coding sequence exchanged between H4 and T3, we determined that the T3 F protein increases H4 proliferation in BmN while the H4 F protein does not improve T3 proliferation in silkworm larvae. Our results suggest that the BmNPV F protein can strongly affect viral proliferation in a genetic background-specific manner and may be an important target for manipulating the proliferation characteristics of BmNPV-based expression vectors.
• A single amino acid replacement of tyrosine with histidine at position 172 in BmNPV T3 GP64 decreases viral proliferation in silkworm larvae despite increasing membrane fusion activity with bmn cells

  Sekiguchi, M., Ishikawa, S., Asano, S.-I., B, o, H., Sato, M.

  Journal of Insect Biotechnology and Sericology 89 (3) 45 - 53 1884-7978 2020/10 [Refereed]
  
• Design and prototyping of a bombyx mori nucleopolyhedrovirus-based genome assembly from pcr-amplified dna fragments

  Harada, N., Ishibashi, D., Asano, S.-I., Sato, M., B, o, H.

  Journal of Insect Biotechnology and Sericology 87 (3) 97 - 108 2018/10 [Refereed][Not invited]
  
• A mutation in plutella xylostella ABCC2 causes resistance to bacillus thuringiensis Cry1Ac by interfering with its receptor function

  Nakaishi, Y., Sato, M., B, o, H., Asano, S.-I.

  Journal of Insect Biotechnology and Sericology 87 (2) 45 - 51 1346-8073 2018 [Refereed]
  
• Transcripts immunoprecipitated with Sxl protein in primordial germ cells of Drosophila embryos

  Ryoma Ota, Shumpei Morita, Masanao Sato, Shuji Shigenobu, Makoto Hayashi, Satoru Kobayashi

  DEVELOPMENT GROWTH & DIFFERENTIATION 59 (9) 713 - 723 0012-1592 2017/12 [Refereed][Not invited]
   

  In Drosophila, Sex lethal (Sxl), an RNA binding protein, is required for induction of female sexual identity in both somatic and germline cells. Although the Sxl-dependent feminizing pathway in the soma was previously elucidated, the downstream targets for Sxl in the germline remained elusive. To identify these target genes, we selected transcripts associated with Sxl in primordial germ cells (PGCs) of embryos using RNA immunoprecipitation coupled to sequencing (RIP-seq) analysis. A total of 308 transcripts encoded by 282 genes were obtained. Seven of these genes, expressed at higher levels in PGCs as determined by microarray and insitu hybridization analyses, were subjected to RNAi-mediated functional analyses. Knockdown of Neos, Kap-alpha3, and CG32075 throughout germline development caused gonadal dysgenesis in a sex-dependent manner, and Su(var)2-10 knockdown caused gonadal dysgenesis in both sexes. Moreover, as with knockdown of Sxl, knockdown of Su(var)2-10 in PGCs gave rise to a tumorous phenotype of germline cells in ovaries. Because this phenotype indicates loss of female identity of germline cells, we consider Su(var)2-10 to be a strong candidate target of Sxl in PGCs. Our results represent a first step toward elucidating the Sxl-dependent feminizing pathway in the germline.
• Identification and functional analysis of outer kinetochore genes in the holocentric insect Bombyx mori

  Hiroaki Mon, Jae Man Lee, Masanao Sato, Takahiro Kusakabe

  INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 86 1 - 8 0965-1748 2017/07 [Refereed][Not invited]
   

  The kinetochore creates chromosomal attachment sites for microtubules. The kinetochore-microtubule interface plays an important role in ensuring accurate transmission of genetic information to daughter cells. Bombyx marl is known"to possess holocentric chromosomes, where spindle microtubules attach along the entire length of the chromosome. Recent evidence suggests that CENP-A and CENP-C, which are essential for centromere structure and function in other species, have lost in holocentric insects, implying that B. mori is able to build its kinetochore regardless of the lack of CENP-A and CENP-C. Here we report the identification of three outer kinetochore genes in the silkworm B. mori by using bioinformatics and RNA interference-based screening. While the homologs of Ndc80 and Mis12 have strong similarity with those of other organisms, the five encoded proteins (BmNuf2, BmSpc24, BmSpc25, BmDsnl and BmNnfl) are highly diverged from their counterparts in other species. Microscopic studies show that the outer kinetochore protein is distributed along the entire length of the chromosomes, which is a key feature of holocentric chromosomes. We also demonstrate that BmDsnl forms a heterotrimeric complex with BmMis12 and BmNnfl, which acts as a receptor of the Ndc80 complex. In addition, our study suggests that a small-scale RNAi-based candidate screening is a useful approach to identify genes which may be highly divergent among different species. (C) 2017 Elsevier Ltd. All rights reserved.
• Distinct intracellular Ca2+ dynamics regulate apical constriction and differentially contribute to neural tube closure

  Makoto Suzuki, Masanao Sato, Hiroshi Koyama, Yusuke Hara, Kentaro Hayashi, Naoko Yasue, Hiromi Imamura, Toshihiko Fujimori, Takeharu Nagai, Robert E. Campbell, Naoto Ueno

  DEVELOPMENT 144 (7) 1307 - 1316 0950-1991 2017/04 [Refereed][Not invited]
   

  Early in the development of the central nervous system, progenitor cells undergo a shape change, called apical constriction, that triggers the neural plate to form a tubular structure. How apical constriction in the neural plate is controlled and how it contributes to tissue morphogenesis are not fully understood. In this study, we show that intracellular calcium ions (Ca2+) are required for Xenopus neural tube formation and that there are two types of Ca(2+)concentrationchanges, a single-cell and a multicellular wave-like fluctuation, in the developing neural plate. Quantitative imaging analyses revealed that transient increases in Ca2+ concentration induced cortical F-actin remodeling, apical constriction and accelerations of the closing movement of the neural plate. We also show that extracellular ATP and N-cadherin (cdh2) participate in the Ca2+-induced apical constriction. Furthermore, our mathematical model suggests that the effect of Ca2+ fluctuations on tissue morphogenesis is independent of fluctuation frequency and that fluctuations affecting individual cells are more efficient than those at the multicellular level. We propose that distinct Ca2+ signaling patterns differentially modulate apical constriction for efficient epithelial folding and that this mechanism has a broad range of physiological outcomes.
• Conserved role of Ovo in germline development in mouse and Drosophila

  Makoto Hayashi, Yuko Shinozuka, Shuji Shigenobu, Masanao Sato, Michihiko Sugimoto, Seiji Ito, Kuniya Abe, Satoru Kobayashi

  SCIENTIFIC REPORTS 7 40056  2045-2322 2017/01 [Refereed][Not invited]
   

  Ovo, which encodes a transcription factor with Zn-finger domains, is evolutionarily conserved among animals. In Drosophila, in addition to its zygotic function for egg production, maternal ovo activity is required in primordial germ cells (PGCs) for expression of germline genes such as vasa and nanos. In this study, we found that maternal Ovo accumulates in PGC nuclei during embryogenesis. In these cells, ovo serves a dual function: activation of genes expressed predominantly in PGCs, and conversely suppression of somatic genes. Reduction of ovo activity in PGCs makes them unable to develop normally into germ cells of both sexes. In mice, knockout of the ovo ortholog, Ovol2, which is expressed in PGCs, decreases the number of PGCs during early embryogenesis. These data strongly suggest that ovo acts as part of an evolutionarily conserved mechanism that regulates germline development in animals.
• Truncated yet functional viral protein produced via RNA polymerase slippage implies underestimated coding capacity of RNA viruses

  Yuka Hagiwara-Komoda, Sun Hee Choi, Masanao Sato, Go Atsumi, Junya Abe, Junya Fukuda, Mie N. Honjo, Atsushi J. Nagano, Keisuke Komoda, Kenji S. Nakahara, Ichiro Uyeda, Satoshi Naito

  SCIENTIFIC REPORTS 6 21411  2045-2322 2016/02 [Refereed][Not invited]
   

  RNA viruses use various strategies to condense their genetic information into small genomes. Potyviruses not only use the polyprotein strategy, but also embed an open reading frame, pipo, in the P3 cistron in the -1 reading frame. PIPO is expressed as a fusion protein with the N-terminal half of P3 (P3N-PIPO) via transcriptional slippage of viral RNA-dependent RNA polymerase (RdRp). We herein show that clover yellow vein virus (ClYVV) produces a previously unidentified factor, P3N-ALT, in the +1 reading frame via transcriptional slippage at a conserved G(1-2)A(6-7) motif, as is the case for P3N-PIPO. The translation of P3N-ALT terminates soon, and it is considered to be a C-terminal truncated form of P3. In planta experiments indicate that P3N-ALT functions in cell-to-cell movement along with P3N-PIPO. Hence, all three reading frames are used to produce functional proteins. Deep sequencing of ClYVV RNA from infected plants endorses the slippage by viral RdRp. Our findings unveil a virus strategy that optimizes the coding capacity.
• Generation of an infectious cDNA clone of Okushiri virus and its derivative capable of expressing an exogenous gene

  Yudistira Wahyu Kurnia, Ryosuke Fujita, Masanao Sato, Haruhiko Isawa, Shin Ichiro Asano, Ngo Dinh Binh, Hisanori Bando

  Journal of Insect Biotechnology and Sericology 85 (2) 39 - 47 1346-8073 2016 [Refereed][Not invited]
   

  © 2016, Journal of Insect Biotechnology and Sericology. All rights reserved. The Okushiri virus (OKV), isolated from Aedes larvae collected on Okushiri Island, Hokkaido, Japan, is a member of the Negevirus family, a newly proposed insect-specific virus group (genus). To enable genetic manipulation of the genome, we constructed an infectious cDNA clone of OKV. RNA synthesized in vitro from pFBOKV, a full-length OKV cDNA, in the presence or absence of cap analogue produced infectious progeny viruses effectively in mosquito C6/36 cells. Subsequently, ORF3 in pFBOKV was replaced with a GFP coding sequence to generate a construct designated as pO2GFP. C6/36 cells transfected with pO2GFP-derived RNA successfully expressed GFP, but failed to produce progeny viruses. Co-transfection of C6/36 cells with pO2GFP- and pFBOKV-derived RNA revealed that it is possible to produce infectious pO2GFP-derived progeny viruses by supplying OKV genetic elements and/or gene product deleted in pO2GFP even though the infectivity appeared to be low. Although improvements are required to construct viral vectors that propagate more efficiently, this is, to our knowledge, the first report of construction of a negevirus-based foreign gene expression system. The cDNA clones constructed and biological insights obtained in this study will be powerful tools allowing for reverse genetics of OKV and providing a basis to develop efficient negevirus-based expression vector systems.
• The distribution pattern of alpha 2,3-and alpha 2,6-linked sialic acids affects host cell preference in Toxoplasma gondii

  Minami Baba, Masanao Sato, Katsuya Kitoh, Yasuhiro Takashima

  EXPERIMENTAL PARASITOLOGY 155 74 - 81 0014-4894 2015/08 [Refereed][Not invited]
   

  Tachyzoites of Toxoplasma gondii, an obligate intracellular parasite, actively invade almost all types of nucleated cells. However, T. gondii tachyzoites preferentially infect particular types of animal tissue cells. The mechanism underlying the host cell preference of T. gondii is not yet known. In this study, we found that enzymatic removal of alpha 2,3- but not alpha 2,6-linked sialic acids on the surface of Vero cells decreased T. gondii tachyzoite adhesion or invasion to the treated cells. Although Chinese hamster ovary (CHO) cells express only alpha 2,3-linked sialic acid, a genetically modified CHO cell line constructed by transfection with the alpha 2,6-sialiltransferase gene contains subpopulations with a variety of expression patterns of alpha 2,3- and alpha 2,6-linked sialic acids. When T gondii tachyzoites were added to the modified CHO cells, the tachyzoites preferentially attached to cells belonging to a subpopulation of cells that highly expressed alpha 2,3-linked sialic acids. Additionally, multiple regression analysis performed to analyse the relationship between the amount of alpha 2,3-linked/alpha 2,6-linked sialic acids and parasite-expressed fluorescence intensity suggested that more tachyzoites adhered to individual alpha 2,3-linked sialic acid rich-cells than to alpha 2,3-linked sialic acid-poor/null cells. The results of confocal laser microscopy confirmed this finding. These results indicate that the host cell preference of T. gondii was, at least partially, affected by the distribution pattern of alpha 2,3-, but almost never alpha 2,6-linked sialic acids on host cells. (C) 2015 Elsevier Inc. All rights reserved.
• Ionotropic Glutamate Receptors Mediate Inducible Defense in the Water Flea Daphnia pulex

  Hitoshi Miyakawa, Masanao Sato, John K. Colbourne, Taisen Iguchi

  PLOS ONE 10 (3) e0121324  1932-6203 2015/03 [Refereed][Not invited]
   

  Phenotypic plasticity is the ability held in many organisms to produce different phenotypes with a given genome in response to environmental stimuli, such as temperature, nutrition and various biological interactions. It seems likely that environmental signals induce a variety of mechanistic responses that influence ontogenetic processes. Inducible defenses, in which prey animals alter their morphology, behavior and/or other traits to help protect against direct or latent predation threats, are among the most striking examples of phenotypic plasticity. The freshwater microcrustacean Daphnia pulex forms tooth-like defensive structures, "neckteeth," in response to chemical cues or signals, referred to as "kairomones," in this case released from phantom midge larvae, a predator of D. pulex. To identify factors involved in the reception and/or transmission of a kairomone, we used microarray analysis to identify genes up-regulated following a short period of exposure to the midge kairomone. In addition to identifying differentially expressed genes of unknown function, we also found significant up-regulation of genes encoding ionotropic glutamate receptors, which are known to be involved in neurotransmission in many animal species. Specific antagonists of these receptors strongly inhibit the formation of neckteeth in D. pulex, although agonists did not induce neckteeth by themselves, indicating that ionotropic glutamate receptors are necessary but not sufficient for early steps of neckteeth formation in D. pulex. Moreover, using co-exposure of D. pulex to antagonists and juvenile hormone (JH), which physiologically mediates neckteeth formation, we found evidence suggesting that the inhibitory effect of antagonists is not due to direct inhibition of JH synthesis/secretion. Our findings not only provide a candidate molecule required for the inducible defense response in D. pulex, but also will contribute to the understanding of complex mechanisms underlying the recognition of environmental changes, which form the basis of phenotypic plasticity.
• Tightly Regulated Expression of Autographa californica Multicapsid Nucleopolyhedrovirus Immediate Early Genes Emerges from Their Interactions and Possible Collective Behaviors

  Chikako Ono, Masanao Sato, Hitomi Taka, Shin-ichiro Asano, Yoshiharu Matsuura, Hisanori Bando

  PLOS ONE 10 (3) e0119580  1932-6203 2015/03 [Refereed][Not invited]
   

  To infect their hosts, DNA viruses must successfully initiate the expression of viral genes that control subsequent viral gene expression and manipulate the host environment. Viral genes that are immediately expressed upon infection play critical roles in the early infection process. In this study, we investigated the expression and regulation of five canonical regulatory immediate-early (IE) genes of Autographa californica multicapsid nucleopolyhedrovirus: ie0, ie1, ie2, me53, and pe38. A systematic transient gene-expression analysis revealed that these IE genes are generally transactivators, suggesting the existence of a highly interactive regulatory network. A genetic analysis using gene knockout viruses demonstrated that the expression of these IE genes was tolerant to the single deletions of activator IE genes in the early stage of infection. A network graph analysis on the regulatory relationships observed in the transient expression analysis suggested that the robustness of IE gene expression is due to the organization of the IE gene regulatory network and how each IE gene is activated. However, some regulatory relationships detected by the genetic analysis were contradictory to those observed in the transient expression analysis, especially for IE0-mediated regulation. Statistical modeling, combined with genetic analysis using knockout alleles for ie0 and ie1, showed that the repressor function of ie0 was due to the interaction between ie0 and ie1, not ie0 itself. Taken together, these systematic approaches provided insight into the topology and nature of the IE gene regulatory network.
• H3K36 Trimethylation-Mediated Epigenetic Regulation is Activated by Bam and Promotes Germ Cell Differentiation During Early Oogenesis in Drosophila

  Masanori Mukai, Seiji Hira, Katsuhiro Nakamura, Shoichi Nakamura, Hiroshi Kimura, Masanao Sato, Satoru Kobayashi

  BIOLOGY OPEN 4 (2) 119 - 124 2046-6390 2015/02 [Refereed][Not invited]
   

  Epigenetic silencing is critical for maintaining germline stem cells in Drosophila ovaries. However, it remains unclear how the differentiation factor, Bag-of-marbles (Bam), counteracts transcriptional silencing. We found that the trimethylation of lysine 36 on histone H3 (H3K36me3), a modification that is associated with gene activation, is enhanced in Bam-expressing cells. H3K36me3 levels were reduced in flies deficient in Bam. Inactivation of the Set2 methyltransferase, which confers the H3K36me3 modification, in germline cells markedly reduced H3K36me3 and impaired differentiation. Genetic analyses revealed that Set2 acts downstream of Bam. Furthermore, orb expression, which is required for germ cell differentiation, was activated by Set2, probably through direct H3K36me3 modification of the orb locus. Our data indicate that H3K36me3-mediated epigenetic regulation is activated by bam, and that this modification facilitates germ cell differentiation, probably through transcriptional activation. This work provides a novel link between Bam and epigenetic transcriptional control.
• Detection of plant viruses in natural environments by using RNA-Seq.

  Atsushi J Nagano, Mie N Honjo, Motohiro Mihara, Masanao Sato M, Hiroshi Kudoh

  Methods in molecular biology (Clifton, N.J.) 1236 89 - 98 1064-3745 2015 [Refereed][Invited]
   

  Sequencing of RNA by next generation sequencers, RNA-Seq, is revolutionizing virus detection. In addition to the unbiased detection of various viruses from wild plants in natural environments, RNA-Seq also allows for the parallel collection of host plant transcriptome data. Host transcriptome data are highly valuable for studying the responses of hosts to viral infections, as well as viral host manipulation. When detecting viruses using RNA-Seq, it is critical to choose appropriate methods for the removal of rRNA from total RNA. Although viruses with polyadenylated genomes can be detected by RNA-Seq following mRNA purification using oligo-dT beads, viruses with non-polyadenylated genomes are not effectively detected. However, such viruses can be detected by RNA-Seq using the rRNA selective depression method. The high-throughput and cost-effective method of RNA-Seq library preparation which is described here allows us to detect a broad range of viruses in wild plants.
• Enrichment of Spermatogonial Stem Cells Using Side Population in Teleost

  Makoto Hayashi, Masanao Sato, Yasuhiko Nagasaka, Sakiko Sadaie, Satoru Kobayashi, Goro Yoshizaki

  BIOLOGY OF REPRODUCTION 91 (1) 23  0006-3363 2014/07 [Refereed][Not invited]
   

  Spermatogenesis originates from a small population of spermatogonial stem cells; this population can maintain continuous sperm production throughout the life of fish via self-renewal and differentiation. Despite their biological importance, spermatogonial stem cells are not thoroughly characterized because they are difficult to distinguish from their progeny cells that become committed to differentiation. We previously established a novel technique for germ cell transplantation to identify spermatogonial stem cells based on their colonizing activity and their ability to initiate donor-derived gametogenesis in the rainbow trout (Oncorhynchus mykiss). Although spermatogonial stem cells can be retrospectively identified after transplantation, there is currently no technique to prospectively enrich for or purify spermatogonial stem cells. Here, we describe a method for spermatogonial stem cell enrichment using a side population. With optimized Hoechst 33342 staining conditions, we successfully identified side-population cells among type A spermatogonia. Side-population cells were transcriptomically and morphologically distinct from non-side-population cells. To functionally determine whether the transplantable spermatogonial stem cells were enriched in the side-population fraction, we compared the colonization activity of side-population cells with that of non-side-population cells. Colonization efficiency was significantly higher with side-population cells than with non-side-population cells or with total type A spermatogonia. In addition, side-population cells could produce billions of sperm in recipients. These results indicated that transplantable spermatogonial stem cells were enriched in the side-population fraction. This method will provide biological information that may advance our understanding of spermatogonial stem cells in teleosts. Additionally, this technique will increase the efficiency of germ cell transplantation used in surrogate broodstock technology.
• An effective method for the inference of reduced S-system models of Genetic Networks

  Shuhei Kimura, Masanao Sato, Mariko Okada-Hatakeyama

  IPSJ Transactions on Bioinformatics 7 30 - 38 1882-6679 2014 [Refereed][Not invited]
   

  The inference of genetic networks is a problem to obtain mathematical models that can explain observed time-series of gene expression levels. A number of models have been proposed to describe genetic networks. The S-system model is one of the most studied models among them. Due to its advantageous features, numerous inference algorithms based on the S-system model have been proposed. The number of the parameters in the S-system model is however larger than those of the other well-studied models. Therefore, when trying to infer S-system models of genetic networks, we need to provide a larger amount of gene expression data to the inference method. In order to reduce the amount of gene expression data required for an inference of genetic networks, this study simplifies the S-system model by fixing some of its parameters to 0. In this study, we call this simplified S-system model a reduced S-system model. We then propose a new inference method that estimates the parameters of the reduced S-system model by minimizing two-dimensional functions. Finally, we check the effectiveness of the proposed method through numerical experiments on artificial and actual genetic network inference problems.
• Inference of Vohradsky's Models of Genetic Networks by Solving Two-Dimensional Function Optimization Problems

  Shuhei Kimura, Masanao Sato, Mariko Okada-Hatakeyama

  PLOS ONE 8 (12) e83308  1932-6203 2013/12 [Refereed][Not invited]
   

  The inference of a genetic network is a problem in which mutual interactions among genes are inferred from time-series of gene expression levels. While a number of models have been proposed to describe genetic networks, this study focuses on a mathematical model proposed by Vohradsky. Because of its advantageous features, several researchers have proposed the inference methods based on Vohradsky's model. When trying to analyze large-scale networks consisting of dozens of genes, however, these methods must solve high-dimensional non-linear function optimization problems. In order to resolve the difficulty of estimating the parameters of the Vohradsky's model, this study proposes a new method that defines the problem as several two-dimensional function optimization problems. Through numerical experiments on artificial genetic network inference problems, we showed that, although the computation time of the proposed method is not the shortest, the method has the ability to estimate parameters of Vohradsky's models more effectively with sufficiently short computation times. This study then applied the proposed method to an actual inference problem of the bacterial SOS DNA repair system, and succeeded in finding several reasonable regulations.
• Complex genetic interactions among non-essential genes of BmNPV revealed by multiple gene knockout analysis

  Hitomi Taka, Chikako Ono, Masanao Sato, Shin-Ichiro Asano, Hisanori Bando

  Journal of Insect Biotechnology and Sericology 82 (1) 25 - 32 1346-8073 2013/08/05 [Not refereed][Not invited]
   

  About two thirds of open reading frames (orfs) predicted on Bombyx mori nucleopolyhedrovirus (BmNPV) genome were dispensable for expression of the reporter gene derived from the polyhedrin promoter in BmN cells when knocked out one at a time (Ono et al., 2012). Effects of removal of multiple genes of BmNPV and genetic interactions of the viral genes have been poorly investigated. In this study, we constructed BmNPV lacking multiple non-essential genes at the orf11-12-13-14 gene cluster and analyzed the expression of EGFP under the control of the polyhedrin gene promoter. Viruses lacking more than two genes except for the one lacking orf13 and orf14 showed distinct phenotypes compared to the single gene knockout viruses. Synergistic, compensatory, and additive relationships were observed in the genetic interaction analyses between pairs of adjacent genes in the gene cluster. In addition, the virus lacking both orf12 and orf13 but carrying the orf12 genomic region at downstream of the polyhedrin locus expressed EGFP at higher levels than the control virus BmGFP (Ono et al., 2012) although the transcription of orf12 was not changed by insertion at the different locus. This increased EGFP expression was not observed with the virus in which the defect of orf12 and orf13 was rescued with orf13 at the same position. These observations suggested that inserting orf12 at the position specifically affected expression of the reporter gene at the polyhedrin locus.
• Development of an efficient parameter estimation method for the inference of Vohradský's neural network models of genetic networks

  Shuhei Kimura, Masanao Sato, Mariko Okada-Hatakeyama

  Proceedings of the International Joint Conference on Neural Networks 2161-4393 2013 [Refereed][Not invited]
   

  Vohradský has proposed a neural network model to describe biochemical networks. Based on this model, several researchers have proposed genetic network inference methods. When trying to analyze large-scale genetic networks, however, these methods must solve high-dimensional function optimization problems. In order to resolve the high-dimensionality in the estimation of the parameters of the Vohradský's neural network model, this study proposes a new method. The proposed method estimates the parameters of the neural network model by solving two-dimensional function optimization problems. Although these two-dimensional problems are non-linear, their low-dimensionality would make the estimation of the model parameters easier. Finally, we confirm the effectiveness of the proposed method through numerical experiments. © 2013 IEEE.
• Dual Regulation of Gene Expression Mediated by Extended MAPK Activation and Salicylic Acid Contributes to Robust Innate Immunity in Arabidopsis thaliana

  Kenichi Tsuda, Akira Mine, Gerit Bethke, Daisuke Igarashi, Christopher J. Botanga, Yayoi Tsuda, Jane Glazebrook, Masanao Sato, Fumiaki Katagiri

  PLoS Genetics 9 (12) e1004015  1553-7390 2013 [Refereed][Not invited]
   

  Network robustness is a crucial property of the plant immune signaling network because pathogens are under a strong selection pressure to perturb plant network components to dampen plant immune responses. Nevertheless, modulation of network robustness is an area of network biology that has rarely been explored. While two modes of plant immunity, Effector-Triggered Immunity (ETI) and Pattern-Triggered Immunity (PTI), extensively share signaling machinery, the network output is much more robust against perturbations during ETI than PTI, suggesting modulation of network robustness. Here, we report a molecular mechanism underlying the modulation of the network robustness in Arabidopsis thaliana. The salicylic acid (SA) signaling sector regulates a major portion of the plant immune response and is important in immunity against biotrophic and hemibiotrophic pathogens. In Arabidopsis, SA signaling was required for the proper regulation of the vast majority of SA-responsive genes during PTI. However, during ETI, regulation of most SA-responsive genes, including the canonical SA marker gene PR1, could be controlled by SA-independent mechanisms as well as by SA. The activation of the two immune-related MAPKs, MPK3 and MPK6, persisted for several hours during ETI but less than one hour during PTI. Sustained MAPK activation was sufficient to confer SA-independent regulation of most SA-responsive genes. Furthermore, the MPK3 and SA signaling sectors were compensatory to each other for inhibition of bacterial growth as well as for PR1 expression during ETI. These results indicate that the duration of the MAPK activation is a critical determinant for modulation of robustness of the immune signaling network. Our findings with the plant immune signaling network imply that the robustness level of a biological network can be modulated by the activities of network components. © 2013 Tsuda et al.
• CBP60g and SARD1 play partially redundant critical roles in salicylic acid signaling

  Lin Wang, Kenichi Tsuda, William Truman, Masanao Sato, Le V. Nguyen, Fumiaki Katagiri, Jane Glazebrook

  PLANT JOURNAL 67 (6) 1029 - 1041 0960-7412 2011/09 [Refereed][Not invited]
   

  Arabidopsis thaliana calmodulin binding protein 60g (CBP60g) contributes to production of salicylic acid (SA) in response to recognition of microbe-associated molecular patterns (MAMPs) such as flg22, a fragment of bacterial flagellin. Calmodulin binding is required for the function of CBP60g in limiting growth of the bacterial pathogen Pseudomonas syringae pv. maculicola (Pma) ES4326 and activation of SA synthesis. Here, we describe a closely related protein, SARD1. Unlike CBP60g, SARD1 does not bind calmodulin. Growth of Pma ES4326 is enhanced in sard1 mutants. In cbp60g sard1 double mutants, growth of Pma ES4326 is greatly enhanced, and SA levels and expression of PR-1 and SID2 are dramatically reduced. Expression profiling placed the CBP60g/SARD1 node between the PAD4/EDS1 and SA nodes in the defense signaling network, and indicated that CBP60g and SARD1 affect defense responses in addition to SA production. A DNA motif bound by CBP60g and SARD1, GAAATTT, was significantly over-represented in promoters of CBP60g/SARD1-dependent genes, suggesting that expression of these genes is modulated by CBP60g/SARD1 binding. Gene expression patterns showed a stronger effect of cbp60g mutations soon after activation of a defense response, and a stronger effect of sard1 mutations at later times. The results are consistent with a model in which CBP60g and SARD1 comprise a partially redundant protein pair that is required for activation of SA production as well as other defense responses, with CBP60g playing a more important role early during the defense response, and SARD1 to playing a more important role later.
• A Putative RNA-Binding Protein Positively Regulates Salicylic Acid-Mediated Immunity in Arabidopsis

  Yiping Qi, Kenichi Tsuda, Anna Joe, Masanao Sato, Le V. Nguyen, Jane Glazebrook, James R. Alfano, Jerry D. Cohen, Fumiaki Katagiri

  MOLECULAR PLANT-MICROBE INTERACTIONS 23 (12) 1573 - 1583 0894-0282 2010/12 [Refereed][Not invited]
   

  RNA-bmdmg proteins (RBP) can control gene expression at both transcriptional and post-transcriptional levels Plants respond to pathogen infection with rapid reprogramming of gene expression However, little is known about how plant RBP function in plant immunity Here, we describe the involvement of an RBP, Arabidopsis thaliana RNA-bind mg protein-defense related 1 (AtRBP-DR1, At4g03110), in resistance to the pathogen Pseudomonas syringae pv tomato DC3000 AtRBP-DR1 loss of function mutants showed enhanced susceptibility to P syringae pv tomato DC3000 Overexpression of AtRBP-DR1 led to enhanced resistance to P syringae pv tomato DC3000 strains and dwarfism The hypersensitive response triggered by P syringae pv tomato DC3000 avrRpt2 was compromised in the Atrbp-dr1 mutant and enhanced in the AtRBP-DR1 overexpression line at early time points AtRBP-DR1 overexpression lines showed higher mRNA levels of SID2 and PR1, which are salicylic acid (SA) inducible, as well as spontaneous cell death in mature leaves Consistent with these observations, the SA level was low in the Atrbp-dr1 mutant but high in the overexpression line The SA-related phenotype in the overexpression line was fully dependent on SID2 Thus, AtRBP-DR1 is a positive regulator of SA-mediated immunity, possibly acting on SA signaling-related genes at a post-transcriptional level
• Network Modeling Reveals Prevalent Negative Regulatory Relationships between Signaling Sectors in Arabidopsis Immune Signaling

  Masanao Sato, Kenichi Tsuda, Lin Wang, John Coller, Yuichiro Watanabe, Jane Glazebrook, Fumiaki Katagiri

  PLOS PATHOGENS 6 (7) e1001011  1553-7366 2010/07 [Refereed][Not invited]
   

  Biological signaling processes may be mediated by complex networks in which network components and network sectors interact with each other in complex ways. Studies of complex networks benefit from approaches in which the roles of individual components are considered in the context of the network. The plant immune signaling network, which controls inducible responses to pathogen attack, is such a complex network. We studied the Arabidopsis immune signaling network upon challenge with a strain of the bacterial pathogen Pseudomonas syringae expressing the effector protein AvrRpt2 (Pto DC3000 AvrRpt2). This bacterial strain feeds multiple inputs into the signaling network, allowing many parts of the network to be activated at once. mRNA profiles for 571 immune response genes of 22 Arabidopsis immunity mutants and wild type were collected 6 hours after inoculation with Pto DC3000 AvrRpt2. The mRNA profiles were analyzed as detailed descriptions of changes in the network state resulting from the genetic perturbations. Regulatory relationships among the genes corresponding to the mutations were inferred by recursively applying a non-linear dimensionality reduction procedure to the mRNA profile data. The resulting static network model accurately predicted 23 of 25 regulatory relationships reported in the literature, suggesting that predictions of novel regulatory relationships are also accurate. The network model revealed two striking features: (i) the components of the network are highly interconnected; and (ii) negative regulatory relationships are common between signaling sectors. Complex regulatory relationships, including a novel negative regulatory relationship between the early microbe-associated molecular pattern-triggered signaling sectors and the salicylic acid sector, were further validated. We propose that prevalent negative regulatory relationships among the signaling sectors make the plant immune signaling network a "sector-switching'' network, which effectively balances two apparently conflicting demands, robustness against pathogenic perturbations and moderation of negative impacts of immune responses on plant fitness.
• Endosome-Associated CRT1 Functions Early in Resistance Gene-Mediated Defense Signaling in Arabidopsis and Tobacco

  Hong-Gu Kang, Chang-Sik Oh, Masanao Sato, Fumiaki Katagiri, Jane Glazebrook, Hideki Takahashi, Pradeep Kachroo, Gregory B. Martin, Daniel F. Klessig

  PLANT CELL 22 (3) 918 - 936 1040-4651 2010/03 [Refereed][Not invited]
   

  Resistance gene-mediated immunity confers protection against pathogen infection in a wide range of plants. A genetic screen for Arabidopsis thaliana mutants compromised for recognition of turnip crinkle virus previously identified CRT1, a member of the GHKL ATPase/kinase superfamily. Here, we demonstrate that CRT1 interacts with various resistance proteins from different structural classes, and this interaction is disrupted when these resistance proteins are activated. The Arabidopsis mutant crt1-2 crh1-1, which lacks CRT1 and its closest homolog, displayed compromised resistance to avirulent Pseudomonas syringae and Hyaloperonospora arabidopsidis. Additionally, resistance-associated hypersensitive cell death was suppressed in Nicotiana benthamiana silenced for expression of CRT1 homolog(s). Thus, CRT1 appears to be a general factor for resistance gene-mediated immunity. Since elevation of cytosolic calcium triggered by avirulent P. syringae was compromised in crt1-2 crh1-1 plants, but cell death triggered by Nt MEK2(DD) was unaffected in CRT1-silenced N. benthamiana, CRT1 likely functions at an early step in this pathway. Genome-wide transcriptome analysis led to identification of CRT1-Associated genes, many of which are associated with transport processes, responses to (a) biotic stress, and the endomembrane system. Confocal microscopy and subcellular fractionation revealed that CRT1 localizes to endosome-like vesicles, suggesting a key process in resistance protein activation/signaling occurs in this subcellular compartment.
• Network Properties of Robust Immunity in Plants

  Kenichi Tsuda, Masanao Sato, Thomas Stoddard, Jane Glazebrook, Fumiaki Katagiri

  PLOS GENETICS 5 (12) e1000772  1553-7390 2009/12 [Refereed][Not invited]
   

  Two modes of plant immunity against biotrophic pathogens, Effector Triggered Immunity (ETI) and Pattern-Triggered Immunity (PTI), are triggered by recognition of pathogen effectors and Microbe-Associated Molecular Patterns (MAMPs), respectively. Although the jasmonic acid (JA)/ethylene (ET) and salicylic acid ( SA) signaling sectors are generally antagonistic and important for immunity against necrotrophic and biotrophic pathogens, respectively, their precise roles and interactions in ETI and PTI have not been clear. We constructed an Arabidopsis dde2/ein2/pad4/sid2-quadruple mutant. DDE2, EIN2, and SID2 are essential components of the JA, ET, and SA sectors, respectively. The pad4 mutation affects the SA sector and a poorly characterized sector. Although the ETI triggered by the bacterial effector AvrRpt2 (AvrRpt2-ETI) and the PTI triggered by the bacterial MAMP flg22 (flg22-PTI) were largely intact in plants with mutations in any one of these genes, they were mostly abolished in the quadruple mutant. For the purposes of this study, AvrRpt2-ETI and flg22-PTI were measured as relative growth of Pseudomonas syringae bacteria within leaves. Immunity to the necrotrophic fungal pathogen Alternaria brassicicola was also severely compromised in the quadruple mutant. Quantitative measurements of the immunity levels in all combinatorial mutants and wild type allowed us to estimate the effects of the wild-type genes and their interactions on the immunity by fitting a mixed general linear model. This signaling allocation analysis showed that, contrary to current ideas, each of the JA, ET, and SA signaling sectors can positively contribute to immunity against both biotrophic and necrotrophic pathogens. The analysis also revealed that while flg22-PTI and AvrRpt2-ETI use a highly overlapping signaling network, the way they use the common network is very different: synergistic relationships among the signaling sectors are evident in PTI, which may amplify the signal; compensatory relationships among the sectors dominate in ETI, explaining the robustness of ETI against genetic and pathogenic perturbations.
• Arabidopsis CaM Binding Protein CBP60g Contributes to MAMP-Induced SA Accumulation and Is Involved in Disease Resistance against Pseudomonas syringae

  Lin Wang, Kenichi Tsuda, Masanao Sato, Jerry D. Cohen, Fumiaki Katagiri, Jane Glazebrook

  PLOS PATHOGENS 5 (2) e1000301  1553-7366 2009/02 [Refereed][Not invited]
   

  Salicylic acid (SA)-induced defense responses are important factors during effector triggered immunity and microbeassociated molecular pattern (MAMP)-induced immunity in plants. This article presents evidence that a member of the Arabidopsis CBP60 gene family, CBP60g, contributes to MAMP-triggered SA accumulation. CBP60g is inducible by both pathogen and MAMP treatments. Pseudomonas syringae growth is enhanced in cbp60g mutants. Expression profiles of a cbp60g mutant after MAMP treatment are similar to those of sid2 and pad4, suggesting a defect in SA signaling. Accordingly, cbp60g mutants accumulate less SA when treated with the MAMP flg22 or a P. syringae hrcC strain that activates MAMP signaling. MAMP-induced production of reactive oxygen species and callose deposition are unaffected in cbp60g mutants. CBP60g is a calmodulin-binding protein with a calmodulin-binding domain located near the N-terminus. Calmodulin binding is dependent on Ca(2+). Mutations in CBP60g that abolish calmodulin binding prevent complementation of the SA production and bacterial growth defects of cbp60g mutants, indicating that calmodulin binding is essential for the function of CBP60g in defense signaling. These studies show that CBP60g constitutes a Ca(2+) link between MAMP recognition and SA accumulation that is important for resistance to P. syringae.
• The Genetic Network Controlling the Arabidopsis Transcriptional Response to Pseudomonas syringae pv. maculicola: Roles of Major Regulators and the Phytotoxin Coronatine

  Lin Wang, Raka M. Mitra, Keegan D. Hasselmann, Masanao Sato, Lisa Lenarz-Wyatt, Jerry D. Cohen, Fumiaki Katagiri, Jane Glazebrook

  MOLECULAR PLANT-MICROBE INTERACTIONS 21 (11) 1408 - 1420 0894-0282 2008/11 [Refereed][Not invited]
   

  Expression profiling of wild-type plants and mutants with defects in key components of the defense signaling network was used to model the Arabidopsis network 24 h after infection by Pseudomonas syringae pv. maculicola ES4326. Results using the Affymetrix ATH1 array revealed that expression levels of most pathogen-responsive genes were affected by mutations in coi1, ein2, npr1, pad4, or sid2. These five mutations defined a small number of different expression patterns displayed by the majority of pathogen-responsive genes. P. syringae pv. tomato strain DC3000 elicited a much weaker salicylic acid (SA) response than ES4326. Additional mutants were profiled using a custom array. Profiles of pbs3 and ndr1 revealed major effects of these mutations and allowed PBS3 and NDR1 to be placed between the EDS1/PAD4 node and the SA synthesis node in the defense network. Comparison of coi1, dde2, and jar1 profiles showed that many genes were affected by coi1 but very few were affected by dde2 or jar1. Profiles of coi1 plants infected with ES4326 were very similar to those of wild-type plants infected with bacteria unable to produce the phytotoxin coronatine, indicating that, essentially, all COI1-dependent gene expression changes in this system are caused by coronatine.
• Interplay between MAMP-triggered and SA-mediated defense responses

  Kenichi Tsuda, Masanao Sato, Jane Glazebrook, Jerry D. Cohen, Fumiaki Katagiri

  PLANT JOURNAL 53 (5) 763 - 775 0960-7412 2008/03 [Refereed][Not invited]
   

  Plants respond to pathogen infection using an innate immune system with at least two distinct recognition mechanisms. One mechanism recognizes microbe-associated molecular patterns (MAMPs). The other is based on resistance (R) genes and specifically recognizes certain pathogen virulence factors, including those delivered through the type III secretion system (TTSS) of bacteria. Salicylic acid (SA)-mediated responses are an important part of the R gene-mediated defense. Substantial overlaps between MAMP-triggered and SA-mediated responses have been reported. However, interactions between MAMP-triggered and SA-mediated signaling mechanisms have not been well documented. Here we report intimate interactions between MAMP-triggered and SA-mediated signaling. We found that SA accumulated at a higher level 6 h after treatment with a MAMP, flg22 or inoculation with Pseudomonas syringae pv. tomato DC3000 (PstDC3000) hrcC mutant, which is deficient in TTSS function. Disruptions of SA signaling components, such as SID2 and PAD4, strongly affected MAMP-triggered responses monitored by expression profiling. We found two groups of genes that were induced by PstDC3000 hrcC in an SA-dependent manner. One group was SID2-dependent at all time points, whereas the other was SID2-independent at early time points and SID2-dependent at later time points. Thus, the expression of the latter genes responds to MAMPs through both SA-independent and SA-dependent signaling mechanisms. Strong resistance to PstDC3000 hrcC was dependent on SA signaling. These results indicate that the SA increase triggered by MAMPs is a major component of the MAMP-triggered signaling mechanism, explaining the overlapping spectra of MAMP-triggered and SA-mediated responses.
• Interplay between MAMP-triggered and SA-mediated defense responses (Plant Journal (2008) 53, (763-775))

  Tsuda, K., Sato, M., Glazebrook, J., Cohen, J.D., Katagiri, F.

  Plant Journal 55 (6) 1061 - 1061 2008
• Point mutations in helper component protease of clover yellow vein virus are associated with the attenuation of RNA-silencing suppression activity and symptom expression in broad bean

  Ma. Leonora M. Yambao, Haruka Yagihashi, Hiroshi Sekiguchi, Toru Sekiguchi, Toru Sasaki, Masanao Sato, Go Atsumi, Yoko Tacahashi, Kenji S. Nakahara, Ichiro Uyeda

  Archives of Virology 153 (1) 105 - 115 0304-8608 2008/01 [Refereed][Not invited]
   

  Helper component protease (HC-Pro) is a potyvirus-encoded multifunctional protein and a major determinant of symptom expression in a susceptible plant. Here, we show the involvement of clover yellow vein virus (ClYVV) HC-Pro in necrotic symptom expression in broad bean (Vicia faba cv. Wase). In this host, lethal necrosis was induced by ClYVV no. 30, from which a spontaneous, mosaic-inducing mutant (MM) was obtained. Mapping with chimeric viruses between ClYVV no. 30 and MM attributed the symptom attenuation to two mutations at the HC-Pro positions 27 (threonine to isoleucine) and 193 (aspartic acid to tyrosine). Although neither mutant with the single amino acid substitution at position 27 or 193 (ClYVV/T27I or D193Y) induced the lethal necrosis, ClYVV/T27I still retained the ability to induce necrotic symptoms, but ClYVV/D193Y scarcely did so. The virus accumulation of ClYVV/D193Y was also lower than that of ClYVV no. 30. The mutations, T27I and D193Y, are located in a putative zinc finger domain and in one (N-terminal) of the two RNA binding domains, respectively, of HC-Pro. RNA-silencing suppression (RSS) activity of P1/HC-Pro in Nicotiana benthamiana was weakened by both mutations. Our results suggest a correlation between viral virulence and RSS function and the importance of the two domains in HC-Pro. © 2007 Springer-Verlag.
• Natural variation in RPS2-mediated resistance among Arabidopsis accessions: Correlation between gene expression profiles and phenotypic responses

  Remco M. P. Van Poecke, Masanao Sato, Lisa Lenarz-Wyatt, Sanford Weisberg, Fumiaki Katagiri

  PLANT CELL 19 (12) 4046 - 4060 1040-4651 2007/12 [Refereed][Not invited]
   

  Natural variation in gene expression (expression traits or e-traits) is increasingly used for the discovery of genes controlling traits. An important question is whether a particular e-trait is correlated with a phenotypic trait. Here, we examined the correlations between phenotypic traits and e-traits among 10 Arabidopsis thaliana accessions. We studied defense against Pseudomonas syringae pv tomato DC3000 (Pst), with a focus on resistance gene-mediated resistance triggered by the type III effector protein AvrRpt2. As phenotypic traits, we measured growth of the bacteria and extent of the hypersensitive response (HR) as measured by electrolyte leakage. Genetic variation among accessions affected growth of Pst both with (Pst avrRpt2) and without (Pst) the AvrRpt2 effector. Variation in HR was not correlated with variation in bacterial growth. We also collected gene expression profiles 6 h after mock and Pst avrRpt2 inoculation using a custom microarray. Clusters of genes whose expression levels are correlated with bacterial growth or electrolyte leakage were identified. Thus, we demonstrated that variation in gene expression profiles of Arabidopsis accessions collected at one time point under one experimental condition has the power to explain variation in phenotypic responses to pathogen attack.
• Two resistance modes to Clover yellow vein virus in pea characterized by a green fluorescent protein-tagged virus

  Marcelo Andrade, Masanao Sato, Ichiro Uyeda

  PHYTOPATHOLOGY 97 (5) 544 - 550 0031-949X 2007/05 [Refereed][Not invited]
   

  This study characterized resistance in pea lines PI 347295 and PI 378159 to Clover yellow vein virus (ClYVV). Genetic cross experiments showed that a single recessive gene controls resistance in both lines. Conventional mechanical inoculation did not result in infection; however, particle bombardment with infectious plasmid or mechanical inoculation with concentrated viral inocula did cause infection. When ClYVV No. 30 isolate was tagged with a green fluorescent protein (GFP) and used to monitor infection, viral cell-to-cell movement differed in the two pea lines. In PI 347595, ClYVV replicated at a single-cell level. but did not move to neighboring cells, indicating that resistance operated at a cell-to-cell step. In PI 378159, the virus moved to cells around the infection site and reached the leaf veins, but viral movement was slower than that in the susceptible line. The viruses observed around the infection sites and in the veins were then recovered and inoculated again by a conventional mechanical inoculation method onto PI 378159 demonstrating that ClYVV probably had mutated and newly emerged mutant viruses can move to neighboring cells and systemically infect the plants. Tagging the virus with GFP was an efficient tool for characterizing resistance modes. Implications of the two resistance modes are discussed.
• Genetic analysis of lethal tip necrosis induced by Clover yellow vein virus infection in pea

  Gerald Ravelo, Uiko Kagaya, Tsuyoshi Inukai, Masanao Sato, Ichiro Uyeda

  Journal of General Plant Pathology 73 (1) 59 - 65 1345-2630 2007/02 [Refereed][Not invited]
   

  Clover yellow vein virus (ClYVV) elicits lethal tip necrosis in the pea line PI 118501. Pea line PI 118501 develops necrotic lesions and veinal necrosis on inoculated leaves, followed by systemic necrosis, leading to plant death. To understand the genetic basis of this lethal tip necrosis, we crossed lines PI 226564 and PI 250438, which develop mosaic symptoms in response to ClYVV inoculation. In reciprocal crosses of PI 118501 with PI 226564, all F 1 plants had mosaic symptoms with slight stem necrosis and early yellowing of upper leaves. Essentially the same symptom was manifested in PI 118501 × PI 250438 F1 plants. In F2 populations from the cross between PI 118501 and PI 226564, the observed ratios of necrosis, mosaic with slight stem necrosis, and mosaic fit the expected 1:2:1 ratio. These results indicate that a single incompletely dominant gene confers the induction of necrosis in PI 118501. This locus in pea, conferring necrosis induction to ClYVV infection, was designated Cyn1 (Clover yellow vein virus-induced necrosis). A linkage analysis using 100 recombinant inbred lines derived from a cross of PI 118501 and PI 226564 demonstrated that Cyn1 was located 7.5 cM from the SSR marker AD174 on linkage group III. © 2007 The Phytopathological Society of Japan and Springer-Verlag.
• A high-performance, small-scale microarray for expression profiling of many samples in Arabidopsis-pathogen studies

  Masanao Sato, Raka M. Mitra, John Coller, Dong Wang, Natalie W. Spivey, Julia Dewdney, Carine Denoux, Jane Glazebrook, Fumiaki Katagiri

  PLANT JOURNAL 49 (3) 565 - 577 0960-7412 2007/02 [Refereed][Not invited]
   

  Studies of the behavior of biological systems often require monitoring of the expression of many genes in a large number of samples. While whole-genome arrays provide high-quality gene-expression profiles, their high cost generally limits the number of samples that can be studied. Although inexpensive small-scale arrays representing genes of interest could be used for many applications, it is challenging to obtain accurate measurements with conventional small-scale microarrays. We have developed a small-scale microarray system that yields highly accurate and reproducible expression measurements. This was achieved by implementing a stable gene-based quantile normalization method for array-to-array normalization, and a probe-printing design that allows use of a statistical model to correct for effects of print tips and uneven hybridization. The array measures expression values in a single sample, rather than ratios between two samples. This allows accurate comparisons among many samples. The array typically yielded correlation coefficients higher than 0.99 between technically duplicated samples. Accuracy was demonstrated by a correlation coefficient of 0.88 between expression ratios determined from this array and an Affymetrix GeneChip, by quantitative RT-PCR, and by spiking known amounts of specific RNAs into the RNA samples used for profiling. The array was used to compare the responses of wild-type, rps2 and ndr1 mutant plants to infection by a Pseudomonas syringae strain expressing avrRpt2. The results suggest that ndr1 affects a defense-signaling pathway(s) in addition to the RPS2-dependent pathway, and indicate that the microarray is a powerful tool for systems analyses of the Arabidopsis disease-signaling network.
• System control in plant defense implicated by expression profiles during pathogen infection

  Sato, M., Katagiri, F.

  Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme 52 (6 Suppl) 2007
• The Arabidopsis gene CAD1 controls programmed cell death in the plant immune system and encodes a protein containing a MACPF domain

  C Morita-Yamamuro, T Tsutsui, M Sato, H Yoshioka, M Tamaoki, D Ogawa, H Matsuura, T Yoshihara, A Ikeda, Uyeda, I, J Yamaguchi

  PLANT AND CELL PHYSIOLOGY 46 (6) 902 - 912 0032-0781 2005/06 [Refereed][Not invited]
   

  To clarify the processes involved in plant immunity, we have isolated and characterized a single recessive Arabidopsis mutant, cad1 (constitutively activated cell death 1), which shows a phenotype that mimics the lesions seen in the hypersensitive response (HR). This mutant shows spontaneously activated expression of pathogenesis-related (PR) genes, and leading to a 32-fold increase in salicylic acid (SA). Inoculation of cad1 mutant plants with Pseudomonas syringae pv tomato DC3000 shows that the cad1 mutation results in the restriction of bacterial growth. Cloning of CAD1 reveals that this gene encodes a protein containing a domain with significant homology to the MACPF (membrane attack complex and perforin) domain of complement components and perforin proteins that are involved in innate immunity in animals. Furthermore, cell death is suppressed in transgenic cad1 plants expressing nahG, which encodes an SA-degrading enzyme. We therefore conclude that the CAD1 protein negatively controls the SA-mediated pathway of programmed cell death in plant immunity.
• Selective involvement of members of the eukaryotic initiation factor 4E family in the infection of Arabidopsis thaliana by potyviruses

  Masanao Sato, Kenji Nakahara, Moyasu Yoshii, Masayuki Ishikawa, Ichiro Uyeda

  FEBS LETTERS 579 (5) 1167 - 1171 0014-5793 2005/02 [Refereed][Not invited]
   

  Arabidopsis thaliana plants with mutations in the genes encoding eukaryotic initiation factor (eIF4E) or isoform of eIF4E (eIF(iso)4E) were tested for susceptibility to Clover yellow vein virus (ClYVV), a member of the genus Potyvirus. ClYVV accumulated in both inoculated and upper uninoculated leaves of mutant plants lacking eIF(iso)4E, but not in mutant plants lacking eIF4E. In contrast, Turnip mosaic virus (TuMV), another member of the genus Potyvirus, multiplied in mutant plants lacking eIF4E but not in mutant plants lacking eIF(iso)4E. These results suggest the selective involvement of members of the eIF4E family in infection by potyviruses. (C) 2005 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.
• The Arabidopsis gene CAD1 controls programmed cell death in the plant immune system and encodes a protein containing a MACPF domain.

  Chizuko Morita-Yamamuro, Tomokazu Tsutsui, Masanao Sato, Hirofumi Yoshioka, Masanori Tamaoki, Daisuke Ogawa, Hideyuki Matsuura, Teruhiko Yoshihara, Akira Ikeda, Ichiro Uyeda, Junji Yamaguchi

  PLANT AND CELL PHYSIOLOGY 46 (6) S120 - S120 0032-0781 2005 [Refereed][Not invited]
  
• Natural resistance to Clover yellow vein virus in beans controlled by a single recessive locus

  Masanao Sato, Chikara Masuta, Ichiro Uyeda

  MOLECULAR PLANT-MICROBE INTERACTIONS 16 (11) 994 - 1002 0894-0282 2003/11 [Refereed][Not invited]
   

  We characterized the resistance of the common bean cv. Jolanda to Clover yellow vein virus no. 30 (ClYVV). After inoculation, the virus was detected in neither inoculated nor upper leaves, suggesting that the resistance operates at either the viral replication or cell-to-cell movement level. To analyze the mechanism of resistance, we developed a green fluorescent protein (GFP)-tagged ClYVV, and monitored GFP fluorescence at sites of infection on ClYVV-inoculated leaves. No GFP fluorescence was detected in Jolanda, whereas its expression in single cells and spread on inoculated leaves were observed clearly in susceptible cultivars. ClYVV-introduced Jolanda cells were found to be still viable; therefore, it is unlikely that the restriction of multiplication was due to rapid cell death. Genetic analysis indicated that a single recessive locus controlled the resistant phenotype of Jolanda. We designated this locus desc (determinant of susceptibility to ClYVV). Meanwhile, a spontaneous mutant virus that overcomes the resistance (ClYVV-Br) was isolated. Inoculation assays using chimeric viruses suggested that a viral genome-linked protein (VPg) might be the avirulence determinant. The resistance mechanism may be associated with the role of VPg in the viral infection cycle.
• Positional effect of gene insertion on genetic stability of a clover yellow vein virus-based expression vector

  Zhen Dong Wang, Shigenori Ueda, Ichiro Uyeda, Haruka Yagihashi, Hiroshi Sekiguchi, Yoko Tacahashi, Masanao Sato, Kenji Ohya, Chihiro Sugimoto, Takeshi Matsumura

  Journal of General Plant Pathology 69 327 - 334 2003/10 [Refereed]
  
• Development of clover yellow vein virus as an efficient, stable gene-expression system for legume species

  Chikara Masuta, Toshikazu Yamana, Yoko Tacahashi, Ichiro Uyeda, Masanao Sato, Shigenori Ueda, Takeshi Matsumura

  PLANT JOURNAL 23 (4) 539 - 546 0960-7412 2000/08 [Refereed][Not invited]
   

  A highly infectious cDNA clone of clover yellow vein virus (pCIYVV) was tested as a viral vector, especially for legume species. The genes for green fluorescent protein (GFP) and soybean glutamine synthetase (GS) were inserted between the genes for pi and HC-Pro on pCIYVV to create three recombinant plasmids: pCIYVV-GFP, pCIYVV-GFP-GS, and pCIYVV-GFP:GS. In the former two constructs all the junctions between the inserted proteins contained the sequences of protease cleavage recognition sites, whereas the third construct expressed a fusion of GFP and GS. Western blot analyses showed that GFP and GS appeared to have been precisely excised from the viral polyprotein with the viral proteases (P1 and Nla). Under UV irradiation, green fluorescence was detected in infected broad bean, kidney bean, and soybean plants. The stability of the constructs in the symptomatic tissues was confirmed by RT-PCR and Western blot analyses. The plants expressing GS together with GFP became tolerant to the herbicide glufosinate, and flowered early. As the GS gene, one of the nodulin genes for nitrogen fixation, is expressed in legume species, this system will be useful for examining the function of genes important to legume plants.

MISC

• カイコゲノム配列解析の現状と展望

  佐藤昌直  日本応用動物昆虫学会大会講演要旨  67th-  2023
• Transplanting the Human TBX5 Regulatory Elements: In Silico Screening and Evaluation of Transcription Factors Independent of Bombyx mori Transcriptional Regulation

  前田麻亜子, 坪田拓也, 門宏明, 増田亮津, 松田拓也, 浅野眞一郎, 伴戸久徳, 瀬筒秀樹, 瀬筒秀樹, 荒川和晴, 荒川和晴, 日下部宜宏, 佐藤昌直, 佐藤昌直  日本分子生物学会年会プログラム・要旨集(Web)  46th-  2023
• カイコ精巣をモデルとした配偶子形成に関与するカオナシ遺伝子の解析

  柿野耕平, 門宏明, 佐藤昌直, 藤井告, 日野真人, 李在萬, 藤田龍介, 日下部宜宏  蚕糸・昆虫機能利用学術講演会・日本蚕糸学会大会講演要旨集  92nd-  2022
• 組織透明化を利用したBmNPV感染観察の高感度化

  佐藤 拓海, 浅野 眞一郎, 佐藤 昌直  東北蚕糸・昆虫利用研究報告  46-  17  -22  2021/12  [Not refereed][Not invited]
  
• 遺伝子間相互作用の定量によって浮き彫りになる遺伝子の役割 : バキュロウイルスimmediate early遺伝子群を例に (特集 定量生物学事始め)

  佐藤 昌直, 小野 慎子, 伴戸 久徳  蚕糸・昆虫バイオテック  89-  (1)  15  -23  2020/04
• 特集「定量生物学事始め」にあたって (特集 定量生物学事始め)

  佐藤 昌直  蚕糸・昆虫バイオテック  89-  (1)  3  -5  2020/04
• グアム産タイワンカブトにおけるOrNV配列の調査

  橋本健太郎, 佐藤昌直, 伴戸久徳, 浅野眞一郎  東北蚕糸・昆虫利用研究報告  45-  (45)  1  -4  2020  [Not refereed]
  
• 機能性糖質によるラット盲腸内細菌叢の改変に基づいたデオキシコール酸生成菌と相互作用する腸内細菌種の同定

  吹谷智, 佐竹実菜子, 佐藤昌直, 石塚敏, 小椋義俊, 林哲也, 横田篤  日本乳酸菌学会誌  30-  (2)  103  2019
• データベースを利用したカイコのもつ遺伝子の相同性検索と分子系統樹の作成

  横井翔, 天竺桂弘子, 天竺桂弘子, 佐藤昌直  生物の科学 遺伝 (生物の科学 遺伝 別冊)  別冊No.23-  122  -128  2019  [Not refereed][Invited]
  
• BmNPV必須遺伝子のリファクタリングとその評価

  石川聡子, 佐藤昌直, 浅野慎一郎, 伴戸久徳  東北蚕糸・昆虫機能利用研究報告  43-  3  -6  2018/12  [Not refereed][Not invited]
  
• Bombyx mori nucleopolyhedrovirus immediate‐early遺伝子ORF上流500塩基による発現制御についての解析

  工藤滉己, 佐藤昌直, 浅野眞一郎, 伴戸久徳  東北蚕糸・昆虫利用研究報告  (42)  8‐11  2017/12/25  [Not refereed][Not invited]
  
• BmNPVゲノムのin vitroアセンブリ

  原田直人, 佐藤昌直, 浅野眞一郎, 伴戸久徳  東北蚕糸・昆虫利用研究報告  (42)  12‐16  2017/12/25  [Not refereed][Not invited]
  
• マメコガネ幼虫におけるCry8Daトキシンの殺虫活性機構について

  山口真, 佐藤昌直, 伴戸久徳, 浅野眞一郎  東北蚕糸・昆虫利用研究報告  (42)  1‐3  2017/12/25  [Not refereed][Not invited]
  
• バキュロウイルスの複数の非必須遺伝子がウイルス増殖に与える影響について

  齋藤諒, 武田ひとみ, 佐藤昌直, 浅野眞一郎, 伴戸久徳  東北蚕糸・昆虫利用研究報告  (42)  4‐7  2017/12/25  [Not refereed][Not invited]
  
• Cry8Daトキシンの殺虫活性機構について

  池田優里恵, 佐藤昌直, 伴戸久徳, 浅野眞一郎  東北蚕糸・昆虫利用研究報告  (41)  12‐13  2016/12/10  [Not refereed][Not invited]
  
• Cry1Iaトキシンのコナガに対する殺虫活性機構について

  佐藤文美, 佐藤昌直, 伴戸久徳, 浅野眞一郎  東北蚕糸・昆虫利用研究報告  (41)  7‐8  2016/12/10  [Not refereed][Not invited]
  
• 教室紹介 北海道大学大学院農学研究院 応用分子昆虫学

  佐藤 昌直  ウイルス  66-  (2)  205  -207  2016/12
• Bridging -omics and reductionist approaches through signaling network modeling at system levels

  Sato, M.  Seikagaku  88-  (1)  54‐60  2016/02/25  [Not refereed][Not invited]
  
• BmSyndecanノックダウンBmN細胞におけるBmNPVの増殖

  宇多桃香, 佐藤昌直, 浅野眞一郎, 伴戸久徳  東北蚕糸・昆虫利用研究報告  (40)  12  -14  2015/12/20  [Not refereed][Not invited]
  
• 摂動に対するカイコ培養細胞株BmN4‐SID1のトランスクリプトーム変化とその情報を利用したネットワークモデリング

  佐藤昌直, 佐藤昌直, 門宏明, 徐剣, 李在萬, 笠嶋めぐみ, 鈴木誉保, 坪田拓也, 小林悟, 瀬筒秀樹, 日下部宜宏  日本生化学会大会(Web)  88th-  1P0798 (WEB ONLY)  -[1P0798]  2015/12  [Not refereed][Not invited]
  
• カイコにおけるTORシグナル経路の解明

  平田一真, 佐藤昌直, 徐剣, 季明明, 祝力, 日野真人, 山下真実, 諸熊大輔, 門宏明, 李在萬, 日下部宜宏  蚕糸・昆虫機能利用学術講演会・日本蚕糸学会大会講演要旨集  85th-  2015
• バキュロウイルスゲノム人工合成系の確立に向けて

  石橋大樹, 佐藤昌直, 高ひとみ, 武内潤一, 浅野眞一郎, 伴戸久徳  東北蚕糸・昆虫利用研究報告  (39)  5  -7  2014/12/10  [Not refereed][Not invited]
  
• Toward a systems understanding of plant-microbe interactions

  Akira Mine, Masanao Sato, Kenichi Tsuda  FRONTIERS IN PLANT SCIENCE  5-  423  2014/08  [Refereed][Not invited]
   

  Plants are closely associated with microorganisms including pathogens and mutualists that influence plant fitness. Molecular genetic approaches have uncovered a number of signaling components from both plants and microbes and their mode of actions. However, signaling pathways are highly interconnected and influenced by diverse sets of environmental factors. Therefore, it is important to have systems views in order to understand the true nature of plant microbe interactions. Indeed, systems biology approaches have revealed previously overlooked or misinterpreted properties of the plant immune signaling network. Experimental reconstruction of biological networks using exhaustive combinatorial perturbations is particularly powerful to elucidate network structure and properties and relationships among network components. Recent advances in metagenomics of microbial communities associated with plants further point to the importance of systems approaches and open a research area of microbial community reconstruction. In this review, we highlight the importance of a systems understanding of plant microbe interactions, with a special emphasis on reconstruction strategies.
• BmNPVの非必須遺伝子(Bm32‐Bm36)間相互作用解析

  高ひとみ, 小野慎子, 佐藤昌直, 浅野眞一郎, 伴戸久徳  東北蚕糸・昆虫利用研究報告  (38)  1  -3  2013/12/30  [Not refereed][Not invited]
  
• Not to be suppressed? Rethinking the host response at a root-parasite interface

  Derek B. Goto, Hikota Miyazawa, Jessica C. Mar, Masanao Sato  PLANT SCIENCE  213-  9  -17  2013/12  [Refereed][Not invited]
   

  Root-knot nematodes are highly efficient plant parasites that establish permanent feeding sites within host roots. The initiation of this feeding site is critical for parasitic success and requires an interaction with multiple signaling pathways involved in plant development and environmental response. Resistance against root-knot nematodes is relatively rare amongst their broad host range and they remain a major threat to agriculture. The development of effective and sustainable control strategies depends on understanding how host signaling pathways are manipulated during invasion of susceptible hosts. It is generally understood that root-knot nematodes either suppress host defense signaling during infestation or are able to avoid detection altogether, explaining their profound success as parasites. However, when compared to the depth of knowledge from other well-studied pathogen interactions, the published data on host responses to root-knot nematode infestation do not yet provide convincing support for this hypothesis and alternative explanations also exist. It is equally possible that defense-like signaling responses are actually induced and required during the early stages of root-knot nematode infestation. We describe how defense-signaling is highly context-dependent and that caution is necessary when interpreting transcriptional responses in the absence of appropriate control data or stringent validation of gene annotation. Further hypothesis-driven studies on host defense-like responses are required to account for these limitations and advance our understanding of root-knot nematode parasitism of plants. (C) 2013 Elsevier Ireland Ltd. All rights reserved.
• カイコ分散型動原体染色体ループドメイン形成へのCTCF,CP190の関与

  益田篤, 佐藤昌直, 末次克行, 山本公子, 門宏明, 李在萬, 日下部宜宏  蚕糸・昆虫機能利用学術講演会・日本蚕糸学会大会講演要旨集  83rd-  2013
• BmDnmt1,BmDnmt2,bMBDの機能阻害細胞におけるDNAのメチル化

  満留卓実, 門宏明, 佐藤昌直, 末次克行, 山本公子, 李志清, 徐剣, 祝力, 李在萬, 日下部宜宏  蚕糸・昆虫機能利用学術講演会・日本蚕糸学会大会講演要旨集  83rd-  2013
• Expression profiles as detailed snapshots of biological states

  Fumiaki Katagiri, Masanao Sato  TRANSGENIC RESEARCH  16-  (4)  399  -403  2007/08  [Refereed][Invited]
  
• 植物と微生物および昆虫との相互作用 遺伝子発現パターンから見た植物の防御応答システム

  佐藤昌直, 片桐文章  蛋白質 核酸 酵素  52-  (6)  654  -659  2007/05/10  [Not refereed][Not invited]
  
• Host factors and its relevance to virus infection in plants

  SATO Masanao, WATANABE Yuichiro  ウイルス  56-  (2)  155  -164  2006/12/22  [Refereed][Not invited]
   

  Virus infection is established when viral proteins can interact with host factors to execute replication and/or cell-to-cell movement. Even after the virus infection has started, host resistance reactions, if trigged, would suppress further virus propagation. We would like to introduce what we understand about host factors as determinants of infection establishment and as key resistance molecules. Genome-wide information of Arabidopsis is providing us much information about such host factors involved in virus infection.

Books etc

• カイコの科学

  日本蚕糸学会 (Joint work)
  朝倉書店 2020/07 (ISBN: 9784254420432) viii, 210p
• カイコの実験単 : カイコで生命科学をまるごと理解!

  「カイコの実験単」企画・編集委員会, 日本蚕糸学会, 金児, 雄, 塩見, 邦博, 天竺桂, 弘子, 外川, 徹, 横山, 岳(蚕糸学) (Joint work)
  エヌ・ティー・エス 2019/03 (ISBN: 9784860435981) 303p

Presentations

• BmNPVにおける膜タンパク質(GP64)のアミノ酸バリアントが増殖に与える影響

  関口真理, 佐藤昌直, 浅野眞一郎, 伴戸久徳

  日本蚕糸学会大会・蚕糸・昆虫機能学術講演会講演要旨集  2020
• 蛍光レポーター発現細胞クラスター認識を自動化・定量化する画像解析アプローチ

  中西登志紀, 関口真理, 浅野眞一郎, 伴戸久徳, 佐藤昌直

  日本蚕糸学会大会・蚕糸・昆虫機能学術講演会講演要旨集  2020
• Identification of key targets and components of PRC2-mediated systemic defense priming in Arabidopsis thaliana

  田島由理, 佐藤昌直, LOO Eliza Po-Iian, 西條雄介

  日本植物病理学会大会プログラム・講演要旨予稿集  2020
• Polycomb repressive complex 2 positively regulates systemic immunity and priming in Arabidopsis thaliana  [Not invited]

  Yuri Tajima, Masanao Sato, Eva-Maria Reimer-Michalski, Eliza Po-iian Loo, Barbara Kracher, Franziska Turck, Yusuke Saijo

  2019 IS-MPMI XVIII Congress  2019/07
• カイコに存在する2つのTOR遺伝子の機能的違い

  小林政彦, 門宏明, 李在萬, 佐藤昌直, 藤田龍介, 日下部宜宏

  日本分子生物学会年会プログラム・要旨集(Web)  2019
• ポリコーム抑制複合体を介した植物免疫プライミング機構

  田島由理, REIMER-MICHALSKI Eva-Maria, LOO Eliza Po-Iian, KRACHER Barbara, TURCK Franziska, 佐藤昌直, 西條雄介, 西條雄介

  日本植物病理学会大会プログラム・講演要旨予稿集  2019
• BmN細胞におけるSmall Molecule Assisted Shutoffの検証

  中西登志紀, 佐藤昌直, 浅野眞一郎, 伴戸久徳

  日本蚕糸学会大会・蚕糸・昆虫機能学術講演会講演要旨集  2019
• カイコ核多角体病ウイルス新規株H4の膜タンパク質GP64の機能解析

  関口真理, 佐藤昌直, 浅野眞一郎, 伴戸久徳

  日本蚕糸学会大会・蚕糸・昆虫機能学術講演会講演要旨集  2019
• カイコRNA-seqデータ自動解析および可視化プログラムの作成と利用

  佐藤昌直, 横井翔, 坪田拓也, 瀬筒秀樹

  日本蚕糸学会大会・蚕糸・昆虫機能学術講演会講演要旨集  2019
• 機能未知遺伝子ライブラリーから得られたカイコ分散型動原体を構成する新規遺伝子の解析

  門宏明, 佐藤昌直, 藤田龍介, 李在萬, 日下部宜宏

  日本蚕糸学会大会・蚕糸・昆虫機能学術講演会講演要旨集  2019
• Gene ontology解析:トランスクリプトーム情報から生物学的解釈を得る

  佐藤昌直

  日本植物病理学会植物感染生理談話会論文集  2019
• 大量ショートリードデータからトランスクリプトーム情報を抽出する

  佐藤昌直

  日本植物病理学会植物感染生理談話会論文集  2019
• 機能性糖質によるラット盲腸内細菌叢の改変に基づいたデオキシコール酸生成菌と相互作用する腸内細菌種の同定

  吹谷智, 佐竹実菜子, 佐藤昌直, 石塚敏, 小椋義俊, 林哲也, 横田篤

  日本乳酸菌学会誌  2019
• Lobe‐less RNAはショウジョウバエの胚発生期において軸索走行制御に寄与する長鎖ノンコーディングRNAである  [Not invited]

  稲垣幸, 門田満隆, KEELEY Sean D, KEELEY Sean D, 中村奈月, 佐藤昌直, 工樂樹洋, 影山裕二, 影山裕二

  日本RNA学会年会要旨集  2018/07
• ネッタイシマカにおけるCry44Aaトキシンレセプターの評価  [Not invited]

  浅野眞一郎, 小野山雄亮, 中神あゆみ, 中尾悠太, 佐藤昌直, 伴戸久徳

  日本蚕糸学会大会・蚕糸・昆虫機能学術講演会講演要旨集  2018/03
• in vitro DNA連結によるBmNPVゲノム構築プラットフォームの確立  [Not invited]

  原田直人, 石橋大樹, 浅野眞一郎, 佐藤昌直, 伴戸久徳

  日本蚕糸学会大会・蚕糸・昆虫機能学術講演会講演要旨集  2018/03
• Pseudomonas syringae pv. tabaciのNicotiana tabacumに対する感染挙動  [Not invited]

  丸山望, 石賀貴子, 石賀康博, 佐藤昌直, 鈴木智子, 加来久敏, 尾花望, 一瀬勇規, 野村暢彦, 別役重之

  日本植物病理学会大会プログラム・講演要旨予稿集  2018/03
• ポリコーム抑制複合体を介した植物免疫プライミングの分子制御機構の解明  [Not invited]

  田島由理, REIMER‐MICHALSKI Eva‐Maria, LOO Eliza Po‐iian, 白石菜月, KRACHER Barbara, TURCK Franziska, 佐藤昌直, 西條雄介, 西條雄介

  日本植物病理学会大会プログラム・講演要旨予稿集  2018/03
• ラットへのコール酸および難消化性オリゴ糖の同時投与による腸内細菌叢改変に基づいたデオキシコール酸生成菌と相互作用する腸内細菌種の探索  [Not invited]

  佐竹実菜子, 吹谷智, 佐藤昌直, 石塚敏, 小椋義俊, 林哲也, 横田篤

  日本農芸化学会大会講演要旨集(Web)  2018/03
• ウイルス感染時におけるAGO1-vsiRNAの標的となる植物mRNAの予測

  堀裕和, 岩橋美穂, 白谷公孝, 佐藤昌直, 峯彰, 峯彰, 竹田篤史, 竹田篤史, 竹田篤史

  日本分子生物学会年会プログラム・要旨集(Web)  2018
• Lobe-less RNAはショウジョウバエの胚発生期において軸索走行制御に寄与する長鎖ノンコーディングRNAである

  稲垣幸, 門田満隆, KEELEY Sean D., KEELEY Sean D., 中村奈月, 佐藤昌直, 工樂樹洋, 影山裕二, 影山裕二

  日本RNA学会年会要旨集  2018
• ショウジョウバエLobe‐less RNAは胚発生期の軸索走行シグナルを制御している  [Not invited]

  稲垣幸, 中野美幸, 中村奈月, 門田満隆, KEELEY Sean D, 佐藤昌直, 工樂樹洋, 影山裕二, 影山裕二

  日本RNA学会年会要旨集  2017/07
• 「顔無し遺伝子」ハンティングパイプラインの構築:配列情報から機能を推定できない遺伝子の機能推定  [Not invited]

  佐藤昌直, 門宏明, 日下部宜宏

  日本蚕糸学会大会・蚕糸・昆虫機能学術講演会講演要旨集  2017/03
• ネッタイシマカにおけるCry44Aaトキシンレセプターについて  [Not invited]

  浅野眞一郎, 中神あゆみ, 中尾悠太, 佐藤昌直, 伴戸久徳

  日本蚕糸学会大会・蚕糸・昆虫機能学術講演会講演要旨集  2017/03
• BmNPV非必須遺伝子arif‐1,pif‐2による補償的な必須遺伝子発現制御  [Not invited]

  高ひとみ, 佐藤昌直, 浅野眞一郎, 伴戸久徳

  日本蚕糸学会大会・蚕糸・昆虫機能学術講演会講演要旨集  2017/03
• 動的なカルシウムシグナルによる頂端収縮と神経管閉鎖の制御

  鈴木誠, 佐藤昌直, 小山宏史, 上野直人

  日本数理生物学会年会(Web)  2017
• ショウジョウバエLobe-less RNAは胚発生期の軸索走行シグナルを制御している

  稲垣幸, 中野美幸, 中村奈月, 門田満隆, KEELEY Sean D., 佐藤昌直, 工樂樹洋, 影山裕二, 影山裕二

  日本RNA学会年会要旨集  2017
• BmNPV非必須遺伝子arif-1,pif-2による補償的な必須遺伝子発現制御

  高ひとみ, 佐藤昌直, 浅野眞一郎, 伴戸久徳

  日本蚕糸学会大会・蚕糸・昆虫機能学術講演会講演要旨集  2017
• カイコ分散型動原体を構成するDNA結合タンパク質の解析  [Not invited]

  門宏明, 佐藤昌直, 李在萬, 日下部宜宏

  日本生化学会大会(Web)  2017
• カイコにおける核多角体病ウイルスの重感染排除の観察,および原因因子の探索  [Not invited]

  諸熊大輔, 門宏明, 佐藤昌直, 李在萬, 伴戸久徳, 日下部宜宏

  日本生化学会大会(Web)  2017
• 植物micro‐RNAの認識特異性に関する研究とその応用  [Not invited]

  白谷公孝, 舛田さくら, 長田怜子, 唐戸俊介, 都筑正行, 佐藤昌直, 渡邊雄一郎, 竹田篤史

  日本植物学会大会研究発表記録  2016/09
• サバ類近縁種間のトランスクリプトーム解析  [Not invited]

  大崎彰梧, 佐藤昌直, 矢澤良輔

  日本水産学会大会講演要旨集  2016/03
• RNA‐seq法を用いた核多角体病ウイルス感染カイコ細胞のトランスクリプトーム解析  [Not invited]

  浜島りな, 佐藤昌直, 小林迪弘, 池田素子

  日本蚕糸学会大会・蚕糸・昆虫機能学術講演会講演要旨集  2016/03
• MAPKの基質となるWRKY型転写因子の葉緑体ROSバーストへの関与  [Not invited]

  安達広明, 波多江健太, 佐藤昌直, 吉岡博文

  日本植物病理学会大会プログラム・講演要旨予稿集  2016/03
• 植物micro-RNAの認識特異性に関する研究とその応用

  白谷公孝, 舛田さくら, 長田怜子, 唐戸俊介, 都筑正行, 佐藤昌直, 渡邊雄一郎, 竹田篤史

  日本植物学会大会研究発表記録  2016
• RNA-seq法を用いた核多角体病ウイルス感染カイコ細胞のトランスクリプトーム解析

  浜島りな, 佐藤昌直, 小林迪弘, 池田素子

  日本蚕糸学会大会・蚕糸・昆虫機能学術講演会講演要旨集  2016
• BmNPVのアクセサリー遺伝子が担うウイルス増殖のロバストネス  [Not invited]

  高ひとみ, 佐藤昌直, 浅野眞一郎, 伴戸久徳

  日本分子生物学会年会プログラム・要旨集(Web)  2016
• 必須性を示すBmNPV非必須遺伝子クラスターの解析  [Not invited]

  高ひとみ, 佐藤昌直, 浅野眞一郎, 伴戸久徳

  日本蚕糸学会大会・蚕糸・昆虫機能学術講演会講演要旨集  2015/09
• カイコにおけるTORシグナル経路の解明  [Not invited]

  平田一真, 佐藤昌直, 徐剣, 季明明, 祝力, 日野真人, 山下真実, 諸熊大輔, 門宏明, 李在萬, 日下部宜宏

  日本蚕糸学会大会・蚕糸・昆虫機能学術講演会講演要旨集  2015/09
• カイコ卵巣由来培養細胞BmN‐BmNPVトランスクリプトームにおけるmRNA配列の推定と評価  [Not invited]

  佐藤昌直, 佐藤昌直, 高ひとみ, 伴戸久徳

  日本蚕糸学会大会・蚕糸・昆虫機能学術講演会講演要旨集  2015/09
• BmSyndecanノックダウンBmN細胞におけるBmNPVの増殖  [Not invited]

  宇多桃香, 佐藤昌直, 浅野眞一郎, 伴戸久徳

  日本蚕糸学会大会・蚕糸・昆虫機能学術講演会講演要旨集  2015/09
• 遺伝子ネットワークのreduced S-systemモデルの効率的同定法の提案

  木村 周平, 佐藤 昌直, 岡田(畠山) 眞里子

  情報処理学会研究報告. BIO, バイオ情報学  2015/03  一般社団法人情報処理学会
   

  遺伝子ネットワーク同定とは,観察された遺伝子発現データに合うような遺伝子ネットワークのモデルのパラメータを推定する問題のことである.遺伝子ネットワークを記述するために多くの数理モデルが提案されているが,中でも S-system モデルは最も使用されてモデルの一つである. S-system モデルは生化学反応を近似したモデルであり,遺伝子ネットワークの記述に適していると考えられている.そのため S-system モデルを用いた遺伝子ネットワーク同定法が,これまでに数多く提案されている.しかしながら S-system に含まれるパラメータ数は,他の頻繁に使用されているモデルのパラメータ数よりも多い.従って遺伝子ネットワークの S-system モデルを同定するためには,より多くの遺伝子発現データを与える必要があると考えられる.遺伝子ネットワーク同定に必要な遺伝子発現データの量を減らすために,本研究では S-system モデルの一部のパラメータを 0 に固定することでモデルを単純化する.本研究では単純化した S-system モデルを,reduced S-system モデルと呼ぶ.次に遺伝子ネットワークの reduced S-system モデルを効率的に同定するための新たな方法を提案する.最後に数値実験を通して,提案手法の有効性を示す.
• 遺伝子ネットワークのreduced S‐systemモデルの効率的同定法の提案  [Not invited]

  木村周平, 佐藤昌直, 岡田(畠山)眞里子

  情報処理学会研究報告(Web)  2015/03
• クローバ葉脈黄化ウイルスがコードするP3N‐PIPOおよび新規タンパク質の発現機構  [Not invited]

  薦田(萩原)優香, CHOI S. H, 佐藤昌直, 厚見剛, 阿部純也, 中原健二, 上田一郎, 内藤哲

  日本植物病理学会大会プログラム・講演要旨予稿集  2015/03
• RNA‐seqによるMAPK‐WRKY経路下流の植物免疫関連遺伝子の探索  [Not invited]

  安達広明, 佐藤昌直, 吉岡博文

  日本植物病理学会大会プログラム・講演要旨予稿集  2015/03
• RNA‐seqによるMAPK‐WRKY経路下流の免疫応答誘導機構の解析  [Not invited]

  安達広明, 佐藤昌直, 吉岡博文

  日本植物生理学会年会要旨集  2015/03
• バキュロウイルスゲノム人工合成系の確立

  石橋大樹, 佐藤昌直, 高ひとみ, 武内潤一, 浅野眞一郎, 伴戸久徳

  日本蚕糸学会大会・蚕糸・昆虫機能学術講演会講演要旨集  2015
• ショウジョウバエ母性因子Mamoと遺伝学的に相互作用する因子の解析  [Not invited]

  中村翔一, 塩田孝祐, 小林悟, 佐藤昌直, 向正則

  日本生化学会大会(Web)  2015
• 摂動に対するカイコ培養細胞株BmN4‐SID1のトランスクリプトーム変化とその情報を利用したネットワークモデリング  [Not invited]

  佐藤昌直, 佐藤昌直, 門宏明, 徐剣, 李在萬, 笠嶋めぐみ, 鈴木誉保, 坪田拓也, 小林悟, 瀬筒秀樹, 日下部宜宏

  日本生化学会大会(Web)  2015
• 植物のmicroRNA‐標的mRNA間に1~3ケ所のミスマッチがある際の認識特異性に関する研究  [Not invited]

  白谷公孝, 舛田さくら, 長田怜子, 唐戸俊介, 都筑正行, 佐藤昌直, 佐藤昌直, 渡邊雄一郎, 竹田篤史, 竹田篤史

  日本生化学会大会(Web)  2015
• 視(み)ることで識(し)る植物免疫応答  [Not invited]

  別役重之, 加藤新平, 佐藤昌直, 浜田紗稀, 福田裕穂

  日本植物病理学会植物感染生理談話会論文集  2014/07
• Lobe‐less RNAはポリコーム複合体と相互作用し,ショウジョウバエにおけるキノコ体の形態形成を制御している  [Not invited]

  稲垣幸, 佐藤昌直, 中村奈月, 小林悟, 影山裕二

  日本RNA学会年会要旨集  2014/07
• 植物exosome因子RRP44/DIS3が作用するRNA  [Not invited]

  熊倉直祐, 大月陽路香, 佐藤昌直, 渡邊雄一郎

  日本RNA学会年会要旨集  2014/07
• AcMNPV IE遺伝子発現のロバストネスを支えるIE遺伝子ネットワークと補償的相互作用  [Not invited]

  小野慎子, 高ひとみ, 佐藤昌直, 浅野眞一郎, 伴戸久徳

  日本蚕糸学会大会・蚕糸・昆虫機能学術講演会講演要旨集  2014/03
• 非必須遺伝子の複数ノックアウトがBmNPV増殖に与える影響について  [Not invited]

  高ひとみ, 小野慎子, 佐藤昌直, 浅野眞一郎, 伴戸久徳

  日本蚕糸学会大会・蚕糸・昆虫機能学術講演会講演要旨集  2014/03
• 非必須遺伝子の多重ノックアウトがBmNPV増殖に与える影響  [Not invited]

  高ひとみ, 小野慎子, 佐藤昌直, 浅野眞一郎, 伴戸久徳

  日本分子生物学会年会プログラム・要旨集(Web)  2014
• カイコDNMT‐1(BmDNMT‐1)の生化学的特性と遺伝子転写制御における役割  [Not invited]

  満留卓実, 門宏明, 佐藤昌直, 末次克行, 山本公子, 李志清, 徐剣, 祝力, LEE Jae M, 日下部宜宏, 益田篤

  日本分子生物学会年会プログラム・要旨集(Web)  2014
• ショウジョウバエPGCにおける母性転写因子Ovoの機能解析  [Not invited]

  篠塚裕子, 佐藤昌直, 小林悟

  日本動物学会大会予稿集  2013/08
• BmDnmt1,BmDnmt2,bMBDの機能阻害細胞におけるDNAのメチル化  [Not invited]

  満留卓実, 門宏明, 佐藤昌直, 末次克行, 山本公子, 李志清, 徐剣, 祝力, 李在萬, 日下部宜宏

  日本蚕糸学会大会・蚕糸・昆虫機能学術講演会講演要旨集  2013/03
• カイコ分散型動原体染色体ループドメイン形成へのCTCF,CP190の関与  [Not invited]

  益田篤, 佐藤昌直, 末次克行, 山本公子, 門宏明, 李在萬, 日下部宜宏

  日本蚕糸学会大会・蚕糸・昆虫機能学術講演会講演要旨集  2013/03
• Lobe‐less RNAはショウジョウバエキノコ体の形態形成を介して学習・記憶を制御している  [Not invited]

  稲垣幸, 佐藤昌直, 宮下知之, 中村奈月, 小林悟, 斉藤実, 影山裕二

  日本分子生物学会年会プログラム・要旨集(Web)  2013
• Side populationを指標にしたニジマス精原幹細胞の濃縮  [Not invited]

  林誠, 佐藤昌直, 岩崎佳子, 小野澤健明, 長坂安彦, 定家咲子, 小林悟, 吉崎悟朗

  日本分子生物学会年会プログラム・要旨集(Web)  2012
• カイコ分散型動原体染色体におけるクロマチンループ形成とその役割  [Not invited]

  益田篤, 佐藤昌直, 門宏明, LEE Jae Man, 日下部宜宏

  日本分子生物学会年会プログラム・要旨集(Web)  2012
• サリチル酸,ジャスモン酸,エチレンのシグナル伝達を司る遺伝子の多重変異体の解析は,植物抵抗性メカニズムにおけるそれらの協調的影響を明らかにした  [Not invited]

  津田賢一, 佐藤昌直, STODDARD Thomas, GLAZEBROOK Jane, 片桐文章

  日本植物病理学会報  2009/08
• mRNA発現プロファイリングおよびネットワーク解析を基盤とした機能ゲノミクス  [Not invited]

  佐藤昌直, LENARZ‐WYATT Lisa, HERNICK Charles, GLAZEBROOK Jane, 渡辺雄一郎, 片桐文章

  日本植物生理学会年会要旨集  2009/03
• 植物ホルモンの情報伝達を司る遺伝子の多重変異が植物の病原体抵抗性に与える影響  [Not invited]

  津田賢一, 佐藤昌直, STODDARD Thomas, GLAZEBROOK Jane, 片桐文章

  日本植物生理学会年会要旨集  2009/03
• (403) Mutual Inhibition between Salicylate-mediated and MAMPs-induced Signaling Revealed by a Network Analysis(Abstracts of the Papers Presented at the Annual Meeting of the Society)

  Sato M., Tsuda K., Glazebrook Jane, Watanabe Y., Katagiri F.

  Annals of the Phytopathological Society of Japan  2008/08  The Phytopathological Society of Japan (PSJ)
  
• MAMPによって誘導される防御応答におけるSAシグナリングの重要性  [Not invited]

  津田賢一, 佐藤昌直, GLAZEBROOK Jane, COHEN Jerry, 片桐文章

  日本植物生理学会年会要旨集  2008/03
• シロイヌナズナの防御応答シグナル伝達のネットワークレベルでの解析  [Not invited]

  佐藤昌直, 津田賢一, GLAZEBROOK Jane, 渡辺雄一郎, 片桐文章

  日本植物生理学会年会要旨集  2008/03
• (283) Statistical Models that Predict the in planta Bacterial Growth based on Early Expression Levels of a Small Number of Arabidopsis Genes in the RPS2-mediated Resistance(Abstracts of the Papers Presented at the Annual Meeting of the Society)

  Sato M., Lenarz-Wtatt Lisa, Watanabe Y., Katagiri F.

  Annals of the Phytopathological Society of Japan  2007/08  The Phytopathological Society of Japan (PSJ)
  
• 遺伝子発現プロファイリングによる,シロイヌナズナのPseudomonas syringae hrcC変異体に対する防御応答解析  [Not invited]

  津田賢一, 佐藤昌直, 片桐文章

  日本植物生理学会年会要旨集  2007/03
• シロイヌナズナのPseudomonas syringaeに対する防御応答を制御するシグナル伝達ネットワークの解析  [Not invited]

  佐藤昌直, LENARZ‐WYATT Lisa, 渡辺雄一郎, 片桐文章

  日本植物生理学会年会要旨集  2007/03
• Analysis of the Arabidopsis thaliana Signaling Network Controlling Defense Responses Against the Bacterial Pathogen Pseudomonas syringae  [Not invited]

  Sato Masanao, Lenarz-Wyatt Lisa, Watanabe Yuichiro, Katagiri Fumiaki

  Plant and Cell Physiology Supplement  2007  The Japanese Society of Plant Physiologists
   

  Elucidation of the plant defense signaling network controlling responses to pathogen infection, has been challenging for several biological reasons. First, plant defense signaling pathways are highly interconnected. Second, plants receive multiple stimuli associated with pathogen infection including pathogen-associated molecular patterns and effectors delivered directly into plant cells. Third, part of the signaling network is robust to perturbations.
  To reveal the structure and function of this signaling network, we have employed a strategy using parallel and quantitative data collection. Our objective is to collect hundreds of observations about the behavior of the system after introducing specific perturbations. To this end, we have developed a high-performance, inexpensive custom microarray and have initiated gene expression profiling combined with a reverse genetics strategy. Analysis of known mutants as reference points within the signaling network revealed a model for the topology of the network and key players controlling signaling pathways utilized to process different stimuli.
• Expression Profile Analysis of Arabidopsis Defense Responses Elicited by The Pseudomonas syringae hrcC Mutant  [Not invited]

  Tsuda Kenichi, Sato Masanao, Katagiri Fumiaki

  Plant and Cell Physiology Supplement  2007  The Japanese Society of Plant Physiologists
   

  Plants change expression of numerous genes upon pathogens attack, and many of the changes compose plant defense mechanisms. The hrcC mutant of the bacterial pathogen Pseudomonas syringae pv. tomato DC3000 is defect in injecting type III effectors (T3Es) into the plant cell, and plant responses induced by the mutant strain is considered mostly based on recognition of pathogen-associated molecular patterns (PAMPs). It is not clear whether PAMPs have any effects on salicylic acid (SA) -mediated responses, which are induced by recognition of some T3Es. Several Arabidopsis defense mutants were analyzed by mRNA profiling using a small-scale custom microarray after inoculation of the hrcC strain. We found that induction of some genes by the hrcC strain depends on the ICS1 gene, which is essential for the pathogen-induced SA synthesis. This strongly suggests that PAMPs can induce SA-mediated defense responses. We will also discuss expression profiles of other Arabidopsis mutants.
• ウイルス感染からみた植物免疫  [Not invited]

  渡邊雄一郎, 稲葉直子, 滝澤真理, 佐藤昌直

  日本生体防御学会学術総会講演抄録集  2007
• (212) Development of an Arabidopsis Pathoarray to Study Arabidopsis thaliana-pathogen Interactions(Abstract of the Paper Presented at the 2006 Annual Meeting in Sapporo)

  Sato M., Mitra Raka M., Poecke Remco M. van, Collar John, Glazebrook Jane, Katagin F.

  Annals of the Phytopathological Society of Japan  2006/11  The Phytopathological Society of Japan (PSJ)
  
• シロイヌナズナ‐病原体相互作用大規模解析用マイクロアレイ“Arabidopsis Pathoarray”の開発  [Not invited]

  佐藤昌直, MITRA Raka M, VAN POECKE Remco M, COLLER John, GLAZEBROOK Jane, 片桐文章

  日本植物病理学会報  2006/11
• (347) Characterization of the Resistance in Pea to Clover Yellow Vein Virus using a Green Fluorescent Protein Tagged Virus(Abstracts of the Papers Presented at the 2005 Annual Meeting in Shizuoka)

  Andrade M., Sato M., Uyeda I.

  Annals of the Phytopathological Society of Japan  2005/08  The Phytopathological Society of Japan (PSJ)
  
• (293) Isolation of Resistance-breaking Strains of Clover yellow vein virus from Pea(Abstracts of the Papers Presented at the Annual Meeting of the Society, Fukuoka, March 28-30, 2004)

  Andrade M., Yambao M. L. M., Sato M., Uyeda I.

  Annals of the Phytopathological Society of Japan  2004/08  The Phytopathological Society of Japan (PSJ)
  
• (7) Resistance to Clover yellow vein virus (C1YVV) in Some Lines of Pea is Governed by a Single Recessive Gene.(Abstracts Presented at the Meeting of the Hokkaido Division) (Abstracts of Papers Presented at the Division Meetings of the Phytopathological Society of Japan, 2003)

  Andrade M., Sato M., Uyeda I.

  Annals of the Phytopathological Society of Japan  2004/02  The Phytopathological Society of Japan (PSJ)
  
• (6)A Point Mutation in the Helper Component-protease (HC-Pro) Gene of Clover yellow vein virus Associates with Symptom Attenuation in Broad Beans.(Abstracts Presented at the Meeting of the Hokkaido Division) (Abstracts of Papers Presented at the Division Meetings of the Phytopathological Society of Japan, 2003)

  Yambao M. L. M., Sato M., Uyeda I.

  Annals of the Phytopathological Society of Japan  2004/02  The Phytopathological Society of Japan (PSJ)
  
• (5) Genetic Analyses of Symptom Determinants in Clover yellow vein virus-infected Pea (Abstracts Presented at the Meeting of the Hokkaido Division) (Abstracts of Papers Presented at the Division Meetings of the Phytopathological Society of Japan, 2003)

  Kagaya U., Sato M., Uyeda I.

  Annals of the Phytopathological Society of Japan  2004/02  The Phytopathological Society of Japan (PSJ)
  
• (427)Fine Mappinf of the Pathogenic Determinants of Clover yellow vein virus Genome(Abstracts of the Papers Presented at the 2003 Annual Meeting in Tokyo)

  Yambo M. L. M., Sasaki T., Ueda I., Sato M., Sekiguchi H., Yagihashi H., Takahashi Y.

  Annals of the Phytopathological Society of Japan  2003/08  The Phytopathological Society of Japan (PSJ)
  
• Comparison of Reactions to Clover yellow vein virus Infection between Different Pea Cultivars(Abstracts of the Papers Presented at the 2003 Annual Meeting in Tokyo)

  Sato M., Ueda I.

  Annals of the Phytopathological Society of Japan  2003/08  The Phytopathological Society of Japan (PSJ)
  
• Symptom Analysis of Chimeric Viruses between Wild and MM Isolates of Clover yellou vein virus

  Yambao M.L.M., Sasaki T., Uyeda I., Sato M., Sekiguchi H., Yagihashi H., Takahashi Y.

  Annals of the Phytopathological Society of Japan  2003/02  The Phytopathological Society of Japan (PSJ)
   

  Wild type Clover yellow vein virus (ClYVV) induces severe necrosis in broad bean plants. A spontaneous mutant (MM) that induces mosaic symptoms with replication efficiency similar to wild type was isolated. To determine the domain in the viral genome involve in necrosis induction, cDNAs to genomic RNA of MM mutant were exchanged with corresponding wild type fragment. Three chimeric clones, pClYVV/CN, pClYVV/NS and pClYVV/SS were made and inoculated to broad beans. Symptom severity was scored and viral accumulation was measured by western blot. pClYVV/NS and pClYVV/SS induced symptoms essentially the same as the wild type. Viral accumulation in broad beans after inoculation of these constructs are also similar to the wild type. On the other hand, pClYVV/CN containing the C-terminal P1 to N-terminal P3 of MM caused a drastic symptom change to mild chlorosis with debilitated infectivity. Sequence analysis of this MM regions showed amino acid substitutions at P1 (E182G), HCPro (T27I, I33V, R51I, D193Y, L327Q, V393I) and P3 (N122S). These results indicate that the ability to induce necrosis and the control of viral accumulation are mapped in the C-terminal P1 to N-terminal P3 region of ClYVV.
• ClYVV Resistance of Common Bean cv. Jolanda Analyzed by Reporter Genes

  Sato M., Masuta C., Uyeda I.

  Annals of the Phytopathological Society of Japan  2003/02  The Phytopathological Society of Japan (PSJ)
   

  インゲンマメ品種Jolandaはクローバー葉脈黄化ウイルス(ClYVV)に対して抵抗性を示す.我々はgreen fluorescent protein(GFP,C3-S65T)を発現するpClYVV/C3-S65Tを構築し,その組み換えウイルスに対してもJolandaが抵抗性を示すことを確認した.pClYVV/C3-S65Tをパーティクルボンバードメントで導入した場合に感受性品種ではウイルス感染の進行と共にGFP蛍光は広がっていったが,Jolandaでは全く観察されなかった.この結果から,1細胞レベルで抵抗性が発揮されていることが明らかになった.次に感染性が失われた欠失クローンpClYVVΔSac/Gを大正金時およびJolandaに導入したところ両者でGFP蛍光は観察されたが,JolandaでのGFP蛍光発現に遅れが見られた.この遺伝子発現の遅れが感受性・抵抗性に関与するかを解析するために,ClYVVの非翻訳領域(NTR)とホタル由来のルシフェラーゼを連結した発現ベクターpClnLを用いた.このルシフェラーゼを用いた解析から,Jolandaの抵抗性とClYVVのNTRによる発現制御は無関係であることが判明した.
• (225)The Genetic Background of Resistance to C1YVV in Jolanda Bean

  Sato M., Masuta C., Uyeda I.

  Annals of the Phytopathological Society of Japan  2002/08  The Phytopathological Society of Japan (PSJ)
  
• Analysis of Clover yellow vein virus Mutant Can Overcome the Resistance in Common Bean Clover yellow vein virus

  Sato M., Masuta C., Uyeda I.

  Annals of the Phytopathological Society of Japan  2001/08  The Phytopathological Society of Japan (PSJ)
  
• Modefication of Clover Yellow Vein Viral Expression Vector and Stability of the Expressed Gene(Abstracts Presented at the Meeting of the Hokkaido Division)

  Wang Z.D., Uyeda I., Ueda S., Sekiguchi H., Takahashi Y., Sato M.

  Annals of the Phytopathological Society of Japan  2000/12  The Phytopathological Society of Japan (PSJ)
  
• Monitoring of Clover Yellow Vein Virus Infection by Green Fluorescent Protein (GFP) (Abstracts Presented at the Meeting of the Hokkaido Division)

  Sato M., Masuta C., Uyeda I.

  Annals of the Phytopathological Society of Japan  1999/12  The Phytopathological Society of Japan (PSJ)
  
• マメ科植物での高発現植物ウイルスベクターの構築  [Not invited]

  山名利一, 増田税, 高橋葉子, 佐藤昌直, 松村健, 上田一郎

  日本植物細胞分子生物学会大会・シンポジウム講演要旨集  1999/07
• Construction of a Plant Virus Based Vector and Highly Efficient Expression of a Foreign Gene in Legume Plants

  Yamana T., Masuta C., Takahashi Y., Sato M., Matsumura T., Uyeda E.

  Annals of the Phytopathological Society of Japan  1999/06  The Phytopathological Society of Japan (PSJ)
  

Research Projects

• Study of virus-mediated and viroid-mediated silencing of host plant genes

  Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research

  Date (from‐to) : 2018/06 -2021/03 

  Author : Takeda Atsushi

   

  To date, it is unclear how AGO1 and AGO2 determine the target mRNAs to be degraded in plants. To predict the target host mRNAs of AGO1-virus-derived siRNAs (vsiRNAs) and AGO2-vsiRNAs more precisely, I analyzed target specificities of AGO1-miRNA and AGO2-miRNA in plants. In case of AGO1-mediated silencing, I tested effects of G:U wobbles between miRNA and mRNAs. Results of a series of transient assay showed that G:U wobble has an intermediate effect between the base paring and the mismatch in a position-dependent manner. In case of AGO2-mediated silencing, I established a transient system to test the requirement of complementarities between miRNA and mRNAs by using a newly generated ago triple mutant of Nicotiana banthamiana. This system allows us to analyze mechanisms of the AGO2 specificity in plants. These basic analyses will help establish algorisms to predict host mRNAs targeted by AGO1-vsiRNAs and AGO2-vsiRNAs in future.
• New approach for studying functional importance of baculovirus nonessential genes

  Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research

  Date (from‐to) : 2015/04 -2018/03 

  Author : Bando Hisanori, TAKA Hitomi, ISHIBASHI Taiki, HARADA Naoto, SAITO Ryo

   

  In Bombyx mori nucleopolyhedrovirus (BmNPV) genome comprised of 143 genes, more than 60 % of them are nonessential genes for efficient multiplication in Bombyx mori cell line BmN. However, a combination of nonessential genes was found to play a critical role in efficient viral multiplication, suggested essentiality of nonessential genes as a collected gene. A study using reverse genetics identified genetic interactions among nonessential gens in such a combination and emphasized importance of a methodology to advance the reverse combinatorial genetics of BmNPVs; thus we established a platform for BmNPV genome assembly from PCR-amplified DNA fragments using Gibson Assembly for further analysis of the essentiality of nonessential genes and for reconstruction of BmNPV vector system based on logical design.
• Molecular basis of formation and regulation of insect holocentric chromosome

  Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research

  Date (from‐to) : 2014/04 -2018/03 

  Author : KUSAKABE TAKAHIRO

   

  Lepidopteran insects are known to have specific chromosomes called heliocentric chromosome having multiple centromeres along the entire length. In this study, we clarified the molecular basis of kinetochore formation of the heliocentric chromosome and newly found six centromere-related genes specific to silkworm using the gene network analysis. Based on these results and analysis on replication related genes, an artificial chromosome functioning by tethering DNA replication factor and kinetochore protein was synthesized. On the other hand, as for the genome-wide gene expression regulation and molecular basis of chromatin structure, we focused on histone acetylation and deacetylation enzymes, and performed gene knockdown on these genes. As a result, we found that HDAC 8 plays an important role in the silkworm.
• Functional genomics on in vivo fitness of BmNPV

  Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research

  Date (from‐to) : 2015/04 -2017/03 

  Author : Hisanori Bando, ASANO SHINICHIRO

   

  Bombyx mori nucleopolyhedrovirus (BmNPV) H4 that had genome sharing high sequence similarity (approx. 97%) with that of the type strain of BmNPV T3 showed marked growth advantage in silkworm larvae. Studies using chimeric recombinant BmNPV between H4 and T3 demonstrated that a viral membrane protein gene gp64 as a determinant in the in vivo fitness of BmNPV H4. Further analyses identified amino acid positions involved in the BmNPV H4 phenotype of efficient growth in silkworm larvae. These results suggested the possibility to control growth ability of BmNPV in silkworm larvae by gp64-targetted genome manipulation.
• Studies of the small RNA specificity and the viral pathogenicity in plants

  Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research

  Date (from‐to) : 2015/04 -2017/03 

  Author : Takeda Atsushi, SATO MASANAO

   

  In plants, viral infection induces RNA silencing, which is a basal immune response against viruses. In the anti-viral pathways of plant RNA silencing, abundant viral-derived small-interfering RNAs (vsiRNAs) are generated through functions of Dicer-like enzymes (DCLs). A class of 21 nt vsiRNAs cleaved by DCL4 is incorporated into Argonaute 1 (AGO1). The AGO1-vsiRNA complex has a potential to cleave not only viral RNAs but also endogenous mRNAs dependent on the complementarity between target RNAs and vsiRNAs in AGO1. However, determinants of target specificity of AGO1-vsiRNA complex are unknown and thus we cannot predict the target mRNAs downregulated upon viral infection. In this study, we examined the AGO1 specificity in plants experimentally by using a massive transient luciferase assay. We identified several determinants of the plant AGO1 specificity, which can help predict the target mRNAs of vsiRNAs in viral-infected plants in future.
• Development of en masse inter-species genetic interaction analysis using a pooled E. coli gene knockout strans

  Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research

  Date (from‐to) : 2015/04 -2017/03 

  Author : Sato Masanao

   

  Microbes and hosts have been co-evolved as they have repeatedly developed a better strategy to infect/defend in infection processes and to counter it. Such coevolution processes result in development of highly complex gene network in both host and microbes. To elucidate the gene network in host or microbe for their interaction, high throughput molecular profiling and genetic interaction analyses have identified thousands of genes in host or microbe. A major next challenge in research on host-microbe interactions is to elucidate interactions between host and microbial gene networks. In this study, I aimed at development of a method to efficiently collect genetic information on how host and microbial gene networks interact in an seamlessly integrated manner. The developed protocol and data analysis pipeline accurately collect readouts in an inter-species genetic interactions en masse.
• Study of population dynamics of host population during viral infection

  Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research

  Date (from‐to) : 2014/04 -2017/03 

  Author : Ueki Shoko, Higashi Aiko, Kobashi Rieko

   

  The initial goal of the project was to analyze the infection process of Heterosigma akashiwo virus (HaV) to its host population, bloom-forming algae, Heterosigma akashiwo, that consisted from strains showing the different reactions to HaV infection. During the project, we completed the whole genome sequencing and gene predictions of HaV, and obtained the insights into the evolutionary and phylogenetical position to other giant double-stranded DNA viruses. In addition, contradicting to the initial understanding, we found out that the host reactions to HaV infection were not only determined by the host genotypes, but also by the presence/absence or the species of the accomplice bacteria associating to the host. The project developed into direction unpredicted when it was initially planed: however, the insights obtained by the project will provide infrastructure for future studies about H. akashiwo and its virus from cellular and molecular biology view points.
• Assembly of baculovirus genome DNA fragments in yeast for improving baculovectors

  Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research

  Date (from‐to) : 2013/04 -2015/03 

  Author : BANDO Hisanori, SATO Masanao

   

  The technologies that enable flexible manipulation of virus genome are very important technical base for improving viral vectors. The aim of this study is to establish a method for assembling baculovirus genome DNA from both synthetic and natural DNA fragments to improve baculovectors. First, we constructed a baculovirus of the silkworm (BmNPV/bacmid) carrying an yeast replication origin (Yori). Second, we cloned 21 overlapping DNA fragments covering whole sequence of the BmNPV/bacmid genome DNA with Yori in bacterial cells using a plasmid vector. Lastly, we assembled the 21 fragments in yeast to form the complete BmNPV genome DNA.
• A systems biology approach for improving baculovector system

  Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research

  Date (from‐to) : 2010/04 -2014/03 

  Author : BANDO Hisanori, KUSAKABE Takahiro, SATOU Masanao

   

  By taking a systems biology approach, a baculovirus gene network models was built and host factors involved in recombinant protein expression from a baculovector system were identified.
• A systems approach to elucidate gene regulatory network for gernline development and fertility

  Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research

  Date (from‐to) : 2011 -2013 

  Author : SATO Masanao

   

  The signaling network in a germline cell was modeled using BmN4, the cell line derived from a Bombyx mori ovary. The network model is composed of genes that are evolutionarily conserved between B. mori and Drosophila melanogaster and that have been known as regulators for signal transduction in D. melanogaster germline or somatic cell development. The model suggested a gene known as a regulator of germline development in D. melanogaster as a hub in the network. In addition, the model inferred roles of genes of which mutations caused sterility by unknown reasons. Furthermore, the model inferred roles of genes, which have been known to function in somatic cells, in germline cells.
• Mechanism regulating GSC niche system in Drosophila ovary and testis

  Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research

  Date (from‐to) : 2008 -2012 

  Author : KOBAYASHI Satoru, ASAOKA Miho, HAYASHI Yoshiki, SATO Masanao, KITADATE Yu, ABE Kuniya

   

  In this study, we have been trying to clarify the mechanisms regulating "GSC Niche System" in Drosophila. We found that 1) heparan sulphate proteoglycans (HSPG) are deeply involved in GSC maintenance by restricting the function of growth factors in a narrow region (Niche field) around "Niche cells", 2) Notch, Sevenless and Egfr signaling are required for proper formation of "Niche cells" in the anterior region of male embryonic gonads, and that 3) maternal Ovo and Sxl are required for germline-specific gene expression and sex determination of primordial germ cells, respectively.