J-GLOBAL         Last updated: Jun 25, 2019 at 14:28
Kyoto University
Master(Science)(The University of Tokyo)

Research Areas


Academic & Professional Experience

Kyoto University 


Chemistry, Graduate School, Division of Science, The University of Tokyo
Chemistry, Faculty of Science, The University of Tokyo

Published Papers

Shinkawa H, Kajikawa M, Nomura Y, Ogura M, Sawaragi Y, Yamano T, Nakagami H, Sugiyama N, Ishihama Y, Kanesaki Y, Yoshikawa H, Fukuzawa H
Plant & cell physiology   60(4) 916-930   Apr 2019   [Refereed]
Sugiyama N, Miyake S, Lin MH, Wakabayashi M, Marusawa H, Nishiumi S, Yoshida M, Ishihama Y
Genes to cells : devoted to molecular & cellular mechanisms   24(2) 139-150   Feb 2019   [Refereed]
Moriya Y, Kawano S, Okuda S, Watanabe Y, Matsumoto M, Takami T, Kobayashi D, Yamanouchi Y, Araki N, Yoshizawa AC, Tabata T, Iwasaki M, Sugiyama N, Tanaka S, Goto S, Ishihama Y
Nucleic acids research   47(D1) D1218-D1224   Jan 2019   [Refereed]
Imamura H, Wagih O, Niinae T, Sugiyama N, Beltrao P, Ishihama Y
Journal of proteome research   16(4) 1825-1830   Apr 2017   [Refereed]
Protein kinase A (PKA or cAMP-dependent protein kinase) is a serine/threonine kinase that plays essential roles in the regulation of proliferation, differentiation, and apoptosis. To better understand the functions of PKA, it is necessary to eluci...
Hiyama A, Takemiya A, Munemasa S, Okuma E, Sugiyama N, Tada Y, Murata Y, Shimazaki KI
Nature communications   8(1) 1284   Nov 2017   [Refereed]
Stomata regulate gas exchange between plants and atmosphere by integrating opening and closing signals. Stomata open in response to low CO2 concentrations to maximize photosynthesis in the light; however, the mechanisms that coordinate photosynthe...
Amagai A, Honda Y, Ishikawa S, Hara Y, Kuwamura M, Shinozawa A, Sugiyama N, Ishihama Y, Takezawa D, Sakata Y, Shinozaki K, Umezawa T
The Plant journal : for cell and molecular biology   94(4) 699-708   May 2018   [Refereed]
Abscisic acid (ABA) and its signaling system are important for land plants to survive in terrestrial conditions. Here, we took a phosphoproteomic approach to elucidate the ABA signaling network in Physcomitrella patens, a model species of basal la...
Okuda S, Watanabe Y, Moriya Y, Kawano S, Yamamoto T, Matsumoto M, Takami T, Kobayashi D, Araki N, Yoshizawa AC, Tabata T, Sugiyama N, Goto S, Ishihama Y
Nucleic acids research   45(D1) D1107-D1111   Jan 2017   [Refereed]
Major advancements have recently been made in mass spectrometry-based proteomics, yielding an increasing number of datasets from various proteomics projects worldwide. In order to facilitate the sharing and reuse of promising datasets, it is impor...
Sugiyama N, Ishihama Y
Journal of pharmaceutical and biomedical analysis   130 264-272   Oct 2016   [Refereed]
Protein phosphorylation mediated by protein kinases plays key roles in cellular signal transduction in both eukaryotic and prokaryotic organisms. Many researches have been conducted to investigate their functions and regulatory mechanisms, but the...
Wagih O, Sugiyama N, Ishihama Y, Beltrao P
Molecular & cellular proteomics : MCP   15(1) 236-245   Jan 2016   [Refereed]
Protein kinases are an important class of enzymes involved in the phosphorylation of their targets, which regulate key cellular processes and are typically mediated by a specificity for certain residues around the target phospho-acceptor residue. ...
Itaba N, Matsumi Y, Okinaka K, Ashla AA, Kono Y, Osaki M, Morimoto M, Sugiyama N, Ohashi K, Okano T, Shiota G
Scientific reports   5 16169   Nov 2015   [Refereed]
Mesenchymal stem cells (MSCs) are an attractive cell source for cell therapy. Based on our hypothesis that suppression of Wnt/β-catenin signal enhances hepatic differentiation of human MSCs, we developed human mesenchymal stem cell-engineered hepa...
Wakabayashi M, Kyono Y, Sugiyama N, Ishihama Y
Analytical chemistry   87(20) 10213-10221   Oct 2015   [Refereed]
We developed a novel approach to enlarge phosphoproteome coverage by selective elution depending on the number of phosphoryl group of peptides from a single titanium dioxide (TiO2) microcolumn using hydrophilic interaction chromatography (HILIC). ...
Lin MH, Sugiyama N, Ishihama Y
Science signaling   8(394) rs10   Sep 2015   [Refereed]
Protein phosphorylation is a crucial posttranslational modification for regulating cellular processes in bacteria; however, it has not been extensively studied because of technical difficulties in the enrichment of phosphopeptides. We devised an e...
Iwano S, Satou A, Matsumura S, Sugiyama N, Ishihama Y, Toyoshima F
Molecular and cellular biology   35(7) 1197-1208   Apr 2015   [Refereed]
Integrin-dependent cell-extracellular matrix (ECM) adhesion is a determinant of spindle orientation. However, the signaling pathways that couple integrins to spindle orientation remain elusive. Here, we show that PCTAIRE-1 kinase (PCTK1), a member...
Masuda K, Chiyoda T, Sugiyama N, Segura-Cabrera A, Kabe Y, Ueki A, Banno K, Suematsu M, Aoki D, Ishihama Y, Saya H, Kuninaka S
PloS one   10(4) e0125308   Apr 2015   [Refereed]
Masuda K, Chiyoda T, Sugiyama N, Segura-Cabrera A, Kabe Y, Ueki A, Banno K, Suematsu M, Aoki D, Ishihama Y, Saya H, Kuninaka S
PloS one   10(2) e0118662   Feb 2015   [Refereed]
In budding yeast, the Mitotic Exit Network (MEN) regulates anaphase promoting complex/cyclosome (APC/C) via the Dbf2-Cdc14 signaling cascade. Dbf2 kinase phosphorylates and activates Cdc14 phosphatase, which removes the inhibitory phosphorylation ...
Imamura H, Sugiyama N, Wakabayashi M, Ishihama Y
Journal of proteome research   13(7) 3410-3419   Jul 2014   [Refereed]
Protein kinase selectivity is largely governed by direct binding to the target site(s) on the substrate. Thus, substrate determinants identified from sequences around phosphorylation sites are desirable resources for matching kinases to their subs...
T. Umezawa; N. Sugiyama; M. Mizoguchi; S. Hayashi; F. Myouga; K. Yamaguchi-Shinozaki; Y. Ishihama; T. Hirayama; K. Shinozaki
Proceedings of the National Academy of Sciences of the United States of America   106(41) 17588-17593   Sep 2009   [Refereed]
Abscisic acid (ABA) signaling is important for stress responses and developmental processes in plants. A subgroup of protein phosphatase 2C (group A PP2C) or SNF1-related protein kinase 2 (subclass III SnRK2) have been known as major negative or p...
Mohamed Helmy, Naoyuki Sugiyama, Masaru Tomita, Yasushi Ishihama
Frontiers in plant science      Apr 2012   [Refereed]
Our recently developed rice proteogenomics database (OryzaPG-DB) is the first sustainable resource for rice shotgun-based proteogenomics, providing information on peptides identified in rice protein digested peptides measured by means of liquid ch...
K. Shinoda; N. Yachie; T. Masuda; N. Sugiyama; M. Sugimoto; T. Soga; M. Tomita
BMC Bioinformatics   7    Oct 2006   [Refereed]
BACKGROUND: Protein identification based on mass spectrometry (MS) has previously been performed using peptide mass fingerprinting (PMF) or tandem MS (MS/MS) database searching. However, these methods cannot identify proteins that are not already ...
K. Shinoda; M. Sugimoto; N. Yachie; N. Sugiyama; T. Masuda; M. Robert; T. Soga; M. Tomita
Journal of Proteome Research   5(12) 3312-3317   Dec 2006   [Refereed]
We developed a computational method to predict the retention times of peptides in HPLC using artificial neural networks (ANN). We performed stepwise multiple linear regressions and selected for ANN input amino acids that significantly affected the...
K. Konoki; N. Sugiyama; M. Murata; K. Tachibana
Tetrahedron Letters   40(5) 887-890   1999   [Refereed]
N. Ishii; K. Nakahigashi; T. Baba; M. Robert; T. Soga; A. Kanai; T. Hirasawa; M. Naba; K. Hirai; A. Hoque; P.Y. Ho; Y. Kakazu; K. Sugawara; S. Igarashi; S. Harada; T. Masuda; N. Sugiyama; T. Togashi; M. Hasegawa; Y. Takai; K. Yugi; K. Arakawa; N. Iwata; Y. Toya; Y. Nakayama; T. Nishioka; K. Shimizu; H. Mori; M. Tomita
Science   316(5824) 593-597   Mar 2007   [Refereed]
Analysis of cellular components at multiple levels of biological information can provide valuable functional insights. We performed multiple high-throughput measurements to study the response of Escherichia coli cells to genetic and environmental ...
K. Konoki; N. Sugiyama; M. Murata; K. Tachibana; Y. Hatanaka
Tetrahedron   56(46) 9003-9014   2000   [Refereed]
N. Sugiyama; K. Konoki; K. Tachibana
Biochemistry   46(40) 11410-11420   Sep 2007   [Refereed]
Okadaic acid, first isolated from the marine sponge Halichondria okadai, is a potent inhibitor of protein phosphatases 1 and 2A (PP1 and PP2A, respectively). Photoaffinity labeling experiments previously performed with biotinylated photoreactive o...
K. Imami; N. Sugiyama; Y. Kyono; M. Tomita; Y. Ishihama
Analytical Sciences   24(1) 161-166   Jan 2008   [Refereed]
We have developed an on-line automated system for phosphoproteome analysis using titania-based phosphopeptide enrichment followed by nanoLC-MS/MS. Titania beads were prepared by calcination of commercial chromatographic titania beads at 800 degree...
N. Sugiyama; H. Nakagami; K. Mochida; A. Daudi; M. Tomita; K. Shirasu; Y. Ishihama
Molecular Systems Biology   4    May 2008   [Refereed]
Protein phosphorylation regulates a wide range of cellular processes. Here, we report the proteome-wide mapping of in vivo phosphorylation sites in Arabidopsis by using complementary phosphopeptide enrichment techniques coupled with high-accuracy ...
N. Sugiyama; T. Masuda; K. Shinoda; A. Nakamura; M. Tomita; Y. Ishihama
Molecular and Cellular Proteomics   6(6) 1103-1109   2007   [Refereed]
Y. Kyono; N. Sugiyama; K. Imami; M. Tomita; Y. Ishihama
Journal of Proteome Research   7(10) 4585-4593   Sep 2008   [Refereed]
We developed a novel approach to enlarge phosphoproteome coverage using successive elution of phosphopeptides with various buffers in series from a single microcolumn packed with hydroxy acid-modified metal oxides, such as titania and zirconia. El...
A. Ravichandran; N. Sugiyama; M. Tomita; S. Swarup; Y. Ishihama
Proteomics   9(10) 2764-2775   May 2009   [Refereed]
Protein phosphorylation on serine, threonine, and tyrosine is well established as a crucial regulatory posttranslational modification in eukaryotes. With the recent whole-genome sequencing projects reporting the presence of serine/threonine kinase...
A. Nock; J.M. Ascano; T. Jones; M.J. Barrero; N. Sugiyama; M. Tomita; Y. Ishihama; S. Malik
Journal of Biological Chemistry   284(30) 19915-19926   May 2009   [Refereed]
Forkhead factors are important regulators of animal development and homeostasis. They are among the earliest to bind quiescent genes, which they activate in conjunction with other transcription factors. Many liver-specific genes are under the cont...
K. Imami; N. Sugiyama; M. Tomita; Y. Ishihama
Molecular BioSystems   6(3) 594-602   Jan 2010   [Refereed]
The use of dialyzed serum is essential in the application of the conventional stable isotope labeling by amino acids in cell culture (SILAC) approach to achieve complete labeling of proteins for quantitative proteomics. Here, we first evaluated th...
H. Nakagami; N. Sugiyama; K. Mochida; A. Daudi; Y. Yoshida; T. Toyoda; M. Tomita; Y. Ishihama; K. Shirasu
Plant Physiology   153(3) 1161-1174   May 2010   [Refereed]
Knowledge of phosphorylation events and their regulation is crucial to understand the functional biology of plants. Here, we report a large-scale phosphoproteome analysis in the model monocot rice (Oryza sativa japonica 'Nipponbare'), an economica...
Y. Kyono; N. Sugiyama; M. Tomita; Y. Ishihama
Rapid Communications in Mass Spectrometry   24(15) 2277-2282   Aug 2010   [Refereed]
We have developed a novel strategy to improve the efficiency of identification of multiply phosphorylated peptides isolated by hydroxy acid modified metal oxide chromatography (HAMMOC). This strategy consists of alkali-induced chemical dephosphory...
K. Konoki; K. Saito; H. Matsuura; N. Sugiyama; Y. Cho; M. Yotsu-Yamashita; K. Tachibana
Bioorganic and Medicinal Chemistry   18(21) 7607-7610   Aug 2010   [Refereed]
Okadaic acid (OA) and dinophysistoxin-1 (DTX1) cause diarrheic shellfish poisoning. This article examines the biochemical interactions of the two toxins with novel okadaic acid binding proteins (OABPs) 2.1 and 2.3, originally isolated from the mar...
S. Ujihara; T. Oishi; R. Mouri; R. Tamate; K. Konoki; N. Matsumori; M. Murata; Y. Oshima; N. Sugiyama; M. Tomita; Y. Ishihama
Bioorganic and Medicinal Chemistry Letters   20(22) 6443-6446   Sep 2010   [Refereed]
As is the case with other ladder-shaped polyether compounds, yessotoxin is produced by marine dinoflagellate, and possesses various biological activities beside potent toxicity. To gain a better understanding of the molecular mechanism for high af...
N. Yachie; R. Saito; N. Sugiyama; M. Tomita; Y. Ishihama
PLoS Computational Biology   7(1)    Jan 2011   [Refereed]
Following recent advances in high-throughput mass spectrometry (MS)-based proteomics, the numbers of identified phosphoproteins and their phosphosites have greatly increased in a wide variety of organisms. Although a critical role of phosphorylati...
T. Masuda; N. Sugiyama; M. Tomita; Y. Ishihama
Analytical Chemistry   83(20) 7698-7703   Sep 2011   [Refereed]
We developed a miniaturized LC-MS system with a high-recovery phosphopeptide enrichment protocol that allows phosphoproteome analysis of 10(4) cells. In the enrichment protocol, the key step is to add sodium deoxycholate and sodium lauroyl sarcosi...
H. Nakagami; N. Sugiyama; Y. Ishihama; K. Shirasu
Plant and Cell Physiology   53(1) 118-124   2012   [Refereed]
The emergence of 'shotgun proteomics' has paved the way for high-throughput proteome analysis, by which thousands of proteins can be identified simultaneously from complex samples. Although the shotgun approach has the potential to monitor many di...
D. Kitagawa; M. Gouda; Y. Kirii; N. Sugiyama; Y. Ishihama; I. Fujii; Y. Narumi; K. Akita; K. Yokota
Journal of Biochemistry   151(1) 47-55   2012   [Refereed]
It is known that some kinase inhibitors are sensitive to the phosphorylation state of the kinase, and therefore those compounds can discriminate between a phosphorylated and unphosphorylated protein. In this study, we prepared two colony stimulati...
M. Iwasaki; N. Sugiyama; N. Tanaka; Y. Ishihama
Journal of Chromatography A   1228 292-297   2012   [Refereed]
We have developed one-dimensional liquid chromatography-tandem mass spectrometry systems with meter-scale reversed phase monolithic silica-C₁₈ capillary columns for human proteome analysis. When tryptic peptides from 4 μg HeLa cell lysate proteins...
F. Inazuka; N. Sugiyama; M. Tomita; T. Abe; G. Shioi; H. Esumi
Journal of Biological Chemistry   287(20) 16379-16389   Mar 2012   [Refereed]
NUAK1 is a member of the AMP-activated protein kinase-related kinase family. Recent studies have shown that NUAK1 is involved in cellular senescence and motility in epithelial cells and fibroblasts. However, the physiological roles of NUAK1 are po...
T. Hoshii; Y. Tadokoro; K. Naka; T. Ooshio; T. Muraguchi; N. Sugiyama; T. Soga; K. Araki; K.-I. Yamamura; A. Hirao
Journal of Clinical Investigation   122(6) 2114-2129   May 2012   [Refereed]
Although dysregulation of mTOR complex 1 (mTORC1) promotes leukemogenesis, how mTORC1 affects established leukemia is unclear. We investigated the role of mTORC1 in mouse hematopoiesis using a mouse model of conditional deletion of Raptor, an esse...
T. Chiyoda; N. Sugiyama; T. Shimizu; H. Naoe; Y. Kobayashi; J. Ishizawa; Y. Arima; H. Tsuda; M. Ito; K. Kaibuchi; D. Aoki; Y. Ishihama; H. Saya; S. Kuninaka
Journal of Cell Biology   197(5) 625-641   May 2012   [Refereed]
In the mitotic exit network of budding yeast, Dbf2 kinase phosphorylates and regulates Cdc14 phosphatase. In contrast, no phosphatase substrates of LATS1/WARTS kinase, the mammalian equivalent of Dbf2, has been reported. To address this discrepanc...
M. Helmy; N. Sugiyama; M. Tomita; Y. Ishihama
Genes to Cells   17(8) 633-644   Jun 2012   [Refereed]
We have developed a novel bioinformatics method called mass spectrum sequential subtraction (MSSS) to search large peptide spectra datasets produced by liquid chromatography/mass spectrometry (LC-MS/MS) against protein and large-sized nucleotide s...
C.-W. Hu; M.-H. Lin; H.-C. Huang; W.-C. Ku; T.-H. Yi; C.-F. Tsai; Y.-J. Chen; N. Sugiyama; Y. Ishihama; H.-F. Juan; S.-H. Wu
Journal of Proteome Research   11(11) 5362-5375   Oct 2012   [Refereed]
Rhodopseudomonas palustris (R. palustris) is a purple nonsulfur anoxygenic phototrophic bacterium with metabolic versatility and is able to grow under photoheterotrophic and chemoheterotrophic states. It has uses in carbon management, carbon recy...
K. Imami; N. Sugiyama; H. Imamura; M. Wakabayashi; M. Tomita; M. Taniguchi; T. Ueno; M. Toi; Y. Ishihama
Molecular and Cellular Proteomics   11(12) 1741-1757   Sep 2012   [Refereed]
Lapatinib is a clinically potent kinase inhibitor for breast cancer patients because of its outstanding selectivity for epidermal growth factor receptor (EGFR) and EGFR2 (also known as HER2). However, there is only limited information about the in...
T. Umezawa; N. Sugiyama; F. Takahashi; J.C. Anderson; Y. Ishihama; S.C. Peck; K. Shinozaki
Science Signaling   6(270)    Apr 2013   [Refereed]
Abscisic acid (ABA) is a phytohormone that regulates diverse plant processes, including seed germination and the response to dehydration. In Arabidopsis thaliana, protein kinases of the SNF1-related protein kinase 2 (SnRK2) family are believed to ...
A. Takemiya; N. Sugiyama; H. Fujimoto; T. Tsutsumi; S. Yamauchi; A. Hiyama; Y. Tada; J.M. Christie; K.-I. Shimazaki
Nature Communications   4    Jan 2013   [Refereed]
Opening of stomata in the plant facilitates photosynthetic CO2 fixation and transpiration. Blue-light perception by phototropins (phot1, phot2) activates the plasma membrane H(+)-ATPase, causing stomata to open. Here we describe a regulator that c...
K. Kami; T. Fujimori; H. Sato; M. Sato; H. Yamamoto; Y. Ohashi; N. Sugiyama; Y. Ishihama; H. Onozuka; A. Ochiai; H. Esumi; T. Soga; M. Tomita
Metabolomics   9(2) 444-453   Apr 2013   [Refereed]
Metabolic microenvironment of tumor cells is influenced by oncogenic signaling and tissue-specific metabolic demands, blood supply, and enzyme expression. To elucidate tumor-specific metabolism, we compared the metabolomics of normal and tumor tis...
Y. Zhou; T. Tanaka; N. Sugiyama; S. Yokoyama; Y. Kawasaki; T. Sakuma; Y. Ishihama; I. Saiki; H. Sakurai
FEBS Letters   588(1) 131-137   2014   [Refereed]
Epidermal growth factor receptor pathway substrate 15 (Eps15) has been suggested to be involved in the endocytosis of cell surface receptors, including epidermal growth factor receptor (EGFR). Eps15 is phosphorylated at Tyr-849 upon stimulation wi...
K. Ikawa; A. Satou; M. Fukuhara; S. Matsumura; N. Sugiyama; H. Goto; M. Fukuda; M. Inagaki; Y. Ishihama; F. Toyoshima
Cell Cycle   13(1) 126-137   2014   [Refereed]
Endocytic vesicle fusion is inhibited during mitosis, but the molecular pathways that mediate the inhibition remain unclear. Here we uncovered an essential role of Polo-like kinase 1 (Plk1) in this mechanism. Phosphoproteomic analysis revealed tha...
M. Wakabayashi; H. Yoshihara; T. Masuda; M. Tsukahara; N. Sugiyama; Y. Ishihama
Journal of Proteome Research   13(2) 915-924   2014   [Refereed]
Formalin-fixed and paraffin-embedded (FFPE) sections mounted on microscope slides are one of the largest available resources for retrospective research on various diseases, but quantitative phosphoproteome analysis of FFPE sections has never been ...


西田紘士, 杉山直幸, 石濱泰
第67回質量分析総合討論会      May 2019
田畑剛, 吉沢明康, 岩崎未央, 杉山直幸, KAELL Lukas, 石濱泰
第67回質量分析総合討論会      May 2019
日本薬学会第139年会      2019
高見祐哉・津曲和哉・Hsin-Yi Chang・杉山直幸・大高章・石濱泰
日本薬学会第139年会      2019
日本薬学会第139年会      2019

Conference Activities & Talks

杉山直幸, 中園純菜, 八児一隆, 坂本大, CHANG Hsin‐Yi, 石濱泰
第67回質量分析総合討論会   May 2019   
Meta-Omics Workshop in Kyoto 2019   2019   
Phosphorylation Network Analysis Based on Kinome Profiling
Mass Spectrometry and Proteomics 2018   18 May 2018   
Human Kinome Profiling using Phosphoproteomic Approaches [Invited]
Naoyuki Sugiyama , Yasushi Ishihama
KBMSS2018   3 Feb 2018   
Direct Profiling of Kinome Activities Using Kinase-Specific Substrate Peptides
Naoyuki Sugiyama, Dai Sakamoto, Junna Nakazono, Kazutaka Yachigo, Hsin-Yi Chang, Yasushi Ishihama
25th International Symposium on Electro- and Liquid Phase-Separation Techniques(ITP2018)   2018   

Research Grants & Projects

Elucidation of Defensive Mechanism against Okadaic Acid within Halichondria okadai
Project Year: 1997 - 2003